Load ncbi (6.1.20040202) into ncbi-tools6/branches/upstream/current.

293 files changed, 54591 insertions, 29496 deletions

diff --git a/VERSION b/VERSION
index ff78c716..17aca6df 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-Wed Oct 29 10:59:56 EST 2003
+Sun Feb  1 10:18:25 EST 2004
diff --git a/access/ent2api.c b/access/ent2api.c
index a036291b..0a0b0e03 100644
--- a/access/ent2api.c
+++ b/access/ent2api.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/29/99
 *
-* $Revision: 1.57 $
+* $Revision: 1.60 $
 *
 * File Description: 
 *
@@ -145,16 +145,52 @@ NLM_EXTERN CONN EntrezOpenConnection (
   Uint2    host_port = e2_host_port;
   CharPtr  host_path = e2_host_path;
   CharPtr  host_service = e2_service;
+#ifdef OS_UNIX
+  CharPtr  env_machine = NULL;
+  CharPtr  env_path = NULL;
+  CharPtr  env_port = NULL;
+  CharPtr  env_service = NULL;
+  int      val = 0;
+#endif
 
+#ifdef OS_UNIX
+  env_machine = (CharPtr) getenv ("NCBI_ENTREZ2_HOST_MACHINE");
+  if (! StringHasNoText (env_machine)) {
+    host_machine = env_machine;
+  }
+#endif
   if (StringHasNoText (host_machine)) {
     host_machine = "www.ncbi.nlm.nih.gov";
   }
+
+#ifdef OS_UNIX
+  env_port = (CharPtr) getenv ("NCBI_ENTREZ2_HOST_PORT");
+  if (! StringHasNoText (env_port)) {
+    if (sscanf (env_port, "%d", &val) == 1) {
+      host_port = (Uint2) val;
+    }
+  }
+#endif
   if (host_port == 0) {
     host_port = 80;
   }
+
+#ifdef OS_UNIX
+  env_path = (CharPtr) getenv ("NCBI_ENTREZ2_HOST_PATH");
+  if (! StringHasNoText (env_path)) {
+    host_path = env_path;
+  }
+#endif
   if (StringHasNoText (host_path)) {
-    host_path = "/entrez/utils/entrez2server.fcgi";
+    host_path = "/entrez/eutils/entrez2server.fcgi";
+  }
+
+#ifdef OS_UNIX
+  env_service = (CharPtr) getenv ("NCBI_ENTREZ2_HOST_SERVICE");
+  if (! StringHasNoText (env_service)) {
+    host_service = env_service;
   }
+#endif
   if (StringHasNoText (host_service)) {
     host_service = "Entrez2";
   }
@@ -932,6 +968,7 @@ NLM_EXTERN Boolean ValidateEntrez2InfoPtr (
   Char                       ch;
   CharPtr                    db;
   Int2                       dbcount;
+  CharPtr                    dbnames [256];
   CharPtr                    dsf;
   Int2                       dsfcount;
   Entrez2DbInfoPtr           e2db;
@@ -941,7 +978,9 @@ NLM_EXTERN Boolean ValidateEntrez2InfoPtr (
   CharPtr                    fld;
   Int2                       fldcount;
   Boolean                    hasLowCase;
+  Int2                       i;
   CharPtr                    last;
+  ValNodePtr                 lastvnp;
   size_t                     len1;
   size_t                     len2;
   CharPtr                    lnk;
@@ -967,6 +1006,19 @@ NLM_EXTERN Boolean ValidateEntrez2InfoPtr (
     return FALSE;
   }
 
+  for (i = 0; i < sizeof (dbnames) / sizeof (CharPtr); i++) {
+    dbnames [i] = "?";
+  }
+  i = 0;
+  for (e2db = e2ip->db_info; e2db != NULL; e2db = e2db->next) {
+    i++;
+    if (! StringHasNoText (e2db->db_name)) {
+      dbnames [i] = e2db->db_name;
+    } else if (! StringHasNoText (e2db->db_menu)) {
+      dbnames [i] = e2db->db_menu;
+    }
+  }
+
   dbcount = 0;
   for (e2db = e2ip->db_info; e2db != NULL; e2db = e2db->next) {
     dbcount++;
@@ -1089,7 +1141,7 @@ NLM_EXTERN Boolean ValidateEntrez2InfoPtr (
         ValNodeCopyStr (head, 0, buf);
         rsult = FALSE;
       } else {
-        ValNodeCopyStr (&menuhead, 0, e2fip->field_menu);
+        ValNodeCopyStr (&menuhead, (Int2) dbcount, e2fip->field_menu);
         if (StringStr (e2fip->field_menu, "Date") != NULL) {
           if (! e2fip->is_date) {
             sprintf (buf, "Database %s field %s does not have is_date set", db, fld);
@@ -1203,12 +1255,13 @@ NLM_EXTERN Boolean ValidateEntrez2InfoPtr (
 
   menuhead = ValNodeSort (menuhead, SortVnpByStr);
   last = NULL;
+  lastvnp = NULL;
   for (vnp = menuhead; vnp != NULL; vnp = vnp->next) {
     str = (CharPtr) vnp->data.ptrvalue;
     if (StringHasNoText (str)) continue;
-    if (last != NULL) {
+    if (last != NULL && lastvnp != NULL) {
       if (StringICmp (last, str) == 0 && StringCmp (last, str) != 0) {
-        sprintf (buf, "Menu names %s and %s differ in capitalization", last, str);
+        sprintf (buf, "Menu names %s [%s] and %s [%s] differ in capitalization", last, dbnames [lastvnp->choice], str, dbnames [vnp->choice]);
         ValNodeCopyStr (head, 0, buf);
         rsult = FALSE;
       } else {
@@ -1224,7 +1277,7 @@ NLM_EXTERN Boolean ValidateEntrez2InfoPtr (
             } else if (StringICmp (last, "Rank") == 0 && StringICmp (str, "Ranked standard deviation") == 0) {
             } else if (StringICmp (last, "Book") == 0 && StringICmp (str, "Book's Topic") == 0) {
             } else {
-              sprintf (buf, "Menu names %s and %s may be unintended variants", last, str);
+              sprintf (buf, "Menu names %s [%s] and %s [%s] may be unintended variants", last, dbnames [lastvnp->choice], str, dbnames [vnp->choice]);
               ValNodeCopyStr (head, 0, buf);
               rsult = FALSE;
             }
@@ -1237,6 +1290,7 @@ NLM_EXTERN Boolean ValidateEntrez2InfoPtr (
       rsult = FALSE;
     }
     last = str;
+    lastvnp = vnp;
   }
   ValNodeFreeData (menuhead);
 
diff --git a/access/pmfapi.c b/access/pmfapi.c
index 02d0198b..f288d240 100644
--- a/access/pmfapi.c
+++ b/access/pmfapi.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   5/5/00
 *
-* $Revision: 1.62 $
+* $Revision: 1.63 $
 *
 * File Description: 
 *
@@ -235,6 +235,12 @@ static void ChangeMedlineAuthorsToISO (
   alp = cap->authors;
   if (alp == NULL || alp->choice != 2) return;
 
+  /* do not convert if too big for buffers */
+
+  for (tmp = alp->names; tmp != NULL; tmp = tmp->next) {
+    if (StringLen ((CharPtr) tmp->data.ptrvalue) > 70) return;
+  }
+
   oldnames = alp->names;
   alp->names = NULL;
   alp->choice = 1; /* make std names */
diff --git a/access/qblastapi.c b/access/qblastapi.c
index 5cf11516..400a73bd 100644
--- a/access/qblastapi.c
+++ b/access/qblastapi.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/28/00
 *
-* $Revision: 1.24 $
+* $Revision: 1.28 $
 *
 * File Description: 
 *
@@ -37,6 +37,18 @@
 * --------------------------------------------------------------------------
 *
 * $Log: qblastapi.c,v $
+* Revision 1.28  2003/11/14 16:23:08  dondosha
+* If query id not local, append title to id to get defline in BLASTGetQuerySummary
+*
+* Revision 1.27  2003/11/12 21:19:03  kans
+* changed query_number to query_num - fixing typo
+*
+* Revision 1.26  2003/11/12 20:49:20  coulouri
+* Replace code accidentally removed between 1.24 and 1.25 in BlastGetQueryBioseqByRIDEx
+*
+* Revision 1.25  2003/11/03 20:50:53  madden
+* Fix problem with content length, remove call to QblastTestRID, add BLASTGetBOByRIDEx
+*
 * Revision 1.24  2003/01/17 20:40:29  madden
 * Put QUERY_NUMBER back in URL for fetching Seqannot
 *
@@ -755,40 +767,6 @@ static void LIBCALLBACK AsnIoErrorFunc(Int2 type, CharPtr message)
     return;
 }
 
-/*
-	Tests the RID to see if it's an in-house job
-	(i.e., indexer) kept in the LL queue, or a
-	normal one.
-
-	External jobs start with a 0 after the first dash
-	(e.g., 1018299345-016645-15460), internal jobs
-	do not.
-
-	Return value is TRUE for internal jobs, FALSE for external.
-
-*/
-static Boolean QblastTestRID(CharPtr RID)
-
-{
-	Boolean retval=TRUE;
-
-	while (*RID != NULLB)
-	{
-		if (*RID == '-')
-		{
-			RID++;
-			if (*RID == '0')
-				retval = FALSE;
-			else
-				retval = TRUE;
-			break;
-		}
-		RID++;
-	}
-
-	return retval;
-}
-
 /* Function to get SeqAnnot for RID. We suupose, that search already
    finished and results are exists on the Qblast repository */
 
@@ -819,8 +797,10 @@ NLM_EXTERN SeqAnnotPtr BLASTGetSeqAnnotByRIDEx(CharPtr RID,
     AsnIoConnPtr aicp;
     EIO_Status   status;
 
-    sprintf(query_string, "FORMAT_TYPE=ASN.1&CMD=Get&RID=%s&QUERY_NUMBER=%ld&FORMAT_OBJECT=Alignment", 
-	RID, (long) query_number);
+    sprintf(query_string,
+            "FORMAT_TYPE=ASN.1&CMD=Get&RID=%s&QUERY_NUMBER=%ld&FORMAT_OBJECT=Alignment", 
+            RID,
+            (long) query_number);
 
     conn = QUERY_OpenUrlQuery ((host_machine == NULL) ? "www.ncbi.nlm.nih.gov" : host_machine, 
 				(host_port <= 0) ? 80 : host_port, 
@@ -829,7 +809,7 @@ NLM_EXTERN SeqAnnotPtr BLASTGetSeqAnnotByRIDEx(CharPtr RID,
                                240, eMIME_T_Application, 
                                eMIME_WwwForm, eENCOD_Url, 0);
     
-    length = StringLen(query_string)+1;
+    length = StringLen(query_string);
     status = CONN_Write (conn, query_string, length , &n_written);    
     QUERY_SendQuery (conn);
     
@@ -860,19 +840,15 @@ NLM_EXTERN BioseqPtr BLASTGetQueryBioseqByRIDEx(CharPtr RID, int query_num)
     Int4         length;
     AsnIoConnPtr aicp;
     EIO_Status   status;
-    
-    /* sprintf(query_string, "RID=%s&ALIGNMENT_VIEW=11", RID); */
-    
-    if (QblastTestRID(RID) == FALSE)
-    	sprintf(query_string, "CMD=Get&RID=%s&FORMAT_OBJECT=Bioseq&FORMAT_TYPE=ASN.1&QUERY_NUMBER=%d", RID, query_num);
-    else
-    	sprintf(query_string, "CMD=Get&RID=%s&FORMAT_OBJECT=Bioseq&FORMAT_TYPE=ASN.1&QUERY_NUMBER=%d&CLIENT=DirSub", RID, query_num);
-    
-    /* conn = QUERY_OpenUrlQuery ("www.ncbi.nlm.nih.gov", 80,  */
+
+    sprintf(query_string,
+            "FORMAT_TYPE=ASN.1&CMD=Get&RID=%s&QUERY_NUMBER=%ld&FORMAT_OBJECT=Bioseq", 
+            RID,
+            (long) query_num);
     
     conn = QUERY_OpenUrlQuery ("www.ncbi.nlm.nih.gov", 80, 
                                "/blast/Blast.cgi", NULL, 
-                               "BLASTGetQueryBioseqByRID()", 
+                               "BLASTGetQueryBioseqByRIDEx()", 
                                30, eMIME_T_Application, 
                                eMIME_WwwForm, eENCOD_Url, 0);
 
@@ -896,7 +872,19 @@ NLM_EXTERN Nlm_Boolean BLASTGetQuerySummary(CharPtr RID, Int4 query_number,
     BioseqPtr bsp = BLASTGetQueryBioseqByRIDEx(RID, query_number);
     if(!bsp)
 	return FALSE;
-    *defline = StringSave(BioseqGetTitle(bsp));
+    if (bsp->id->choice == SEQID_LOCAL) {
+       *defline = StringSave(BioseqGetTitle(bsp));
+    } else {
+#define SEQID_LENGTH 255
+       Int4 id_length;
+       Char tmp[SEQID_LENGTH+1];
+       Int4 title_length = StringLen(BioseqGetTitle(bsp));
+       SeqIdWrite(bsp->id, tmp, PRINTID_FASTA_LONG, SEQID_LENGTH);
+       id_length = StringLen(tmp);
+       title_length += id_length + 3;
+       *defline = (CharPtr) MemNew(title_length*sizeof(Char));
+       sprintf(*defline, "%s %s", tmp, BioseqGetTitle(bsp));
+    }
     *query_length = BioseqGetLen(bsp);
     BioseqFree(bsp);
     return TRUE;
@@ -906,7 +894,13 @@ NLM_EXTERN Nlm_Boolean BLASTGetQuerySummary(CharPtr RID, Int4 query_number,
 /* Function to get BlastObject for RID. We suupose, that search already
    finished and results are exists on the Qblast repository. Blast Object
    ASN.1 will be returned as CharPtr buffer*/
-NLM_EXTERN CharPtr BLASTGetBOByRID(CharPtr RID)
+/*
+ * retrive blast object
+ */
+NLM_EXTERN CharPtr BLASTGetBOByRIDEx(CharPtr RID,
+                                     Nlm_CharPtr host_machine,
+                                     Nlm_Uint2 host_port,
+                                     Nlm_CharPtr host_path)
 {
     Char         query_string[256];
     CONN         conn;
@@ -916,21 +910,17 @@ NLM_EXTERN CharPtr BLASTGetBOByRID(CharPtr RID)
     EIO_Status   status;
     CharPtr      in_buff;
     
-/*
-    sprintf(query_string, "RID=%s&ALIGNMENT_VIEW=13", RID);
-*/
-    if (QblastTestRID(RID) == FALSE)
-    	sprintf(query_string, "CMD=Get&RID=%s&FORMAT_OBJECT=BlastObject&FORMAT_TYPE=ASN.1", RID);
-    else
-    	sprintf(query_string, "CMD=Get&RID=%s&FORMAT_OBJECT=BlastObject&FORMAT_TYPE=ASN.1&CLIENT=DirSub", RID);
-    
-    conn = QUERY_OpenUrlQuery ("www.ncbi.nlm.nih.gov", 80, 
-                               "/blast/Blast.cgi", NULL, 
-                               "BLASTGetBOByRID()", 
+    sprintf(query_string, "CMD=Get&RID=%s&FORMAT_OBJECT=BlastObject&FORMAT_TYPE=ASN.1", RID);
+
+    conn = QUERY_OpenUrlQuery ((host_machine == NULL) ? "www.ncbi.nlm.nih.gov" : host_machine,
+                                (host_port <= 0) ? 80 : host_port,
+                                (host_path == NULL) ? "/blast/Blast.cgi" : host_path,
+				NULL,
+                               "BLASTGetBOByRIDEx()", 
                                30, eMIME_T_Application, 
                                eMIME_WwwForm, eENCOD_Url, 0);
 
-    length = StringLen(query_string) + 1;
+    length = StringLen(query_string);
     status = CONN_Write (conn, query_string, length , &n_written);    
     QUERY_SendQuery (conn);
     
@@ -960,3 +950,8 @@ NLM_EXTERN CharPtr BLASTGetBOByRID(CharPtr RID)
     CONN_Close(conn);
     return in_buff;
 }
+
+NLM_EXTERN CharPtr BLASTGetBOByRID(CharPtr RID)
+{
+	return BLASTGetBOByRIDEx(RID, NULL, 0, NULL);
+}
diff --git a/access/qblastapi.h b/access/qblastapi.h
index 54f87b72..0904c86c 100644
--- a/access/qblastapi.h
+++ b/access/qblastapi.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/28/00
 *
-* $Revision: 1.10 $
+* $Revision: 1.11 $
 *
 * File Description: 
 *
@@ -37,6 +37,9 @@
 * --------------------------------------------------------------------------
 *
 * $Log: qblastapi.h,v $
+* Revision 1.11  2003/11/03 20:51:04  madden
+* add BLASTGetBOByRIDEx
+*
 * Revision 1.10  2003/01/15 22:04:50  madden
 * Moved BLASTGetSeqAnnotByRIDEx from internal
 *
@@ -212,6 +215,7 @@ NLM_EXTERN Nlm_Boolean BLASTGetQuerySummary(CharPtr RID, Int4 query_number,
    ASN.1 will be returned as CharPtr buffer
 */
 NLM_EXTERN CharPtr BLASTGetBOByRID(CharPtr RID);
+NLM_EXTERN CharPtr BLASTGetBOByRIDEx(CharPtr RID, Nlm_CharPtr host_machine, Nlm_Uint2 host_port, Nlm_CharPtr host_path);
 
 #ifdef __cplusplus
 }
diff --git a/access/vecscnapi.c b/access/vecscnapi.c
index cb7de159..79e2c5a8 100644
--- a/access/vecscnapi.c
+++ b/access/vecscnapi.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/13/00
 *
-* $Revision: 1.13 $
+* $Revision: 1.15 $
 *
 * File Description: 
 *
@@ -467,8 +467,11 @@ NLM_EXTERN Int4 VecScreenCheckQueue (
 
           /* estimated wait time has expired, so queue another check */
 
-          if (curr->secondsToWait < 60) {
+          if (curr->secondsToWait < 300) {
             curr->secondsToWait *= 2;
+            if (curr->secondsToWait > 300) {
+              curr->secondsToWait = 300;
+            }
           }
           curr->postedTime = GetSecs ();
 
diff --git a/algo/blast/api/Makefile b/algo/blast/api/Makefile
deleted file mode 100644
index fb2efdd7..00000000
--- a/algo/blast/api/Makefile
+++ /dev/null
@@ -1,19 +0,0 @@
-.PHONY: all install
-
-all:
-	cd ../lib && make -f Makefile.blast_lib
-	make -f Makefile.blast_app
-
-# Solaris only!
-CXX = purify /netopt/forte6u2/bin/CC
-blast.pure:
-	cd ../lib && make -f Makefile.blast_lib
-	make APP=$@ CXX="$(CXX)" -f Makefile.blast_app
-
-clean:
-	make -f Makefile.blast_app clean
-	rm -fr blast.pure
-
-install: blast
-	test -d ../bin || mkdir ../bin
-	install blast ../bin/
diff --git a/algo/blast/api/Makefile.blast_app b/algo/blast/api/Makefile.blast_app
deleted file mode 100644
index cb26ab53..00000000
--- a/algo/blast/api/Makefile.blast_app
+++ /dev/null
@@ -1,50 +0,0 @@
-#
-# Makefile:  
-#
-# This file was originally generated by shell script "new_project.sh"
-# 
-#
-
-include ../NewBlast.mk
-
-###  PATH TO A PRE-BUILT C++ TOOLKIT
-builddir = $(NCBI)/$(VERSION_STABILITY)/$(BUILD_TYPE)/build
-
-
-###  DEFAULT COMPILATION FLAGS  -- DON'T EDIT OR MOVE THESE 4 LINES !!!
-include $(builddir)/Makefile.mk
-srcdir = .
-BINCOPY = @:
-LOCAL_CPPFLAGS = $(BLAST_CPPFLAGS)
-
-#############################################################################
-###  EDIT SETTINGS FOR THE DEFAULT (APPLICATION) TARGET HERE              ### 
-APP = blast
-SRC = blast_app blast_format blast_input blast_seq blast_seqalign seqsrc_readdb
-# OBJ =
-
-# PRE_LIBS = $(NCBI_C_LIBPATH) .....
-
-LIB = $(SEQ_LIBS) pub medline biblio general dbapi_driver xser xutil \
-    xconnect xncbi
-
-# LIB      = xser xhtml xcgi xconnect xutil xncbi
-
-## If you need the C toolkit...
-LIBS     = $(NCBI_C_LIBPATH) -lncbitool -lncbiobj -lncbi -lblast $(NETWORK_LIBS) $(ORIG_LIBS)
-CPPFLAGS = $(ORIG_CPPFLAGS) -I. -I../include $(NCBI_C_INCLUDE)
-LDFLAGS  = $(ORIG_LDFLAGS) $(BLAST_PROFILE) -L../lib
-
-# CFLAGS   = $(ORIG_CFLAGS)
-# CXXFLAGS = $(ORIG_CXXFLAGS)
-# LDFLAGS  = $(ORIG_LDFLAGS)
-#                                                                         ###
-#############################################################################
-
-
-###  APPLICATION BUILD RULES  -- DON'T EDIT OR MOVE THIS LINE !!!
-include $(builddir)/Makefile.app
-MAKEFILE = Makefile.blast_app
-
-
-###  PUT YOUR OWN ADDITIONAL TARGETS (MAKE COMMANDS/RULES) HERE
diff --git a/algo/blast/api/blast_format.c b/algo/blast/api/blast_format.c
index 277e3355..24191c3e 100644
--- a/algo/blast/api/blast_format.c
+++ b/algo/blast/api/blast_format.c
@@ -1,4 +1,4 @@
-/* $Id: blast_format.c,v 1.29 2003/10/23 20:15:37 dondosha Exp $
+/* $Id: blast_format.c,v 1.36 2003/12/09 15:31:23 kans Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -34,13 +34,13 @@ Contents: Formatting of BLAST results (SeqAlign)
 Detailed Contents: 
 
 ******************************************************************************
- * $Revision: 1.29 $
+ * $Revision: 1.36 $
  * */
 
-static char const rcsid[] = "$Id: blast_format.c,v 1.29 2003/10/23 20:15:37 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_format.c,v 1.36 2003/12/09 15:31:23 kans Exp $";
 
-#include "blast_format.h"
-#include "blast_seq.h"
+#include <algo/blast/api/blast_format.h>
+#include <algo/blast/api/blast_seq.h>
 #include <algo/blast/core/blast_filter.h>
 #include <algo/blast/core/blast_util.h>
 #include <sequtil.h>
@@ -83,6 +83,14 @@ BlastPrintReference PROTO((Boolean html, Int4 line_length, FILE *outfp));
 extern Boolean LIBCALL 
 MegaBlastPrintReference PROTO((Boolean html, Int4 line_length, FILE *outfp));
 
+extern void MBXmlClose(MBXml* mbxp, ValNodePtr other_returns, 
+                       Boolean ungapped);
+
+extern CharPtr BlastGetReference (Boolean html);
+
+extern CharPtr LIBCALL BlastGetVersionNumber PROTO((void));
+extern CharPtr LIBCALL BlastGetReleaseDate PROTO((void));
+
 typedef struct TxDfDbInfo {
    struct TxDfDbInfo* next;
    Boolean   is_protein;
@@ -106,8 +114,31 @@ Int2 BlastFormattingOptionsNew(Uint1 program_number, char* file_out,
         calloc(1, sizeof(BlastFormattingOptions))) == NULL)
       return -1;
    format_options->believe_query = FALSE;
-   if ((format_options->outfp = FileOpen(file_out, "w")) == NULL)
-      return -1;
+   if (align_view != 7 && align_view < 10) {
+      FILE* outfp;
+      if ((outfp = FileOpen(file_out, "w")) == NULL)
+         return -1;
+      format_options->outfp = (void *) outfp;
+   } else {
+      AsnIoPtr aip;
+      char write_mode[3];
+
+      switch (align_view) {
+      case 7:
+         strcpy(write_mode, "wx"); break;
+      case 10:
+         strcpy(write_mode, "w"); break;
+      case 11:
+         strcpy(write_mode, "wb"); break;
+      default:
+         return -1;
+      }
+      
+      if ((aip = AsnIoOpen(file_out, write_mode)) == NULL)
+         return -1;
+      format_options->outfp = (void *) aip;
+   }
+
    format_options->number_of_descriptions = num_descriptions;
    format_options->number_of_alignments = num_alignments;
    
@@ -132,14 +163,219 @@ Int2 BlastFormattingOptionsNew(Uint1 program_number, char* file_out,
 BlastFormattingOptions* 
 BlastFormattingOptionsFree(BlastFormattingOptions* format_options)
 {
-   FileClose(format_options->outfp);
+   if (format_options->align_view != 7 && format_options->align_view < 10)
+      FileClose( (FILE *)format_options->outfp);
+   else
+      AsnIoClose( (AsnIoPtr)format_options->outfp);
+
    sfree(format_options);
    return NULL;
 }
 
+#define BXML_INCLUDE_QUERY 0x1
+
+static BlastOutputPtr 
+CreateBlastOutputHead(CharPtr program, CharPtr database, 
+                      SeqLocPtr query_loc, Int4 flags)
+{
+    BlastOutputPtr boutp;
+    Char buffer[1024];
+    SeqPortPtr spp;
+    Boolean is_aa = FALSE;
+    Int4 i;
+    
+    if((boutp = BlastOutputNew()) == NULL)
+        return FALSE;
+    
+    /* For optimization BLOSUM62 may be loaded ones */
+    if (query_loc) {
+       SeqIdPtr sip = SeqLocId(query_loc);
+       BioseqPtr bsp;
+       SeqIdWrite(sip, buffer, PRINTID_FASTA_LONG, sizeof(buffer));
+       boutp->query_ID = StringSave(buffer);
+
+       bsp = BioseqLockById(sip);
+       if(!bsp ||
+          (boutp->query_def = StringSave(BioseqGetTitle(bsp))) == NULL) {
+          boutp->query_def = StringSave("No definition line found");
+       }
+       BioseqUnlock(bsp);
+
+       boutp->query_len = SeqLocLen(query_loc);
+
+       if(flags & BXML_INCLUDE_QUERY) {
+          boutp->query_seq = MemNew(boutp->query_len+1);
+          is_aa = (strcmp(program, "blastp") || strcmp(program, "tblastn"));
+          spp = SeqPortNewByLoc(query_loc, 
+                   (is_aa) ? Seq_code_ncbieaa : Seq_code_iupacna);
+          
+          for (i = 0; i < boutp->query_len; i++) {
+             boutp->query_seq[i] = SeqPortGetResidue(spp);
+          }
+          spp = SeqPortFree(spp);
+       } else {
+          boutp->query_seq = NULL;    /* Do we need sequence here??? */
+       }
+    }
+    /* Program name */
+    boutp->program = StringSave(program);
+
+    /* Database name */
+    boutp->db = StringSave(database);
+
+    /* Version text */
+    sprintf(buffer, "%s %s [%s]", program, BlastGetVersionNumber(), 
+            BlastGetReleaseDate());
+    boutp->version = StringSave(buffer);
+
+    /* Reference */
+    boutp->reference = BlastGetReference(FALSE);
+
+    /* Filling parameters */
+    
+    boutp->param = ParametersNew();    
+    /* THE FOLLOWING IS NOT IMPLEMENTED. JUST FILL DEFAULT NUMBERS */
+    boutp->param->expect = 10;
+    boutp->param->gap_open = 0;
+    boutp->param->gap_extend = 0;
+    
+    return boutp;
+}
+
+#define MACRO_atp_find(atp,name)\
+        if((atp = AsnTypeFind(amp, #name))==NULL){\
+                ErrPostEx(SEV_ERROR,0,0,\
+                        "Could not find type <%s>", #name);\
+                return NULL; \
+        }
+
+static MBXml* MBXmlInit(AsnIoPtr aip, CharPtr program, CharPtr database, 
+                          SeqLocPtr query_loc, Int4 flags)
+{
+    MBXml* mbxp;
+    AsnModulePtr amp;
+    DataVal av;
+    AsnTypePtr atp;
+    Boolean retval = FALSE;
+
+    AsnTypePtr       BLASTOUTPUT;
+    AsnTypePtr       BLASTOUTPUT_program;
+    AsnTypePtr       BLASTOUTPUT_version;
+    AsnTypePtr       BLASTOUTPUT_reference;
+    AsnTypePtr       BLASTOUTPUT_db;
+    AsnTypePtr       BLASTOUTPUT_query_ID;
+    AsnTypePtr       BLASTOUTPUT_query_def;
+    AsnTypePtr       BLASTOUTPUT_query_len;
+    AsnTypePtr       BLASTOUTPUT_query_seq;
+    AsnTypePtr       BLASTOUTPUT_param;
+    AsnTypePtr       BLASTOUTPUT_iterations;
+    AsnTypePtr       BLASTOUTPUT_iterations_E;
+    AsnTypePtr       BLASTOUTPUT_mbstat;
+
+    mbxp = (MBXml*) MemNew(sizeof(MBXml));
+    
+    mbxp->aip = aip;
+    
+    if (! bxmlobjAsnLoad()) {
+        return NULL;
+    }
+    
+    amp = AsnAllModPtr();
+
+    MACRO_atp_find(BLASTOUTPUT,BlastOutput);
+    MACRO_atp_find(BLASTOUTPUT_program,BlastOutput.program);
+    MACRO_atp_find(BLASTOUTPUT_version,BlastOutput.version);
+    MACRO_atp_find(BLASTOUTPUT_reference,BlastOutput.reference);
+    MACRO_atp_find(BLASTOUTPUT_db,BlastOutput.db);
+    MACRO_atp_find(BLASTOUTPUT_query_ID,BlastOutput.query-ID);
+    MACRO_atp_find(BLASTOUTPUT_query_def,BlastOutput.query-def);
+    MACRO_atp_find(BLASTOUTPUT_query_len,BlastOutput.query-len);
+    MACRO_atp_find(BLASTOUTPUT_query_seq,BlastOutput.query-seq);
+    MACRO_atp_find(BLASTOUTPUT_param,BlastOutput.param);
+    MACRO_atp_find(BLASTOUTPUT_iterations,BlastOutput.iterations);
+    MACRO_atp_find(BLASTOUTPUT_iterations_E,BlastOutput.iterations.E);
+    MACRO_atp_find(BLASTOUTPUT_mbstat,BlastOutput.mbstat);
+
+    /* Start of iterations structure */
+    mbxp->atp = BLASTOUTPUT_iterations_E;
+
+    /* Head of all BlastOutput structure */
+    mbxp->BlastOutput = BLASTOUTPUT;
+    
+    /* Head of iterations strucure */
+    mbxp->BlastOutput_iterations = BLASTOUTPUT_iterations;
+
+    /* Head of the final statistics for Mega BLAST */
+    mbxp->BlastOutput_mbstat = BLASTOUTPUT_mbstat;
+    
+    mbxp->boutp = CreateBlastOutputHead(program, database, query_loc, flags);
+    
+    atp = AsnLinkType(NULL, BLASTOUTPUT);   /* link local tree */
+    
+    if (atp == NULL) {
+        return NULL;
+    }
+    
+    if (! AsnOpenStruct(mbxp->aip, atp, (Pointer) mbxp->boutp)) {
+        return NULL;
+    }
+
+    if (mbxp->boutp->program != NULL) {
+        av.ptrvalue = mbxp->boutp -> program;
+        retval = AsnWrite(mbxp->aip, BLASTOUTPUT_program,  &av);
+    }
+    
+    if (mbxp->boutp->version != NULL) {
+        av.ptrvalue = mbxp->boutp->version;
+        retval = AsnWrite(mbxp->aip, BLASTOUTPUT_version,  &av);
+    }
+    
+    if (mbxp->boutp->reference != NULL) {
+        av.ptrvalue = mbxp->boutp->reference;
+        retval = AsnWrite(mbxp->aip, BLASTOUTPUT_reference,  &av);
+    }
+
+    if (mbxp->boutp -> db != NULL) {
+        av.ptrvalue = mbxp->boutp->db;
+        retval = AsnWrite(mbxp->aip, BLASTOUTPUT_db,  &av);
+    }
+
+    if (mbxp->boutp -> query_ID != NULL) {
+        av.ptrvalue = mbxp->boutp->query_ID;
+        retval = AsnWrite(mbxp->aip, BLASTOUTPUT_query_ID,  &av);
+    }
+
+    if (mbxp->boutp->query_def != NULL) {
+        av.ptrvalue = mbxp->boutp->query_def;
+        retval = AsnWrite(mbxp->aip, BLASTOUTPUT_query_def,  &av);
+    }
+
+    av.intvalue = mbxp->boutp->query_len;
+    retval = AsnWrite(mbxp->aip, BLASTOUTPUT_query_len,  &av);
+
+    if (mbxp->boutp->query_seq != NULL) {
+        av.ptrvalue = mbxp->boutp->query_seq;
+        retval = AsnWrite(mbxp->aip, BLASTOUTPUT_query_seq,  &av);
+    }
+
+    if (mbxp->boutp->param != NULL) {
+        if (!ParametersAsnWrite(mbxp->boutp->param, 
+                                mbxp->aip, BLASTOUTPUT_param)) {
+            return NULL;
+        }
+    }
+
+    if(!AsnOpenStruct(mbxp->aip, BLASTOUTPUT_iterations, NULL))
+        return NULL;
+    
+    AsnIoFlush(mbxp->aip);
+    
+    return mbxp;
+}
+
 Int2 BLAST_FormatResults(SeqAlignPtr head, char* blast_database,
         char* blast_program, Int4 num_queries, 
-        SeqLocPtr query_slp, BlastMask* blast_mask, 
+        SeqLocPtr query_slp, BlastMaskLoc* blast_mask, 
         BlastFormattingOptions* format_options, Boolean is_ooframe)
 {  
    SeqAlignPtr seqalign = head, sap, next_seqalign;
@@ -154,12 +390,16 @@ Int2 BLAST_FormatResults(SeqAlignPtr head, char* blast_database,
    BlastPruneSapStruct* prune;
    SeqAnnotPtr seqannot;
    MBXml* mbxp = NULL;
-   FILE *outfp;
+   FILE *outfp = NULL;
 
    if (!format_options || !format_options->outfp || !query_slp)
       return -1;
 
-   outfp = format_options->outfp;
+   if (format_options->align_view != 7 && format_options->align_view < 10)
+      outfp = (FILE *) format_options->outfp;
+   else 
+      aip = (AsnIoPtr) format_options->outfp; 
+
    align_type = BlastGetTypes(blast_program, &query_is_na, &db_is_na);
    BlastProgram2Number(blast_program, &program_number);
    
@@ -169,12 +409,16 @@ Int2 BLAST_FormatResults(SeqAlignPtr head, char* blast_database,
    query_index = 0;
    slp = query_slp;
    mask_loc_head = mask_loc = 
-      BlastMaskToSeqLoc(program_number, blast_mask, slp);
+      BlastMaskLocToSeqLoc(program_number, blast_mask, slp);
 
    if (!seqalign && format_options->align_view < 7) {
       fprintf(outfp, "\n\n ***** No hits found ******\n\n");
    }
       
+   if (format_options->align_view == 7) {
+      mbxp = MBXmlInit(aip, "megablast", blast_database, slp, 0);
+   }
+
    while (seqalign) {
       /* Find which query the current SeqAlign is for */
       query_id = TxGetQueryIdFromSeqAlign(seqalign);
@@ -246,9 +490,8 @@ Int2 BLAST_FormatResults(SeqAlignPtr head, char* blast_database,
             outfp, (format_options->align_view == 9));
          
          SeqAlignSetFree(seqalign);
-      } else if(format_options->align_view == 7 || 
-                format_options->align_view == 10 || 
-                format_options->align_view == 11) {
+      } else if(format_options->align_view == 7) {
+         /* XML printout - NOT IMPLEMENTED YET */
          IterationPtr iterp;
          
          iterp = BXMLBuildOneQueryIteration(seqalign, NULL, FALSE, 
@@ -265,37 +508,37 @@ Int2 BLAST_FormatResults(SeqAlignPtr head, char* blast_database,
          if (aip) {
             SeqAnnotAsnWrite((SeqAnnotPtr) seqannot, aip, NULL);
             AsnIoReset(aip);
+         } else if (outfp) {
+            /* Uncacheing causes problems with ordinal nos. vs. gi's. */
+            prune = BlastPruneHitsFromSeqAlign(seqalign, 
+                       format_options->number_of_descriptions, NULL);
+            ObjMgrSetHold();
+            init_buff_ex(85);
+            PrintDefLinesFromSeqAlign(prune->sap, 80, outfp, 
+               format_options->print_options, FIRST_PASS, NULL);
+            free_buff();
+            
+            prune = BlastPruneHitsFromSeqAlign(seqalign, 
+                       format_options->number_of_alignments, prune);
+            seqannot->data = prune->sap;
+            if(is_ooframe) {
+               OOFShowBlastAlignment(prune->sap, mask_loc, outfp, 
+                                     format_options->align_options, NULL);
+            } else if (format_options->align_view != 0) {
+               ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL, NULL, 
+                  format_options->align_options, NULL, mask_loc, NULL);
+            } else {
+               ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL, NULL, 
+                  format_options->align_options, NULL, mask_loc, 
+                  FormatScoreFunc);
+            }
+            seqannot->data = seqalign;
+            prune = BlastPruneSapStructDestruct(prune);
+            ObjMgrClearHold();
+            ObjMgrFreeCache(0);
          }
-         /* Uncacheing causes problems with ordinal nos. vs. gi's. */
-         prune = BlastPruneHitsFromSeqAlign(seqalign, 
-                    format_options->number_of_descriptions, NULL);
-         ObjMgrSetHold();
-         init_buff_ex(85);
-         PrintDefLinesFromSeqAlign(prune->sap, 80, outfp, 
-            format_options->print_options, FIRST_PASS, NULL);
-         free_buff();
-         
-         prune = BlastPruneHitsFromSeqAlign(seqalign, 
-                    format_options->number_of_alignments, prune);
-         seqannot->data = prune->sap;
-         if(is_ooframe) {
-            OOFShowBlastAlignment(prune->sap, mask_loc, outfp, 
-                                  format_options->align_options, NULL);
-         } else if (format_options->align_view != 0) {
-            ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL, NULL, 
-               format_options->align_options, NULL, mask_loc, NULL);
-         } else {
-            ShowTextAlignFromAnnot(seqannot, 60, outfp, NULL, NULL, 
-               format_options->align_options, NULL, mask_loc, 
-               FormatScoreFunc);
-         }
-         seqannot->data = seqalign;
-         prune = BlastPruneSapStructDestruct(prune);
-         ObjMgrClearHold();
-         ObjMgrFreeCache(0);
          seqannot = SeqAnnotFree(seqannot);
       }
-
       seqalign = next_seqalign;
       /* Relink the mask locations so chain can be freed in the end.
        The 'tmp_loc' variable points to the location that was unlinked. */
@@ -306,6 +549,10 @@ Int2 BLAST_FormatResults(SeqAlignPtr head, char* blast_database,
 
    } /* End loop on seqaligns for different queries */
 
+   if (format_options->align_view == 7 && mbxp) {
+      MBXmlClose(mbxp, NULL, format_options->ungapped);
+   }
+
    /* Free the mask locations. Note that mask_loc is not a real SeqLoc, 
       but a ValNode wrapper around the actual masking locations. */
    for (mask_loc = mask_loc_head; mask_loc; ) {
@@ -469,7 +716,7 @@ FormatBlastParameters(Uint1 program_number,
       add_string_to_buffer(buffer, &ret_buffer, &ret_buffer_length);
    }
 
-   if (hit_options->gapped_calculation) {
+   if (score_options->gapped_calculation) {
       sprintf(buffer, "Gap Penalties: Existence: %ld, Extension: %ld",
               (long) score_options->gap_open, 
               (long) score_options->gap_extend);
@@ -508,7 +755,7 @@ FormatBlastParameters(Uint1 program_number,
       }
       add_string_to_buffer(buffer, &ret_buffer, &ret_buffer_length);
    
-      if (hit_options->gapped_calculation) {
+      if (score_options->gapped_calculation) {
          sprintf(buffer, 
                  "Number of HSP's better than %4.1f without gapping: %ld", 
                  hit_options->expect_value, 
@@ -521,7 +768,8 @@ FormatBlastParameters(Uint1 program_number,
       }
    }
    BlastNumber2Program(program_number, &prog_name);
-   qlen = query_info->total_length;
+   /* Total query length does not include the first and last sentinel byte */
+   qlen = query_info->context_offsets[query_info->last_context+1] - 1;
    sfree(prog_name);
    sprintf(buffer, "length of query: %ld", (long)qlen);
    add_string_to_buffer(buffer, &ret_buffer, &ret_buffer_length);
@@ -540,7 +788,7 @@ FormatBlastParameters(Uint1 program_number,
    add_string_to_buffer(buffer, &ret_buffer, &ret_buffer_length);
    
    if (program_number == blast_type_blastn || 
-       !hit_options->gapped_calculation)
+       !score_options->gapped_calculation)
       kbp = sbp->kbp[query_info->first_context];
    else
       kbp = sbp->kbp_gap[query_info->first_context];
@@ -548,7 +796,7 @@ FormatBlastParameters(Uint1 program_number,
    sprintf(buffer, "X1: %ld (%4.1f bits)", 
            (long)return_stats->x_drop_ungapped, word_options->x_dropoff);
    add_string_to_buffer(buffer, &ret_buffer, &ret_buffer_length);
-   if (hit_options->gapped_calculation) {
+   if (score_options->gapped_calculation) {
       sprintf(buffer, "X2: %ld (%4.1f bits)", 
               (long)return_stats->x_drop_gap, ext_options->gap_x_dropoff);
       add_string_to_buffer(buffer, &ret_buffer, &ret_buffer_length);
@@ -565,9 +813,9 @@ FormatBlastParameters(Uint1 program_number,
    cutoff = 0;
    if (single_query) {
       evalue = hit_options->expect_value;
-      BLAST_Cutoffs_simple(&cutoff, &evalue, kbp,
+      BLAST_Cutoffs(&cutoff, &evalue, kbp,
          (double) query_info->eff_searchsp_array[query_info->first_context], 
-         FALSE);
+         FALSE, 0);
       sprintf(buffer, "S2: %ld (%4.1f bits)", (long) cutoff, 
               (((cutoff)*(kbp->Lambda))-(kbp->logK))/NCBIMATH_LN2);
       add_string_to_buffer(buffer, &ret_buffer, &ret_buffer_length);
@@ -771,7 +1019,7 @@ static void ScoreAndEvalueToBuffers(double bit_score, double evalue,
  * that prints results before the traceback stage, e.g. the on-the-fly 
  * tabular output, a la the -D3 option of the old megablast.
  */
-void BLAST_PrintIntermediateResults(BlastResults* results, 
+void BLAST_PrintIntermediateResults(BlastHSPResults* results, 
         BlastQueryInfo* query_info, SeqLocPtr query_slp, 
         ReadDBFILEPtr rdfp, SeqIdPtr seqid, BlastScoreBlk* sbp, 
         char* filename)
diff --git a/algo/blast/api/blast_format.h b/algo/blast/api/blast_format.h
index 3128a53a..8e1da44b 100644
--- a/algo/blast/api/blast_format.h
+++ b/algo/blast/api/blast_format.h
@@ -1,4 +1,4 @@
-/* $Id: blast_format.h,v 1.15 2003/08/25 22:25:46 dondosha Exp $
+/* $Id: blast_format.h,v 1.17 2003/12/03 17:30:24 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@ Author: Ilya Dondoshansky
 Contents: Functions needed for formatting of BLAST results
 
 ******************************************************************************
- * $Revision: 1.15 $
+ * $Revision: 1.17 $
  * */
 #ifndef __BLAST_FORMAT__
 #define __BLAST_FORMAT__
@@ -61,7 +61,7 @@ typedef struct BlastFormattingOptions {
    Uint4 print_options;
    Boolean believe_query;
    Boolean html;
-   FILE *outfp;
+   void* outfp; /**< Output file: either FILE* or AsnIoPtr */
    Int4 number_of_descriptions;
    Int4 number_of_alignments;
    Boolean ungapped; /**< Should this be here????? */
@@ -116,7 +116,7 @@ typedef struct MBXml {
  */
 Int2 BLAST_FormatResults(SeqAlignPtr head, char* blast_database,
         char* blast_program, Int4 num_queries, 
-        SeqLocPtr query_slp, BlastMask* mask_loc, 
+        SeqLocPtr query_slp, BlastMaskLoc* mask_loc, 
         BlastFormattingOptions* format_options, Boolean is_ooframe);
 
 /** Print the summary at the end of the BLAST report.
@@ -145,7 +145,7 @@ Int2 PrintOutputFooter(Uint1 program_number,
 Int2 BLAST_PrintOutputHeader(BlastFormattingOptions* format_options,
         Boolean greedy_extension, ReaddbNewArgs* readdb_args);
 
-void BLAST_PrintIntermediateResults(BlastResults* results, 
+void BLAST_PrintIntermediateResults(BlastHSPResults* results, 
         BlastQueryInfo* query_info, SeqLocPtr query_slp, 
         ReadDBFILEPtr rdfp, SeqIdPtr seqid, BlastScoreBlk* sbp, 
         char* filename);
diff --git a/algo/blast/api/blast_input.c b/algo/blast/api/blast_input.c
index 04836b73..dcf2edbc 100644
--- a/algo/blast/api/blast_input.c
+++ b/algo/blast/api/blast_input.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: blast_input.c,v 1.8 2003/09/15 21:18:30 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_input.c,v 1.10 2003/12/03 17:30:25 dondosha Exp $";
 /* ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -31,30 +31,30 @@ Author: Ilya Dondoshansky
 
 Contents: Reading FASTA sequences for BLAST
 
-$Revision: 1.8 $
+$Revision: 1.10 $
 
 ******************************************************************************/
 #include <objloc.h>
 #include <tofasta.h>
-#include "blast_input.h"
-#include "blast_seq.h"
+#include <algo/blast/api/blast_input.h>
+#include <algo/blast/api/blast_seq.h>
 
 #define MAX_NUM_QUERIES 16383 /* == 1/2 INT2_MAX */
 #define MAX_TOTAL_LENGTH 20000000
 
 Boolean
 BLAST_GetQuerySeqLoc(FILE *infp, Boolean query_is_na, Uint1 strand,
-   Int4 start, Int4 end, BlastMask** lcase_mask, SeqLocPtr* query_slp, 
+   Int4 start, Int4 end, BlastMaskLoc** lcase_mask, SeqLocPtr* query_slp, 
    Int4 ctr_start, Int4* num_queries)
 {
    Int8 total_length;
    BioseqPtr query_bsp;
    SeqLocPtr mask_slp, last_slp;
-   BlastMask* last_mask;
+   BlastMaskLoc* last_mask;
    char prefix[2];     /* for FastaToSeqEntryForDb */
    Int2 ctr = ctr_start + 1; /* Counter for FastaToSeqEntryForDb */
    Int4 query_index = 0;
-   BlastMask* new_mask;
+   BlastMaskLoc* new_mask;
    SeqEntryPtr sep;
    Boolean done = TRUE;
    Int4 from, to;
@@ -79,7 +79,7 @@ BLAST_GetQuerySeqLoc(FILE *infp, Boolean query_is_na, Uint1 strand,
                                     &ctr, (lcase_mask ? &mask_slp : NULL))) != NULL)
    {
       if (mask_slp) {
-         new_mask = BlastMaskFromSeqLoc(mask_slp, query_index);
+         new_mask = BlastMaskLocFromSeqLoc(mask_slp, query_index);
          
          if (!last_mask)
             *lcase_mask = last_mask = new_mask;
diff --git a/algo/blast/api/blast_input.h b/algo/blast/api/blast_input.h
index 60f3be47..2db0736d 100644
--- a/algo/blast/api/blast_input.h
+++ b/algo/blast/api/blast_input.h
@@ -1,4 +1,4 @@
-/* $Id: blast_input.h,v 1.9 2003/08/25 22:25:46 dondosha Exp $
+/* $Id: blast_input.h,v 1.10 2003/12/03 17:30:25 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -31,7 +31,7 @@ Author: Ilya Dondoshansky
 
 Contents: Reading FASTA sequences for BLAST
 
-$Revision: 1.9 $
+$Revision: 1.10 $
 
 ******************************************************************************/
 
@@ -65,7 +65,7 @@ extern "C" {
  */
 Boolean
 BLAST_GetQuerySeqLoc(FILE *infp, Boolean query_is_na, Uint1 strand,
-   Int4 from, Int4 to, BlastMask** lcase_mask, SeqLocPtr* query_slp, Int4 ctr_start,
+   Int4 from, Int4 to, BlastMaskLoc** lcase_mask, SeqLocPtr* query_slp, Int4 ctr_start,
    Int4* num_queries);
 
 /** Given a file containing sequence(s) in fasta format,
diff --git a/algo/blast/api/blast_seq.c b/algo/blast/api/blast_seq.c
index a905801d..d3a2ced0 100644
--- a/algo/blast/api/blast_seq.c
+++ b/algo/blast/api/blast_seq.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: blast_seq.c,v 1.26 2003/09/17 16:20:56 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_seq.c,v 1.33 2003/12/03 17:30:25 dondosha Exp $";
 /*
 * ===========================================================================
 *
@@ -33,20 +33,20 @@ Author: Ilya Dondoshansky
 Contents: Functions converting between SeqLocs and structures used in BLAST.
 
 ******************************************************************************
- * $Revision: 1.26 $
+ * $Revision: 1.33 $
  * */
 
 #include <seqport.h>
 #include <sequtil.h>
 #include <objloc.h>
-#include "blast_seq.h"
+#include <algo/blast/api/blast_seq.h>
 #include <algo/blast/core/blast_filter.h>
 #include <algo/blast/core/blast_util.h>
 #include <algo/blast/core/blast_stat.h> /* Needed for NCBI4NA_TO_BLASTNA definition only */
 
-BlastMask* BlastMaskFromSeqLoc(SeqLocPtr mask_slp, Int4 index)
+BlastMaskLoc* BlastMaskLocFromSeqLoc(SeqLocPtr mask_slp, Int4 index)
 {
-   BlastMask* new_mask = (BlastMask*) calloc(1, sizeof(BlastMask));
+   BlastMaskLoc* new_mask = (BlastMaskLoc*) calloc(1, sizeof(BlastMaskLoc));
    BlastSeqLoc* loc,* last_loc = NULL,* head_loc = NULL;
    SeqIntPtr si;
 
@@ -69,7 +69,7 @@ BlastMask* BlastMaskFromSeqLoc(SeqLocPtr mask_slp, Int4 index)
    return new_mask;
 }
 
-SeqLocPtr BlastMaskToSeqLoc(Uint1 program_number, BlastMask* mask_loc, 
+SeqLocPtr BlastMaskLocToSeqLoc(Uint1 program_number, BlastMaskLoc* mask_loc, 
                             SeqLocPtr slp)
 {
    BlastSeqLoc* loc;
@@ -142,10 +142,10 @@ SeqLocPtr BlastMaskToSeqLoc(Uint1 program_number, BlastMask* mask_loc,
    return mask_head;
 }
 
-Int2 BlastMaskDNAToProtein(BlastMask** mask_loc_ptr, SeqLocPtr slp)
+Int2 BlastMaskLocDNAToProtein(BlastMaskLoc** mask_loc_ptr, SeqLocPtr slp)
 {
    Int2 status = 0;
-   BlastMask* last_mask = NULL,* head_mask = NULL,* mask_loc; 
+   BlastMaskLoc* last_mask = NULL,* head_mask = NULL,* mask_loc; 
    Int4 dna_length;
    BlastSeqLoc* dna_loc,* prot_loc_head,* prot_loc_last;
    DoubleInt* dip;
@@ -168,9 +168,9 @@ Int2 BlastMaskDNAToProtein(BlastMask** mask_loc_ptr, SeqLocPtr slp)
          coordinates */
       for (context = 0; context < NUM_FRAMES; ++context) {
          if (!last_mask) {
-            head_mask = last_mask = (BlastMask *) calloc(1, sizeof(BlastMask));
+            head_mask = last_mask = (BlastMaskLoc *) calloc(1, sizeof(BlastMaskLoc));
          } else {
-            last_mask->next = (BlastMask *) calloc(1, sizeof(BlastMask));
+            last_mask->next = (BlastMaskLoc *) calloc(1, sizeof(BlastMaskLoc));
             last_mask = last_mask->next;
          }
          
@@ -203,7 +203,7 @@ Int2 BlastMaskDNAToProtein(BlastMask** mask_loc_ptr, SeqLocPtr slp)
    }
 
    /* Free the mask with nucleotide coordinates */
-   BlastMaskFree(*mask_loc_ptr);
+   BlastMaskLocFree(*mask_loc_ptr);
    /* Return the new mask with protein coordinates */
    *mask_loc_ptr = head_mask;
 
@@ -211,11 +211,11 @@ Int2 BlastMaskDNAToProtein(BlastMask** mask_loc_ptr, SeqLocPtr slp)
 }
 
 
-Int2 BlastMaskProteinToDNA(BlastMask** mask_loc_ptr, SeqLocPtr slp)
+Int2 BlastMaskLocProteinToDNA(BlastMaskLoc** mask_loc_ptr, SeqLocPtr slp)
 {
    Int2 status = 0;
    Int4 index;
-   BlastMask* mask_loc;
+   BlastMaskLoc* mask_loc;
    BlastSeqLoc* loc;
    DoubleInt* dip;
    Int4 dna_length;
@@ -270,6 +270,7 @@ static Int4 BLAST_SetUpQueryInfo(SeqLocPtr slp, Uint1 program,
    BlastQueryInfo* query_info;
    Int4* context_offsets;
    Int4 index;
+   Int4 total_contexts;
 
    if (translate)
       num_frames = 6;
@@ -285,6 +286,8 @@ static Int4 BLAST_SetUpQueryInfo(SeqLocPtr slp, Uint1 program,
    query_info->first_context = 0;
    query_info->num_queries = ValNodeLen(slp);
    query_info->last_context = query_info->num_queries*num_frames - 1;
+   total_contexts = query_info->last_context + 1;
+
    if ((strand = SeqLocStrand(slp)) == Seq_strand_minus) {
       if (translate)
          query_info->first_context = 3;
@@ -298,14 +301,14 @@ static Int4 BLAST_SetUpQueryInfo(SeqLocPtr slp, Uint1 program,
    }
 
    if ((context_offsets = (Int4*) 
-      malloc((query_info->last_context+2)*sizeof(Int4))) == NULL)
+      malloc((total_contexts+1)*sizeof(Int4))) == NULL)
       return -1;
 
    if ((query_info->eff_searchsp_array = 
-      (Int8*) malloc((query_info->last_context+1)*sizeof(Int8))) == NULL)
+      (Int8*) malloc(total_contexts*sizeof(Int8))) == NULL)
       return -1;
    if ((query_info->length_adjustments =
-        (Int4*) malloc((query_info->last_context+1)*sizeof(Int4))) == NULL)
+        (Int4*) malloc(total_contexts*sizeof(Int4))) == NULL)
        return -1;
 
    context_offsets[0] = 0;
@@ -352,7 +355,6 @@ static Int4 BLAST_SetUpQueryInfo(SeqLocPtr slp, Uint1 program,
          context_offsets[index+1] = context_offsets[index] + length + 1;
       }
    }
-   query_info->total_length = context_offsets[index];
 
    *query_info_ptr = query_info;
    return 0;
diff --git a/algo/blast/api/blast_seq.h b/algo/blast/api/blast_seq.h
index 967e48c6..54065509 100644
--- a/algo/blast/api/blast_seq.h
+++ b/algo/blast/api/blast_seq.h
@@ -1,4 +1,4 @@
-/* $Id: blast_seq.h,v 1.8 2003/08/25 22:25:46 dondosha Exp $
+/* $Id: blast_seq.h,v 1.9 2003/12/03 17:30:25 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -35,7 +35,7 @@ Contents: Functions converting from SeqLocs to structures used in BLAST and
 Detailed Contents: 
 
 ******************************************************************************
- * $Revision: 1.8 $
+ * $Revision: 1.9 $
  * */
 #ifndef __BLAST_SEQ__
 #define __BLAST_SEQ__
@@ -54,18 +54,18 @@ extern "C" {
 
 #define NUM_FRAMES 6
 
-/** Convert a SeqLoc of type int or packed_int to a BlastMask structure.
+/** Convert a SeqLoc of type int or packed_int to a BlastMaskLoc structure.
  * @param mask_slp The SeqLoc to be converted [in]
  * @param index The ordinal number of the sequence to be assigned to the new 
- *              BlastMask
- * @return Pointer to the allocated BlastMask structure.
+ *              BlastMaskLoc
+ * @return Pointer to the allocated BlastMaskLoc structure.
  */
-BlastMask* BlastMaskFromSeqLoc(SeqLocPtr mask_slp, Int4 index);
+BlastMaskLoc* BlastMaskLocFromSeqLoc(SeqLocPtr mask_slp, Int4 index);
 
-/** Convert a BlastMask list to a list of SeqLocs, used for formatting 
+/** Convert a BlastMaskLoc list to a list of SeqLocs, used for formatting 
  * BLAST results.
  */
-SeqLocPtr BlastMaskToSeqLoc(Uint1 program_number, BlastMask* mask_loc, 
+SeqLocPtr BlastMaskLocToSeqLoc(Uint1 program_number, BlastMaskLoc* mask_loc, 
                             SeqLocPtr slp);
 
 /** Duplicate masks in 6 frames for each nucleotide sequence, converting
@@ -73,13 +73,13 @@ SeqLocPtr BlastMaskToSeqLoc(Uint1 program_number, BlastMask* mask_loc,
  * @param mask_loc_ptr Masks list to be modified [in] [out]
  * @param slp List of nucleotide query SeqLoc's [in]
  */
-Int2 BlastMaskDNAToProtein(BlastMask** mask_loc_ptr, SeqLocPtr slp);
+Int2 BlastMaskLocDNAToProtein(BlastMaskLoc** mask_loc_ptr, SeqLocPtr slp);
 
 /** Convert all masks' protein coordinates to nucleotide.
  * @param mask_loc_ptr Masks list to be modified [in] [out]
  * @param slp List of nucleotide query SeqLoc's [in]
  */
-Int2 BlastMaskProteinToDNA(BlastMask** mask_loc_ptr, SeqLocPtr slp);
+Int2 BlastMaskLocProteinToDNA(BlastMaskLoc** mask_loc_ptr, SeqLocPtr slp);
 
 /** Given a list of query SeqLoc's, create the sequence block and the query
  * info structure. This is the last time SeqLoc is needed before formatting.
diff --git a/algo/blast/api/blast_seqalign.c b/algo/blast/api/blast_seqalign.c
index d9754dc0..36445ec9 100644
--- a/algo/blast/api/blast_seqalign.c
+++ b/algo/blast/api/blast_seqalign.c
@@ -1,4 +1,4 @@
-/* $Id: blast_seqalign.c,v 1.24 2003/09/15 21:18:30 dondosha Exp $
+/* $Id: blast_seqalign.c,v 1.27 2003/12/03 17:30:25 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,12 +32,12 @@ Author: Ilya Dondoshansky
 Contents: Conversion of BLAST results to the SeqAlign form
 
 ******************************************************************************
- * $Revision: 1.24 $
+ * $Revision: 1.27 $
  * */
 
-static char const rcsid[] = "$Id: blast_seqalign.c,v 1.24 2003/09/15 21:18:30 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_seqalign.c,v 1.27 2003/12/03 17:30:25 dondosha Exp $";
 
-#include "blast_seqalign.h"
+#include <algo/blast/api/blast_seqalign.h>
 
 extern Int4 LIBCALL HspArrayPurge PROTO((BlastHSP** hsp_array, 
                        Int4 hspcnt, Boolean clear_num));
@@ -1321,7 +1321,7 @@ BLAST_GapInfoToSeqAlign(Uint1 program_number, BlastHSPList* hsp_list,
 }
 
 Int2 BLAST_ResultsToSeqAlign(Uint1 program_number, 
-        BlastResults* results, SeqLocPtr query_slp, 
+        BlastHSPResults* results, SeqLocPtr query_slp, 
         BlastSeqSrc* bssp, SeqLocPtr subject_slp,
         BlastScoringOptions* score_options, BlastScoreBlk* sbp,
         Boolean is_gapped, SeqAlignPtr* head_seqalign)
@@ -1357,6 +1357,7 @@ Int2 BLAST_ResultsToSeqAlign(Uint1 program_number,
             char* id_str = BLASTSeqSrcGetSeqIdStr(bssp, (void*) &hsp_list->oid);
             subject_id = SeqIdParse(id_str);
             subject_length = BLASTSeqSrcGetSeqLen(bssp, (void*) &hsp_list->oid); 
+            sfree(id_str);
          }
          if (is_gapped) {
             BLAST_GapInfoToSeqAlign(program_number, hsp_list, query_id, 
diff --git a/algo/blast/api/blast_seqalign.h b/algo/blast/api/blast_seqalign.h
index 76c83b04..3a6fa3e0 100644
--- a/algo/blast/api/blast_seqalign.h
+++ b/algo/blast/api/blast_seqalign.h
@@ -1,4 +1,4 @@
-/* $Id: blast_seqalign.h,v 1.11 2003/08/25 22:25:46 dondosha Exp $
+/* $Id: blast_seqalign.h,v 1.12 2003/12/03 17:30:26 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@ Author: Ilya Dondoshansky
 Contents: Functions to convert BLAST results to the SeqAlign form
 
 ******************************************************************************
- * $Revision: 1.11 $
+ * $Revision: 1.12 $
  * */
 #ifndef __BLAST_SEQALIGN__
 #define __BLAST_SEQALIGN__
@@ -62,7 +62,7 @@ extern "C" {
  * @param is_gapped Is this a gapped alignment search? [in]
  * @param head_seqalign List of SeqAlign's [out]
  */
-Int2 BLAST_ResultsToSeqAlign(Uint1 program_number, BlastResults* results, 
+Int2 BLAST_ResultsToSeqAlign(Uint1 program_number, BlastHSPResults* results, 
         SeqLocPtr query_slp, BlastSeqSrc* bssp, SeqLocPtr subject_slp, 
         BlastScoringOptions* score_options, BlastScoreBlk* sbp,
         Boolean is_gapped, SeqAlignPtr* head_seqalign);
diff --git a/algo/blast/api/nmakefile b/algo/blast/api/nmakefile
deleted file mode 100644
index 19547aad..00000000
--- a/algo/blast/api/nmakefile
+++ /dev/null
@@ -1,35 +0,0 @@
-CC=cl.exe
-CFLAGS=/nologo /DWIN32 -I\\dizzy\public\ncbi\include /I..\include
-LIB=lib.exe
-LINK=link.exe
-LDFLAGS=/nologo /libpath:\\dizzy\public\ncbi\Release /libpath:. /nodefaultlib:msvcrt.lib
-LIBS=blast.lib ncbitool.lib ncbiobj.lib ncbimmdb.lib ncbimain.lib ncbi.lib user32.lib
-
-OBJ=aa_lookup.obj\
-aa_ungapped.obj\
-blast_dust.obj\
-blast_engine.obj\
-blast_extend.obj\
-blast_filter.obj\
-blast_format.obj\
-blast_gapalign.obj\
-blast_hits.obj\
-blast_message.obj\
-blast_seg.obj\
-blast_seqalign.obj\
-blast_traceback.obj\
-blast_util.obj\
-mb_lookup.obj\
-na_lookup.obj\
-util.obj
-
-all: blast.lib blast_driver.exe
-
-blast.lib : $(OBJ)
-	$(LIB) /out:blast.lib $(OBJ)
-
-blast_driver.exe : blast_driver.obj blast_options.obj blast_setup.obj blast.lib
-	$(LINK) $(LDFLAGS) /out:blast_driver.exe blast_driver.obj blast_options.obj blast_setup.obj $(LIBS)
-
-clean:
-	del *.obj blast_driver.exe
diff --git a/algo/blast/api/seqsrc_readdb.c b/algo/blast/api/seqsrc_readdb.c
index f7e367d9..eff22dfd 100644
--- a/algo/blast/api/seqsrc_readdb.c
+++ b/algo/blast/api/seqsrc_readdb.c
@@ -1,4 +1,4 @@
-/*  $Id: seqsrc_readdb.c,v 1.9 2003/09/15 21:18:30 dondosha Exp $
+/*  $Id: seqsrc_readdb.c,v 1.16 2004/01/30 23:50:27 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -30,9 +30,9 @@
 *
 */
 
-static char const rcsid[] = "$Id: seqsrc_readdb.c,v 1.9 2003/09/15 21:18:30 dondosha Exp $";
+static char const rcsid[] = "$Id: seqsrc_readdb.c,v 1.16 2004/01/30 23:50:27 dondosha Exp $";
 
-#include "seqsrc_readdb.h"
+#include <algo/blast/api/seqsrc_readdb.h>
 #include <algo/blast/core/blast_def.h>
 #include <algo/blast/core/blast_util.h>
 
@@ -74,6 +74,53 @@ static Int8 ReaddbGetTotLen(void* readdb_handle, void* ignoreme)
     return dblength;
 }
 
+/** Retrieves the name of the BLAST database.
+ * @param readdb_handle Pointer to initialized ReadDBFILEPtr structure [in]
+ * @param ignoreme Unused by this implementation [in]
+ */
+static char* ReaddbGetName(void* readdb_handle, void* ignoreme)
+{
+    ReadDBFILEPtr rdfp = (ReadDBFILEPtr) readdb_handle;
+
+    return strdup(readdb_get_filename(rdfp));
+}
+
+/** Retrieves the definition of the BLAST database.
+ * @param readdb_handle Pointer to initialized ReadDBFILEPtr structure [in]
+ * @param ignoreme Unused by this implementation [in]
+ */
+static char* ReaddbGetDefinition(void* readdb_handle, void* ignoreme)
+{
+    ReadDBFILEPtr rdfp = (ReadDBFILEPtr) readdb_handle;
+    char* definition = NULL;
+    
+    if ((definition = readdb_get_title(rdfp)) == NULL)
+       definition = readdb_get_filename(rdfp);
+    return strdup(definition);
+}
+
+/** Retrieves the date of the BLAST database.
+ * @param readdb_handle Pointer to initialized ReadDBFILEPtr structure [in]
+ * @param ignoreme Unused by this implementation [in]
+ */
+static char* ReaddbGetDate(void* readdb_handle, void* ignoreme)
+{
+    ReadDBFILEPtr rdfp = (ReadDBFILEPtr) readdb_handle;
+
+    return strdup(readdb_get_date(rdfp));
+}
+
+/** Retrieves the date of the BLAST database.
+ * @param readdb_handle Pointer to initialized ReadDBFILEPtr structure [in]
+ * @param ignoreme Unused by this implementation [in]
+ */
+static Boolean ReaddbGetIsProt(void* readdb_handle, void* ignoreme)
+{
+    ReadDBFILEPtr rdfp = (ReadDBFILEPtr) readdb_handle;
+
+    return readdb_is_prot(rdfp);
+}
+
 /** Retrieves the sequence meeting the criteria defined by its second argument.
  * @param readdb_handle Pointer to initialized ReadDBFILEPtr structure [in]
  * @param args Pointer to GetSeqArg structure [in]
@@ -153,6 +200,31 @@ static char* ReaddbGetSeqIdStr(void* readdb_handle, void* args)
     return seqid_str;
 }
 
+/** Retrieves the sequence identifier meeting the criteria defined by its 
+ * second argument. Currently it is an ordinal id (integer value).
+ * Client code is responsible for deallocating the return value. 
+ * @param readdb_handle Pointer to initialized ReadDBFILEPtr structure [in]
+ * @param args Pointer to integer indicating ordinal id [in]
+ * @return Sequence id structure generated from ASN.1 spec, 
+ *         cast to a void pointer.
+ */
+static void* ReaddbGetSeqId(void* readdb_handle, void* args)
+{
+    ReadDBFILEPtr rdfp = (ReadDBFILEPtr) readdb_handle;
+    Int4* oid = (Int4*) args;
+    SeqIdPtr sip = NULL;
+    char *seqid_str = NULL;
+
+    if (!rdfp || !oid)
+        return NULL;
+
+    if (!readdb_get_descriptor(rdfp, *oid, &sip, NULL)) {
+        return NULL;
+    }
+
+    return (void*) sip;
+}
+
 /** Retrieve length of a given database sequence.
  * @param readdb_handle Pointer to initialized ReadDBFILEPtr structure [in]
  * @param args Pointer to integer indicating ordinal id [in]
@@ -222,18 +294,35 @@ static Int2 ReaddbGetNextChunk(void* readdb_handle, BlastSeqSrcIterator* itr)
 {
     ReadDBFILEPtr rdfp = (ReadDBFILEPtr) readdb_handle;
     OIDListPtr oidlist = ReaddbFetchFirstOIDList(rdfp);
-    static unsigned int current_oid = 0;
     unsigned int nseqs;
 
     if (!rdfp || !itr)
         return BLAST_SEQSRC_ERROR;
 
-    /* call get_totals_ex2?: need a less expensive and accurate way of doing 
-     * this */
-    nseqs = ReaddbGetNumberOfSeqs(rdfp);
-    if (current_oid >= nseqs) {
-        return BLAST_SEQSRC_EOF;
+
+    if (itr->next_oid < rdfp->start)
+       itr->next_oid = rdfp->start;
+
+    while (rdfp) {
+       if (rdfp->stop > 0) {
+          nseqs = rdfp->stop + 1;
+       } else {
+          /* call get_totals_ex2?: need a less expensive and accurate way of 
+             doing this */
+          nseqs = ReaddbGetNumberOfSeqs(rdfp);
+       }
+
+
+       if (itr->next_oid >= nseqs) {
+          if (nseqs < rdfp->num_seqs)
+             itr->next_oid = UINT4_MAX;
+          rdfp = rdfp->next;
+       } else {
+          break;
+       }
     }
+    if (!rdfp)
+       return BLAST_SEQSRC_EOF;
 
     if (oidlist) {
         itr->itr_type = eOidList;
@@ -243,9 +332,9 @@ static Int2 ReaddbGetNextChunk(void* readdb_handle, BlastSeqSrcIterator* itr)
     } else {
         itr->itr_type = eOidRange;
         NlmMutexLockEx(&ReaddbMutex);
-        itr->current_pos = itr->oid_range[0] = current_oid;
-        itr->oid_range[1] = MIN(current_oid + itr->chunk_sz, nseqs);
-        current_oid = itr->oid_range[1];
+        itr->current_pos = itr->oid_range[0] = itr->next_oid;
+        itr->oid_range[1] = MIN(itr->next_oid + itr->chunk_sz, nseqs);
+        itr->next_oid = itr->oid_range[1];
         NlmMutexUnlock(ReaddbMutex);
     }
 
@@ -305,19 +394,30 @@ BlastSeqSrc* ReaddbSeqSrcNew(BlastSeqSrc* retval, void* args)
     if ( !(rdfp = readdb_new(rargs->dbname, rargs->is_protein)))
         return NULL;
 
-    /* Initialize the BlastSeqSrc structure fields with used-defined function
+    /* Initialize the BlastSeqSrc structure fields with user-defined function
      * pointers and rdfp */
     SetDeleteFnPtr(retval, &ReaddbSeqSrcFree);
     SetDataStructure(retval, (void*) rdfp);
     SetGetNumSeqs(retval, &ReaddbGetNumSeqs);
     SetGetMaxSeqLen(retval, &ReaddbGetMaxLength);
     SetGetTotLen(retval, &ReaddbGetTotLen);
+    SetGetName(retval, &ReaddbGetName);
+    SetGetDefinition(retval, &ReaddbGetDefinition);
+    SetGetDate(retval, &ReaddbGetDate);
+    SetGetIsProt(retval, &ReaddbGetIsProt);
     SetGetSequence(retval, &ReaddbGetSequence);
     SetGetSeqIdStr(retval, &ReaddbGetSeqIdStr);
+    SetGetSeqId(retval, &ReaddbGetSeqId);
     SetGetSeqLen(retval, &ReaddbGetSeqLen);
     SetGetNextChunk(retval, &ReaddbGetNextChunk);
     SetIterNext(retval, &ReaddbIteratorNext);
 
+    /* Set the range, if it is specified */
+    if (rargs->first_db_seq > 0)
+       rdfp->start = rargs->first_db_seq;
+    if (rargs->final_db_seq > 0)
+       rdfp->stop = rargs->final_db_seq;
+
     return retval;
 }
 
diff --git a/algo/blast/api/seqsrc_readdb.h b/algo/blast/api/seqsrc_readdb.h
index 6aa6abe7..cf0d5bf2 100644
--- a/algo/blast/api/seqsrc_readdb.h
+++ b/algo/blast/api/seqsrc_readdb.h
@@ -1,4 +1,4 @@
-/*  $Id: seqsrc_readdb.h,v 1.7 2003/08/19 22:05:44 camacho Exp $
+/*  $Id: seqsrc_readdb.h,v 1.8 2003/12/03 16:50:37 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -51,6 +51,8 @@ extern "C" {
 typedef struct ReaddbNewArgs {
     char* dbname;     /**< Database name */
     Boolean is_protein; /**< Is this database protein? */
+   Int4 first_db_seq; /**< Ordinal id of the first sequence to search */
+   Int4 final_db_seq; /**< Ordinal id of the last sequence to search */
 } ReaddbNewArgs;
 
 /** Readdb sequence source constructor 
diff --git a/algo/blast/core/blast_def.h b/algo/blast/core/blast_def.h
index b605815b..c097ca8c 100644
--- a/algo/blast/core/blast_def.h
+++ b/algo/blast/core/blast_def.h
@@ -1,4 +1,4 @@
-/* $Id: blast_def.h,v 1.27 2003/10/15 16:59:43 coulouri Exp $
+/* $Id: blast_def.h,v 1.29 2003/12/03 16:31:45 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@ Contents: Definitions of major structures used throughout BLAST
 Detailed Contents: 
 
 ******************************************************************************
- * $Revision: 1.27 $
+ * $Revision: 1.29 $
  * */
 #ifndef __BLAST_DEF__
 #define __BLAST_DEF__
@@ -73,11 +73,11 @@ void __sfree(void** x); /* implemented in lib/util.c */
 #endif
 
 /** Structure for keeping the query masking information */
-typedef struct BlastMask {
+typedef struct BlastMaskLoc {
    Int4 index; /**< Index of the query sequence this mask is applied to */
    ListNode* loc_list; /**< List of mask locations */
-   struct BlastMask* next; /**< Pointer to the next query mask */
-} BlastMask;
+   struct BlastMaskLoc* next; /**< Pointer to the next query mask */
+} BlastMaskLoc;
 
 /** Structure to hold a sequence. */
 typedef struct BLAST_SequenceBlk {
@@ -94,7 +94,7 @@ typedef struct BLAST_SequenceBlk {
                                         for sequence_start */
    Uint1* oof_sequence; /**< Mixed-frame protein representation of a
                              nucleotide sequence for out-of-frame alignment */
-   BlastMask* lcase_mask; /**< Locations to be masked from operations on this 
+   BlastMaskLoc* lcase_mask; /**< Locations to be masked from operations on this 
                            sequence: lookup table for query; scanning for
                            subject. */
 } BLAST_SequenceBlk;
@@ -105,7 +105,6 @@ typedef struct BlastQueryInfo {
    Int2 first_context; /**< Index of the first element of the context array */
    Int2 last_context;  /**< Index of the last element of the context array */
    int num_queries;   /**< Number of query sequences */
-   Int4 total_length; /**< Total length of all query sequences/strands/frames */
    Int4* context_offsets; /**< Offsets of the individual queries in the
                                concatenated super-query */
    Int4* length_adjustments; /**< Length adjustments for boundary conditions */
diff --git a/algo/blast/core/blast_dust.c b/algo/blast/core/blast_dust.c
index becb7636..48eec873 100644
--- a/algo/blast/core/blast_dust.c
+++ b/algo/blast/core/blast_dust.c
@@ -30,7 +30,7 @@ static char const rcsid[] = "$Id";
 *   
 * Version Creation Date: 05/28/2003
 *
-* $Revision: 1.16 $
+* $Revision: 1.17 $
 *
 * File Description: A utility to find low complexity NA regions.
 *                   This parallels functionality of dust.c from the C toolkit,
@@ -206,7 +206,6 @@ dust_triplet_find (Uint1* seq_start, Int4 icur, Int4 max, Uint1* s1)
    Int4 n;
    Uint1* s2,* s3;
    Int2 c;
-   Boolean flagVD;
    Uint1* seq = &seq_start[icur];
    Uint1 end_byte = NCBI4NA_TO_BLASTNA[NULLB];
    
@@ -232,7 +231,6 @@ dust_triplet_find (Uint1* seq_start, Int4 icur, Int4 max, Uint1* s1)
    *s2 |= c;
    
    /* triplet fill loop */
-   flagVD = TRUE;
    while ((c = *seq++) != end_byte && n < max) {
       c &= NCBI_2NA_MASK;
       *s1 <<= 2;
diff --git a/algo/blast/core/blast_engine.c b/algo/blast/core/blast_engine.c
index c894e41f..864ca6e9 100644
--- a/algo/blast/core/blast_engine.c
+++ b/algo/blast/core/blast_engine.c
@@ -1,4 +1,4 @@
-/* $Id: blast_engine.c,v 1.86 2003/10/27 23:50:29 dondosha Exp $
+/* $Id: blast_engine.c,v 1.97 2003/12/10 21:31:26 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@ Contents: High level BLAST functions
 
 ******************************************************************************/
 
-static char const rcsid[] = "$Id: blast_engine.c,v 1.86 2003/10/27 23:50:29 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_engine.c,v 1.97 2003/12/10 21:31:26 dondosha Exp $";
 
 #include <algo/blast/core/blast_engine.h>
 #include <algo/blast/core/lookup_wrap.h>
@@ -195,6 +195,11 @@ BLAST_SearchEngineCore(Uint1 program_number, BLAST_SequenceBlk* query,
       combined_hsp_list = NULL;
       
       for (chunk = 0; chunk < num_chunks; ++chunk) {
+         if (chunk > 0) {
+            offset += subject->length - DBSEQ_CHUNK_OVERLAP;
+            subject->sequence += 
+               (subject->length - DBSEQ_CHUNK_OVERLAP)/COMPRESSION_RATIO;
+         }
          subject->length = MIN(total_subject_length - offset, 
                                MAX_DBSEQ_LEN);
          
@@ -203,7 +208,7 @@ BLAST_SearchEngineCore(Uint1 program_number, BLAST_SequenceBlk* query,
          return_stats->db_hits +=
             aux_struct->WordFinder(subject, query, lookup, 
                gap_align->sbp->matrix, word_params, ewp, query_offsets, 
-               subject_offsets, OFFSET_ARRAY_SIZE, init_hitlist);
+               subject_offsets, GetOffsetArraySize(lookup), init_hitlist);
             
          if (init_hitlist->total == 0)
             continue;
@@ -249,7 +254,7 @@ BLAST_SearchEngineCore(Uint1 program_number, BLAST_SequenceBlk* query,
          if (hit_options->do_sum_stats == TRUE) {
             status = BLAST_LinkHsps(program_number, hsp_list, query_info,
                         subject, gap_align->sbp, hit_params, 
-                        hit_options->gapped_calculation);
+                        score_options->gapped_calculation);
          } else if (hit_options->phi_align) {
             /* These e-values will not be accurate yet, since we don't know
                the number of pattern occurrencies in the database. That
@@ -259,7 +264,7 @@ BLAST_SearchEngineCore(Uint1 program_number, BLAST_SequenceBlk* query,
             /* Calculate e-values for all HSPs */
             status = 
                BLAST_GetNonSumStatsEvalue(program_number, query_info, 
-                  hsp_list, hit_options, gap_align->sbp);
+                  hsp_list, score_options, gap_align->sbp);
          }
 
          /* Discard HSPs that don't pass the e-value test */
@@ -269,13 +274,10 @@ BLAST_SearchEngineCore(Uint1 program_number, BLAST_SequenceBlk* query,
          /* Allow merging of HSPs either if traceback is already 
             available, or if it is an ungapped search */
          if (MergeHSPLists(hsp_list, &combined_hsp_list, offset,
-             (Uint1) (hsp_list->traceback_done || !hit_options->gapped_calculation), FALSE)) {
+             (Uint1) (hsp_list->traceback_done || !score_options->gapped_calculation), FALSE)) {
             /* HSPs from this list are moved elsewhere, reset count to 0 */
             hsp_list->hspcnt = 0;
          }
-         offset += subject->length - DBSEQ_CHUNK_OVERLAP;
-         subject->sequence += 
-            (subject->length - DBSEQ_CHUNK_OVERLAP)/COMPRESSION_RATIO;
       } /* End loop on chunks of subject sequence */
       
       MergeHSPLists(combined_hsp_list, hsp_list_out, 0, 
@@ -312,28 +314,80 @@ FillReturnXDropoffsInfo(BlastReturnStat* return_stats,
    return 0;
 }
 
+/* Computes the effective search space for the given parameters */
+static
+Int8 ComputeEffectiveSearchSpace(BLAST_KarlinBlk* kbp, /* [in] */
+                                 Uint1 program_number, /* [in] */
+                                 Int4 query_length,    /* [in] */
+                                 const BlastScoringOptions* 
+                                 scoring_options,      /* [in] */
+                                 double alpha,         /* [in] */
+                                 double beta,          /* [in] */
+                                 Int8 db_length,       /* [in] */
+                                 Int4 db_num_seqs,     /* [in] */
+                                 Int4* length_adjustment_out  /* [out] */
+                                )
+{
+    Int4 length_adjustment = 0;  /* length adjustment for current iteration. */
+    Int4 last_length_adjustment = 0;/* length adjustment in previous iteration.*/
+    Int4 min_query_length;   /* lower bound on query length. */
+    Int2 i; /* Iteration index for calculating length adjustment */
+    Int8 effective_length, effective_db_length; /* effective lengths of 
+                                                  query and database */
+    Int8 retval = 0;
+
+    ASSERT(kbp);
+
+    min_query_length = (Int4) (1/(kbp->K));
+
+    for (i=0; i<5; i++) {
+
+        if (program_number != blast_type_blastn && 
+            scoring_options->gapped_calculation) {
+
+            length_adjustment = BLAST_Nint((((kbp->logK)+log((double)(query_length-last_length_adjustment)*(double)MAX(db_num_seqs, db_length-db_num_seqs*last_length_adjustment)))*alpha/kbp->Lambda) + beta);
+
+        } else {
+
+            length_adjustment = BLAST_Nint((kbp->logK+log((double)(query_length-last_length_adjustment)*(double)MAX(1, db_length-db_num_seqs*last_length_adjustment)))/(kbp->H));
+        }
+
+        if (length_adjustment >= query_length-min_query_length) {
+            length_adjustment = query_length-min_query_length;
+            break;
+        }
+        
+        if (ABS(last_length_adjustment-length_adjustment) <= 1)
+            break;
+        last_length_adjustment = length_adjustment;
+    }
+    effective_length = 
+        MAX(query_length - length_adjustment, min_query_length);
+    effective_db_length = MAX(1, db_length - db_num_seqs*length_adjustment);
+     
+    retval = effective_length * effective_db_length;
+
+    if (length_adjustment_out) {
+        *length_adjustment_out = length_adjustment;
+    }
+
+    return retval;
+}
+
 Int2 BLAST_CalcEffLengths (Uint1 program_number, 
    const BlastScoringOptions* scoring_options,
    const BlastEffectiveLengthsOptions* eff_len_options, 
    const BlastScoreBlk* sbp, BlastQueryInfo* query_info)
 {
-   double alpha, beta; /*alpha and beta for new scoring system */
-   Int4 min_query_length;   /* lower bound on query length. */
+   double alpha=0, beta=0; /*alpha and beta for new scoring system */
    Int4 length_adjustment = 0;  /* length adjustment for current iteration. */
-   Int4 last_length_adjustment;/* length adjustment in previous iteration.*/
    Int4 index;		/* loop index. */
    Int4	db_num_seqs;	/* number of sequences in database. */
    Int8	db_length;	/* total length of database. */
    BLAST_KarlinBlk* *kbp_ptr; /* Array of Karlin block pointers */
-   BLAST_KarlinBlk* kbp; /* Karlin-Blk pointer from ScoreBlk. */
    Int4 query_length;   /* length of an individual query sequence */
-   Int8 effective_length, effective_db_length; /* effective lengths of 
-                                                  query and database */
-   Int8 effective_search_space; /* Effective search space for a given 
+   Int8 effective_search_space = 0; /* Effective search space for a given 
                                    sequence/strand/frame */
-   Int2 i; /* Iteration index for calculating length adjustment */
-   Uint1 num_strands;
-   Boolean skip = FALSE;
 
    if (sbp == NULL || eff_len_options == NULL)
       return 1;
@@ -359,67 +413,32 @@ Int2 BLAST_CalcEffLengths (Uint1 program_number,
    else
       kbp_ptr = sbp->kbp_std; 
    
-   if (program_number == blast_type_blastn)
-      num_strands = 2;
-   else
-      num_strands = 1;
+   for (index = query_info->first_context;
+        index <= query_info->last_context;
+        index++) {
 
-   for (index = query_info->first_context; 
-        index <= query_info->last_context; index++) {
-      if ((index % num_strands) == 0) 
-         skip = FALSE;
       if (eff_len_options->searchsp_eff) {
          effective_search_space = eff_len_options->searchsp_eff;
       } else {
-         query_length = BLAST_GetQueryLength(query_info, index);
-         
-         if (query_length <= 0) {
-            /* This strand of this query is not searched */
-            query_info->eff_searchsp_array[index] = 0;
-            query_info->length_adjustments[index] = 0;
-            continue;
-         }
-
-         if (!skip) {
-            /* Use the correct Karlin block. For blastn, two identical Karlin
-               blocks are allocated for each sequence (one per strand), but we
-               only need one of them.
-            */
-            kbp = kbp_ptr[index];
-            length_adjustment = 0;
-            last_length_adjustment = 0;
-            min_query_length = (Int4) (1/(kbp->K));
-            
-            for (i=0; i<5; i++) {
-               if (program_number != blast_type_blastn && 
-                   scoring_options->gapped_calculation) {
-                  length_adjustment = BLAST_Nint((((kbp->logK)+log((double)(query_length-last_length_adjustment)*(double)MAX(db_num_seqs, db_length-db_num_seqs*last_length_adjustment)))*alpha/kbp->Lambda) + beta);
-               } else {
-                  length_adjustment = (Int4) ((kbp->logK+log((double)(query_length-last_length_adjustment)*(double)MAX(1, db_length-db_num_seqs*last_length_adjustment)))/(kbp->H));
-               }
-               
-               if (length_adjustment >= query_length-min_query_length) {
-                  length_adjustment = query_length-min_query_length;
-                  break;
-               }
-               
-               if (ABS(last_length_adjustment-length_adjustment) <= 1)
-                  break;
-               last_length_adjustment = length_adjustment;
-            }
-            effective_length = 
-               MAX(query_length - length_adjustment, min_query_length);
-            effective_db_length = MAX(1, db_length - db_num_seqs*length_adjustment);
-            
-            effective_search_space = effective_length * effective_db_length;
-            skip = TRUE;
+         if ( (query_length = BLAST_GetQueryLength(query_info, index)) <= 0) {
+             continue;
          }
+         /* Use the correct Karlin block. For blastn, two identical Karlin
+            blocks are allocated for each sequence (one per strand), but we
+            only need one of them.
+         */
+         effective_search_space = ComputeEffectiveSearchSpace(kbp_ptr[index],
+                                                              program_number,
+                                                              query_length,
+                                                              scoring_options,
+                                                              alpha, beta,
+                                                              db_length,
+                                                              db_num_seqs,
+                                                              &length_adjustment);
       }
-
       query_info->eff_searchsp_array[index] = effective_search_space;
       query_info->length_adjustments[index] = length_adjustment;
 
-
    }
 
    return 0;
@@ -504,7 +523,8 @@ BLAST_SetUpAuxStructures(Uint1 program_number,
                                query_info, hit_params);
 
    BlastInitialWordParametersNew(program_number, word_options, *hit_params, 
-      *ext_params, sbp, query_info, eff_len_options, word_params);
+      *ext_params, sbp, query_info, eff_len_options, 
+      scoring_options->gapped_calculation, word_params);
 
    if ((status = BLAST_GapAlignStructNew(scoring_options, *ext_params, 
                     max_subject_length, query->length, sbp, gap_align))) {
@@ -685,7 +705,7 @@ BLAST_DatabaseSearchEngine(Uint1 program_number,
    const BlastEffectiveLengthsOptions* eff_len_options,
    const PSIBlastOptions* psi_options, 
    const BlastDatabaseOptions* db_options,
-   BlastResults* results, BlastReturnStat* return_stats)
+   BlastHSPResults* results, BlastReturnStat* return_stats)
 {
    BlastCoreAuxStruct* aux_struct = NULL;
    BlastThrInfo* thr_info = NULL;
@@ -781,11 +801,11 @@ BLAST_DatabaseSearchEngine(Uint1 program_number,
    /* Now sort the hit lists for all queries */
    BLAST_SortResults(results);
 
-   if (hit_options->gapped_calculation) {
+   if (!ext_options->skip_traceback && score_options->gapped_calculation) {
       status = 
          BLAST_ComputeTraceback(program_number, results, query, query_info,
             bssp, gap_align, score_options, ext_params, hit_params,
-            db_options);
+            db_options, psi_options);
    }
 
    /* Do not destruct score block here */
@@ -812,7 +832,7 @@ BLAST_TwoSequencesEngine(Uint1 program_number,
    const BlastEffectiveLengthsOptions* eff_len_options,
    const PSIBlastOptions* psi_options, 
    const BlastDatabaseOptions* db_options,
-   BlastResults* results, BlastReturnStat* return_stats)
+   BlastHSPResults* results, BlastReturnStat* return_stats)
 {
    BlastCoreAuxStruct* aux_struct = NULL;
    BlastHSPList* hsp_list; 
@@ -850,7 +870,7 @@ BLAST_TwoSequencesEngine(Uint1 program_number,
    BlastCoreAuxStructFree(aux_struct);
    sfree(word_params);
 
-   if (hit_options->gapped_calculation) {
+   if (score_options->gapped_calculation) {
       status = 
          BLAST_TwoSequencesTraceback(program_number, results, query, 
             query_info, subject, gap_align, score_options, ext_params, 
diff --git a/algo/blast/core/blast_engine.h b/algo/blast/core/blast_engine.h
index bfb2c845..b072d537 100644
--- a/algo/blast/core/blast_engine.h
+++ b/algo/blast/core/blast_engine.h
@@ -1,4 +1,4 @@
-/* $Id: blast_engine.h,v 1.24 2003/09/10 19:41:02 dondosha Exp $
+/* $Id: blast_engine.h,v 1.25 2003/12/03 16:31:45 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@ Author: Ilya Dondoshansky
 Contents: High level BLAST functions
 
 ******************************************************************************
- * $Revision: 1.24 $
+ * $Revision: 1.25 $
  * */
 #ifndef __BLAST_ENGINE__
 #define __BLAST_ENGINE__
@@ -78,7 +78,7 @@ BLAST_DatabaseSearchEngine(Uint1 program_number,
    const BlastEffectiveLengthsOptions* eff_len_options,
    const PSIBlastOptions* psi_options, 
    const BlastDatabaseOptions* db_options,
-   BlastResults* results, BlastReturnStat* return_stats);
+   BlastHSPResults* results, BlastReturnStat* return_stats);
 
 /** The high level function performing BLAST comparison of two sequences,
  * after all the setup has been done.
@@ -111,7 +111,7 @@ BLAST_TwoSequencesEngine(Uint1 program_number,
    const BlastEffectiveLengthsOptions* eff_len_options,
    const PSIBlastOptions* psi_options, 
    const BlastDatabaseOptions* db_options,
-   BlastResults* results, BlastReturnStat* return_stats);
+   BlastHSPResults* results, BlastReturnStat* return_stats);
 
 /** Function to calculate effective query length and db length as well as
  * effective search space. 
diff --git a/algo/blast/core/blast_extend.c b/algo/blast/core/blast_extend.c
index 16cc1d53..64f7871b 100644
--- a/algo/blast/core/blast_extend.c
+++ b/algo/blast/core/blast_extend.c
@@ -1,4 +1,4 @@
-/* $Id: blast_extend.c,v 1.42 2003/10/22 15:32:09 dondosha Exp $
+/* $Id: blast_extend.c,v 1.47 2004/01/13 16:20:04 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,10 +32,10 @@ Author: Ilya Dondoshansky
 Contents: Functions to initialize structures used for BLAST extension
 
 ******************************************************************************
- * $Revision: 1.42 $
+ * $Revision: 1.47 $
  * */
 
-static char const rcsid[] = "$Id: blast_extend.c,v 1.42 2003/10/22 15:32:09 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_extend.c,v 1.47 2004/01/13 16:20:04 dondosha Exp $";
 
 #include <algo/blast/core/blast_extend.h>
 #include <algo/blast/core/blast_options.h>
@@ -565,59 +565,61 @@ BlastnWordUngappedExtend(BLAST_SequenceBlk* query,
    Int4 q_off, Int4 s_off, Int4 cutoff, Int4 X, 
    BlastUngappedData** ungapped_data)
 {
-	Uint1* q;
-	Int4 sum, score;
-	Uint1 ch;
-	Uint1* subject0,* sf,* q_beg,* q_end,* s_end,* s,* start;
-	Int2 remainder, base;
-	Int4 q_avail, s_avail;
-
+   Uint1* q;
+   Int4 sum, score;
+   Uint1 ch;
+   Uint1* subject0,* sf,* q_beg,* q_end,* s_end,* s,* start;
+   Int2 remainder, base;
+   Int4 q_avail, s_avail;
+   
    base = 3 - (s_off % 4);
-
-	subject0 = subject->sequence;
+   
+   subject0 = subject->sequence;
    q_avail = query->length - q_off;
    s_avail = subject->length - s_off;
 
-	q = q_beg = q_end = query->sequence + q_off;
-	s = s_end = subject0 + s_off/COMPRESSION_RATIO;
-	if (q_off < s_off) {
+   q = q_beg = q_end = query->sequence + q_off;
+   s = s_end = subject0 + s_off/COMPRESSION_RATIO;
+   if (q_off < s_off) {
       start = subject0 + (s_off-q_off)/COMPRESSION_RATIO;
       remainder = 3 - ((s_off-q_off)%COMPRESSION_RATIO);
-	} else {
+   } else {
       start = subject0;
       remainder = 3;
-	}
-
-	/* Find where positive scoring starts & ends within the word hit */
-	score = 0;
+   }
+   
+   /* Find where positive scoring starts & ends within the word hit */
+   score = 0;
    sum = 0;
 
-	/* extend to the left */
-	do {
+   /* extend to the left */
+   while ((s > start) || (s == start && base < remainder)) {
       if (base == 3) {
          s--;
          base = 0;
-      } else
-         base++;
+      } else {
+         ++base;
+      }
       ch = *s;
       if ((sum += matrix[*--q][READDB_UNPACK_BASE_N(ch, base)]) > 0) {
          q_beg = q;
          score += sum;
          sum = 0;
-      } else if (sum < X)
+      } else if (sum < X) {
          break;
-	} while ((s > start) || (s == start && base < remainder));
+      }
+   }
    
    if (score >= cutoff && !ungapped_data) 
       return FALSE;
    
-	if (ungapped_data) {
+   if (ungapped_data) {
       *ungapped_data = (BlastUngappedData*) 
          malloc(sizeof(BlastUngappedData));
-	   (*ungapped_data)->q_start = q_beg - query->sequence;
-	   (*ungapped_data)->s_start = 
-	      s_off - (q_off - (*ungapped_data)->q_start);
-	}
+      (*ungapped_data)->q_start = q_beg - query->sequence;
+      (*ungapped_data)->s_start = 
+         s_off - (q_off - (*ungapped_data)->q_start);
+   }
 
    if (q_avail < s_avail) {
       sf = subject0 + (s_off + q_avail)/COMPRESSION_RATIO;
@@ -626,13 +628,14 @@ BlastnWordUngappedExtend(BLAST_SequenceBlk* query,
       sf = subject0 + (subject->length)/COMPRESSION_RATIO;
       remainder = 3 - ((subject->length)%COMPRESSION_RATIO);
    }
-	/* extend to the right */
-	q = q_end;
-	s = s_end;
-	sum = 0;
+	
+   /* extend to the right */
+   q = q_end;
+   s = s_end;
+   sum = 0;
    base = 3 - (s_off % COMPRESSION_RATIO);
-
-	while (s < sf || (s == sf && base > remainder)) {
+   
+   while (s < sf || (s == sf && base > remainder)) {
       ch = *s;
       if ((sum += matrix[*q++][READDB_UNPACK_BASE_N(ch, base)]) > 0) {
          q_end = q;
@@ -645,14 +648,14 @@ BlastnWordUngappedExtend(BLAST_SequenceBlk* query,
          s++;
       } else
          base--;
-	}
+   }
    
-	if (ungapped_data) {
-	   (*ungapped_data)->length = q_end - q_beg;
-	   (*ungapped_data)->score = score;
+   if (ungapped_data) {
+      (*ungapped_data)->length = q_end - q_beg;
+      (*ungapped_data)->score = score;
       (*ungapped_data)->frame = 0;
-	}
-
+   }
+   
    return (score < cutoff);
 }
 
@@ -781,7 +784,6 @@ Int4 BlastNaWordFinder(BLAST_SequenceBlk* subject,
    Int4 i;
    Uint1* s,* s_end;
    Uint1* q_start = query->sequence;
-   Uint1* q_end = query->sequence + query->length;
    Int4 hitsfound, total_hits = 0;
    Uint4 word_size, compressed_wordsize, reduced_word_length;
    Uint4 extra_bytes_needed;
@@ -789,20 +791,17 @@ Int4 BlastNaWordFinder(BLAST_SequenceBlk* subject,
    Uint1* q;
    Int4 start_offset, last_start, next_start, last_end;
    Uint1 max_bases;
-   Int4 bases_in_last_byte, bases_in_extra_bytes;
 
    word_size = COMPRESSION_RATIO*lookup->wordsize;
    last_start = subject->length - word_size;
    s_end = subject->sequence + subject->length/COMPRESSION_RATIO;
    start_offset = 0;
-   bases_in_last_byte = subject->length % COMPRESSION_RATIO;
 
    compressed_wordsize = lookup->reduced_wordsize;
    extra_bytes_needed = lookup->wordsize - compressed_wordsize;
-   bases_in_extra_bytes = COMPRESSION_RATIO*extra_bytes_needed;
    reduced_word_length = COMPRESSION_RATIO*compressed_wordsize;
    extra_bases = lookup->word_length - word_size;
-   last_end = subject->length - (word_size - reduced_word_length);
+   last_end = subject->length - word_size;
 
    while (start_offset <= last_start) {
       /* Pass the last word ending offset */
@@ -812,42 +811,41 @@ Int4 BlastNaWordFinder(BLAST_SequenceBlk* subject,
       
       total_hits += hitsfound;
       for (i = 0; i < hitsfound; ++i) {
+         /* Here it is guaranteed that subject offset is divisible by 4,
+            because we only extend to the right, so scanning stride must be
+            equal to 4. */
+         s = abs_start + (s_offsets[i])/COMPRESSION_RATIO;
          q = q_start + q_offsets[i];
-         s = abs_start + s_offsets[i]/COMPRESSION_RATIO;
 	    
-	 /* Check for extra bytes if required for longer words. */
-	 if (extra_bytes_needed && 
-	     !BlastNaCompareExtraBytes(q, s, extra_bytes_needed))
-	    continue;
-         if (s_offsets[i] > reduced_word_length) {
-            /* mini extension to the left */
-            max_bases = 
-               MIN(4, q_offsets[i] - reduced_word_length);
-            left = BlastNaMiniExtendLeft(q-reduced_word_length, 
-                      s-compressed_wordsize-1, max_bases);
-         } else {
-            left = 0;
-         }
-         s += extra_bytes_needed;
-         if (s <= s_end) {
-            /* mini extension to the right */
-            q += COMPRESSION_RATIO*extra_bytes_needed;
-            max_bases = MIN(4, q_end - q);
-            if (s == s_end)
-               max_bases = MIN(max_bases, bases_in_last_byte);
+         /* Check for extra bytes if required for longer words. */
+         if (extra_bytes_needed && 
+             !BlastNaCompareExtraBytes(q+reduced_word_length, 
+                 s+compressed_wordsize, extra_bytes_needed))
+            continue;
+         /* mini extension to the left */
+         max_bases = 
+            MIN(COMPRESSION_RATIO, MIN(q_offsets[i], s_offsets[i]));
+         left = BlastNaMiniExtendLeft(q, s-1, max_bases);
+
+         /* mini extension to the right */
+         max_bases =
+            MIN(COMPRESSION_RATIO, 
+                MIN(subject->length - s_offsets[i] - lookup->wordsize,
+                    query->length - q_offsets[i] - word_size));
+
+         if (max_bases > 0) {
+            s += lookup->wordsize;
+            q += word_size;
             right = BlastNaMiniExtendRight(q, s, max_bases);
-         } else {
-            right = 0;
          }
 
-	 if (left + right >= extra_bases) {
-	    /* Check if this diagonal has already been explored. */
-	    BlastnExtendInitialHit(query, subject, lookup_wrap, 
+         if (left + right >= extra_bases) {
+            /* Check if this diagonal has already been explored. */
+            BlastnExtendInitialHit(query, subject, lookup_wrap, 
                word_params, matrix, ewp, q_offsets[i], 
-               s_offsets[i] + bases_in_extra_bytes + right, 
+               s_offsets[i] + word_size + right, 
                s_offsets[i], init_hitlist);
          }
-	 
       }
       start_offset = next_start;
    }
@@ -872,34 +870,16 @@ BlastNaExactMatchExtend(Uint1* q_start, Uint1* s_start,
    Uint4 max_bases_left, Uint4 max_bases_right, Uint4 max_length, 
    Boolean extend_partial_byte, Uint4* extended_right)
 {
-   Uint4 length = 0, extended_left = 0;
+   Uint4 length;
    Uint1* q,* s;
    
    *extended_right = 0;
 
-   /* Extend to the left; start with previous byte */
-   q = q_start - COMPRESSION_RATIO;
-   s = s_start - 1;
-   while (length < max_length && max_bases_left >= COMPRESSION_RATIO) {
-      if (*s != PACK_WORD(q))
-         break;
-      length += COMPRESSION_RATIO;
-      --s;
-      q -= COMPRESSION_RATIO;
-      max_bases_left -= COMPRESSION_RATIO;
-   }
-   extended_left = length;
-   if (length >= max_length)
-      return TRUE;
-   if (extend_partial_byte && max_bases_left > 0) {
-      length += BlastNaMiniExtendLeft(q+COMPRESSION_RATIO, s, 
-                   (Uint1) MIN(max_bases_left, COMPRESSION_RATIO));
-   }
-   if (length >= max_length)
-      return TRUE;
+   length = 0;
+
+   /* Extend to the right; start from the firstt byte (it must be the 
+      first one that's guaranteed to match by the lookup table hit). */
 
-   /* Extend to the right; start after the end of the word */
-   max_bases_right = MIN(max_bases_right, max_length - length);
    q = q_start;
    s = s_start;
    while (length < max_length && max_bases_right >= COMPRESSION_RATIO) {
@@ -911,14 +891,39 @@ BlastNaExactMatchExtend(Uint1* q_start, Uint1* s_start,
       max_bases_right -= COMPRESSION_RATIO;
    }
    if (extend_partial_byte) {
-      if (length >= max_length)
-         return TRUE;
       if (max_bases_right > 0) {
          length += BlastNaMiniExtendRight(q, s, 
                       (Uint1) MIN(max_bases_right, COMPRESSION_RATIO));
       }
    }
-   *extended_right = length - extended_left;
+
+   *extended_right = length;
+
+   if (length >= max_length)
+      return TRUE;
+
+   if (max_bases_left < max_length - length)
+      return FALSE;
+   else
+      max_bases_left = max_length - length;
+
+   /* Extend to the left; start with the byte just before the first. */
+   q = q_start - COMPRESSION_RATIO;
+   s = s_start - 1;
+   while (length < max_length && max_bases_left >= COMPRESSION_RATIO) {
+      if (*s != PACK_WORD(q))
+         break;
+      length += COMPRESSION_RATIO;
+      --s;
+      q -= COMPRESSION_RATIO;
+      max_bases_left -= COMPRESSION_RATIO;
+   }
+   if (length >= max_length)
+      return TRUE;
+   if (extend_partial_byte && max_bases_left > 0) {
+      length += BlastNaMiniExtendLeft(q+COMPRESSION_RATIO, s, 
+                   (Uint1) MIN(max_bases_left, COMPRESSION_RATIO));
+   }
 
    return (length >= max_length);
 }
@@ -940,31 +945,35 @@ Int4 MB_WordFinder(BLAST_SequenceBlk* subject,
    MBLookupTable* mb_lt = (MBLookupTable*) lookup->lut;
    Uint1* s_start,* q_start,* q,* s;
    Int4 hitsfound=0;
-   Int4 hit_counter=0, i;
+   Int4 hit_counter=0, index;
    Int4 start_offset, next_start, last_start, last_end;
-   Uint4 word_length, reduced_word_length;
+   Uint4 word_length;
    Uint4 max_bases_left, max_bases_right;
    Int4 query_length = query->length;
+   Int4 subject_length = subject->length;
    Boolean ag_blast, variable_wordsize;
    Uint4 extended_right;
+   Uint4 q_off, s_off; 
+   Uint1 remainder;
 
    s_start = subject->sequence;
    q_start = query->sequence;
    word_length = mb_lt->word_length;
-   reduced_word_length = COMPRESSION_RATIO*mb_lt->compressed_wordsize;
    ag_blast = (Boolean) (word_options->extension_method == eRightAndLeft);
-   variable_wordsize = word_options->variable_wordsize;
+   variable_wordsize = (Boolean) word_options->variable_wordsize;
 
    start_offset = 0;
    if (mb_lt->discontiguous) {
-      last_start = subject->length - mb_lt->template_length;
+      last_start = subject_length - mb_lt->template_length;
       last_end = last_start + mb_lt->word_length;
    } else {
-      last_end = subject->length;
-      if (ag_blast)
-         last_start = last_end - reduced_word_length;
-      else
+      last_end = subject_length;
+      if (ag_blast) {
+         last_start = 
+            last_end - COMPRESSION_RATIO*mb_lt->compressed_wordsize;
+      } else {
          last_start = last_end - mb_lt->word_length;
+      }
    }
 
    /* start_offset points to the beginning of the word */
@@ -983,29 +992,36 @@ Int4 MB_WordFinder(BLAST_SequenceBlk* subject,
 	    q_offsets, s_offsets, max_hits, &next_start);
       }
       if (ag_blast) {
-         for (i = 0; i < hitsfound; ++i) {
-            q = q_start + q_offsets[i] - s_offsets[i]%COMPRESSION_RATIO;
-            s = s_start + s_offsets[i]/COMPRESSION_RATIO;
+         for (index = 0; index < hitsfound; ++index) {
+            /* Adjust offsets to the start of the next full byte in the
+               subject sequence */
+            remainder = (-s_offsets[index])%COMPRESSION_RATIO;
+            q_off = q_offsets[index] + remainder;
+            s_off = s_offsets[index] + remainder;
+            s = s_start + s_off/COMPRESSION_RATIO;
+            q = q_start + q_off;
 	    
-            max_bases_left = MIN(word_length, MIN(q_offsets[i], s_offsets[i]));
-
+            max_bases_left = 
+               MIN(word_length, MIN(q_off, s_off));
             max_bases_right = MIN(word_length, 
-               MIN(query_length-q_offsets[i], last_end-s_offsets[i]));
+               MIN(query_length-q_off, subject_length-s_off));
                                                 
-            if (BlastNaExactMatchExtend(q, s, max_bases_left, max_bases_right,
-                   word_length, (Boolean) !variable_wordsize, &extended_right)) {
+            if (BlastNaExactMatchExtend(q, s, max_bases_left, 
+                   max_bases_right, word_length, !variable_wordsize, 
+                   &extended_right))
+            {
                /* Check if this diagonal has already been explored and save
                   the hit if needed. */
                BlastnExtendInitialHit(query, subject, lookup,
-                  word_params, matrix, ewp, q_offsets[i], 
-                  s_offsets[i] + extended_right, s_offsets[i], 
+                  word_params, matrix, ewp, q_offsets[index], 
+                  s_off + extended_right, s_offsets[index], 
                   init_hitlist);
             }
          }
       } else {
-         for (i = 0; i < hitsfound; ++i) {
+         for (index = 0; index < hitsfound; ++index) {
             MB_ExtendInitialHit(query, subject, lookup, word_params,
-               matrix, ewp, q_offsets[i], s_offsets[i], init_hitlist);
+               matrix, ewp, q_offsets[index], s_offsets[index], init_hitlist);
          }
       }
       /* next_start returned from the ScanSubject points to the beginning
@@ -1014,7 +1030,7 @@ Int4 MB_WordFinder(BLAST_SequenceBlk* subject,
       hit_counter += hitsfound;
    }
 
-   MB_ExtendWordExit(ewp, subject->length);
+   MB_ExtendWordExit(ewp, subject_length);
 
    return hit_counter;
 }
@@ -1034,30 +1050,24 @@ Int4 BlastNaWordFinder_AG(BLAST_SequenceBlk* subject,
    BlastInitialWordOptions* word_options = word_params->options;
    LookupTable* lookup = (LookupTable*) lookup_wrap->lut;
    Uint1* s_start = subject->sequence;
-   Int4 i;
-   Uint1* s,* s_end;
    Uint1* q_start = query->sequence;
+   Int4 index;
+   Uint1* q;
+   Uint1* s;
    Int4 query_length = query->length;
    Int4 subject_length = subject->length;
    Int4 hitsfound, total_hits = 0;
-   Uint4 extra_length, reduced_word_length, min_extra_length;
-   Uint1* q;
+   Uint4 word_length;
    Int4 start_offset, end_offset, next_start;
    Uint1 max_bases_left, max_bases_right;
-   Int4 bases_in_last_byte;
    Boolean variable_wordsize = word_options->variable_wordsize;
-   Int4 extended_right;
-   Uint1* q_tmp,* s_tmp;
-   Uint4 length;
-
-   s_end = subject->sequence + subject_length/COMPRESSION_RATIO;
-   bases_in_last_byte = subject_length % COMPRESSION_RATIO;
+   Uint4 extended_right;
+   Uint4 q_off, s_off; /* Adjusted offsets */
+   Uint1 remainder; 
 
-   reduced_word_length = COMPRESSION_RATIO*lookup->reduced_wordsize;
-   min_extra_length = reduced_word_length - COMPRESSION_RATIO;
-   extra_length = lookup->word_length - min_extra_length;
+   word_length = lookup->word_length;
    start_offset = 0;
-   end_offset = subject_length - reduced_word_length;
+   end_offset = subject_length - COMPRESSION_RATIO*lookup->reduced_wordsize;
 
    /* start_offset points to the beginning of the word; end_offset is the
       beginning of the last word */
@@ -1066,58 +1076,25 @@ Int4 BlastNaWordFinder_AG(BLAST_SequenceBlk* subject,
                      q_offsets, s_offsets, max_hits, &next_start); 
       
       total_hits += hitsfound;
-      for (i = 0; i < hitsfound; ++i) {
-         q = q_start + q_offsets[i] - s_offsets[i]%COMPRESSION_RATIO;
-         s = s_start + s_offsets[i]/COMPRESSION_RATIO;
+      for (index = 0; index < hitsfound; ++index) {
+         remainder = (-s_offsets[index])%COMPRESSION_RATIO;
+         q_off = q_offsets[index] + remainder;
+         s_off = s_offsets[index] + remainder;
+         s = s_start + s_off/COMPRESSION_RATIO;
+         q = q_start + q_off;
 	    
          max_bases_left = 
-            MIN(extra_length, MIN(q_offsets[i], s_offsets[i]) 
-                - min_extra_length);
-
-         max_bases_right = MIN(extra_length, 
-            MIN(query_length-q_offsets[i], subject_length-s_offsets[i]));
-                                 
-
-         q_tmp = q - reduced_word_length;
-         s_tmp = s - lookup->reduced_wordsize;
-         length = 0;
-         while (max_bases_left >= COMPRESSION_RATIO) {
-            if (*s_tmp != PACK_WORD(q_tmp))
-               break;
-            length += COMPRESSION_RATIO;
-            --s_tmp;
-            q_tmp -= COMPRESSION_RATIO;
-            max_bases_left -= COMPRESSION_RATIO;
-         }
-         if (!variable_wordsize) {
-            length += BlastNaMiniExtendLeft(q_tmp+COMPRESSION_RATIO, s_tmp, 
-                                            max_bases_left);
-         }
-         extended_right = 0;
-        /* Extend to the right; start after the end of the word */
-         max_bases_right = MIN(max_bases_right, extra_length - length);
-         q_tmp = q;
-         s_tmp = s;
-         while (max_bases_right >= COMPRESSION_RATIO) {
-            if (*s_tmp != PACK_WORD(q_tmp))
-               break;
-            extended_right += COMPRESSION_RATIO;
-            ++s_tmp;
-            q_tmp += COMPRESSION_RATIO;
-            max_bases_right -= COMPRESSION_RATIO;
-         }
-         if (!variable_wordsize) {
-            extended_right += BlastNaMiniExtendRight(q_tmp, s_tmp, 
-                                             max_bases_right);
-         }
-               
-         length += extended_right;
-
-         if (length >= extra_length) {
-	    /* Check if this diagonal has already been explored. */
-	    BlastnExtendInitialHit(query, subject, lookup_wrap, 
-               word_params, matrix, ewp, q_offsets[i], 
-               s_offsets[i] + extended_right, s_offsets[i], init_hitlist);
+            MIN(word_length, MIN(q_off, s_off));
+         max_bases_right = MIN(word_length, 
+            MIN(query_length-q_off, subject_length-s_off));
+         
+         if (BlastNaExactMatchExtend(q, s, max_bases_left, max_bases_right,
+                word_length, !variable_wordsize, &extended_right)) 
+         {
+            /* Check if this diagonal has already been explored. */
+            BlastnExtendInitialHit(query, subject, lookup_wrap, 
+               word_params, matrix, ewp, q_offsets[index], 
+               s_off + extended_right, s_offsets[index], init_hitlist);
          }
       }
       start_offset = next_start;
diff --git a/algo/blast/core/blast_filter.c b/algo/blast/core/blast_filter.c
index 3431eca6..262683ea 100644
--- a/algo/blast/core/blast_filter.c
+++ b/algo/blast/core/blast_filter.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: blast_filter.c,v 1.34 2003/10/17 20:12:50 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_filter.c,v 1.38 2004/01/07 21:17:30 dondosha Exp $";
 /*
 * ===========================================================================
 *
@@ -33,7 +33,7 @@ Author: Ilya Dondoshansky
 Contents: All code related to query sequence masking/filtering for BLAST
 
 ******************************************************************************
- * $Revision: 1.34 $
+ * $Revision: 1.38 $
  * */
 
 #include <algo/blast/core/blast_def.h>
@@ -73,9 +73,9 @@ BlastSeqLoc* BlastSeqLocFree(BlastSeqLoc* loc)
    return NULL;
 }
 
-BlastMask* BlastMaskFree(BlastMask* mask_loc)
+BlastMaskLoc* BlastMaskLocFree(BlastMaskLoc* mask_loc)
 {
-   BlastMask* next_loc;
+   BlastMaskLoc* next_loc;
    while (mask_loc) {
       next_loc = mask_loc->next;
       BlastSeqLocFree(mask_loc->loc_list);
@@ -103,7 +103,8 @@ static int DoubleIntSortByStartPosition(const void *vp1, const void *vp2)
 
 /* This will go in place of CombineSeqLocs to combine filtered locations */
 Int2
-CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out)
+CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out,
+                     Int4 link_value)
 {
    Int2 status=0;		/* return value. */
    Int4 start, stop;	/* USed to merge overlapping SeqLoc's. */
@@ -118,12 +119,12 @@ CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out)
 
    /* Put all the SeqLoc's into one big linked list. */
    loc_head = last_loc = 
-      (BlastSeqLoc*) MemDup(mask_loc, sizeof(BlastSeqLoc));
+      (BlastSeqLoc*) BlastMemDup(mask_loc, sizeof(BlastSeqLoc));
          
    /* Copy all locations, so loc points at the end of the chain */
    while (last_loc->next) {		
       last_loc->next = 
-         (BlastSeqLoc*)MemDup(last_loc->next, sizeof(BlastSeqLoc));
+         (BlastSeqLoc*) BlastMemDup(last_loc->next, sizeof(BlastSeqLoc));
       last_loc = last_loc->next;
    }
    
@@ -141,7 +142,7 @@ CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out)
       di = loc_var->ptr;
       if (loc_var->next)
          di_next = loc_var->next->ptr;
-      if (di_next && stop+1 >= di_next->i1) {
+      if (di_next && ((stop + link_value) > di_next->i1)) {
          stop = MAX(stop, di_next->i2);
       } else {
          di_tmp = (DoubleInt*) malloc(sizeof(DoubleInt));
@@ -152,8 +153,8 @@ CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out)
          else
             new_loc_last = ListNodeAddPointer(&new_loc_last, 0, di_tmp);
          if (loc_var->next) {
-               start = di_next->i1;
-               stop = di_next->i2;
+             start = di_next->i1;
+             stop = di_next->i2;
          }
       }
       loc_var = loc_var->next;
@@ -174,7 +175,7 @@ CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out)
 Int2 
 BLAST_ComplementMaskLocations(Uint1 program_number, 
    BlastQueryInfo* query_info, 
-   BlastMask* mask_loc, BlastSeqLoc* *complement_mask) 
+   BlastMaskLoc* mask_loc, BlastSeqLoc* *complement_mask) 
 {
    Int4 start_offset, end_offset, filter_start, filter_end;
    Int4 context, index;
@@ -191,6 +192,9 @@ BLAST_ComplementMaskLocations(Uint1 program_number,
         context <= query_info->last_context; ++context) {
       start_offset = query_info->context_offsets[context];
       end_offset = query_info->context_offsets[context+1] - 2;
+      /* For blastn: check if this strand is not searched at all */
+      if (end_offset < start_offset)
+          continue;
       index = (is_na ? context / 2 : context);
       reverse = (is_na && ((context & 1) != 0));
       first = TRUE;
@@ -218,7 +222,7 @@ BLAST_ComplementMaskLocations(Uint1 program_number,
          /* Reverse the order of the locations */
          for (start_loc = mask_loc->loc_list; start_loc; 
               start_loc = start_loc->next) {
-            loc = (BlastSeqLoc*) MemDup(start_loc, sizeof(BlastSeqLoc));
+            loc = (BlastSeqLoc*) BlastMemDup(start_loc, sizeof(BlastSeqLoc));
             loc->next = prev_loc;
             prev_loc = loc;
          }
diff --git a/algo/blast/core/blast_filter.h b/algo/blast/core/blast_filter.h
index fcad4449..7f1e4dc7 100644
--- a/algo/blast/core/blast_filter.h
+++ b/algo/blast/core/blast_filter.h
@@ -1,4 +1,4 @@
-/* $Id: blast_filter.h,v 1.9 2003/08/11 14:57:16 dondosha Exp $
+/* $Id: blast_filter.h,v 1.11 2004/01/07 21:17:17 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@ Contents: BLAST filtering functions.
 Detailed Contents: 
 
 ******************************************************************************
- * $Revision: 1.9 $
+ * $Revision: 1.11 $
  * */
 #ifndef __BLAST_FILTER__
 #define __BLAST_FILTER__
@@ -55,17 +55,20 @@ BlastSeqLoc* BlastSeqLocNew(Int4 from, Int4 to);
 /** Deallocate a BlastSeqLoc structure */
 BlastSeqLoc* BlastSeqLocFree(BlastSeqLoc* loc);
 
-/** Deallocate memory for a list of BlastMask structures */
-BlastMask* BlastMaskFree(BlastMask* mask_loc);
+/** Deallocate memory for a list of BlastMaskLoc structures */
+BlastMaskLoc* BlastMaskLocFree(BlastMaskLoc* mask_loc);
 
 /** Go through all mask locations in one sequence, 
  * combine any that overlap. Deallocate the memory for the locations that 
  * were on the list, produce a new (merged) list of locations. 
  * @param mask_loc The list of masks to be merged [in] 
  * @param mask_loc_out The new (merged) list of masks. [out]
+ * @param link_value Largest gap size between locations fow which they
+ *                   should be linked together [in] 
 */
 Int2
-CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out);
+CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out,
+                     Int4 link_value);
 
 /** This function takes the list of mask locations (i.e., regions that 
  * should not be searched or not added to lookup table) and makes up a set 
@@ -82,7 +85,7 @@ CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out);
 */
 Int2 
 BLAST_ComplementMaskLocations(Uint1 program_number, 
-   BlastQueryInfo* query_info, BlastMask* mask_loc, 
+   BlastQueryInfo* query_info, BlastMaskLoc* mask_loc, 
    BlastSeqLoc* *complement_mask);
 
 /** Runs filtering functions, according to the string "instructions", on the
diff --git a/algo/blast/core/blast_gapalign.c b/algo/blast/core/blast_gapalign.c
index c4953b1a..0fe388ad 100644
--- a/algo/blast/core/blast_gapalign.c
+++ b/algo/blast/core/blast_gapalign.c
@@ -1,4 +1,4 @@
-/* $Id: blast_gapalign.c,v 1.52 2003/10/27 20:48:49 dondosha Exp $
+/* $Id: blast_gapalign.c,v 1.63 2004/01/22 15:30:30 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,10 +32,10 @@ Author: Ilya Dondoshansky
 Contents: Functions to perform gapped alignment
 
 ******************************************************************************
- * $Revision: 1.52 $
+ * $Revision: 1.63 $
  * */
 
-static char const rcsid[] = "$Id: blast_gapalign.c,v 1.52 2003/10/27 20:48:49 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_gapalign.c,v 1.63 2004/01/22 15:30:30 dondosha Exp $";
 
 #include <algo/blast/core/blast_options.h>
 #include <algo/blast/core/blast_def.h>
@@ -44,12 +44,6 @@ static char const rcsid[] = "$Id: blast_gapalign.c,v 1.52 2003/10/27 20:48:49 do
 #include <algo/blast/core/blast_setup.h>
 #include <algo/blast/core/greedy_align.h>
 
-static Int2 BLAST_GreedyNtGappedAlignment(Uint1* query, Uint1* subject,
-   Int4 query_length, Int4 subject_length,
-   BlastGapAlignStruct* gap_align,
-   const BlastScoringOptions* score_options, 
-   const BlastExtensionOptions* ext_options,
-   Int4 q_off, Int4 s_off, Boolean compressed_subject);
 static Int2 BLAST_DynProgNtGappedAlignment(BLAST_SequenceBlk* query_blk, 
    BLAST_SequenceBlk* subject_blk, BlastGapAlignStruct* gap_align, 
    const BlastScoringOptions* score_options, BlastInitHSP* init_hsp);
@@ -832,7 +826,8 @@ static Int4 SEMI_G_ALIGN_EX(Uint1* A, Uint1* B, Int4 M, Int4 N,
   BlastGapDP* dp;
   Uint1* Bptr;
   Int4 B_increment=1;
-  
+  Int4 next_c, next_f;
+
   if(!score_only) {
     return ALIGN_EX(A, B, M, N, S, pei, pej, sapp, gap_align, score_options, 
                     query_offset, reversed, reverse_sequence);
@@ -856,12 +851,12 @@ static Int4 SEMI_G_ALIGN_EX(Uint1* A, Uint1* B, Int4 M, Int4 N,
   dyn_prog = (BlastGapDP*)malloc(j);
 
   dyn_prog[0].CC = 0; c = dyn_prog[0].DD = -m;
-  dyn_prog[0].FF = -m;
+  dyn_prog[0].FF = -m - decline_penalty;
   for(i = 1; i <= N; i++) {
     if(c < -X) break;
     dyn_prog[i].CC = c;
     dyn_prog[i].DD = c - m; 
-    dyn_prog[i].FF = c-m;
+    dyn_prog[i].FF = c - m - decline_penalty;
     c -= h;
   }
 
@@ -872,87 +867,68 @@ static Int4 SEMI_G_ALIGN_EX(Uint1* A, Uint1* B, Int4 M, Int4 N,
 
   tt = 0;  j = i;
   for (j_r = 1; j_r <= M; j_r++) {
-      if (!(gap_align->positionBased)){ /*AAS*/
+     if ((reverse_sequence && (A[M-j_r] == NULLB)) ||
+         (!reverse_sequence && (A[j_r] == NULLB)))
+        break;
+
+     if (!(gap_align->positionBased)){ /*AAS*/
         if(reverse_sequence)
-            wa = matrix[A[M-j_r]];
+           wa = matrix[A[M-j_r]];
         else
-            wa = matrix[A[j_r]];
-      }
-      else {
-	  if(reversed || reverse_sequence)
-	  {
-	      wa = gap_align->sbp->posMatrix[M - j_r];
-		if (A[M-j_r] == NULLB)  /* Prevents gapping through a NULL byte in rps-blast. */
-			break;
-	  }
-	  else
-	  {
-	      wa = gap_align->sbp->posMatrix[j_r + query_offset];
-		if (A[j_r] == NULLB)
-			break;
-	  }
-      }
+           wa = matrix[A[j_r]];
+     }
+     else {
+        if(reversed || reverse_sequence)
+           wa = gap_align->sbp->posMatrix[M - j_r];
+        else
+           wa = gap_align->sbp->posMatrix[j_r + query_offset];
+     }
       e = c =f = MININT;
       Bptr = &B[tt];
       if(reverse_sequence)
-	Bptr = &B[N-tt];
+         Bptr = &B[N-tt];
       for (cb = i = tt, dp = &dyn_prog[i]; i < j; i++) {
-	Bptr += B_increment;
-	  d = dp->DD;
-	  if (e < f) e = f;
-	  if (d < f) d = f;
-	  if (c < d || c < e) {
-	      if (d < e) {
-		  c = e;
-	      } else {
-		  c = d; 
-	      }
-	      if (best_score - c > X) {
-		  c = dp->CC+wa[*Bptr]; f = dp->FF;
-		  if (tt == i) tt++;
-		  else { dp->CC =dp->FF= MININT;}
-	      } else {
-		  cb = i;
-                  if ((c-=m) > (d-=h)) {
-                      dp->DD = c;
-                  } else {
-                      dp->DD = d;
-                  }
-                  if (c > (e-=h)) {
-                      e = c;
-                  }
-                  c+=m;
-		  d = dp->CC+wa[*Bptr]; dp->CC = c; c=d;
-		  d = dp->FF; dp->FF = f-decline_penalty; f = d;
-	      }
-	  } else {
-	      if (best_score - c > X){
-		  c = dp->CC+wa[*Bptr]; f= dp->FF;
-		  if (tt == i) tt++;
-		  else { dp->CC =dp->FF= MININT;}
-	      } else {
-		  cb = i; 
-		  if (c > best_score) {
-		      best_score = c;
-		      *pei = j_r; *pej = i;
-		  } 
-		  if ((c-=m) > (d-=h)) {
-		      dp->DD = c; 
-		  } else {
-		      dp->DD = d;
-		  } 
-		  if (c > (e-=h)) {
-		      e = c;
-		  } 
-		  c+=m;
-		  d = dp->FF;
-		  if (c-g>f) dp->FF = c-g-decline_penalty; else dp->FF = f-decline_penalty;
-		  f = d;
-		  d = dp->CC+wa[*Bptr]; dp->CC = c; c = d;
-	      }
-	  }
-	  dp++;
+         d = dp->DD;
+         Bptr += B_increment;
+         next_c = dp->CC+wa[*Bptr];   /* Bptr is & B[i+1]; */
+         next_f = dp->FF;
+         if (c < f) c = f;
+         if (f > d) d = f;
+         else if (c < d) c= d;
+
+         if (f > e) e = f;
+         else if (c < e) c=e;
+
+         if (best_score - c > X){
+            if (tt == i) tt++;
+            else { dp->CC =  MININT; }
+         } else {
+            cb = i;
+            if (c > best_score) {
+               best_score = c;
+               *pei = j_r; *pej = i;
+            }
+            if ((c-=m) > (d-=h)) {
+               dp->DD = c; 
+            } else {
+               dp->DD = d;
+            } 
+            if (c > (e-=h)) {
+               e = c; 
+            }
+            c+=m; 
+            if (f < c-g) { 
+               dp->FF = c-g-decline_penalty; 
+            } else {
+               dp->FF = f-decline_penalty;
+            }
+            dp->CC = c;
+         }
+         c = next_c;
+         f = next_f;
+         dp++;
       }
+
       if (tt == j) break;
       if (cb < j-1) { j = cb+1;}
       else while (e >= best_score-X && j <= N) {
@@ -1280,6 +1256,7 @@ static Int4 OOF_SEMI_G_ALIGN(Uint1* A, Uint1* B, Int4 M, Int4 N,
   Int4* wa;
   BlastGapDP* dp;
   Int4 factor = 1;
+  Int4 NN;
   
   if(!score_only)
       return OOF_ALIGN(A, B, M, N, S, pei, pej, sapp, gap_align, score_options,
@@ -1304,12 +1281,12 @@ static Int4 OOF_SEMI_G_ALIGN(Uint1* A, Uint1* B, Int4 M, Int4 N,
 	X = m;
 
   if(N <= 0 || M <= 0) return 0;
-  N+=2;
+  NN = N + 2;
 
   j = (N + 5) * sizeof(BlastGapDP);
   CD = (BlastGapDP*)calloc(1, j);
   CD[0].CC = 0; c = CD[0].DD = -m;
-  for(i = 3; i <= N; i+=3) {
+  for(i = 3; i <= NN; i+=3) {
     CD[i].CC = c;
     CD[i].DD = c - m; 
     CD[i-1].CC = CD[i-2].CC = CD[i-1].DD = CD[i-2].DD = MININT;
@@ -1331,9 +1308,9 @@ static Int4 OOF_SEMI_G_ALIGN(Uint1* A, Uint1* B, Int4 M, Int4 N,
     }
     s1 = s2 = s3 = f1= f2 = MININT; f1=f2=e1 = e2 = e3 = MININT; sc = MININT;
     for(cb = i = tt, dp = &CD[i-1]; 1;) {
-	if (i >= j) break;
-   sc = MAX(MAX(f1, f2)-shift, s3)+wa[B[factor*i]];
-   ++i;
+	if (i >= j || i > N) break;
+        sc = MAX(MAX(f1, f2)-shift, s3)+wa[B[factor*i]];
+        ++i;
 
 	f1 = s3; 
 	s3 = (++dp)->CC; f1 = MAX(f1, s3);
@@ -1389,7 +1366,7 @@ static Int4 OOF_SEMI_G_ALIGN(Uint1* A, Uint1* B, Int4 M, Int4 N,
 		dp->DD = MAX(sc, d-h);
 	    }
 	}
-	if (i >= j) { c = e2; e2 = e1; e1 = e3; e3 = c; break; }
+	if (i >= j || i > N) { c = e2; e2 = e1; e1 = e3; e3 = c; break; }
 
    sc = MAX(MAX(f1, f2)-shift, s1)+wa[B[factor*i]];
    ++i;
@@ -1426,7 +1403,7 @@ static Int4 OOF_SEMI_G_ALIGN(Uint1* A, Uint1* B, Int4 M, Int4 N,
     if(cb < j) { j = cb;}
     else {
 	c = (MAX(e1, MAX(e2, e3))+X-best_score)/h+j;
-	if (c > N) c = N;
+	if (c > NN) c = NN;
 	if (c > j)
 	while (1) {
 	    CD[j].CC = e1;
@@ -1441,7 +1418,7 @@ static Int4 OOF_SEMI_G_ALIGN(Uint1* A, Uint1* B, Int4 M, Int4 N,
 	}
     }
     c = j+4;
-    if (c > N+1) c = N+1;
+    if (c > NN+1) c = NN+1;
     while (j < c) {
 	CD[j].DD = CD[j].CC = MININT;
 	j++;
@@ -1525,10 +1502,11 @@ Int2 BLAST_MbGetGappedScore(Uint1 program_number,
       if (!delete_hsp) {
          Boolean good_hit = TRUE;
             
-         BLAST_GreedyNtGappedAlignment(query->sequence, subject->sequence,
+         BLAST_GreedyGappedAlignment(query->sequence, subject->sequence,
             query->length, subject->length, gap_align, 
-            score_options, ext_options, init_hsp->q_off, init_hsp->s_off, 
-            TRUE);
+            score_options, init_hsp->q_off, init_hsp->s_off, 
+            TRUE, (ext_options->algorithm_type == EXTEND_GREEDY ? 
+                   TRUE : FALSE));
          /* For neighboring we have a stricter criterion to keep an HSP */
          if (hit_options->is_neighboring) {
             Int4 hsp_length;
@@ -1589,28 +1567,11 @@ MBToGapEditScript (MBGapEditScript* ed_script)
 
 }
 
-/** Greedy gapped alignment, with or without traceback.
- * Given two sequences, relevant options and an offset pair, fills the
- * gap_align structure with alignment endpoints and, if traceback is 
- * performed, gap information.
- * @param query The query sequence [in]
- * @param subject The subject sequence [in]
- * @param query_length The query sequence length [in]
- * @param subject The subject sequence length [in]
- * @param gap_align The structure holding various information and memory 
- *        needed for gapped alignment [in] [out]
- * @param score_options Options related to scoring alignments [in]
- * @param ext_options Options related to alignment extension [in]
- * @param q_off Starting offset in query [in]
- * @param s_off Starting offset in subject [in]
- * @param compressed_subject Is subject sequence compressed? [in]
- */
-static Int2 
-BLAST_GreedyNtGappedAlignment(Uint1* query, Uint1* subject, 
+Int2 
+BLAST_GreedyGappedAlignment(Uint1* query, Uint1* subject, 
    Int4 query_length, Int4 subject_length, BlastGapAlignStruct* gap_align,
    const BlastScoringOptions* score_options, 
-   const BlastExtensionOptions* ext_options,
-   Int4 q_off, Int4 s_off, Boolean compressed_subject)
+   Int4 q_off, Int4 s_off, Boolean compressed_subject, Boolean do_traceback)
 {
    Uint1* q;
    Uint1* s;
@@ -1622,11 +1583,6 @@ BLAST_GreedyNtGappedAlignment(Uint1* query, Uint1* subject,
    MBGapEditScript *ed_script_fwd=NULL, *ed_script_rev=NULL;
    Uint1 rem;
    GapEditScript* esp = NULL;
-   /* Traceback is needed either when greedy extension does traceback
-      immediately from the initial word hits, or if this is a 
-      final alignment. */
-   Boolean do_traceback = (!compressed_subject ||
-      (ext_options->algorithm_type == EXTEND_GREEDY) );
    
    q_avail = query_length - q_off;
    s_avail = subject_length - s_off;
@@ -1747,7 +1703,7 @@ static Int2 BLAST_DynProgNtGappedAlignment(BLAST_SequenceBlk* query_blk,
    Boolean found_start, found_end;
    Int4 q_length=0, s_length=0, score_right, score_left, 
       private_q_start, private_s_start;
-   Int4 offset_adjustment;
+   Uint1 offset_adjustment;
    Uint1* query,* subject;
    
    found_start = FALSE;
@@ -1759,9 +1715,10 @@ static Int2 BLAST_DynProgNtGappedAlignment(BLAST_SequenceBlk* query_blk,
    /* If subject offset is not at the start of a full byte, 
       BLAST_AlignPackedNucl won't work, so shift the alignment start
       to the left */
-   offset_adjustment = init_hsp->s_off % COMPRESSION_RATIO;
-   q_length = init_hsp->q_off - offset_adjustment;
-   s_length = init_hsp->s_off - offset_adjustment;
+   offset_adjustment = 
+      COMPRESSION_RATIO - (init_hsp->s_off % COMPRESSION_RATIO);
+   q_length = init_hsp->q_off + offset_adjustment;
+   s_length = init_hsp->s_off + offset_adjustment;
    if (q_length != 0 && s_length != 0) {
       found_start = TRUE;
       score_left = BLAST_AlignPackedNucl(query, subject, q_length, s_length, 
@@ -1779,7 +1736,7 @@ static Int2 BLAST_DynProgNtGappedAlignment(BLAST_SequenceBlk* query_blk,
    {
       found_end = TRUE;
       score_right = BLAST_AlignPackedNucl(query+q_length-1, 
-         subject+(s_length-1)/COMPRESSION_RATIO, 
+         subject+(s_length+3)/COMPRESSION_RATIO - 1, 
          query_blk->length-q_length, 
          subject_blk->length-s_length, &(gap_align->query_stop),
          &(gap_align->subject_stop), gap_align, score_options, FALSE);
@@ -2494,6 +2451,7 @@ static Int2 BLAST_ProtGappedAlignment(Uint1 program,
    Int4 private_q_start, private_s_start;
    Uint1* query=NULL,* subject=NULL;
    Boolean switch_seq = FALSE;
+   Int4 query_length, subject_length;
     
    if (gap_align == NULL)
       return FALSE;
@@ -2504,16 +2462,22 @@ static Int2 BLAST_ProtGappedAlignment(Uint1 program,
       if (program == blast_type_blastx) {
          subject = subject_blk->sequence + s_length;
          query = query_blk->oof_sequence + CODON_LENGTH + q_length;
+         query_length = query_blk->length - CODON_LENGTH + 1;
+         subject_length = subject_blk->length;
          switch_seq = TRUE;
       } else if (program == blast_type_tblastn) {
          subject = subject_blk->oof_sequence + CODON_LENGTH + s_length;
          query = query_blk->sequence + q_length;
+         query_length = query_blk->length;
+         subject_length = subject_blk->length - CODON_LENGTH + 1;
       }
    } else {
       q_length = init_hsp->q_off + 1;
       s_length = init_hsp->s_off + 1;
       query = query_blk->sequence;
       subject = subject_blk->sequence;
+      query_length = query_blk->length;
+      subject_length = subject_blk->length;
    }
 
    found_start = FALSE;
@@ -2542,12 +2506,11 @@ static Int2 BLAST_ProtGappedAlignment(Uint1 program,
    }
 
    score_right = 0;
-   if (init_hsp->q_off < query_blk->length && 
-       init_hsp->s_off < subject_blk->length) {
+   if (q_length < query_length && s_length < subject_length) {
       found_end = TRUE;
       if(score_options->is_ooframe) {
          score_right = OOF_SEMI_G_ALIGN_EX(query-1, subject-1, 
-            query_blk->length-q_length, subject_blk->length-s_length,
+            query_length-q_length, subject_length-s_length,
             NULL, &(gap_align->query_stop), &(gap_align->subject_stop), 
             TRUE, NULL, gap_align, 
             score_options, q_length, FALSE, switch_seq);
@@ -2555,12 +2518,14 @@ static Int2 BLAST_ProtGappedAlignment(Uint1 program,
          gap_align->subject_stop += s_length;
       } else {
          score_right = SEMI_G_ALIGN_EX(query+init_hsp->q_off,
-            subject+init_hsp->s_off, query_blk->length-q_length, 
-            subject_blk->length-s_length, NULL, &(gap_align->query_stop), 
+            subject+init_hsp->s_off, query_length-q_length, 
+            subject_length-s_length, NULL, &(gap_align->query_stop), 
             &(gap_align->subject_stop), TRUE, NULL, gap_align, 
             score_options, init_hsp->q_off, FALSE, FALSE);
-         gap_align->query_stop += init_hsp->q_off;
-         gap_align->subject_stop += init_hsp->s_off;
+         /* Make end offsets point to the byte after the end of the 
+            alignment */
+         gap_align->query_stop += init_hsp->q_off + 1;
+         gap_align->subject_stop += init_hsp->s_off + 1;
       }
    }
    
@@ -2751,11 +2716,11 @@ BLAST_OOFTracebackToGapEditBlock(Int4* S, Int4 q_length,
 Int2 BLAST_GappedAlignmentWithTraceback(Uint1 program, Uint1* query, 
         Uint1* subject, BlastGapAlignStruct* gap_align, 
         const BlastScoringOptions* score_options,
-        const BlastExtensionOptions* ext_options,
         Int4 q_start, Int4 s_start, Int4 query_length, Int4 subject_length)
 {
     Boolean found_start, found_end;
     Int4 score_right, score_left, private_q_length, private_s_length, tmp;
+    Int4 q_length, s_length;
     Int4 prev;
     Int4* tback,* tback1,* p = NULL,* q;
     Boolean is_ooframe = score_options->is_ooframe;
@@ -2765,25 +2730,30 @@ Int2 BLAST_GappedAlignmentWithTraceback(Uint1 program, Uint1* query,
     if (gap_align == NULL)
         return -1;
     
-    /* If greedy extension was performed without traceback for preliminary
-       gapped alignment, use greedy algorithm for final alignment as well. */
-    if (ext_options->algorithm_type == EXTEND_GREEDY_NO_TRACEBACK) {
-       return BLAST_GreedyNtGappedAlignment(query, subject, 
-                 query_length, subject_length, gap_align, 
-                 score_options, ext_options, q_start, s_start, FALSE);
-    }
-
     found_start = FALSE;
     found_end = FALSE;
     
+    q_length = query_length;
+    s_length = subject_length;
+    if (is_ooframe) {
+       /* The mixed frame sequence is shifted to the 3rd position, so its 
+          maximal available length for extension is less by 2 than its 
+          total length. */
+       switch_seq = (program == blast_type_blastx);
+       if (switch_seq) {
+          q_length -= CODON_LENGTH - 1;
+       } else {
+          s_length -= CODON_LENGTH - 1;
+       }
+    }
+
     tback = tback1 = (Int4*)
-       malloc((subject_length + query_length)*sizeof(Int4));
+       malloc((s_length + q_length)*sizeof(Int4));
 
     score_left = 0; prev = 3;
     found_start = TRUE;
         
     if(is_ooframe) {
-       switch_seq = (program == blast_type_blastx);
        /* NB: Left extension does not include starting point corresponding
           to the offset pair; the right extension does. */
        score_left =
@@ -2818,12 +2788,12 @@ Int2 BLAST_GappedAlignmentWithTraceback(Uint1 program, Uint1* query,
     
     score_right = 0;
 
-    if ((q_start < query_length) && (s_start < subject_length)) {
+    if ((q_start < q_length) && (s_start < s_length)) {
        found_end = TRUE;
        if(is_ooframe) {
           score_right = 
              OOF_SEMI_G_ALIGN_EX(query+q_start-1, subject+s_start-1, 
-                query_length-q_start, subject_length-s_start, 
+                q_length-q_start, s_length-s_start, 
                 tback1, &private_q_length, &private_s_length, FALSE,
                 &tback1, gap_align, score_options, q_start, FALSE, switch_seq);
             if (prev != 3 && p) {
@@ -2833,7 +2803,7 @@ Int2 BLAST_GappedAlignmentWithTraceback(Uint1 program, Uint1* query,
         } else {
             score_right = 
                SEMI_G_ALIGN_EX(query+q_start, subject+s_start, 
-                  query_length-q_start-1, subject_length-s_start-1, 
+                  q_length-q_start-1, s_length-s_start-1, 
                   tback1, &private_q_length, &private_s_length, FALSE, 
                   &tback1, gap_align, score_options, q_start, FALSE, FALSE);
         }
@@ -2897,11 +2867,8 @@ Int2 PHIGappedAlignmentWithTraceback(Uint1 program,
 {
     Boolean found_end;
     Int4 score_right, score_left, private_q_length, private_s_length, tmp;
-    Int4 prev;
     Int4* tback,* tback1,* p = NULL,* q;
-    Boolean is_ooframe = score_options->is_ooframe;
     Int2 status = 0;
-    Boolean switch_seq = FALSE;
     Int4 pat_length;
     
     if (gap_align == NULL)
@@ -2912,7 +2879,7 @@ Int2 PHIGappedAlignmentWithTraceback(Uint1 program,
     tback = tback1 = (Int4*)
        malloc((subject_length + query_length)*sizeof(Int4));
 
-    score_left = 0; prev = 3;
+    score_left = 0;
         
     score_left = 
        SEMI_G_ALIGN_EX(query, subject, q_start, s_start, tback, 
@@ -3016,7 +2983,6 @@ static Int2 PHIGappedAlignment(Uint1 program,
    Int4 q_length=0, s_length=0, score_right, score_left;
    Int4 private_q_start, private_s_start;
    Uint1* query,* subject;
-   Boolean switch_seq = FALSE;
     
    if (gap_align == NULL)
       return FALSE;
@@ -3089,12 +3055,11 @@ Int2 PHIGetGappedScore (Uint1 program_number,
         BlastHSPList** hsp_list_ptr)
 
 {
-   Boolean is_prot;
    BlastHSPList* hsp_list;
    BlastInitHSP** init_hsp_array;
    BlastInitHSP* init_hsp;
    Int4 index;
-   Int4 q_start, s_start, q_end, s_end;
+   Int4 q_start, s_start;
    Int2 status = 0;
    BlastHitSavingOptions* hit_options = hit_params->options;
 
@@ -3105,7 +3070,6 @@ Int2 PHIGetGappedScore (Uint1 program_number,
    if (init_hitlist->total == 0)
       return 0;
 
-   is_prot = (program_number != blast_type_blastn);
 
    if (*hsp_list_ptr == NULL)
       *hsp_list_ptr = hsp_list = BlastHSPListNew();
@@ -3123,13 +3087,11 @@ Int2 PHIGetGappedScore (Uint1 program_number,
       init_hsp = init_hsp_array[index];
 
       if (!init_hsp->ungapped_data) {
-         q_start = q_end = init_hsp->q_off;
-         s_start = s_end = init_hsp->s_off;
+         q_start = init_hsp->q_off;
+         s_start = init_hsp->s_off;
       } else {
          q_start = init_hsp->ungapped_data->q_start;
-         q_end = q_start + init_hsp->ungapped_data->length - 1;
          s_start = init_hsp->ungapped_data->s_start;
-         s_end = s_start + init_hsp->ungapped_data->length - 1;
       }
 
       status =  PHIGappedAlignment(program_number, query, 
diff --git a/algo/blast/core/blast_gapalign.h b/algo/blast/core/blast_gapalign.h
index 2a8fa913..39362ae9 100644
--- a/algo/blast/core/blast_gapalign.h
+++ b/algo/blast/core/blast_gapalign.h
@@ -1,4 +1,4 @@
-/* $Id: blast_gapalign.h,v 1.27 2003/10/27 20:50:20 dondosha Exp $
+/* $Id: blast_gapalign.h,v 1.28 2003/12/10 23:14:34 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@ Author: Ilya Dondoshansky
 Contents: Structures and functions prototypes used for BLAST gapped extension
 
 ******************************************************************************
- * $Revision: 1.27 $
+ * $Revision: 1.28 $
  * */
 
 #ifndef __BLAST_GAPALIGN__
@@ -246,8 +246,6 @@ Int2 BLAST_GetGappedScore (Uint1 program_number, BLAST_SequenceBlk* query,
  * @param subject The subject sequence [in]
  * @param gap_align The gapped alignment structure [in] [out]
  * @param score_options Scoring parameters [in]
- * @param ext_options Extension options, specifying which algorithm to use
- *                     for gapped extension [in]
  * @param q_start Offset in query where to start alignment [in]
  * @param s_start Offset in subject where to start alignment [in]
  * @param subject_length Maximal allowed extension in subject [in]
@@ -256,9 +254,30 @@ Int2 BLAST_GappedAlignmentWithTraceback(Uint1 program,
         Uint1* query, Uint1* subject, 
         BlastGapAlignStruct* gap_align, 
         const BlastScoringOptions* score_options,
-        const BlastExtensionOptions* ext_options,
         Int4 q_start, Int4 s_start, Int4 query_length, Int4 subject_length);
 
+/** Greedy gapped alignment, with or without traceback.
+ * Given two sequences, relevant options and an offset pair, fills the
+ * gap_align structure with alignment endpoints and, if traceback is 
+ * performed, gap information.
+ * @param query The query sequence [in]
+ * @param subject The subject sequence [in]
+ * @param query_length The query sequence length [in]
+ * @param subject The subject sequence length [in]
+ * @param gap_align The structure holding various information and memory 
+ *        needed for gapped alignment [in] [out]
+ * @param score_options Options related to scoring alignments [in]
+ * @param q_off Starting offset in query [in]
+ * @param s_off Starting offset in subject [in]
+ * @param compressed_subject Is subject sequence compressed? [in]
+ * @param do_traceback Should traceback be saved? [in]
+ */
+Int2 
+BLAST_GreedyGappedAlignment(Uint1* query, Uint1* subject, 
+   Int4 query_length, Int4 subject_length, BlastGapAlignStruct* gap_align,
+   const BlastScoringOptions* score_options, 
+   Int4 q_off, Int4 s_off, Boolean compressed_subject, Boolean do_traceback);
+
 /** Perform a gapped alignment with traceback for PHI BLAST
  * @param program Type of BLAST program [in]
  * @param query The query sequence [in]
diff --git a/algo/blast/core/blast_hits.c b/algo/blast/core/blast_hits.c
index 63d18c0e..81a93ce0 100644
--- a/algo/blast/core/blast_hits.c
+++ b/algo/blast/core/blast_hits.c
@@ -1,4 +1,4 @@
-/* $Id: blast_hits.c,v 1.46 2003/10/21 22:15:34 camacho Exp $
+/* $Id: blast_hits.c,v 1.64 2004/01/21 16:11:27 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -37,10 +37,10 @@ Detailed Contents:
           alignment
 
 ******************************************************************************
- * $Revision: 1.46 $
+ * $Revision: 1.64 $
  * */
 
-static char const rcsid[] = "$Id: blast_hits.c,v 1.46 2003/10/21 22:15:34 camacho Exp $";
+static char const rcsid[] = "$Id: blast_hits.c,v 1.64 2004/01/21 16:11:27 dondosha Exp $";
 
 #include <algo/blast/core/blast_options.h>
 #include <algo/blast/core/blast_extend.h>
@@ -116,7 +116,7 @@ BlastHSP* BlastHSPFree(BlastHSP* hsp)
 }
 
 Int2 BLAST_GetNonSumStatsEvalue(Uint1 program, BlastQueryInfo* query_info,
-        BlastHSPList* hsp_list, BlastHitSavingOptions* hit_options, 
+        BlastHSPList* hsp_list, const BlastScoringOptions* score_options, 
         BlastScoreBlk* sbp)
 {
    BlastHSP* hsp;
@@ -124,18 +124,15 @@ Int2 BLAST_GetNonSumStatsEvalue(Uint1 program, BlastQueryInfo* query_info,
    BLAST_KarlinBlk** kbp;
    Int4 hsp_cnt;
    Int4 index;
-   Uint1 factor;
    
    if (hsp_list == NULL)
       return 1;
    
-   if (hit_options->gapped_calculation && program != blast_type_blastn)
+   if (score_options->gapped_calculation && program != blast_type_blastn)
       kbp = sbp->kbp_gap_std;
    else
       kbp = sbp->kbp_std;
    
-   factor = ((program == blast_type_blastn) ? 2 : 1);
-
    hsp_cnt = hsp_list->hspcnt;
    hsp_array = hsp_list->hsp_array;
    for (index=0; index<hsp_cnt; index++) {
@@ -151,7 +148,7 @@ Int2 BLAST_GetNonSumStatsEvalue(Uint1 program, BlastQueryInfo* query_info,
       } else {
          hsp->evalue = 
             BLAST_KarlinStoE_simple(hsp->score, kbp[hsp->context],
-               (double)query_info->eff_searchsp_array[hsp->context/factor]);
+               (double)query_info->eff_searchsp_array[hsp->context]);
       }
    }
    
@@ -260,7 +257,6 @@ BlastHSPGetNumIdentical(Uint1* query, Uint1* subject,
    Int4* align_length_ptr)
 {
    Int4 i, num_ident, align_length, q_off, s_off;
-   Int2 context;
    Uint1* q,* s;
    GapEditBlock* gap_info;
    GapEditScript* esp;
@@ -270,7 +266,6 @@ BlastHSPGetNumIdentical(Uint1* query, Uint1* subject,
    if (!gap_info && is_gapped)
       return -1;
 
-   context = hsp->context;
    q_off = hsp->query.offset;
    s_off = hsp->subject.offset;
 
@@ -322,26 +317,45 @@ BlastHSPGetNumIdentical(Uint1* query, Uint1* subject,
 
 /** Comparison callback function for sorting HSPs by e-value */
 static int
-evalue_compare_hsps(const void* v1, const void* v2)
+score_compare_hsps(const void* v1, const void* v2)
 {
    BlastHSP* h1,* h2;
    
    h1 = *((BlastHSP**) v1);
    h2 = *((BlastHSP**) v2);
 
-   if (h1->evalue < h2->evalue)
-      return -1;
-   else if (h1->evalue > h2->evalue)
-      return 1;
+   /* No need to check e-values, because for the same subject sequence e-value
+      is always inverse proportional to score. However e-values are less 
+      sensitive, since they both can be 0, when scores are large but 
+      different. */
    if (h1->score > h2->score)
       return -1;
    else if (h1->score < h2->score)
       return 1;
+   /* Tie-breakers: decreasing subject offsets; decreasing subject ends, 
+      decreasing query offsets, decreasing query ends */
+   else if (h1->subject.offset > h2->subject.offset)
+      return -1;
+   else if (h1->subject.offset < h2->subject.offset)
+      return 1;
+   else if (h1->subject.end > h2->subject.end)
+      return -1;
+   else if (h1->subject.end < h2->subject.end)
+      return 1;
+   else if (h1->query.offset > h2->query.offset)
+      return -1;
+   else if (h1->query.offset < h2->query.offset)
+      return 1;
+   else if (h1->query.end > h2->query.end)
+      return -1;
+   else if (h1->query.end < h2->query.end)
+      return 1;
+
    return 0;
 }
 
-/** Comparison callback function for sorting HSPs by diagonal and removing
- * the HSPs contained in or identical to other HSPs.
+/** Comparison callback function for sorting HSPs by diagonal and flagging
+ * the HSPs contained in or identical to other HSPs for future deletion.
 */
 static int
 diag_uniq_compare_hsps(const void* v1, const void* v2)
@@ -364,13 +378,6 @@ diag_uniq_compare_hsps(const void* v1, const void* v2)
    else if (h1->context > h2->context)
       return 1;
    
-   /* If the two HSP's have same coordinates, they are equal */
-   if (h1->query.offset == h2->query.offset && 
-       h1->query.end == h2->query.end && 
-       h1->subject.offset == h2->subject.offset &&
-       h1->subject.end == h2->subject.end)
-      return 0;
-   
    /* Check if one HSP is contained in the other, if so, 
       leave only the longer one, given it has lower evalue */
    if (h1->query.offset >= h2->query.offset && 
@@ -378,21 +385,33 @@ diag_uniq_compare_hsps(const void* v1, const void* v2)
        h1->subject.offset >= h2->subject.offset && 
        h1->subject.end <= h2->subject.end && 
        h1->evalue >= h2->evalue) { 
-      *hp1 = BlastHSPFree(*hp1);
-      return 1; 
+      (*hp1)->score = 0;
    } else if (h1->query.offset <= h2->query.offset &&  
               h1->query.end >= h2->query.end &&  
               h1->subject.offset <= h2->subject.offset && 
               h1->subject.end >= h2->subject.end && 
               h1->evalue <= h2->evalue) { 
-      *hp2 = BlastHSPFree(*hp2);
-      return -1; 
+      (*hp2)->score = 0;
    }
    
    return (h1->query.offset - h1->subject.offset) -
       (h2->query.offset - h2->subject.offset);
 }
 
+static int
+null_compare_hsps(const void* v1, const void* v2)
+{
+   BlastHSP* h1,* h2;
+   
+   h1 = *((BlastHSP**) v1);
+   h2 = *((BlastHSP**) v2);
+   
+   if ((h1 && h2) || (!h1 && !h2))
+      return 0;
+   else if (!h1) return 1;
+   else return -1;
+}
+
 /** Are the two HSPs within a given diagonal distance of each other? */
 #define MB_HSP_CLOSE(q1, q2, s1, s2, c) (ABS(((q1)-(s1)) - ((q2)-(s2))) < (c))
 
@@ -406,11 +425,22 @@ BlastSortUniqHspArray(BlastHSPList* hsp_list)
    Int2 context;
    double evalue;
 
-   qsort(hsp_list->hsp_array, hsp_list->hspcnt, sizeof(BlastHSP*), 
-            diag_uniq_compare_hsps);
+   qsort(hsp_array, hsp_list->hspcnt, sizeof(BlastHSP*), 
+         diag_uniq_compare_hsps);
+   /* Delete all HSPs that were flagged in qsort */
+   for (index = 0, new_hspcnt = 0; index < hsp_list->hspcnt; ++index) {
+      if (hsp_array[index]->score == 0) {
+         hsp_array[index] = BlastHSPFree(hsp_array[index]);
+      }
+   }      
+   /* Move all nulled out HSPs to the end */
+   qsort(hsp_array, hsp_list->hspcnt, sizeof(BlastHSP*),
+         null_compare_hsps);
+
    for (index=1, new_hspcnt=0; index<hsp_list->hspcnt; index++) {
-      if (hsp_array[index]==NULL) 
-	 continue;
+      if (!hsp_array[index])
+         break;
+
       q_off = hsp_array[index]->query.offset;
       s_off = hsp_array[index]->subject.offset;
       q_end = hsp_array[index]->query.end;
@@ -461,64 +491,31 @@ BlastSortUniqHspArray(BlastHSPList* hsp_list)
    return 0;
 }
 
-/** Reevaluate the HSPs in an HSP list, using ambiguity information. 
- * This is/can only done either for an ungapped search, or if traceback is 
- * already available.
- * Subject sequence is uncompressed and saved here. Number of identities is
- * calculated for each HSP along the way. 
- * @param hsp_list The list of HSPs for one subject sequence [in] [out]
- * @param query_blk The query sequence [in]
- * @param subject_blk The subject sequence [in] [out]
- * @param hit_options The options related to saving hits [in]
- * @param query_info Auxiliary query information [in]
- * @param sbp The statistical information [in]
- * @param score_options The scoring options [in]
- * @param rdfp The BLAST database structure (for retrieving uncompressed
- *             sequence) [in]
- */
-static Int2 
-BLAST_ReevaluateWithAmbiguities(BlastHSPList* hsp_list,
-   BLAST_SequenceBlk* query_blk, BLAST_SequenceBlk* subject_blk, 
-   const BlastHitSavingOptions* hit_options, BlastQueryInfo* query_info, 
-   BlastScoreBlk* sbp, const BlastScoringOptions* score_options, 
-   const BlastSeqSrc* bssp)
+Boolean ReevaluateHSPWithAmbiguities(BlastHSP* hsp, 
+           Uint1* query_start, Uint1* subject_start, 
+           const BlastHitSavingOptions* hit_options, 
+           const BlastScoringOptions* score_options, 
+           BlastQueryInfo* query_info, BlastScoreBlk* sbp)
 {
    Int4 sum, score, gap_open, gap_extend;
    Int4** matrix;
-   BlastHSP** hsp_array,* hsp;
-   Uint1* query,* subject,* query_start,* subject_start = NULL;
+   Uint1* query,* subject;
    Uint1* new_q_start,* new_s_start,* new_q_end,* new_s_end;
-   Int4 index, context, hspcnt, i;
+   Int4 index;
    Int2 factor = 1;
    Uint1 mask = 0x0f;
-   GapEditScript* esp,* last_esp,* prev_esp,* first_esp;
-   Boolean purge, delete_hsp;
+   GapEditScript* esp,* last_esp = NULL,* prev_esp,* first_esp = NULL;
+   Boolean delete_hsp;
    double searchsp_eff;
-   Int4 last_esp_num;
-   Int2 status = 0;
+   Int4 last_esp_num = 0;
    Int4 align_length;
-   BLAST_KarlinBlk** kbp;
-   GetSeqArg seq_arg;
-
-   if (!hsp_list)
-      return status;
-
-   hspcnt = hsp_list->hspcnt;
-   hsp_array = hsp_list->hsp_array;
-   memset((void*) &seq_arg, 0, sizeof(seq_arg));
-
-   /* In case of no traceback, return without doing anything */
-   if (!hsp_list->traceback_done && hit_options->gapped_calculation) {
-      return status;
-   }
-
-   if (hsp_list->hspcnt == 0)
-      /* All HSPs have been deleted */
-      return status;
+   BLAST_KarlinBlk* kbp;
+   Boolean gapped_calculation = score_options->gapped_calculation;
 
    /* NB: this function is called only for BLASTn, so we know where the 
       Karlin block is */
-   kbp = sbp->kbp_std;
+   kbp = sbp->kbp_std[hsp->context];
+   searchsp_eff = (double)query_info->eff_searchsp_array[hsp->context];
 
    if (score_options->gap_open == 0 && score_options->gap_extend == 0) {
       if (score_options->reward % 2 == 1) 
@@ -533,79 +530,70 @@ BLAST_ReevaluateWithAmbiguities(BlastHSPList* hsp_list,
 
    matrix = sbp->matrix;
 
-   /* Retrieve the unpacked subject sequence and save it in the 
-      sequence_start element of the subject structure.
-      NB: for the BLAST 2 Sequences case, the uncompressed sequence must 
-      already be there */
-   if (bssp) {
-      seq_arg.oid = subject_blk->oid;
-      seq_arg.encoding = BLASTNA_ENCODING;
-      BLASTSeqSrcGetSequence(bssp, (void*) &seq_arg);
-
-#if 0
-      readdb_get_sequence_ex(rdfp, subject_blk->oid, 
-         &subject_blk->sequence_start, &buf_len, TRUE);
-      subject_blk->sequence = subject_blk->sequence_start + 1;
-      subject_blk->sequence_start_allocated = TRUE;
-#endif
-      subject_blk->sequence_start = seq_arg.seq->sequence_start;
-      subject_blk->sequence = seq_arg.seq->sequence_start + 1;
-   }
-   /* The sequence in blastna encoding is now stored in sequence_start */
-   subject_start = subject_blk->sequence_start + 1;
-
-   purge = FALSE;
-   for (index=0; index<hspcnt; index++) {
-      if (hsp_array[index] == NULL)
-         continue;
-      else
-         hsp = hsp_array[index];
-
-      context = hsp->context;
-
-      query_start = query_blk->sequence + query_info->context_offsets[context];
-      searchsp_eff = (double)query_info->eff_searchsp_array[context/2];
-      
-      query = query_start + hsp->query.offset; 
-      subject = subject_start + hsp->subject.offset;
-      score = 0;
-      sum = 0;
-      new_q_start = new_q_end = query;
-      new_s_start = new_s_end = subject;
-      i = 0;
-
+   query = query_start + hsp->query.offset; 
+   subject = subject_start + hsp->subject.offset;
+   score = 0;
+   sum = 0;
+   new_q_start = new_q_end = query;
+   new_s_start = new_s_end = subject;
+   index = 0;
+   
+   if (!gapped_calculation) {
+      for (index = 0; index < hsp->subject.length; ++index) {
+         sum += factor*matrix[*query & mask][*subject];
+         query++;
+         subject++;
+         if (sum < 0) {
+            if (BLAST_KarlinStoE_simple(score, kbp, searchsp_eff)
+                > hit_options->expect_value) {
+               /* Start from new offset */
+               new_q_start = query;
+               new_s_start = subject;
+               score = sum = 0;
+            } else {
+               /* Stop here */
+               break;
+            }
+         } else if (sum > score) {
+            /* Remember this point as the best scoring end point */
+            score = sum;
+            new_q_end = query;
+            new_s_end = subject;
+         }
+      }
+   } else {
       esp = hsp->gap_info->esp;
       prev_esp = NULL;
       last_esp = first_esp = esp;
       last_esp_num = 0;
-
+      
       while (esp) {
          if (esp->op_type == GAPALIGN_SUB) {
             sum += factor*matrix[*query & mask][*subject];
             query++;
             subject++;
-            i++;
+            index++;
          } else if (esp->op_type == GAPALIGN_DEL) {
             sum -= gap_open + gap_extend * esp->num;
             subject += esp->num;
-            i += esp->num;
+            index += esp->num;
          } else if (esp->op_type == GAPALIGN_INS) {
             sum -= gap_open + gap_extend * esp->num;
             query += esp->num;
-            i += esp->num;
+            index += esp->num;
          }
          
          if (sum < 0) {
-            if (BLAST_KarlinStoE_simple(score, kbp[context],
-                   searchsp_eff) > hit_options->expect_value) {
+            if (BLAST_KarlinStoE_simple(score, kbp, searchsp_eff)
+                > hit_options->expect_value) {
                /* Start from new offset */
                new_q_start = query;
                new_s_start = subject;
                score = sum = 0;
-               if (i < esp->num) {
-                  esp->num -= i;
+               if (index < esp->num) {
+                  esp->num -= index;
                   first_esp = esp;
-                  i = 0;
+                  index = 0;
                } else {
                   first_esp = esp->next;
                }
@@ -622,32 +610,34 @@ BLAST_ReevaluateWithAmbiguities(BlastHSPList* hsp_list,
             /* Remember this point as the best scoring end point */
             score = sum;
             last_esp = esp;
-            last_esp_num = i;
+            last_esp_num = index;
             new_q_end = query;
             new_s_end = subject;
          }
-         if (i >= esp->num) {
-            i = 0;
+         if (index >= esp->num) {
+            index = 0;
             prev_esp = esp;
             esp = esp->next;
          }
-      }
-
-      score /= factor;
+      } /* loop on edit scripts */
+   } /* if (gapped_calculation) */
 
-      delete_hsp = FALSE;
-      hsp->score = score;
-      hsp->evalue = 
-         BLAST_KarlinStoE_simple(score, kbp[context], searchsp_eff);
-      if (hsp->evalue > hit_options->expect_value) {
-         delete_hsp = TRUE;
-      } else {
-         hsp->query.length = new_q_end - new_q_start;
-         hsp->subject.length = new_s_end - new_s_start;
-         hsp->query.offset = new_q_start - query_start;
-         hsp->query.end = hsp->query.offset + hsp->query.length;
-         hsp->subject.offset = new_s_start - subject_start;
-         hsp->subject.end = hsp->subject.offset + hsp->subject.length;
+   score /= factor;
+   
+   delete_hsp = FALSE;
+   hsp->score = score;
+   hsp->evalue = 
+      BLAST_KarlinStoE_simple(score, kbp, searchsp_eff);
+   if (hsp->evalue > hit_options->expect_value) {
+      delete_hsp = TRUE;
+   } else {
+      hsp->query.length = new_q_end - new_q_start;
+      hsp->subject.length = new_s_end - new_s_start;
+      hsp->query.offset = new_q_start - query_start;
+      hsp->query.end = hsp->query.offset + hsp->query.length;
+      hsp->subject.offset = new_s_start - subject_start;
+      hsp->subject.end = hsp->subject.offset + hsp->subject.length;
+      if (gapped_calculation) {
          /* Make corrections in edit block and free any parts that
             are no longer needed */
          if (first_esp != hsp->gap_info->esp) {
@@ -659,17 +649,103 @@ BLAST_ReevaluateWithAmbiguities(BlastHSPList* hsp_list,
             last_esp->next = NULL;
          }
          last_esp->num = last_esp_num;
-         BlastHSPGetNumIdentical(query_start, subject_start, hsp, 
-            hit_options->gapped_calculation, &hsp->num_ident, &align_length);
-         /* Check if this HSP passes the percent identity test */
-         if (((double)hsp->num_ident) / align_length * 100 < 
-             hit_options->percent_identity)
-            delete_hsp = TRUE;
       }
+      BlastHSPGetNumIdentical(query_start, subject_start, hsp, 
+         gapped_calculation, &hsp->num_ident, &align_length);
+      /* Check if this HSP passes the percent identity test */
+      if (((double)hsp->num_ident) / align_length * 100 < 
+          hit_options->percent_identity)
+         delete_hsp = TRUE;
+   }
+   
+   if (delete_hsp) { /* This HSP is now below the cutoff */
+      if (gapped_calculation && first_esp != NULL && 
+          first_esp != hsp->gap_info->esp)
+         GapEditScriptDelete(first_esp);
+   }
+  
+   return delete_hsp;
+} 
+
+/** Reevaluate all HSPs in an HSP list, using ambiguity information. 
+ * This is/can only done either for an ungapped search, or if traceback is 
+ * already available.
+ * Subject sequence is uncompressed and saved here. Number of identities is
+ * calculated for each HSP along the way. 
+ * @param hsp_list The list of HSPs for one subject sequence [in] [out]
+ * @param query_blk The query sequence [in]
+ * @param subject_blk The subject sequence [in] [out]
+ * @param hit_options The options related to saving hits [in]
+ * @param query_info Auxiliary query information [in]
+ * @param sbp The statistical information [in]
+ * @param score_options The scoring options [in]
+ * @param rdfp The BLAST database structure (for retrieving uncompressed
+ *             sequence) [in]
+ */
+static Int2 
+ReevaluateHSPListWithAmbiguities(BlastHSPList* hsp_list,
+   BLAST_SequenceBlk* query_blk, BLAST_SequenceBlk* subject_blk, 
+   const BlastHitSavingOptions* hit_options, BlastQueryInfo* query_info, 
+   BlastScoreBlk* sbp, const BlastScoringOptions* score_options, 
+   const BlastSeqSrc* bssp)
+{
+   BlastHSP** hsp_array,* hsp;
+   Uint1* query_start,* subject_start = NULL;
+   Int4 index, context, hspcnt;
+   Boolean purge, delete_hsp;
+   Int2 status = 0;
+   GetSeqArg seq_arg;
+   Boolean gapped_calculation = score_options->gapped_calculation;
 
+   if (!hsp_list)
+      return status;
+
+   hspcnt = hsp_list->hspcnt;
+   hsp_array = hsp_list->hsp_array;
+   memset((void*) &seq_arg, 0, sizeof(seq_arg));
+
+   /* In case of no traceback, return without doing anything */
+   if (!hsp_list->traceback_done && gapped_calculation) {
+      if (hsp_list->hspcnt > 1)
+         status = BlastSortUniqHspArray(hsp_list);
+      return status;
+   }
+
+   if (hsp_list->hspcnt == 0)
+      /* All HSPs have been deleted */
+      return status;
+
+   /* Retrieve the unpacked subject sequence and save it in the 
+      sequence_start element of the subject structure.
+      NB: for the BLAST 2 Sequences case, the uncompressed sequence must 
+      already be there */
+   if (bssp) {
+      seq_arg.oid = subject_blk->oid;
+      seq_arg.encoding = BLASTNA_ENCODING;
+      BLASTSeqSrcGetSequence(bssp, (void*) &seq_arg);
+
+      subject_blk->sequence_start = seq_arg.seq->sequence_start;
+      subject_blk->sequence = seq_arg.seq->sequence_start + 1;
+   }
+   /* The sequence in blastna encoding is now stored in sequence_start */
+   subject_start = subject_blk->sequence_start + 1;
+
+   purge = FALSE;
+   for (index=0; index<hspcnt; index++) {
+      if (hsp_array[index] == NULL)
+         continue;
+      else
+         hsp = hsp_array[index];
+
+      context = hsp->context;
+
+      query_start = query_blk->sequence + query_info->context_offsets[context];
+
+      delete_hsp = 
+         ReevaluateHSPWithAmbiguities(hsp, query_start, subject_start,
+            hit_options, score_options, query_info, sbp);
+      
       if (delete_hsp) { /* This HSP is now below the cutoff */
-         if (first_esp != NULL && first_esp != hsp->gap_info->esp)
-            GapEditScriptDelete(first_esp);
          hsp_array[index] = BlastHSPFree(hsp_array[index]);
          purge = TRUE;
       }
@@ -758,8 +834,10 @@ evalue_compare_hsp_lists(const void* v1, const void* v2)
    h2 = *(BlastHSPList**) v2;
    
    /* If any of the HSP lists is empty, it is considered "worse" than the 
-      other */
-   if (h1->hspcnt == 0)
+      other, unless the other is also empty. */
+   if (h1->hspcnt == 0 && h2->hspcnt == 0)
+      return 0;
+   else if (h1->hspcnt == 0)
       return 1;
    else if (h2->hspcnt == 0)
       return -1;
@@ -827,6 +905,7 @@ static void InsertBlastHSPListInHeap(BlastHitList* hit_list,
       }
       hit_list->worst_evalue = 
          hit_list->hsplist_array[0]->hsp_array[0]->evalue;
+      hit_list->low_score = hit_list->hsplist_array[0]->hsp_array[0]->score;
 }
 
 /** Insert a new HSP list into the hit list.
@@ -858,7 +937,11 @@ static Int2 BLAST_UpdateHitList(BlastHitList* hit_list,
       hit_list->hsplist_array[hit_list->hsplist_count++] = hsp_list;
       hit_list->worst_evalue = 
          MAX(hsp_list->hsp_array[0]->evalue, hit_list->worst_evalue);
-   } else if (hsp_list->hsp_array[0]->evalue >= hit_list->worst_evalue) {
+      hit_list->low_score = 
+         MIN(hsp_list->hsp_array[0]->score, hit_list->low_score);
+   } else if ((hsp_list->hsp_array[0]->evalue > hit_list->worst_evalue) ||
+              ((hsp_list->hsp_array[0]->evalue == hit_list->worst_evalue) &&
+               (hsp_list->hsp_array[0]->score <= hit_list->low_score))) {
       /* This hit list is less significant than any of those already saved;
          discard it */
       BlastHSPListFree(hsp_list);
@@ -887,6 +970,7 @@ static BlastHitList* BLAST_HitListNew(Int4 hitlist_size)
    BlastHitList* new_hitlist = (BlastHitList*) 
       calloc(1, sizeof(BlastHitList));
    new_hitlist->hsplist_max = hitlist_size;
+   new_hitlist->low_score = INT4_MAX;
    return new_hitlist;
 }
 
@@ -908,9 +992,9 @@ static BlastHitList* BLAST_HitListFree(BlastHitList* hitlist)
 static BlastHSPList* BlastHSPListDup(BlastHSPList* hsp_list)
 {
    BlastHSPList* new_hsp_list = (BlastHSPList*) 
-      MemDup(hsp_list, sizeof(BlastHSPList));
+      BlastMemDup(hsp_list, sizeof(BlastHSPList));
    new_hsp_list->hsp_array = (BlastHSP**) 
-      MemDup(hsp_list->hsp_array, hsp_list->hspcnt*sizeof(BlastHSP*));
+      BlastMemDup(hsp_list->hsp_array, hsp_list->hspcnt*sizeof(BlastHSP*));
    new_hsp_list->allocated = hsp_list->hspcnt;
 
    return new_hsp_list;
@@ -918,7 +1002,7 @@ static BlastHSPList* BlastHSPListDup(BlastHSPList* hsp_list)
 
 /* Documentation in blast_hits.h */
 Int2 BLAST_SaveHitlist(Uint1 program, BLAST_SequenceBlk* query,
-        BLAST_SequenceBlk* subject, BlastResults* results, 
+        BLAST_SequenceBlk* subject, BlastHSPResults* results, 
         BlastHSPList* hsp_list, BlastHitSavingParameters* hit_parameters, 
         BlastQueryInfo* query_info, BlastScoreBlk* sbp, 
         const BlastScoringOptions* score_options, const BlastSeqSrc* bssp,
@@ -935,7 +1019,7 @@ Int2 BLAST_SaveHitlist(Uint1 program, BLAST_SequenceBlk* query,
       return 0;
 
    if (program == blast_type_blastn) {
-      status = BLAST_ReevaluateWithAmbiguities(hsp_list, query, subject, 
+      status = ReevaluateHSPListWithAmbiguities(hsp_list, query, subject, 
                   hit_options, query_info, sbp, score_options, bssp);
       context_factor = 2;
    } else if (program == blast_type_blastx || 
@@ -948,7 +1032,7 @@ Int2 BLAST_SaveHitlist(Uint1 program, BLAST_SequenceBlk* query,
    /* Sort the HSPs by e-value */
    if (hsp_list->hspcnt > 1) {
       qsort(hsp_list->hsp_array, hsp_list->hspcnt, sizeof(BlastHSP*), 
-               evalue_compare_hsps);
+               score_compare_hsps);
    }
 
    /* *******************************************************************
@@ -1037,12 +1121,12 @@ Int2 BLAST_SaveHitlist(Uint1 program, BLAST_SequenceBlk* query,
    return 0; 
 }
 
-Int2 BLAST_ResultsInit(Int4 num_queries, BlastResults** results_ptr)
+Int2 BLAST_ResultsInit(Int4 num_queries, BlastHSPResults** results_ptr)
 {
-   BlastResults* results;
+   BlastHSPResults* results;
    Int2 status = 0;
 
-   results = (BlastResults*) malloc(sizeof(BlastResults));
+   results = (BlastHSPResults*) malloc(sizeof(BlastHSPResults));
 
    results->num_queries = num_queries;
    results->hitlist_array = (BlastHitList**) 
@@ -1052,7 +1136,7 @@ Int2 BLAST_ResultsInit(Int4 num_queries, BlastResults** results_ptr)
    return status;
 }
 
-BlastResults* BLAST_ResultsFree(BlastResults* results)
+BlastHSPResults* BLAST_ResultsFree(BlastHSPResults* results)
 {
    Int4 index;
 
@@ -1066,7 +1150,25 @@ BlastResults* BLAST_ResultsFree(BlastResults* results)
    return NULL;
 }
 
-Int2 BLAST_SortResults(BlastResults* results)
+static void BlastHitListPurge(BlastHitList* hit_list)
+{
+   Int4 index, hsplist_count;
+   
+   if (!hit_list)
+      return;
+   
+   hsplist_count = hit_list->hsplist_count;
+   for (index = 0; index < hsplist_count && 
+           hit_list->hsplist_array[index]->hspcnt > 0; ++index);
+   
+   hit_list->hsplist_count = index;
+   /* Free all empty HSP lists */
+   for ( ; index < hsplist_count; ++index) {
+      BlastHSPListFree(hit_list->hsplist_array[index]);
+   }
+}
+
+Int2 BLAST_SortResults(BlastHSPResults* results)
 {
    Int4 index;
    BlastHitList* hit_list;
@@ -1077,6 +1179,7 @@ Int2 BLAST_SortResults(BlastResults* results)
          qsort(hit_list->hsplist_array, hit_list->hsplist_count, 
                   sizeof(BlastHSPList*), evalue_compare_hsp_lists);
       }
+      BlastHitListPurge(hit_list);
    }
    return 0;
 }
@@ -1287,8 +1390,7 @@ BLAST_MergeHsps(BlastHSP* hsp1, BlastHSP* hsp2, Int4 start)
       if (new_segment1->s_end <= new_segment2->s_end) {
          new_segment1 = new_segment1->next;
          num1++;
-      }
-      if (new_segment1->s_end >= new_segment2->s_end) {
+      } else {
          new_segment2 = new_segment2->next;
          num2++;
       }
diff --git a/algo/blast/core/blast_hits.h b/algo/blast/core/blast_hits.h
index 17b0bfa6..f10f6edf 100644
--- a/algo/blast/core/blast_hits.h
+++ b/algo/blast/core/blast_hits.h
@@ -1,4 +1,4 @@
-/* $Id: blast_hits.h,v 1.13 2003/09/25 15:15:55 dondosha Exp $
+/* $Id: blast_hits.h,v 1.18 2003/12/12 22:57:31 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@ Author: Ilya Dondoshansky
 Contents: Structures used for saving BLAST hits
 
 ******************************************************************************
- * $Revision: 1.13 $
+ * $Revision: 1.18 $
  * */
 #ifndef __BLAST_HITS__
 #define __BLAST_HITS__
@@ -49,18 +49,19 @@ typedef struct BlastHitList {
    Int4 hsplist_count; /**< Filled size of the HSP lists array */
    Int4 hsplist_max; /**< Maximal allowed size of the HSP lists array */
    double worst_evalue; /**< Highest of the best e-values among the HSP 
-                            lists */
+                           lists */
+   Int4 low_score; /**< The lowest of the best scores among the HSP lists */
    Boolean heapified; /**< Is this hit list already heapified? */
    BlastHSPList** hsplist_array; /**< Array of HSP lists for individual
                                           database hits */
 } BlastHitList;
 
 /** The structure to contain all BLAST results, for multiple queries */
-typedef struct BlastResults {
+typedef struct BlastHSPResults {
    Int4 num_queries; /**< Number of query sequences */
    BlastHitList** hitlist_array; /**< Array of results for individual
                                           query sequences */
-} BlastResults;
+} BlastHSPResults;
 
 /** BLAST_SaveHitlist
  *  Save the current hit list to appropriate places in the results structure
@@ -81,7 +82,7 @@ typedef struct BlastResults {
  * @param thr_info Information shared between multiple search threads [in]
  */
 Int2 BLAST_SaveHitlist(Uint1 program, BLAST_SequenceBlk* query, 
-        BLAST_SequenceBlk* subject, BlastResults* results, 
+        BLAST_SequenceBlk* subject, BlastHSPResults* results, 
         BlastHSPList* hsp_list, BlastHitSavingParameters* hit_parameters, 
         BlastQueryInfo* query_info, BlastScoreBlk* sbp, 
         const BlastScoringOptions* score_options, const BlastSeqSrc* bssp,
@@ -92,10 +93,10 @@ Int2 BLAST_SaveHitlist(Uint1 program, BLAST_SequenceBlk* query,
  *                    for [in]
  * @param results_ptr The allocated structure [out]
  */
-Int2 BLAST_ResultsInit(Int4 num_queries, BlastResults** results_ptr);
+Int2 BLAST_ResultsInit(Int4 num_queries, BlastHSPResults** results_ptr);
 
 /** Sort each hit list in the BLAST results by best e-value */
-Int2 BLAST_SortResults(BlastResults* results);
+Int2 BLAST_SortResults(BlastHSPResults* results);
 
 /** Calculate the expected values for all HSPs in a hit list. In case of 
  * multiple queries, the offsets are assumed to be already adjusted to 
@@ -104,11 +105,11 @@ Int2 BLAST_SortResults(BlastResults* results);
  * @param query_info Auxiliary query information - needed only for effective
                      search space calculation if it is not provided [in]
  * @param hsp_list List of HSPs for one subject sequence [in] [out]
- * @param hit_options Options containing the e-value cut-off [in]
+ * @param score_options Needed only to check if gapped calculation is done [in]
  * @param sbp Structure containing statistical information [in]
  */
 Int2 BLAST_GetNonSumStatsEvalue(Uint1 program, BlastQueryInfo* query_info,
-        BlastHSPList* hsp_list, BlastHitSavingOptions* hit_options, 
+        BlastHSPList* hsp_list, const BlastScoringOptions* score_options, 
         BlastScoreBlk* sbp);
 
 /** Calculate e-value for an HSP found by PHI BLAST.
@@ -132,6 +133,26 @@ void PHIGetEvalue(BlastHSPList* hsp_list, BlastScoreBlk* sbp);
 Int2 BLAST_ReapHitlistByEvalue(BlastHSPList* hsp_list, 
                                BlastHitSavingOptions* hit_options);
 
+/** Reevaluate the HSP's score, e-value and percent identity after taking
+ * into account the ambiguity information. Needed for blastn only, either
+ * after a greedy gapped extension, or for ungapped search.
+ * @param hsp The HSP structure [in] [out]
+ * @param query_start Pointer to the start of the query sequence [in]
+ * @param subject_start Pointer to the start of the subject sequence [in]
+ * @param hit_options Hit saving options with e-value cut-off [in]
+ * @param score_options Scoring options [in]
+ * @param query_info Query information structure, containing effective search
+ *                   space(s) [in]
+ * @param sbp Score block with Karlin-Altschul parameters [in]
+ * @return Should this HSP be deleted after the score reevaluation?
+ */
+Boolean ReevaluateHSPWithAmbiguities(BlastHSP* hsp, 
+           Uint1* query_start, Uint1* subject_start, 
+           const BlastHitSavingOptions* hit_options, 
+           const BlastScoringOptions* score_options, 
+           BlastQueryInfo* query_info, BlastScoreBlk* sbp);
+
+
 /** Cleans out the NULLed out HSP's from the HSP array,
  *	moving the BLAST_HSPPtr's up to fill in the gaps.
  * @param hsp_array Array of pointers to HSP structures [in]
@@ -193,7 +214,7 @@ BlastHSP* BlastHSPFree(BlastHSP* hsp);
 BlastHSPList* BlastHSPListFree(BlastHSPList* hsp_list);
 
 /** Deallocate memory for BLAST results */
-BlastResults* BLAST_ResultsFree(BlastResults* results);
+BlastHSPResults* BLAST_ResultsFree(BlastHSPResults* results);
 
 #ifdef __cplusplus
 }
diff --git a/algo/blast/core/blast_lookup.c b/algo/blast/core/blast_lookup.c
index 9177a990..3215ec7a 100644
--- a/algo/blast/core/blast_lookup.c
+++ b/algo/blast/core/blast_lookup.c
@@ -1,4 +1,4 @@
-/* $Id: blast_lookup.c,v 1.3 2003/10/22 16:45:28 dondosha Exp $
+/* $Id: blast_lookup.c,v 1.16 2004/01/26 19:39:27 coulouri Exp $
 
 * ===========================================================================
 *
@@ -29,9 +29,9 @@
 #include <algo/blast/core/blast_def.h>
 #include <algo/blast/core/blast_options.h>
 #include <algo/blast/core/blast_lookup.h>
-#include <algo/blast/core/util.h>
+#include <algo/blast/core/lookup_util.h>
 
-static char const rcsid[] = "$Id: blast_lookup.c,v 1.3 2003/10/22 16:45:28 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_lookup.c,v 1.16 2004/01/26 19:39:27 coulouri Exp $";
 
 static void AddWordHits( LookupTable *lookup,
 			 Int4** matrix,
@@ -65,12 +65,21 @@ Int4 LookupTableNew(const LookupTableOptions* opt,
 		      Boolean is_protein)
 {
    LookupTable* lookup = *lut = 
-      (LookupTable*) malloc(sizeof(LookupTable));
+      (LookupTable*) calloc(1, sizeof(LookupTable));
+
+   ASSERT(lookup != NULL);
 
   if (is_protein) {
+    Int4 i;
+
     lookup->charsize = ilog2(opt->alphabet_size) + 1;
     lookup->wordsize = opt->word_size;
-    lookup->backbone_size = iexp(2,lookup->charsize*opt->word_size);
+
+    lookup->backbone_size = 0;
+    for(i=0;i<lookup->wordsize;i++)
+        lookup->backbone_size |= (opt->alphabet_size - 1) << (i * lookup->charsize);
+    lookup->backbone_size += 1;
+
     lookup->mask = makemask(opt->word_size * lookup->charsize);
   } else {
      lookup->word_length = opt->word_size;
@@ -90,8 +99,11 @@ Int4 LookupTableNew(const LookupTableOptions* opt,
   lookup->threshold = opt->threshold;
   lookup->thin_backbone = 
      (Int4**) calloc(lookup->backbone_size , sizeof(Int4*));
-  lookup->use_pssm = opt->use_pssm;
+  ASSERT(lookup->thin_backbone != NULL);
 
+  lookup->use_pssm = opt->use_pssm;
+  lookup->neighbors=NULL;
+  lookup->overflow=NULL;
   return 0;
 }
 
@@ -105,16 +117,18 @@ Int4 BlastAaLookupAddWordHit(LookupTable* lookup, /* in/out: the lookup table */
   Int4 * chain = NULL;
     
   /* compute its index, */
+
   _ComputeIndex(lookup->wordsize,lookup->charsize,lookup->mask, w, &index);
 
   ASSERT(index < lookup->backbone_size);
-      
+
   /* if backbone cell is null, initialize a new chain */
   if (lookup->thin_backbone[index] == NULL)
     {
       chain_size = 8;
       hits_in_chain = 0;
-      chain = (Int4*) malloc( chain_size * sizeof(Int4) );
+      chain = (Int4*) calloc( chain_size, sizeof(Int4) );
+      ASSERT(chain != NULL);
       chain[0] = chain_size;
       chain[1] = hits_in_chain;
       lookup->thin_backbone[index] = chain;
@@ -132,6 +146,8 @@ Int4 BlastAaLookupAddWordHit(LookupTable* lookup, /* in/out: the lookup table */
     {
       chain_size = chain_size * 2;
       chain = (Int4*) realloc(chain, chain_size * sizeof(Int4) );
+      ASSERT(chain != NULL);
+
       lookup->thin_backbone[index] = chain;
       chain[0] = chain_size;
     }
@@ -156,10 +172,12 @@ Int4 _BlastAaLookupFinalize(LookupTable* lookup)
 /* allocate the new lookup table */
  lookup->thick_backbone = (LookupBackboneCell *)
     calloc(lookup->backbone_size , sizeof(LookupBackboneCell));
+    ASSERT(lookup->thick_backbone != NULL);
 
  /* allocate the pv_array */
  lookup->pv = (PV_ARRAY_TYPE *)
-    calloc((lookup->backbone_size >> PV_ARRAY_BTS) , sizeof(PV_ARRAY_TYPE));
+    calloc((lookup->backbone_size >> PV_ARRAY_BTS) + 1 , sizeof(PV_ARRAY_TYPE));
+  ASSERT(lookup->pv != NULL);
 
  /* find out how many cells have >3 hits */
  for(i=0;i<lookup->backbone_size;i++)
@@ -175,7 +193,8 @@ Int4 _BlastAaLookupFinalize(LookupTable* lookup)
  lookup->longest_chain = longest_chain;
 
  /* allocate the overflow array */
- lookup->overflow = (Int4*) malloc( overflow_cells_needed * sizeof(Int4) );
+ lookup->overflow = (Int4*) calloc( overflow_cells_needed, sizeof(Int4) );
+ ASSERT(lookup->overflow != NULL);
 
 /* for each position in the lookup table backbone, */
 for(i=0;i<lookup->backbone_size;i++)
@@ -207,7 +226,7 @@ for(i=0;i<lookup->backbone_size;i++)
 	      num_overflows++;
 
 	      lookup->thick_backbone[i].num_used = lookup->thin_backbone[i][1];
-	      lookup->thick_backbone[i].payload.overflow = & (lookup->overflow[overflow_cursor]);
+	      lookup->thick_backbone[i].payload.overflow_cursor = overflow_cursor;
 	      for(j=0;j<lookup->thin_backbone[i][1];j++)
 		{
                 lookup->overflow[overflow_cursor] = lookup->thin_backbone[i][j+2];
@@ -260,6 +279,7 @@ static NCBI_INLINE void  _ComputeIndex(Int4 wordsize,
   Int4 i;
 
   *index = 0;
+
   for(i=0;i<wordsize;i++)
 {
     *index = ((*index << charsize) | word[i]) & mask;
@@ -337,7 +357,7 @@ Int4 BlastAaScanSubject(const LookupTableWrap* lookup_wrap,
 		src = lookup->thick_backbone[index].payload.entries;
 	      else
 		/* hits live in overflow array */
-		src = lookup->thick_backbone[index].payload.overflow;
+		src = & (lookup->overflow [ lookup->thick_backbone[index].payload.overflow_cursor ] );
 	      
 	      /* copy the hits. */
 	      for(i=0;i<numhits;i++)
@@ -390,8 +410,8 @@ Int4 BlastAaLookupIndexQueries(LookupTable* lookup,
     }
 
   /* free neighbor array*/
-  sfree(lookup->neighbors);
-  lookup->neighbors=NULL;
+  if (lookup->neighbors != NULL)
+    sfree(lookup->neighbors);
 
   return 0;
 }
@@ -408,7 +428,7 @@ Int4 _BlastAaLookupIndexQuery(LookupTable* lookup,
   for(loc=location; loc; loc=loc->next)
     {
       from = ((DoubleInt*) loc->ptr)->i1;
-      to = ((DoubleInt*) loc->ptr)->i2 - lookup->wordsize;
+      to = ((DoubleInt*) loc->ptr)->i2 - lookup->wordsize + 1;
 
       for(w=from;w<=to;w++)
 	{
@@ -436,6 +456,7 @@ Int4 MakeAllWordSequence(LookupTable* lookup)
   lookup->neighbors_length = len;
 
   lookup->neighbors = (Uint1*) malloc( len );
+  ASSERT(lookup->neighbors != NULL);
 
   /* generate the de Bruijn sequence */
 
@@ -444,30 +465,34 @@ Int4 MakeAllWordSequence(LookupTable* lookup)
   /* unwrap it */
 
   for(i=0;i<(n-1);i++)
-    lookup->neighbors[len-((n-1)+1)+i] = lookup->neighbors[i];
+    lookup->neighbors[len-n+1+i] = lookup->neighbors[i];
   
   return 0;
 }
 
 Int4 AddNeighboringWords(LookupTable* lookup, Int4 ** matrix, BLAST_SequenceBlk* query, Int4 offset)
 {
-  Uint1* w = NULL;
-
-
-  if (query)
-	w = query->sequence + offset;
   
-  if (lookup->threshold == 0)
+  if (lookup->use_pssm)
+  {
+      AddPSSMWordHits(lookup, matrix, offset);
+  }
+  else
+  {
+    Uint1* w = NULL;
+    ASSERT(query != NULL);
+    w = query->sequence + offset;
+  
+    if (lookup->threshold == 0)
     {
       BlastAaLookupAddWordHit(lookup, w, offset);
       lookup->exact_matches++;
-      return 0;
     }
-  
-  if (lookup->use_pssm)
-      AddPSSMWordHits(lookup, matrix, offset);
-  else
+    else
+    {
       AddWordHits(lookup, matrix, w, offset);
+    }
+  }
   return 0;
 }
 
@@ -475,7 +500,7 @@ static void AddWordHits(LookupTable* lookup, Int4** matrix,
 			Uint1* word, Int4 offset)
 {
   Uint1* s = lookup->neighbors;
-  Uint1* s_end=s + lookup->neighbors_length - lookup->wordsize;
+  Uint1* s_end=s + lookup->neighbors_length - lookup->wordsize + 1;
   Uint1* w = word;
   Uint1 different;
   Int4 score;
@@ -500,7 +525,13 @@ static void AddWordHits(LookupTable* lookup, Int4** matrix,
         while (s < s_end)
           {
             if ( (s[0] == w[0]) || (p0[s[0]] >= threshold) )
+	    {
                 BlastAaLookupAddWordHit(lookup,s,offset);
+		if (s[0] == w[0])
+		    lookup->exact_matches++;
+		else
+		    lookup->neighbor_matches++;
+	    }
             s++;
   	  }
 
@@ -516,7 +547,13 @@ static void AddWordHits(LookupTable* lookup, Int4** matrix,
 	    different = (w[0] ^ s[0]) | (w[1] ^ s[1]);
   
             if ( !different || (score >= threshold) )
+	    {
                 BlastAaLookupAddWordHit(lookup,s,offset);
+		if (!different)
+		    lookup->exact_matches++;
+		else
+		    lookup->neighbor_matches++;
+	    }
             s++;
 	  }
 
@@ -533,7 +570,13 @@ static void AddWordHits(LookupTable* lookup, Int4** matrix,
 	    different = (w[0] ^ s[0]) | (w[1] ^ s[1]) | (w[2] ^ s[2]);
   
             if ( !different || (score >= threshold) )
+	    {
                 BlastAaLookupAddWordHit(lookup,s,offset);
+		if (!different)
+		    lookup->exact_matches++;
+		else
+		    lookup->neighbor_matches++;
+	    }
             s++;
   	  }
 
@@ -551,7 +594,13 @@ static void AddWordHits(LookupTable* lookup, Int4** matrix,
               }
   
             if ( !different || (score >= threshold) )
+	    {
                 BlastAaLookupAddWordHit(lookup,s,offset);
+		if (!different)
+		    lookup->exact_matches++;
+		else
+		    lookup->neighbor_matches++;
+	    }
             s++;
   	  }
 
@@ -731,8 +780,7 @@ Int4 BlastNaScanSubject_AG(const LookupTableWrap* lookup_wrap,
          
          if (NA_PV_TEST(pv_array, index, PV_ARRAY_BTS)) {
             num_hits = lookup->thick_backbone[index].num_used;
-            if (num_hits == 0)
-               continue;
+            ASSERT(num_hits != 0);
             if (num_hits > (max_hits - total_hits))
                break;
             if ( num_hits <= HITS_ON_BACKBONE )
@@ -740,11 +788,9 @@ Int4 BlastNaScanSubject_AG(const LookupTableWrap* lookup_wrap,
                lookup_pos = lookup->thick_backbone[index].payload.entries;
             else
                /* hits live in overflow array */
-               lookup_pos = (Int4*)
-                  (lookup->thick_backbone[index].payload.overflow);
+               lookup_pos = & ( lookup->overflow[lookup->thick_backbone[index].payload.overflow_cursor] );
             
-            s_off = 
-               ((s - abs_start) + compressed_wordsize)*COMPRESSION_RATIO;
+            s_off = (s - abs_start)*COMPRESSION_RATIO;
             while (num_hits) {
                q_off = *((Uint4 *) lookup_pos); /* get next query offset */
                lookup_pos++;
@@ -770,13 +816,13 @@ Int4 BlastNaScanSubject_AG(const LookupTableWrap* lookup_wrap,
          index = 0;
          for (i = 0; i < compressed_wordsize; ++i)
             index = ((index)<<FULL_BYTE_SHIFT) | (*s++);
+
          adjusted_index = 
-            (((index)<<bit) & lookup->mask) | ((*s)>>(FULL_BYTE_SHIFT-bit));
+            BlastNaLookupAdjustIndex(s, index, lookup->mask, bit);
          
          if (NA_PV_TEST(pv_array, adjusted_index, PV_ARRAY_BTS)) {
             num_hits = lookup->thick_backbone[adjusted_index].num_used;
-            if (num_hits == 0)
-               continue;
+            ASSERT(num_hits != 0);
             if (num_hits > (max_hits - total_hits))
                break;
             if ( num_hits <= HITS_ON_BACKBONE )
@@ -784,8 +830,7 @@ Int4 BlastNaScanSubject_AG(const LookupTableWrap* lookup_wrap,
                lookup_pos = lookup->thick_backbone[adjusted_index].payload.entries;
             else
                /* hits live in overflow array */
-               lookup_pos = (Int4*)
-                 (lookup->thick_backbone[adjusted_index].payload.overflow);
+               lookup_pos = & (lookup->overflow [ lookup->thick_backbone[adjusted_index].payload.overflow_cursor]);
             
             while (num_hits) {
                q_off = *((Uint4 *) lookup_pos); /* get next query offset */
@@ -793,7 +838,7 @@ Int4 BlastNaScanSubject_AG(const LookupTableWrap* lookup_wrap,
                num_hits--;
                
                q_offsets[total_hits] = q_off;
-               s_offsets[total_hits++] = s_off + reduced_word_length;
+               s_offsets[total_hits++] = s_off;
             }
          }
       }
@@ -818,105 +863,54 @@ Int4 BlastNaScanSubject(const LookupTableWrap* lookup_wrap,
    Int4 q_off;
    PV_ARRAY_TYPE *pv_array = lookup->pv;
    Int4 total_hits = 0;
-   Boolean full_byte_scan = (lookup->scan_step % COMPRESSION_RATIO == 0);
+   Int4 reduced_word_length = lookup->reduced_wordsize*COMPRESSION_RATIO;
    Int4 i;
 
    abs_start = subject->sequence;
    s = abs_start + start_offset/COMPRESSION_RATIO;
    /* s_end points to the place right after the last full sequence byte */ 
-   s_end = abs_start + (*end_offset)/COMPRESSION_RATIO;
+   s_end = 
+      abs_start + (*end_offset + reduced_word_length)/COMPRESSION_RATIO;
+
    index = 0;
    
    /* Compute the first index */
    for (i = 0; i < lookup->reduced_wordsize; ++i)
       index = ((index)<<FULL_BYTE_SHIFT) | *s++;
 
-   if (full_byte_scan) {
-      /* s points to the byte right after the end of the current word */
-      while (s <= s_end) {
-         if (NA_PV_TEST(pv_array, index, PV_ARRAY_BTS)) {
-            num_hits = lookup->thick_backbone[index].num_used;
-            if (num_hits == 0)
-               continue;
-            if (num_hits > (max_hits - total_hits))
-               break;
-            if ( num_hits <= HITS_ON_BACKBONE )
-               /* hits live in thick_backbone */
-               lookup_pos = lookup->thick_backbone[index].payload.entries;
-            else
-               /* hits live in overflow array */
-               lookup_pos = 
-                  (Int4*)(lookup->thick_backbone[index].payload.overflow);
-            
-            /* Save the hits offsets */
-            s_off = (s - abs_start)*COMPRESSION_RATIO;
-            while (num_hits) {
-               q_off = *((Uint4 *) lookup_pos); /* get next query offset */
-               lookup_pos++;
-               num_hits--;
-               
-               q_offsets[total_hits] = q_off;
-               s_offsets[total_hits++] = s_off;
-            }
-         }
-
-         /* Compute the next value of the index */
-         index = (((index)<<FULL_BYTE_SHIFT) & lookup->mask) | (*s++);  
-
-      }
-      /* Ending offset should point to the start of the word that ends 
-         at s */
-      *end_offset = ((s - abs_start) - lookup->reduced_wordsize)*COMPRESSION_RATIO;
-   } else {
-      Int4 scan_shift = 2*lookup->scan_step;
-      Uint1 bit = 2*(start_offset % COMPRESSION_RATIO);
-      Int4 adjusted_index;
-
-      /* s points to the byte right after the end of the current word */
-      while (s <= s_end) {
-         /* Adjust the word index by the base within a byte */
-         adjusted_index = BlastNaLookupAdjustIndex(s, index, lookup->mask,
-                                                   bit);
+   /* s points to the byte right after the end of the current word */
+   while (s <= s_end) {
+      if (NA_PV_TEST(pv_array, index, PV_ARRAY_BTS)) {
+         num_hits = lookup->thick_backbone[index].num_used;
+         ASSERT(num_hits != 0);
+         if (num_hits > (max_hits - total_hits))
+            break;
+         if ( num_hits <= HITS_ON_BACKBONE )
+            /* hits live in thick_backbone */
+            lookup_pos = lookup->thick_backbone[index].payload.entries;
+         else
+            /* hits live in overflow array */
+            lookup_pos = & (lookup->overflow[lookup->thick_backbone[index].payload.overflow_cursor]);
          
-         if (NA_PV_TEST(pv_array, index, PV_ARRAY_BTS)) {
-            num_hits = lookup->thick_backbone[index].num_used;
-            if (num_hits == 0)
-               continue;
-            if (num_hits > (max_hits - total_hits))
-               break;
-            if ( num_hits <= HITS_ON_BACKBONE )
-               /* hits live in thick_backbone */
-               lookup_pos = lookup->thick_backbone[index].payload.entries;
-            else
-               /* hits live in overflow array */
-               lookup_pos = 
-                  (Int4*)(lookup->thick_backbone[index].payload.overflow);
+         /* Save the hits offsets */
+         s_off = (s - abs_start)*COMPRESSION_RATIO - reduced_word_length;
+         while (num_hits) {
+            q_off = *((Uint4 *) lookup_pos); /* get next query offset */
+            lookup_pos++;
+            num_hits--;
             
-            /* Save the hits offsets */
-            s_off = (s - abs_start)*COMPRESSION_RATIO + bit/2;
-            while (num_hits) {
-               q_off = *((Uint4 *) lookup_pos); /* get next query offset */
-               lookup_pos++;
-               num_hits--;
-               
-               q_offsets[total_hits] = q_off;
-               s_offsets[total_hits++] = s_off;
-            }
-         }
-         bit += scan_shift;
-         if (bit >= FULL_BYTE_SHIFT) {
-            /* Advance to the next full byte */
-            bit -= FULL_BYTE_SHIFT;
-            index = BlastNaLookupComputeIndex(FULL_BYTE_SHIFT, 
-                                lookup->mask, s++, index);
+            q_offsets[total_hits] = q_off;
+            s_offsets[total_hits++] = s_off;
          }
       }
-      /* Ending offset should point to the start of the word that ends 
-         at s */
-      *end_offset = 
-         ((s - abs_start) - lookup->reduced_wordsize)*COMPRESSION_RATIO
-         + bit/2;
+
+      /* Compute the next value of the index */
+      index = (((index)<<FULL_BYTE_SHIFT) & lookup->mask) | (*s++);  
+
    }
+   /* Ending offset should point to the start of the word that ends 
+      at s */
+   *end_offset = (s - abs_start)*COMPRESSION_RATIO - reduced_word_length;
 
    return total_hits;
 }
@@ -981,7 +975,8 @@ static Int4 BlastNaLookupAddWordHit(LookupTable* lookup, Uint1* w,
     {
       chain_size = 8;
       hits_in_chain = 0;
-      chain = malloc( chain_size * sizeof(Int4) );
+      chain = calloc( chain_size, sizeof(Int4) );
+      ASSERT(chain != NULL);
       chain[0] = chain_size;
       chain[1] = hits_in_chain;
       lookup->thin_backbone[index] = chain;
@@ -999,6 +994,7 @@ static Int4 BlastNaLookupAddWordHit(LookupTable* lookup, Uint1* w,
     {
       chain_size = chain_size * 2;
       chain = realloc(chain, chain_size * sizeof(Int4) );
+      ASSERT(chain != NULL);
       lookup->thin_backbone[index] = chain;
       chain[0] = chain_size;
     }
@@ -1025,12 +1021,12 @@ Int4 BlastNaLookupIndexQuery(LookupTable* lookup, BLAST_SequenceBlk* query,
 
   for(loc=location; loc; loc=loc->next) {
      from = ((DoubleInt*) loc->ptr)->i1;
-     to = ((DoubleInt*) loc->ptr)->i2;
+     to = ((DoubleInt*) loc->ptr)->i2 + 1;
      
      sequence = query->sequence + from;
-     /* Make the offsets point to the ends of the words */
-     from += lookup->reduced_wordsize*COMPRESSION_RATIO;
-     for(offset = from; offset < to; offset++) {
+     /* Last offset is such that full word fits in the sequence */
+     to -= lookup->reduced_wordsize*COMPRESSION_RATIO;
+     for(offset = from; offset <= to; offset++) {
 	BlastNaLookupAddWordHit(lookup, sequence, offset);
 	++sequence;
      }
diff --git a/algo/blast/core/blast_lookup.h b/algo/blast/core/blast_lookup.h
index 1d6deba1..77c7d027 100644
--- a/algo/blast/core/blast_lookup.h
+++ b/algo/blast/core/blast_lookup.h
@@ -1,4 +1,4 @@
-/* $Id: blast_lookup.h,v 1.1 2003/09/10 19:37:26 dondosha Exp $
+/* $Id: blast_lookup.h,v 1.2 2004/01/26 19:39:27 coulouri Exp $
 
 * ===========================================================================
 *
@@ -75,7 +75,7 @@ extern "C" {
     Int4 num_used;       /* num valid positions */
 
     union {
-      Int4* overflow;
+      Int4 overflow_cursor;
       Int4 entries[HITS_ON_BACKBONE];
     } payload;
 
diff --git a/algo/blast/core/blast_options.c b/algo/blast/core/blast_options.c
index 083e7896..e773bce5 100644
--- a/algo/blast/core/blast_options.c
+++ b/algo/blast/core/blast_options.c
@@ -26,6 +26,27 @@
 **************************************************************************
  *
  * $Log: blast_options.c,v $
+ * Revision 1.75  2003/12/31 20:04:47  dondosha
+ * Round best stride to a number divisible by 4 for all values except 6 and 7
+ *
+ * Revision 1.74  2003/12/31 16:04:37  coulouri
+ * use -1 to disable protein neighboring words
+ *
+ * Revision 1.73  2003/12/08 16:03:05  coulouri
+ * Propagate protein neighboring threshold even if it is zero
+ *
+ * Revision 1.72  2003/11/24 23:18:32  dondosha
+ * Added gap_decay_rate argument to BLAST_Cutoffs; removed BLAST_Cutoffs_simple
+ *
+ * Revision 1.71  2003/11/12 18:17:46  dondosha
+ * Correction in calculating scanning stride
+ *
+ * Revision 1.70  2003/11/04 23:22:47  dondosha
+ * Do not calculate hit saving cutoff score for PHI BLAST
+ *
+ * Revision 1.69  2003/10/30 19:34:01  dondosha
+ * Removed gapped_calculation from BlastHitSavingOptions structure
+ *
  * Revision 1.68  2003/10/24 20:55:10  camacho
  * Rename GetDefaultStride
  *
@@ -328,7 +349,7 @@
  *
 */
 
-static char const rcsid[] = "$Id: blast_options.c,v 1.68 2003/10/24 20:55:10 camacho Exp $";
+static char const rcsid[] = "$Id: blast_options.c,v 1.75 2003/12/31 20:04:47 dondosha Exp $";
 
 #include <algo/blast/core/blast_options.h>
 #include <algo/blast/core/blast_gapalign.h>
@@ -473,7 +494,7 @@ BlastInitialWordParametersNew(Uint1 program_number,
    BlastExtensionParameters* ext_params, BlastScoreBlk* sbp, 
    BlastQueryInfo* query_info, 
    const BlastEffectiveLengthsOptions* eff_len_options, 
-   BlastInitialWordParameters* *parameters)
+   Boolean gapped_calculation, BlastInitialWordParameters* *parameters)
 {
    Int4 context = query_info->first_context;
    Int4 cutoff_score = 0, s2 = 0;
@@ -493,8 +514,7 @@ BlastInitialWordParametersNew(Uint1 program_number,
    (*parameters)->x_dropoff = (Int4)
       ceil(word_options->x_dropoff*NCBIMATH_LN2/sbp->kbp_std[context]->Lambda);
 
-   if (hit_params->options->gapped_calculation && 
-       program_number != blast_type_blastn)
+   if (program_number != blast_type_blastn && gapped_calculation)
       kbp = sbp->kbp_gap[context];
    else
       kbp = sbp->kbp_std[context];
@@ -507,14 +527,14 @@ BlastInitialWordParametersNew(Uint1 program_number,
       eff_len_options->dbseq_num;
 
    e2 = UNGAPPED_CUTOFF_EVALUE;
-   BLAST_Cutoffs(&s2, &e2, kbp, MIN(avglen, qlen), avglen, TRUE);
+   BLAST_Cutoffs(&s2, &e2, kbp, MIN(avglen, qlen)*avglen, TRUE, 
+                 hit_params->gap_decay_rate);
 
    cutoff_score = MIN(hit_params->cutoff_score, s2);
 
    /* For non-blastn programs, the cutoff score should not be larger than 
       gap trigger */
-   if (hit_params->options->gapped_calculation && 
-       program_number != blast_type_blastn) {
+   if (gapped_calculation && program_number != blast_type_blastn) {
       (*parameters)->cutoff_score = 
          MIN((Int4)ext_params->gap_trigger, cutoff_score);
    } else {
@@ -741,6 +761,16 @@ BlastScoringOptionsValidate(Uint1 program_number,
 	if (options == NULL)
 		return 1;
 
+   if (program_number == blast_type_tblastx && 
+              options->gapped_calculation)
+   {
+		Int4 code=2;
+		Int4 subcode=1;
+      Blast_MessageWrite(blast_msg, 2, code, subcode, 
+         "Gapped search is not allowed for tblastx");
+		return (Int2) code;
+   }
+
 	if (program_number == blast_type_blastn)
 	{
 		if (options->penalty >= 0)
@@ -893,6 +923,8 @@ Int4 CalculateBestStride(Int4 word_size, Boolean var_words, Int4 lut_type)
 {
    Int4 lut_width;
    Int4 extra = 1;
+   Uint1 remainder;
+   Int4 stride;
 
    if (lut_type == MB_LOOKUP_TABLE)
       lut_width = 12;
@@ -901,10 +933,18 @@ Int4 CalculateBestStride(Int4 word_size, Boolean var_words, Int4 lut_type)
    else
       lut_width = 4;
 
-   if (var_words && ((word_size % COMPRESSION_RATIO) == 0) )
+   remainder = word_size % COMPRESSION_RATIO;
+
+   if (var_words && (remainder == 0) )
       extra = COMPRESSION_RATIO;
 
-   return word_size - lut_width + extra;
+   stride = word_size - lut_width + extra;
+
+   remainder = stride % 4;
+
+   if (stride > 8 || (stride > 4 && remainder == 1) ) 
+      stride -= remainder;
+   return stride;
 }
 
 Int2 
@@ -927,8 +967,16 @@ BLAST_FillLookupTableOptions(LookupTableOptions* options,
       }
    }
 
-   if (threshold)
+   /* if the supplied threshold is -1, disable neighboring words */
+   if (threshold == -1)
+      options->threshold = 0;
+
+   /* if the supplied threshold is > 0, use it */
+   if (threshold > 0)
       options->threshold = threshold;
+
+   /* otherwise, use the default */
+
    if (use_pssm)
       options->use_pssm = use_pssm;
    if (word_size)
@@ -937,7 +985,7 @@ BLAST_FillLookupTableOptions(LookupTableOptions* options,
       if (!ag_blast) {
          options->scan_step = COMPRESSION_RATIO;
       } else {
-         options->scan_step = CalculateBestStride(word_size, variable_wordsize,
+         options->scan_step = CalculateBestStride(options->word_size, variable_wordsize,
                                                   options->lut_type);
       }
    }
@@ -1070,7 +1118,6 @@ BLAST_FillHitSavingOptions(BlastHitSavingOptions* options,
    if (!options)
       return 1;
 
-   options->gapped_calculation = is_gapped;
    if (hitlist_size)
       options->hitlist_size = hitlist_size;
    if (evalue)
@@ -1087,14 +1134,6 @@ BlastHitSavingOptionsValidate(Uint1 program_number,
 	if (options == NULL)
 		return 1;
 
-   if (program_number == blast_type_tblastx && options->gapped_calculation) {
-		Int4 code=2;
-		Int4 subcode=1;
-      Blast_MessageWrite(blast_msg, 2, code, subcode, 
-         "Gapped search is not allowed for tblastx");
-		return (Int2) code;
-   }
-
 	if (options->hitlist_size < 1)
 	{
 		Int4 code=1;
@@ -1135,6 +1174,7 @@ BlastHitSavingParametersNew(Uint1 program_number,
    BlastHitSavingParameters* params;
    BLAST_KarlinBlk* kbp;
    double evalue = options->expect_value;
+   Boolean gapped_calculation = TRUE;
 
    if (!options || !parameters)
       return 1;
@@ -1149,20 +1189,24 @@ BlastHitSavingParametersNew(Uint1 program_number,
 
    params->handle_results = handle_results;
 
-   if (sbp->kbp_gap && sbp->kbp_gap[query_info->first_context])
+   if (sbp->kbp_gap && sbp->kbp_gap[query_info->first_context]) {
       kbp = sbp->kbp_gap[query_info->first_context];
-   else
+   } else {
       kbp = sbp->kbp[query_info->first_context];
+      gapped_calculation = FALSE;
+   }
 
    if (options->cutoff_score > 0) {
       params->cutoff_score = options->cutoff_score;
-   } else {
-      BLAST_Cutoffs_simple(&(params->cutoff_score), &evalue, kbp, 
+   } else if (!options->phi_align) {
+      BLAST_Cutoffs(&(params->cutoff_score), &evalue, kbp, 
          (double)query_info->eff_searchsp_array[query_info->first_context], 
-         FALSE);
+         FALSE, 0);
+   } else {
+      params->cutoff_score = 0;
    }
    
-   if (program_number == blast_type_blastn || !options->gapped_calculation) {
+   if (program_number == blast_type_blastn || !gapped_calculation) {
       params->gap_prob = BLAST_GAP_PROB;
       params->gap_decay_rate = BLAST_GAP_DECAY_RATE;
    } else {
diff --git a/algo/blast/core/blast_options.h b/algo/blast/core/blast_options.h
index bfc60f28..14ff03fb 100644
--- a/algo/blast/core/blast_options.h
+++ b/algo/blast/core/blast_options.h
@@ -1,4 +1,4 @@
-/* $Id: blast_options.h,v 1.49 2003/10/24 20:54:54 camacho Exp $
+/* $Id: blast_options.h,v 1.51 2003/12/03 16:25:01 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -36,7 +36,7 @@ Detailed Contents:
 	- Options to be used for different tasks of the BLAST search
 
 ******************************************************************************
- * $Revision: 1.49 $
+ * $Revision: 1.51 $
  * */
 
 #ifndef __BLASTOPTIONS__
@@ -221,6 +221,7 @@ typedef struct BlastExtensionOptions {
    double gap_trigger;/**< Score in bits for starting gapped extension */
    Int4 algorithm_type; /**< E.g. for blastn: dynamic programming; 
                            greedy without traceback; greedy with traceback */
+   Boolean skip_traceback; /**< Is traceback information needed in results? */
 } BlastExtensionOptions;
 
 typedef struct BlastExtensionParameters {
@@ -277,8 +278,6 @@ typedef struct BlastHitSavingOptions {
    Boolean is_neighboring; /**< FIXME: neighboring is specified by a percent 
                              identity and a minimum hit length */
 
-   Boolean gapped_calculation;	/**< gapping is used. */
-
    /* Will be dealt with when needed *
    Uint1 handle_results_method; **< Formatting results on the fly if set to 
                                    non-zero */
@@ -464,6 +463,7 @@ BlastInitialWordParametersFree(BlastInitialWordParameters* parameters);
  * @param sbp Statistical (Karlin-Altschul) information [in]
  * @param query_info Query information [in]
  * @param eff_len_options Effective lengths options [in]
+ * @param gapped_calculation Is gapped calculation used for statistics? [in]
  * @param parameters Resulting parameters [out]
 */
 Int2
@@ -473,7 +473,7 @@ BlastInitialWordParametersNew(Uint1 program_number,
    BlastExtensionParameters* ext_params, BlastScoreBlk* sbp, 
    BlastQueryInfo* query_info, 
    const BlastEffectiveLengthsOptions* eff_len_options, 
-   BlastInitialWordParameters* *parameters);
+   Boolean gapped_calculation, BlastInitialWordParameters* *parameters);
 
 /** Deallocate memory for BlastExtensionOptions.
  * @param options Structure to free [in]
diff --git a/algo/blast/core/blast_seqsrc.c b/algo/blast/core/blast_seqsrc.c
index 9b276076..942953a2 100644
--- a/algo/blast/core/blast_seqsrc.c
+++ b/algo/blast/core/blast_seqsrc.c
@@ -1,4 +1,4 @@
-/*  $Id: blast_seqsrc.c,v 1.13 2003/08/25 22:27:40 dondosha Exp $
+/*  $Id: blast_seqsrc.c,v 1.15 2003/12/08 22:43:50 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -30,7 +30,7 @@
 *
 */
 
-static char const rcsid[] = "$Id: blast_seqsrc.c,v 1.13 2003/08/25 22:27:40 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_seqsrc.c,v 1.15 2003/12/08 22:43:50 dondosha Exp $";
 
 #include <algo/blast/core/blast_seqsrc.h>
 
@@ -40,15 +40,26 @@ struct BlastSeqSrc {
     BlastSeqSrcConstructor NewFnPtr;       /**< Constructor */
     BlastSeqSrcDestructor  DeleteFnPtr;    /**< Destructor */
 
+   /* Functions to get information about database as a whole */
     GetInt4FnPtr      GetNumSeqs;     /**< Get number of sequences in set */
     GetInt4FnPtr      GetMaxSeqLen;   /**< Get length of longest seq in set */
     GetInt8FnPtr      GetTotLen;      /**< Get tot length of all seqs in set */
+    GetStrFnPtr       GetName;        /**< Get the name of the database */
+    GetStrFnPtr       GetDefinition;  /**< Get the database definition */
+    GetStrFnPtr       GetDate;        /**< Get the date of the database */
+    GetBoolFnPtr      GetIsProt;      /**< Find if database is a protein or 
+                                         nucleotide */
+
+   /* Functions to get information about individual sequences */
     GetSeqBlkFnPtr    GetSequence;    /**< Retrieve individual sequence */
-    GetSeqIdFnPtr     GetSeqIdStr;    /**< Retrieve sequence identifier */
+    GetStrFnPtr  GetSeqIdStr;  /**< Retrieve sequence identifier string */
+    GetSeqIdFnPtr     GetSeqId;       /**< Retrieve sequence identifier */
     GetInt4FnPtr      GetSeqLen;      /**< Retrieve given sequence length */
+
+   /* Functions to iterate over sequences in the database */
     GetNextChunkFnPtr GetNextChunk;   /**< Get next chunk of seq indices */
     AdvanceIteratorFnPtr IterNext;    /**< Gets next oid from the iterator */
-
+   
     void*             DataStructure;  /**< ADT holding the sequence data */
 
 };
@@ -166,8 +177,15 @@ DEFINE_MEMBER_FUNCTIONS(void*, DataStructure, BlastSeqSrc*)
 DEFINE_MEMBER_FUNCTIONS(GetInt4FnPtr, GetNumSeqs, BlastSeqSrc*)
 DEFINE_MEMBER_FUNCTIONS(GetInt4FnPtr, GetMaxSeqLen, BlastSeqSrc*)
 DEFINE_MEMBER_FUNCTIONS(GetInt8FnPtr, GetTotLen, BlastSeqSrc*)
+
+DEFINE_MEMBER_FUNCTIONS(GetStrFnPtr, GetName, BlastSeqSrc*)
+DEFINE_MEMBER_FUNCTIONS(GetStrFnPtr, GetDefinition, BlastSeqSrc*)
+DEFINE_MEMBER_FUNCTIONS(GetStrFnPtr, GetDate, BlastSeqSrc*)
+DEFINE_MEMBER_FUNCTIONS(GetBoolFnPtr, GetIsProt, BlastSeqSrc*)
+
 DEFINE_MEMBER_FUNCTIONS(GetSeqBlkFnPtr, GetSequence, BlastSeqSrc*)
-DEFINE_MEMBER_FUNCTIONS(GetSeqIdFnPtr, GetSeqIdStr, BlastSeqSrc*)
+DEFINE_MEMBER_FUNCTIONS(GetStrFnPtr, GetSeqIdStr, BlastSeqSrc*)
+DEFINE_MEMBER_FUNCTIONS(GetSeqIdFnPtr, GetSeqId, BlastSeqSrc*)
 DEFINE_MEMBER_FUNCTIONS(GetInt4FnPtr, GetSeqLen, BlastSeqSrc*)
 DEFINE_MEMBER_FUNCTIONS(GetNextChunkFnPtr, GetNextChunk, BlastSeqSrc*)
 DEFINE_MEMBER_FUNCTIONS(AdvanceIteratorFnPtr, IterNext, BlastSeqSrc*)
diff --git a/algo/blast/core/blast_seqsrc.h b/algo/blast/core/blast_seqsrc.h
index 4455eee5..c5cf24fb 100644
--- a/algo/blast/core/blast_seqsrc.h
+++ b/algo/blast/core/blast_seqsrc.h
@@ -1,4 +1,4 @@
-/*  $Id: blast_seqsrc.h,v 1.9 2003/08/21 19:38:50 camacho Exp $
+/*  $Id: blast_seqsrc.h,v 1.12 2003/12/15 18:20:46 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -76,10 +76,23 @@ typedef Int4 (*GetInt4FnPtr) (void*, void*);
  * passed to user-defined implementation */
 typedef Int8 (*GetInt8FnPtr) (void*, void*);
 
-/** Function pointer typedef to return a null terminated string containing a
- * sequence identifier. First argument is the BlastSeqSrc structure used, second
+/** Function pointer typedef to return a null terminated string. 
+ * First argument is the BlastSeqSrc structure used, second
  * argument is passed to user-defined implementation. */
-typedef char* (*GetSeqIdFnPtr) (void*, void*);
+typedef char* (*GetStrFnPtr) (void*, void*);
+
+
+/** Function pointer typedef to return a boolean value. 
+ * First argument is the BlastSeqSrc structure used, second
+ * argument is passed to user-defined implementation. */
+typedef Boolean (*GetBoolFnPtr) (void*, void*);
+
+
+/** Function pointer typedef to return a sequence identifier. The returned SeqId
+ * is cast to a void pointer.
+ * First argument is the BlastSeqSrc structure used, second
+ * argument is passed to user-defined implementation. */
+typedef void* (*GetSeqIdFnPtr) (void*, void*);
 
 /** Function pointer typedef to retrieve sequences from data structure embedded
  * in the BlastSeqSrc structure.
@@ -128,6 +141,8 @@ typedef struct BlastSeqSrcIterator {
     /** Size of the chunks to advance over the BlastSeqSrc, also size of 
       * oid_list member */
     unsigned int  chunk_sz;
+    /* Starting oid for the next chunk/range */
+    unsigned int next_oid;
 } BlastSeqSrcIterator;
 
 /** Allocated and initialized an iterator over a BlastSeqSrc. 
@@ -199,10 +214,20 @@ BlastSeqSrc* BlastSeqSrcFree(BlastSeqSrc* bssp);
     (*GetGetMaxSeqLen(bssp))(GetDataStructure(bssp), NULL)
 #define BLASTSeqSrcGetTotLen(bssp) \
     (*GetGetTotLen(bssp))(GetDataStructure(bssp), NULL)
+#define BLASTSeqSrcGetName(bssp) \
+    (*GetGetName(bssp))(GetDataStructure(bssp), NULL)
+#define BLASTSeqSrcGetDefinition(bssp) \
+    (*GetGetDefinition(bssp))(GetDataStructure(bssp), NULL)
+#define BLASTSeqSrcGetDate(bssp) \
+    (*GetGetDate(bssp))(GetDataStructure(bssp), NULL)
+#define BLASTSeqSrcGetIsProt(bssp) \
+    (*GetGetIsProt(bssp))(GetDataStructure(bssp), NULL)
 #define BLASTSeqSrcGetSequence(bssp, arg) \
     (*GetGetSequence(bssp))(GetDataStructure(bssp), arg)
 #define BLASTSeqSrcGetSeqIdStr(bssp, arg) \
     (*GetGetSeqIdStr(bssp))(GetDataStructure(bssp), arg)
+#define BLASTSeqSrcGetSeqId(bssp, arg) \
+    (*GetGetSeqId(bssp))(GetDataStructure(bssp), arg)
 #define BLASTSeqSrcGetSeqLen(bssp, arg) \
     (*GetGetSeqLen(bssp))(GetDataStructure(bssp), arg)
 #define BLASTSeqSrcGetNextChunk(bssp, iterator) \
@@ -225,8 +250,13 @@ DECLARE_MEMBER_FUNCTIONS(void*, DataStructure, BlastSeqSrc*);
 DECLARE_MEMBER_FUNCTIONS(GetInt4FnPtr, GetNumSeqs, BlastSeqSrc*);
 DECLARE_MEMBER_FUNCTIONS(GetInt4FnPtr, GetMaxSeqLen, BlastSeqSrc*);
 DECLARE_MEMBER_FUNCTIONS(GetInt8FnPtr, GetTotLen, BlastSeqSrc*);
+DECLARE_MEMBER_FUNCTIONS(GetStrFnPtr, GetName, BlastSeqSrc*);
+DECLARE_MEMBER_FUNCTIONS(GetStrFnPtr, GetDefinition, BlastSeqSrc*);
+DECLARE_MEMBER_FUNCTIONS(GetStrFnPtr, GetDate, BlastSeqSrc*);
+DECLARE_MEMBER_FUNCTIONS(GetBoolFnPtr, GetIsProt, BlastSeqSrc*);
 DECLARE_MEMBER_FUNCTIONS(GetSeqBlkFnPtr, GetSequence, BlastSeqSrc*);
-DECLARE_MEMBER_FUNCTIONS(GetSeqIdFnPtr, GetSeqIdStr, BlastSeqSrc*);
+DECLARE_MEMBER_FUNCTIONS(GetStrFnPtr, GetSeqIdStr, BlastSeqSrc*);
+DECLARE_MEMBER_FUNCTIONS(GetSeqIdFnPtr, GetSeqId, BlastSeqSrc*);
 DECLARE_MEMBER_FUNCTIONS(GetInt4FnPtr, GetSeqLen, BlastSeqSrc*);
 DECLARE_MEMBER_FUNCTIONS(GetNextChunkFnPtr, GetNextChunk, BlastSeqSrc*);
 DECLARE_MEMBER_FUNCTIONS(AdvanceIteratorFnPtr, IterNext, BlastSeqSrc*);
diff --git a/algo/blast/core/blast_setup.c b/algo/blast/core/blast_setup.c
index 6cda6a1e..3e478246 100644
--- a/algo/blast/core/blast_setup.c
+++ b/algo/blast/core/blast_setup.c
@@ -1,5 +1,5 @@
 static char const rcsid[] =
-    "$Id: blast_setup.c,v 1.62 2003/10/27 23:02:11 dondosha Exp $";
+    "$Id: blast_setup.c,v 1.65 2004/01/07 21:44:36 dondosha Exp $";
 /* ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@ Author: Tom Madden
 
 Contents: Utilities initialize/setup BLAST.
 
-$Revision: 1.62 $
+$Revision: 1.65 $
 
 ******************************************************************************/
 
@@ -394,7 +394,7 @@ Int2 BLAST_MainSetUp(Uint1 program_number,
                      const BlastHitSavingOptions * hit_options,
                      BLAST_SequenceBlk * query_blk,
                      BlastQueryInfo * query_info,
-                     BlastSeqLoc ** lookup_segments, BlastMask * *filter_out,
+                     BlastSeqLoc ** lookup_segments, BlastMaskLoc * *filter_out,
                      BlastScoreBlk * *sbpp, Blast_Message * *blast_message)
 {
     BlastScoreBlk *sbp;
@@ -407,10 +407,10 @@ Int2 BLAST_MainSetUp(Uint1 program_number,
     BlastSeqLoc *filter_slp = NULL;     /* SeqLocPtr computed for filtering. */
     BlastSeqLoc *filter_slp_combined;   /* Used to hold combined SeqLoc's */
     BlastSeqLoc *loc;           /* Iterator variable */
-    BlastMask *last_filter_out = NULL;
+    BlastMaskLoc *last_filter_out = NULL;
     Uint1 *buffer;              /* holds sequence for plus strand or protein. */
     Boolean reverse;            /* Indicates the strand when masking filtered locations */
-    BlastMask *mask_slp, *next_mask_slp; /* Auxiliary locations for lower 
+    BlastMaskLoc *mask_slp, *next_mask_slp; /* Auxiliary locations for lower 
                                             case masks */
     Int4 context_offset;
     Boolean no_forward_strand; 
@@ -502,15 +502,20 @@ Int2 BLAST_MainSetUp(Uint1 program_number,
 
             /* Attach the lower case mask locations to the filter locations 
                and combine them */
-            if (filter_slp && mask_slp) {
-                for (loc = filter_slp; loc->next; loc = loc->next) ;
-                loc->next = mask_slp->loc_list;
+            if (mask_slp) {
+                if (filter_slp) {
+                    for (loc = filter_slp; loc->next; loc = loc->next);
+                    loc->next = mask_slp->loc_list;
+                } else {
+                    filter_slp = mask_slp->loc_list;
+                }
                 /* Set location list to NULL, to allow safe memory deallocation */
                 mask_slp->loc_list = NULL;
             }
 
             filter_slp_combined = NULL;
-            CombineMaskLocations(filter_slp, &filter_slp_combined);
+            CombineMaskLocations(filter_slp, &filter_slp_combined, 0);
+
             filter_slp = BlastSeqLocFree(filter_slp);
 
             /* NB: for translated searches filter locations are returned in 
@@ -520,10 +525,10 @@ Int2 BLAST_MainSetUp(Uint1 program_number,
             if (filter_slp_combined) {
                 if (!last_filter_out) {
                     last_filter_out = *filter_out =
-                        (BlastMask *) calloc(1, sizeof(BlastMask));
+                        (BlastMaskLoc *) calloc(1, sizeof(BlastMaskLoc));
                 } else {
                     last_filter_out->next =
-                        (BlastMask *) calloc(1, sizeof(BlastMask));
+                        (BlastMaskLoc *) calloc(1, sizeof(BlastMaskLoc));
                     last_filter_out = last_filter_out->next;
                 }
                 last_filter_out->index = index;
@@ -561,7 +566,7 @@ Int2 BLAST_MainSetUp(Uint1 program_number,
 
     /* Free the filtering locations if masking done for lookup table only */
     if (mask_at_hash) {
-        *filter_out = BlastMaskFree(*filter_out);
+        *filter_out = BlastMaskLocFree(*filter_out);
     }
 
     /* Get "ideal" values if the calculated Karlin-Altschul params bad. */
diff --git a/algo/blast/core/blast_setup.h b/algo/blast/core/blast_setup.h
index 601de5b1..9ee94279 100644
--- a/algo/blast/core/blast_setup.h
+++ b/algo/blast/core/blast_setup.h
@@ -30,13 +30,16 @@ Author: Tom Madden
 
 Contents: Utilities initialize/setup BLAST.
 
-$Revision: 1.25 $
+$Revision: 1.26 $
 
 ******************************************************************************/
 
 /*
  *
 * $Log: blast_setup.h,v $
+* Revision 1.26  2003/12/03 16:31:46  dondosha
+* Renamed BlastMask to BlastMaskLoc, BlastResults to BlastHSPResults, to avoid name conflicts
+*
 * Revision 1.25  2003/09/10 19:43:05  dondosha
 * Changed #includes in accordance with lookup table code reorganization
 *
@@ -216,7 +219,7 @@ Int2 BLAST_MainSetUp(Uint1 program_number,
         const BlastHitSavingOptions* hit_options,
         BLAST_SequenceBlk* query_blk,
         BlastQueryInfo* query_info, BlastSeqLoc* *lookup_segments,
-        BlastMask* *filter_slp_out,
+        BlastMaskLoc* *filter_slp_out,
         BlastScoreBlk* *sbpp, Blast_Message* *blast_message);
 
 #ifdef __cplusplus
diff --git a/algo/blast/core/blast_stat.c b/algo/blast/core/blast_stat.c
index 6d87f656..e338b124 100644
--- a/algo/blast/core/blast_stat.c
+++ b/algo/blast/core/blast_stat.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: blast_stat.c,v 1.39 2003/10/16 15:55:22 coulouri Exp $";
+static char const rcsid[] = "$Id: blast_stat.c,v 1.45 2003/12/05 16:03:57 camacho Exp $";
 
 /* ===========================================================================
 *
@@ -49,8 +49,26 @@ Detailed Contents:
 	- calculate pseuod-scores from p-values.
 
 ****************************************************************************** 
- * $Revision: 1.39 $
+ * $Revision: 1.45 $
  * $Log: blast_stat.c,v $
+ * Revision 1.45  2003/12/05 16:03:57  camacho
+ * Remove compiler warnings
+ *
+ * Revision 1.44  2003/11/28 22:39:11  camacho
+ * + static keyword to BlastKarlinLtoH
+ *
+ * Revision 1.43  2003/11/28 15:03:48  camacho
+ * Added static keyword to BlastKarlinLtoH
+ *
+ * Revision 1.42  2003/11/26 19:12:13  madden
+ * code to simplify some routines and use NlmKarlinLambdaNR in place of BlastKarlinLambdaBis (following Mike Gertzs changes to blastkar.c )
+ *
+ * Revision 1.41  2003/11/24 23:18:32  dondosha
+ * Added gap_decay_rate argument to BLAST_Cutoffs; removed BLAST_Cutoffs_simple
+ *
+ * Revision 1.40  2003/11/19 15:17:42  dondosha
+ * Removed unused members from Karlin block structure
+ *
  * Revision 1.39  2003/10/16 15:55:22  coulouri
  * fix uninitialized variables
  *
@@ -271,9 +289,11 @@ static Uint1 ncbieaa_to_ncbistdaa[128]={
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
 
+#if 0  /* Is this really needed ? */
 static Uint1 ncbistdaa_to_ncbieaa[BLASTAA_SIZE]={
 '-','A','B','C','D','E','F','G','H','I','K','L','M',
 'N','P','Q','R','S','T','V','W','X','Y','Z','U','*'};
+#endif
 
 /* Used in BlastKarlinBlkGappedCalc */
 typedef double array_of_8[8];
@@ -1392,6 +1412,10 @@ typedef struct BLAST_LetterProb {
 		double	p;
 	} BLAST_LetterProb;
 
+#if 0
+
+/* Unused for right now, but do not remove */
+
 /*  M. O. Dayhoff amino acid background frequencies   */
 static BLAST_LetterProb	Dayhoff_prob[] = {
 		{ 'A', 87.13 },
@@ -1439,6 +1463,7 @@ static BLAST_LetterProb Altschul_prob[] = {
 		{ 'W', 13.00 },
 		{ 'Y', 32.00 }
 	};
+#endif
 
 /* amino acid background frequencies from Robinson and Robinson */
 static BLAST_LetterProb Robinson_prob[] = {
@@ -1817,6 +1842,7 @@ BlastScoreFreqCalc(BlastScoreBlk* sbp, BLAST_ScoreFreq* sfp, BLAST_ResFreq* rfp1
 #define DIMOFP0	(iter*range + 1)
 #define DIMOFP0_MAX (BLAST_KARLIN_K_ITER_MAX*BLAST_SCORE_RANGE_MAX+1)
 
+
 static double
 BlastKarlinLHtoK(BLAST_ScoreFreq* sfp, double	lambda, double H)
 {
@@ -1835,8 +1861,8 @@ BlastKarlinLHtoK(BLAST_ScoreFreq* sfp, double	lambda, double H)
 	double	Sum, av, oldsum, oldsum2, score_avg;
 	int		iter;
 	double	sumlimit;
-	double* p,* ptrP,* ptr1,* ptr2,* ptr1e;
-	double	etolami, etolam;
+	double* p, * ptrP, * ptr1, * ptr2, * ptr1e;
+	double	x;
         Boolean         bi_modal_score = FALSE;
 
 	if (lambda <= 0. || H <= 0.) {
@@ -1865,7 +1891,7 @@ BlastKarlinLHtoK(BLAST_ScoreFreq* sfp, double	lambda, double H)
 	range = high - low;
 
 	av = H/lambda;
-	etolam = exp((double)lambda);
+	x = exp((double) -lambda);
 
 	if (low == -1 || high == 1) {
            if (high == 1)
@@ -1874,7 +1900,7 @@ BlastKarlinLHtoK(BLAST_ScoreFreq* sfp, double	lambda, double H)
               score_avg = sfp->score_avg / d;
               K = (score_avg * score_avg) / av;
            }
-           return K * (1.0 - 1./etolam);
+           return K * (1.0 - x);
 	}
 
 	sumlimit = BLAST_KARLIN_K_SUMLIMIT_DEFAULT;
@@ -1917,11 +1943,13 @@ BlastKarlinLHtoK(BLAST_ScoreFreq* sfp, double	lambda, double H)
               if (ptrP - P0 <= range)
                  --last;
            }
-           etolami = BLAST_Powi((double)etolam, lo - 1);
-           for (sum = 0., i = lo; i != 0; ++i) {
-              etolami *= etolam;
-              sum += *++ptrP * etolami;
-           }
+					 /* Horner's rule */
+					 sum = *++ptrP;
+					 for( i = lo + 1; i < 0; i++ ) {
+						 sum = *++ptrP + sum * x;
+					 }
+					 sum *= x;
+
            for (; i <= hi; ++i)
               sum += *++ptrP;
            oldsum2 = oldsum;
@@ -1942,157 +1970,168 @@ BlastKarlinLHtoK(BLAST_ScoreFreq* sfp, double	lambda, double H)
            }
         }
 
-	if (etolam > 0.05) 
-	{
-           etolami = 1 / etolam;
-           K = exp((double)-2.0*Sum) / (av*(1.0 - etolami));
+	if (x <  1.0 / 0.05 ) {
+		K = exp((double)-2.0*Sum) / (av*(1.0 - x));
+	} else {
+		K = -exp((double)-2.0*Sum) / (av*BLAST_Expm1(-(double)lambda));
 	}
-	else
-           K = -exp((double)-2.0*Sum) / (av*BLAST_Expm1(-(double)lambda));
 
 CleanUp:
 #ifndef BLAST_KARLIN_K_STACKP
 	if (P0 != NULL)
 		sfree(P0);
 #endif
+
 	return K;
 }
 
-/******************* Fast Lambda Calculation Subroutine ************************
-	Version 1.0	May 16, 1991
-	Program by:	Stephen Altschul
-
-	Uses Newton-Raphson method (fast) to solve for Lambda, given an initial
-	guess (lambda0) obtained perhaps by the bisection method.
-*******************************************************************************/
-
-/*
-	BlastKarlinLambdaBis
+/**
+ * Find positive solution to sum_{i=low}^{high} exp(i lambda) = 1.
+ * 
+ * @param probs probabilities of a score occuring 
+ * @param d the gcd of the possible scores. This equals 1 if the scores
+ * are not a lattice
+ * @param low the lowest possible score
+ * @param high the highest possible score
+ * @param lambda0 an initial value for lambda
+ * @param tolx the tolerance to which lambda must be computed
+ * @param itmax the maximum number of times the function may be
+ * evaluated
+ * @param maxNewton the maximum permissible number of Newton
+ * iteration. After that the computation will proceed by bisection.
+ * @param itn a pointer to an integer that will receive the actually
+ * number of iterations performed.
+ *
+ * Let phi(lambda) =  sum_{i=low}^{high} exp(i lambda) - 1. Then phi(lambda)
+ * may be written
+ *
+ *     phi(lamdba) = exp(u lambda) p( exp(-lambda) )
+ *
+ * where p(x) is a polynomial that has exactly two zeros, one at x = 1
+ * and one at y = exp(-lamdba). It is simpler, more numerically
+ * efficient and stable to apply Newton's method to p(x) than to
+ * phi(lambda).
+ *
+ * We define a safeguarded Newton iteration as follows. Let the
+ * initial interval of uncertainty be [0,1]. If p'(x) >= 0, we bisect
+ * the interval. Otherwise we try a Newton step. If the Newton iterate
+ * lies in the current interval of uncertainty and it reduces the
+ * value of | p(x) | by at least 10%, we accept the new
+ * point. Otherwise, we bisect the current interval of uncertainty.
+ * It is clear that this method converges to a zero of p(x).  Since
+ * p'(x) > 0 in an interval containing x = 1, the method cannot
+ * converge to x = 1 and therefore converges to the only other zero,
+ * y.
+ */
 
-	Calculate Lambda using the bisection method (slow).
-*/
-static double
-BlastKarlinLambdaBis(BLAST_ScoreFreq* sfp)
+static double 
+NlmKarlinLambdaNR( double* probs, Int4 d, Int4 low, Int4 high, double lambda0, double tolx,
+									 Int4 itmax, Int4 maxNewton, Int4 * itn ) 
 {
-	register double* sprob;
-	double	lambda, up, newval;
-	Int4	i, low, high, d;
-	int		j;
-	register double	sum, x0, x1;
-
-	if (sfp->score_avg >= 0.) {
-		return -1.;
-	}
-	low = sfp->obs_min;
-	high = sfp->obs_max;
-	if (BlastScoreChk(low, high) != 0)
-		return -1.;
+  Int4 k;
+  double x0, x, a = 0, b = 1;
+  double f = 4;  /* Larger than any possible value of the poly in [0,1] */
+  Int4 isNewton = 0; /* we haven't yet taken a Newton step. */
 
-	sprob = sfp->sprob;
-
-        /* Find greatest common divisor of all scores */
-    	for (i = 1, d = -low; i <= high-low && d > 1; ++i) {
-           if (sprob[i+low] != 0)
-              d = BLAST_Gcd(d, i);
-        }
+  assert( d > 0 );
 
-        high = high / d;
-        low = low / d;
-
-	up = BLAST_KARLIN_LAMBDA0_DEFAULT;
-	for (lambda=0.; ; ) {
-		up *= 2;
-		x0 = exp((double)up);
-		x1 = BLAST_Powi((double)x0, low - 1);
-		if (x1 > 0.) {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i*d] * (x1 *= x0);
-		}
-		else {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i*d] * exp(up * i);
-		}
-		if (sum >= 1.0)
-			break;
-		lambda = up;
-	}
+	x0 = exp( -lambda0 );
+  x = ( 0 < x0 && x0 < 1 ) ? x0 : .5;
+  
+  for( k = 0; k < itmax; k++ ) { /* all iteration indices k */
+    Int4 i;
+    double g, fold = f;
+    Int4 wasNewton = isNewton; /* If true, then the previous step was a */
+                              /* Newton step */
+    isNewton  = 0;            /* Assume that this step is not */
+    
+    /* Horner's rule for evaluating a polynomial and its derivative */
+    g = 0;
+    f = probs[low];
+    for( i = low + d; i < 0; i += d ) {
+      g = x * g + f;
+      f = f * x + probs[i];
+    }
+    g = x * g + f;
+    f = f * x + probs[0] - 1;
+    for( i = d; i <= high; i += d ) {
+      g = x * g + f;
+      f = f * x + probs[i];
+    }
+    /* End Horner's rule */
+
+    if( f > 0 ) {
+      a = x; /* move the left endpoint */
+    } else if( f < 0 ) { 
+      b = x; /* move the right endpoint */
+    } else { /* f == 0 */
+      break; /* x is an exact solution */
+    }
+    if( b - a < 2 * a * ( 1 - b ) * tolx ) {
+      /* The midpoint of the interval converged */
+      x = (a + b) / 2; break;
+    }
 
-	for (j=0; j<BLAST_KARLIN_LAMBDA_ITER_DEFAULT; ++j) {
-		newval = (lambda + up) / 2.;
-		x0 = exp((double)newval);
-		x1 = BLAST_Powi((double)x0, low - 1);
-		if (x1 > 0.) {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i*d] * (x1 *= x0);
-		}
-		else {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i*d] * exp(newval * i);
-		}
-		if (sum > 1.0)
-			up = newval;
-		else
-			lambda = newval;
-	}
-	return (lambda + up) / (2. * d);
+    if( k >= maxNewton ||
+        /* If convergence of Newton's method appears to be failing; or */
+				( wasNewton && fabs( f ) > .9 * fabs(fold) ) ||  
+        /* if the previous iteration was a Newton step but didn't decrease 
+         * f sufficiently; or */
+        g >= 0 
+        /* if a Newton step will move us away from the desired solution */
+        ) { /* then */
+      /* bisect */
+      x = (a + b)/2;
+    } else {
+      /* try a Newton step */
+      double p = - f/g;
+      double y = x + p;
+      if( y <= a || y >= b ) { /* The proposed iterate is not in (a,b) */
+        x = (a + b)/2;
+      } else { /* The proposed iterate is in (a,b). Accept it. */
+        isNewton = 1;
+        x = y;
+        if( fabs( p ) < tolx * x * (1-x) ) break; /* Converged */
+      } /* else the proposed iterate is in (a,b) */
+    } /* else try a Newton step. */ 
+  } /* end for all iteration indices k */
+	*itn = k; 
+  return -log(x)/d;
 }
 
+
 static double
 BlastKarlinLambdaNR(BLAST_ScoreFreq* sfp)
 {
 	Int4	low;			/* Lowest score (must be negative)  */
 	Int4	high;			/* Highest score (must be positive) */
-	int		j;
+	Int4		itn;
 	Int4	i, d;
-	double*	sprob;
-	double	lambda0, sum, slope, temp, x0, x1, amt;
+	double* 	sprob;
+	double	returnValue;
 
 	low = sfp->obs_min;
 	high = sfp->obs_max;
 	if (sfp->score_avg >= 0.) {	/* Expected score must be negative */
 		return -1.0;
 	}
-	if (BlastScoreChk(low, high) != 0)
-		return -1.;
-
-	lambda0 = BLAST_KARLIN_LAMBDA0_DEFAULT;
-
+	if (BlastScoreChk(low, high) != 0) return -1.;
+	
 	sprob = sfp->sprob;
-        /* Find greatest common divisor of all scores */
-    	for (i = 1, d = -low; i <= high-low && d > 1; ++i) {
-           if (sprob[i+low] != 0)
-              d = BLAST_Gcd(d, i);
-        }
-
-        high = high / d;
-        low = low / d;
-	/* Calculate lambda */
-
-	for (j=0; j<20; ++j) { /* limit of 20 should never be close-approached */
-		sum = -1.0;
-		slope = 0.0;
-		if (lambda0 < 0.01)
-			break;
-		x0 = exp((double)lambda0);
-		x1 = BLAST_Powi((double)x0, low - 1);
-		if (x1 == 0.)
-			break;
-		for (i=low; i<=high; i++) {
-			sum += (temp = sprob[i*d] * (x1 *= x0));
-			slope += temp * i;
-		}
-		lambda0 -= (amt = sum/slope);
-		if (ABS(amt/lambda0) < BLAST_KARLIN_LAMBDA_ACCURACY_DEFAULT) {
-			/*
-			Does it appear that we may be on the verge of converging
-			to the ever-present, zero-valued solution?
-			*/
-			if (lambda0 > BLAST_KARLIN_LAMBDA_ACCURACY_DEFAULT)
-				return lambda0 / d;
-			break;
+	/* Find greatest common divisor of all scores */
+	for (i = 1, d = -low; i <= high-low && d > 1; ++i) {
+		if (sprob[i+low] != 0) {
+			d = BLAST_Gcd(d, i);
 		}
 	}
-	return BlastKarlinLambdaBis(sfp);
+	returnValue =
+		NlmKarlinLambdaNR( sprob, d, low, high,
+											 BLAST_KARLIN_LAMBDA0_DEFAULT,
+											 BLAST_KARLIN_LAMBDA_ACCURACY_DEFAULT,
+											 20, 20 + BLAST_KARLIN_LAMBDA_ITER_DEFAULT, &itn );
+
+
+	return returnValue;
 }
 
 /*
@@ -2100,34 +2139,33 @@ BlastKarlinLambdaNR(BLAST_ScoreFreq* sfp)
 
 	Calculate H, the relative entropy of the p's and q's
 */
-static double
+static double 
 BlastKarlinLtoH(BLAST_ScoreFreq* sfp, double	lambda)
 {
 	Int4	score;
-	double	av, etolam, etolami;
+	double	H, etonlam, sum, scale;
+
+	double *probs = sfp->sprob;
+	Int4 low   = sfp->obs_min,  high  = sfp->obs_max;
 
 	if (lambda < 0.) {
 		return -1.;
 	}
-	if (BlastScoreChk(sfp->obs_min, sfp->obs_max) != 0)
-		return -1.;
-
-	etolam = exp((double)lambda);
-	etolami = BLAST_Powi((double)etolam, sfp->obs_min - 1);
-	if (etolami > 0.) 
-	{
-	    av = 0.0;
-	    for (score=sfp->obs_min; score<=sfp->obs_max; score++)
-   			av += sfp->sprob[score] * score * (etolami *= etolam);
-	}
-	else 
-	{
-	    av = 0.0;
-	    for (score=sfp->obs_min; score<=sfp->obs_max; score++)
-   			av += sfp->sprob[score] * score * exp(lambda * score);
-	}
-
-    	return lambda * av;
+	if (BlastScoreChk(low, high) != 0) return -1.;
+
+	etonlam = exp( - lambda );
+  sum = low * probs[low];
+  for( score = low + 1; score <= high; score++ ) {
+    sum = score * probs[score] + etonlam * sum;
+  }
+
+  scale = BLAST_Powi( etonlam, high );
+  if( scale > 0 ) {
+    H = lambda * sum/scale;
+  } else { /* Underflow of exp( -lambda * high ) */
+    H = lambda * exp( lambda * high + log(sum) );
+  }
+	return H;
 }
 
 /**************** Statistical Significance Parameter Subroutine ****************
@@ -2203,35 +2241,34 @@ BlastKarlinBlkCalc(BLAST_KarlinBlk* kbp, BLAST_ScoreFreq* sfp)
 
 	/* Calculate the parameter Lambda */
 
-	kbp->Lambda_real = kbp->Lambda = BlastKarlinLambdaNR(sfp);
+	kbp->Lambda = BlastKarlinLambdaNR(sfp);
 	if (kbp->Lambda < 0.)
 		goto ErrExit;
 
 
 	/* Calculate H */
 
-	kbp->H_real = kbp->H = BlastKarlinLtoH(sfp, kbp->Lambda);
+	kbp->H = BlastKarlinLtoH(sfp, kbp->Lambda);
 	if (kbp->H < 0.)
 		goto ErrExit;
 
 
 	/* Calculate K and log(K) */
 
-	kbp->K_real = kbp->K = BlastKarlinLHtoK(sfp, kbp->Lambda, kbp->H);
+	kbp->K = BlastKarlinLHtoK(sfp, kbp->Lambda, kbp->H);
 	if (kbp->K < 0.)
 		goto ErrExit;
-	kbp->logK_real = kbp->logK = log(kbp->K);
+	kbp->logK = log(kbp->K);
 
 	/* Normal return */
 	return 0;
 
 ErrExit:
-	kbp->Lambda = kbp->H = kbp->K
-		= kbp->Lambda_real = kbp->H_real = kbp->K_real = -1.;
+	kbp->Lambda = kbp->H = kbp->K = -1.;
 #ifdef BLASTKAR_HUGE_VAL
-	kbp->logK_real = kbp->logK = BLASTKAR_HUGE_VAL;
+	kbp->logK = BLASTKAR_HUGE_VAL;
 #else
-	kbp->logK_real = kbp->logK = 1.e30;
+	kbp->logK = 1.e30;
 #endif
 	return 1;
 }
@@ -2741,10 +2778,10 @@ BLAST_KarlinkGapBlkFill(BLAST_KarlinBlk* kbp, Int4 gap_open, Int4 gap_extend, In
 			{
 				if (kbp)
 				{
-					kbp->Lambda_real = kbp->Lambda = values[index][3];
-					kbp->K_real = kbp->K = values[index][4];
-					kbp->logK_real = kbp->logK = log(kbp->K);
-					kbp->H_real = kbp->H = values[index][5];
+					kbp->Lambda = values[index][3];
+					kbp->K = values[index][4];
+					kbp->logK = log(kbp->K);
+					kbp->H = values[index][5];
 				}
 				found_values = TRUE;
 				break;
@@ -2867,24 +2904,6 @@ BlastGapDecay(double pvalue, unsigned nsegs, double decayrate)
 	return pvalue / ((1. - decayrate) * BLAST_Powi(decayrate, nsegs - 1));
 }
 
-/*
-	BlastCutoffs
-
-	Calculate the cutoff score, S, and the highest expected score.
-
-	WRG (later modified by TLM).
-*/
-Int2
-BLAST_Cutoffs(Int4 *S, /* cutoff score */
-	double* E, /* expected no. of HSPs scoring at or above S */
-	BLAST_KarlinBlk* kbp,
-	double qlen, /* length of query sequence */
-	double dblen, /* length of database or database sequence */
-	Boolean dodecay) /* TRUE ==> use gapdecay feature */
-{
-	return BLAST_Cutoffs_simple(S, E, kbp, qlen*dblen, dodecay);
-}
-
 /* Smallest float that might not cause a floating point exception in
 	S = (Int4) (ceil( log((double)(K * searchsp / E)) / Lambda ));
 below.
@@ -2913,12 +2932,18 @@ BlastKarlinEtoS_simple(double	E,	/* Expect value */
 	return S;
 }
 
+/*
+	BlastCutoffs
+	Calculate the cutoff score, S, and the highest expected score.
+	WRG (later modified by TLM).
+*/
 Int2
-BLAST_Cutoffs_simple(Int4 *S, /* cutoff score */
+BLAST_Cutoffs(Int4 *S, /* cutoff score */
 	double* E, /* expected no. of HSPs scoring at or above S */
 	BLAST_KarlinBlk* kbp,
 	double searchsp, /* size of search space. */
-	Boolean dodecay) /* TRUE ==> use gapdecay feature */
+	Boolean dodecay,  /* TRUE ==> use gapdecay feature */
+   double gap_decay_rate)
 {
 	Int4	s = *S, es;
 	double	e = *E, esave;
@@ -2936,7 +2961,7 @@ BLAST_Cutoffs_simple(Int4 *S, /* cutoff score */
 	if (e > 0.) 
 	{
 		if (dodecay)
-			e = BlastGapDecayInverse(e, 1, 0.5);
+			e = BlastGapDecayInverse(e, 1, gap_decay_rate);
 		es = BlastKarlinEtoS_simple(e, kbp, searchsp);
 	}
 	/*
@@ -2955,7 +2980,7 @@ BLAST_Cutoffs_simple(Int4 *S, /* cutoff score */
 	{
 		e = BLAST_KarlinStoE_simple(s, kbp, searchsp);
 		if (dodecay)
-			e = BlastGapDecay(e, 1, 0.5);
+			e = BlastGapDecay(e, 1, gap_decay_rate);
 		*E = e;
 	}
 
diff --git a/algo/blast/core/blast_stat.h b/algo/blast/core/blast_stat.h
index bee0d836..fc0cacc7 100644
--- a/algo/blast/core/blast_stat.h
+++ b/algo/blast/core/blast_stat.h
@@ -1,4 +1,4 @@
-/* $Id: blast_stat.h,v 1.17 2003/08/11 14:57:16 dondosha Exp $
+/* $Id: blast_stat.h,v 1.19 2003/11/24 23:18:18 dondosha Exp $
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
@@ -32,7 +32,7 @@ Contents: definitions and prototypes used by blastkar.c to calculate BLAST
 
 ******************************************************************************/
 
-/* $Revision: 1.17 $ 
+/* $Revision: 1.19 $ 
  * */
 #ifndef __BLASTKAR__
 #define __BLASTKAR__
@@ -105,9 +105,6 @@ typedef struct BLAST_KarlinBlk {
 		double	Lambda; /* Lambda value used in statistics */
 		double	K, logK; /* K value used in statistics */
 		double	H; /* H value used in statistics */
-		/* "real" values are ones actually found, may be replaced by above */
-		double	Lambda_real, K_real, logK_real, H_real;
-		Int4 q_frame, s_frame; /* reading frame for query and subject.*/
 		double	paramC;	/* for use in seed. */
 	} BLAST_KarlinBlk;
 
@@ -273,10 +270,16 @@ char* BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_exten
 
 double BLAST_KarlinStoE_simple (Int4 S, BLAST_KarlinBlk* kbp, double  searchsp);
 
-Int2 BLAST_Cutoffs (Int4 *S, double* E, BLAST_KarlinBlk* kbp, double qlen, double dblen, Boolean dodecay);
-
-
-Int2 BLAST_Cutoffs_simple (Int4 *S, double* E, BLAST_KarlinBlk* kbp, double search_sp, Boolean dodecay);
+/** Calculate the cutoff score from the expected number of HSPs or vice versa.
+ * @param S The calculated score [in] [out]
+ * @param E The calculated e-value [in] [out]
+ * @param kbp The Karlin-Altschul statistical parameters [in]
+ * @param searchsp The effective search space [in]
+ * @param dodecay Use gap decay feature? [in]
+ * @param gap_decay_rate Gap decay rate to use, if dodecay is set [in]
+ */
+Int2 BLAST_Cutoffs (Int4 *S, double* E, BLAST_KarlinBlk* kbp, 
+                    double searchsp, Boolean dodecay, double gap_decay_rate);
 
 /* Functions to calculate SumE (for large and small gaps). */
 double BLAST_SmallGapSumE (BLAST_KarlinBlk* kbp, Int4 gap, double gap_prob, double gap_decay_rate, Int2 num,  double xsum, Int4 query_length, Int4 subject_length);
diff --git a/algo/blast/core/blast_toolkit.h b/algo/blast/core/blast_toolkit.h
new file mode 100644
index 00000000..0213cff5
--- /dev/null
+++ b/algo/blast/core/blast_toolkit.h
@@ -0,0 +1,7 @@
+#ifndef _BLAST_TOOLKIT__H_
+#define _BLAST_TOOLKIT__H_
+
+/* C toolkit */
+#include <ncbistd.h>
+
+#endif
diff --git a/algo/blast/core/blast_traceback.c b/algo/blast/core/blast_traceback.c
index 4ef15360..2e6d8dd9 100644
--- a/algo/blast/core/blast_traceback.c
+++ b/algo/blast/core/blast_traceback.c
@@ -1,4 +1,4 @@
-/* $Id: blast_traceback.c,v 1.58 2003/10/29 05:13:02 camacho Exp $
+/* $Id: blast_traceback.c,v 1.70 2004/01/28 22:07:13 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -41,7 +41,7 @@ Detailed Contents:
 #include <algo/blast/core/blast_util.h>
 #include <algo/blast/core/link_hsps.h>
 
-static char const rcsid[] = "$Id: blast_traceback.c,v 1.58 2003/10/29 05:13:02 camacho Exp $";
+static char const rcsid[] = "$Id: blast_traceback.c,v 1.70 2004/01/28 22:07:13 dondosha Exp $";
 
 /** Comparison function for sorting HSPs by score. 
  * Ties are broken based on subject sequence offsets.
@@ -239,7 +239,6 @@ BlastHSPGetNumIdentical(Uint1* query, Uint1* subject, BlastHSP* hsp,
    Boolean gapped_calculation, Int4* num_ident_ptr, Int4* align_length_ptr)
 {
    Int4 i, num_ident, align_length, q_off, s_off;
-   Int2 context;
    Uint1* q,* s;
    GapEditBlock* gap_info;
    GapEditScript* esp;
@@ -249,7 +248,6 @@ BlastHSPGetNumIdentical(Uint1* query, Uint1* subject, BlastHSP* hsp,
    if (!gap_info && gapped_calculation)
       return -1;
 
-   context = hsp->context;
    q_off = hsp->query.offset;
    s_off = hsp->subject.offset;
 
@@ -300,26 +298,20 @@ BlastOOFGetNumIdentical(Uint1* query_seq, Uint1* subject_seq,
    BlastHSP* hsp, Uint1 program, 
    Int4* num_ident_ptr, Int4* align_length_ptr)
 {
-   Int4 i, num_ident, align_length, q_off, s_off;
-   Int2 context;
+   Int4 i, num_ident, align_length;
    Uint1* q,* s;
    GapEditScript* esp;
 
    if (!hsp->gap_info || !subject_seq || !query_seq)
       return -1;
 
-   context = hsp->context;
 
    if (program == blast_type_tblastn) {
-       q_off = hsp->query.offset;
-       s_off = hsp->subject.offset;
-       q = &query_seq[q_off];
-       s = &subject_seq[s_off];
+       q = &query_seq[hsp->query.offset];
+       s = &subject_seq[hsp->subject.offset];
    } else {
-       s_off = hsp->query.offset;
-       q_off = hsp->subject.offset;
-       s = &query_seq[q_off];
-       q = &subject_seq[s_off];
+       s = &query_seq[hsp->query.offset];
+       q = &subject_seq[hsp->subject.offset];
    }
    num_ident = 0;
    align_length = 0;
@@ -383,6 +375,9 @@ static void SavePatternLengthInGapAlignStruct(Int4 length,
    gap_align->query_stop = length;
 }
 
+
+#define MAX_FULL_TRANSLATION 2100
+
 /** Compute gapped alignment with traceback for all HSPs from a single
  * query/subject sequence pair.
  * @param program_number Type of BLAST program [in]
@@ -405,10 +400,11 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
    const BlastScoringOptions* score_options,
    const BlastExtensionOptions* ext_options,
    BlastHitSavingParameters* hit_params,
-   const BlastDatabaseOptions* db_options)
+   const BlastDatabaseOptions* db_options,
+   const PSIBlastOptions* psi_options)
 {
    Int4 index, index1, index2;
-   Boolean hsp_start_is_contained, hsp_end_is_contained, do_not_do;
+   Boolean hsp_start_is_contained, hsp_end_is_contained;
    BlastHSP* hsp,* hsp1=NULL,* hsp2;
    Uint1* query,* subject,* subject_start = NULL;
    Int4 query_length, query_length_orig;
@@ -419,9 +415,7 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
    BlastHitSavingOptions* hit_options = hit_params->options;
    Int4 min_score_to_keep = hit_params->cutoff_score;
    Int4 align_length;
-   /** THE FOLLOWING HAS TO BE PASSED IN THE ARGUMENTS!!!!! 
-       DEFINED INSIDE TEMPORARILY, ONLY TO ALLOW COMPILATION */
-   double scalingFactor = 1.0;
+   double scalingFactor = ((psi_options) ? psi_options->scalingFactor : 1.0);
    Int4 new_hspcnt = 0;
    Boolean is_ooframe = score_options->is_ooframe;
    Int4 context_offset;
@@ -433,6 +427,9 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
    Uint1* nucl_sequence = NULL;
    BLAST_KarlinBlk** kbp;
    Boolean phi_align = (hit_options->phi_align);
+   Boolean greedy_traceback;
+   Boolean partial_translation = FALSE;
+   Int4 start_shift = 0, translation_length;
 
    if (hsp_list->hspcnt == 0) {
       return 0;
@@ -443,22 +440,31 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
    if (translate_subject) {
       if (!db_options)
          return -1;
+      partial_translation = (subject_blk->length > MAX_FULL_TRANSLATION);
+      
+      /* If mixed-frame sequence is already available, then no need to translate
+         again */
+      if (is_ooframe && subject_blk->oof_sequence)
+         partial_translation = FALSE;
+
       nucl_sequence = subject_blk->sequence_start;
-      if (is_ooframe) {
-         BLAST_GetAllTranslations(nucl_sequence, NCBI4NA_ENCODING,
-            subject_blk->length, db_options->gen_code_string,
-            &translation_buffer, &frame_offsets, &subject_blk->oof_sequence);
-      } else {
-         BLAST_GetAllTranslations(nucl_sequence, NCBI4NA_ENCODING,
-            subject_blk->length, db_options->gen_code_string, 
-            &translation_buffer, &frame_offsets, NULL);
+      if (!partial_translation) {
+         if (is_ooframe) {
+            BLAST_GetAllTranslations(nucl_sequence, NCBI4NA_ENCODING,
+               subject_blk->length, db_options->gen_code_string,
+               &translation_buffer, &frame_offsets, 
+               &subject_blk->oof_sequence);
+         } else {
+            BLAST_GetAllTranslations(nucl_sequence, NCBI4NA_ENCODING,
+               subject_blk->length, db_options->gen_code_string, 
+               &translation_buffer, &frame_offsets, NULL);
+         }
       }
    }
 
    if (!is_ooframe) {
       if (!translate_subject) {
          subject_start = subject_blk->sequence;
-         subject_length = subject_blk->length;
       }
    } else {
       /* Out-of-frame gapping: need to use a mixed-frame sequence */
@@ -467,8 +473,8 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
       } else {
          subject = subject_start = subject_blk->oof_sequence + CODON_LENGTH;
       }
-      subject_length = subject_blk->length;
    }
+   subject_length = subject_blk->length;
    
    for (index=0; index < hsp_list->hspcnt; index++) {
       hsp_start_is_contained = FALSE;
@@ -526,18 +532,57 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
          }
       }
       
-      if (translate_subject && !is_ooframe) {
-         Int2 context = FrameToContext(hsp->subject.frame);
-         subject_start = translation_buffer + frame_offsets[context] + 1;
-         subject_length = 
-            frame_offsets[context+1] - frame_offsets[context] - 1;
-      }
-
-      do_not_do = FALSE;
-      
-      if (do_not_do == FALSE && (hsp_start_is_contained == FALSE || 
+      if ((hsp_start_is_contained == FALSE || 
            hsp_end_is_contained == FALSE || hsp->score > hsp1->score)) {
-         if (!is_ooframe && 
+
+         if (translate_subject && partial_translation) {
+            Int4 nucl_shift;
+            sfree(translation_buffer);
+            start_shift = 
+               MAX(0, 3*hsp->subject.offset - MAX_FULL_TRANSLATION);
+            translation_length =
+               MIN(3*hsp->subject.end + MAX_FULL_TRANSLATION, 
+                   subject_blk->length) - start_shift;
+            if (hsp->subject.frame > 0) {
+               nucl_shift = start_shift;
+            } else {
+               nucl_shift = subject_blk->length - start_shift 
+                  - translation_length;
+            }
+               
+            if (is_ooframe) {
+               sfree(subject_blk->oof_sequence);
+               GetPartialTranslation(nucl_sequence+nucl_shift, 
+                  translation_length, hsp->subject.frame, 
+                  db_options->gen_code_string, &translation_buffer, 
+                  NULL, &subject_blk->oof_sequence);
+            } else {
+               GetPartialTranslation(nucl_sequence+nucl_shift, 
+                  translation_length, hsp->subject.frame,
+                  db_options->gen_code_string, &translation_buffer, 
+                  &subject_length, NULL);
+            }
+            /* Below, the start_shift will be used for the protein
+               coordinates, so need to divide it by 3 */
+            start_shift /= CODON_LENGTH;
+            hsp->subject.offset -= start_shift;
+            hsp->subject.gapped_start -= start_shift;
+         }
+
+         if (translate_subject && !is_ooframe) {
+            if (!partial_translation) {
+               Int2 context = FrameToContext(hsp->subject.frame);
+               subject_start = translation_buffer + frame_offsets[context] + 1;
+               subject_length = 
+                  frame_offsets[context+1] - frame_offsets[context] - 1;
+            } else {
+               subject_start = translation_buffer + 1;
+               /* Subject length is already assigned in call to 
+                  GetPartialTranslation. */
+            }
+         }
+
+         if (!phi_align && !is_ooframe && 
              (((hsp->query.gapped_start == 0 && 
                 hsp->subject.gapped_start == 0) ||
                !BLAST_CheckStartForGappedAlignment(hsp, query, 
@@ -565,6 +610,9 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
          
          subject = subject_start;
 
+         greedy_traceback = (ext_options->algorithm_type ==
+                             EXTEND_GREEDY_NO_TRACEBACK);
+
          /* Perform the gapped extension with traceback */
          if (phi_align) {
             Int4 pat_length = GetPatternLengthFromBlastHSP(hsp);
@@ -572,9 +620,13 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
             PHIGappedAlignmentWithTraceback(program_number, query, subject,
                gap_align, score_options, q_start, s_start, query_length, 
                subject_length);
+         } else if (greedy_traceback) {
+            BLAST_GreedyGappedAlignment(query, subject, 
+                 query_length, subject_length, gap_align, 
+                 score_options, q_start, s_start, FALSE, TRUE);
          } else {
             BLAST_GappedAlignmentWithTraceback(program_number, query, subject, 
-               gap_align, score_options, ext_options, q_start, s_start, 
+               gap_align, score_options, q_start, s_start, 
                query_length, subject_length);
          }
 
@@ -590,6 +642,11 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
             
             hsp->gap_info = gap_align->edit_block;
             gap_align->edit_block = NULL;
+
+            if (greedy_traceback) {
+               ReevaluateHSPWithAmbiguities(hsp, query, subject, hit_options,
+                                            score_options, query_info, sbp);
+            }
             
             if (hsp->gap_info) {
                hsp->gap_info->frame1 = hsp->query.frame;
@@ -620,6 +677,14 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
                   &align_length);
             }
 
+            if (start_shift > 0) {
+               hsp->subject.offset += start_shift;
+               hsp->subject.end += start_shift;
+               hsp->subject.gapped_start += start_shift;
+               if (hsp->gap_info)
+                  hsp->gap_info->start2 += start_shift;
+            }
+
             if (hsp->num_ident * 100 < 
                 align_length * hit_options->percent_identity) {
                keep = FALSE;
@@ -627,7 +692,7 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
             
             if (program_number == blast_type_blastp ||
                 program_number == blast_type_blastn) {
-               if (hit_options->gapped_calculation && 
+               if (score_options->gapped_calculation && 
                    program_number != blast_type_blastn)
                   kbp = sbp->kbp_gap;
                else
@@ -724,7 +789,7 @@ BlastHSPListGetTraceback(Uint1 program_number, BlastHSPList* hsp_list,
            PHIGetEvalue(hsp_list, sbp);
         } else {
            BLAST_GetNonSumStatsEvalue(program_number, query_info, hsp_list, 
-                                      hit_options, sbp);
+                                      score_options, sbp);
         }
         
         BLAST_ReapHitlistByEvalue(hsp_list, hit_options);
@@ -775,13 +840,14 @@ static Uint1 GetTracebackEncoding(Uint1 program_number)
    return encoding;
 }
 
-Int2 BLAST_ComputeTraceback(Uint1 program_number, BlastResults* results, 
+Int2 BLAST_ComputeTraceback(Uint1 program_number, BlastHSPResults* results, 
         BLAST_SequenceBlk* query, BlastQueryInfo* query_info, 
         const BlastSeqSrc* bssp, BlastGapAlignStruct* gap_align,
         const BlastScoringOptions* score_options,
         const BlastExtensionParameters* ext_params,
         BlastHitSavingParameters* hit_params,
-        const BlastDatabaseOptions* db_options)
+        const BlastDatabaseOptions* db_options,
+        const PSIBlastOptions* psi_options)
 {
    Int2 status = 0;
    Int4 query_index, subject_index;
@@ -827,7 +893,7 @@ Int2 BLAST_ComputeTraceback(Uint1 program_number, BlastResults* results,
 
             BlastHSPListGetTraceback(program_number, hsp_list, query, 
                seq_arg.seq, query_info, gap_align, sbp, score_options, 
-               ext_params->options, hit_params, db_options);
+               ext_params->options, hit_params, db_options, psi_options);
          }
       }
    }
@@ -841,7 +907,7 @@ Int2 BLAST_ComputeTraceback(Uint1 program_number, BlastResults* results,
 }
 
 Int2 BLAST_TwoSequencesTraceback(Uint1 program_number, 
-        BlastResults* results, 
+        BlastHSPResults* results, 
         BLAST_SequenceBlk* query, BlastQueryInfo* query_info, 
         BLAST_SequenceBlk* subject, 
         BlastGapAlignStruct* gap_align,
@@ -855,7 +921,6 @@ Int2 BLAST_TwoSequencesTraceback(Uint1 program_number,
    BlastHitList* hit_list;
    BlastHSPList* hsp_list;
    BlastScoreBlk* sbp;
-   Uint1 encoding=ERROR_ENCODING;
    Boolean db_is_na;
    
    if (!results || !query_info || !subject) {
@@ -874,8 +939,6 @@ Int2 BLAST_TwoSequencesTraceback(Uint1 program_number,
 
    sbp = gap_align->sbp;
 
-   encoding = GetTracebackEncoding(program_number);
-
    if (db_is_na) {
       /* Two sequences case: free the compressed sequence */
       sfree(subject->sequence);
@@ -895,7 +958,7 @@ Int2 BLAST_TwoSequencesTraceback(Uint1 program_number,
       if (!hsp_list->traceback_done) {
          BlastHSPListGetTraceback(program_number, hsp_list, query, subject, 
             query_info, gap_align, sbp, score_options, ext_params->options, 
-            hit_params, db_options);
+            hit_params, db_options, NULL);
       }
    }
 
diff --git a/algo/blast/core/blast_traceback.h b/algo/blast/core/blast_traceback.h
index fecef7d7..7226e3fa 100644
--- a/algo/blast/core/blast_traceback.h
+++ b/algo/blast/core/blast_traceback.h
@@ -1,4 +1,4 @@
-/* $Id: blast_traceback.h,v 1.13 2003/10/29 05:13:38 camacho Exp $
+/* $Id: blast_traceback.h,v 1.15 2003/12/03 16:31:46 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@ Contents: Functions to do gapped alignment with traceback and/or convert
           results to the SeqAlign form
 
 ******************************************************************************
- * $Revision: 1.13 $
+ * $Revision: 1.15 $
  * */
 #ifndef __BLAST_TRACEBACK__
 #define __BLAST_TRACEBACK__
@@ -57,14 +57,16 @@ extern "C" {
  * @param ext_params Gapped extension parameters [in]
  * @param hit_params Parameters for saving hits [in]
  * @param db_options Options containing database genetic code string [in]
+ * @param psi_options Options specific to PSI BLAST [in]
  */
-Int2 BLAST_ComputeTraceback(Uint1 program_number, BlastResults* results, 
+Int2 BLAST_ComputeTraceback(Uint1 program_number, BlastHSPResults* results, 
         BLAST_SequenceBlk* query, BlastQueryInfo* query_info, 
         const BlastSeqSrc* bssp, BlastGapAlignStruct* gap_align,
         const BlastScoringOptions* score_options,
         const BlastExtensionParameters* ext_params,
         BlastHitSavingParameters* hit_params,
-        const BlastDatabaseOptions* db_options);
+        const BlastDatabaseOptions* db_options,
+        const PSIBlastOptions* psi_options);
 
 /** Given the preliminary alignment results from a two sequences search
  * (possibly with multiple query sequences), redo the gapped alignment
@@ -81,7 +83,7 @@ Int2 BLAST_ComputeTraceback(Uint1 program_number, BlastResults* results,
  * @param db_options Options containing database genetic code string [in]
  */
 Int2 BLAST_TwoSequencesTraceback(Uint1 program_number, 
-        BlastResults* results, BLAST_SequenceBlk* query, 
+        BlastHSPResults* results, BLAST_SequenceBlk* query, 
         BlastQueryInfo* query_info, BLAST_SequenceBlk* subject, 
         BlastGapAlignStruct* gap_align, 
         const BlastScoringOptions* score_options,
diff --git a/algo/blast/core/blast_util.c b/algo/blast/core/blast_util.c
index b6c8fe4b..42c43ef2 100644
--- a/algo/blast/core/blast_util.c
+++ b/algo/blast/core/blast_util.c
@@ -1,4 +1,4 @@
-/* $Id: blast_util.c,v 1.51 2003/10/21 13:02:36 camacho Exp $
+/* $Id: blast_util.c,v 1.55 2004/01/28 02:57:35 ucko Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@ Author: Ilya Dondoshansky
 Contents: Various BLAST utilities
 
 ******************************************************************************
- * $Revision: 1.51 $
+ * $Revision: 1.55 $
  * */
 
 #include <algo/blast/core/blast_def.h>
@@ -40,7 +40,7 @@ Contents: Various BLAST utilities
 #include <algo/blast/core/blast_stat.h>
 #include <algo/blast/core/blast_filter.h>
 
-static char const rcsid[] = "$Id: blast_util.c,v 1.51 2003/10/21 13:02:36 camacho Exp $";
+static char const rcsid[] = "$Id: blast_util.c,v 1.55 2004/01/28 02:57:35 ucko Exp $";
 
 Int2
 BlastSetUp_SeqBlkNew (const Uint1* buffer, Int4 length, Int2 context,
@@ -93,6 +93,7 @@ Int2 BlastSeqBlkSetSequence(BLAST_SequenceBlk* seq_blk,
     seq_blk->sequence_start = (Uint1*) sequence;
     seq_blk->sequence = (Uint1*) sequence + 1;
     seq_blk->length = seqlen;
+    seq_blk->oof_sequence = NULL;
 
     return 0;
 }
@@ -106,6 +107,7 @@ Int2 BlastSeqBlkSetCompressedSequence(BLAST_SequenceBlk* seq_blk,
 
     seq_blk->sequence_allocated = TRUE;
     seq_blk->sequence = (Uint1*) sequence;
+    seq_blk->oof_sequence = NULL;
 
     return 0;
 }
@@ -136,12 +138,14 @@ MakeBlastSequenceBlk(ReadDBFILEPtr db, BLAST_SequenceBlk** seq_blk,
 Int2 BlastSequenceBlkClean(BLAST_SequenceBlk* seq_blk)
 {
    if (!seq_blk)
-      return 1;
+       return 1;
 
    if (seq_blk->sequence_allocated) 
-      sfree(seq_blk->sequence);
+       sfree(seq_blk->sequence);
    if (seq_blk->sequence_start_allocated)
-      sfree(seq_blk->sequence_start);
+       sfree(seq_blk->sequence_start);
+   if (seq_blk->oof_sequence)
+       sfree(seq_blk->oof_sequence);
 
    return 0;
 }
@@ -152,7 +156,7 @@ BLAST_SequenceBlk* BlastSequenceBlkFree(BLAST_SequenceBlk* seq_blk)
       return NULL;
 
    BlastSequenceBlkClean(seq_blk);
-   BlastMaskFree(seq_blk->lcase_mask);
+   BlastMaskLocFree(seq_blk->lcase_mask);
    sfree(seq_blk);
    return NULL;
 }
@@ -894,6 +898,60 @@ Int2 BLAST_GetAllTranslations(const Uint1* nucl_seq, Uint1 encoding,
    return 0;
 }
 
+int GetPartialTranslation(const Uint1* nucl_seq,
+        Int4 nucl_length, Int2 frame, Uint1* genetic_code,
+        Uint1** translation_buffer_ptr, Int4* protein_length, 
+        Uint1** mixed_seq_ptr)
+{
+   Uint1* translation_buffer;
+   Uint1* nucl_seq_rev = NULL;
+   Int4 length;
+   
+   if ((*translation_buffer_ptr = translation_buffer = 
+        (Uint1*) malloc(2*(nucl_length+1)+1)) == NULL)
+      return -1;
+
+   if (frame < 0) {
+      /* First produce the reverse strand of the nucleotide sequence */
+      GetReverseNuclSequence(nucl_seq, nucl_length, &nucl_seq_rev);
+   } 
+
+   if (!mixed_seq_ptr) {
+      length = 
+         BLAST_GetTranslation(nucl_seq, nucl_seq_rev, 
+            nucl_length, frame, translation_buffer, genetic_code);
+      if (protein_length)
+         *protein_length = length;
+   } else {
+      Int4 index;
+      Int2 frame_sign = ((frame < 0) ? -1 : 1);
+      Int4 offset = 0;
+      Int4 frame_offsets[3];
+      Uint1* seq;
+
+      for (index = 1; index <= 3; ++index) {
+         length = 
+            BLAST_GetTranslation(nucl_seq, nucl_seq_rev, 
+               nucl_length, frame_sign*index, translation_buffer+offset, 
+               genetic_code);
+         frame_offsets[index-1] = offset;
+         offset += length + 1;
+      }
+
+      *mixed_seq_ptr = (Uint1*) malloc(2*(nucl_length+1));
+
+      for (index = 0, seq = *mixed_seq_ptr; index <= nucl_length; 
+           ++index, ++seq) {
+         *seq = translation_buffer[frame_offsets[index%3]+(index/3)];
+      }
+   }
+
+   sfree(nucl_seq_rev);
+
+   return 0;
+}
+
+
 Int2 FrameToContext(Int2 frame) 
 {
    if (frame > 0)
diff --git a/algo/blast/core/blast_util.h b/algo/blast/core/blast_util.h
index 5f360812..b5f8f418 100644
--- a/algo/blast/core/blast_util.h
+++ b/algo/blast/core/blast_util.h
@@ -1,4 +1,4 @@
-/* $Id: blast_util.h,v 1.34 2003/10/21 13:02:28 camacho Exp $
+/* $Id: blast_util.h,v 1.36 2004/01/28 02:57:29 ucko Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@ Contents: Various auxiliary BLAST utility functions
 Detailed Contents: 
 
 ******************************************************************************
- * $Revision: 1.34 $
+ * $Revision: 1.36 $
  * */
 #ifndef __BLAST_UTIL__
 #define __BLAST_UTIL__
@@ -152,6 +152,8 @@ Int4 BLAST_GetTranslation(const Uint1* query_seq,
    const Uint1* query_seq_rev, Int4 nt_length, Int2 frame, Uint1* buffer, 
    const Uint1* genetic_code);
 
+
+
 /** Translate a nucleotide sequence without ambiguity codes.
  * This is used for the first-pass translation of the database.
  * The genetic code to be used is determined by the translation_table
@@ -270,6 +272,25 @@ Int2 BLAST_GetAllTranslations(const Uint1* nucl_seq, Uint1 encoding,
         Uint1** translation_buffer_ptr, Int4** frame_offsets_ptr,
         Uint1** mixed_seq_ptr);
 
+/** Get one frame translation - needed when only parts of subject sequences
+ * are translated. 
+ * @param nucl_seq Pointer to start of nucleotide sequence to be translated [in]
+ * @param nucl_length Length of nucleotide sequence to be translated [in]
+ * @param frame What frame to translate into [in]
+ * @param genetic_code What genetic code to use? [in]
+ * @param translation_buffer_ptr Pointer to buffer with translated 
+ *                               sequence [out]
+ * @param protein_length Length of the translation buffer [out] 
+ * @param mixed_seq_ptr Pointer to buffer with mixed frame sequence, in case
+ *                      of out-of-frame gapping; buffer filled only if argument
+ *                      not NULL. [out]
+ */
+int GetPartialTranslation(const Uint1* nucl_seq,
+        Int4 nucl_length, Int2 frame, Uint1* genetic_code,
+        Uint1** translation_buffer_ptr, Int4* protein_length, 
+        Uint1** mixed_seq_ptr);
+
+
 /** Convert translation frame into a context for the concatenated translation
  * buffer.
  */
diff --git a/algo/blast/core/link_hsps.c b/algo/blast/core/link_hsps.c
index e47f2149..bce27428 100644
--- a/algo/blast/core/link_hsps.c
+++ b/algo/blast/core/link_hsps.c
@@ -1,4 +1,4 @@
-/* $Id: link_hsps.c,v 1.16 2003/10/16 15:52:08 coulouri Exp $
+/* $Id: link_hsps.c,v 1.18 2004/01/27 16:50:41 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -38,7 +38,7 @@ Detailed Contents:
 #include <algo/blast/core/link_hsps.h>
 #include <algo/blast/core/blast_util.h>
 
-static char const rcsid[] = "$Id: link_hsps.c,v 1.16 2003/10/16 15:52:08 coulouri Exp $";
+static char const rcsid[] = "$Id: link_hsps.c,v 1.18 2004/01/27 16:50:41 dondosha Exp $";
 
 #define WINDOW_SIZE 20
 static double 
@@ -497,6 +497,7 @@ link_hsps(Uint1 program_number, BlastHSPList* hsp_list,
      for (index=0;index<number_of_hsps;index++) 
      {
         H=hsp_array[index];
+        H->start_of_chain = FALSE;
         hp_frame_number[cur_frame]++;
 
         H->prev= index ? hsp_array[index-1] : NULL;
@@ -1231,7 +1232,6 @@ new_link_hsps(Uint1 program_number, BlastHSPList* hsp_list,
       hsp->next = score_hsp_array[index];
    }
 
-   sfree(subject_seq);
    sfree(score_hsp_array);
    sfree(offset_hsp_array);
    sfree(end_hsp_array);
diff --git a/algo/blast/core/lookup_util.c b/algo/blast/core/lookup_util.c
index 96e65430..9facc84c 100644
--- a/algo/blast/core/lookup_util.c
+++ b/algo/blast/core/lookup_util.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: util.c,v 1.6 2003/08/11 15:02:00 dondosha Exp $";
+static char const rcsid[] = "$Id: lookup_util.c,v 1.7 2003/11/20 15:29:12 coulouri Exp $";
 
 /*
 
@@ -28,7 +28,7 @@ static char const rcsid[] = "$Id: util.c,v 1.6 2003/08/11 15:02:00 dondosha Exp
 
 */
 
-#include <algo/blast/core/util.h>
+#include <algo/blast/core/lookup_util.h>
 
 void __sfree(void **x)
 {
diff --git a/algo/blast/core/lookup_util.h b/algo/blast/core/lookup_util.h
index 63cec11d..c443f681 100644
--- a/algo/blast/core/lookup_util.h
+++ b/algo/blast/core/lookup_util.h
@@ -1,4 +1,4 @@
-/* $Id: util.h,v 1.7 2003/08/11 14:57:16 dondosha Exp $
+/* $Id: lookup_util.h,v 1.7 2003/08/11 14:57:16 dondosha Exp $
 
 * ===========================================================================
 *
diff --git a/algo/blast/core/mb_lookup.c b/algo/blast/core/mb_lookup.c
index 45e20c9c..50488e9d 100644
--- a/algo/blast/core/mb_lookup.c
+++ b/algo/blast/core/mb_lookup.c
@@ -1,4 +1,4 @@
-/* $Id: mb_lookup.c,v 1.20 2003/10/20 20:41:14 dondosha Exp $
+/* $Id: mb_lookup.c,v 1.26 2004/01/05 19:23:58 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -34,14 +34,14 @@ Contents: Functions responsible for the creation of a lookup table
 Detailed Contents: 
 
 ******************************************************************************
- * $Revision: 1.20 $
+ * $Revision: 1.26 $
  */
 #include <algo/blast/core/blast_options.h>
 #include <algo/blast/core/blast_def.h>
 #include <algo/blast/core/mb_lookup.h>
 
 
-static char const rcsid[] = "$Id: mb_lookup.c,v 1.20 2003/10/20 20:41:14 dondosha Exp $";
+static char const rcsid[] = "$Id: mb_lookup.c,v 1.26 2004/01/05 19:23:58 dondosha Exp $";
 
 MBLookupTable* MBLookupTableDestruct(MBLookupTable* mb_lt)
 {
@@ -103,6 +103,9 @@ static DiscTemplateType GetDiscTemplateType(Int2 weight, Uint1 length,
    return TEMPL_CONTIGUOUS; /* All unsupported cases default to 0 */
 }
 
+#define SMALL_QUERY_CUTOFF 15000
+#define LARGE_QUERY_CUTOFF 800000
+
 /** Documentation in mb_lookup.h */
 Int2 MB_LookupTableNew(BLAST_SequenceBlk* query, ListNode* location,
         MBLookupTable** mb_lt_ptr,
@@ -121,6 +124,7 @@ Int2 MB_LookupTableNew(BLAST_SequenceBlk* query, ListNode* location,
    Int4 pv_shift, pv_array_bts, pv_size, pv_index;
    Int2 word_length, extra_length;
    Int4 last_offset;
+   Int4 table_entries;
 #ifdef USE_HASH_TABLE
    Int4 hash_shift, hash_mask, crc, size, length;
    Uint1* hash_buf;
@@ -166,8 +170,51 @@ Int2 MB_LookupTableNew(BLAST_SequenceBlk* query, ListNode* location,
    mb_lt->hashsize = 1<<size;
    hash_shift = (32 - size)/2;
    hash_mask = mb_lt->hashsize - 1;
+   pv_shift = 0;
+
 #else
-   mb_lt->hashsize = (1<<(8*width));
+
+   if (width == 2) {
+      mb_lt->hashsize = 1 << 16;
+      pv_shift = 0;
+   }
+   else {
+
+      /* determine the approximate number of hashtable entries */
+      table_entries = 0;
+      for (loc = location; loc; loc = loc->next) {
+         from = ((DoubleInt*) loc->ptr)->i1;
+         to = ((DoubleInt*) loc->ptr)->i2;
+         table_entries += (to - from);
+      }
+
+      /* To fit in the external cache of latter-day micro-
+         processors, the PV array must be compressed. pv_shift
+	 below is the power of two that the array size is
+	 divided by. The target PV array size is 128 kBytes.
+
+	 If the query is too small or too large, the compression 
+	 should be higher. Small queries don't reuse the PV array,
+	 and large queries saturate it. In either case, cache
+	 is better used on other data. */
+
+      if (lookup_options->word_size == 11 && lookup_options->mb_template_length > 0) {
+         mb_lt->hashsize = 1 << 22;
+         if( table_entries <= SMALL_QUERY_CUTOFF ||
+	     table_entries >= LARGE_QUERY_CUTOFF )
+            pv_shift = 3;
+	 else
+            pv_shift = 2;
+      }
+      else {
+         mb_lt->hashsize = 1 << 24;
+         if( table_entries <= SMALL_QUERY_CUTOFF ||
+	     table_entries >= LARGE_QUERY_CUTOFF )
+            pv_shift = 5;
+	 else
+            pv_shift = 4;
+      }
+   }
 #endif
 
    if (lookup_options->mb_template_length > 0) {
@@ -210,14 +257,10 @@ Int2 MB_LookupTableNew(BLAST_SequenceBlk* query, ListNode* location,
    }
 
    if (two_templates) {
-      if (lookup_options->word_size >= 12) {
-         if ((mb_lt->hashtable2 = (Int4*) 
-              calloc(mb_lt->hashsize, sizeof(Int4))) == NULL) {
-            MBLookupTableDestruct(mb_lt);
-            return -1;
-         }
-      } else {/* For weight 11 no need for extra main table */
-         mb_lt->hashtable2 = mb_lt->hashtable;
+      if ((mb_lt->hashtable2 = (Int4*) 
+           calloc(mb_lt->hashsize, sizeof(Int4))) == NULL) {
+         MBLookupTableDestruct(mb_lt);
+         return -1;
       }
       if ((mb_lt->next_pos2 = (Int4*) 
            calloc((query_length+1), sizeof(Int4))) == NULL) {
@@ -227,18 +270,24 @@ Int2 MB_LookupTableNew(BLAST_SequenceBlk* query, ListNode* location,
    }
 
    for (loc = location; loc; loc = loc->next) {
+      /* We want index to be always pointing to the start of the word.
+         Since sequence pointer points to the end of the word, subtract
+         word length from the loop boundaries. 
+      */
       from = ((DoubleInt*) loc->ptr)->i1;
-      to = ((DoubleInt*) loc->ptr)->i2;
+      to = ((DoubleInt*) loc->ptr)->i2 - word_length;
 
       seq = query->sequence_start + from;
       pos = seq + word_length;
       
       ecode = 0;
-
-      last_offset = to + 1 - extra_length;
+      /* Also add 1 to all indices, because lookup table indices count 
+         from 1. */
+      from -= word_length - 2;
+      last_offset = to + 2 - extra_length;
       amb_cond = TRUE;
 
-      for (index = from + 1; index <= last_offset; index++) {
+      for (index = from; index <= last_offset; index++) {
          val = *++seq;
          if ((val & nuc_mask) != 0) { /* ambiguity or gap */
             ecode = 0;
@@ -326,15 +375,14 @@ Int2 MB_LookupTableNew(BLAST_SequenceBlk* query, ListNode* location,
                   if (two_templates) {
                      switch (template_type) {
                      case TEMPL_11_16:
-                        ecode2 = GET_WORD_INDEX_11_16_OPT(ecode) | 
-                           SECOND_TEMPLATE_BIT;
+                        ecode2 = GET_WORD_INDEX_11_16_OPT(ecode);
                         break;
                      case TEMPL_12_16:
                         ecode2 = GET_WORD_INDEX_12_16_OPT(ecode);
                         break;
                      case TEMPL_11_18:
                         ecode2 = (GET_WORD_INDEX_11_18_OPT(ecode)) |
-                           (GET_EXTRA_CODE_18_OPT(seq)) | SECOND_TEMPLATE_BIT;
+                           (GET_EXTRA_CODE_18_OPT(seq));
                         break;
                      case TEMPL_12_18:
                         ecode2 = (GET_WORD_INDEX_12_18_OPT(ecode)) |
@@ -342,7 +390,7 @@ Int2 MB_LookupTableNew(BLAST_SequenceBlk* query, ListNode* location,
                         break;
                      case TEMPL_11_21:
                         ecode2 = (GET_WORD_INDEX_11_21_OPT(ecode)) |
-                           (GET_EXTRA_CODE_21_OPT(seq)) | SECOND_TEMPLATE_BIT;
+                           (GET_EXTRA_CODE_21_OPT(seq));
                         break;
                      case TEMPL_12_21:
                         ecode2 = (GET_WORD_INDEX_12_21_OPT(ecode)) |
@@ -374,16 +422,7 @@ Int2 MB_LookupTableNew(BLAST_SequenceBlk* query, ListNode* location,
       }
    }
    
-#ifdef USE_HASH_TABLE
-   /* If hash table is used instead of index table, no need for extra reduction
-      of pv_array size */
-   pv_shift = 0;
-#else
-   /* For 12-mer based lookup table need to make presense bit array much 
-      smaller, so it stays in cache, even though this allows for collisions */
-   pv_shift = (width < 3) ? 0 : 5;
-#endif
-   mb_lt->pv_array_bts = pv_array_bts = PV_ARRAY_BTS + pv_shift;
+   mb_lt->pv_array_bts = pv_array_bts = PV_ARRAY_BTS + pv_shift; 
 
 #ifdef QUESTION_PV_ARRAY_USE
    if (mb_lt->num_unique_pos_added < 
@@ -443,7 +482,6 @@ Int2 MB_LookupTableNew(BLAST_SequenceBlk* query, ListNode* location,
 
    mb_lt->longest_chain = longest_chain;
 
-
    *mb_lt_ptr = mb_lt;
 
    return 0;
@@ -500,6 +538,10 @@ Int4 MB_AG_ScanSubject(const LookupTableWrap* lookup_wrap,
    Boolean full_byte_scan = mb_lt->full_byte_scan;
    Uint1 pv_array_bts = mb_lt->pv_array_bts;
    
+   /* Since the test for number of hits here is done after adding them, 
+      subtract the longest chain length from the allowed offset array size. */
+   max_hits -= mb_lt->longest_chain;
+
    abs_start = subject->sequence;
    s = abs_start + start_offset/COMPRESSION_RATIO;
    compressed_scan_step = mb_lt->scan_step / COMPRESSION_RATIO;
@@ -518,15 +560,14 @@ Int4 MB_AG_ScanSubject(const LookupTableWrap* lookup_wrap,
          
          if (NA_PV_TEST(pv_array, index, pv_array_bts)) {
             q_off = mb_lt->hashtable[index];
-            s_off = 
-               ((s - abs_start) + compressed_wordsize)*COMPRESSION_RATIO;
+            s_off = (s - abs_start)*COMPRESSION_RATIO;
+            if (q_off && (total_hits >= max_hits))
+               break;
             while (q_off) {
-               q_offsets[total_hits] = q_off;
+               q_offsets[total_hits] = q_off - 1;
                s_offsets[total_hits++] = s_off;
                q_off = mb_lt->next_pos[q_off];
             }
-            if (total_hits >= max_hits)
-               break;
          }
       }
       *end_offset = (s - abs_start)*COMPRESSION_RATIO;
@@ -544,16 +585,15 @@ Int4 MB_AG_ScanSubject(const LookupTableWrap* lookup_wrap,
          /* Adjust the word index by the base within a byte */
          adjusted_index = BlastNaLookupAdjustIndex(s, index, mb_lt->mask,
                                                    bit);
-         
          if (NA_PV_TEST(pv_array, adjusted_index, pv_array_bts)) {
             q_off = mb_lt->hashtable[adjusted_index];
+            if (q_off && (total_hits >= max_hits))
+               break;
             while (q_off) {
-               q_offsets[total_hits] = q_off;
-               s_offsets[total_hits++] = s_off + word_size; 
+               q_offsets[total_hits] = q_off - 1;
+               s_offsets[total_hits++] = s_off; 
                q_off = mb_lt->next_pos[q_off];
             }
-            if (total_hits >= max_hits)
-               break;
          }
       }
       *end_offset = s_off;
@@ -568,33 +608,30 @@ Int4 MB_AG_ScanSubject(const LookupTableWrap* lookup_wrap,
  *        the word (needed when word template is longer than 16 bases) [in]
  * @param word A piece of the sequence packed into an integer [in]
  * @param template_type What type of discontiguous word template to use [in]
- * @param second_template_bit When index has fewer bits than the lookup table 
- *        width, the indices for the second template are distinguished from 
- *        those for the first template by setting a special bit. [in]
  * @return The lookup table index of the discontiguous word [out]
  */
 static NCBI_INLINE Int4 ComputeDiscontiguousIndex(Uint1* subject, Int4 word,
-                  Uint1 template_type, Int4 second_template_bit)
+                  Uint1 template_type)
 {
    Int4 index;
    Int4 extra_code;   
 
    switch (template_type) {
    case TEMPL_11_16:
-      index = GET_WORD_INDEX_11_16(word) | second_template_bit;
+      index = GET_WORD_INDEX_11_16(word);
       break;
    case TEMPL_12_16:
       index = GET_WORD_INDEX_12_16(word);
       break;
    case TEMPL_11_16_OPT:
-      index = GET_WORD_INDEX_11_16_OPT(word) | second_template_bit;
+      index = GET_WORD_INDEX_11_16_OPT(word);
       break;
    case TEMPL_12_16_OPT:
       index = GET_WORD_INDEX_12_16_OPT(word);
       break;
    case TEMPL_11_18: 
      extra_code = (Int4) GET_EXTRA_CODE_PACKED_4_18(subject);
-     index = (GET_WORD_INDEX_11_18(word) | extra_code) | second_template_bit;
+     index = (GET_WORD_INDEX_11_18(word) | extra_code);
      break;
    case TEMPL_12_18: 
       extra_code = (Int4) GET_EXTRA_CODE_PACKED_4_18(subject);
@@ -602,8 +639,7 @@ static NCBI_INLINE Int4 ComputeDiscontiguousIndex(Uint1* subject, Int4 word,
       break;
    case TEMPL_11_18_OPT: 
       extra_code = (Int4) GET_EXTRA_CODE_PACKED_4_18_OPT(subject);
-      index = (GET_WORD_INDEX_11_18_OPT(word) | extra_code) | 
-         second_template_bit;
+      index = (GET_WORD_INDEX_11_18_OPT(word) | extra_code);
       break;
    case TEMPL_12_18_OPT:
       extra_code = (Int4) GET_EXTRA_CODE_PACKED_4_18_OPT(subject);
@@ -611,8 +647,7 @@ static NCBI_INLINE Int4 ComputeDiscontiguousIndex(Uint1* subject, Int4 word,
       break;
    case TEMPL_11_21: 
       extra_code = (Int4) GET_EXTRA_CODE_PACKED_4_21(subject);
-      index = (GET_WORD_INDEX_11_21(word) | extra_code) | 
-         second_template_bit;
+      index = (GET_WORD_INDEX_11_21(word) | extra_code);
       break;
    case TEMPL_12_21:
       extra_code = (Int4) GET_EXTRA_CODE_PACKED_4_21(subject);
@@ -620,8 +655,7 @@ static NCBI_INLINE Int4 ComputeDiscontiguousIndex(Uint1* subject, Int4 word,
       break;
    case TEMPL_11_21_OPT: 
       extra_code = (Int4) GET_EXTRA_CODE_PACKED_4_21_OPT(subject);
-      index = (GET_WORD_INDEX_11_21_OPT(word) | extra_code) | 
-         second_template_bit;
+      index = (GET_WORD_INDEX_11_21_OPT(word) | extra_code);
       break;
    case TEMPL_12_21_OPT:
       extra_code = (Int4) GET_EXTRA_CODE_PACKED_4_21_OPT(subject);
@@ -650,13 +684,10 @@ static NCBI_INLINE Int4 ComputeDiscontiguousIndex(Uint1* subject, Int4 word,
  *        a compressed sequence byte [in]
  * @param template_type What discontiguous word template to use for index 
  *        computation [in]
- * @param second_template_bit Bit to set if this index is for a second 
- *        template [in]
  * @return The lookup index for the discontiguous word.
 */
 static NCBI_INLINE Int4 ComputeDiscontiguousIndex_1b(const Uint1* word_start, 
-                      Int4 word, Uint1 sequence_bit, Uint1 template_type,
-                      Int4 second_template_bit)
+                      Int4 word, Uint1 sequence_bit, Uint1 template_type)
 {
    Int4 index;
    Uint1* subject = (Uint1 *) word_start;
@@ -672,21 +703,20 @@ static NCBI_INLINE Int4 ComputeDiscontiguousIndex_1b(const Uint1* word_start,
 
    switch (template_type) {
    case TEMPL_11_16:
-      index = GET_WORD_INDEX_11_16(word) | second_template_bit;
+      index = GET_WORD_INDEX_11_16(word);
       break;
    case TEMPL_12_16:
       index = GET_WORD_INDEX_12_16(word);
       break;
    case TEMPL_11_16_OPT:
-      index = GET_WORD_INDEX_11_16_OPT(word) | second_template_bit;
+      index = GET_WORD_INDEX_11_16_OPT(word);
       break;
    case TEMPL_12_16_OPT:
       index = GET_WORD_INDEX_12_16_OPT(word);
       break;
    case TEMPL_11_18: 
       GET_EXTRA_CODE_PACKED_18(subject, bit, tmpval, extra_code);
-      index = (GET_WORD_INDEX_11_18(word) | extra_code) | 
-         second_template_bit;
+      index = (GET_WORD_INDEX_11_18(word) | extra_code);
       break;
    case TEMPL_12_18: 
       GET_EXTRA_CODE_PACKED_18(subject, bit, tmpval, extra_code);
@@ -694,8 +724,7 @@ static NCBI_INLINE Int4 ComputeDiscontiguousIndex_1b(const Uint1* word_start,
       break;
    case TEMPL_11_18_OPT: 
       GET_EXTRA_CODE_PACKED_18_OPT(subject, bit, tmpval, extra_code);
-      index = (GET_WORD_INDEX_11_18_OPT(word) | extra_code) | 
-         second_template_bit;
+      index = (GET_WORD_INDEX_11_18_OPT(word) | extra_code);
       break;
    case TEMPL_12_18_OPT:
       GET_EXTRA_CODE_PACKED_18_OPT(subject, bit, tmpval, extra_code);
@@ -703,8 +732,7 @@ static NCBI_INLINE Int4 ComputeDiscontiguousIndex_1b(const Uint1* word_start,
       break;
    case TEMPL_11_21: 
       GET_EXTRA_CODE_PACKED_21(subject, bit, tmpval, extra_code);
-      index = (GET_WORD_INDEX_11_21(word) | extra_code) | 
-         second_template_bit;
+      index = (GET_WORD_INDEX_11_21(word) | extra_code);
       break;
    case TEMPL_12_21:
       GET_EXTRA_CODE_PACKED_21(subject, bit, tmpval, extra_code);
@@ -712,8 +740,7 @@ static NCBI_INLINE Int4 ComputeDiscontiguousIndex_1b(const Uint1* word_start,
       break;
    case TEMPL_11_21_OPT: 
       GET_EXTRA_CODE_PACKED_21_OPT(subject, bit, tmpval, extra_code);
-      index = (GET_WORD_INDEX_11_21_OPT(word) | extra_code) | 
-         second_template_bit;
+      index = (GET_WORD_INDEX_11_21_OPT(word) | extra_code);
       break;
    case TEMPL_12_21_OPT:
       GET_EXTRA_CODE_PACKED_21_OPT(subject, bit, tmpval, extra_code);
@@ -747,33 +774,42 @@ Int4 MB_ScanSubject(const LookupTableWrap* lookup,
    Uint4* q_ptr = q_offsets,* s_ptr = s_offsets;
    PV_ARRAY_TYPE *pv_array = mb_lt->pv_array;
    Uint1 pv_array_bts = mb_lt->pv_array_bts;
+   Int4 compressed_wordsize = mb_lt->compressed_wordsize;
 
 #ifdef DEBUG_LOG
    FILE *logfp0 = fopen("new0.log", "a");
 #endif   
 
+   /* Since the test for number of hits here is done after adding them, 
+      subtract the longest chain length from the allowed offset array size.
+   */
+   max_hits -= mb_lt->longest_chain;
+
    abs_start = subject->sequence;
    s = abs_start + start_offset/COMPRESSION_RATIO;
    s_end = abs_start + (*end_offset)/COMPRESSION_RATIO;
 
    s = BlastNaLookupInitIndex(mb_lt->compressed_wordsize, s, &index);
 
+   /* In the following code, s points to the byte right after the end of 
+      the word. */
    while (s <= s_end) {
       if (NA_PV_TEST(pv_array, index, pv_array_bts)) {
          query_offset = mb_lt->hashtable[index];
-         subject_offset = (s - abs_start)*COMPRESSION_RATIO;
+         subject_offset = 
+            ((s - abs_start) - compressed_wordsize)*COMPRESSION_RATIO;
+         if (query_offset && (hitsfound >= max_hits))
+            break;
          while (query_offset) {
 #ifdef DEBUG_LOG
             fprintf(logfp0, "%ld\t%ld\t%ld\n", query_offset, 
                     subject_offset, index);
 #endif
-            *(q_ptr++) = query_offset;
+            *(q_ptr++) = query_offset - 1;
             *(s_ptr++) = subject_offset;
             ++hitsfound;
             query_offset = mb_lt->next_pos[query_offset];
          }
-         if (hitsfound >= max_hits)
-            break;
       }
       /* Compute the next value of the lookup index 
          (shifting sequence by a full byte) */
@@ -782,7 +818,7 @@ Int4 MB_ScanSubject(const LookupTableWrap* lookup,
    }
 
    *end_offset = 
-     ((s - abs_start) - mb_lt->compressed_wordsize)*COMPRESSION_RATIO;
+     ((s - abs_start) - compressed_wordsize)*COMPRESSION_RATIO;
 #ifdef DEBUG_LOG
    fclose(logfp0);
 #endif
@@ -808,11 +844,16 @@ Int4 MB_DiscWordScanSubject(const LookupTableWrap* lookup,
    Uint1 second_template_type = mb_lt->second_template_type;
    PV_ARRAY_TYPE *pv_array = mb_lt->pv_array;
    Uint1 pv_array_bts = mb_lt->pv_array_bts;
+   Int4 compressed_wordsize = mb_lt->compressed_wordsize;
 
 #ifdef DEBUG_LOG
    FILE *logfp0 = fopen("new0.log", "a");
 #endif   
    
+   /* Since the test for number of hits here is done after adding them, 
+      subtract the longest chain length from the allowed offset array size. */
+   max_hits -= mb_lt->longest_chain;
+
    abs_start = subject->sequence;
    s_start = abs_start + start_offset/COMPRESSION_RATIO;
    s_end = abs_start + (*end_offset)/COMPRESSION_RATIO;
@@ -823,33 +864,36 @@ Int4 MB_DiscWordScanSubject(const LookupTableWrap* lookup,
    if (full_byte_scan) {
 
      while (s <= s_end) {
-       index = ComputeDiscontiguousIndex(s, word, template_type, 0);
+       index = ComputeDiscontiguousIndex(s, word, template_type);
 
        if (two_templates) {
-          index2 = ComputeDiscontiguousIndex(s, word, second_template_type, 
-                                             SECOND_TEMPLATE_BIT);
+          index2 = ComputeDiscontiguousIndex(s, word, second_template_type);
        }
        if (NA_PV_TEST(pv_array, index, pv_array_bts)) {
           query_offset = mb_lt->hashtable[index];
-          subject_offset = (s - abs_start)*COMPRESSION_RATIO;
+          subject_offset = 
+             ((s - abs_start) - compressed_wordsize)*COMPRESSION_RATIO;
+          if (query_offset && (hitsfound >= max_hits))
+             break;
           while (query_offset) {
 #ifdef DEBUG_LOG
              fprintf(logfp0, "%ld\t%ld\t%ld\n", query_offset, 
                      subject_offset, index);
 #endif
-             *(q_ptr++) = query_offset;
+             *(q_ptr++) = query_offset - 1;
              *(s_ptr++) = subject_offset;
              ++hitsfound;
              query_offset = mb_lt->next_pos[query_offset];
           }
-          if (hitsfound >= max_hits)
-             break;
        }
        if (two_templates && NA_PV_TEST(pv_array, index2, pv_array_bts)) {
           query_offset = mb_lt->hashtable2[index2];
-          subject_offset = (s - abs_start)*COMPRESSION_RATIO;
+          subject_offset = 
+             ((s - abs_start) - compressed_wordsize)*COMPRESSION_RATIO;
+          if (query_offset && (hitsfound >= max_hits))
+             break;
           while (query_offset) {
-             q_offsets[hitsfound] = query_offset;
+             q_offsets[hitsfound] = query_offset - 1;
              s_offsets[hitsfound++] = subject_offset;
              query_offset = mb_lt->next_pos2[query_offset];
           }
@@ -868,33 +912,39 @@ Int4 MB_DiscWordScanSubject(const LookupTableWrap* lookup,
                                          bit);
    
          index = ComputeDiscontiguousIndex_1b(s, adjusted_word, bit,
-                    template_type, 0);
+                    template_type);
        
          if (two_templates)
             index2 = ComputeDiscontiguousIndex_1b(s, adjusted_word, bit,
-                        second_template_type, SECOND_TEMPLATE_BIT);
+                        second_template_type);
 
          if (NA_PV_TEST(pv_array, index, pv_array_bts)) {
             query_offset = mb_lt->hashtable[index];
-            subject_offset = (s - abs_start)*COMPRESSION_RATIO + bit/2;
+            subject_offset = 
+               ((s - abs_start) - compressed_wordsize)*COMPRESSION_RATIO
+               + bit/2;
+            if (query_offset && (hitsfound >= max_hits))
+               break;
             while (query_offset) {
 #ifdef DEBUG_LOG
                fprintf(logfp0, "%ld\t%ld\t%ld\n", query_offset, 
                        subject_offset, index);
 #endif
-               *(q_ptr++) = query_offset;
+               *(q_ptr++) = query_offset - 1;
                *(s_ptr++) = subject_offset;
                ++hitsfound;
                query_offset = mb_lt->next_pos[query_offset];
             }
-            if (hitsfound >= max_hits)
-               break;
          }
          if (two_templates && NA_PV_TEST(pv_array, index2, pv_array_bts)) {
             query_offset = mb_lt->hashtable2[index2];
-            subject_offset = (s - abs_start)*COMPRESSION_RATIO + bit/2;
+            subject_offset = 
+               ((s - abs_start) - compressed_wordsize)*COMPRESSION_RATIO
+               + bit/2;
+            if (query_offset && (hitsfound >= max_hits))
+               break;
             while (query_offset) {
-               q_offsets[hitsfound] = query_offset;
+               q_offsets[hitsfound] = query_offset - 1;
                s_offsets[hitsfound++] = subject_offset;
                query_offset = mb_lt->next_pos2[query_offset];
             }
@@ -909,7 +959,7 @@ Int4 MB_DiscWordScanSubject(const LookupTableWrap* lookup,
       }
    }
    *end_offset = 
-     ((s - abs_start) - mb_lt->compressed_wordsize)*COMPRESSION_RATIO;
+     ((s - abs_start) - compressed_wordsize)*COMPRESSION_RATIO;
 #ifdef DEBUG_LOG
    fclose(logfp0);
 #endif
diff --git a/algo/blast/core/ncbi_math.c b/algo/blast/core/ncbi_math.c
index d5a62a80..a0c05a02 100644
--- a/algo/blast/core/ncbi_math.c
+++ b/algo/blast/core/ncbi_math.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/23/91
 *
-* $Revision: 1.6 $
+* $Revision: 1.7 $
 *
 * File Description:
 *   	portable math functions
@@ -42,6 +42,9 @@
 * 12-22-93 Schuler     Converted ERRPOST((...)) to ErrPostEx(...)
 *
 * $Log: ncbi_math.c,v $
+* Revision 1.7  2003/12/05 16:03:57  camacho
+* Remove compiler warnings
+*
 * Revision 1.6  2003/09/26 20:39:32  dondosha
 * Rearranged code so it compiles
 *
@@ -110,8 +113,10 @@
 
 #include <algo/blast/core/ncbi_math.h>
 
+#if 0
 extern char * g_corelib;
 static char * _this_file = __FILE__;
+#endif
 
 
 /*
diff --git a/algo/blast/core/ncbi_std.c b/algo/blast/core/ncbi_std.c
index 52562500..7935e05a 100644
--- a/algo/blast/core/ncbi_std.c
+++ b/algo/blast/core/ncbi_std.c
@@ -1,7 +1,7 @@
 #include <algo/blast/core/blast_def.h> /* for sfree() macro */
 #include <algo/blast/core/ncbi_std.h>
 
-void * MemDup (const void *orig, size_t size)
+void * BlastMemDup (const void *orig, size_t size)
 {
 	void*	copy;
 
diff --git a/algo/blast/core/ncbi_std.h b/algo/blast/core/ncbi_std.h
index e95105d9..0f272a8d 100644
--- a/algo/blast/core/ncbi_std.h
+++ b/algo/blast/core/ncbi_std.h
@@ -1,4 +1,4 @@
-/* $Id: ncbi_std.h,v 1.19 2003/09/11 16:58:42 dondosha Exp $
+/* $Id: ncbi_std.h,v 1.23 2003/12/09 18:51:40 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -35,7 +35,7 @@ Contents: Type and macro definitions from C toolkit that are not defined in
 Detailed Contents: 
 
 ******************************************************************************
- * $Revision: 1.19 $
+ * $Revision: 1.23 $
  * */
 #ifndef __NCBI_STD__
 #define __NCBI_STD__
@@ -44,19 +44,12 @@ Detailed Contents:
 #include <stdlib.h>
 #include <string.h>
 
-#ifndef _MSC_VER
-#include <strings.h>
-#endif
-
 #include <math.h>
 #include <ctype.h>
 #include <assert.h>
 
-#ifndef NCBI_C_TOOLKIT
-#include <corelib/ncbitype.h>
-#else
-#include <ncbistd.h>
-#endif
+/* which toolkit are we using? */
+#include "blast_toolkit.h"
 
 #include <algo/blast/core/ncbi_math.h>
 
@@ -88,7 +81,7 @@ extern "C" {
 #define strdup _strdup
 #endif
 
-#ifndef NCBI_C_TOOLKIT
+#ifndef _NCBISTD_ /* if we're not in the C toolkit... */
 typedef Uint1 Boolean;
 #ifndef TRUE
 #define TRUE 1
@@ -120,7 +113,7 @@ typedef Uint1 Boolean;
 
 /* low-level ANSI-style functions */
 
-#ifndef NCBI_C_TOOLKIT
+#ifndef _NCBISTD_ /* if we're not in the C toolkit ... */
 #define UINT4_MAX     4294967295U
 #define INT4_MAX    2147483647
 #define INT4_MIN    (-2147483647-1)
@@ -142,9 +135,9 @@ typedef Uint1 Boolean;
 
 #else
 
-#endif /* NCBI_C_TOOLKIT */
+#endif /* _NCBISTD_ */
 
-extern void* MemDup (const void *orig, size_t size);
+extern void* BlastMemDup (const void *orig, size_t size);
 
 
 /******************************************************************************/
diff --git a/algo/blast/core/pattern.c b/algo/blast/core/pattern.c
index f1dd2f0a..b569520b 100644
--- a/algo/blast/core/pattern.c
+++ b/algo/blast/core/pattern.c
@@ -1,4 +1,4 @@
-/* $Id: pattern.c,v 1.6 2003/10/16 15:52:08 coulouri Exp $
+/* $Id: pattern.c,v 1.8 2003/12/04 16:27:13 camacho Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,13 +32,13 @@ Author: Ilya Dondoshansky
 Contents: Functions for finding pattern matches in sequence.
 
 ******************************************************************************
- * $Revision: 1.6 $
+ * $Revision: 1.8 $
  * */
 
 #include <algo/blast/core/blast_def.h>
 #include <algo/blast/core/pattern.h>
 
-static char const rcsid[] = "$Id: pattern.c,v 1.6 2003/10/16 15:52:08 coulouri Exp $";
+static char const rcsid[] = "$Id: pattern.c,v 1.8 2003/12/04 16:27:13 camacho Exp $";
 
 /*Looks for 1 bits in the same position of s and mask
   Let rightOne be the rightmost position where s and mask both have
@@ -147,7 +147,8 @@ static Int4 find_hitsS_DNA(Int4* hitArray, const Uint1* seq, Int4 pos, Int4 len,
     remain = len % 4;
   }
   for (i = 0; i < end; i++) {
-    if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) {
+    if ( (tmp = (prefixMatchedBitPattern &
+                 patternSearch->DNAwhichPrefixPosPtr[seq[i]]))) {
       for (j = 0; j < 4; j++) {
 	if (tmp & patternSearch->match_mask) {
 	  hitArray[twiceNumHits++] = i*4+j + pos;
@@ -160,7 +161,8 @@ static Int4 find_hitsS_DNA(Int4* hitArray, const Uint1* seq, Int4 pos, Int4 len,
     prefixMatchedBitPattern = (((prefixMatchedBitPattern << 4) | mask2) & patternSearch->DNAwhichSuffixPosPtr[seq[i]]);
   }
   /* In the last byte check bits only up to 'remain' */
-  if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) {
+  if ( (tmp = (prefixMatchedBitPattern &
+               patternSearch->DNAwhichPrefixPosPtr[seq[i]]))) {
      for (j = 0; j < remain; j++) {
         if (tmp & patternSearch->match_mask) {
            hitArray[twiceNumHits++] = i*4+j + pos;
@@ -223,7 +225,7 @@ static Int4 and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearc
     Int4 returnValue = 0;
 
     for (i = 0; i < patternSearch->numWords; i++) 
-      if (result[i] = (a[i] & b[i])) 
+      if ( (result[i] = (a[i] & b[i]) ) ) 
 	returnValue = 1;
     return returnValue;
 }
@@ -386,7 +388,7 @@ static Int4 find_hitsLL(Int4 *hitArray, const Uint1* seq, Int4 len, Boolean is_d
     return twiceNumHits;
 }
 
-Int4 find_hits(Int4 *hitArray, const Uint1* seq, Int4 len, 
+Int4 FindPatternHits(Int4 *hitArray, const Uint1* seq, Int4 len, 
                Boolean is_dna, patternSearchItems * patternSearch)
 {
     if (patternSearch->flagPatternLength == ONE_WORD_PATTERN) 
diff --git a/algo/blast/core/pattern.h b/algo/blast/core/pattern.h
index dcdf12c3..48b23448 100644
--- a/algo/blast/core/pattern.h
+++ b/algo/blast/core/pattern.h
@@ -1,4 +1,4 @@
-/* $Id: pattern.h,v 1.1 2003/09/09 22:03:54 dondosha Exp $
+/* $Id: pattern.h,v 1.2 2003/12/03 16:22:55 dondosha Exp $
 
 * ===========================================================================
 *
@@ -34,7 +34,7 @@ Contents: Functions for finding pattern matches in sequence.
 Detailed Contents: 
 
 ******************************************************************************
- * $Revision: 1.1 $
+ * $Revision: 1.2 $
  * */
 
 #include <algo/blast/core/blast_def.h>
@@ -130,7 +130,7 @@ typedef struct seedSearchItems {
  * @param patternSearch Pattern information [in]
  * @return Twice the number of hits (length of hitArray filled in)
 */
-Int4 find_hits(Int4 *hitArray, const Uint1* seq, Int4 len, 
+Int4 FindPatternHits(Int4 *hitArray, const Uint1* seq, Int4 len, 
                Boolean is_dna, patternSearchItems * patternSearch);
 
 #ifdef __cplusplus
diff --git a/algo/blast/core/phi_lookup.c b/algo/blast/core/phi_lookup.c
index 48e6d21e..37251294 100644
--- a/algo/blast/core/phi_lookup.c
+++ b/algo/blast/core/phi_lookup.c
@@ -1,4 +1,4 @@
-/* $Id: phi_lookup.c,v 1.6 2003/10/16 15:52:08 coulouri Exp $
+/* $Id: phi_lookup.c,v 1.7 2003/12/03 16:23:08 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@ Author: Ilya Dondoshansky
 Contents: Functions for accessing the lookup table for PHI-BLAST
 
 ******************************************************************************
- * $Revision: 1.6 $
+ * $Revision: 1.7 $
  * */
 
 #include <algo/blast/core/blast_def.h>
@@ -41,7 +41,7 @@ Contents: Functions for accessing the lookup table for PHI-BLAST
 #include <algo/blast/core/phi_lookup.h>
 #include <algo/blast/core/blast_message.h>
 
-static char const rcsid[] = "$Id: phi_lookup.c,v 1.6 2003/10/16 15:52:08 coulouri Exp $";
+static char const rcsid[] = "$Id: phi_lookup.c,v 1.7 2003/12/03 16:23:08 dondosha Exp $";
 
 #define seedepsilon 0.00001
 #define allone  ((1 << ALPHABET_SIZE) - 1)
@@ -689,8 +689,8 @@ Int4 PHIBlastIndexQuery(PHILookupTable* lookup,
       offset = 0;
       sequence = query->sequence + from;
       
-      twiceNumHits = find_hits(hitArray, sequence, loc_length, is_dna,
-                               pattern_info);
+      twiceNumHits = FindPatternHits(hitArray, sequence, loc_length, is_dna,
+                                     pattern_info);
       
       for (i = 0; i < twiceNumHits; i += 2) {
          PHIBlastAddPatternHit(lookup, hitArray[i+1]+from, 
@@ -734,8 +734,8 @@ Int4 PHIBlastScanSubject(const LookupTableWrap* lookup_wrap,
    */
    *offset_ptr = subject_blk->length;
 
-   twiceNumHits = find_hits(hitArray, subject, subject_blk->length, 
-                            lookup->is_dna, lookup->pattern_info);
+   twiceNumHits = FindPatternHits(hitArray, subject, subject_blk->length, 
+                                  lookup->is_dna, lookup->pattern_info);
 
 
    for (i = 0; i < twiceNumHits; i += 2) {
diff --git a/api/alignval.c b/api/alignval.c
index bf3a64b7..cd926db3 100644
--- a/api/alignval.c
+++ b/api/alignval.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/3/99
 *
-* $Revision: 6.37 $
+* $Revision: 6.38 $
 *
 * File Description:  To validate sequence alignment.
 *
@@ -67,6 +67,7 @@ typedef struct saval {
   Boolean     delete_salp;
   Boolean     delete_bsp;
   Boolean     retdel;
+  Boolean     do_hist_assembly;
   ValNodePtr  ids;
   Uint2       entityID;
   Boolean     dirty;
@@ -1840,6 +1841,7 @@ NLM_EXTERN Boolean ValidateSeqAlign (SeqAlignPtr salp, Uint2 entityID, Boolean m
      sv.delete_salp = delete_salp;
      sv.delete_bsp = delete_bsp;
      sv.retdel = TRUE;
+     sv.do_hist_assembly = FALSE;
      sv.ids = NULL;
      sv.entityID = entityID; 
      sv.dirty = FALSE;   
@@ -1963,7 +1965,7 @@ NLM_EXTERN Int2 LIBCALLBACK ValidateSeqAlignFromData (Pointer data)
      ValidateSeqAlign (salp, 0, TRUE, TRUE, TRUE, FALSE, FALSE, NULL);
   }
   if (sep!=NULL) {
-     ValidateSeqAlignInSeqEntry (sep, TRUE, TRUE, TRUE, TRUE, FALSE);
+     ValidateSeqAlignInSeqEntry (sep, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE);
   }
   return OM_MSG_RET_DONE;
 }
@@ -2008,7 +2010,9 @@ static void ValidateSeqAlignCallback (SeqEntryPtr sep, Pointer mydata,
         bsp = (BioseqPtr) sep->data.ptrvalue;
         if (bsp!=NULL) {
            ValidateSeqAlignInAnnot (bsp->annot, svp);
-           ValidateSeqAlignInHist (bsp->hist, svp);
+           if (svp != NULL && svp->do_hist_assembly) {
+              ValidateSeqAlignInHist (bsp->hist, svp);
+           }
         }
      }   
      else if(IS_Bioseq_set(sep)) {
@@ -2024,7 +2028,8 @@ static void ValidateSeqAlignCallback (SeqEntryPtr sep, Pointer mydata,
 
 NLM_EXTERN Boolean ValidateSeqAlignInSeqEntry (SeqEntryPtr sep, Boolean message, 
                                  Boolean msg_success, Boolean find_remote_bsp, 
-                                 Boolean delete_bsp, Boolean delete_salp)
+                                 Boolean delete_bsp, Boolean delete_salp,
+                                 Boolean do_hist_assembly)
 {
   SeqEntryPtr      sep_head;
   Uint2            entityID;
@@ -2042,6 +2047,7 @@ NLM_EXTERN Boolean ValidateSeqAlignInSeqEntry (SeqEntryPtr sep, Boolean message,
         sv.delete_salp = delete_salp;
         sv.delete_bsp = delete_bsp;
         sv.retdel = TRUE;
+        sv.do_hist_assembly = do_hist_assembly;
         sv.ids = NULL;
         sv.entityID = entityID; 
         sv.dirty = FALSE;
@@ -2058,9 +2064,10 @@ NLM_EXTERN Boolean ValidateSeqAlignInSeqEntry (SeqEntryPtr sep, Boolean message,
 
 
 /* alignment validator private for regular validator */
-NLM_EXTERN Boolean ValidateSeqAlignWithinValidator (ValidStructPtr vsp, SeqEntryPtr sep);
 
-NLM_EXTERN Boolean ValidateSeqAlignWithinValidator (ValidStructPtr vsp, SeqEntryPtr sep)
+NLM_EXTERN Boolean ValidateSeqAlignWithinValidator (ValidStructPtr vsp, SeqEntryPtr sep, Boolean find_remote_bsp, Boolean do_hist_assembly);
+
+NLM_EXTERN Boolean ValidateSeqAlignWithinValidator (ValidStructPtr vsp, SeqEntryPtr sep, Boolean find_remote_bsp, Boolean do_hist_assembly)
 
 {
   GatherContext  gc;
@@ -2076,7 +2083,7 @@ NLM_EXTERN Boolean ValidateSeqAlignWithinValidator (ValidStructPtr vsp, SeqEntry
   vsp->sfp = NULL;
   vsp->descr = NULL;
   MemSet ((Pointer) &gc, 0, sizeof (GatherContext));
-  rsult = ValidateSeqAlignInSeqEntry (sep, FALSE, FALSE, TRUE, FALSE, FALSE);
+  rsult = ValidateSeqAlignInSeqEntry (sep, FALSE, FALSE, find_remote_bsp, FALSE, FALSE, do_hist_assembly);
   useLockByID = TRUE;
   useValErr = FALSE;
   useVsp = NULL;
diff --git a/api/alignval.h b/api/alignval.h
index 764bccdc..f73a04b6 100644
--- a/api/alignval.h
+++ b/api/alignval.h
@@ -29,13 +29,16 @@
 *
 * Version Creation Date:   6/3/99
 *
-* $Revision: 6.13 $
+* $Revision: 6.14 $
 *
 * File Description:
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: alignval.h,v $
+* Revision 6.14  2003/11/14 18:06:42  kans
+* added do_hist_assembly parameter
+*
 * Revision 6.13  1999/11/23 21:47:31  vakatov
 * Fixed for C++ and/or DLL compilation
 *
@@ -79,8 +82,8 @@ NLM_EXTERN Boolean ValidateSeqAlign (SeqAlignPtr salp, Uint2 entityID, Boolean m
 
 NLM_EXTERN Boolean ValidateSeqAlignInSeqEntry (SeqEntryPtr sep, Boolean message, 
                                  Boolean msg_success, Boolean find_remote_bsp, 
-                                 Boolean delete_bsp, Boolean delete_salp);
-
+                                 Boolean delete_bsp, Boolean delete_salp,
+                                 Boolean do_hist_assembly);
 
 
 #define Err_SeqId 1
diff --git a/api/aliread.c b/api/aliread.c
index 7af5ffe4..5c1bcbfb 100644
--- a/api/aliread.c
+++ b/api/aliread.c
@@ -383,7 +383,7 @@ CharPtr ReadAlignFileLine (FILE PNTR        alignFilePtr,
   Int4    segmentLen = 0;
   Int4    segmentCount = 1;
   Boolean done = FALSE;
-  Char    ch;
+  Char    ch = 0;
 
   /* Allocate memory for the line.  More */
   /* can be added later as necessary.    */
@@ -408,11 +408,14 @@ CharPtr ReadAlignFileLine (FILE PNTR        alignFilePtr,
 	{
 	  done = TRUE;
 	  ch = (Char) NLM_GETC (alignFilePtr);
-	  if (ch != '\r')
+	  if (ch != '\r') {
 	    ungetc (ch, alignFilePtr);
+	  
+	  }
 	}
-      else if (ch == '\r')
-	done = TRUE;
+      else if (ch == '\r') {
+        done = TRUE;
+      }
       else
 	{
 	  lineStr[totalLen] = ch;
@@ -450,6 +453,7 @@ CharPtr ReadAlignFileLine (FILE PNTR        alignFilePtr,
     *isEOF = TRUE;
 
   lineStr[totalLen] = '\0';
+
   return lineStr;
 }
 
@@ -1160,8 +1164,9 @@ ValNodePtr Ali_ReadLines (FILE PNTR        alignFilePtr,
 
       lineStr = ReadAlignFileLine(alignFilePtr, errorListPtr,
 				  configPtr, &isEOF);
-      if (lineStr == NULL)
+      if (lineStr == NULL) {
 	return NULL;
+      }
 
       rowNum++;
 
diff --git a/api/asn2gnb1.c b/api/asn2gnb1.c
index deccca09..3108ce82 100644
--- a/api/asn2gnb1.c
+++ b/api/asn2gnb1.c
@@ -1,4 +1,4 @@
-/*   asn2gnbk.c
+/*   asn2gnb1.c
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -23,14 +23,14 @@
 *
 * ===========================================================================
 *
-* File Name:  asn2gnbk.c
+* File Name:  asn2gnb1.c
 *
 * Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans,
 *          Mati Shomrat
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 6.729 $
+* $Revision: 1.2 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -55,7 +55,7 @@
 #include <gbftdef.h>
 #include <edutil.h>
 #include <alignmgr2.h>
-#include <asn2gnbp.h>
+#include <asn2gnbi.h>
 
 #ifdef WIN_MAC
 #if __profile__
@@ -63,1183 +63,324 @@
 #endif
 #endif
 
-#define ASN2FF_EMBL_MAX 78
-#define ASN2FF_GB_MAX   79
-#define SEQID_MAX_LEN   41
-
-#define TILDE_IGNORE     0
-#define TILDE_TO_SPACES  1
-#define TILDE_EXPAND     2
-#define TILDE_OLD_EXPAND 3
-
-
-/* flags set by mode to customize behavior */
-
-typedef struct asn2gbflags {
-  Boolean             suppressLocalID;
-  Boolean             validateFeats;
-  Boolean             ignorePatPubs;
-  Boolean             dropShortAA;
-  Boolean             avoidLocusColl;
-  Boolean             iupacaaOnly;
-  Boolean             dropBadCitGens;
-  Boolean             noAffilOnUnpub;
-  Boolean             dropIllegalQuals;
-  Boolean             checkQualSyntax;
-  Boolean             needRequiredQuals;
-  Boolean             needOrganismQual;
-  Boolean             needAtLeastOneRef;
-  Boolean             citArtIsoJta;
-  Boolean             dropBadDbxref;
-  Boolean             useEmblMolType;
-  Boolean             hideBankItComment;
-  Boolean             checkCDSproductID;
-  Boolean             suppressSegLoc;
-  Boolean             srcQualsToNote;
-  Boolean             hideEmptySource;
-  Boolean             goQualsToNote;
-  Boolean             geneSynsToNote;
-  Boolean             selenocysteineToNote;
-  Boolean             forGbRelease;
-} Asn2gbFlags, PNTR Asn2gbFlagsPtr;
-
-/* internal Asn2gbSect structure has fields on top of Asn2gbSect fields */
-
-typedef struct int_Asn2gbSect {
-  Asn2gbSect  asp;
-  SeqPortPtr  spp;
-} IntAsn2gbSect, PNTR IntAsn2gbSectPtr;
-
-/* string structure */
-
-#define STRING_BUF_LEN  1024
-
-typedef struct stringitem {
-  struct stringitem  *curr;
-  struct stringitem  *next;
-  Pointer            iajp;
-  Char               buf [STRING_BUF_LEN];
-  Int4               pos;
-} StringItem, PNTR StringItemPtr;
-
-/* internal asn2gbjob structure has fields on top of Asn2gbJob fields */
-
-typedef struct int_asn2gb_job {
-  Asn2gbJob      ajp;
-  FmtType        format;
-  ModType        mode;
-  Asn2gbFlags    flags;
-  Boolean        showFarTransl;
-  Boolean        transIfNoProd;
-  Boolean        alwaysTranslCds;
-  Boolean        showTranscript;
-  Boolean        showPeptide;
-  Boolean        transientSeqPort;
-  Boolean        masterStyle;
-  Boolean        newSourceOrg;
-  ValNodePtr     lockedBspList;
-  Boolean        relModeError;
-  Boolean        skipProts;
-  Boolean        skipMrnas;
-  IndxPtr        index;
-  GBSeqPtr       gbseq;
-  StringItemPtr  pool;
-  Boolean        www;
-} IntAsn2gbJob, PNTR IntAsn2gbJobPtr;
-
-/* structure for storing working parameters while building asn2gb_job structure */
-
-typedef struct asn2gbwork {
-  IntAsn2gbJobPtr  ajp;
-  Uint2            entityID;
-
-  FmtType          format;
-  ModType          mode;
-  StlType          style;
-
-  ValNodePtr       pubhead;    /* for collecting publications */
-  ValNodePtr       srchead;    /* for collecting biosources */
-
-  /* linked lists of paragraphs, sections, blocks */
-
-  ValNodePtr       sectionList;
-  ValNodePtr       blockList;    /* reset for each new section */
-
-  /* most recent node of linked lists, for quickly adding next node */
-
-  ValNodePtr       lastsection;
-  ValNodePtr       lastblock;    /* reset for each new section */
-
-  Int4             currsection;
-
-  /* section fields needed for populating blocks */
-
-  Asn2gbSectPtr    asp;
-
-  BioseqPtr        target;
-  BioseqPtr        parent;
-  BioseqPtr        bsp;
-  BioseqPtr        refs;
-  SeqLocPtr        slp;
-  Uint2            seg;
-  Int4             numsegs;
-  Int4             partcount;
-  Int4             from;
-  Int4             to;
-  Boolean          showAllFeats;
-
-  Boolean          contig;
-  Boolean          showconfeats;
-  Boolean          showconsource;
-
-  Boolean          onlyNearFeats;
-  Boolean          farFeatsSuppress;
-  Boolean          nearFeatsSuppress;
-
-  Boolean          citSubsFirst;
-  Boolean          hideGeneFeats;
-  Boolean          newLocusLine;
-  Boolean          showBaseCount;
-
-  Boolean          hideImpFeats;
-  Boolean          hideRemImpFeats;
-  Boolean          hideSnpFeats;
-  Boolean          hideExonFeats;
-  Boolean          hideIntronFeats;
-  Boolean          hideMiscFeats;
-  Boolean          hideCddFeats;
-  Boolean          hideCdsProdFeats;
-
-  Boolean          hideGeneRIFs;
-  Boolean          onlyGeneRIFs;
-  Boolean          latestGeneRIFs;
-
-  Boolean          showRefs;
+/* utility functions */
 
-  Boolean          isGPS;
-  Boolean          copyGpsCdsUp;
-  Boolean          copyGpsGeneDown;
+NLM_EXTERN ValNodePtr ValNodeCopyStrToHead (ValNodePtr PNTR head, Int2 choice, CharPtr str)
 
-  Boolean          showContigAndSeq;
+{
+  ValNodePtr newnode;
 
-  Char             basename [SEQID_MAX_LEN];
+  if (head == NULL || str == NULL) return NULL;
 
-  SeqFeatPtr       lastsfp;
-  SeqAnnotPtr      lastsap;
-  Int4             lastleft;
-  Int4             lastright;
+  newnode = ValNodeNew (NULL);
+  if (newnode == NULL) return NULL;
 
-  Boolean          firstfeat;
-  Boolean          featseen;
+  newnode->choice = (Uint1) choice;
+  newnode->data.ptrvalue = StringSave (str);
 
-  SeqSubmitPtr     ssp;
-  Boolean          hup;
+  newnode->next = *head;
+  *head = newnode;
 
-  Boolean          stream;
+  return newnode;
+}
 
-  Boolean          failed;
-} Asn2gbWork, PNTR Asn2gbWorkPtr;
+/* the val node strings mechanism will be replaced by a more efficient method later  */
 
-/* array for assigning biosource and feature data fields to qualifiers */
-/* should be allocated to MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR) */
+NLM_EXTERN CharPtr MergeFFValNodeStrs (
+  ValNodePtr list
+)
 
-typedef union qualval {
-  CharPtr        str;
-  Boolean        ble;
-  Int4           num;
-  ValNodePtr     vnp;
-  GBQualPtr      gbq;
-  OrgModPtr      omp;
-  SubSourcePtr   ssp;
-  CodeBreakPtr   cbp;
-  SeqLocPtr      slp;
-  SeqIdPtr       sip;
-  tRNAPtr        trp;
-  UserObjectPtr  uop;
-  UserFieldPtr   ufp;
-} QualVal, PNTR QualValPtr;
+{
+  size_t      len;
+  CharPtr     ptr;
+  CharPtr     str;
+  CharPtr     tmp;
+  ValNodePtr  vnp;
 
-/* structure passed to individual paragraph format functions */
 
-typedef struct asn2gbformat {
-  IntAsn2gbJobPtr ajp;
-  Asn2gbSectPtr   asp;
-  QualValPtr      qvp;
-
-  FmtType         format;
-} Asn2gbFormat, PNTR Asn2gbFormatPtr;
-
-
-/* Seq-hist replacedBy is preformatted into string field, */
-/* then comment descriptors, Map location:, and Region:, */
-/* then comment features, finally HTGS */
-
-typedef struct comment_block {
-  ASN2GB_BASE_BLOCK
-  Boolean           first;
-} CommentBlock, PNTR CommentBlockPtr;
-
-/* internal reference block has fields on top of RefBlock fields */
-
-typedef struct int_ref_block {
-  RefBlock   rb;
-  DatePtr    date;     /* internal sorting use only */
-  SeqLocPtr  loc;      /* final location on target bioseq */
-  CharPtr    authstr;  /* author string */
-  Uint2      index;    /* index if feature on target bioseq */
-  Boolean    justuids; /* gibb pub with uids and Figure, etc. */
-  CharPtr    fig;      /* figure string from equivalent gibb pub */
-  CharPtr    maploc;   /* maploc string from equivalent gibb pub */
-  Boolean    poly_a;   /* poly_a field from equivalent gibb pub */
-} IntRefBlock, PNTR IntRefBlockPtr;
-
-/* internal source block has fields on top of BaseBlock fields */
-
-typedef struct int_src_block {
-  BaseBlock         bb;
-  Boolean           is_descriptor;
-  Boolean           is_focus;
-  Boolean           is_synthetic;
-  BioSourcePtr      biop;
-  Uint4             orghash;
-  Uint4             modhash;
-  Uint4             subhash;
-  Uint4             xrfhash;
-  SeqLocPtr         loc;     /* final location on target bioseq */
-  CharPtr           taxname;
-  CharPtr           comment;
-  OrgModPtr         omp;
-  SubSourcePtr      ssp;
-  ValNodePtr        vnp;
-  Int4              left;
-  Int4              right;
-} IntSrcBlock, PNTR IntSrcBlockPtr;
-
-/* internal feature block has fields on top of FeatBlock fields */
-
-typedef struct int_feat_block {
-  FeatBlock  fb;
-  Boolean     mapToNuc;
-  Boolean     mapToProt;
-  Boolean     mapToGen;
-  Boolean     mapToMrna;
-  Boolean     mapToPep;
-  Boolean     isCDS;     /* set if using IntCdsBlock */
-  Boolean     firstfeat;
-} IntFeatBlock, PNTR IntFeatBlockPtr;
-
-/* internal cds block has fields on top of IntFeatBlock fields */
-
-typedef struct int_cds_block {
-  IntFeatBlock  ifb;
-  FeatBlock     fb;
-  CharPtr       fig;    /* figure string from pub */
-  CharPtr       maploc; /* maploc string from pub */
-} IntCdsBlock, PNTR IntCdsBlockPtr;
-
-
-/* enumerated qualifier category definitions */
-
-typedef enum {
-  Qual_class_ignore = 0,
-  Qual_class_string,
-  Qual_class_tilde,
-  Qual_class_sgml,
-  Qual_class_boolean,
-  Qual_class_int,
-  Qual_class_evidence,
-  Qual_class_valnode,
-  Qual_class_EC_valnode,
-  Qual_class_xtraprds,
-  Qual_class_quote,
-  Qual_class_EC_quote,
-  Qual_class_noquote,
-  Qual_class_label,
-  Qual_class_number,
-  Qual_class_paren,
-  Qual_class_region,
-  Qual_class_replace,
-  Qual_class_consplice,
-  Qual_class_bond,
-  Qual_class_site,
-  Qual_class_L_R_B,
-  Qual_class_rpt,
-  Qual_class_organelle,
-  Qual_class_orgmod,
-  Qual_class_subsource,
-  Qual_class_code_break,
-  Qual_class_anti_codon,
-  Qual_class_codon,
-  Qual_class_method,
-  Qual_class_pubset,
-  Qual_class_db_xref,
-  Qual_class_seq_id,
-  Qual_class_seq_loc,
-  Qual_class_its,
-  Qual_class_sec_str,
-  Qual_class_trna_codons,
-  Qual_class_translation,
-  Qual_class_transcription,
-  Qual_class_peptide,
-  Qual_class_protnames,
-  Qual_class_illegal,
-  Qual_class_note,
-  Qual_class_rpt_unit,
-  Qual_class_product,
-  Qual_class_model_ev,
-  Qual_class_gene_syn,
-  Qual_class_locus_tag,
-  Qual_class_go
-}  QualType;
-
-/* source 'feature' */
-
-/* some qualifiers will require additional content verification not
-   explicitly indicated by the class type */
-
-typedef enum {
-  SCQUAL_acronym = 1,
-  SCQUAL_anamorph,
-  SCQUAL_authority,
-  SCQUAL_biotype,
-  SCQUAL_biovar,
-  SCQUAL_breed,
-  SCQUAL_cell_line,
-  SCQUAL_cell_type,
-  SCQUAL_chemovar,
-  SCQUAL_chromosome,
-  SCQUAL_citation,
-  SCQUAL_clone,
-  SCQUAL_clone_lib,
-  SCQUAL_common,
-  SCQUAL_common_name,
-  SCQUAL_country,
-  SCQUAL_cultivar,
-  SCQUAL_db_xref,
-  SCQUAL_org_xref,
-  SCQUAL_dev_stage,
-  SCQUAL_dosage,
-  SCQUAL_ecotype,
-  SCQUAL_endogenous_virus_name,
-  SCQUAL_environmental_sample,
-  SCQUAL_extrachrom,
-  SCQUAL_focus,
-  SCQUAL_forma,
-  SCQUAL_forma_specialis,
-  SCQUAL_frequency,
-  SCQUAL_gb_acronym,
-  SCQUAL_gb_anamorph,
-  SCQUAL_gb_synonym,
-  SCQUAL_genotype,
-  SCQUAL_germline,
-  SCQUAL_group,
-  SCQUAL_haplotype,
-  SCQUAL_ins_seq_name,
-  SCQUAL_isolate,
-  SCQUAL_isolation_source,
-  SCQUAL_lab_host,
-  SCQUAL_label,
-  SCQUAL_macronuclear,
-  SCQUAL_map,
-  SCQUAL_mol_type,
-  SCQUAL_note,
-  SCQUAL_old_lineage,
-  SCQUAL_old_name,
-  SCQUAL_organism,
-  SCQUAL_organelle,
-  SCQUAL_orgmod_note,
-  SCQUAL_pathovar,
-  SCQUAL_plasmid_name,
-  SCQUAL_plastid_name,
-  SCQUAL_pop_variant,
-  SCQUAL_rearranged,
-  SCQUAL_segment,
-  SCQUAL_seqfeat_note,
-  SCQUAL_sequenced_mol,
-  SCQUAL_serogroup,
-  SCQUAL_serotype,
-  SCQUAL_serovar,
-  SCQUAL_sex,
-  SCQUAL_spec_or_nat_host,
-  SCQUAL_specimen_voucher,
-  SCQUAL_strain,
-  SCQUAL_sub_clone,
-  SCQUAL_sub_group,
-  SCQUAL_sub_species,
-  SCQUAL_sub_strain,
-  SCQUAL_sub_type,
-  SCQUAL_subsource_note,
-  SCQUAL_synonym,
-  SCQUAL_teleomorph,
-  SCQUAL_tissue_lib,
-  SCQUAL_tissue_type,
-  SCQUAL_transgenic,
-  SCQUAL_transposon_name,
-  SCQUAL_type,
-  SCQUAL_unstructured,
-  SCQUAL_usedin,
-  SCQUAL_variety,
-  SCQUAL_zero_orgmod,
-  SCQUAL_one_orgmod,
-  SCQUAL_zero_subsrc,
-  ASN2GNBK_TOTAL_SOURCE
-}  SourceType;
-
-/* ordering arrays for qualifiers and note components */
-
-static Uint1 source_qual_order [] = {
-  SCQUAL_organism,
-
-  SCQUAL_organelle,
-
-  SCQUAL_mol_type,
-
-  SCQUAL_strain,
-  SCQUAL_sub_strain,
-  SCQUAL_variety,
-  SCQUAL_serotype,
-  SCQUAL_serovar,
-  SCQUAL_cultivar,
-  SCQUAL_isolate,
-  SCQUAL_isolation_source,
-  SCQUAL_spec_or_nat_host,
-  SCQUAL_sub_species,
-  SCQUAL_specimen_voucher,
-
-  SCQUAL_db_xref,
-  SCQUAL_org_xref,
-
-  SCQUAL_chromosome,
-
-  SCQUAL_segment,
-
-  SCQUAL_map,
-  SCQUAL_clone,
-  SCQUAL_sub_clone,
-  SCQUAL_haplotype,
-  SCQUAL_sex,
-  SCQUAL_cell_line,
-  SCQUAL_cell_type,
-  SCQUAL_tissue_type,
-  SCQUAL_clone_lib,
-  SCQUAL_dev_stage,
-  SCQUAL_ecotype,
-  SCQUAL_frequency,
-
-  SCQUAL_germline,
-  SCQUAL_rearranged,
-  SCQUAL_transgenic,
-  SCQUAL_environmental_sample,
-
-  SCQUAL_lab_host,
-  SCQUAL_pop_variant,
-  SCQUAL_tissue_lib,
-
-  SCQUAL_plasmid_name,
-  SCQUAL_transposon_name,
-  SCQUAL_ins_seq_name,
-
-  SCQUAL_country,
-
-  SCQUAL_focus,
-
-  SCQUAL_note,
-
-  SCQUAL_sequenced_mol,
-  SCQUAL_label,
-  SCQUAL_usedin,
-  SCQUAL_citation,
-  0
-};
+  if (list == NULL) return NULL;
 
-static Uint1 source_desc_note_order [] = {
-  SCQUAL_seqfeat_note,
-  SCQUAL_orgmod_note,
-  SCQUAL_subsource_note,
-
-  SCQUAL_type,
-  SCQUAL_sub_type,
-  SCQUAL_serogroup,
-  SCQUAL_pathovar,
-  SCQUAL_chemovar,
-  SCQUAL_biovar,
-  SCQUAL_biotype,
-  SCQUAL_group,
-  SCQUAL_sub_group,
-  SCQUAL_common,
-  SCQUAL_acronym,
-  SCQUAL_dosage,
-
-  SCQUAL_authority,
-  SCQUAL_forma,
-  SCQUAL_forma_specialis,
-  SCQUAL_synonym,
-  SCQUAL_anamorph,
-  SCQUAL_teleomorph,
-  SCQUAL_breed,
-
-  SCQUAL_genotype,
-  SCQUAL_plastid_name,
-
-  SCQUAL_endogenous_virus_name,
-
-  SCQUAL_common_name,
-
-  SCQUAL_zero_orgmod,
-  SCQUAL_one_orgmod,
-  SCQUAL_zero_subsrc,
-
-  /* SCQUAL_old_lineage, */
-
-  /* SCQUAL_old_name, */
-  0
-};
+  for (vnp = list, len = 0; vnp != NULL; vnp = vnp->next) {
+    str = (CharPtr) vnp->data.ptrvalue;
+    len += StringLen (str);
+  }
+  if (len == 0) return NULL;
 
-static Uint1 source_feat_note_order [] = {
-  SCQUAL_unstructured,
-
-  SCQUAL_type,
-  SCQUAL_sub_type,
-  SCQUAL_serogroup,
-  SCQUAL_pathovar,
-  SCQUAL_chemovar,
-  SCQUAL_biovar,
-  SCQUAL_biotype,
-  SCQUAL_group,
-  SCQUAL_sub_group,
-  SCQUAL_common,
-  SCQUAL_acronym,
-  SCQUAL_dosage,
-
-  SCQUAL_authority,
-  SCQUAL_forma,
-  SCQUAL_forma_specialis,
-  SCQUAL_synonym,
-  SCQUAL_anamorph,
-  SCQUAL_teleomorph,
-  SCQUAL_breed,
-
-  SCQUAL_genotype,
-  SCQUAL_plastid_name,
-
-  SCQUAL_endogenous_virus_name,
-
-  SCQUAL_seqfeat_note,
-  SCQUAL_orgmod_note,
-  SCQUAL_subsource_note,
-
-  SCQUAL_common_name,
-
-  SCQUAL_zero_orgmod,
-  SCQUAL_one_orgmod,
-  SCQUAL_zero_subsrc,
-
-  /* SCQUAL_old_lineage, */
-
-  /* SCQUAL_old_name, */
-  0
-};
+  ptr = MemNew (sizeof (Char) * (len + 2));
+  if (ptr == NULL) return NULL;
 
-typedef struct sourcequal {
-  CharPtr     name;
-  Uint1       qualclass;
-} SourceQual, PNTR SourceQualPtr;
-
-static SourceQual asn2gnbk_source_quals [ASN2GNBK_TOTAL_SOURCE] = {
-  { "",                     Qual_class_ignore    },
-  { "acronym",              Qual_class_orgmod    },
-  { "anamorph",             Qual_class_orgmod    },
-  { "authority",            Qual_class_orgmod    },
-  { "biotype",              Qual_class_orgmod    },
-  { "biovar",               Qual_class_orgmod    },
-  { "breed",                Qual_class_orgmod    },
-  { "cell_line",            Qual_class_subsource },
-  { "cell_type",            Qual_class_subsource },
-  { "chemovar",             Qual_class_orgmod    },
-  { "chromosome",           Qual_class_subsource },
-  { "citation",             Qual_class_pubset    },
-  { "clone",                Qual_class_subsource },
-  { "clone_lib",            Qual_class_subsource },
-  { "common",               Qual_class_orgmod    },
-  { "common",               Qual_class_string    },
-  { "country",              Qual_class_subsource },
-  { "cultivar",             Qual_class_orgmod    },
-  { "db_xref",              Qual_class_db_xref   },
-  { "db_xref",              Qual_class_db_xref   },
-  { "dev_stage",            Qual_class_subsource },
-  { "dosage",               Qual_class_orgmod    },
-  { "ecotype",              Qual_class_orgmod    },
-  { "endogenous_virus",     Qual_class_subsource },
-  { "environmental_sample", Qual_class_subsource },
-  { "extrachromosomal",     Qual_class_boolean   },
-  { "focus",                Qual_class_boolean   },
-  { "forma",                Qual_class_orgmod    },
-  { "forma_specialis",      Qual_class_orgmod    },
-  { "frequency",            Qual_class_subsource },
-  { "gb_acronym",           Qual_class_orgmod    },
-  { "gb_anamorph",          Qual_class_orgmod    },
-  { "gb_synonym",           Qual_class_orgmod    },
-  { "genotype",             Qual_class_subsource },
-  { "germline",             Qual_class_subsource },
-  { "group",                Qual_class_orgmod    },
-  { "haplotype",            Qual_class_subsource },
-  { "insertion_seq",        Qual_class_subsource },
-  { "isolate",              Qual_class_orgmod    },
-  { "isolation_source",     Qual_class_subsource },
-  { "lab_host",             Qual_class_subsource },
-  { "label",                Qual_class_label     },
-  { "macronuclear",         Qual_class_boolean   },
-  { "map",                  Qual_class_subsource },
-  { "mol_type",             Qual_class_string    },
-  { "note",                 Qual_class_note      },
-  { "old_lineage",          Qual_class_orgmod    },
-  { "old_name",             Qual_class_orgmod    },
-  { "organism",             Qual_class_string    },
-  { "organelle",            Qual_class_organelle },
-  { "orgmod_note",          Qual_class_orgmod    },
-  { "pathovar",             Qual_class_orgmod    },
-  { "plasmid",              Qual_class_subsource },
-  { "plastid",              Qual_class_subsource },
-  { "pop_variant",          Qual_class_subsource },
-  { "rearranged",           Qual_class_subsource },
-  { "segment",              Qual_class_subsource },
-  { "seqfeat_note",         Qual_class_string    },
-  { "sequenced_mol",        Qual_class_quote     },
-  { "serogroup",            Qual_class_orgmod    },
-  { "serotype",             Qual_class_orgmod    },
-  { "serovar",              Qual_class_orgmod    },
-  { "sex",                  Qual_class_subsource },
-  { "specific_host",        Qual_class_orgmod    },
-  { "specimen_voucher",     Qual_class_orgmod    },
-  { "strain",               Qual_class_orgmod    },
-  { "sub_clone",            Qual_class_subsource },
-  { "subgroup",             Qual_class_orgmod    },
-  { "sub_species",          Qual_class_orgmod    },
-  { "sub_strain",           Qual_class_orgmod    },
-  { "subtype",              Qual_class_orgmod    },
-  { "subsource_note",       Qual_class_subsource },
-  { "synonym",              Qual_class_orgmod    },
-  { "teleomorph",           Qual_class_orgmod    },
-  { "tissue_lib",           Qual_class_subsource },
-  { "tissue_type",          Qual_class_subsource },
-  { "transgenic",           Qual_class_subsource },
-  { "transposon",           Qual_class_subsource },
-  { "type",                 Qual_class_orgmod    },
-  { "unstructured",         Qual_class_valnode   },
-  { "usedin",               Qual_class_quote     },
-  { "variety",              Qual_class_orgmod    },
-  { "?",                    Qual_class_orgmod    },
-  { "?",                    Qual_class_orgmod    },
-  { "?",                    Qual_class_subsource },
-};
+  for (vnp = list, tmp = ptr; vnp != NULL; vnp = vnp->next) {
+    str = (CharPtr) vnp->data.ptrvalue;
+    tmp = StringMove (tmp, str);
+  }
 
-static Int2 subSourceToSourceIdx [30] = {
-  SCQUAL_zero_subsrc,
-  SCQUAL_chromosome,
-  SCQUAL_map,
-  SCQUAL_clone,
-  SCQUAL_sub_clone,
-  SCQUAL_haplotype,
-  SCQUAL_genotype,
-  SCQUAL_sex,
-  SCQUAL_cell_line,
-  SCQUAL_cell_type,
-  SCQUAL_tissue_type,
-  SCQUAL_clone_lib,
-  SCQUAL_dev_stage,
-  SCQUAL_frequency,
-  SCQUAL_germline,
-  SCQUAL_rearranged,
-  SCQUAL_lab_host,
-  SCQUAL_pop_variant,
-  SCQUAL_tissue_lib,
-  SCQUAL_plasmid_name,
-  SCQUAL_transposon_name,
-  SCQUAL_ins_seq_name,
-  SCQUAL_plastid_name,
-  SCQUAL_country,
-  SCQUAL_segment,
-  SCQUAL_endogenous_virus_name,
-  SCQUAL_transgenic,
-  SCQUAL_environmental_sample,
-  SCQUAL_isolation_source,
-  SCQUAL_subsource_note
-};
+  return ptr;
+}
 
-typedef enum {
-  FTQUAL_allele = 1,
-  FTQUAL_anticodon,
-  FTQUAL_bond,
-  FTQUAL_bond_type,
-  FTQUAL_bound_moiety,
-  FTQUAL_cds_product,
-  FTQUAL_citation,
-  FTQUAL_clone,
-  FTQUAL_coded_by,
-  FTQUAL_codon,
-  FTQUAL_codon_start,
-  FTQUAL_cons_splice,
-  FTQUAL_db_xref,
-  FTQUAL_derived_from,
-  FTQUAL_direction,
-  FTQUAL_EC_number,
-  FTQUAL_evidence,
-  FTQUAL_exception,
-  FTQUAL_exception_note,
-  FTQUAL_figure,
-  FTQUAL_frequency,
-  FTQUAL_function,
-  FTQUAL_gene,
-  FTQUAL_gene_desc,
-  FTQUAL_gene_allele,
-  FTQUAL_gene_map,
-  FTQUAL_gene_syn,
-  FTQUAL_gene_syn_refseq,
-  FTQUAL_gene_note,
-  FTQUAL_gene_xref,
-  FTQUAL_go_component,
-  FTQUAL_go_function,
-  FTQUAL_go_process,
-  FTQUAL_heterogen,
-  FTQUAL_illegal_qual,
-  FTQUAL_insertion_seq,
-  FTQUAL_label,
-  FTQUAL_locus_tag,
-  FTQUAL_map,
-  FTQUAL_maploc,
-  FTQUAL_mod_base,
-  FTQUAL_modelev,
-  FTQUAL_note,
-  FTQUAL_number,
-  FTQUAL_operon,
-  FTQUAL_organism,
-  FTQUAL_partial,
-  FTQUAL_PCR_conditions,
-  FTQUAL_peptide,
-  FTQUAL_phenotype,
-  FTQUAL_product,
-  FTQUAL_product_quals,
-  FTQUAL_prot_activity,
-  FTQUAL_prot_comment,
-  FTQUAL_prot_EC_number,
-  FTQUAL_prot_note,
-  FTQUAL_prot_method,
-  FTQUAL_prot_conflict,
-  FTQUAL_prot_desc,
-  FTQUAL_prot_missing,
-  FTQUAL_prot_name,
-  FTQUAL_prot_names,
-  FTQUAL_protein_id,
-  FTQUAL_pseudo,
-  FTQUAL_region,
-  FTQUAL_region_name,
-  FTQUAL_replace,
-  FTQUAL_rpt_family,
-  FTQUAL_rpt_type,
-  FTQUAL_rpt_unit,
-  FTQUAL_rrna_its,
-  FTQUAL_sec_str_type,
-  FTQUAL_selenocysteine,
-  FTQUAL_selenocysteine_note,
-  FTQUAL_seqfeat_note,
-  FTQUAL_site,
-  FTQUAL_site_type,
-  FTQUAL_standard_name,
-  FTQUAL_transcription,
-  FTQUAL_transcript_id,
-  FTQUAL_transcript_id_note, /* !!! remove October 15, 2003 !!! */
-  FTQUAL_transl_except,
-  FTQUAL_transl_table,
-  FTQUAL_translation,
-  FTQUAL_transposon,
-  FTQUAL_trna_aa,
-  FTQUAL_trna_codons,
-  FTQUAL_usedin,
-  FTQUAL_xtra_prod_quals,
-  ASN2GNBK_TOTAL_FEATUR
-}  FtQualType;
-
-/* ordering arrays for qualifiers and note components */
-
-static Uint1 feat_qual_order [] = {
-  FTQUAL_partial,
-  FTQUAL_gene,
-
-  FTQUAL_locus_tag,
-  FTQUAL_gene_syn_refseq,
-
-  FTQUAL_gene_allele,
-
-  FTQUAL_operon,
-
-  FTQUAL_product,
-
-  FTQUAL_prot_EC_number,
-  FTQUAL_prot_activity,
-
-  FTQUAL_standard_name,
-  FTQUAL_coded_by,
-  FTQUAL_derived_from,
-
-  FTQUAL_prot_name,
-  FTQUAL_region_name,
-  FTQUAL_bond_type,
-  FTQUAL_site_type,
-  FTQUAL_sec_str_type,
-  FTQUAL_heterogen,
-
-  FTQUAL_note, 
-  FTQUAL_citation,
-
-  FTQUAL_number,
-
-  FTQUAL_pseudo,
-  FTQUAL_selenocysteine,
-
-  FTQUAL_codon_start,
-
-  FTQUAL_anticodon,
-  FTQUAL_bound_moiety,
-  FTQUAL_clone,
-  FTQUAL_cons_splice,
-  FTQUAL_direction,
-  FTQUAL_function,
-  FTQUAL_evidence,
-  FTQUAL_exception,
-  FTQUAL_frequency,
-  FTQUAL_EC_number,
-  FTQUAL_gene_map,
-  FTQUAL_allele,
-  FTQUAL_map,
-  FTQUAL_mod_base,
-  FTQUAL_PCR_conditions,
-  FTQUAL_phenotype,
-  FTQUAL_rpt_family,
-  FTQUAL_rpt_type,
-  FTQUAL_rpt_unit,
-  FTQUAL_insertion_seq,
-  FTQUAL_transposon,
-  FTQUAL_usedin,
-
-  FTQUAL_illegal_qual,
-
-  FTQUAL_replace,
-
-  FTQUAL_transl_except,
-  FTQUAL_transl_table,
-  FTQUAL_codon,
-  FTQUAL_organism,
-  FTQUAL_label,
-  FTQUAL_cds_product,
-  FTQUAL_protein_id,
-  FTQUAL_transcript_id,
-  FTQUAL_db_xref, 
-  FTQUAL_gene_xref,
-  FTQUAL_translation,
-  FTQUAL_transcription,
-  FTQUAL_peptide,
-  0
-};
 
-/*
-prot_names after seqfeat_note - gi|4210642|emb|AJ005084.1|HBVAJ5084
-prot_conflict after prot_desc - gi|61183|emb|V01135.1|PIVM02
-figure after prot_desc - gi|400553|gb|S64006.1|
-seqfeat_note after prot_desc - gi|431713|gb|L20354.1|STVPATPOLB
-  but prot_desc after seqfeat_note - AF252556.1
-prot_names after figure - gi|234022|gb|S56149.1|S56149
-seqfeat_note after prot_conflict after figure - gi|234046|gb|S51392.1|S51392
-prot_method after prot_comment (descriptor) after prot_note after prot_desc
-region after seqfeat_note - gi|6554164|gb|AF043644.3|AF043644
-prot_desc after prot_names - gi|6581069|gb|AF202541.1|AF202541 - cannot do !!!
-gene_syn after gene_desc - gi|3386543|gb|AF079528.1|AF079528
-pseudo after note - gi|6598562|gb|AC006419.3|AC006419
-*/
+NLM_EXTERN void AddValNodeString (
+  ValNodePtr PNTR head,
+  CharPtr prefix,
+  CharPtr string,
+  CharPtr suffix
+)
 
-static Uint1 feat_note_order [] = {
-  FTQUAL_transcript_id_note, /* !!! remove October 15, 2003 !!! */
-  FTQUAL_gene_desc,
-  FTQUAL_gene_syn,
-  FTQUAL_trna_codons,
-  FTQUAL_prot_desc,
-  FTQUAL_prot_note,
-  FTQUAL_prot_comment,
-  FTQUAL_prot_method,
-  FTQUAL_figure,
-  FTQUAL_maploc,
-  FTQUAL_prot_conflict,
-  FTQUAL_prot_missing,
-  FTQUAL_seqfeat_note,
-  FTQUAL_exception_note,
-  FTQUAL_region,
-  FTQUAL_selenocysteine_note,
-  FTQUAL_prot_names,
-  FTQUAL_bond,
-  FTQUAL_site,
-  FTQUAL_rrna_its,
-  FTQUAL_xtra_prod_quals,
-  FTQUAL_modelev,
-  /* GO terms appear as own qualifiers in RefSeq records, Sequin or Dump mode */
-  FTQUAL_go_component,
-  FTQUAL_go_function,
-  FTQUAL_go_process,
-  0
-};
+{
+  Char     buf [256];
+  CharPtr  freeme = NULL;
+  size_t   len;
+  CharPtr  newstr;
+  CharPtr  strptr;
 
-typedef struct featurqual {
-  CharPtr     name;
-  Uint1       qualclass;
-} FeaturQual, PNTR FeaturQualPtr;
-
-static FeaturQual asn2gnbk_featur_quals [ASN2GNBK_TOTAL_FEATUR] = {
-  { "",               Qual_class_ignore        },
-  { "allele",         Qual_class_quote         },
-  { "anticodon",      Qual_class_anti_codon    },
-  { "bond",           Qual_class_bond          },
-  { "bond_type",      Qual_class_bond          },
-  { "bound_moiety",   Qual_class_quote         },
-  { "product",        Qual_class_string        },
-  { "citation",       Qual_class_pubset        },
-  { "clone",          Qual_class_quote         },
-  { "coded_by",       Qual_class_seq_loc       },
-  { "codon",          Qual_class_codon         },
-  { "codon_start",    Qual_class_int           },
-  { "cons_splice",    Qual_class_consplice     },
-  { "db_xref",        Qual_class_db_xref       },
-  { "derived_from",   Qual_class_seq_loc       },
-  { "direction",      Qual_class_L_R_B         },
-  { "EC_number",      Qual_class_EC_quote      },
-  { "evidence",       Qual_class_evidence      },
-  { "exception",      Qual_class_string        },
-  { "exception_note", Qual_class_string        },
-  { "figure",         Qual_class_string        },
-  { "frequency",      Qual_class_quote         },
-  { "function",       Qual_class_quote         },
-  { "gene",           Qual_class_sgml          },
-  { "gene_desc",      Qual_class_string        },
-  { "allele",         Qual_class_string        },
-  { "map",            Qual_class_string        },
-  { "gene_syn",       Qual_class_gene_syn      },
-  { "synonym",        Qual_class_gene_syn      },
-  { "gene_note",      Qual_class_string        },
-  { "db_xref",        Qual_class_db_xref       },
-  { "go_component",   Qual_class_go            },
-  { "go_function",    Qual_class_go            },
-  { "go_process",     Qual_class_go            },
-  { "heterogen",      Qual_class_string        },
-  { "illegal",        Qual_class_illegal       },
-  { "insertion_seq",  Qual_class_quote         },
-  { "label",          Qual_class_label         },
-  { "locus_tag",      Qual_class_locus_tag     },
-  { "map",            Qual_class_quote         },
-  { "maploc",         Qual_class_string        },
-  { "mod_base",       Qual_class_noquote       },
-  { "model_evidence", Qual_class_model_ev      },
-  { "note",           Qual_class_note          },
-  { "number",         Qual_class_number        },
-  { "operon",         Qual_class_quote         },
-  { "organism",       Qual_class_quote         },
-  { "partial",        Qual_class_boolean       },
-  { "PCR_conditions", Qual_class_quote         },
-  { "peptide",        Qual_class_peptide       },
-  { "phenotype",      Qual_class_quote         },
-  { "product",        Qual_class_product       },
-  { "product",        Qual_class_quote         },
-  { "function",       Qual_class_valnode       },
-  { "prot_comment",   Qual_class_string        },
-  { "EC_number",      Qual_class_EC_valnode    },
-  { "prot_note",      Qual_class_string        },
-  { "prot_method",    Qual_class_method        },
-  { "prot_conflict",  Qual_class_string        },
-  { "prot_desc",      Qual_class_string        },
-  { "prot_missing",   Qual_class_string        },
-  { "name",           Qual_class_tilde         },
-  { "prot_names",     Qual_class_protnames     },
-  { "protein_id",     Qual_class_seq_id        },
-  { "pseudo",         Qual_class_boolean       },
-  { "region",         Qual_class_region        },
-  { "region_name",    Qual_class_string        },
-  { "replace",        Qual_class_replace       },
-  { "rpt_family",     Qual_class_quote         },
-  { "rpt_type",       Qual_class_rpt           },
-  { "rpt_unit",       Qual_class_rpt_unit      },
-  { "rrna_its",       Qual_class_its           },
-  { "sec_str_type",   Qual_class_sec_str       },
-  { "selenocysteine", Qual_class_boolean       },
-  { "selenocysteine", Qual_class_string        },
-  { "seqfeat_note",   Qual_class_string        },
-  { "site",           Qual_class_site          },
-  { "site_type",      Qual_class_site          },
-  { "standard_name",  Qual_class_quote         },
-  { "transcription",  Qual_class_transcription },
-  { "transcript_id",  Qual_class_seq_id        },
-  { "tscpt_id_note",  Qual_class_seq_id        }, /* !!! remove October 15, 2003 !!! */
-  { "transl_except",  Qual_class_code_break    },
-  { "transl_table",   Qual_class_int           },
-  { "translation",    Qual_class_translation   },
-  { "transposon",     Qual_class_quote         },
-  { "trna_aa",        Qual_class_ignore        },
-  { "trna_codons",    Qual_class_trna_codons   },
-  { "usedin",         Qual_class_paren         },
-  { "xtra_products",  Qual_class_xtraprds      }
-};
+  len = StringLen (prefix) + StringLen (string) + StringLen (suffix);
+  if (len == 0) return;
 
-static Boolean AllowedValQual (Uint2 featureKey, FtQualType qualKey);
+  if (len < sizeof (buf)) {
 
+    /* if new string fits in stack buffer, no need to allocate */
 
-/* ********************************************************************** */
+    MemSet ((Pointer) buf, 0, sizeof (buf));
+    newstr = buf;
 
-/* URLs */
+  } else {
 
-#define MAX_WWWBUF 328
+    /* new string bigger than stack buffer, so allocate sufficient string */
 
-static Char link_feat [MAX_WWWBUF];
-#define DEF_LINK_FEAT  "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
+    newstr = (CharPtr) MemNew (sizeof (Char) * (len + 2));
+    if (newstr == NULL) return;
 
-static Char link_seq [MAX_WWWBUF];
-#define DEF_LINK_SEQ  "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
+    /* allocated string will be freed at end of function */
 
-static Char link_wgs [MAX_WWWBUF];
-#define DEF_LINK_WGS  "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?"
+    freeme = newstr;
+  }
 
-static Char link_omim [MAX_WWWBUF];
-#define DEF_LINK_OMIM "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id="
+  strptr = newstr;
 
-static Char ref_link [MAX_WWWBUF];
-#define DEF_LINK_REF  "http://www.ncbi.nlm.nih.gov/RefSeq/"
+  if (prefix != NULL) {
+    strptr = StringMove (strptr, prefix);
+  }
 
-static Char nt_link [MAX_WWWBUF];
-#define DEF_LINK_NT  "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?view=graph&val="
+  if (string != NULL) {
+    strptr = StringMove (strptr, string);
+  }
 
-static Char doc_link [MAX_WWWBUF];
-#define DEF_LINK_DOC  "http://www.ncbi.nlm.nih.gov/genome/guide/build.html"
+  if (suffix != NULL) {
+    strptr = StringMove (strptr, suffix);
+  }
 
-static Char ev_link [MAX_WWWBUF];
-#define DEF_LINK_EV  "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?"
+  /* currently just makes a valnode list, to be enhanced later */
 
-static Char ec_link [MAX_WWWBUF];
-#define DEF_LINK_EC "http://www.expasy.ch/cgi-bin/nicezyme.pl?"
+  ValNodeCopyStr (head, 0, newstr);
 
-static Char link_tax [MAX_WWWBUF];
-#define DEF_LINK_TAX "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?"
+  /* if large string was allocated, free it now */
 
-static Char link_ff [MAX_WWWBUF];
-#define DEF_LINK_FF  "/cgi-bin/Entrez/getfeat?"
+  if (freeme != NULL) {
+    MemFree (freeme);
+  }
+}
 
-static Char link_muid [MAX_WWWBUF];
-#define DEF_LINK_MUID  "/entrez/utils/qmap.cgi?"
 
-static Char link_ace [MAX_WWWBUF];
-#define DEF_LINK_ACE  "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=gene&q="
+NLM_EXTERN void FFAddString_NoRedund (
+  StringItemPtr unique,
+  CharPtr prefix,
+  CharPtr string,
+  CharPtr suffix
+)
+{
+  CharPtr    str = string;
+  Int4       foundPos = 0;
+  Boolean    wholeWord = FALSE;
 
-static Char link_code [MAX_WWWBUF];
-#define DEF_LINK_CODE "http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?"
+  if ( StringHasNoText(prefix)  &&
+       StringHasNoText(string)  &&
+       StringHasNoText(suffix)  ) return;
 
-static Char link_fly [MAX_WWWBUF];
-#define DEF_LINK_FLY "http://flybase.bio.indiana.edu/.bin/fbidq.html?"
+  if (StringNICmp (string, "tRNA-", 5) == 0) {
+    str = string+5;
+    }
 
-static Char link_fly_fban [MAX_WWWBUF];
-#define DEF_LINK_FBAN "http://www.fruitfly.org/cgi-bin/annot/fban?"
+  while ( foundPos >= 0 && !wholeWord ) {
+    foundPos = FFStringSearch(unique, str, foundPos);
+    if ( foundPos >= 0 ) {
+      wholeWord = IsWholeWordSubstr(unique, foundPos, str);
+      foundPos += StringLen(str);
+    }
+  }
 
-static Char link_fly_fbgn [MAX_WWWBUF];
-#define DEF_LINK_FBGN "http://flybase.bio.indiana.edu/.bin/fbidq.html?"
+  if ( foundPos < 0 || !wholeWord ) {
+      FFAddTextToString(unique, prefix, string, suffix, FALSE, FALSE, TILDE_IGNORE);
+  }
+}
 
-static Char link_cog [MAX_WWWBUF];
-#define DEF_LINK_COG "http://www.ncbi.nlm.nih.gov/cgi-bin/COG/palox?"
 
-static Char link_sgd [MAX_WWWBUF];
-#define DEF_LINK_SGD "/cgi-bin/Entrez/referer?http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus="
 
-static Char link_gdb [MAX_WWWBUF];
-#define DEF_LINK_GDB "http://gdbwww.gdb.org/gdb-bin/genera/genera/hgd/DBObject/GDB:"
+/* s_AddPeriodToEnd () -- Adds a '.' to the end of a given string if */
+/*                        there is not already one there.            */
+/*                                                                   */
+/*                        Note that this adds one character to the   */
+/*                        length of the string, leading to a         */
+/*                        memory overrun if space was not previously */
+/*                        allocated for this.                        */
 
-static Char link_ck [MAX_WWWBUF];
-#define DEF_LINK_CK "http://flybane.berkeley.edu/cgi-bin/cDNA/CK_clone.pl?db=CK&dbid="
+NLM_EXTERN void s_AddPeriodToEnd (CharPtr someString)
+{
+  Int4  len;
 
-static Char link_rice [MAX_WWWBUF];
-#define DEF_LINK_RICE "http://ars-genome.cornell.edu/cgi-bin/WebAce/webace?db=ricegenes&class=Marker&object="
+  if (StringHasNoText (someString)) return;
+  len = StringLen (someString);
+  if (len < 1) return;
+  if (someString[len-1] != '.')
+    {
+      someString[len] = '.';
+      someString[len+1] = '\0';
+    }
+}
 
-static Char link_sp [MAX_WWWBUF];
-#define DEF_LINK_SP "/cgi-bin/Entrez/referer?http://expasy.hcuge.ch/cgi-bin/sprot-search-ac%3f"
+/* s_RemovePeriodFromEnd () -- If the last character in a given      */
+/*                             string is a '.', removes it.          */
 
-static Char link_pdb [MAX_WWWBUF];
-#define DEF_LINK_PDB "/cgi-bin/Entrez/referer?http://expasy.hcuge.ch/cgi-bin/get-pdb-entry%3f"
+NLM_EXTERN Boolean s_RemovePeriodFromEnd (CharPtr someString)
+{
+  Int4  len;
 
-static Char link_UniSTS [MAX_WWWBUF];
-#define DEF_LINK_UniSTS "http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid="
+  if (StringHasNoText (someString)) return FALSE;
+  len = StringLen (someString);
+  if (len < 1) return FALSE;
+  if (someString[len-1] == '.') {
+    someString[len-1] = '\0';
+    return TRUE;
+  }
+  return FALSE;
+}
 
-static Char link_dbSTS [MAX_WWWBUF];
-#define DEF_LINK_dbSTS "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
+/**/
+/*   isEllipsis () - Determines if a string ends in an ellipses */
+/**/
 
-static Char link_dbEST [MAX_WWWBUF];
-#define DEF_LINK_dbEST "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
+NLM_EXTERN Boolean IsEllipsis (
+  CharPtr str
+)
 
-static Char link_omim [MAX_WWWBUF];
-#define DEF_LINK_OMIM "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id="
+{
+  size_t   len;
+  CharPtr  ptr;
 
-static Char link_locus [MAX_WWWBUF];
-#define DEF_LINK_LOCUS "http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l="
+  if (StringHasNoText (str)) return FALSE;
+  len = StringLen (str);
+  if (len < 3) return FALSE;
+  ptr = str + len - 3;
+  return (Boolean) (ptr [0] == '.' && ptr [1] == '.' && ptr [2] == '.');
+}
 
-static Char link_snp [MAX_WWWBUF];
-#define DEF_LINK_SNP "http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs="
+NLM_EXTERN void A2GBSeqLocReplaceID (
+  SeqLocPtr newloc,
+  SeqLocPtr ajpslp
+)
 
-static Char link_ratmap [MAX_WWWBUF];
-#define DEF_LINK_RATMAP "http://ratmap.gen.gu.se/action.lasso?-database=RATMAPfmPro&-layout=Detail&-response=/RM/Detail+Format.html&-search&-recid="
+{
+  BioseqPtr  bsp;
+  SeqIdPtr   sip;
 
-static Char link_rgd [MAX_WWWBUF];
-#define DEF_LINK_RGD "http://rgd.mcw.edu/query/query.cgi?id="
+  bsp = BioseqFindFromSeqLoc (ajpslp);
+  if (bsp == NULL) return;
+  sip = SeqIdFindBest (bsp->id, 0);
+  SeqLocReplaceID (newloc, sip);
+}
 
-static Char link_mgd [MAX_WWWBUF];
-#define DEF_LINK_MGD "http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:"
+NLM_EXTERN CharPtr asn2gb_PrintDate (
+  DatePtr dp
+)
 
-static Char link_cdd [MAX_WWWBUF];
-#define DEF_LINK_CDD "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid="
+{
+  Char    buf [30];
+  size_t  len;
 
-static Char link_niaest [MAX_WWWBUF];
-#define DEF_LINK_NIAEST "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1="
+  if (dp == NULL) return NULL;
 
-static Char link_worm_base [MAX_WWWBUF];
-#define DEF_LINK_WORM_BASE "http://www.wormbase.org/db/get?class=Sequence;name="
+  if (DatePrint (dp, buf)) {
+    if (StringICmp (buf, "Not given") != 0) {
+      len = StringLen (buf);
+      if (len > 0) {
+        if (buf [len - 1] == '\n') {
+          if (buf [len - 2] == '.') {
+            buf [len - 2] = '\0';
+          } else {
+            buf [len - 1] = '\0';
+          }
+        }
+      }
+      return StringSave (buf);
+    }
+  }
 
-static Char link_worfdb [MAX_WWWBUF];
-#define DEF_LINK_WORFDB "http://worfdb.dfci.harvard.edu/search.pl?form=1&search="
+  return NULL;
+}
 
-static Char link_nextdb [MAX_WWWBUF];
-#define DEF_LINK_NEXTDB "http://nematode.lab.nig.ac.jp/cgi-bin/db/ShowGeneInfo.sh?celk="
+static CharPtr month_names [] = {
+  "JAN", "FEB", "MAR", "APR", "MAY", "JUN",
+  "JUL", "AUG", "SEP", "OCT", "NOV", "DEC",
+  "??"
+};
 
-static Char link_imgt [MAX_WWWBUF];
-#define DEF_LINK_IMGT "http://imgt.cines.fr:8104/cgi-bin/IMGTlect.jv?query=202+"
+NLM_EXTERN CharPtr DateToFF (
+  CharPtr buf,
+  DatePtr dp,
+  Boolean citSub
+)
 
-static Char link_ifo [MAX_WWWBUF];
-#define DEF_LINK_IFO "http://www.ifo.or.jp/index_e.html"
+{
+  Int2  day;
+  Int2  month;
+  Int2  year;
 
-static Char link_jcm [MAX_WWWBUF];
-#define DEF_LINK_JCM "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM="
+  if (buf != NULL) {
+    *buf = '\0';
+  }
+  if (dp == NULL) return NULL;
 
-static Char link_isfinder [MAX_WWWBUF];
-#define DEF_LINK_ISFINDER "http://www-is.biotoul.fr/scripts/is/is_spec.idc?name="
+  if (dp->data [0] == 0) {
 
-static Char link_gabi [MAX_WWWBUF];
-#define DEF_LINK_GABI "https://gabi.rzpd.de/cgi-bin-protected/GreenCards.pl.cgi?Mode=ShowBioObject&BioObjectName="
+    StringCpy (buf, dp->str);
 
-static Char link_fantom [MAX_WWWBUF];
-#define DEF_LINK_FANTOM "http://fantom.gsc.riken.go.jp/db/view/main.cgi?masterid="
+  } else if (dp->data [0] == 1) {
 
-static Char link_interpro [MAX_WWWBUF];
-#define DEF_LINK_INTERPRO "http://www.ebi.ac.uk/interpro/ISearch?mode=ipr&query="
+    year = 1900 + (Int2) dp->data [1];
+    month = (Int2) dp->data [2];
+    day = (Int2) dp->data [3];
 
-static Char link_genedb [MAX_WWWBUF];
-#define DEF_LINK_GENEDB "http://www.genedb.org/genedb/Dispatcher?formType=navBar&submit=Search+for&organism=All%3Apombe%3Acerevisiae%3Adicty%3Aasp%3Atryp%3Aleish%3Amalaria%3Astyphi%3Aglossina&desc=yes&ohmr=%2F&name="
+    if (citSub) {
+      if (month < 1 || month > 12) {
+        month = 13;
+      }
+      if (day < 1 || day > 31) {
+        day = 0;
+      }
+    } else {
+      if (month < 1 || month > 12) {
+        month = 1;
+      }
+      if (day < 1 || day > 31) {
+        day = 1;
+      }
+    }
 
-static Char link_zfin [MAX_WWWBUF];
-#define DEF_LINK_ZFIN "http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID="
+    if (day < 1) {
+      sprintf (buf, "??-%s-%ld",
+               month_names [month-1], (long) year);
+    } else if (day < 10) {
+      sprintf (buf, "0%ld-%s-%ld",
+               (long) day, month_names [month-1], (long) year);
+    } else {
+      sprintf(buf, "%ld-%s-%ld",
+               (long) day, month_names [month-1], (long) year);
+    }
+  }
 
-static Char link_rebase [MAX_WWWBUF];
-#define DEF_LINK_REBASE "http://rebase.neb.com/rebase/enz/"
+  return buf;
+}
 
-/* utility functions */
 
-static StringItemPtr FFGetString (IntAsn2gbJobPtr ajp)
+NLM_EXTERN StringItemPtr FFGetString (IntAsn2gbJobPtr ajp)
 
 {
   StringItemPtr  sip;
@@ -1260,7 +401,7 @@ static StringItemPtr FFGetString (IntAsn2gbJobPtr ajp)
   return sip;
 }
 
-static void FFRecycleString (IntAsn2gbJobPtr ajp, StringItemPtr ffstring)
+NLM_EXTERN void FFRecycleString (IntAsn2gbJobPtr ajp, StringItemPtr ffstring)
 
 {
   StringItemPtr  nxt;
@@ -1280,7 +421,7 @@ static void FFRecycleString (IntAsn2gbJobPtr ajp, StringItemPtr ffstring)
   ffstring->curr = NULL;
 }
 
-static void FFAddOneChar (
+NLM_EXTERN void FFAddOneChar (
   StringItemPtr sip, 
   Char ch,
   Boolean convertQuotes
@@ -1302,11 +443,11 @@ static void FFAddOneChar (
   current->pos++;
 }
 
-static void FFAddNewLine(StringItemPtr ffstring) {
+NLM_EXTERN void FFAddNewLine(StringItemPtr ffstring) {
   FFAddOneChar(ffstring, '\n', FALSE);
 }
 
-static void FFAddNChar (
+NLM_EXTERN void FFAddNChar (
   StringItemPtr sip, 
   Char ch,
   Int4 n,
@@ -1321,7 +462,7 @@ static void FFAddNChar (
 }
   
 
-static void FFExpandTildes (StringItemPtr sip, CharPtr PNTR cpp) {
+NLM_EXTERN void FFExpandTildes (StringItemPtr sip, CharPtr PNTR cpp) {
   Char replace = **cpp;
 
   if ( **cpp == '~' ) {
@@ -1337,7 +478,7 @@ static void FFExpandTildes (StringItemPtr sip, CharPtr PNTR cpp) {
 }
 
 
-static void FFReplaceTildesWithSpaces (StringItemPtr ffstring, CharPtr PNTR cpp) {
+NLM_EXTERN void FFReplaceTildesWithSpaces (StringItemPtr ffstring, CharPtr PNTR cpp) {
   Char replace = **cpp, lookahead;
   CharPtr cptr = *cpp;
   
@@ -1363,7 +504,7 @@ static void FFReplaceTildesWithSpaces (StringItemPtr ffstring, CharPtr PNTR cpp)
   FFAddOneChar(ffstring, replace, FALSE);
 }
 
-static void FFOldExpand (StringItemPtr sip, CharPtr PNTR cpp) {
+NLM_EXTERN void FFOldExpand (StringItemPtr sip, CharPtr PNTR cpp) {
   /* "~" -> "\n", "~~" or "~~ ~~" -> "\n\n" */ 
   CharPtr cp = *cpp;
   Char current = *cp;
@@ -1399,7 +540,44 @@ static void FFOldExpand (StringItemPtr sip, CharPtr PNTR cpp) {
   }
 }
 
-static void AddStringWithTildes (StringItemPtr ffstring, CharPtr string)
+NLM_EXTERN void AddCommentStringWithTildes (StringItemPtr ffstring, CharPtr string)
+{
+/* One "~" is a  new line, "~~" or "~~ ~~" means 2 returns */       
+
+    /* Int2  i; */
+
+    while (*string != '\0') {
+        if (*string == '`' && *(string+1) == '~') {
+            FFAddOneChar(ffstring, '~', FALSE);
+            string += 2;
+        } else if (*string == '~') {
+            FFAddOneChar(ffstring, '\n', FALSE);
+            string++;
+            if (*string == '~') {
+                /*
+                for (i = 0; i < 12; i++) {
+                    FFAddOneChar(ffstring, ' ', FALSE);
+                }
+                */
+                FFAddOneChar(ffstring, '\n', FALSE);
+                string++;
+            if (*string == ' ' && *(string+1) == '~' && *(string+2) == '~') {
+                    string += 3;
+            }
+          }
+        } else if (*string == '\"') {   
+            *string = '\'';
+            FFAddOneChar(ffstring, *string, FALSE);
+            string++;
+        } else {  
+            FFAddOneChar(ffstring, *string, FALSE);
+            string++;
+        }
+    }
+}    /* AddCommentStringWithTildes */
+
+
+NLM_EXTERN void AddStringWithTildes (StringItemPtr ffstring, CharPtr string)
 {
 /* One "~" is a  new line, "~~" or "~~ ~~" means 2 returns */       
 
@@ -1429,7 +607,7 @@ static void AddStringWithTildes (StringItemPtr ffstring, CharPtr string)
 }    /* AddStringWithTildes */
 
 
-static void FFProcessTildes (StringItemPtr sip, CharPtr PNTR cpp, Int2 tildeAction) {
+NLM_EXTERN void FFProcessTildes (StringItemPtr sip, CharPtr PNTR cpp, Int2 tildeAction) {
     
   switch (tildeAction) {
 
@@ -1452,7 +630,7 @@ static void FFProcessTildes (StringItemPtr sip, CharPtr PNTR cpp, Int2 tildeActi
   }
 }
 
-static void FFAddPeriod (StringItemPtr sip) {
+NLM_EXTERN void FFAddPeriod (StringItemPtr sip) {
   Int4 i;
   Char ch  = '\0';
   StringItemPtr riter = sip->curr, prev;
@@ -1491,7 +669,7 @@ static void FFAddPeriod (StringItemPtr sip) {
   }
 }
 
-static void FFAddOneString (
+NLM_EXTERN void FFAddOneString (
   StringItemPtr sip, 
   CharPtr string,
   Boolean addPeriod, 
@@ -1517,10 +695,7 @@ static void FFAddOneString (
   }
 }
 
-static Boolean GetWWW (IntAsn2gbJobPtr ajp);
-static Boolean FFIsStartOfLink (StringItemPtr iter, Int4 pos);
-
-static void FFCatenateSubString (
+NLM_EXTERN void FFCatenateSubString (
   StringItemPtr dest,
   StringItemPtr start_sip, Int4 start_pos,
   StringItemPtr end_sip, Int4 end_pos
@@ -1596,7 +771,7 @@ static void FFCatenateSubString (
 }
 
 
-static CharPtr FFToCharPtr (StringItemPtr sip) {
+NLM_EXTERN CharPtr FFToCharPtr (StringItemPtr sip) {
   Int4 size = 0, i;
   StringItemPtr iter;
   CharPtr result, temp;
@@ -1623,7 +798,7 @@ static CharPtr FFToCharPtr (StringItemPtr sip) {
 
 /* word wrap functions */
 
-static void FFSkipLink (StringItemPtr PNTR iterp, Int4Ptr ip) {
+NLM_EXTERN void FFSkipLink (StringItemPtr PNTR iterp, Int4Ptr ip) {
   StringItemPtr iter = *iterp;
   Int4 i = *ip;
 
@@ -1645,14 +820,13 @@ static void FFSkipLink (StringItemPtr PNTR iterp, Int4Ptr ip) {
   *ip = i;
 }
 
-static Boolean FFIsStartOfLink (StringItemPtr iter, Int4 pos)  {
+NLM_EXTERN Boolean FFIsStartOfLink (StringItemPtr iter, Int4 pos)  {
   static CharPtr start_link = "<A HREF";
   static CharPtr end_link = "</A>";
   Int4 start_len = StringLen(start_link);
   Int4 end_len = StringLen(end_link);
   Char temp[10];
   Int4 i;
-  StringItemPtr current = NULL;
 
   if ( iter == NULL || pos >= iter->pos ) return FALSE;
   if ( iter->buf[pos] != '<' ) return FALSE;
@@ -1683,13 +857,13 @@ static Boolean FFIsStartOfLink (StringItemPtr iter, Int4 pos)  {
 }
 
 
-static void FFSavePosition(StringItemPtr ffstring, StringItemPtr PNTR bufptr, Int4 PNTR posptr) {
+NLM_EXTERN void FFSavePosition(StringItemPtr ffstring, StringItemPtr PNTR bufptr, Int4 PNTR posptr) {
   *bufptr = ffstring->curr;
   *posptr = ffstring->curr->pos;
 }
 
 
-static void FFTrim (
+NLM_EXTERN void FFTrim (
     StringItemPtr ffstring,
     StringItemPtr line_start,
     Int4 line_pos,
@@ -1752,7 +926,8 @@ static void FFTrim (
 /* already exists in the line, in such case we break at the 'new-line'       */
 /* spaces, dashes and new-lines will be broken at that character wheras for  */
 /* commas we break at the character following the comma.                     */
-static void FFCalculateLineBreak (
+
+NLM_EXTERN void FFCalculateLineBreak (
   StringItemPtr PNTR break_sip, Int4 PNTR break_pos,
   Int4 init_indent, Int4 visible
 )
@@ -1876,7 +1051,7 @@ static void FFCalculateLineBreak (
   }
 }
 
-static void FFLineWrap (
+NLM_EXTERN void FFLineWrap (
   StringItemPtr dest, 
   StringItemPtr src, 
   Int4 init_indent,
@@ -1935,7 +1110,7 @@ static void FFLineWrap (
 
 /* === */
 
-static void FFStartPrint (
+NLM_EXTERN void FFStartPrint (
   StringItemPtr sip,
   FmtType format,
   Int4 gb_init_indent,
@@ -1962,7 +1137,7 @@ static void FFStartPrint (
   }
 }
 
-static void FFAddTextToString (
+NLM_EXTERN void FFAddTextToString (
   StringItemPtr ffstring, 
   CharPtr prefix,
   CharPtr string,
@@ -1983,7 +1158,7 @@ static void FFAddTextToString (
 }
    
 
-static CharPtr FFEndPrint (
+NLM_EXTERN CharPtr FFEndPrint (
   IntAsn2gbJobPtr ajp,
   StringItemPtr ffstring,
   FmtType format,
@@ -2010,7 +1185,7 @@ static CharPtr FFEndPrint (
   return result;
 }
 
-static Uint4 FFLength(StringItemPtr ffstring) {
+NLM_EXTERN Uint4 FFLength(StringItemPtr ffstring) {
   Uint4 len = 0;
   StringItemPtr current;
 
@@ -2022,7 +1197,7 @@ static Uint4 FFLength(StringItemPtr ffstring) {
 }
 
 
-static Char FFCharAt(StringItemPtr ffstring, Uint4 pos) {
+NLM_EXTERN Char FFCharAt(StringItemPtr ffstring, Uint4 pos) {
   Uint4 count = 0, inbufpos;
   StringItemPtr current = NULL;
 
@@ -2041,7 +1216,7 @@ static Char FFCharAt(StringItemPtr ffstring, Uint4 pos) {
 }
 
 
-static Char FFFindChar (
+NLM_EXTERN Char FFFindChar (
   StringItemPtr ffstring,   /* StringItem to search in */
   StringItemPtr start_buf,  /* the position of the last char searched for (buffer) */
   Uint4 start_pos,          /* the position of the last char searched for (pos) */
@@ -2086,7 +1261,7 @@ static Char FFFindChar (
   return result;
 }
 
-static Boolean FFEmpty(StringItemPtr ffstring) {
+NLM_EXTERN Boolean FFEmpty(StringItemPtr ffstring) {
   if ( ffstring != NULL && ffstring->pos != 0 ) {
     return FALSE;
   }
@@ -2182,7 +1357,7 @@ static void ComputeGoodSuffix(const CharPtr pattern, Uint4 good_suffix[])
  * searches for a pattern in a StringItem.
  * Using the Boyer-Moore algorithm for the search.
  */
-static Int4 FFStringSearch (
+NLM_EXTERN Int4 FFStringSearch (
   StringItemPtr text,
   const CharPtr pattern,
   Uint4 position )
@@ -2227,7 +1402,8 @@ static Int4 FFStringSearch (
 /*                         word or phrase -- i.e. is it both         */
 /*                         preceded and followed by white space.     */
 /*                                                                   */
-static Boolean IsWholeWordSubstr (
+
+NLM_EXTERN Boolean IsWholeWordSubstr (
   StringItemPtr searchStr,
   Uint4 foundPos,
   CharPtr subStr
@@ -2258,8576 +1434,9 @@ static Boolean IsWholeWordSubstr (
 }
 
 
-/* www utility functions */
-
-static Boolean GetWWW (IntAsn2gbJobPtr ajp) {
-    return ajp->www;
-}
-
-static void FiniWWW (IntAsn2gbJobPtr ajp) {
-    ajp->www = FALSE;
-}
-
-static void InitWWW (IntAsn2gbJobPtr ajp)
-{
-  ajp->www = TRUE;
-
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FEAT", DEF_LINK_FEAT, link_feat, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_WGS", DEF_LINK_WGS, link_wgs, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_OMIM", DEF_LINK_OMIM, link_omim, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_REF", DEF_LINK_REF, ref_link, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_NT", DEF_LINK_NT, nt_link, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_DOC", DEF_LINK_DOC, doc_link, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_EV", DEF_LINK_EV, ev_link, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_EC", DEF_LINK_EC, ec_link, 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_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, 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_SEQ", DEF_LINK_SEQ, link_seq, 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);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FLY", DEF_LINK_FLY, link_fly, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_COG", DEF_LINK_COG, link_cog, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SGD", DEF_LINK_SGD, link_sgd, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SGD", DEF_LINK_GDB, link_gdb, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_CK", DEF_LINK_CK, link_ck, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_RICE", DEF_LINK_RICE, link_rice, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SP", DEF_LINK_SP, link_sp, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_PDB", DEF_LINK_PDB, link_pdb, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_OMIM", DEF_LINK_OMIM, link_omim, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_UniSTS", DEF_LINK_UniSTS, link_UniSTS, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_dbSTS", DEF_LINK_dbSTS, link_dbSTS, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_dbEST", DEF_LINK_dbEST, link_dbEST, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_LOCUS", DEF_LINK_LOCUS, link_locus, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SNP", DEF_LINK_SNP, link_snp, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_RATMAP", DEF_LINK_RATMAP, link_ratmap, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_RGD", DEF_LINK_RGD, link_rgd, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_MGD", DEF_LINK_MGD, link_mgd, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FBGN", DEF_LINK_FBGN, link_fly_fbgn, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FBAN", DEF_LINK_FBAN, link_fly_fban, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_CDD", DEF_LINK_CDD, link_cdd, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_NIAEST", DEF_LINK_NIAEST, link_niaest, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_WORM_BASE", DEF_LINK_WORM_BASE, link_worm_base, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_WORFDB", DEF_LINK_WORFDB, link_worfdb, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_NEXTDB", DEF_LINK_NEXTDB, link_nextdb, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_IMGT", DEF_LINK_IMGT, link_imgt, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_IFO", DEF_LINK_IFO, link_ifo, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_JCM", DEF_LINK_JCM, link_jcm, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_ISFINDER", DEF_LINK_ISFINDER, link_isfinder, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_GABI", DEF_LINK_GABI, link_gabi, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FANTOM", DEF_LINK_FANTOM, link_fantom, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_INTERPRO", DEF_LINK_INTERPRO, link_interpro, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_GENEDB", DEF_LINK_GENEDB, link_genedb, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_ZFIN", DEF_LINK_ZFIN, link_zfin, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_REBASE", DEF_LINK_REBASE, link_rebase, MAX_WWWBUF);
-}
-
-
-static void FF_www_gcode (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  CharPtr gcode
-)
-{
-
-  if ( GetWWW(ajp) ) {
-    FFAddOneString(ffstring, "<a href=", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, link_code, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, "mode=c#SG", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, gcode, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneChar(ffstring, '>', FALSE);  
-    FFAddOneString(ffstring, gcode, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-  } else {
-    FFAddOneString(ffstring, gcode, FALSE, FALSE, TILDE_IGNORE);
-  }
-}
-
-static void FF_AddECnumber (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  CharPtr str
-)
-{
-  if ( GetWWW(ajp) ) {
-    FFAddOneString(ffstring, "<a href=", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, ec_link, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneChar(ffstring, '>', FALSE);  
-    FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-  } else {
-    FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
-  }
-}
-
-
-
-static void FF_www_featloc(StringItemPtr ffstring, CharPtr loc)
-{
-  CharPtr ptr;
-
-  if (loc == NULL) return;
-
-  for ( ptr = loc; *ptr != '\0'; ++ptr ) {
-    switch (*ptr) {
-    case '<' :
-      /*FFAddOneString(ffstring, "<", FALSE, FALSE, TILDE_IGNORE);*/
-      FFAddOneString(ffstring, "&lt;", FALSE, FALSE, TILDE_IGNORE);
-      break;
-    case '>' :
-      /*FFAddOneString(ffstring, ">", FALSE, FALSE, TILDE_IGNORE);*/
-      FFAddOneString(ffstring, "&gt;", FALSE, FALSE, TILDE_IGNORE);
-      break;
-    default:
-      FFAddOneChar(ffstring, *ptr, FALSE);
-      break;
-    }
-  }
-}
-
-
-static void FF_www_db_xref_std (
-  StringItemPtr ffstring,
-  CharPtr db,
-  CharPtr identifier,
-  CharPtr link
-)
-{
-  while (*identifier == ' ')
-    identifier++;
-
-  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, "<a href=", link, identifier, FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, ">", identifier, "</a>", FALSE, FALSE, TILDE_IGNORE);
-}
-
-static void FF_www_db_xref_fly (
-  StringItemPtr ffstring,
-  CharPtr db, 
-  CharPtr identifier
-)
-{
-  CharPtr link = link_fly;
-  
-  if ( StringStr(identifier, "FBa") != NULL ) {
-    link = link_fly_fban;
-  }
-  if ( StringStr(identifier, "FBg") != NULL ) {
-    link = link_fly_fbgn;
-  }
-
-  FF_www_db_xref_std(ffstring, db, identifier, link);
-}
-
-static void FF_www_db_xref_mgd (
-  StringItemPtr ffstring,
-  CharPtr db, 
-  CharPtr identifier
-)
-{
-  if (StringNICmp (identifier, "MGI:", 4) == 0) {
-    identifier += 4;
-  }
-
-  FF_www_db_xref_std(ffstring, "MGI", identifier, link_mgd);
-}
-
-static void FF_www_db_xref_pid(
-  StringItemPtr ffstring,
-  CharPtr db, 
-  CharPtr identifier
-)
-{
-  if ( *identifier != 'g' ) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_seq);
-    return;
-  }
-  ++identifier;
-
-  FFAddTextToString(ffstring, NULL, db, ":g", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, "<a href=", link_seq, "val=", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, identifier, ">", identifier, FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-}
-
-/*prefix = "<a href=%sval=gnl|dbest|%s>"; */
-static void FF_www_db_xref_dbEST(
-  StringItemPtr ffstring,
-  CharPtr db, 
-  CharPtr identifier
-)
-{
-  while (*identifier == ' ')
-    identifier++;
-
-  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, "<a href=", link_dbEST, "val=gnl|dbest|", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, identifier, ">", identifier, FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-}
-
-static void FF_www_db_xref_dbSTS(
-  StringItemPtr ffstring,
-  CharPtr db, 
-  CharPtr identifier
-)
-{
-  while (*identifier == ' ')
-    identifier++;
-
-  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, "<a href=", link_dbSTS, "val=gnl|dbsst|", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, identifier, ">", identifier, FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-}
-
-static void FF_www_db_xref_niaEST(
-  StringItemPtr ffstring,
-  CharPtr db, 
-  CharPtr identifier
-)
-{
-  while (*identifier == ' ')
-    identifier++;
-
-  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, "<a href=", link_niaest, identifier, FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, "&val=1>", FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, identifier, FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-}
-
-
-static void FF_www_db_xref_ifo(
-  StringItemPtr ffstring,
-  CharPtr db, 
-  CharPtr identifier
-)
-{
-  while (*identifier == ' ')
-    identifier++;
-
-  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, "<a href=", link_ifo, ">", FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, identifier, FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-}
-
-
-static void FF_www_db_xref_gdb(
-  StringItemPtr ffstring,
-  CharPtr db, 
-  CharPtr identifier
-)
-{
-  CharPtr start;
-  Char id[20], PNTR idp = id;
-
-  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
-
-  if ( (start = StringStr(identifier, "G00-")) != NULL ) {
-    /* G00-id-id */
-    start += StringLen("G00-");
-    while ( *start != '\0' ) {
-      if ( *start != '-' ) {
-        *idp++ = *start++;
-      } else {
-        *start++;
-      }
-    }
-    *idp = '\0';
-    FFAddTextToString(ffstring, "<a href=", link_gdb, id, FALSE, FALSE, TILDE_IGNORE);  
-    FFAddTextToString(ffstring, ">", identifier, "</a>", FALSE, FALSE, TILDE_IGNORE);
-  } else if ( IS_DIGIT(*identifier) ) {
-    /* id */
-    FFAddTextToString(ffstring, "<a href=", link_gdb, identifier, FALSE, FALSE, TILDE_IGNORE);  
-    FFAddTextToString(ffstring, ">", identifier, "</a>", FALSE, FALSE, TILDE_IGNORE);
-  } else {
-    FFAddOneString(ffstring, identifier, FALSE, FALSE, TILDE_IGNORE);
-  }
-}
-
-static void FF_www_db_xref_rebase (
-  StringItemPtr ffstring,
-  CharPtr db,
-  CharPtr identifier
-)
-{
-  while (*identifier == ' ')
-    identifier++;
-
-  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, "<a href=", link_rebase, identifier, FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, ".html>", identifier, "</a>", FALSE, FALSE, TILDE_IGNORE);
-}
-
-
-static void Do_www_db_xref(
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  CharPtr db, CharPtr identifier
-)
-{
-  if ( ffstring == NULL || db == NULL || identifier == NULL ) return;
-
-  if ( StringCmp(db, "FLYBASE") == 0) {
-    FF_www_db_xref_fly(ffstring, db, identifier);
-  } else if ( StringCmp(db , "COG") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_cog);
-  } else if ( StringCmp(db , "UniSTS") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_UniSTS);
-  } else if ( StringCmp(db , "LocusID") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_locus);
-  } else if ( StringCmp(db , "InterimID") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_locus);
-  } else if ( StringCmp(db , "MIM") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_omim);
-  } else if ( StringCmp(db , "SGD") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_sgd);
-  } else if ( StringCmp(db , "IMGT/LIGM") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_imgt);
-  } else if ( StringCmp(db , "CK") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_ck);
-  } else if ( StringCmp(db , "RiceGenes") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_rice);
-  } else if ( StringCmp(db , "dbSNP") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_snp);
-  } else if ( StringCmp(db , "RATMAP") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_ratmap);
-  } else if ( StringCmp(db , "RGD") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_rgd);
-  } else if ( StringCmp(db , "MGD") == 0) {
-    FF_www_db_xref_mgd(ffstring, db, identifier);
-  } else if ( StringCmp(db , "CDD") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_cdd);
-  } else if ( StringCmp(db , "JCM") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_jcm);
-  } else if ( StringCmp(db , "ISFinder") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_isfinder);
-  } else if ( StringCmp(db , "GABI") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_gabi);
-  } else if ( StringCmp(db , "ZFIN") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_zfin);
-  } else if ( StringCmp(db , "FANTOM_DB") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_fantom);
-  } else if ( StringCmp(db , "Interpro") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_interpro);
-  } else if ( StringCmp(db , "GeneDB") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_genedb);
-  } else if ( StringCmp(db , "PID") == 0) {
-    FF_www_db_xref_pid(ffstring, db, identifier);
-  } else if ( StringCmp(db , "dbEST") == 0) {
-    FF_www_db_xref_dbEST(ffstring, db, identifier);
-  } else if ( StringCmp(db , "dbSTS") == 0) {
-    FF_www_db_xref_dbSTS(ffstring, db, identifier);
-  } else if ( StringCmp(db , "niaEST") == 0) {
-    FF_www_db_xref_niaEST(ffstring, db, identifier);
-  } else if ( StringCmp(db , "WormBase") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_worm_base);
-  } else if ( StringCmp(db , "AceView/WormGenes") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_ace);
-  } else if ( StringCmp(db , "WorfDB") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_worfdb);
-  } else if ( StringCmp(db , "NextDB") == 0) {
-    FF_www_db_xref_std(ffstring, db, identifier, link_nextdb);
-  } else if ( StringCmp(db , "IFO") == 0) {
-    FF_www_db_xref_ifo(ffstring, db, identifier);
-  } else if ( StringCmp(db , "GDB") == 0) {
-    FF_www_db_xref_gdb(ffstring, db, identifier);
-  } else if ( StringCmp(db , "REBASE") == 0) {
-    FF_www_db_xref_rebase(ffstring, db, identifier);
-
-  } else {  
-    /* default: no link just the text */
-    FFAddTextToString(ffstring, db, ":", identifier, FALSE, FALSE, TILDE_IGNORE);
-  }             
-}
-
-static void FF_www_db_xref(
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  CharPtr db, CharPtr identifier
-)
-{
-  if ( ffstring == NULL || db == NULL || identifier == NULL ) return;
-  
-  if ( GetWWW(ajp) ) {
-    Do_www_db_xref (ajp, ffstring, db, identifier);
-  } else { /* not in www mode */
-    if (StringCmp(db , "MGD") == 0) {
-      if (StringNICmp (identifier, "MGI:", 4) == 0) {
-        identifier += 4;
-      }
-      FFAddTextToString(ffstring, "MGI", ":", identifier, FALSE, FALSE, TILDE_IGNORE);
-    } else {
-      FFAddTextToString(ffstring, db, ":", identifier, FALSE, FALSE, TILDE_IGNORE);
-    }
-  }
-}
-
-/* public function to get URLs for collaboration-approved db_xrefs */
-
-static Boolean links_loaded = FALSE;
-
-NLM_EXTERN CharPtr asn2gnbk_dbxref (
-  DbtagPtr dbt
-)
-
-{
-  IntAsn2gbJobPtr  ajp;
-  Char             buf [80];
-  StringItemPtr    ffstring;
-  ObjectIdPtr      oip;
-  CharPtr          ptr;
-  CharPtr          str;
-  CharPtr          tmp;
-
-  if (dbt == NULL) return NULL;
-  if (StringHasNoText (dbt->db)) return NULL;
-  oip = dbt->tag;
-  if (oip == NULL) return NULL;
-
-  if (! StringHasNoText (oip->str)) {
-    if (StringLen (dbt->db) + StringLen (oip->str) < 80) {
-      sprintf (buf, "%s", oip->str);
-    }
-  } else {
-    sprintf (buf, "%ld", (long) oip->id);
-  }
-
-  ajp = (IntAsn2gbJobPtr) MemNew (sizeof (IntAsn2gbJob));
-  if (ajp == NULL) return NULL;
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return NULL;
-
-  if (! links_loaded) {
-    InitWWW (ajp);
-    links_loaded = TRUE;
-  }
-  ajp->www = TRUE;
-
-  Do_www_db_xref (ajp, ffstring, dbt->db, buf);
-
-  ajp->www = FALSE;
-
-  str = FFToCharPtr (ffstring);
-
-  FFRecycleString (ajp, ffstring);
-  MemFree (ajp);
-
-  tmp = StringChr (str, '<');
-  if (tmp != NULL) {
-    ptr = StringSave (tmp);
-    tmp = StringChr (ptr, '>');
-    if (tmp != NULL) {
-      tmp++;
-      *tmp = '\0';
-    }
-    MemFree (str);
-    str = ptr;
-  } else {
-    str = MemFree (str);
-  }
-
-  return str;
-}
-
-static void FF_www_protein_id(
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  CharPtr seqid
-)
-{
-
-  if ( GetWWW(ajp) ) {
-    FFAddOneString(ffstring, "<a href=", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, link_seq, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, "val=", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, seqid, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneChar(ffstring, '>', FALSE);  
-    FFAddOneString(ffstring, seqid, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-  } else {
-    FFAddOneString(ffstring, seqid, FALSE, FALSE, TILDE_IGNORE);
-  }
-}
-
-static void  FF_www_muid(
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  Int4 muid
-)
-{
-  Char numbuf[40];
-  
-  if ( GetWWW(ajp) ) {
-    FFAddTextToString(ffstring, "<a href=", link_muid, NULL, FALSE, FALSE, TILDE_IGNORE);
-    sprintf(numbuf, "%ld", (long)muid);
-    FFAddTextToString(ffstring, "uid=", numbuf, "&form=6&db=m&Dopt=r>", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, numbuf, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-  } else {
-    sprintf(numbuf, "%ld", (long)muid);
-    FFAddOneString(ffstring, numbuf, FALSE, FALSE, TILDE_IGNORE);
-  }
-}
-
-static void FF_www_accession (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  CharPtr cstring
-)
-{
-  if (cstring == NULL || ffstring == NULL) return;
-
-  if ( GetWWW(ajp) ) {
-    FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
-    FFAddTextToString(ffstring, "val=", cstring, ">", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, cstring, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-  } else {
-    FFAddOneString(ffstring, cstring, FALSE, FALSE, TILDE_IGNORE);
-  }
-  return;
-}
-
-static CharPtr TxtSave (CharPtr text, size_t len)
-
-{
-   CharPtr str = NULL;
-
-   if ((text == NULL) || (len == 0))
-      return str;
-
-   str = MemNew((size_t)(len + 1));
-   MemCopy(str, text, (size_t)len);
-
-   return (str);
-}
-
-static Boolean FF_www_dbsource(
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  CharPtr str,
-  Boolean first,
-  Uint1 choice
-)
-{
-  CharPtr  temp, end, text, loc, link=NULL;
-  Int2 j;
-
-  if( GetWWW(ajp) ) {
-    if (choice == SEQID_PIR /*|| choice == SEQID_SWISSPROT */) {
-      link = link_seq;
-    } else if (choice == SEQID_PDB || choice == SEQID_PRF) {
-      link = link_seq;
-    } else if (choice == SEQID_EMBL || choice == SEQID_GENBANK || 
-        choice == SEQID_DDBJ || choice == SEQID_GIBBSQ || 
-        choice == SEQID_GIBBMT || choice == SEQID_GI || 
-        choice == SEQID_GIIM || choice == SEQID_OTHER ||
-        choice == SEQID_TPG || choice == SEQID_TPE || choice == SEQID_TPD)  {
-      link = link_seq;
-    } else {
-      AddStringWithTildes(ffstring, str);
-      return TRUE;
-    }
-  
-    if ((text = StringStr(str, "accession")) != NULL) {
-      end = text + 9;
-      j = 9;
-      while (*end == ' ') {
-        ++end;
-        j++;
-      }
-      if (first == FALSE) {
-        FFAddOneString(ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
-      }
-      loc = TxtSave (str, end-str - j);
-      FFAddOneString(ffstring, loc, FALSE, FALSE, TILDE_IGNORE);
-      MemFree (loc);
-      for (; text != end; ++text ) {
-        FFAddOneChar(ffstring, *text, FALSE);
-      }
-
-      temp = text;
-      end += StringLen(text) - 1;
-      if ( *end != ';' ) {
-        ++end;
-      }
-
-      FFAddTextToString(ffstring, "<a href=", link, "val=", FALSE, FALSE, TILDE_IGNORE);
-      for (text = temp; text != end; ++text ) {
-        FFAddOneChar(ffstring, *text, FALSE);
-      }
-      FFAddOneString(ffstring, ">", FALSE, FALSE, TILDE_IGNORE);
-
-      text = temp;
-      FFAddOneString(ffstring, text, FALSE, FALSE, TILDE_IGNORE);
-      FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-    } else {
-      if (first == FALSE) {
-        FFAddOneString(ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
-      }
-      FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
-    }
-  } else {
-    AddStringWithTildes(ffstring, str);
-  }
-  return TRUE;
-}
-
-
-/* old utility functions */
-
-static ValNodePtr ValNodeCopyStrToHead (ValNodePtr PNTR head, Int2 choice, CharPtr str)
-
-{
-  ValNodePtr newnode;
-
-  if (head == NULL || str == NULL) return NULL;
-
-  newnode = ValNodeNew (NULL);
-  if (newnode == NULL) return NULL;
-
-  newnode->choice = (Uint1) choice;
-  newnode->data.ptrvalue = StringSave (str);
-
-  newnode->next = *head;
-  *head = newnode;
-
-  return newnode;
-}
-
-/* the val node strings mechanism will be replaced by a more efficient method later  */
-
-static CharPtr MergeValNodeStrings (
-  ValNodePtr list
-)
-
-{
-  size_t      len;
-  CharPtr     ptr;
-  CharPtr     str;
-  CharPtr     tmp;
-  ValNodePtr  vnp;
-
-
-  if (list == NULL) return NULL;
-
-  for (vnp = list, len = 0; vnp != NULL; vnp = vnp->next) {
-    str = (CharPtr) vnp->data.ptrvalue;
-    len += StringLen (str);
-  }
-  if (len == 0) return NULL;
-
-  ptr = MemNew (sizeof (Char) * (len + 2));
-  if (ptr == NULL) return NULL;
-
-  for (vnp = list, tmp = ptr; vnp != NULL; vnp = vnp->next) {
-    str = (CharPtr) vnp->data.ptrvalue;
-    tmp = StringMove (tmp, str);
-  }
-
-  return ptr;
-}
-
-
-static void AddValNodeString (
-  ValNodePtr PNTR head,
-  CharPtr prefix,
-  CharPtr string,
-  CharPtr suffix
-)
-
-{
-  Char     buf [256];
-  CharPtr  freeme = NULL;
-  size_t   len;
-  CharPtr  newstr;
-  CharPtr  strptr;
-
-  len = StringLen (prefix) + StringLen (string) + StringLen (suffix);
-  if (len == 0) return;
-
-  if (len < sizeof (buf)) {
-
-    /* if new string fits in stack buffer, no need to allocate */
-
-    MemSet ((Pointer) buf, 0, sizeof (buf));
-    newstr = buf;
-
-  } else {
-
-    /* new string bigger than stack buffer, so allocate sufficient string */
-
-    newstr = (CharPtr) MemNew (sizeof (Char) * (len + 2));
-    if (newstr == NULL) return;
-
-    /* allocated string will be freed at end of function */
-
-    freeme = newstr;
-  }
-
-  strptr = newstr;
-
-  if (prefix != NULL) {
-    strptr = StringMove (strptr, prefix);
-  }
-
-  if (string != NULL) {
-    strptr = StringMove (strptr, string);
-  }
-
-  if (suffix != NULL) {
-    strptr = StringMove (strptr, suffix);
-  }
-
-  /* currently just makes a valnode list, to be enhanced later */
-
-  ValNodeCopyStr (head, 0, newstr);
-
-  /* if large string was allocated, free it now */
-
-  if (freeme != NULL) {
-    MemFree (freeme);
-  }
-}
-
-
-static void FFAddString_NoRedund (
-  StringItemPtr unique,
-  CharPtr prefix,
-  CharPtr string,
-  CharPtr suffix
-)
-{
-  CharPtr    str = string;
-  Int4       foundPos = 0;
-  Boolean    wholeWord = FALSE;
-
-  if ( StringHasNoText(prefix)  &&
-       StringHasNoText(string)  &&
-       StringHasNoText(suffix)  ) return;
-
-  if (StringNICmp (string, "tRNA-", 5) == 0) {
-    str = string+5;
-    }
-
-  while ( foundPos >= 0 && !wholeWord ) {
-    foundPos = FFStringSearch(unique, str, foundPos);
-    if ( foundPos >= 0 ) {
-      wholeWord = IsWholeWordSubstr(unique, foundPos, str);
-      foundPos += StringLen(str);
-    }
-  }
-
-  if ( foundPos < 0 || !wholeWord ) {
-      FFAddTextToString(unique, prefix, string, suffix, FALSE, FALSE, TILDE_IGNORE);
-  }
-}
-
-
-
-/* s_AddPeriodToEnd () -- Adds a '.' to the end of a given string if */
-/*                        there is not already one there.            */
-/*                                                                   */
-/*                        Note that this adds one character to the   */
-/*                        length of the string, leading to a         */
-/*                        memory overrun if space was not previously */
-/*                        allocated for this.                        */
-
-static void s_AddPeriodToEnd (CharPtr someString)
-{
-  Int4  len;
-
-  if (StringHasNoText (someString)) return;
-  len = StringLen (someString);
-  if (len < 1) return;
-  if (someString[len-1] != '.')
-    {
-      someString[len] = '.';
-      someString[len+1] = '\0';
-    }
-}
-
-/* s_RemovePeriodFromEnd () -- If the last character in a given      */
-/*                             string is a '.', removes it.          */
-
-static Boolean s_RemovePeriodFromEnd (CharPtr someString)
-{
-  Int4  len;
-
-  if (StringHasNoText (someString)) return FALSE;
-  len = StringLen (someString);
-  if (len < 1) return FALSE;
-  if (someString[len-1] == '.') {
-    someString[len-1] = '\0';
-    return TRUE;
-  }
-  return FALSE;
-}
-
-/**/
-/*   isEllipsis () - Determines if a string ends in an ellipses */
-/**/
-
-static Boolean IsEllipsis (
-  CharPtr str
-)
-
-{
-  size_t   len;
-  CharPtr  ptr;
-
-  if (StringHasNoText (str)) return FALSE;
-  len = StringLen (str);
-  if (len < 3) return FALSE;
-  ptr = str + len - 3;
-  return (Boolean) (ptr [0] == '.' && ptr [1] == '.' && ptr [2] == '.');
-}
-
-static void A2GBSeqLocReplaceID (
-  SeqLocPtr newloc,
-  SeqLocPtr ajpslp
-)
-
-{
-  BioseqPtr  bsp;
-  SeqIdPtr   sip;
-
-  bsp = BioseqFindFromSeqLoc (ajpslp);
-  if (bsp == NULL) return;
-  sip = SeqIdFindBest (bsp->id, 0);
-  SeqLocReplaceID (newloc, sip);
-}
-
-static CharPtr asn2gb_PrintDate (
-  DatePtr dp
-)
-
-{
-  Char    buf [30];
-  size_t  len;
-
-  if (dp == NULL) return NULL;
-
-  if (DatePrint (dp, buf)) {
-    if (StringICmp (buf, "Not given") != 0) {
-      len = StringLen (buf);
-      if (len > 0) {
-        if (buf [len - 1] == '\n') {
-          if (buf [len - 2] == '.') {
-            buf [len - 2] = '\0';
-          } else {
-            buf [len - 1] = '\0';
-          }
-        }
-      }
-      return StringSave (buf);
-    }
-  }
-
-  return NULL;
-}
-
-static CharPtr month_names [] = {
-  "JAN", "FEB", "MAR", "APR", "MAY", "JUN",
-  "JUL", "AUG", "SEP", "OCT", "NOV", "DEC",
-  "??"
-};
-
-static CharPtr DateToGB (
-  CharPtr buf,
-  DatePtr dp,
-  Boolean citSub
-)
-
-{
-  Int2  day;
-  Int2  month;
-  Int2  year;
-
-  if (buf != NULL) {
-    *buf = '\0';
-  }
-  if (dp == NULL) return NULL;
-
-  if (dp->data [0] == 0) {
-
-    StringCpy (buf, dp->str);
-
-  } else if (dp->data [0] == 1) {
-
-    year = 1900 + (Int2) dp->data [1];
-    month = (Int2) dp->data [2];
-    day = (Int2) dp->data [3];
-
-    if (citSub) {
-      if (month < 1 || month > 12) {
-        month = 13;
-      }
-      if (day < 1 || day > 31) {
-        day = 0;
-      }
-    } else {
-      if (month < 1 || month > 12) {
-        month = 1;
-      }
-      if (day < 1 || day > 31) {
-        day = 1;
-      }
-    }
-
-    if (day < 1) {
-      sprintf (buf, "??-%s-%ld",
-               month_names [month-1], (long) year);
-    } else if (day < 10) {
-      sprintf (buf, "0%ld-%s-%ld",
-               (long) day, month_names [month-1], (long) year);
-    } else {
-      sprintf(buf, "%ld-%s-%ld",
-               (long) day, month_names [month-1], (long) year);
-    }
-  }
-
-  return buf;
-}
-
-
-/* ********************************************************************** */
-
-/* format functions allocate printable string for given paragraph */
-
-static CharPtr DefaultFormatBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  if (afp == NULL || bbp == NULL) return NULL;
-
-  /* default format function assumes string pre-allocated by add block function */
-
-  return StringSaveNoNull (bbp->string);
-}
-
-/* superset of http://www.ncbi.nlm.nih.gov/collab/db_xref.html and RefSeq db_xrefs */
-
-static CharPtr legalDbXrefs [] = {
-  "PIDe", "PIDd", "PIDg", "PID",
-  "AceView/WormGenes",
-  "ATCC",
-  "ATCC(in host)",
-  "ATCC(dna)",
-  "BDGP_EST",
-  "BDGP_INS",
-  "CDD",
-  "CK",
-  "COG",
-  "dbEST",
-  "dbSNP",
-  "dbSTS",
-  "ENSEMBL",
-  "ESTLIB",
-  "FANTOM_DB",
-  "FLYBASE",
-  "GABI",
-  "GDB",
-  "GeneDB",
-  "GeneID",
-  "GI",
-  "GO",
-  "GOA",
-  "IFO",
-  "IMGT/LIGM",
-  "IMGT/HLA",
-  "InterimID",
-  "Interpro",
-  "ISFinder",
-  "JCM",
-  "LocusID",
-  "MaizeDB",
-  "MGD",
-  "MGI",
-  "MIM",
-  "NextDB",
-  "niaEST",
-  "PIR",
-  "PSEUDO",
-  "RATMAP",
-  "RiceGenes",
-  "REMTREMBL",
-  "RGD",
-  "RZPD",
-  "SGD",
-  "SoyBase",
-  "SPTREMBL",
-  "SWISS-PROT",
-  "taxon",
-  "UniGene",
-  "UniSTS",
-  "WorfDB",
-  "WormBase",
-  "ZFIN",
-  NULL
-};
-
-static CharPtr legalRefSeqDbXrefs [] = {
-  "REBASE",
-  NULL
-};
-
-static CharPtr organellePrefix [] = {
-  NULL,
-  NULL,
-  "Chloroplast ",
-  "Chromoplast ",
-  "Kinetoplast ",
-  "Mitochondrion ",
-  "Plastid ",
-  NULL,
-  NULL,
-  NULL,
-  NULL,
-  NULL,
-  "Cyanelle ",
-  NULL,
-  NULL,
-  "Nucleomorph ",
-  "Apicoplast ",
-  "Leucoplast ",
-  "Proplastid ",
-  NULL
-};
-
-static CharPtr newOrganellePrefix [] = {
-  NULL,
-  NULL,
-  "chloroplast ",
-  "chromoplast ",
-  "kinetoplast ",
-  "mitochondrion ",
-  "plastid ",
-  NULL,
-  NULL,
-  NULL,
-  NULL,
-  NULL,
-  "cyanelle ",
-  NULL,
-  NULL,
-  "nucleomorph ",
-  "apicoplast ",
-  "leucoplast ",
-  "proplastid ",
-  NULL
-};
-
-static CharPtr FormatSourceBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  CharPtr            acr = NULL;
-  Boolean            addPeriod = TRUE;
-  IntAsn2gbJobPtr    ajp;
-  CharPtr            ana = NULL;
-  Asn2gbSectPtr      asp;
-  BioSourcePtr       biop = NULL;
-  CharPtr            com = NULL;
-  CharPtr            common = NULL;
-  SeqMgrDescContext  dcontext;
-  SeqMgrFeatContext  fcontext;
-  CharPtr            gbacr = NULL;
-  CharPtr            gbana = NULL;
-  GBBlockPtr         gbp = NULL;
-  GBSeqPtr           gbseq;
-  CharPtr            gbsyn = NULL;
-  Uint1              genome;
-  ValNodePtr         mod = NULL;
-  OrgModPtr          omp = NULL;
-  OrgNamePtr         onp;
-  CharPtr            organelle = NULL;
-  OrgRefPtr          orp;
-  CharPtr            prefix = " (";
-  SeqDescrPtr        sdp;
-  CharPtr            second = NULL;
-  SeqFeatPtr         sfp;
-  CharPtr            str;
-  CharPtr            syn = NULL;
-  CharPtr            taxname = NULL;
-  Boolean            using_anamorph = FALSE;
-  StringItemPtr      ffstring, temp;
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-
-  if (! StringHasNoText (bbp->string)) return StringSave (bbp->string);
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return NULL;
-
-  if (bbp->itemtype == OBJ_SEQDESC) {
-    sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext);
-    if (sdp != NULL) {
-      if (dcontext.seqdesctype == Seq_descr_source) {
-        biop = (BioSourcePtr) sdp->data.ptrvalue;
-      } else if (dcontext.seqdesctype == Seq_descr_genbank) {
-        gbp = (GBBlockPtr) sdp->data.ptrvalue;
-      }
-    }
-  } else if (bbp->itemtype == OBJ_SEQFEAT) {
-    sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
-    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_BIOSRC) {
-      biop = (BioSourcePtr) sfp->data.value.ptrvalue;
-    }
-  }
-  if (gbp != NULL) {
-    common = gbp->source;
-  }
-
-  if (biop != NULL) {
-    genome = biop->genome;
-    if (genome <= 19) {
-      if (ajp->newSourceOrg && (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT)) {
-        organelle = newOrganellePrefix [genome];
-      } else {
-        organelle = organellePrefix [genome];
-      }
-    }
-    orp = biop->org;
-    if (orp != NULL) {
-      taxname = orp->taxname;
-      common = orp->common;
-      mod = orp->mod;
-      onp = orp->orgname;
-      if (onp != NULL) {
-
-        if (ajp->newSourceOrg) {
-          for (omp = onp->mod; omp != NULL; omp = omp->next) {
-            switch (omp->subtype) {
-              case ORGMOD_common :
-                com = omp->subname;
-                break;
-              case ORGMOD_acronym :
-                acr = omp->subname;
-                break;
-              case ORGMOD_synonym :
-                syn = omp->subname;
-                break;
-              case ORGMOD_anamorph :
-                ana = omp->subname;
-                break;
-              case ORGMOD_gb_acronym :
-                gbacr = omp->subname;
-                break;
-              case ORGMOD_gb_anamorph :
-                gbana = omp->subname;
-                break;
-              case ORGMOD_gb_synonym :
-                gbsyn = omp->subname;
-                break;
-              default :
-                break;
-            }
-          }
-
-          if (StringHasNoText (second)) {
-            second = syn;
-            using_anamorph = FALSE;
-          }
-           if (StringHasNoText (second)) {
-             second = acr;
-             using_anamorph = FALSE;
-          }
-          if (StringHasNoText (second)) {
-            second = ana;
-            using_anamorph = TRUE;
-          }
-          if (StringHasNoText (second)) {
-            second = com;
-            using_anamorph = FALSE;
-          }
-
-          if (StringHasNoText (second)) {
-            second = gbsyn;
-            using_anamorph = FALSE;
-          }
-          if (StringHasNoText (second)) {
-            second = gbacr;
-            using_anamorph = FALSE;
-          }
-          if (StringHasNoText (second)) {
-            second = gbana;
-            using_anamorph = TRUE;
-          }
-
-          if (StringHasNoText (second)) {
-            second = common;
-            using_anamorph = FALSE;
-          }
-          if (using_anamorph) {
-            prefix = " (anamorph: ";
-          }
-        }
-      }
-    }
-  }
-
-  /* If the organelle prefix is already on the */
-  /* name, don't add it.                       */
-
-  if (StringNCmp (organelle, taxname, StringLen (organelle)) == 0)
-    organelle = "";
-
-  if (StringHasNoText (common)) {
-    common = taxname;
-  }
-  if (StringHasNoText (common)) {
-    common = "Unknown.";
-  }
-  if (StringHasNoText (taxname)) {
-    taxname = "Unknown.";
-  }
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-    
-    temp = FFGetString(ajp);
-
-    if (ajp->newSourceOrg) {
-
-      if (! StringHasNoText (organelle)) {
-        FFAddTextToString(temp, NULL, organelle, NULL, FALSE, FALSE, TILDE_IGNORE);
-      }
-      FFAddTextToString(temp, NULL, taxname, NULL, FALSE, FALSE, TILDE_IGNORE);
-      if (! StringHasNoText (second)) {
-        FFAddTextToString(temp, prefix, second, ")", FALSE, FALSE, TILDE_IGNORE);
-      }
-      addPeriod = FALSE;
-
-    } else {
-      FFAddTextToString(temp, NULL, common, NULL, FALSE, FALSE, TILDE_IGNORE);
-      while (mod != NULL) {
-        str = (CharPtr) mod->data.ptrvalue;
-        if (! StringHasNoText (str)) {
-          FFAddTextToString(temp, " ", str, NULL, FALSE, FALSE, TILDE_IGNORE);
-        }
-        mod = mod->next;
-      }
-    }
-
-    str = FFToCharPtr(temp);
-    if (StringCmp (str, ".") == 0) {
-      str = MemFree (str);
-    }
-    FFRecycleString(ajp, temp);
-    /* optionally populate gbseq for XML-ized GenBank format */
-
-    if (ajp->gbseq) {
-      gbseq = &asp->gbseq;
-    } else {
-      gbseq = NULL;
-    }
-
-    if (gbseq != NULL) {
-      gbseq->source = StringSave (str);
-    }
-
-    
-    FFStartPrint(ffstring, afp->format, 0, 12, "SOURCE", 12, 5, 5, "OS", TRUE);
-    if (str != NULL) {
-      FFAddTextToString(ffstring, NULL, str, NULL, addPeriod, FALSE, TILDE_TO_SPACES);
-    } else {
-      FFAddOneChar(ffstring, '.', FALSE);
-    }
-    
-    MemFree (str);
-
-  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-
-    FFStartPrint(ffstring, afp->format, 0, 12, "SOURCE", 12, 5, 5, "OS", TRUE);
-    FFAddTextToString(ffstring, organelle, taxname, NULL, FALSE, FALSE, TILDE_TO_SPACES);
-    FFAddTextToString(ffstring, " (", common, ")", FALSE, FALSE, TILDE_TO_SPACES);
-    
-  }
-  
-  str = FFEndPrint(ajp, ffstring, afp->format, 12, 12, 0, 5, "OS");
-  FFRecycleString(ajp, ffstring);
-  return str;
-}
-
-static CharPtr FormatOrganismBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  BioSourcePtr       biop = NULL;
-  Char               ch;
-  CharPtr            common = NULL;
-  DbtagPtr           dbt;
-  SeqMgrDescContext  dcontext;
-  SeqMgrFeatContext  fcontext;
-  GBSeqPtr           gbseq;
-  Uint1              genome;
-  CharPtr            lineage = NULL;
-  ObjectIdPtr        oip;
-  OrgNamePtr         onp;
-  CharPtr            organelle = NULL;
-  OrgRefPtr          orp;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp;
-  CharPtr            str;
-  Int4               taxid = -1;
-  CharPtr            taxname = NULL;
-  CharPtr            tmp;
-  CharPtr            ptr;
-  ValNodePtr         vnp;
-  StringItemPtr      ffstring, temp;
-  Char               buf [16];
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-
-
-  if (! StringHasNoText (bbp->string)) return StringSave (bbp->string);
-
-  if (bbp->itemtype == OBJ_SEQDESC) {
-    sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext);
-    if (sdp != NULL && dcontext.seqdesctype == Seq_descr_source) {
-      biop = (BioSourcePtr) sdp->data.ptrvalue;
-    }
-  } else if (bbp->itemtype == OBJ_SEQFEAT) {
-    sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
-    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_BIOSRC) {
-      biop = (BioSourcePtr) sfp->data.value.ptrvalue;
-    }
-  }
-  if (biop != NULL) {
-    genome = biop->genome;
-    if (genome <= 19) {
-      organelle = organellePrefix [genome];
-    }
-    orp = biop->org;
-    if (orp != NULL) {
-      taxname = orp->taxname;
-      common = orp->common;
-      onp = orp->orgname;
-      if (onp != NULL) {
-        lineage = onp->lineage;
-      }
-      for (vnp = orp->db; vnp != NULL; vnp = vnp->next) {
-        dbt = (DbtagPtr) vnp->data.ptrvalue;
-        if (dbt == NULL) continue;
-        if (StringCmp (dbt->db, "taxon") == 0) {
-          oip = dbt->tag;
-          if (oip != NULL) {
-            taxid = oip->id;
-          }
-        }
-      }
-    }
-  }
-
-  /* If the organelle prefix is already on the */
-  /* name, don't add it.                       */
-
-  if (StringNCmp (organelle, taxname, StringLen (organelle)) == 0)
-    organelle = "";
-
-  if (StringHasNoText (common)) {
-    common = taxname;
-  }
-  if (StringHasNoText (common)) {
-    common = "Unknown.";
-  }
-  if (StringHasNoText (taxname)) {
-    taxname = "Unknown.";
-  }
-  if (StringHasNoText (lineage)) {
-    lineage = "Unclassified.";
-  }
-
-  ffstring = FFGetString(ajp);
-  temp = FFGetString(ajp);
-  if ( ffstring == NULL || temp == NULL ) return NULL;
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-    
-    FFStartPrint(temp, afp->format, 2, 12, "ORGANISM", 12, 5, 5, "OC", FALSE);
-    if (! ajp->newSourceOrg) {
-      FFAddOneString(temp, organelle, FALSE, FALSE, TILDE_IGNORE);
-    }
-    if (StringNICmp (taxname, "Unknown", 7) != 0) {
-      if ( GetWWW(ajp) ) { 
-        if (taxid != -1) {
-          FFAddOneString(temp, "<a href=", FALSE, FALSE, TILDE_IGNORE);
-          FFAddOneString(temp, link_tax, FALSE, FALSE, TILDE_IGNORE);
-          FFAddOneString(temp, "id=", FALSE, FALSE, TILDE_IGNORE);
-          sprintf (buf, "%ld", (long) taxid);
-          FFAddOneString(temp, buf, FALSE, FALSE, TILDE_IGNORE);
-          FFAddOneString(temp, ">", FALSE, FALSE, TILDE_IGNORE);
-        } else {
-          FFAddOneString(temp, "<a href=", FALSE, FALSE, TILDE_IGNORE);
-          FFAddOneString(temp, link_tax, FALSE, FALSE, TILDE_IGNORE);
-          FFAddOneString(temp, "name=", FALSE, FALSE, TILDE_IGNORE);
-          tmp = StringSave (taxname);
-          if (tmp != NULL) {
-            ptr = tmp;
-            ch = *ptr;
-            while (ch != '\0') {
-              if (IS_WHITESP (ch)) {
-                *ptr = '+';
-              }
-              ptr++;
-              ch = *ptr;
-            }
-            FFAddOneString(temp, tmp, FALSE, FALSE, TILDE_IGNORE);
-            MemFree (tmp);
-          }
-          FFAddOneString(temp, ">", FALSE, FALSE, TILDE_IGNORE);
-        }
-        FFAddOneString(temp, taxname, FALSE, FALSE, TILDE_IGNORE);
-        FFAddOneString(temp, "</a>", FALSE, FALSE, TILDE_IGNORE);
-      } else {
-        FFAddOneString(temp, taxname, FALSE, FALSE, TILDE_IGNORE);
-      }
-    } else {
-      FFAddOneString(temp, taxname, FALSE, FALSE, TILDE_IGNORE);
-    }
-    FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-    FFRecycleString(ajp, temp);
-
-    temp = FFGetString(ajp);
-    FFStartPrint(temp, afp->format, 12, 12, NULL, 0, 5, 5, "OC", FALSE);
-    FFAddTextToString(temp, NULL, lineage, NULL, TRUE, FALSE, TILDE_TO_SPACES);
-    FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-    FFRecycleString(ajp, temp);
-    /* optionally populate gbseq for XML-ized GenBank format */
-
-    if (ajp->gbseq) {
-      gbseq = &asp->gbseq;
-    } else {
-      gbseq = NULL;
-    }
-
-    if (gbseq != NULL) {
-      temp = FFGetString(ajp);
-      if (! ajp->newSourceOrg) {
-        FFAddOneString(temp, organelle, FALSE, FALSE, TILDE_IGNORE);
-      }
-      FFAddOneString(temp, taxname, FALSE, FALSE, TILDE_IGNORE);
-      gbseq->organism = FFToCharPtr(temp);
-      gbseq->taxonomy = StringSave (lineage);
-      FFRecycleString(ajp, temp);
-    }
-
-  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-    FFStartPrint(temp, afp->format, 12, 12, NULL, 0, 5, 5, "OC", FALSE);
-    FFAddTextToString(temp, NULL, lineage, NULL, TRUE, FALSE, TILDE_TO_SPACES);
-    FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "OC");
-  }
-
-  
-  str = FFToCharPtr(ffstring);
-  FFRecycleString(ajp, ffstring);
-  return str;
-}
-
-/* format references section */
-
-static AuthListPtr GetAuthListPtr (
-  PubdescPtr pdp,
-  CitSubPtr csp
-)
-
-{
-  AuthListPtr  alp = NULL;
-  CitArtPtr    cap;
-  CitBookPtr   cbp;
-  CitGenPtr    cgp;
-  CitPatPtr    cpp;
-  ValNodePtr   vnp;
-
-  if (csp != NULL) {
-    alp = csp->authors;
-    if (alp != NULL) return alp;
-  }
-  if (pdp == NULL) return NULL;
-
-  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-    switch (vnp->choice) {
-      case PUB_Gen :
-        cgp = (CitGenPtr) vnp->data.ptrvalue;
-        if (cgp != NULL) {
-          alp = cgp->authors;
-        }
-        break;
-      case PUB_Sub :
-        csp = (CitSubPtr) vnp->data.ptrvalue;
-        if (csp != NULL) {
-          alp = csp->authors;
-        }
-        break;
-      case PUB_Article :
-        cap = (CitArtPtr) vnp->data.ptrvalue;
-        if (cap != NULL) {
-          alp = cap->authors;
-        }
-        break;
-      case PUB_Book :
-      case PUB_Proc :
-      case PUB_Man :
-        cbp = (CitBookPtr) vnp->data.ptrvalue;
-        if (cbp != NULL) {
-          alp = cbp->authors;
-        }
-        break;
-      case PUB_Patent :
-        cpp = (CitPatPtr) vnp->data.ptrvalue;
-        if (cpp != NULL) {
-          alp = cpp->authors;
-        }
-        break;
-      default :
-        break;
-    }
-
-    if (alp != NULL) return alp;
-  }
-
-  return NULL;
-}
-
-static CharPtr MakeSingleAuthorString (
-  FmtType format,
-  CharPtr prefix,
-  CharPtr name,
-  CharPtr initials,
-  CharPtr suffix,
-  IndxPtr index,
-  GBReferencePtr gbref
-)
-
-{
-  Char     ch;
-  Char     dummy [10];
-  size_t   len;
-  CharPtr  nametoindex;
-  CharPtr  ptr;
-  CharPtr  str;
-  CharPtr  tmp;
-
-  if (name == NULL) return NULL;
-
-  /* !!! clean up 'et al' as (presumably) last author !!! */
-
-  /* !!! temporary to suppress diff !!! */
-  {
-  if (StringLen (name) <= 6 &&
-      (StringNICmp (name, "et al", 5) == 0 || StringNICmp (name, "et,al", 5) == 0)) {
-    if (StringCmp (prefix, " and ") == 0) {
-      prefix = NULL;
-      dummy [0] = ' ';
-      StringNCpy_0 (dummy + 1, name, sizeof (dummy) - 1);
-      name = dummy;
-    }
-  }
-  }
-  /*
-  if (StringLen (name) <= 6 &&
-      (StringNICmp (name, "et al", 5) == 0 || StringNICmp (name, "et,al", 5) == 0)) {
-    name = "et al.";
-    if (StringCmp (prefix, " and ") == 0) {
-      prefix = ", ";
-    }
-  }
-  */
-
-  len = StringLen (name) + StringLen (initials) + StringLen (suffix) + StringLen (prefix);
-  str = MemNew (sizeof (Char) * (len + 4));
-  if (str == NULL) return NULL;
-
-  ptr = str;
-  if (! StringHasNoText (prefix)) {
-    ptr = StringMove (ptr, prefix);
-  }
-  nametoindex = ptr;
-
-  /* initials and suffix to support structured name fields */
-
-  tmp = StringMove (ptr, name);
-  if (! StringHasNoText (initials)) {
-    tmp = StringMove (tmp, ",");
-    tmp = StringMove (tmp, initials);
-  }
-  if (! StringHasNoText (suffix)) {
-    tmp = StringMove (tmp, " ");
-    tmp = StringMove (tmp, suffix);
-  }
-
-  /* optionally populate indexes for NCBI internal database */
-
-  if (index != NULL) {
-    ValNodeCopyStrToHead (&(index->authors), 0, nametoindex);
-  }
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (gbref != NULL) {
-    ValNodeCopyStr (&(gbref->authors), 0, nametoindex);
-  }
-
-  /* if embl, remove commas in individual names, starting after prefix */
-
-  if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-    tmp = ptr;
-    ch = *tmp;
-    while (ch != '\0') {
-      if (ch == ',') {
-        *tmp = ' ';
-      }
-      tmp++;
-      ch = *tmp;
-    }
-  }
-
-  return str;
-}
-
-static CharPtr GetAuthorsString (
-  FmtType format,
-  AuthListPtr alp,
-  CharPtr PNTR consortP,
-  IndxPtr index,
-  GBReferencePtr gbref
-)
-
-{
-  AuthorPtr    ap;
-  ValNodePtr   conslist;
-  Int2         count;
-  ValNodePtr   head = NULL;
-  ValNodePtr   names;
-  ValNodePtr   next;
-  NameStdPtr   nsp;
-  PersonIdPtr  pid;
-  ValNodePtr   pidlist;
-  CharPtr      prefix = NULL;
-  CharPtr      str;
-  ValNodePtr   vnp;
-
-  if (alp == NULL) return NULL;
-
-  alp = AsnIoMemCopy ((Pointer) alp,
-                      (AsnReadFunc) AuthListAsnRead,
-                      (AsnWriteFunc) AuthListAsnWrite);
-  if (alp == NULL) return NULL;
-
-  count = 0;
-  if (alp->choice == 1) {
-
-    pidlist = NULL;
-    conslist = NULL;
-
-    for (names = alp->names; names != NULL; names = names->next) {
-      ap = (AuthorPtr) names->data.ptrvalue;
-      if (ap == NULL) continue;
-      pid = ap->name;
-      if (pid == NULL) continue;
-      if (pid->choice == 2 || pid->choice == 3 || pid->choice == 4) {
-        ValNodeAddPointer (&pidlist, 0, (Pointer) pid);
-      } else if (pid->choice == 5) {
-        ValNodeAddPointer (&conslist, 0, (Pointer) pid);
-      }
-    }
-
-    for (vnp = pidlist; vnp != NULL; vnp = vnp->next) {
-      next = vnp->next;
-      if (next == NULL) {
-        if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-          if (count == 0) {
-            prefix = NULL;
-          } else {
-            prefix = " and ";
-          }
-        }
-      }
-      str = NULL;
-      pid = (PersonIdPtr) vnp->data.ptrvalue;
-      if (pid->choice == 2) {
-        nsp = (NameStdPtr) pid->data;
-        if (nsp != NULL) {
-          if (! StringHasNoText (nsp->names [0])) {
-            str = MakeSingleAuthorString (format, prefix, nsp->names [0], nsp->names [4], nsp->names [5], index, gbref);
-          } else if (! StringHasNoText (nsp->names [3])) {
-            str = MakeSingleAuthorString (format, prefix, nsp->names [3], NULL, NULL, index, gbref);
-          }
-        }
-      } else if (pid->choice == 3 || pid->choice == 4) {
-        str = MakeSingleAuthorString (format, prefix, (CharPtr) pid->data, NULL, NULL, index, gbref);
-      }
-      if (str != NULL) {
-        ValNodeAddStr (&head, 0, str);
-        count++;
-      }
-      prefix = ", ";
-    }
-
-    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);
-        }
-
-        /* optionally populate gbseq for XML-ized GenBank format */
-
-        if (gbref != NULL) {
-          gbref->consortium = StringSave (str);
-        }
-
-        str = MemFree (str);
-      }
-    }
-
-    ValNodeFree (pidlist);
-    ValNodeFree (conslist);
-
-  } else if (alp->choice == 2 || alp->choice == 3) {
-    for (vnp = alp->names; vnp != NULL; vnp = vnp->next) {
-      next = vnp->next;
-      if (next == NULL) {
-        if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-          if (count == 0) {
-            prefix = NULL;
-          } else {
-            prefix = " and ";
-          }
-        }
-      }
-      str = MakeSingleAuthorString (format, prefix, (CharPtr) vnp->data.ptrvalue, NULL, NULL, index, gbref);
-      if (str != NULL) {
-        ValNodeAddStr (&head, 0, str);
-        count++;
-      }
-      prefix = ", ";
-    }
-  }
-
-  str = MergeValNodeStrings (head);
-
-  ValNodeFreeData (head);
-
-  AuthListFree (alp);
-
-  return str;
-}
-
-/*
-Strips all spaces in string in following manner. If the function
-meet several spaces (spaces and tabs) in succession it replaces them
-with one space. Strips all spaces after '(' and before ')'
-*/
-
-static void StrStripSpaces (
-  CharPtr str
-)
-
-{
-  CharPtr  new_str;
-
-  if (str == NULL) return;
-
-  new_str = str;
-  while (*str != '\0') {
-    *new_str++ = *str;
-    if (*str == ' ' || *str == '\t' || *str == '(') {
-      for (str++; *str == ' ' || *str == '\t'; str++) continue;
-      if (*str == ')' || *str == ',') {
-        new_str--;
-      }
-    } else {
-      str++;
-    }
-  }
-  *new_str = '\0';
-}
-
-static Boolean AllCaps (
-  CharPtr p
-)
-
-{
-  if (p == NULL) return FALSE;
-
-  for (p++; p != NULL && *p != '\0'; p++) {
-    if (IS_LOWER (*p)) return FALSE;
-  }
-  return TRUE;
-}
-
-static void CleanEquals (
-  CharPtr p
-)
-
-{
-  if (p == NULL) return;
-
-  for (; *p != '\0'; p++) {
-    if (*p == '\"') {
-      *p = '\'';
-    }
-  }
-}
-
-static CharPtr GetPubTitle (
-  FmtType format,
-  PubdescPtr pdp,
-  CitSubPtr csp
-)
-
-{
-  CitArtPtr        cap;
-  CitBookPtr       cbp;
-  CitGenPtr        cgp;
-  Char             ch;
-  CitPatPtr        cpp;
-  MedlineEntryPtr  mep;
-  CharPtr          ptr;
-  CharPtr          title = NULL;
-  ValNodePtr       ttl = NULL;
-  ValNodePtr       vnp;
-
-  if (csp != NULL) {
-    if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-      title = "Direct Submission";
-      return StringSave (title);
-    } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-      return NULL;
-    }
-  }
-  if (pdp == NULL) return NULL;
-
-  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-    switch (vnp->choice) {
-      case PUB_Gen :
-        cgp = (CitGenPtr) vnp->data.ptrvalue;
-        if (cgp != NULL) {
-          if (! StringHasNoText (cgp->title)) return StringSave (cgp->title);
-          if (! StringHasNoText (cgp->cit)) {
-            ptr = StringStr (cgp->cit, "Title=\"");
-            if (ptr != NULL) {
-              title = StringSave (ptr + 7);
-              for (ptr = title; *ptr != '\0'; ptr++) {
-                if (*ptr == '"') {
-                  *ptr = '\0';
-                  break;
-                }
-              }
-              return title;
-            }
-          }
-        }
-        break;
-      case PUB_Sub :
-        csp = (CitSubPtr) vnp->data.ptrvalue;
-        if (csp != NULL) {
-          if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-            title = "Direct Submission";
-            return StringSave (title);
-          } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-            return NULL;
-          }
-        }
-        break;
-      case PUB_Medline :
-        mep = (MedlineEntryPtr) vnp->data.ptrvalue;
-        if (mep != NULL) {
-          cap = mep->cit;
-          if (cap != NULL) {
-            ttl = cap->title;
-          }
-        }
-        break;
-      case PUB_Article :
-        cap = (CitArtPtr) vnp->data.ptrvalue;
-        if (cap != NULL) {
-          ttl = cap->title;
-        }
-        break;
-      /* case PUB_Book : */
-      case PUB_Proc :
-      case PUB_Man :
-        cbp = (CitBookPtr) vnp->data.ptrvalue;
-        if (cbp != NULL) {
-          ttl = cbp->title;
-          if (ttl != NULL) {
-            title = (CharPtr) ttl->data.ptrvalue;
-            if (! StringHasNoText (title)) {
-              title = StringSave (title);
-              if (StringLen (title) > 3) {
-                ch = *title;
-                if (IS_LOWER (ch)) {
-                  *title = TO_UPPER (ch);
-                }
-                ptr = title;
-                if (AllCaps (ptr)) {
-                  for (ptr++; ptr != NULL && *ptr != '\0'; ptr++) {
-                    ch = *ptr;
-                    *ptr = TO_LOWER (ch);
-                  }
-                }
-              }
-              return title;
-            }
-          }
-        }
-        break;
-      case PUB_Patent :
-        cpp = (CitPatPtr) vnp->data.ptrvalue;
-        if (cpp != NULL) {
-          title = cpp->title;
-          if (! StringHasNoText (title)) {
-            return StringSave (title);
-          }
-        }
-        break;
-      default :
-        break;
-    }
-
-    if (ttl != NULL) {
-      title = (CharPtr) ttl->data.ptrvalue;
-      if (! StringHasNoText (title)) {
-        return StringSave (title);
-      }
-    }
-  }
-
-  return NULL;
-}
-
-static void CleanPubTitle (
-  CharPtr title
-)
-
-{
-  CharPtr  p;
-  Boolean  remove_it;
-
-  if (title == NULL) return;
-
-  CleanEquals (title);
-
-  for (p = title + StringLen (title) - 1; p > title + 2; p--) {
-    if (*p == ' ') {
-      *p = '\0';
-    } else if (*p == '.') {
-      remove_it = FALSE;
-      if (p > title + 5) {
-        if (*(p - 1) != '.' || *(p - 2) != '.') {
-          remove_it = TRUE;
-        }
-      }
-      if (remove_it) {
-        *p = '\0';
-      }
-      break;
-    } else {
-      break;
-    }
-  }
-}
-
-/*
-medline type page numbering is expanded (e.g., 125-35 -> 125-135,
-F124-34 -> F124-F134, 12a-c -> 12a-12c).
-If only one page is given, this is output without a dash.
-Expanded numbering is validated to ensure that the
-first number is smaller than or equal to the second and
-that the first letter is less than or identical to the second
-(i.e., a < c).  If the input is all letters (i.e., roman numerals)
-this is not validated.
-
-Return values:
- 0 : valid page numbering.
--1 : invalid page numbering.
-*/
-
-#define MAX_PAGE_DIGITS 12
-
-static Int2 FixPages (
-  CharPtr out_pages,
-  CharPtr in_pages
-)
-
-{
-  Boolean dash=TRUE, first_alpha;
-  Char firstbegin[MAX_PAGE_DIGITS];
-  Char secondbegin[MAX_PAGE_DIGITS];
-  Char firstend[MAX_PAGE_DIGITS];
-  Char secondend[MAX_PAGE_DIGITS];
-  Char temp[MAX_PAGE_DIGITS];
-  CharPtr alphabegin, numbegin, alphaend, numend, ptr, in=in_pages;
-  Int2 diff, index, retval=0;
-  Int2 length_nb, length_ab, length_ne, length_ae;
-  Int4 num1=0, num2=0;
-
-  if (in_pages == NULL) return retval;
-
-  while (*in != '\0')
-  {      /* Check for digits in input*/
-    if (IS_DIGIT(*in))
-      break;
-    in++;
-  }
-
-  if (*in == '\0' || (in != in_pages && *(in-1) == ' '))
-  {    /* if all letters (i.e. roman numerals), put out. */
-    out_pages = StringCpy(out_pages, in_pages);
-    return retval;
-  }
-
-  in = in_pages;
-  if (IS_DIGIT(*in))
-  {      /* Do digits come first? */
-    first_alpha = FALSE;
-    index=0;
-    while (IS_DIGIT(*in) || *in == ' ')
-    {
-      firstbegin[index] = *in;
-      if (*in != ' ')
-        index++;
-      in++;
-      if (*in == '-')
-        break;
-
-    }
-    firstbegin[index] = '\0';
-    index=0;
-    if (*in != '-')
-    {    /* After digits look for letters. */
-      while (IS_ALPHA(*in)  || *in == ' ')
-      {
-        secondbegin[index] = *in;
-        index++;
-        in++;
-        if (*in == '-')
-          break;
-      }
-    }
-    secondbegin[index] = '\0';
-    if (*in == '-')    /* if dash is not present, note */
-      in++;
-    else
-      dash=FALSE;
-    index=0;
-    while (IS_DIGIT(*in) || *in == ' ')
-    {      /* Look for digits.  */
-      firstend[index] = *in;
-      if (*in != ' ')
-        index++;
-      in++;
-    }
-    firstend[index] = '\0';
-    index=0;
-    if (*in != '\0')
-    {      /* Look for letters again. */
-      while (IS_ALPHA(*in)  || *in == ' ')
-      {
-        secondend[index] = *in;
-        index++;
-        in++;
-      }
-    }
-    secondend[index] = '\0';
-  }
-  else
-  {      /* Do letters come first? */
-    first_alpha = TRUE;
-    index=0;
-    while (IS_ALPHA(*in) || *in == ' ')
-    {
-      firstbegin[index] = *in;
-      index++;
-      in++;
-      if (*in == '-')
-        break;
-    }
-    firstbegin[index] = '\0';
-    index=0;
-    if (*in != '-')
-    {    /* After letters look for digits.   */
-      while (IS_DIGIT(*in)  || *in == ' ')
-      {
-        secondbegin[index] = *in;
-        if (*in != ' ')
-          index++;
-        in++;
-        if (*in == '-')
-          break;
-      }
-    }
-    secondbegin[index] = '\0';
-    if (*in == '-')    /* Note if dash is missing. */
-      in++;
-    else
-      dash=FALSE;
-    index=0;
-    while (IS_ALPHA(*in) || *in == ' ')
-    {    /* Look for letters again. */
-      firstend[index] = *in;
-      index++;
-      in++;
-    }
-    firstend[index] = '\0';
-    index=0;
-    if (*in != '\0')
-    {    /* Any digits here? */
-      while (IS_DIGIT(*in)  || *in == ' ')
-      {
-        secondend[index] = *in;
-        if (*in != ' ')
-          index++;
-        in++;
-      }
-    }
-    secondend[index] = '\0';
-  }
-
-  if (first_alpha)
-  {
-    alphabegin = firstbegin;
-    numbegin = secondbegin;
-    alphaend = firstend;
-    numend = secondend;
-  }
-  else
-  {
-    numbegin = firstbegin;
-    alphabegin = secondbegin;
-    numend = firstend;
-    alphaend = secondend;
-  }
-
-  length_nb = StringLen(numbegin);
-  length_ab = StringLen(alphabegin);
-  length_ne = StringLen(numend);
-  length_ae = StringLen(alphaend);
-
-  /* If no dash, but second letters or numbers present, reject. */
-  if (dash == FALSE)
-  {
-    if (length_ne != 0 || length_ae != 0)
-      retval = -1;
-  }
-  /* Check for situations like "AAA-123" or "222-ABC". */
-  if (dash == TRUE)
-  {
-    if (length_ne == 0 && length_ab == 0)
-      retval = -1;
-    else if (length_ae == 0 && length_nb == 0)
-      retval = -1;
-  }
-
-  /* The following expands "F502-512" into "F502-F512" and
-  checks, for entries like "12a-12c" that a > c.  "12aa-12ab",
-  "125G-137A", "125-G137" would be rejected. */
-  if (retval == 0)
-  {
-    if (length_ab > 0)
-    {
-      if (length_ae > 0)
-      {
-        if (StringCmp(alphabegin, alphaend) != 0)
-        {
-          if (length_ab != 1 || length_ae != 1)
-            retval = -1;
-          else if (*alphabegin > *alphaend)
-            retval = -1;
-        }
-      }
-      else
-      {
-        alphaend = alphabegin;
-        length_ae = length_ab;
-      }
-    }
-    else if (length_ae > 0)
-      retval = -1;
-  }
-
-/* The following expands "125-37" into "125-137".  */
-  if (retval == 0)
-  {
-    if (length_nb > 0)
-    {
-      if (length_ne > 0)
-      {
-        diff = length_nb - length_ne;
-        if (diff > 0)
-        {
-          index=0;
-          while (numend[index] != '\0')
-          {
-            temp[index+diff] = numend[index];
-            index++;
-          }
-          temp[index+diff] = numend[index];
-          for (index=0; index<diff; index++)
-            temp[index] = numbegin[index];
-          index=0;
-          while (temp[index] != '\0')
-          {
-            numend[index] = temp[index];
-            index++;
-          }
-          numend[index] = temp[index];
-        }
-      }
-      else
-      {
-        numend = numbegin;
-        length_ne = length_nb;
-      }
-
-    }
-    else if (length_ne > 0)
-      retval = -1;
-  /* Check that the first number is <= the second (expanded) number. */
-    if (retval == 0)
-    {
-  /*    sscanf(numbegin, "%ld", &num_type);
-      num1 = (Int4) num_type;
-      sscanf(  numend, "%ld", &num_type);
-      num2 = (Int4) num_type;
-  */
-      num1 = (Int4) atol(numbegin);
-      num2 = (Int4) atol(numend);
-      if (num2 < num1)
-        retval = -1;
-    }
-  }
-
-  if (retval == -1)
-  {
-    out_pages = StringCpy(out_pages, in_pages);
-  }
-  else
-  {
-    ptr = out_pages;
-  /* Place expanded and validated page numbers into "out_pages". */
-    if (first_alpha)
-    {
-      while (*alphabegin != '\0')
-      {
-        *ptr = *alphabegin;
-        alphabegin++;
-        ptr++;
-      }
-      while (*numbegin != '\0')
-      {
-        *ptr = *numbegin;
-        numbegin++;
-        ptr++;
-      }
-      if (dash == TRUE)
-      {
-        *ptr = '-';
-        ptr++;
-        while (*alphaend != '\0')
-        {
-          *ptr = *alphaend;
-          alphaend++;
-          ptr++;
-        }
-        while (*numend != '\0')
-        {
-          *ptr = *numend;
-          numend++;
-          ptr++;
-        }
-      }
-      *ptr = '\0';
-    }
-    else
-    {
-      while (*numbegin != '\0')
-      {
-        *ptr = *numbegin;
-        numbegin++;
-        ptr++;
-      }
-      while (*alphabegin != '\0')
-      {
-        *ptr = *alphabegin;
-        alphabegin++;
-        ptr++;
-      }
-      if (dash == TRUE)
-      {
-        *ptr = '-';
-        ptr++;
-        while (*numend != '\0')
-        {
-          *ptr = *numend;
-          numend++;
-          ptr++;
-        }
-        while (*alphaend != '\0')
-        {
-          *ptr = *alphaend;
-          alphaend++;
-          ptr++;
-        }
-      }
-      *ptr = '\0';
-    }
-  }
-  return retval;
-}
-
-/* !!! still need to add StripParanthesis equivalent !!! */
-
-static void DoSup (
-  ValNodePtr PNTR head,
-  CharPtr issue,
-  CharPtr part_sup,
-  CharPtr part_supi
-)
-
-{
-  size_t   len;
-  CharPtr  str;
-  CharPtr  temp;
-
-  len = StringLen (issue) + StringLen (part_sup) + StringLen (part_supi) + 25;
-  str = MemNew (sizeof (Char) * len);
-  if (str == NULL) return;
-  temp = str;
-
-  if (! StringHasNoText (part_sup)) {
-    *temp = ' ';
-    temp++;
-    temp = StringMove (temp, part_sup);
-  }
-  if (StringHasNoText (issue) && StringHasNoText (part_supi)) {
-    ValNodeCopyStr (head, 0, str);
-    MemFree (str);
-    return;
-  }
-  *temp = ' ';
-  temp++;
-  *temp = '(';
-  temp++;
-  if (! StringHasNoText (issue)) {
-    temp = StringMove (temp, issue);
-  }
-  if (! StringHasNoText (part_supi)) {
-    *temp = ' ';
-    temp++;
-    temp = StringMove (temp, part_supi);
-  }
-  *temp = ')';
-  temp++;
-  ValNodeCopyStr (head, 0, str);
-  MemFree (str);
-}
-
-static CharPtr FormatCitJour (
-  FmtType format,
-  Boolean citArtIsoJta,
-  CitJourPtr cjp
-)
-
-{
-  Char        buf [256];
-  DatePtr     dp;
-  ValNodePtr  head = NULL;
-  ImprintPtr  imp;
-  CharPtr     issue = NULL;
-  Char        pages [128];
-  CharPtr     part_sup = NULL;
-  CharPtr     part_supi = NULL;
-  CharPtr     rsult = NULL;
-  CharPtr     title;
-  ValNodePtr  ttl;
-  CharPtr     volume;
-  Char        year [8];
-
-  if (cjp == NULL) return NULL;
-
-  ttl = cjp->title;
-  if (ttl == NULL) return NULL;
-
-  /* always use iso_jta title if present */
-
-  while (ttl != NULL && ttl->choice != Cit_title_iso_jta) {
-    ttl = ttl->next;
-  }
-
-  /* release mode requires iso_jta title */
-
-  if (ttl == NULL) {
-    if (citArtIsoJta) return NULL;
-    ttl = cjp->title;
-  }
-
-  imp = cjp->imp;
-  if (imp == NULL) return NULL;
-
-  dp = imp->date;
-  year [0] = '\0';
-  if (dp != NULL) {
-    if (dp->data [0] == 1) {
-      if (dp->data [1] != 0) {
-        sprintf (year, " (%ld)", (long) (1900 + dp->data [1]));
-      }
-    } else {
-      StringCpy (year, " (");
-      StringNCat (year, dp->str, 4);
-      StringCat (year, ")");
-    }
-  }
-
-  if (imp->prepub == 1 || imp->prepub == 255) {
-    sprintf (buf, "Unpublished %s", year);
-    return StringSave (buf);
-  }
-
-  title = (CharPtr) ttl->data.ptrvalue;
-  if (StringLen (title) < 3) return StringSave (".");
-
-  ValNodeCopyStr (&head, 0, title);
-
-  volume = imp->volume;
-  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-    issue = imp->issue;
-    part_sup = imp->part_sup;
-    part_supi = imp->part_supi;
-  }
-  pages [0] = '\0';
-  FixPages (pages, imp->pages);
-
-  if (! StringHasNoText (volume)) {
-    AddValNodeString (&head, " ", volume, NULL);
-  }
-
-  if ((! StringHasNoText (volume)) || (! StringHasNoText (pages))) {
-    DoSup (&head, issue, part_sup, part_supi);
-  }
-
-  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-    if (! StringHasNoText (pages)) {
-      AddValNodeString (&head, ", ", pages, NULL);
-    }
-  } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-    if (! StringHasNoText (pages)) {
-      AddValNodeString (&head, ":", pages, NULL);
-    } else if (imp->prepub == 2 || (StringHasNoText (volume))) {
-      ValNodeCopyStr (&head, 0, " 0:0-0");
-    }
-  }
-
-  ValNodeCopyStr (&head, 0, year);
-
-  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-    if (imp->prepub == 2) {
-      ValNodeCopyStr (&head, 0, " In press");
-    }
-  }
-
-  rsult = MergeValNodeStrings (head);
-  ValNodeFreeData (head);
-
-  return rsult;
-}
-
-static CharPtr MakeAffilStr (
-  AffilPtr afp
-)
-
-{
-  ValNodePtr  head = NULL;
-  CharPtr     prefix = "";
-  CharPtr     rsult = NULL;
-
-  if (afp == NULL) return NULL;
-
-  if (! StringHasNoText (afp->affil)) {
-    ValNodeCopyStr (&head, 0, afp->affil);
-    prefix = ", ";
-  }
-
-  if (afp->choice == 2) {
-    if (! StringHasNoText (afp->div)) {
-      AddValNodeString (&head, prefix, afp->div, NULL);
-      prefix = ", ";
-    }
-    if (! StringHasNoText (afp->street)) {
-      AddValNodeString (&head, prefix, afp->street, NULL);
-      prefix = ", ";
-    }
-    if (! StringHasNoText (afp->city)) {
-      AddValNodeString (&head, prefix, afp->city, NULL);
-      prefix = ", ";
-    }
-    if (! StringHasNoText (afp->sub)) {
-      AddValNodeString (&head, prefix, afp->sub, NULL);
-      prefix = ", ";
-    }
-    if (! StringHasNoText (afp->country)) {
-      AddValNodeString (&head, prefix, afp->country, NULL);
-      prefix = ", ";
-    }
-  }
-
-  rsult = MergeValNodeStrings (head);
-  ValNodeFreeData (head);
-
-  return rsult;
-}
-
-static CharPtr GetAffil (
-  AffilPtr afp
-)
-
-{
-  Boolean need_comma=FALSE;
-  CharPtr string=NULL, temp, ptr;
-  Char ch;
-  Int2 aflen=15;
-
-  if (afp == NULL) return NULL;
-  if (afp) {
-    if (afp -> choice == 1){
-      if (afp -> affil){
-        aflen += StringLen(afp -> affil);
-      }
-    }else if (afp -> choice == 2){
-      aflen += StringLen (afp -> affil) +
-      StringLen (afp -> div) +
-      StringLen (afp -> city) +
-      StringLen (afp -> sub) +
-      StringLen (afp -> street) +
-      StringLen (afp -> country) + StringLen(afp->postal_code);
-    }
-
-    temp = string = MemNew(aflen);
-
-    if ( afp -> choice == 1){
-       if (afp -> affil){
-        ptr = afp->affil;
-        while ((*temp = *ptr) != '\0')
-        {
-          temp++; ptr++;
-        }
-       }
-    }else if (afp -> choice == 2){
-
-      if( afp -> div) {
-        if (need_comma)
-        {
-          *temp = ','; temp++;
-          *temp = ' '; temp++;
-        }
-        ptr = afp->div;
-        while ((*temp = *ptr) != '\0')
-        {
-          temp++; ptr++;
-        }
-        need_comma = TRUE;
-      }
-
-      if(afp -> affil) {
-        if (need_comma)
-        {
-          *temp = ','; temp++;
-          *temp = ' '; temp++;
-        }
-        ptr = afp->affil;
-        while ((*temp = *ptr) != '\0')
-        {
-          temp++; ptr++;
-        }
-        need_comma = TRUE;
-      }
-
-      if(afp -> street) {
-        if (need_comma)
-        {
-          *temp = ','; temp++;
-          *temp = ' '; temp++;
-        }
-        ptr = afp->street;
-        while ((*temp = *ptr) != '\0')
-        {
-          temp++; ptr++;
-        }
-        need_comma = TRUE;
-      }
-
-      if( afp -> city) {
-        if (need_comma)
-        {
-          *temp = ','; temp++;
-          *temp = ' '; temp++;
-        }
-        ptr = afp->city;
-        while ((*temp = *ptr) != '\0')
-        {
-          temp++; ptr++;
-        }
-        need_comma = TRUE;
-      }
-
-      if( afp -> sub) {
-        if (need_comma)
-        {
-          *temp = ','; temp++;
-          *temp = ' '; temp++;
-        }
-        ptr = afp->sub;
-        while ((*temp = *ptr) != '\0')
-        {
-          temp++; ptr++;
-        }
-        need_comma = TRUE;
-      }
-
-      if( afp -> postal_code){
-        *temp = ' ';
-        temp++;
-        ptr = afp->postal_code;
-        while ((*temp = *ptr) != '\0')
-        {
-          temp++; ptr++;
-        }
-      }
-
-      if( afp -> country){
-        if (need_comma)
-        {
-          *temp = ','; temp++;
-          *temp = ' '; temp++;
-        }
-        ptr = afp->country;
-        while ((*temp = *ptr) != '\0')
-        {
-          temp++; ptr++;
-        }
-        need_comma = TRUE;
-      }
-    }
-    temp++;
-    *temp = '\0';
-  }
-
-    /* convert double quotes to single quotes */
-
-    ptr = string;
-    ch = *ptr;
-    while (ch != '\0') {
-      if (ch == '\"') {
-        *ptr = '\'';
-      }
-      ptr++;
-      ch = *ptr;
-    }
-
-  return string;
-}
-
-static CharPtr FormatCitBookArt (
-  FmtType format,
-  CitBookPtr cbp
-)
-
-{
-  AffilPtr     afp;
-  AuthListPtr  alp;
-  CharPtr      book_title = NULL;
-  Char         buf [256];
-  Char         ch;
-  DatePtr      dp;
-  ValNodePtr   head = NULL;
-  ImprintPtr   imp;
-  CharPtr      issue = NULL;
-  ValNodePtr   names = NULL;
-  Char         pages [128];
-  CharPtr      part_sup = NULL;
-  CharPtr      part_supi = NULL;
-  CharPtr      rsult = NULL;
-  CharPtr      str;
-  CharPtr      title;
-  ValNodePtr   ttl;
-  ValNodePtr   vnp;
-  CharPtr      volume;
-  Char         year [8];
-
-  if (cbp == NULL) return NULL;
-
-  ttl = cbp->title;
-  if (ttl == NULL) return NULL;
-
-  imp = cbp->imp;
-  if (imp == NULL) return NULL;
-
-  dp = imp->date;
-  year [0] = '\0';
-  if (dp != NULL) {
-    if (dp->data [0] == 1) {
-      if (dp->data [1] != 0) {
-        sprintf (year, "(%ld)", (long) (1900 + dp->data [1]));
-      }
-    } else {
-      StringCpy (year, "(");
-      StringNCat (year, dp->str, 4);
-      StringCpy (year, ")");
-    }
-  }
-
-  if (imp->prepub == 1 || imp->prepub == 255) {
-    sprintf (buf, "Unpublished %s", year);
-    return StringSave (buf);
-  }
-
-  title = (CharPtr) ttl->data.ptrvalue;
-  if (StringLen (title) < 3) return StringSave (".");
-
-  ValNodeCopyStr (&head, 0, "(in) ");
-
-  alp = cbp->authors;
-  if (alp != NULL) {
-    str = GetAuthorsString (format, alp, NULL, NULL, NULL);
-    if (str != NULL) {
-      ValNodeCopyStr (&head, 0, str);
-      names = alp->names;
-      if (names != NULL) {
-        if (names->next != NULL) {
-          ValNodeCopyStr (&head, 0, " (Eds.);");
-        } else {
-          ValNodeCopyStr (&head, 0, " (Ed.);");
-        }
-      }
-      ValNodeCopyStr (&head, 0, "\n");
-    }
-    MemFree (str);
-  }
-
-  book_title = StringSaveNoNull (title);
-  vnp = ValNodeAddStr (&head, 0, book_title);
-  if (book_title != NULL) {
-
-    /* make book title all caps */
-
-    title = book_title;
-    ch = *title;
-    while (ch != '\0') {
-      *title = TO_UPPER (ch);
-      title++;
-      ch = *title;
-    }
-  }
-
-  volume = imp->volume;
-  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-    issue = imp->issue;
-    part_sup = imp->part_sup;
-    part_supi = imp->part_supi;
-  }
-  pages [0] = '\0';
-  FixPages (pages, imp->pages);
-
-  if ((! StringHasNoText (volume)) && (StringCmp (volume, "0") != 0)) {
-    AddValNodeString (&head, ", Vol. ", volume, NULL);
-    DoSup (&head, issue, part_sup, part_supi);
-  }
-
-  if (! StringHasNoText (pages)) {
-    AddValNodeString (&head, ": ", pages, NULL);
-  }
-
-  if (book_title != NULL) {
-    ValNodeCopyStr (&head, 0, ";\n");
-  }
-
-  afp = imp->pub;
-  if (afp != NULL) {
-    str = MakeAffilStr (afp);
-    if (str != NULL) {
-      ValNodeCopyStr (&head, 0, str);
-      ValNodeCopyStr (&head, 0, " ");
-      MemFree (str);
-    }
-  }
-
-  AddValNodeString (&head, NULL, year, NULL);
-
-  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-    if (imp->prepub == 2) {
-      ValNodeCopyStr (&head, 0, " In press");
-    }
-  }
-
-  rsult = MergeValNodeStrings (head);
-  ValNodeFreeData (head);
-
-  return rsult;
-}
-
-static CharPtr FormatCitBook (
-  FmtType format,
-  CitBookPtr cbp
-)
-
-{
-  AffilPtr   afp;
-  char       year[5];
-  CharPtr    bookTitle=NULL;
-  CharPtr    retval = NULL;
-  CharPtr    temp;
-  DatePtr    dp;
-  ImprintPtr ip;
-  int        aflen = 0;
-  CharPtr    p;
-  CharPtr    affilStr = NULL;
-
-  /* Check parameters */
-
-  if (cbp == NULL)
-    return NULL;
-
-  if ( cbp -> othertype != 0)
-    return NULL;
-
-  ip = cbp -> imp;
-
-  /* Format the year */
-
-  dp = ip -> date;
-  year[0] = '\0';
-
-  if ( dp -> data[0] == 1)
-    sprintf(year,"%ld",(long) ( 1900+dp -> data[1]));
-  else
-    {
-      StringNCpy( (CharPtr) year, (CharPtr) dp -> str, (size_t) 4);
-      year[4] = '\0';
-    }
-
-  /* Get the book title */
-
-  if (cbp->title)
-    bookTitle = StringSave(cbp -> title -> data.ptrvalue);
-
-  /* Get the affiliation length */
-
-  if ( ip -> pub){
-    afp = ip -> pub;
-    aflen = StringLen(afp -> affil)+ 5;
-    if ( afp -> choice == 2){
-      aflen += 3 + StringLen(afp -> div);
-      aflen += 3 + StringLen(afp -> street);
-      aflen += 3 + StringLen(afp -> city);
-      aflen += 3 + StringLen(afp -> sub);
-      aflen += 3 + StringLen(afp -> country);
-    }
-  } else{
-    aflen = 22;
-  }
-  if (ip->prepub == 2)
-    aflen += 10;
-
-  /* Create a Char String big enough to hold */
-  /* the title, year, and affiliation.       */
-
-  temp = retval = MemNew( (size_t) (30+StringLen( bookTitle)+StringLen( year) + aflen) );
-
-  /* Convert the title to upper case and */
-  /* add it to the string.               */
-
-  for ( p = bookTitle; *p; p++)
-    *p = TO_UPPER(*p);
-
-  /* temp = StringMove(temp, "Book: "); */
-  temp = StringMove(temp, "(in) ");
-  temp = StringMove(temp, bookTitle);
-  temp = StringMove(temp, ".");
-
-  /* Add the affiliation to the string */
-
-  if ( ip -> pub)
-    {
-      afp = ip -> pub;
-      *temp = ' ';
-      temp++;
-      affilStr = MakeAffilStr(afp);
-      temp = StringMove(temp,affilStr);
-    }
-
-  /* Add the year to the string */
-
-  if (year[0] != '\0')
-    {
-      if (affilStr != NULL)
-        temp = StringMove(temp," (");
-      else
-        temp = StringMove(temp, "(");
-      temp = StringMove(temp, year);
-      temp = StringMove(temp, ")");
-    }
-
-  /* If in press, add note */
-
-  if (ip->prepub == 2)
-    temp = StringMove(temp, ", In press");
-
-  /* Clean up and return */
-
-  if (bookTitle)
-    MemFree(bookTitle);
-
-  return retval;
-
-}
-
-static CharPtr FormatThesis (
-  FmtType format,
-  CitBookPtr cbp
-)
-
-{
-  AffilPtr     afp;
-  Char         ch;
-  DatePtr      dp;
-  ValNodePtr   head = NULL;
-  ImprintPtr   imp;
-  CharPtr      ptr;
-  CharPtr      rsult = NULL;
-  CharPtr      str;
-  CharPtr      suffix = NULL;
-  Char         year [8];
-
-  if (cbp == NULL) return NULL;
-  if (cbp->othertype != 2 || cbp->let_type != 3) return NULL;
-
-  imp = cbp->imp;
-  if (imp == NULL) return NULL;
-
-  dp = imp->date;
-  year [0] = '\0';
-  if (dp != NULL) {
-    if (dp->data [0] == 1) {
-      if (dp->data [1] != 0) {
-        sprintf (year, "%ld", (long) (1900 + dp->data [1]));
-      }
-    } else {
-      StringNCpy (year, dp->str, (size_t) 4);
-      year [4] = '\0';
-    }
-  }
-
-  AddValNodeString (&head, "Thesis (", year, ")");
-
-  if (imp->prepub == 2) {
-    suffix = ", In press";
-  }
-
-  str = NULL;
-  afp = imp->pub;
-  if (afp != NULL) {
-    if (afp->choice == 1) {
-      if (StringLen (afp->affil) > 7) {
-        str = StringSave (afp->affil);
-      }
-    } else if (afp->choice == 2) {
-      str = MakeAffilStr (afp);
-    }
-  }
-
-  if (str != NULL) {
-
-    /* convert double quotes to single quotes */
-
-    ptr = str;
-    ch = *ptr;
-    while (ch != '\0') {
-      if (ch == '\"') {
-        *ptr = '\'';
-      }
-      ptr++;
-      ch = *ptr;
-    }
-    AddValNodeString (&head, " ", str, suffix);
-    MemFree (str);
-  }
-
-  rsult = MergeValNodeStrings (head);
-  ValNodeFreeData (head);
-
-  return rsult;
-}
-
-static CharPtr FormatCitArt (
-  FmtType format,
-  Boolean citArtIsoJta,
-  CitArtPtr cap
-)
-
-{
-  CitBookPtr  cbp;
-  CitJourPtr  cjp;
-  CharPtr     rsult = NULL;
-
-  if (cap == NULL) return NULL;
-
-  switch (cap->from) {
-    case 1 :
-      cjp = (CitJourPtr) cap->fromptr;
-      if (cjp != NULL) {
-        rsult = FormatCitJour (format, citArtIsoJta, cjp);
-      }
-      break;
-    case 2 :
-      cbp = (CitBookPtr) cap->fromptr;
-      if (cbp != NULL) {
-        rsult = FormatCitBookArt (format, cbp);
-      }
-      break;
-    case 3 :
-      cbp = (CitBookPtr) cap->fromptr;
-      if (cbp != NULL) {
-        rsult = FormatCitBookArt (format, cbp);
-      }
-      break;
-    default :
-      break;
-  }
-
-  return rsult;
-}
-
-static CharPtr FormatCitPat (
-  FmtType   format,
-  CitPatPtr cpp,
-  SeqIdPtr  seqidp
-)
-
-{
-  AffilPtr       afp;
-  AuthListPtr    alp;
-  Char           date [40];
-  ValNodePtr     head = NULL;
-  CharPtr        prefix = NULL;
-  CharPtr        rsult = NULL;
-  SeqIdPtr       sip;
-  CharPtr        suffix = NULL;
-  PatentSeqIdPtr psip;
-  Int4           pat_seqid = 0;
-  Char           buf[10];
-
-  if (cpp == NULL) return NULL;
-
-  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-    ValNodeCopyStr (&head, 0, "Patent: ");
-    suffix = " ";
-  } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-    ValNodeCopyStr (&head, 0, "Patent number ");
-  }
-
-  if (! StringHasNoText (cpp->country)) {
-    AddValNodeString (&head, NULL, cpp->country, suffix);
-  }
-
-  if (! StringHasNoText (cpp->number)) {
-    ValNodeCopyStr (&head, 0, cpp->number);
-  } else if (! StringHasNoText (cpp->app_number)) {
-    AddValNodeString (&head, "(", cpp->app_number, ")");
-  }
-
-  if (! StringHasNoText (cpp->doc_type)) {
-    AddValNodeString (&head, "-", cpp->doc_type, NULL);
-  }
-
-  /* pat_seqid test */
-
-  for (sip = seqidp; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_PATENT) {
-      psip = (PatentSeqIdPtr) sip -> data.ptrvalue;
-      if (psip != NULL) {
-        pat_seqid = psip->seqid;
-      }
-    }
-  }
-  if (pat_seqid > 0) {
-    if (format == EMBL_FMT) {
-      sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", ");
-      ValNodeCopyStr (&head, 0, buf);
-    } else {
-      sprintf(buf,"%s%ld ", " ", (long) pat_seqid);
-      ValNodeCopyStr (&head, 0, buf);
-    }
-  } else {
-    ValNodeCopyStr (&head, 0, " ");
-  }
-
-  /* Date */
-
-  date [0] = '\0';
-  if (cpp->date_issue != NULL) {
-    DateToGB (date, cpp->date_issue, FALSE);
-  } else if (cpp->app_date != NULL) {
-    DateToGB (date, cpp->app_date, FALSE);
-  }
-  if (! StringHasNoText (date)) {
-    ValNodeCopyStr (&head, 0, date);
-  }
-
-  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-    ValNodeCopyStr (&head, 0, ";");
-  } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-    ValNodeCopyStr (&head, 0, ".");
-  }
-
-  alp = cpp->authors;
-  if (alp != NULL) {
-    afp = alp->affil;
-    if (afp != NULL) {
-      suffix = NULL;
-      if (afp->choice == 2) {
-        suffix = ";";
-      }
-
-      /* If and of the affiliation fields are */
-      /* non-blank, put them on a new line.   */
-
-      if ((! StringHasNoText (afp->affil)) ||
-          (! StringHasNoText (afp->street)) ||
-          (! StringHasNoText (afp->div)) ||
-          (! StringHasNoText (afp->city)) ||
-          (! StringHasNoText (afp->sub)) ||
-          (! StringHasNoText (afp->country)))
-        ValNodeCopyStr (&head, 0, "\n");
-
-      /* Write out the affiliation fields */
-
-      if (! StringHasNoText (afp->affil)) {
-        AddValNodeString (&head, NULL, afp->affil, suffix);
-        prefix = " ";
-      }
-      if (! StringHasNoText (afp->street)) {
-        AddValNodeString (&head, prefix, afp->street, ";");
-        prefix = " ";
-      }
-      if (! StringHasNoText (afp->div)) {
-        AddValNodeString (&head, prefix, afp->div, ";");
-        prefix = " ";
-      }
-      if (! StringHasNoText (afp->city)) {
-        AddValNodeString (&head, prefix, afp->city, NULL);
-        prefix = ", ";
-      }
-      if (! StringHasNoText (afp->sub)) {
-        AddValNodeString (&head, prefix, afp->sub, NULL);
-      }
-      if (! StringHasNoText (afp->country)) {
-        AddValNodeString (&head, ";\n", afp->country, ";");
-      }
-    }
-  }
-
-  rsult = MergeValNodeStrings (head);
-  ValNodeFreeData (head);
-
-  /*
-  s_StringCleanup(rsult);
-  */
-
-  return rsult;
-}
-
-static CharPtr FormatCitGen (
-  FmtType format,
-  Boolean dropBadCitGens,
-  Boolean noAffilOnUnpub,
-  CitGenPtr cgp
-)
-
-{
-  CharPtr      affil = NULL;
-  AuthListPtr  alp = NULL;
-  Char         ch;
-  DatePtr      dp;
-  ValNodePtr   head = NULL;
-  CharPtr      inpress = NULL;
-  CharPtr      journal = NULL;
-  Char         pages [128];
-  CharPtr      prefix = NULL;
-  CharPtr      ptr;
-  CharPtr      rsult = NULL;
-  Char         year [8];
-
-  if (cgp == NULL) return NULL;
-
-  if (cgp->journal == NULL && StringNICmp (cgp->cit, "unpublished", 11) == 0) {
-    if (noAffilOnUnpub) {
-
-      /* !!! temporarily put date in unpublished citation for QA !!! */
-
-      if (dropBadCitGens) {
-        year [0] = '\0';
-        dp = cgp->date;
-        if (dp != NULL) {
-          if (dp->data [0] == 1) {
-            if (dp->data [1] != 0) {
-              sprintf (year, " (%ld)", (long) (1900 + dp->data [1]));
-            }
-          } else {
-            StringCpy (year, " (");
-            StringNCat (year, dp->str, 4);
-            StringCat (year, ")");
-          }
-        }
-        AddValNodeString (&head, NULL, "Unpublished", NULL);
-        AddValNodeString (&head, NULL, year, NULL);
-        rsult = MergeValNodeStrings (head);
-        ValNodeFreeData (head);
-        return rsult;
-      }
-
-      /* !!! remove above section once QA against asn2ff is done !!! */
-
-      return StringSave ("Unpublished");
-    }
-
-    alp = cgp->authors;
-    if (alp != NULL) {
-      affil = GetAffil (alp->affil);
-      if (! StringHasNoText (affil)) {
-        rsult = MemNew ((size_t) StringLen (affil) + (size_t) StringLen (cgp->cit) + 15);
-        StringCpy (rsult, "Unpublished ");
-        StringCat (rsult, affil);
-        TrimSpacesAroundString (rsult);
-        return rsult;
-      }
-    }
-
-    rsult = StringSave (cgp->cit);
-    TrimSpacesAroundString (rsult);
-    return rsult;
-  }
-
-  year [0] = '\0';
-  dp = cgp->date;
-  if (dp != NULL) {
-    if (dp->data [0] == 1) {
-      if (dp->data [1] != 0) {
-        sprintf (year, " (%ld)", (long) (1900 + dp->data [1]));
-      }
-    } else {
-      StringCpy (year, " (");
-      StringNCat (year, dp->str, 4);
-      StringCat (year, ")");
-    }
-  }
-
-  pages [0] = '\0';
-  if (cgp->pages != NULL) {
-    FixPages (pages, cgp->pages);
-  }
-
-  if (cgp->journal != NULL) {
-    journal = (CharPtr) cgp->journal->data.ptrvalue;
-  }
-  if (cgp->cit != NULL) {
-    ptr = StringStr (cgp->cit, "Journal=\"");
-    if (ptr != NULL) {
-      journal = ptr + 9;
-    } else if (StringNICmp (cgp->cit, "submitted", 8) == 0 ||
-               StringNICmp (cgp->cit, "unpublished", 11) == 0) {
-
-      if ((! dropBadCitGens) || journal != NULL) {
-        inpress = cgp->cit;
-      } else {
-        inpress = "Unpublished";
-      }
-    } else if (StringNICmp (cgp->cit, "Online Publication", 18) == 0 ||
-               StringNICmp (cgp->cit, "Published Only in DataBase", 26) == 0) {
-
-      inpress = cgp->cit;
-    } else if ((! dropBadCitGens) && journal == NULL) {
-      journal = cgp->cit;
-    }
-  }
-  if (journal != NULL) {
-    journal = StringSave (journal);
-    for (ptr = journal, ch = *ptr; ch != '\0'; ptr++, ch = *ptr) {
-      if (ch == '=' || ch == '\"') {
-        *ptr = '\0';
-      }
-    }
-    ValNodeAddStr (&head, 0, journal);
-    prefix = " ";
-  }
-
-  if (! StringHasNoText (inpress)) {
-    AddValNodeString (&head, prefix, inpress, NULL);
-    prefix = " ";
-  }
-
-  if (! StringHasNoText (cgp->volume)) {
-    AddValNodeString (&head, prefix, cgp->volume, NULL);
-  }
-
-  if (! StringHasNoText (pages)) {
-    if (format == GENBANK_FMT) {
-      AddValNodeString (&head, ", ", pages, NULL);
-    } else if (format == EMBL_FMT) {
-      AddValNodeString (&head, ":", pages, NULL);
-    }
-  }
-
-  if (! StringHasNoText (year)) {
-    AddValNodeString (&head, NULL, year, NULL);
-  }
-
-  rsult = MergeValNodeStrings (head);
-  ValNodeFreeData (head);
-
-  return rsult;
-}
-
-static CharPtr FormatCitSub (
-  FmtType format,
-  CitSubPtr csp
-)
-
-{
-  CharPtr      affil;
-  AffilPtr     afp;
-  AuthListPtr  alp;
-  Char         buf [256];
-  Char         date [40];
-  ValNodePtr   head = NULL;
-  CharPtr      rsult = NULL;
-
-  if (csp == NULL) return NULL;
-
-  date [0] = '\0';
-  if (csp->date != NULL) {
-    DateToGB (date, csp->date, TRUE);
-  }
-  if (StringHasNoText (date)) {
-    StringCpy (date, "??-???-????");
-  }
-
-  sprintf (buf, "Submitted (%s)", date);
-  ValNodeCopyStr (&head, 0, buf);
-
-  alp = csp->authors;
-  if (alp != NULL) {
-    afp = alp->affil;
-    if (afp != NULL) {
-      affil = GetAffil (afp);
-      if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-        if (StringNCmp(affil, " to the EMBL/GenBank/DDBJ databases.", 36) != 0) {
-          ValNodeCopyStr (&head, 0, " to the EMBL/GenBank/DDBJ databases.\n");
-        } else {
-          ValNodeCopyStr (&head, 0, " ");
-        }
-      } else {
-        ValNodeCopyStr (&head, 0, " ");
-      }
-      ValNodeCopyStr (&head, 0, affil);
-      MemFree (affil);
-    } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-      ValNodeCopyStr (&head, 0, " to the EMBL/GenBank/DDBJ databases.\n");
-    }
-  }
-
-  rsult = MergeValNodeStrings (head);
-  ValNodeFreeData (head);
-
-  return rsult;
-}
-
-static CharPtr GetPubJournal (
-  FmtType format,
-  Boolean dropBadCitGens,
-  Boolean noAffilOnUnpub,
-  Boolean citArtIsoJta,
-  PubdescPtr pdp,
-  CitSubPtr csp,
-  SeqIdPtr  seqidp,
-  IndxPtr index
-)
-
-{
-  CitArtPtr        cap;
-  CitBookPtr       cbp;
-  CitGenPtr        cgp;
-  CitPatPtr        cpp;
-  CharPtr          journal = NULL;
-  MedlineEntryPtr  mep;
-  ValNodePtr       vnp;
-
-  if (csp != NULL) {
-    return FormatCitSub (format, csp);
-  }
-  if (pdp == NULL) return NULL;
-
-  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-    switch (vnp->choice) {
-      case PUB_Gen :
-        cgp = (CitGenPtr) vnp->data.ptrvalue;
-        if (cgp != NULL) {
-          if (StringNICmp ("BackBone id_pub", cgp->cit, 15) != 0) {
-            if (cgp->cit == NULL && cgp->journal == NULL && cgp->date == NULL && cgp->serial_number) {
-              break; /* skip just serial number */
-            }
-          }
-          journal = FormatCitGen (format, dropBadCitGens, noAffilOnUnpub, cgp);
-        }
-        break;
-      case PUB_Sub :
-        csp = (CitSubPtr) vnp->data.ptrvalue;
-        if (csp != NULL) {
-          journal = FormatCitSub (format, csp);
-        }
-        break;
-      case PUB_Medline :
-        mep = (MedlineEntryPtr) vnp->data.ptrvalue;
-        if (mep != NULL) {
-          cap = mep->cit;
-          if (cap != NULL) {
-            journal = FormatCitArt (format, citArtIsoJta, cap);
-          }
-        }
-        break;
-      case PUB_Article :
-        cap = (CitArtPtr) vnp->data.ptrvalue;
-        if (cap != NULL) {
-          journal = FormatCitArt (format, citArtIsoJta, cap);
-        }
-        break;
-      case PUB_Book :
-      case PUB_Proc :
-        cbp = (CitBookPtr) vnp->data.ptrvalue;
-        if (cbp != NULL) {
-          journal = FormatCitBook (format, cbp);
-        }
-        break;
-      case PUB_Man :
-        cbp = (CitBookPtr) vnp->data.ptrvalue;
-        if (cbp != NULL) {
-          journal = FormatThesis (format, cbp);
-        }
-        break;
-      case PUB_Patent :
-        cpp = (CitPatPtr) vnp->data.ptrvalue;
-        if (cpp != NULL) {
-          journal = FormatCitPat (format, cpp, seqidp);
-        }
-        break;
-      default :
-        break;
-    }
-
-    /* optionally populate indexes for NCBI internal database */
-
-    if (index != NULL && journal != NULL) {
-
-      /* skip non-informative cit-gens */
-
-      if (StringNICmp (journal, "submitted", 8) == 0 ||
-          StringNICmp (journal, "unpublished", 11) == 0 ||
-          StringNICmp (journal, "Online Publication", 18) == 0 ||
-          StringNICmp (journal, "Published Only in DataBase", 26) == 0) {
-      } else {
-        ValNodeCopyStrToHead (&(index->journals), 0, journal);
-      }
-    }
-
-    if (journal != NULL) return journal;
-  }
-
-  return NULL;
-}
-
-static Int4 GetMuid (
-  PubdescPtr pdp
-)
-
-{
-  MedlineEntryPtr  mep;
-  ValNodePtr       vnp;
-
-  if (pdp == NULL) return 0;
-
-  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-    switch (vnp->choice) {
-      case PUB_Medline :
-        mep = (MedlineEntryPtr) vnp->data.ptrvalue;
-        if (mep != NULL) {
-          return mep->uid;
-        }
-        break;
-      case PUB_Muid :
-        return vnp->data.intvalue;
-      default :
-        break;
-    }
-  }
-
-  return 0;
-}
-
-static Int4 GetPmid (
-  PubdescPtr pdp
-)
-
-{
-  MedlineEntryPtr  mep;
-  ValNodePtr       vnp;
-
-  if (pdp == NULL) return 0;
-
-  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-    switch (vnp->choice) {
-      case PUB_Medline :
-        mep = (MedlineEntryPtr) vnp->data.ptrvalue;
-        if (mep != NULL) {
-          return mep->pmid;
-        }
-        break;
-      case PUB_PMid :
-        return vnp->data.intvalue;
-      default :
-        break;
-    }
-  }
-
-  return 0;
-}
-
-static CharPtr CleanQualValue (
-  CharPtr str
-)
-
-{
-  Char     ch;
-  CharPtr  dst;
-  CharPtr  ptr;
-
-  if (str == NULL || str [0] == '\0') return NULL;
-
-  dst = str;
-  ptr = str;
-  ch = *ptr;
-  while (ch != '\0') {
-    if (ch == '\n' || ch == '\r' || ch == '\t' || ch == '"') {
-      *dst = ' ';
-      dst++;
-    } else {
-      *dst = ch;
-      dst++;
-    }
-    ptr++;
-    ch = *ptr;
-  }
-  *dst = '\0';
-
-  return str;
-}
-
-static CharPtr Asn2gnbkCompressSpaces (CharPtr str)
-
-{
-  Char     ch;
-  CharPtr  dst;
-  Char     last;
-  CharPtr  ptr;
-
-  if (str != NULL && str [0] != '\0') {
-    dst = str;
-    ptr = str;
-    ch = *ptr;
-    while (ch != '\0' && ch <= ' ') {
-      ptr++;
-      ch = *ptr;
-    }
-    while (ch != '\0') {
-      *dst = ch;
-      dst++;
-      ptr++;
-      last = ch;
-      ch = *ptr;
-      if (ch != '\0' && ch < ' ') {
-        *ptr = ' ';
-        ch = *ptr;
-      }
-      while (ch != '\0' && last <= ' ' && ch <= ' ') {
-        ptr++;
-        ch = *ptr;
-      }
-    }
-    *dst = '\0';
-    dst = NULL;
-    ptr = str;
-    ch = *ptr;
-    while (ch != '\0') {
-      if (ch != ' ') {
-        dst = NULL;
-      } else if (dst == NULL) {
-        dst = ptr;
-      }
-      ptr++;
-      ch = *ptr;
-    }
-    if (dst != NULL) {
-      *dst = '\0';
-    }
-  }
-  return str;
-}
-
-static CharPtr StripAllSpaces (
-  CharPtr str
-)
-
-{
-  Char     ch;
-  CharPtr  dst;
-  CharPtr  ptr;
-
-  if (str == NULL || str [0] == '\0') return NULL;
-
-  dst = str;
-  ptr = str;
-  ch = *ptr;
-  while (ch != '\0') {
-    if (ch == ' ' || ch == '\t') {
-    } else {
-      *dst = ch;
-      dst++;
-    }
-    ptr++;
-    ch = *ptr;
-  }
-  *dst = '\0';
-
-  return str;
-}
-
-static CharPtr remarksText [] = {
-  "full automatic", "full staff_review", "full staff_entry",
-  "simple staff_review", "simple staff_entry", "simple automatic",
-  "unannotated automatic", "unannotated staff_review", "unannotated staff_entry",
-  NULL
-};
-
-static void AddReferenceToGbseq (
-  GBSeqPtr gbseq,
-  GBReferencePtr gbref,
-  CharPtr str
-)
-
-{
-  CharPtr  copy;
-  CharPtr  ptr;
-  CharPtr  ref;
-
-  if (gbseq == NULL || gbref == NULL || StringHasNoText (str)) return;
-
-  copy = StringSave (str);
-
-  /* link in reverse order, to be reversed in slash block */
-
-  gbref->next = gbseq->references;
-  gbseq->references = gbref;
-
-  /* now parse or make ASN required default values for remaining fields */
-
-  if (StringNCmp (copy, "REFERENCE   ", 12) == 0) {
-    ref = copy + 12;
-    ptr = StringStr (ref, "\n  AUTHORS");
-    if (ptr == NULL) {
-      ptr = StringStr (ref, ")\n");
-    }
-    if (ptr != NULL) {
-      *ptr = '\0';
-      gbref->reference = StringSave (ref);
-    }
-  }
-
-  if (gbref->reference == NULL) {
-    gbref->reference = StringSave ("?");
-  }
-
-  CleanQualValue (gbref->reference);
-  Asn2gnbkCompressSpaces (gbref->reference);
-
-  if (gbref->journal == NULL) {
-    gbref->journal = StringSave ("?");
-  }
-
-  CleanQualValue (gbref->journal);
-  Asn2gnbkCompressSpaces (gbref->journal);
-
-  MemFree (copy);
-}
-
-static Boolean IsCitSub (
-  PubdescPtr pdp,
-  CitSubPtr csp
-)
-
-{
-  ValNodePtr  vnp;
-
-  if (csp != NULL) return TRUE;
-  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-    if (vnp->choice == PUB_Sub) return TRUE;
-  }
-  return FALSE;
-}
-
-static CharPtr FormatReferenceBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  AuthListPtr        alp;
-  Asn2gbSectPtr      asp;
-  BioseqPtr          bsp;
-  Char               buf [150];
-  CitArtPtr          cap;
-  Char               ch;
-  CitJourPtr         cjp;
-  Boolean            citArtIsoJta;
-  CharPtr            consortium;
-  CitRetractPtr      crp;
-  CitSubPtr          csp = NULL;
-  SeqMgrDescContext  dcontext;
-  SeqMgrFeatContext  fcontext;
-  Int4               gibbsq;
-  GBReferencePtr     gbref = NULL;
-  GBSeqPtr           gbseq;
-  Int2               i;
-  ImprintPtr         imp;
-  IndxPtr            index;
-  IntRefBlockPtr     irp;
-  size_t             len;
-  SeqLocPtr          loc = NULL;
-  MedlineEntryPtr    mep;
-  Int4               muid = 0;
-  Boolean            needsPeriod = FALSE;
-  SeqLocPtr          nextslp;
-  Boolean            notFound;
-  ObjMgrDataPtr      omdp;
-  PubdescPtr         pdp = NULL;
-  PubdescPtr         pdpcopy = NULL;
-  PubmedEntryPtr     pep = NULL;
-  Int4               pmid = 0;
-  CharPtr            prefix = NULL;
-  RefBlockPtr        rbp;
-  SubmitBlockPtr     sbp;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp = NULL;
-  SeqIdPtr           sip;
-  SeqLocPtr          slp;
-  SeqSubmitPtr       ssp;
-  Int4               start;
-  Int4               stop;
-  CharPtr            str;
-  Boolean            strict_isojta;
-  CharPtr            suffix = NULL;
-  CharPtr            tmp;
-  Boolean            trailingPeriod = TRUE;
-  ValNodePtr         vnp;
-  StringItemPtr      ffstring, temp;
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  rbp = (RefBlockPtr) bbp;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-  bsp = asp->bsp;
-  if (bsp == NULL) return NULL;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return NULL;
-
-  if (ajp->index) {
-    index = &asp->index;
-  } else {
-    index = NULL;
-  }
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (! StringHasNoText (rbp->string)) return StringSave (rbp->string);
-
-  /* could be descriptor, feature, or submit block citation */
-
-  if (rbp->itemtype == OBJ_SEQDESC) {
-
-    sdp = SeqMgrGetDesiredDescriptor (rbp->entityID, NULL, rbp->itemID, 0, NULL, &dcontext);
-    if (sdp != NULL && dcontext.seqdesctype == Seq_descr_pub) {
-      pdp = (PubdescPtr) sdp->data.ptrvalue;
-    }
-
-  } else if (rbp->itemtype == OBJ_SEQFEAT) {
-
-    sfp = SeqMgrGetDesiredFeature (rbp->entityID, NULL, rbp->itemID, 0, NULL, &fcontext);
-    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_PUB) {
-      pdp = (PubdescPtr) sfp->data.value.ptrvalue;
-    }
-
-  } else if (rbp->itemtype == OBJ_SEQSUB_CIT) {
-
-    omdp = ObjMgrGetData (rbp->entityID);
-    if (omdp != NULL && omdp->datatype == OBJ_SEQSUB) {
-      ssp = (SeqSubmitPtr) omdp->dataptr;
-      if (ssp != NULL && ssp->datatype == 1) {
-        sbp = ssp->sub;
-        if (sbp != NULL) {
-          csp = sbp->cit;
-        }
-      }
-    }
-  }
-
-  if (pdp == NULL && csp == NULL) return NULL;
-
-  temp = FFGetString(ajp);
-  if ( temp == NULL ) {
-    FFRecycleString(ajp, ffstring);
-    return NULL;
-  }
-
-  /* any justuids left at this point is RefSeq protein, and should be fetched */
-
-  irp = (IntRefBlockPtr) rbp;
-  if (irp->justuids) {
-    if (rbp->pmid != 0) {
-      pep = GetPubMedForUid (rbp->pmid);
-    } else if (rbp->muid != 0) {
-      pep = GetPubMedForUid (rbp->muid);
-    }
-    if (pep != NULL) {
-      mep = (MedlineEntryPtr) pep->medent;
-      if (mep != NULL && mep->cit != NULL) {
-        pdpcopy = AsnIoMemCopy ((Pointer) pdp,
-                                 (AsnReadFunc) PubdescAsnRead,
-                                 (AsnWriteFunc) PubdescAsnWrite);
-        cap = AsnIoMemCopy ((Pointer) mep->cit,
-                            (AsnReadFunc) CitArtAsnRead,
-                            (AsnWriteFunc) CitArtAsnWrite);
-        vnp = ValNodeAddPointer (&(pdpcopy->pub), PUB_Article, (Pointer) cap);
-        pdp = pdpcopy;
-      }
-    }
-  }
-
-  /* print serial number */
-  FFStartPrint(temp, afp->format, 0, 12, "REFERENCE", 12, 5, 5, "RN", TRUE);
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-    if (rbp->serial > 99) {
-      sprintf (buf, "%d ", (int) rbp->serial);
-    } else {
-      sprintf (buf, "%d", (int) rbp->serial);
-    }
-  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-    sprintf (buf, "[%d]", (int) rbp->serial);
-  }
-
-  FFAddOneString(temp, buf, FALSE, FALSE, TILDE_TO_SPACES);
-
-  /* print base range */
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-
-    if (rbp->sites != 3) {
-      FFAddNChar(temp, ' ', 15 - temp->pos, FALSE);
-    }
-  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-
-    if (rbp->sites == 0) {
-      FFLineWrap(ffstring, temp, 0, 5, ASN2FF_EMBL_MAX, "RN");   
-      FFRecycleString(ajp, temp);
-      temp = FFGetString(ajp);
-      FFStartPrint(temp, afp->format, 0, 0, NULL, 0, 5, 5, "RP", FALSE);
-    }
-  }
-
-  if (rbp->sites == 1 || rbp->sites == 2) {
-
-    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-      FFAddOneString(temp, "(sites)", FALSE, FALSE, TILDE_TO_SPACES);
-      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-    } else {
-      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RP");
-    }
-  } else if (rbp->sites == 3) {
-    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-    } else {
-      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RP");
-    }
-  } else {
-    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-      FFAddNChar(temp, ' ', 15 - temp->pos, FALSE);
-      if (afp->format == GENBANK_FMT) {
-        FFAddOneString(temp, "(bases ", FALSE, FALSE, TILDE_TO_SPACES);
-      } else {
-        FFAddOneString(temp, "(residues ", FALSE, FALSE, TILDE_TO_SPACES);
-      }
-    }
-
-    irp = (IntRefBlockPtr) rbp;
-    loc = irp->loc;
-
-    if (loc != NULL) {
-      if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-        suffix = "; ";
-      } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-        suffix = ", ";
-      }
-
-      slp = SeqLocFindNext (loc, NULL);
-      while (slp != NULL) {
-        nextslp = SeqLocFindNext (loc, slp);
-        start = SeqLocStart (slp) + 1;
-        stop = SeqLocStop (slp) + 1;
-        if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-          sprintf (buf, "%ld to %ld", (long) start, (long) stop);
-        } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-          sprintf (buf, "%ld-%ld", (long) start, (long) stop);
-        }
-        if (nextslp == NULL) {
-          suffix = NULL;
-        }
-        FFAddTextToString(temp, NULL, buf, suffix, FALSE, FALSE, TILDE_TO_SPACES);
-        slp = nextslp;
-      }
-
-    } else {
-
-      /* code still used for ssp->cit */
-
-      start = 1;
-      stop = bsp->length;
-      if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-        sprintf (buf, "%ld to %ld", (long) start, (long) stop);
-      } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-        sprintf (buf, "%ld-%ld", (long) start, (long) stop);
-      }
-      FFAddOneString(temp, buf, FALSE, FALSE, TILDE_TO_SPACES);
-    }
-
-    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-      FFAddOneString(temp, ")", FALSE, FALSE, TILDE_TO_SPACES);
-    }
-    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-    } else {
-      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RP");
-    }
-  }
-
-  if (gbseq != NULL) {
-    gbref = GBReferenceNew ();
-  }
-
-  /* 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;
-
-  alp = GetAuthListPtr (pdp, csp);
-  if (alp != NULL) {
-    str = GetAuthorsString (afp->format, alp, &consortium, index, gbref);
-    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 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);
-    } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-      FFAddOneChar(temp, ';', FALSE);
-    }    
-  }
-
-  MemFree (str);
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-  } else {
-      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RA");
-  }
-
-  /* print consortium */
-
-  FFRecycleString(ajp, temp);
-  temp = FFGetString(ajp);
-  if (! StringHasNoText (consortium)) {
-    FFStartPrint (temp, afp->format, 2, 12, "CONSRTM", 12, 5, 5, "CM", FALSE);
-    FFAddTextToString (temp, NULL, consortium, suffix, FALSE, FALSE, TILDE_TO_SPACES);
-    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-    } else {
-      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "CM");
-    }
-  }
-  MemFree (consortium);
-
-  /* print title */
-  FFRecycleString(ajp, temp);
-  temp = FFGetString(ajp);
-
-  str = GetPubTitle (afp->format, pdp, csp);
-  CleanPubTitle (str);
-  StrStripSpaces (str);
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-    prefix = NULL;
-    suffix = NULL;
-  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-    if (str != NULL) {
-      prefix = "\"";
-      suffix = "\";";
-    } else {
-      prefix = NULL;
-      suffix = ";";
-    }
-  }
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-    if (! StringHasNoText (str)) {
-      FFStartPrint (temp, afp->format, 2, 12, "TITLE", 12, 5, 5, "RT", FALSE);
-
-      FFAddTextToString (temp, prefix, str, suffix, FALSE, FALSE, TILDE_TO_SPACES);
-      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-    }
-  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-    FFStartPrint (temp, afp->format, 2, 12, "TITLE", 12, 5, 5, "RT", FALSE);
-    if (! StringHasNoText (str)) {
-
-      FFAddTextToString (temp, prefix, str, suffix, FALSE, FALSE, TILDE_TO_SPACES);
-
-    } else {
-      FFAddOneChar (temp, ';', FALSE);
-    }
-    FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RT");
-  }
-
-  if (gbseq != NULL) {
-    if (gbref != NULL) {
-      gbref->title = StringSaveNoNull (str);
-    }
-  }
-
-  MemFree (str);
-
-  /* print journal */
-  FFRecycleString(ajp, temp);
-  temp = FFGetString(ajp);
-
-  FFStartPrint (temp, afp->format, 2, 12, "JOURNAL", 12, 5, 5, "RL", FALSE);
-
-  /* Only GenBank/EMBL/DDBJ require ISO JTA in ENTREZ/RELEASE modes (RefSeq should later) */
-
-  citArtIsoJta = ajp->flags.citArtIsoJta;
-  strict_isojta = FALSE;
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_GENBANK ||
-        sip->choice == SEQID_EMBL ||
-        sip->choice == SEQID_DDBJ ||
-        /* sip->choice == SEQID_OTHER || */
-        sip->choice == SEQID_TPG ||
-        sip->choice == SEQID_TPE ||
-        sip->choice == SEQID_TPD) {
-      strict_isojta = TRUE;
-    }
-  }
-  if (! strict_isojta) {
-    citArtIsoJta = FALSE;
-  }
-
-  str = GetPubJournal (afp->format, ajp->flags.dropBadCitGens,
-                       ajp->flags.noAffilOnUnpub, citArtIsoJta,
-                       pdp, csp, bsp->id, index);
-  if (str == NULL) {
-    str = StringSave ("Unpublished");
-  }
-  StrStripSpaces (str);
-  TrimSpacesAroundString (str);
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-    needsPeriod = FALSE;
-  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-    if (! IsCitSub (pdp, csp)) {
-      needsPeriod = TRUE;
-    }
-  }
-
-  FFAddOneString (temp, str, FALSE, FALSE, TILDE_IGNORE);
-  if (needsPeriod) {
-    FFAddOneChar(temp, '.', FALSE);
-  }
-
-  if (gbseq != NULL) {
-    if (gbref != NULL) {
-      gbref->journal = StringSaveNoNull (str);
-      tmp = gbref->journal;
-      if (tmp != NULL) {
-        ch = *tmp;
-        while (ch != '\0') {
-          if (ch == '\n' || ch == '\r' || ch == '\t') {
-            *tmp = ' ';
-          }
-          tmp++;
-          ch = *tmp;
-        }
-        TrimSpacesAroundString (gbref->journal);
-      }
-    }
-  }
-
-  MemFree (str);
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-    FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-  } else {
-    FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RL");
-  }
-
-  /* print muid */
-  FFRecycleString(ajp, temp);
-  temp = FFGetString(ajp);
-  
-  muid = GetMuid (pdp);
-  if (muid > 0) {
-    FFStartPrint (temp, afp->format, 2, 12, "MEDLINE", 12, 5, 5, "RX", FALSE);
-
-    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-      FF_www_muid (ajp, temp, muid);
-      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-    } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-      sprintf (buf, "MEDLINE; %ld.", (long) muid);
-      FFAddOneString (temp, buf, FALSE, FALSE, TILDE_TO_SPACES);
-      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RX");
-    }
-  }
-
-  FFRecycleString(ajp, temp);
-  temp = FFGetString(ajp);
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-    pmid = GetPmid (pdp);
-    if (pmid > 0) {
-      FFStartPrint (temp, afp->format, 3, 12, "PUBMED", 12, 5, 5, "RX", FALSE);
-
-      FF_www_muid (ajp, temp, pmid);
-      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-    }
-  }
-
-  if (gbseq != NULL) {
-    if (gbref != NULL) {
-      gbref->medline = muid;
-      gbref->pubmed = pmid;
-    }
-  }
-
-  if (pdp == NULL) {
-    str = FFToCharPtr(ffstring);
-
-    if (gbseq != NULL) {
-      if (gbref != NULL) {
-        AddReferenceToGbseq (gbseq, gbref, str);
-      }
-    }
-
-    FFRecycleString(ajp, ffstring);
-    FFRecycleString(ajp, temp);
-    if (pep != NULL) {
-      PubmedEntryFree (pep);
-    }
-    if (pdpcopy != NULL) {
-      PubdescFree (pdpcopy);
-    }
-
-    return str;
-  }
-
-
-  /* !!! remainder of fields are only for GenBank !!! */
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-
-    prefix = "REMARK";
-
-    if (pdp->comment != NULL) {
-      for (i = 0, notFound = TRUE; notFound && remarksText [i] != NULL; i++) {
-        if (StringCmp (pdp->comment, remarksText [i]) == 0) {
-          notFound = FALSE;
-        }
-      }
-      if (notFound) {
-        FFRecycleString(ajp, temp);
-        temp = FFGetString(ajp);
-
-        FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
-        FFAddOneString (temp, pdp->comment, FALSE, TRUE, TILDE_EXPAND);
-        FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-        prefix = NULL;
-
-        if (gbseq != NULL) {
-          if (gbref != NULL) {
-            gbref->remark = StringSave (pdp->comment);
-          }
-        }
-
-      }
-    }
-
-    gibbsq = 0;
-    for (sip = bsp->id; sip != NULL; sip = sip->next) {
-      if (sip->choice == SEQID_GIBBSQ) {
-        gibbsq = sip->data.intvalue;
-      }
-    }
-    csp = NULL;
-    for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-      if (vnp->choice == PUB_Sub) {
-        csp = (CitSubPtr) vnp->data.ptrvalue;
-      }
-    }
-    if (gibbsq > 0 /* && csp == NULL */) {
-      FFRecycleString(ajp, temp);
-      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);
-      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);
-      prefix = NULL;
-
-      /* gibbsq comment section (fields may be copied from degenerate pubdesc) */
-
-      str = pdp->fig;
-      if (StringHasNoText (str)) {
-        str = irp->fig;
-      }
-      if (! StringHasNoText (str)) {
-        FFRecycleString(ajp, temp);
-        temp = FFGetString(ajp);
-
-        sprintf (buf, "This sequence comes from %s", str);
-        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);
-        prefix = NULL;
-      }
-
-      if (pdp->poly_a || irp->poly_a) {
-        FFRecycleString(ajp, temp);
-        temp = FFGetString(ajp);
-
-        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;
-      }
-
-      str = pdp->maploc;
-      if (StringHasNoText (str)) {
-        str = irp->maploc;
-      }
-      if (! StringHasNoText (str)) {
-        FFRecycleString(ajp, temp);
-        temp = FFGetString(ajp);
-
-        sprintf (buf, "Map location: %s", str);
-        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);
-        prefix = NULL;
-      }
-
-    }
-
-    for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-      if (vnp->choice == PUB_Article) {
-        cap = (CitArtPtr) vnp->data.ptrvalue;
-        if (cap != NULL && cap->from == 1) {
-          cjp = (CitJourPtr) cap->fromptr;
-          if (cjp != NULL) {
-            imp = cjp->imp;
-            if (imp != NULL) {
-              crp = imp->retract;
-              if (crp != NULL && crp->type == 3) {
-                FFRecycleString(ajp, temp);
-                temp = FFGetString(ajp);
-
-                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);
-                FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-                prefix = NULL;
-              }
-            }
-          }
-        }
-      } else if (vnp->choice == PUB_Sub) {
-        csp = (CitSubPtr) vnp->data.ptrvalue;
-        if (csp != NULL) {
-          if (! StringHasNoText (csp->descr)) {
-            FFRecycleString(ajp, temp);
-            temp = FFGetString(ajp);
-
-            FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
-            FFAddOneString (temp, csp->descr, FALSE, TRUE, TILDE_EXPAND);
-            FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-            prefix = NULL;
-          }
-        }
-      }
-    }
-
-  }
-
-  str = FFToCharPtr(ffstring);
-
-  if (gbseq != NULL) {
-    if (gbref != NULL) {
-      AddReferenceToGbseq (gbseq, gbref, str);
-    }
-  }
-
-  FFRecycleString(ajp, ffstring);
-  FFRecycleString(ajp, temp);
-  if (pep != NULL) {
-    PubmedEntryFree (pep);
-  }
-  if (pdpcopy != NULL) {
-    PubdescFree (pdpcopy);
-  }
-
-  return str;
-}
-
-/* A tilde is not an EOL if it is found in a sring of the form:    */
-/* /~alpahnumdot/ where alphanumdot is either alpha numeric or '.' */
-/*                                                                 */
-/* str points to the tilde in question.                            */
-static Boolean IsTildeEOL(CharPtr str) {
-  CharPtr ptr;
-
-  if ( *(str - 1) != '/' ) return TRUE;
-
-  ++str;
-
-  
-  for ( ptr = str; 
-    IS_ALPHANUM(*ptr) || *ptr == '_' || *ptr == '-' || *ptr == '.';
-    ++ptr) continue;
-
-  return *ptr == '/' ? FALSE : TRUE;
-}
-
-
-/* returns a pointer to the first character past the url */
-static CharPtr FindUrlEnding(CharPtr str) {
-  CharPtr ptr;
-
-  for ( ptr = str;
-        !IS_WHITESP(*ptr) && *ptr != '\0' && *ptr != '(' && *ptr != '\"';
-        ++ptr  ) {
-    if ( *ptr == '~' ) {
-      if ( IsTildeEOL(ptr) ) break;
-    }
-  }
-
-  --ptr;
-
-  /* back up over any trailing periods, commas, or parentheses */
-  while ( (*ptr == '.') || (*ptr == ',') || (*ptr == ')') ) {
-    --ptr;
-  }
-
-  ++ptr;
-
-  return ptr;
-}
-
-static void AddCommentWithURLlinks (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  CharPtr prefix,
-  CharPtr str,
-  CharPtr suffix
-)
-
-{
-  Char     ch;
-  CharPtr  ptr;
-
-  while (! StringHasNoText (str)) {
-    ptr = StringStr (str, "http://");
-    if (ptr == NULL) {
-      if (prefix != NULL) {
-        FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      }
-      AddStringWithTildes (ffstring, str);
-      if (suffix != NULL) {
-        FFAddOneString(ffstring, suffix, FALSE, FALSE, TILDE_IGNORE);
-      }
-      return;
-    }
-
-    *ptr = '\0';
-    AddStringWithTildes (ffstring, str); 
-    *ptr = 'h';
-
-    str = ptr;
-    ptr = FindUrlEnding(str);
-
-
-    ch = *ptr;
-    *ptr = '\0';
-    if ( GetWWW(ajp) ) {
-      FFAddTextToString(ffstring, "<a href=", str, ">", FALSE, FALSE, TILDE_IGNORE);
-      FFAddTextToString(ffstring, NULL, str, "</a>", FALSE, FALSE, TILDE_IGNORE);
-    } else {
-      FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
-    }
-
-    *ptr = ch;
-    str = ptr;
-  }
-}
-
-static void CatenateCommentInGbseq (
-  GBSeqPtr gbseq,
-  CharPtr str
-)
-
-{
-  Char     ch;
-  CharPtr  tmp;
-
-  if (gbseq == NULL || StringHasNoText (str)) return;
-
-  if (StringNCmp (str, "COMMENT     ", 12) == 0) {
-    str += 12;
-  }
-  if (gbseq->comment == NULL) {
-    gbseq->comment = StringSave (str);
-  } else {
-    tmp = (CharPtr) MemNew (StringLen (gbseq->comment) + StringLen (str) + 4);
-    StringCpy (tmp, gbseq->comment);
-    StringCat (tmp, "; ");
-    StringCat (tmp, str);
-    gbseq->comment = MemFree (gbseq->comment);
-    gbseq->comment = tmp;
-  }
-
-  tmp = gbseq->comment;
-  if (tmp == NULL) return;
-  ch = *tmp;
-  while (ch != '\0') {
-    if (ch == '\n' || ch == '\r' || ch == '\t') {
-      *tmp = ' ';
-    }
-    tmp++;
-    ch = *tmp;
-  }
-  TrimSpacesAroundString (gbseq->comment);
-  Asn2gnbkCompressSpaces (gbseq->comment);
-}
-
-
-static CharPtr FormatCommentBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  Boolean            add_period;
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  CommentBlockPtr    cbp;
-  CharPtr            db;
-  DbtagPtr           dbt;
-  SeqMgrDescContext  dcontext;
-  SeqMgrFeatContext  fcontext;
-  GBSeqPtr           gbseq;
-  size_t             len;
-  ObjectIdPtr        oip;
-  CharPtr            prefix;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp;
-  Char               sfx [32];
-  CharPtr            str;
-  CharPtr            suffix;
-  CharPtr            title;
-  StringItemPtr      ffstring;
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-
-  cbp = (CommentBlockPtr) bbp;
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  /* some comments are allocated (along with possible first COMMENT label) */
-
-  if (! StringHasNoText (bbp->string)) {
-    str = StringSave (bbp->string);
-    CatenateCommentInGbseq (gbseq, str);
-    return str;
-  }
-
-  title = NULL;
-  prefix = NULL;
-  suffix = NULL;
-  add_period = FALSE;
-  sfx [0] = '\0';
-
-  if (bbp->itemtype == OBJ_SEQDESC) {
-
-    /* usually should reference comment, maploc, or region descriptor IDs */
-
-    sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext);
-    if (sdp != NULL) {
-
-      if (dcontext.seqdesctype == Seq_descr_comment) {
-
-        title = (CharPtr) sdp->data.ptrvalue;
-
-      } else if (dcontext.seqdesctype == Seq_descr_maploc) {
-
-        dbt = (DbtagPtr) sdp->data.ptrvalue;
-        if (dbt != NULL) {
-          db = dbt->db;
-          oip = dbt->tag;
-          if (oip != NULL) {
-            if (oip->str != NULL) {
-
-              title = oip->str;
-              prefix = ("Map location: ");
-
-            } else if (db != NULL && oip->id != 0) {
-
-              title = db;
-              prefix = ("Map location: (Database ");
-              sprintf (sfx, "; id # %ld).", (long) oip->id);
-              suffix = sfx;
-
-            }
-          }
-        }
-
-      } else if (dcontext.seqdesctype == Seq_descr_region) {
-
-        title = (CharPtr) sdp->data.ptrvalue;
-        prefix = "Region: ";
-
-      }
-    }
-
-  } else if (bbp->itemtype == OBJ_SEQFEAT) {
-
-    /* also have to deal with comment feature across entire sequence */
-
-    sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
-    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_COMMENT) {
-
-      title = sfp->comment;
-    }
-  }
-
-  if (title == NULL) return NULL;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return NULL;
-
-  if (cbp->first) {
-    FFStartPrint (ffstring, afp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-  } else {
-    FFStartPrint (ffstring, afp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-  }
-
-  str = StringSave (title);
-  TrimSpacesAndJunkFromEnds (str, TRUE);
-  if (! IsEllipsis (str)) {
-    s_RemovePeriodFromEnd (str);
-    len = StringLen (str);
-    if (len > 0 && str [len - 1] != '.') {
-      add_period = TRUE;
-    }
-  }
-  AddCommentWithURLlinks(ajp, ffstring, prefix, str, suffix);
-  /*
-  if ( GetWWW(ajp) && prefix == NULL && suffix == NULL) {
-    
-    AddCommentWithURLlinks (ffstring, str);
-  } else {
-    FFAddTextToString (ffstring, prefix, str, suffix, FALSE, TRUE, TILDE_OLD_EXPAND);
-  }
-  */
-  if (add_period) {
-    FFAddOneChar (ffstring, '.',FALSE);
-  }
-  MemFree (str);
-
-  str = FFEndPrint(ajp, ffstring, afp->format, 12, 12, 5, 5, "CC");
-
-  CatenateCommentInGbseq (gbseq, str);
-
-  FFRecycleString(ajp, ffstring);
-  return str;
-}
-
-/* format features section */
-
-static Boolean is_real_id (
-  SeqIdPtr sip,
-  SeqIdPtr this_sip
-)
-
-{
-  BioseqPtr  bsp;
-
-  if (sip == NULL || this_sip == NULL) return FALSE;
-
-  if (! SeqIdIn (sip, this_sip)) {
-    bsp = BioseqFind (sip);
-    if (bsp == NULL) return TRUE;  /* ??? */
-    if (bsp->repr == Seq_repr_virtual) return FALSE;
-  }
-
-  return TRUE;
-}
-
-static Boolean FlatVirtLoc (
-  BioseqPtr bsp,
-  SeqLocPtr location
-)
-
-{
-  SeqIntPtr  sintp;
-  SeqIdPtr   sip;
-  SeqPntPtr  spp;
-
-  if (bsp == NULL || location == NULL) return FALSE;
-
-  switch (location->choice) {
-    case SEQLOC_WHOLE :
-      sip = (SeqIdPtr) location->data.ptrvalue;
-      if (sip == NULL) return TRUE;
-      if (! is_real_id (sip, bsp->id)) return TRUE;
-      break;
-    case SEQLOC_INT :
-      sintp = (SeqIntPtr) location->data.ptrvalue;
-      if (sintp == NULL) return TRUE;
-      sip = sintp->id;
-      if (sip == NULL) return TRUE;
-      if (! is_real_id (sip, bsp->id)) return TRUE;
-      break;
-    case SEQLOC_PNT :
-      spp = (SeqPntPtr) location->data.ptrvalue;
-      if (spp == NULL) return TRUE;
-      sip = spp->id;
-      if (sip == NULL) return TRUE;
-      if (! is_real_id (sip, bsp->id)) return TRUE;
-      break;
-    default :
-      break;
-  }
-
-  return FALSE;
-}
-
-static Uint1    order [NUM_SEQID];
-static Boolean  order_initialized = FALSE;
-
-static CharPtr lim_str [5] = { "", ">","<", ">", "<" };
-
-static Boolean GetAccnVerFromServer (Int4 gi, CharPtr buf)
-
-{
-  AccnVerLookupFunc  func;
-  SeqMgrPtr          smp;
-  CharPtr            str;
-
-  if (buf == NULL) return FALSE;
-  *buf = '\0';
-  smp = SeqMgrWriteLock ();
-  if (smp == NULL) return FALSE;
-  func = smp->accn_ver_lookup_func;
-  SeqMgrUnlock ();
-  if (func == NULL) return FALSE;
-  str = (*func) (gi);
-  if (str == NULL) return FALSE;
-  if (StringLen (str) < 40) {
-    StringCpy (buf, str);
-  }
-  MemFree (str);
-  return TRUE;
-}
-
-
-/******************************************************************************/
-/*                              FlatLoc functions  .                          */
-/******************************************************************************/
-
-static Boolean FF_FlatNullAhead (
-  BioseqPtr bsp,
-  ValNodePtr location
-)
-
-{
-  SeqLocPtr  next;
-
-  if (bsp == NULL || location == NULL) return FALSE;
-
-  next = location->next;
-  if (next == NULL) return TRUE;
-  if (next->choice == SEQLOC_NULL) return TRUE;
-  if (FlatVirtLoc (bsp, next)) return TRUE;
-
-  return FALSE;
-}
-
-
-
-static void FlatLocSeqId (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  SeqIdPtr sip
-)
-
-{
-  BioseqPtr    bsp;
-  Char         buf [40];
-  ObjectIdPtr  oip;
-  SeqIdPtr     use_id = NULL;
-  Boolean      was_lock = FALSE;
-
-  if (ffstring == NULL || sip == NULL) return;
-
-  buf [0] = '\0';
-  bsp = BioseqFind (sip);
-  if (bsp != NULL) {
-    use_id = SeqIdSelect (bsp->id, order, NUM_SEQID);
-  } else if (sip->choice == SEQID_GI) {
-    if (GetAccnVerFromServer (sip->data.intvalue, buf)) {
-      FFAddTextToString(ffstring, NULL, buf, ":", FALSE, FALSE, TILDE_IGNORE);
-      /*AddValNodeString (head, NULL, buf, ":");*/
-      return;
-    }
-    use_id = GetSeqIdForGI (sip->data.intvalue);
-  }
-  if (use_id == NULL && bsp == NULL) {
-    bsp = BioseqLockById (sip);
-    was_lock = TRUE;
-    if (bsp != NULL) {
-      use_id = SeqIdSelect (bsp->id, order, NUM_SEQID);
-    }
-  }
-  if (use_id != NULL) {
-    SeqIdWrite (use_id, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
-    if (use_id->choice == SEQID_GI) {
-      ajp->relModeError = TRUE;
-    }
-  } else if (sip->choice == SEQID_GI) {
-    SeqIdWrite (sip, buf, PRINTID_FASTA_LONG, sizeof (buf) - 1);
-    ajp->relModeError = TRUE;
-  } else {
-    SeqIdWrite (sip, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
-    if (sip->choice == SEQID_GI) {
-      ajp->relModeError = TRUE;
-    }
-  }
-  if (was_lock) {
-    BioseqUnlock (bsp);
-  }
-  if (StringHasNoText (buf)) {
-    StringCpy (buf, "?00000");
-    ajp->relModeError = TRUE;
-    if (use_id != NULL && use_id->choice == SEQID_LOCAL) {
-      oip = (ObjectIdPtr) use_id->data.ptrvalue;
-      if (oip != NULL && (! StringHasNoText (oip->str))) {
-        StringNCpy_0 (buf, oip->str, 13);
-      }
-    }
-  }
-  FFAddTextToString(ffstring, NULL, buf, ":", FALSE, FALSE, TILDE_IGNORE);
-}
-
-
-
-static void FlatLocCaret (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  SeqIdPtr sip,
-  SeqIdPtr this_sip,
-  Int4 point,
-  IntFuzzPtr fuzz
-)
-
-{
-  Char   buf [128];
-  Uint1  index;
-
-  if (ffstring == NULL) return;
-
-  if (sip != NULL && (! SeqIdIn (sip, this_sip))) {
-    FlatLocSeqId (ajp, ffstring, sip);
-  }
-
-  buf [0] = '\0';
-  point++; /* orginal FlatLocHalfCaret was called with point + 1 */
-
-  if (fuzz != NULL) {
-    switch (fuzz->choice) {
-      case 1 :
-        sprintf (buf, "(%ld.%ld)..(%ld.%ld)",
-                 (long) (point - fuzz->a),
-                 (long) point,
-                 (long) point,
-                 (long) (point + fuzz->a));
-        break;
-      case 2 :
-        sprintf (buf, "%ld^%ld",
-                 (long) (1 + fuzz->b),
-                 (long) (1 + fuzz->a));
-        break;
-      case 3 :
-        sprintf (buf, "%ld^%ld",
-                 (long) (point - point * ((double) fuzz->a / 1000.0)),
-                 (long) (point + point * ((double) fuzz->a / 1000.0)));
-        break;
-      case 4 :
-        if (fuzz->a == 3) { /* space to right */
-          sprintf (buf, "%ld^%ld", (long) (point), (long) (point + 1));
-        } else if (fuzz->a == 4 && point > 1) { /* space to left */
-          sprintf (buf, "%ld^%ld", (long) (point - 1), (long) point);
-        } else {
-          index = (Uint1) fuzz->a;
-          if (index > 4) {
-            index = 0;
-          }
-          sprintf (buf, "%s%ld", lim_str [index], (long) point);
-        }
-        break;
-      default :
-        sprintf (buf, "%ld", (long) point);
-        break;
-    }
-  } else {
-    sprintf (buf, "%ld", (long) point);
-  }
-
-  FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
-}
-
-
-static void FlatLocPoint (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  SeqIdPtr sip,
-  SeqIdPtr this_sip,
-  Int4 point,
-  IntFuzzPtr fuzz
-)
-
-{
-  Char   buf [128];
-  Uint1  index;
-
-  if (ffstring == NULL) return;
-
-  if (sip != NULL && (! SeqIdIn (sip, this_sip))) {
-    FlatLocSeqId (ajp, ffstring, sip);
-  }
-
-  buf [0] = '\0';
-  point++;
-
-  if (fuzz != NULL) {
-    switch (fuzz->choice) {
-      case 1 :
-        sprintf (buf, "(%ld.%ld)",
-                 (long) (point - fuzz->a),
-                 (long) (point + fuzz->a));
-        break;
-      case 2 :
-        sprintf (buf, "(%ld.%ld)",
-                 (long) (1 + fuzz->b),
-                 (long) (1 + fuzz->a));
-        break;
-      case 3 :
-        sprintf (buf, "(%ld.%ld)",
-                 (long) (point - point * ((double) fuzz->a / 1000.0)),
-                 (long) (point + point * ((double) fuzz->a / 1000.0)));
-        break;
-      case 4 :
-        index = (Uint1) fuzz->a;
-        if (index > 4) {
-          index = 0;
-        }
-        sprintf (buf, "%s%ld", lim_str [index], (long) point);
-        break;
-      default :
-        sprintf (buf, "%ld", (long) point);
-        break;
-    }
-  } else {
-    sprintf (buf, "%ld", (long) point);
-  }
-
-  FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
-}
-
-
-static void FlatLocElement (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  BioseqPtr bsp,
-  SeqLocPtr location
-)
-
-{
-  Boolean     minus_strand = FALSE;
-  SeqBondPtr  sbp;
-  SeqIntPtr   sintp;
-  SeqIdPtr    sip;
-  SeqPntPtr   spp;
-  BioseqPtr   wholebsp;
-
-  if (ffstring == NULL || bsp == NULL || location == NULL) return;
-
-  switch (location->choice) {
-    case SEQLOC_WHOLE :
-      sip = (SeqIdPtr) location->data.ptrvalue;
-      if (sip == NULL) return;
-      wholebsp = BioseqFind (sip);
-      if (wholebsp == NULL) return;
-      if (is_real_id (sip, bsp->id)) {
-        FlatLocPoint (ajp, ffstring, sip, bsp->id, 0, NULL);
-        if (bsp->length > 0) {
-          FFAddOneString(ffstring, "..", FALSE, FALSE, TILDE_IGNORE);
-          FlatLocPoint (ajp, ffstring, NULL, bsp->id, bsp->length - 1, NULL);
-        }
-      }
-      break;
-    case SEQLOC_INT :
-      sintp = (SeqIntPtr) location->data.ptrvalue;
-      if (sintp == NULL) return;
-      sip = sintp->id;
-      if (sip == NULL) return;
-      if (is_real_id (sip, bsp->id)) {
-        minus_strand = (Boolean) (sintp->strand == Seq_strand_minus);
-        if (minus_strand) {
-          FFAddOneString(ffstring, "complement(", FALSE, FALSE, TILDE_IGNORE);
-        }
-        FlatLocPoint (ajp, ffstring, sip, bsp->id, sintp->from, sintp->if_from);
-        if (sintp->to > 0 &&
-            (sintp->to != sintp->from ||
-             sintp->if_from != NULL ||
-             sintp->if_to != NULL)) {
-          FFAddOneString(ffstring, "..", FALSE, FALSE, TILDE_IGNORE);
-          FlatLocPoint (ajp, ffstring, NULL, bsp->id, sintp->to, sintp->if_to);
-        }
-        if (minus_strand) {
-          FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
-        }
-      }
-      break;
-    case SEQLOC_PNT :
-      spp = (SeqPntPtr) location->data.ptrvalue;
-      if (spp == NULL) return;
-      sip = spp->id;
-      if (sip == NULL) return;
-      if (is_real_id (sip, bsp->id)) {
-        minus_strand = (Boolean) (spp->strand == Seq_strand_minus);
-        if (minus_strand) {
-          FFAddOneString(ffstring, "complement(", FALSE, FALSE, TILDE_IGNORE);
-        }
-        if (spp->fuzz != NULL) {
-          FlatLocCaret (ajp, ffstring, sip, bsp->id, spp->point, spp->fuzz);
-        } else {
-          FlatLocPoint (ajp, ffstring, sip, bsp->id, spp->point, NULL);
-        }
-        if (minus_strand) {
-          FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
-        }
-      }
-      break;
-    case SEQLOC_BOND :
-      sbp = (SeqBondPtr) location->data.ptrvalue;
-      if (sbp == NULL) return;
-      spp = sbp->a;
-      if (spp == NULL) return;
-      sip = spp->id;
-      if (sip == NULL) return;
-      FFAddOneString(ffstring, "bond(", FALSE, FALSE, TILDE_IGNORE);
-      FlatLocPoint (ajp, ffstring, sip, bsp->id, spp->point, spp->fuzz);
-      spp = sbp->b;
-      if (spp != NULL) {
-        FFAddOneString(ffstring, ",", FALSE, FALSE, TILDE_IGNORE);
-        FlatLocPoint (ajp, ffstring, NULL, bsp->id, spp->point, spp->fuzz);
-      }
-      FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
-      break;
-    default :
-      /* unexpected internal complex type or unimplemented SEQLOC_FEAT */
-      return;
-  }
-}
-
-
-
-static void FF_FlatPackedPoint (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  PackSeqPntPtr pspp,
-  BioseqPtr bsp
-)
-
-{
-  Uint1  dex;
-
-  if (ffstring == NULL || pspp == NULL || bsp == NULL) return;
-
-  for (dex = 0; dex < pspp->used; dex++) {
-    FlatLocPoint (ajp, ffstring, pspp->id, bsp->id, pspp->pnts [dex], pspp->fuzz);
-  }
-}
-
-
-static void FF_DoFlatLoc (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  BioseqPtr bsp,
-  SeqLocPtr location,
-  Boolean ok_to_complement
-);
-
-static void FF_GroupFlatLoc (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  BioseqPtr bsp,
-  SeqLocPtr location,
-  CharPtr prefix,
-  Boolean is_flat_order
-)
-
-{
-  Boolean        found_non_virt = FALSE;
-  SeqIdPtr       hold_next;
-  Int2           parens = 1;
-  PackSeqPntPtr  pspp;
-  SeqLocPtr      slp;
-  Boolean        special_mode = FALSE; /* join in order */
-
-  if (ffstring == NULL || bsp == NULL || location == NULL) return;
-
-  /* prefix will have the first parenthesis */
-
-  FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-
-  for (slp = (SeqLocPtr) location->data.ptrvalue; slp != NULL; slp = slp->next) {
-
-    if (slp->choice == SEQLOC_NULL || FlatVirtLoc (bsp, slp)) {
-      if (slp != location && slp->next != NULL) {
-        if (special_mode) {
-          special_mode = FALSE;
-          FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
-          parens--;
-        }
-      }
-      continue;
-    }
-
-    if (found_non_virt && slp->choice != SEQLOC_EMPTY && slp->choice != SEQLOC_NULL) {
-      FFAddOneString(ffstring, ",", FALSE, FALSE, TILDE_IGNORE);
-    }
-
-    switch (slp->choice) {
-      case SEQLOC_WHOLE :
-      case SEQLOC_PNT :
-      case SEQLOC_BOND :
-      case SEQLOC_FEAT :
-        found_non_virt = TRUE;
-        if (FlatVirtLoc (bsp, slp)) {
-          if (slp != location && slp->next != NULL) {
-            if (special_mode) {
-              special_mode = FALSE;
-              FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
-              parens--;
-            }
-          }
-        } else {
-          FlatLocElement (ajp, ffstring, bsp, slp);
-        }
-        break;
-      case SEQLOC_INT :
-        found_non_virt = TRUE;
-        if (is_flat_order && (! FF_FlatNullAhead (bsp, slp))) {
-          special_mode = TRUE;
-          FFAddOneString(ffstring, "join(", FALSE, FALSE, TILDE_IGNORE);
-          parens++;
-        }
-        FlatLocElement (ajp, ffstring, bsp, slp);
-        break;
-      case SEQLOC_PACKED_PNT :
-        found_non_virt = TRUE;
-        pspp = (PackSeqPntPtr) slp->data.ptrvalue;
-        if (pspp != NULL) {
-          FF_FlatPackedPoint (ajp, ffstring, pspp, bsp);
-        }
-        break;
-      case SEQLOC_PACKED_INT :
-      case SEQLOC_MIX :
-      case SEQLOC_EQUIV :
-        found_non_virt = TRUE;
-        hold_next = slp->next;
-        slp->next = NULL;
-        FF_DoFlatLoc (ajp, ffstring, bsp, slp, FALSE);
-        slp->next = hold_next;
-        break;
-      default :
-        break;
-    }
-
-  }
-
-  while (parens > 0) {
-    FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
-    parens--;
-  }
-}
-
-
-
-
-static void FF_DoFlatLoc (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  BioseqPtr bsp,
-  SeqLocPtr location,
-  Boolean ok_to_complement
-)
-
-{
-  Boolean        found_null;
-  SeqLocPtr      next_loc;
-  PackSeqPntPtr  pspp;
-  SeqLocPtr      slp;
-
-  if (ffstring == NULL || bsp == NULL || location == NULL) return;
-
-  /* deal with complement of entire location */
-
-  if (ok_to_complement && SeqLocStrand (location) == Seq_strand_minus) {
-    slp = AsnIoMemCopy ((Pointer) location,
-                        (AsnReadFunc) SeqLocAsnRead,
-                        (AsnWriteFunc) SeqLocAsnWrite);
-    if (slp != NULL) {
-      SeqLocRevCmp (slp);
-      FFAddOneString(ffstring, "complement(", FALSE, FALSE, TILDE_IGNORE);
-      FF_DoFlatLoc (ajp, ffstring, bsp, slp, FALSE);
-      FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
-    }
-    SeqLocFree (slp);
-    return;
-  }
-
-  /* handle each location component */
-
-  for (slp = location; slp != NULL; slp = slp->next) {
-
-    if (slp->choice == SEQLOC_NULL || FlatVirtLoc (bsp, slp)) continue;
-
-    /* print comma between components */
-
-    if (slp != location) {
-      FFAddOneString(ffstring, ",", FALSE, FALSE, TILDE_IGNORE);
-    }
-
-    switch (slp->choice) {
-      case SEQLOC_MIX :
-      case SEQLOC_PACKED_INT :
-        found_null = FALSE;
-        for (next_loc = (SeqLocPtr) slp->data.ptrvalue;
-         next_loc != NULL;
-         next_loc = next_loc->next) {
-          if (next_loc->choice == SEQLOC_NULL ||
-              FlatVirtLoc (bsp, next_loc) /* ||
-              LocationHasNullsBetween (slp) */ )
-            found_null = TRUE;
-        }
-        if (found_null) {
-          FF_GroupFlatLoc (ajp, ffstring, bsp, slp, "order(", TRUE);
-        } else {
-          FF_GroupFlatLoc (ajp, ffstring, bsp, slp, "join(", FALSE);
-        }
-        break;
-      case SEQLOC_EQUIV :
-        FF_GroupFlatLoc (ajp, ffstring, bsp, slp, "one-of(", FALSE);
-        break;
-      case SEQLOC_PACKED_PNT :
-        pspp = (PackSeqPntPtr) slp->data.ptrvalue;
-        if (pspp != NULL) {
-          FF_FlatPackedPoint (ajp, ffstring, pspp, bsp);
-        }
-        break;
-      default :
-        FlatLocElement (ajp, ffstring, bsp, slp);
-        break;
-    }
-
-  }
-}
-
-
-
-
-static CharPtr FlatLoc (
-  IntAsn2gbJobPtr ajp,
-  BioseqPtr bsp,
-  SeqLocPtr location,
-  Boolean masterStyle
-)
-
-{
-  Boolean     hasNulls;
-  IntFuzzPtr  fuzz = NULL;
-  SeqLocPtr   loc;
-  Boolean     noLeft;
-  Boolean     noRight;
-  Uint1       num = 1;
-  SeqPntPtr   spp;
-  CharPtr     str;
-  SeqLocPtr   tmp;
-  StringItemPtr ffstring = NULL;
-
-  if (bsp == NULL || location == NULL) return NULL;
-
-  ffstring = FFGetString(ajp);
-
-  if (! order_initialized) {
-    order [SEQID_GENBANK] = num++;
-    order [SEQID_EMBL] = num++;
-    order [SEQID_DDBJ] = num++;
-    order [SEQID_OTHER] = num++;
-    order [SEQID_TPG] = num++;
-    order [SEQID_TPE] = num++;
-    order [SEQID_TPD] = num++;
-    order [SEQID_GIBBSQ] = num++;
-    order [SEQID_GIBBMT] = num++;
-    order [SEQID_PRF] = num++;
-    order [SEQID_PDB] = num++;
-    order [SEQID_PIR] = num++;
-    order [SEQID_SWISSPROT] = num++;
-    order [SEQID_PATENT] = num++;
-    order [SEQID_GI] = num++;;
-    order [SEQID_GENERAL] = num++;
-    order [SEQID_LOCAL] = num++;
-    order [SEQID_GIIM] = num++;
-    order_initialized = TRUE;
-  }
-
-  if (masterStyle) {
-
-    /* map location from parts to segmented bioseq */
-
-    if (location->choice == SEQLOC_PNT) {
-      spp = (SeqPntPtr) location->data.ptrvalue;
-      if (spp != NULL) {
-        fuzz = spp->fuzz;
-      }
-    }
-
-    CheckSeqLocForPartial (location, &noLeft, &noRight);
-    hasNulls = LocationHasNullsBetween (location);
-    loc = SeqLocMerge (bsp, location, NULL, FALSE, TRUE, hasNulls);
-    if (loc == NULL) {
-      tmp = TrimLocInSegment (bsp, location, &noLeft, &noRight);
-      loc = SeqLocMerge (bsp, tmp, NULL, FALSE, TRUE, hasNulls);
-      SeqLocFree (tmp);
-    }
-    if (loc == NULL) {
-      return StringSave ("?");
-    }
-    FreeAllFuzz (loc);
-    SetSeqLocPartial (loc, noLeft, noRight);
-
-    if (loc->choice == SEQLOC_PNT && fuzz != NULL) {
-      spp = (SeqPntPtr) loc->data.ptrvalue;
-      if (spp != NULL && spp->fuzz == NULL) {
-        spp->fuzz = AsnIoMemCopy ((Pointer) fuzz,
-                                  (AsnReadFunc) IntFuzzAsnRead,
-                                  (AsnWriteFunc) IntFuzzAsnWrite);
-      }
-    }
-
-    FF_DoFlatLoc (ajp, ffstring, bsp, loc, TRUE);
-
-    SeqLocFree (loc);
-
-  } else {
-    FF_DoFlatLoc (ajp, ffstring, bsp, location, TRUE);
-  }
-
-  str = FFToCharPtr(ffstring);
-  FFRecycleString(ajp, ffstring);
-  return str;
-}
-
-
-
-
-static void PromoteSeqId (SeqIdPtr sip, Pointer userdata)
-
-{
-  SeqIdPtr  bestid, newid, oldid;
-
-  bestid = (SeqIdPtr) userdata;
-
-  newid = SeqIdDup (bestid);
-  if (newid == NULL) return;
-
-  oldid = ValNodeNew (NULL);
-  if (oldid == NULL) return;
-
-  MemCopy (oldid, sip, sizeof (ValNode));
-  oldid->next = NULL;
-
-  sip->choice = newid->choice;
-  sip->data.ptrvalue = newid->data.ptrvalue;
-
-  SeqIdFree (oldid);
-  ValNodeFree (newid);
-
-  SeqIdStripLocus (sip);
-}
-
-static SeqLocPtr SeqLocReMapEx (SeqIdPtr newid, SeqLocPtr seq_loc, SeqLocPtr location, Int4 offset, Boolean rev, Boolean masterStyle)
-
-{
-  BioseqPtr    bsp;
-  Boolean      hasNulls;
-  IntFuzzPtr   fuzz = NULL;
-  SeqLocPtr    loc;
-  Boolean      noLeft;
-  Boolean      noRight;
-  Uint1        num = 1;
-  SeqEntryPtr  scope;
-  SeqIdPtr     sip;
-  SeqLocPtr    slp = NULL;
-  SeqPntPtr    spp;
-  SeqLocPtr    tmp;
-
-  if (newid == NULL || seq_loc == NULL || location == NULL) return NULL;
-
-  if (masterStyle) {
-
-    sip = SeqLocId (seq_loc);
-    if (sip == NULL) return NULL;
-    bsp = BioseqFind (sip);
-    if (bsp == NULL) {
-      scope = SeqEntrySetScope (NULL);
-      bsp = BioseqFind (sip);
-      SeqEntrySetScope (scope);
-    }
-    if (bsp == NULL) return NULL;
-    sip = SeqIdFindBest (bsp->id, 0);
-
-    /* map location from parts to segmented bioseq */
-
-    if (location->choice == SEQLOC_PNT) {
-      spp = (SeqPntPtr) location->data.ptrvalue;
-      if (spp != NULL) {
-        fuzz = spp->fuzz;
-      }
-    }
-
-    CheckSeqLocForPartial (location, &noLeft, &noRight);
-    hasNulls = LocationHasNullsBetween (location);
-    loc = SeqLocMerge (bsp, location, NULL, FALSE, TRUE, hasNulls);
-    if (loc == NULL) {
-      tmp = TrimLocInSegment (bsp, location, &noLeft, &noRight);
-      loc = SeqLocMerge (bsp, tmp, NULL, FALSE, TRUE, hasNulls);
-      SeqLocFree (tmp);
-    }
-    if (loc == NULL) {
-      return NULL;
-    }
-    FreeAllFuzz (loc);
-    SetSeqLocPartial (loc, noLeft, noRight);
-
-    if (loc->choice == SEQLOC_PNT && fuzz != NULL) {
-      spp = (SeqPntPtr) loc->data.ptrvalue;
-      if (spp != NULL && spp->fuzz == NULL) {
-        spp->fuzz = AsnIoMemCopy ((Pointer) fuzz,
-                                  (AsnReadFunc) IntFuzzAsnRead,
-                                  (AsnWriteFunc) IntFuzzAsnWrite);
-      }
-    }
-
-    scope = SeqEntrySetScope (NULL);
-    slp = SeqLocReMap (newid, seq_loc, loc, offset, rev);
-    SeqEntrySetScope (scope);
-
-    SeqLocFree (loc);
-
-    VisitSeqIdsInSeqLoc (slp, (Pointer) sip, PromoteSeqId);
-  } else {
-
-    scope = SeqEntrySetScope (NULL);
-    slp = SeqLocReMap (newid, seq_loc, location, offset, rev);
-    SeqEntrySetScope (scope);
-  }
-
-  return slp;
-}
-
-
-/******************************************************************************/
-/*                            End FlatLoc functions.                          */
-/******************************************************************************/
-
-
-
-static void SubSourceToQualArray (
-  SubSourcePtr ssp,
-  QualValPtr qvp
-)
-
-{
-  Int2   idx;
-  Uint1  subtype;
-
-  if (ssp == NULL || qvp == NULL) return;
-
-  while (ssp != NULL) {
-    subtype = ssp->subtype;
-    if (subtype == 255) {
-      subtype = 29;
-    }
-    if (subtype < 30) {
-      idx = subSourceToSourceIdx [subtype];
-      if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) {
-        if (qvp [idx].ssp == NULL) {
-          qvp [idx].ssp = ssp;
-        }
-      }
-    }
-    ssp = ssp->next;
-  }
-}
-
-static Int2 orgModToSourceIdx [38] = {
-  SCQUAL_zero_orgmod,
-  SCQUAL_one_orgmod,
-  SCQUAL_strain,
-  SCQUAL_sub_strain,
-  SCQUAL_type,
-  SCQUAL_sub_type,
-  SCQUAL_variety,
-  SCQUAL_serotype,
-  SCQUAL_serogroup,
-  SCQUAL_serovar,
-  SCQUAL_cultivar,
-  SCQUAL_pathovar,
-  SCQUAL_chemovar,
-  SCQUAL_biovar,
-  SCQUAL_biotype,
-  SCQUAL_group,
-  SCQUAL_sub_group,
-  SCQUAL_isolate,
-  SCQUAL_common,
-  SCQUAL_acronym,
-  SCQUAL_dosage,
-  SCQUAL_spec_or_nat_host,
-  SCQUAL_sub_species,
-  SCQUAL_specimen_voucher,
-  SCQUAL_authority,
-  SCQUAL_forma,
-  SCQUAL_forma_specialis,
-  SCQUAL_ecotype,
-  SCQUAL_synonym,
-  SCQUAL_anamorph,
-  SCQUAL_teleomorph,
-  SCQUAL_breed,
-  SCQUAL_gb_acronym,
-  SCQUAL_gb_anamorph,
-  SCQUAL_gb_synonym,
-  SCQUAL_old_lineage,
-  SCQUAL_old_name,
-  SCQUAL_orgmod_note
-};
-
-static void OrgModToQualArray (
-  OrgModPtr omp,
-  QualValPtr qvp
-)
-
-{
-  Int2   idx;
-  Uint1  subtype;
-
-  if (omp == NULL || qvp == NULL) return;
-
-  while (omp != NULL) {
-    subtype = omp->subtype;
-    if (subtype == 253) {
-      subtype = 35;
-    } else if (subtype == 254) {
-      subtype = 36;
-    } else if (subtype == 255) {
-      subtype = 37;
-    }
-    if (subtype < 38) {
-      idx = orgModToSourceIdx [subtype];
-      if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) {
-        if (qvp [idx].omp == NULL) {
-          qvp [idx].omp = omp;
-        }
-      }
-    }
-    omp = omp->next;
-  }
-}
-
-static CharPtr organelleQual [] = {
-  NULL,
-  NULL,
-  "/organelle=\"plastid:chloroplast\"",
-  "/organelle=\"plastid:chromoplast\"",
-  "/organelle=\"mitochondrion:kinetoplast\"",
-  "/organelle=\"mitochondrion\"",
-  "/organelle=\"plastid\"",
-  "/macronuclear",
-  NULL,
-  "/plasmid=\"\"",
-  "/transposon=\"\"",
-  "/insertion_seq=\"\"",
-  "/organelle=\"plastid:cyanelle\"",
-  "/proviral",
-  "/virion",
-  "/organelle=\"nucleomorph\"",
-  "/organelle=\"plastid:apicoplast\"",
-  "/organelle=\"plastid:leucoplast\"",
-  "/organelle=\"plastid:proplastid\"",
-  NULL
-};
-
-static Boolean StringIsJustQuotes (
-  CharPtr str
-)
-
-{
-  Nlm_Uchar  ch;    /* to use 8bit characters in multibyte languages */
-
-  if (str != NULL) {
-    ch = *str;
-    while (ch != '\0') {
-      if (ch > ' ' && ch != '"' && ch != '\'') {
-        return FALSE;
-      }
-      str++;
-      ch = *str;
-    }
-  }
-  return TRUE;
-}
-
-static CharPtr RemoveAllSpaces (
-  CharPtr str
-)
-
-{
-  Char     ch;
-  CharPtr  dst;
-  CharPtr  ptr;
-
-  if (str == NULL || str [0] == '\0') return NULL;
-
-  dst = str;
-  ptr = str;
-  ch = *ptr;
-  while (ch != '\0') {
-    if (ch != ' ') {
-      *dst = ch;
-      dst++;
-    }
-    ptr++;
-    ch = *ptr;
-  }
-  *dst = '\0';
-
-  return str;
-}
-
-static void AddFeatureToGbseq (
-  GBSeqPtr gbseq,
-  GBFeaturePtr gbfeat,
-  CharPtr str,
-  SeqFeatPtr sfp
-)
-
-{
-  Char            ch;
-  CharPtr         copy;
-  GBQualifierPtr  gbqual;
-  GBQualifierPtr  last = NULL;
-  CharPtr         ptr;
-  CharPtr         qual;
-  CharPtr         val;
-
-  if (gbseq == NULL || gbfeat == NULL || StringHasNoText (str)) return;
-
-  copy = StringSave (str);
-
-  /* link in reverse order, to be reversed in slash block */
-
-  gbfeat->next = gbseq->feature_table;
-  gbseq->feature_table = gbfeat;
-
-  /* now parse qualifiers */
-
-  ptr = StringStr (copy, "                     /");
-  while (ptr != NULL) {
-    qual = ptr + 22;
-    val = qual;
-    ch = *val;
-    while (ch != '=' && ch != '\n' && ch != '\0') {
-      val++;
-      ch = *val;
-    }
-    /*
-    val = StringChr (qual, '=');
-    if (val == NULL) {
-      val = StringChr (qual, '\n');
-    }
-    */
-    if (ch != '\0' /* val != NULL */) {
-      *val = '\0';
-      val++;
-      if (ch == '=') {
-        if (*val == '"') {
-          val++;
-        }
-        ptr = StringStr (val, "\n                     /");
-        if (ptr != NULL) {
-          *ptr = '\0';
-          ptr++;
-        }
-      } else {
-        ptr = StringStr (val, "                     /");
-        val = NULL;
-      }
-      gbqual = GBQualifierNew ();
-      if (gbqual != NULL) {
-        gbqual->name = StringSave (qual);
-        if (! StringHasNoText (val)) {
-          gbqual->value = StringSave (val);
-          CleanQualValue (gbqual->value);
-          Asn2gnbkCompressSpaces (gbqual->value);
-          if (sfp != NULL) {
-            if (sfp->data.choice == SEQFEAT_CDREGION &&
-                StringICmp (qual, "translation") == 0) {
-              RemoveAllSpaces (gbqual->value);
-            } else if (sfp->data.choice == SEQFEAT_RNA &&
-                       StringICmp (qual, "transcription") == 0) {
-              RemoveAllSpaces (gbqual->value);
-            } else if (sfp->data.choice == SEQFEAT_PROT &&
-                       StringICmp (qual, "peptide") == 0) {
-              RemoveAllSpaces (gbqual->value);
-            }
-          }
-        }
-      }
-    } else {
-      gbqual = GBQualifierNew ();
-      if (gbqual != NULL) {
-        gbqual->name = StringSave (qual);
-      }
-    }
-    if (gbfeat->quals == NULL) {
-      gbfeat->quals = gbqual;
-    } else if (last != NULL) {
-      last->next = gbqual;
-    }
-    last = gbqual;
-  }
-
-  MemFree (copy);
-}
-
-static CharPtr GetMolTypeQual (
-  BioseqPtr bsp
-)
-
-{
-  SeqMgrDescContext  dcontext;
-  MolInfoPtr         mip;
-  SeqDescrPtr        sdp;
-
-  if (bsp == NULL) return NULL;
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
-  if (sdp == NULL) return NULL;
-  mip = (MolInfoPtr) sdp->data.ptrvalue;
-  if (mip == NULL) return NULL;
-
-  switch (mip->biomol) {
-    case 0 :
-      switch (bsp->mol) {
-        case Seq_mol_dna :
-          return "unassigned DNA";
-        case Seq_mol_rna :
-          return "unassigned RNA";
-        case Seq_mol_na :
-          break;
-        default :
-          break;
-      }
-      break;
-    case MOLECULE_TYPE_GENOMIC :
-      switch (bsp->mol) {
-        case Seq_mol_dna :
-          return "genomic DNA";
-        case Seq_mol_rna :
-          return "genomic RNA";
-        case Seq_mol_na :
-          break;
-        default :
-          break;
-      }
-      break;
-    case MOLECULE_TYPE_PRE_MRNA :
-      return "pre-RNA";
-    case MOLECULE_TYPE_MRNA :
-      return "mRNA";
-    case MOLECULE_TYPE_RRNA :
-      return "rRNA";
-    case MOLECULE_TYPE_TRNA :
-      return "tRNA";
-    case MOLECULE_TYPE_SNRNA :
-      return "snRNA";
-    case MOLECULE_TYPE_SCRNA :
-      return "scRNA";
-    case MOLECULE_TYPE_PEPTIDE :
-      break;
-    case MOLECULE_TYPE_OTHER_GENETIC_MATERIAL :
-      switch (bsp->mol) {
-        case Seq_mol_dna :
-          return "other DNA";
-        case Seq_mol_rna :
-          return "other RNA";
-        case Seq_mol_na :
-          break;
-        default :
-          break;
-      }
-      break;
-    case MOLECULE_TYPE_GENOMIC_MRNA_MIX :
-      break;
-    case MOLECULE_TYPE_CRNA :
-      return "other RNA";
-      break;
-    case MOLECULE_TYPE_SNORNA :
-      return "snoRNA";
-      break;
-    case MOLECULE_TYPE_TRANSCRIBED_RNA :
-      return "other RNA";
-      break;
-    case 255 :
-      switch (bsp->mol) {
-        case Seq_mol_dna :
-          return "other DNA";
-        case Seq_mol_rna :
-          return "other RNA";
-        case Seq_mol_na :
-          break;
-        default :
-          break;
-      }
-      break;
-    default :
-      break;
-  }
-
-  return NULL;
-}
-
-static CharPtr FormatSourceFeatBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  Boolean            add_period;
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  BioSourcePtr       biop = NULL;
-  BioseqPtr          bsp;
-  Char               buf [80];
-  CharPtr            common = NULL;
-  DbtagPtr           dbt;
-  SeqMgrDescContext  dcontext;
-  SeqMgrFeatContext  fcontext;
-  GBFeaturePtr       gbfeat = NULL;
-  GBSeqPtr           gbseq;
-  Int2               i;
-  Uint1              idx;
-  IntSrcBlockPtr     isp;
-  Boolean            is_desc = TRUE;
-  Int2               j;
-  Uint1              jdx;
-  Uint1              lastomptype;
-  Uint1              lastssptype;
-  SeqLocPtr          location = NULL;
-  CharPtr            notestr;
-  Uint1Ptr           notetbl = NULL;
-  Boolean            okay;
-  ObjectIdPtr        oip;
-  OrgModPtr          omp;
-  OrgNamePtr         onp = NULL;
-  OrgRefPtr          orp = NULL;
-  CharPtr            prefix;
-  Uint1Ptr           qualtbl = NULL;
-  QualValPtr         qvp;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp = NULL;
-  SubSourcePtr       ssp;
-  CharPtr            str;
-  CharPtr            taxname = NULL;
-  ValNodePtr         vnp;
-  StringItemPtr      ffstring, unique;
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-  bsp = asp->bsp;
-  if (bsp == NULL) return NULL;
-  qvp = afp->qvp;
-  if (qvp == NULL) return NULL;
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (! StringHasNoText (bbp->string)) return StringSave (bbp->string);
-
-  isp = (IntSrcBlockPtr) bbp;
-
-  /* could be descriptor or feature */
-
-  if (bbp->itemtype == OBJ_SEQDESC) {
-    sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext);
-    if (sdp != NULL && dcontext.seqdesctype == Seq_descr_source) {
-      biop = (BioSourcePtr) sdp->data.ptrvalue;
-    }
-  } else if (bbp->itemtype == OBJ_SEQFEAT) {
-    sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
-    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_BIOSRC) {
-      biop = (BioSourcePtr) sfp->data.value.ptrvalue;
-    }
-    is_desc = FALSE;
-  }
-
-  if (biop == NULL) return NULL;
-
-  unique = FFGetString(ajp);
-  if ( unique == NULL ) return NULL;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return NULL;
-
-  FFStartPrint (ffstring, afp->format, 5, 21, NULL, 0, 5, 21, "FT", FALSE);
-  FFAddOneString (ffstring, "source", FALSE, FALSE, TILDE_IGNORE);
-  FFAddNChar(ffstring, ' ', 21 - 5 - StringLen("source"), FALSE);
-
-  if (gbseq != NULL) {
-    gbfeat = GBFeatureNew ();
-    if (gbfeat != NULL) {
-      gbfeat->key = StringSave ("source");
-    }
-  }
-
-  location = isp->loc;
-
-  str = FlatLoc (ajp, bsp, location, ajp->masterStyle);
-  if ( GetWWW(ajp) ) {
-    FF_www_featloc (ffstring, str);
-  } else {
-    FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_IGNORE);
-  }
-  FFAddOneChar(ffstring, '\n', FALSE);
-
-  if (gbseq != NULL) {
-    if (gbfeat != NULL) {
-      if (! StringHasNoText (str)) {
-        gbfeat->location = StringSave (str);
-      } else {
-        gbfeat->location = StringSave ("");
-      }
-    }
-  }
-
-  MemFree (str);
-
-  orp = biop->org;
-  if (orp != NULL) {
-    taxname = orp->taxname;
-    /* common = orp->common; */
-  }
-  if (StringHasNoText (taxname)) {
-    if (ajp->flags.needOrganismQual) {
-      taxname = "unknown";
-      common = orp->common;
-#ifdef ASN2GNBK_PRINT_UNKNOWN_ORG
-    } else {
-      taxname = "unknown";
-      common = orp->common;
-#endif
-    }
-  }
-
-  /* populate qualifier table from biosource fields */
-
-  qvp [SCQUAL_organism].str = taxname;
-  qvp [SCQUAL_common_name].str = common;
-
-  if (biop->is_focus) {
-    qvp [SCQUAL_focus].ble = TRUE;
-  }
-
-  str = GetMolTypeQual (bsp);
-  if (str == NULL) {
-    switch (bsp->mol) {
-      case Seq_mol_dna :
-        str = "unassigned DNA";
-        break;
-      case Seq_mol_rna :
-        str = "unassigned RNA";
-        break;
-      case Seq_mol_aa :
-        break;
-      default :
-        str = "unassigned DNA";
-        break;
-    }
-  }
-  qvp [SCQUAL_mol_type].str = str;
-
-  SubSourceToQualArray (biop->subtype, qvp);
-
-  if (orp != NULL) {
-    onp = orp->orgname;
-    if (onp != NULL) {
-      OrgModToQualArray (onp->mod, qvp);
-    }
-
-    if (! is_desc) {
-      qvp [SCQUAL_unstructured].vnp = orp->mod;
-    }
-    qvp [SCQUAL_db_xref].vnp = orp->db;
-  }
-
-  if (sfp != NULL) {
-    qvp [SCQUAL_org_xref].vnp = sfp->dbxref;
-  }
-
-  /* organelle currently prints /mitochondrion, /virion, etc. */
-
-  qvp [SCQUAL_organelle].num = biop->genome;
-
-  /* some qualifiers are flags in genome and names in subsource, print once with name */
-
-  if (qvp [SCQUAL_ins_seq_name].ssp != NULL &&
-      qvp [SCQUAL_organelle].num == GENOME_insertion_seq) {
-    qvp [SCQUAL_organelle].num = 0;
-  }
-  if (qvp [SCQUAL_plasmid_name].ssp != NULL &&
-      qvp [SCQUAL_organelle].num == GENOME_plasmid) {
-    qvp [SCQUAL_organelle].num = 0;
-  }
-  /* AF095904.1
-  if (qvp [SCQUAL_plastid_name].ssp != NULL &&
-      qvp [SCQUAL_organelle].num == GENOME_plastid) {
-    qvp [SCQUAL_organelle].num = 0;
-  }
-  */
-  if (qvp [SCQUAL_transposon_name].ssp != NULL &&
-      qvp [SCQUAL_organelle].num == GENOME_transposon) {
-    qvp [SCQUAL_organelle].num = 0;
-  }
-
-  if (sfp != NULL) {
-    qvp [SCQUAL_seqfeat_note].str = sfp->comment;
-  }
-
-  /* now print qualifiers from table */
-
-  qualtbl = source_qual_order;
-  if (is_desc) {
-    notetbl = source_desc_note_order;
-  } else {
-    notetbl = source_feat_note_order;
-  }
-
-  for (i = 0, idx = qualtbl [i]; idx != 0; i++, idx = qualtbl [i]) {
-
-    lastomptype = 0;
-    lastssptype = 0;
-    switch (asn2gnbk_source_quals [idx].qualclass) {
-
-      case Qual_class_ignore :
-        break;
-
-      case Qual_class_string :
-        if (! StringHasNoText (qvp [idx].str)) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=", 
-                            FALSE, FALSE, TILDE_IGNORE);
-          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"", 
-                            FALSE, FALSE, TILDE_TO_SPACES);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_boolean :
-        if (qvp [idx].ble) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "\n",
-                            FALSE, TRUE, TILDE_IGNORE);
-        }
-        break;
-
-      case Qual_class_organelle :
-        j = (Int2) qvp [idx].num;
-        if (organelleQual [j] != NULL) {
-          FFAddTextToString(ffstring, NULL, organelleQual[j], "\n",
-                            FALSE, FALSE, TILDE_IGNORE);
-        }
-        break;
-
-      case Qual_class_orgmod :
-        omp = qvp [idx].omp;
-        if (lastomptype == 0 && omp != NULL) {
-          lastomptype = omp->subtype;
-        }
-        while (omp != NULL && omp->subtype == lastomptype) {
-          if (StringIsJustQuotes (omp->subname)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=\"\"\n",
-                              FALSE, TRUE, TILDE_IGNORE);
-          } else if (! StringHasNoText (omp->subname)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=",
-                              FALSE, TRUE, TILDE_IGNORE);
-            FFAddTextToString(ffstring, "\"", omp->subname, "\"\n",
-                              FALSE, TRUE, TILDE_TO_SPACES);
-          }
-          omp = omp->next;
-        }
-        break;
-
-      case Qual_class_subsource :
-        ssp = qvp [idx].ssp;
-        if (lastssptype == 0 && ssp != NULL) {
-          lastssptype = ssp->subtype;
-        }
-        while (ssp != NULL && ssp->subtype == lastssptype) {
-          if (ssp->subtype == SUBSRC_germline ||
-              ssp->subtype == SUBSRC_rearranged ||
-              ssp->subtype == SUBSRC_transgenic ||
-              ssp->subtype == SUBSRC_environmental_sample) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "\n",
-                              FALSE, TRUE, TILDE_TO_SPACES);
-          } else if (StringIsJustQuotes (ssp->name)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=\"\"\n",
-                              FALSE, TRUE, TILDE_IGNORE);
-          } else if (! StringHasNoText (ssp->name)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=",
-                              FALSE, TRUE, TILDE_IGNORE);
-            FFAddTextToString(ffstring, "\"", ssp->name, "\"\n",
-                              FALSE, TRUE, TILDE_TO_SPACES);
-          }
-          ssp = ssp->next;
-        }
-        break;
-
-      case Qual_class_pubset :
-        break;
-
-      case Qual_class_quote :
-        break;
-
-      case Qual_class_noquote :
-        break;
-
-      case Qual_class_label :
-        break;
-
-      case Qual_class_db_xref :
-        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
-          buf [0] = '\0';
-          dbt = (DbtagPtr) vnp->data.ptrvalue;
-          if (dbt != NULL && (! StringHasNoText (dbt->db))) {
-            oip = dbt->tag;
-            if (oip != NULL) {
-
-              okay = TRUE;
-              if (ajp->flags.dropBadDbxref) {
-                /* if RELEASE_MODE, drop unknown dbtag */
-                okay = FALSE;
-                for (j = 0; legalDbXrefs [j] != NULL; j++) {
-                  if (StringCmp (dbt->db, legalDbXrefs [j]) == 0) {
-                    okay = TRUE;
-                  }
-                }
-              }
-
-              if (okay) {
-                if (! StringHasNoText (oip->str)) {
-                  if (StringLen (dbt->db) + StringLen (oip->str) < 80) {
-                    sprintf (buf, "%s", oip->str);
-                  }
-                } else {
-                  sprintf (buf, "%ld", (long) oip->id);
-                }
-              }
-            }
-          }
-          if (! StringHasNoText (buf)) {
-            FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-            FF_www_db_xref(ajp, ffstring, dbt->db, buf);
-            FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-          }
-        }
-        break;
-
-      case Qual_class_illegal :
-        break;
-
-      case Qual_class_note :
-        if (! ajp->flags.srcQualsToNote) {
-
-          /* in sequin_mode and dump_mode, all orgmods and subsources show up as separate /qualifiers */
-
-          for (j = 0, jdx = notetbl [j]; jdx != 0; j++, jdx = notetbl [j]) {
-
-            lastomptype = 0;
-            lastssptype = 0;
-            switch (asn2gnbk_source_quals [jdx].qualclass) {
-
-              case Qual_class_orgmod :
-                if (jdx == SCQUAL_orgmod_note) break;
-                omp = qvp [jdx].omp;
-                if (lastomptype == 0 && omp != NULL) {
-                  lastomptype = omp->subtype;
-                }
-                while (omp != NULL && omp->subtype == lastomptype) {
-                  if (StringIsJustQuotes (omp->subname)) {
-                    FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [jdx].name, "=\"\"\n",
-                              FALSE, TRUE, TILDE_IGNORE);
-                  } else if (! StringHasNoText (omp->subname)) {
-                    FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [jdx].name, "=",
-                                      FALSE, TRUE, TILDE_IGNORE);
-                    FFAddTextToString(ffstring, "\"", omp->subname, "\"\n",
-                                      FALSE, TRUE, TILDE_TO_SPACES);
-                  }
-                  omp = omp->next;
-                }
-                break;
-
-              case Qual_class_subsource :
-                if (jdx == SCQUAL_subsource_note) break;
-                ssp = qvp [jdx].ssp;
-                if (lastssptype == 0 && ssp != NULL) {
-                  lastssptype = ssp->subtype;
-                }
-                while (ssp != NULL && ssp->subtype == lastssptype) {
-                  if (StringIsJustQuotes (ssp->name)) {
-                    FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [jdx].name, "=\"\"\n",
-                                      FALSE, TRUE, TILDE_IGNORE);
-
-                  } else if (! StringHasNoText (ssp->name)) {
-                    FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [jdx].name, "=",
-                                      FALSE, TRUE, TILDE_IGNORE);
-                    FFAddTextToString(ffstring, "\"", ssp->name, "\"\n",
-                                      FALSE, TRUE, TILDE_TO_SPACES);
-                  }
-                  ssp = ssp->next;
-                }
-                break;
-
-              default :
-                break;
-            }
-          }
-        }
-
-        notestr = NULL;
-        prefix = "";
-        add_period = FALSE;
-
-        if (biop->genome == 8) {
-          FFAddTextToString(unique, "", "extrachromosomal", NULL, FALSE, FALSE, TILDE_IGNORE); 
-          prefix = "\n";
-        }
-
-        for (j = 0, jdx = notetbl [j]; jdx != 0; j++, jdx = notetbl [j]) {
-
-          lastomptype = 0;
-          lastssptype = 0;
-          switch (asn2gnbk_source_quals [jdx].qualclass) {
-
-            case Qual_class_string :
-              if (! StringHasNoText (qvp [jdx].str)) {
-                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, NULL);
-                add_period = FALSE;
-                prefix = "\n";
-              }
-              break;
-
-            case Qual_class_orgmod :
-              if ((! ajp->flags.srcQualsToNote) && jdx != SCQUAL_orgmod_note) break;
-              omp = qvp [jdx].omp;
-              if (lastomptype == 0 && omp != NULL) {
-                lastomptype = omp->subtype;
-              }
-              while (omp != NULL && omp->subtype == lastomptype) {
-                if (! StringHasNoText (omp->subname)) {
-                  if (jdx == SCQUAL_orgmod_note) {
-                    sprintf (buf, "%s", prefix);
-                  } else {
-                    sprintf (buf, "%s%s: ", prefix, asn2gnbk_source_quals [jdx].name);
-                  }
-
-                  str = StringSave (omp->subname);
-                  add_period = s_RemovePeriodFromEnd (str);
-                  if (jdx == SCQUAL_orgmod_note) {
-                    FFAddString_NoRedund (unique, buf, str, NULL);
-                  } else {
-                    FFAddTextToString(unique, buf, str, NULL, FALSE, FALSE, TILDE_IGNORE);
-                  }
-                  MemFree (str);
-
-                  if (jdx == SCQUAL_orgmod_note) {
-                    if (add_period) {
-                      prefix = ".\n";
-                    } else {
-                      prefix = "\n";
-                    }
-                  } else {
-                    prefix = "; ";
-                  }
-                }
-                omp = omp->next;
-              }
-              break;
-
-            case Qual_class_subsource :
-              if ((! ajp->flags.srcQualsToNote) && jdx != SCQUAL_subsource_note) break;
-              ssp = qvp [jdx].ssp;
-              if (lastssptype == 0 && ssp != NULL) {
-                lastssptype = ssp->subtype;
-              }
-              while (ssp != NULL && ssp->subtype == lastssptype) {
-                if (! StringHasNoText (ssp->name)) {
-                  if (jdx == SCQUAL_subsource_note) {
-                    sprintf (buf, "%s", prefix);
-                  } else {
-                    sprintf (buf, "%s%s: ", prefix, asn2gnbk_source_quals [jdx].name);
-                  }
-
-                  str = StringSave (ssp->name);
-                  add_period = s_RemovePeriodFromEnd (str);
-                  if (jdx == SCQUAL_subsource_note) {
-                    FFAddString_NoRedund (unique, buf, str, NULL);
-                  } else {
-                    FFAddTextToString(unique, buf, str, NULL, FALSE, FALSE, TILDE_IGNORE);
-                  }
-                  MemFree (str);
-
-                  if (jdx == SCQUAL_subsource_note) {
-                    if (add_period) {
-                      prefix = ".\n";
-                    } else {
-                      prefix = "\n";
-                    }
-                  } else {
-                    prefix = "; ";
-                 }
-                }
-                ssp = ssp->next;
-              }
-              break;
-
-            case Qual_class_valnode :
-              for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
-                str = (CharPtr) vnp->data.ptrvalue;
-                if (! StringHasNoText (str)) {
-                  FFAddString_NoRedund (unique, prefix, str, NULL);
-                  add_period = FALSE;
-                  prefix = "; ";
-                }
-              }
-              break;
-
-            default :
-              break;
-          }
-        }
-        if ( !FFEmpty(unique) ) {
-          notestr = FFToCharPtr(unique);
-        
-          if (add_period) {
-            s_AddPeriodToEnd (notestr);
-          }
-
-#ifdef ASN2GNBK_STRIP_NOTE_PERIODS
-          if (! IsEllipsis (notestr))
-            s_RemovePeriodFromEnd (notestr);
-#endif
-
-          FFAddOneString (ffstring, "/note=\"", FALSE, FALSE, TILDE_IGNORE);
-          if (is_desc) {
-            /* AB055064.1 says TILDE_IGNORE on descriptors */
-            FFAddOneString (ffstring, notestr, FALSE, TRUE, TILDE_IGNORE);
-          } else {
-            /* ASZ93724.1 says TILDE_EXPAND on features */
-            FFAddOneString (ffstring, notestr, FALSE, TRUE, TILDE_EXPAND);
-          }
-          FFAddOneString (ffstring, "\"", FALSE, FALSE, TILDE_IGNORE);
-
-          MemFree (notestr);
-        }
-        break;
-      default :
-        break;
-    }
-  }
-
-  /* and then deal with the various note types separately (not in order table) */
-
-  str = FFEndPrint(ajp, ffstring, afp->format, 21, 21, 5, 21, "FT"); 
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (gbseq != NULL) {
-    if (gbfeat != NULL) {
-      AddFeatureToGbseq (gbseq, gbfeat, str, NULL);
-    }
-  }
-
-  FFRecycleString(ajp, unique);
-  FFRecycleString(ajp, ffstring);
-  return str;
-}
-
-
-typedef struct qualfeatur {
-  CharPtr     name;
-  Uint1       featurclass;
-} QualFeatur, PNTR QualFeaturPtr;
-
-#define NUM_GB_QUALS 26
-
-static QualFeatur qualToFeature [NUM_GB_QUALS] = {
-  { "allele",         FTQUAL_allele         },
-  { "bound_moiety",   FTQUAL_bound_moiety   },
-  { "clone",          FTQUAL_clone          },
-  { "codon",          FTQUAL_codon          },
-  { "cons_splice",    FTQUAL_cons_splice    },
-  { "direction",      FTQUAL_direction      },
-  { "EC_number",      FTQUAL_EC_number      },
-  { "frequency",      FTQUAL_frequency      },
-  { "function",       FTQUAL_function       },
-  { "insertion_seq",  FTQUAL_insertion_seq  },
-  { "label",          FTQUAL_label          },
-  { "map",            FTQUAL_map            },
-  { "mod_base",       FTQUAL_mod_base       },
-  { "number",         FTQUAL_number         },
-  { "operon",         FTQUAL_operon         },
-  { "organism",       FTQUAL_organism       },
-  { "PCR_conditions", FTQUAL_PCR_conditions },
-  { "phenotype",      FTQUAL_phenotype      },
-  { "product",        FTQUAL_product_quals  },
-  { "replace",        FTQUAL_replace        },
-  { "rpt_family",     FTQUAL_rpt_family     },
-  { "rpt_type",       FTQUAL_rpt_type       },
-  { "rpt_unit",       FTQUAL_rpt_unit       },
-  { "standard_name",  FTQUAL_standard_name  },
-  { "transposon",     FTQUAL_transposon     },
-  { "usedin",         FTQUAL_usedin         }
-};
-
-static Int2 GbqualToFeaturIndex (
-  CharPtr qualname
-)
-
-{
-  Int2  L, R, mid;
-
-  if (qualname == NULL || *qualname == '\0') return 0;
-
-  L = 0;
-  R = NUM_GB_QUALS - 1;
-
-  while (L < R) {
-    mid = (L + R) / 2;
-    if (StringICmp (qualToFeature [mid].name, qualname) < 0) {
-      L = mid + 1;
-    } else {
-      R = mid;
-    }
-  }
-
-  if (StringICmp (qualToFeature [R].name, qualname) == 0) {
-    return qualToFeature [R].featurclass;
-  }
-
-  return 0;
-}
-
-#define NUM_ILLEGAL_QUALS 14
-
-static FeaturQual illegalGbqualList [NUM_ILLEGAL_QUALS] = {
-  { "anticodon",      Qual_class_noquote },
-  { "citation",       Qual_class_noquote },
-  { "codon_start",    Qual_class_noquote },
-  { "db_xref",        Qual_class_quote   },
-  { "evidence",       Qual_class_noquote },
-  { "exception",      Qual_class_quote   },
-  { "gene",           Qual_class_quote   },
-  { "note",           Qual_class_quote   },
-  { "protein_id",     Qual_class_quote   },
-  { "pseudo",         Qual_class_noquote },
-  { "transcript_id",  Qual_class_quote   },
-  { "transl_except",  Qual_class_noquote },
-  { "transl_table",   Qual_class_noquote },
-  { "translation",    Qual_class_quote   },
-};
-
-static Int2 IllegalGbqualToClass (
-  CharPtr qualname
-)
-
-{
-  Int2  L, R, mid;
-
-  if (qualname == NULL || *qualname == '\0') return 0;
-
-  L = 0;
-  R = NUM_ILLEGAL_QUALS - 1;
-
-  while (L < R) {
-    mid = (L + R) / 2;
-    if (StringICmp (illegalGbqualList [mid].name, qualname) < 0) {
-      L = mid + 1;
-    } else {
-      R = mid;
-    }
-  }
-
-  if (StringICmp (illegalGbqualList [R].name, qualname) == 0) {
-    return illegalGbqualList [R].qualclass;
-  }
-
-  return 0;
-}
-
-static CharPtr trnaList [] = {
-  "tRNA-Gap",
-  "tRNA-Ala",
-  "tRNA-Asx",
-  "tRNA-Cys",
-  "tRNA-Asp",
-  "tRNA-Glu",
-  "tRNA-Phe",
-  "tRNA-Gly",
-  "tRNA-His",
-  "tRNA-Ile",
-  "tRNA-Lys",
-  "tRNA-Leu",
-  "tRNA-Met",
-  "tRNA-Asn",
-  "tRNA-Pro",
-  "tRNA-Gln",
-  "tRNA-Arg",
-  "tRNA-Ser",
-  "tRNA-Thr",
-  "tRNA-Sec",
-  "tRNA-Val",
-  "tRNA-Trp",
-  "tRNA-OTHER",
-  "tRNA-Tyr",
-  "tRNA-Glx",
-  "tRNA-TERM",
-  NULL
-};
-
-static CharPtr evidenceText [] = {
-  NULL, "experimental", "not_experimental"
-};
-
-static CharPtr secStrText [] = {
-  NULL, "helix", "sheet", "turn"
-};
-
-static CharPtr  oops = "?";
-
-static CharPtr SeqCodeNameGet (
-  SeqCodeTablePtr table,
-  Uint1 residue
-)
-
-{
-  Uint1  index;
-
-  if (table != NULL) {
-    index = residue - table->start_at;
-    if ( /*index >= 0 && */ index < table->num) {
-      return (table->names) [index];
-    }
-  }
-
-  return oops;
-}
-
-static CharPtr Get3LetterSymbol (
-  IntAsn2gbJobPtr  ajp,
-  Uint1 seq_code,
-  SeqCodeTablePtr table,
-  Uint1 residue
-)
-
-{
-  Uint1            code = Seq_code_ncbieaa;
-  Int2             index;
-  Uint1            new_residue;
-  CharPtr          ptr;
-  CharPtr          retval = NULL;
-  SeqMapTablePtr   smtp;
-  SeqCodeTablePtr  table_3aa;
-
-  if (residue == 42) { /* stop codon in NCBIeaa */
-    retval = "TERM";
-    return retval;
-  }
-
-  if (ajp->flags.iupacaaOnly) {
-    code = Seq_code_iupacaa;
-  } else {
-    code = Seq_code_ncbieaa;
-  }
-
-  if (seq_code != code) {
-    /* if code and seq_code are identical, then smtp is NULL?? */
-    smtp = SeqMapTableFind (code, seq_code);
-    new_residue = SeqMapTableConvert (smtp, residue);
-  } else {
-    new_residue = residue;
-  }
-
-  /* The following looks for non-symbols (255) and "Undetermined" (88) */
-  if ((int) new_residue == 255 || (int) new_residue == 88) {
-    retval = "OTHER";
-    return retval;
-  } else {
-    ptr = SeqCodeNameGet (table, residue);
-    table_3aa=SeqCodeTableFind  (Seq_code_iupacaa3);
-    if (ptr != NULL && table_3aa != NULL) {
-      for (index=0; index < (int) table_3aa->num; index++) {
-        if (StringCmp(ptr, (table_3aa->names) [index]) == 0) {
-          retval = (table_3aa->symbols) [index];
-          return retval;
-        }
-      }
-    }
-  }
-
-  retval = "OTHER";
-  return retval;
-}
-
-static Boolean MatchCit (
-  ValNodePtr ppr,
-  RefBlockPtr rbp
-)
-
-{
-  Char        buf [121];
-  size_t      len;
-  Int4        uid;
-  ValNodePtr  vnp;
-
-  if (ppr == NULL || rbp == NULL) return FALSE;
-  switch (ppr->choice) {
-    case PUB_Muid :
-      uid = ppr->data.intvalue;
-      if (rbp->muid == uid) return TRUE;
-      break;
-    case PUB_PMid :
-      uid = ppr->data.intvalue;
-      if (rbp->pmid == uid) return TRUE;
-      break;
-    case PUB_Equiv :
-      for (vnp = (ValNodePtr) ppr->data.ptrvalue; vnp != NULL; vnp = vnp->next) {
-        if (MatchCit (vnp, rbp)) return TRUE;
-      }
-      break;
-    default :
-      PubLabelUnique (ppr, buf, sizeof (buf) - 1, OM_LABEL_CONTENT, TRUE);
-      len = StringLen (buf);
-      if (len > 0 && buf [len - 1] == '>') {
-        buf [len - 1] = '\0';
-        len--;
-      }
-      len = MIN (len, StringLen (rbp->uniquestr));
-      if (StringNICmp (rbp->uniquestr, buf, len) == 0) return TRUE;
-      break;
-  }
-  return FALSE;
-}
-
-static Int2 MatchRef (
-  ValNodePtr ppr,
-  RefBlockPtr PNTR rbpp,
-  Int2 numReferences
-)
-
-{
-  Int2         j;
-  RefBlockPtr  rbp;
-
-  if (ppr == NULL || rbpp == NULL) return 0;
-
-  for (j = 0; j < numReferences; j++) {
-    rbp = rbpp [j];
-    if (rbp == NULL) continue;
-    if (MatchCit (ppr, rbp)) return j + 1;
-  }
-  return 0;
-}
-
-/* taken from asn2ff4.c */
-
-static Boolean LookForFuzz (SeqLocPtr head)
-{
-  Boolean retval=FALSE;
-  IntFuzzPtr ifp;
-  PackSeqPntPtr pspp;
-  SeqIntPtr sip;
-  SeqLocPtr slp;
-  SeqPntPtr spp;
-
-  if (head == NULL)
-    return retval;
-
-  slp=NULL;
-  while ((slp = SeqLocFindNext(head, slp)) != NULL)
-  {
-    switch (slp->choice)
-    {
-      case SEQLOC_INT:
-        sip = (SeqIntPtr)(slp->data.ptrvalue);
-        ifp = sip->if_from;
-        if (ifp != NULL)
-        {
-          if (ifp->choice == 4)
-          {
-            if (ifp->a != 0)
-              retval=TRUE;
-          }
-          else
-            retval = TRUE;
-        }
-        ifp = sip->if_to;
-        if (ifp != NULL)
-        {
-          if (ifp->choice == 4)
-          {
-            if (ifp->a != 0)
-              retval=TRUE;
-          }
-          else
-            retval = TRUE;
-        }
-        break;
-      case SEQLOC_PNT:
-        spp = (SeqPntPtr)(slp->data.ptrvalue);
-        ifp = spp->fuzz;
-        if (ifp != NULL)
-        {
-          if (ifp->choice == 4)
-          {
-            if (ifp->a != 0)
-              retval=TRUE;
-          }
-          else
-            retval = TRUE;
-        }
-        break;
-      case SEQLOC_PACKED_PNT:
-        pspp = (PackSeqPntPtr)(slp->data.ptrvalue);
-        ifp = pspp->fuzz;
-        if (ifp != NULL)
-        {
-          if (ifp->choice == 4)
-          {
-            if (ifp->a != 0)
-              retval=TRUE;
-          }
-          else
-            retval = TRUE;
-        }
-        break;
-      default:
-        break;
-    }
-    if (retval == TRUE)
-      break;
-  }
-  return retval;
-}
-
-static CharPtr bondList [] = {
-  NULL,
-  "disulfide",
-  "thiolester",
-  "xlink",
-  "thioether",
-  "unclassified"
-};
-
-static CharPtr siteList [] = {
-  NULL,
-  "active",
-  "binding",
-  "cleavage",
-  "inhibit",
-  "modified",
-  "glycosylation",
-  "myristoylation",
-  "mutagenized",
-  "metal-binding",
-  "phosphorylation",
-  "acetylation",
-  "amidation",
-  "methylation",
-  "hydroxylation",
-  "sulfatation",
-  "oxidative-deamination",
-  "pyrrolidone-carboxylic-acid",
-  "gamma-carboxyglutamic-acid",
-  "blocked",
-  "lipid-binding",
-  "np-binding",
-  "DNA binding",
-  "signal-peptide",
-  "transit-peptide",
-  "transmembrane-region",
-  "unclassified"
-};
-
-static CharPtr conflict_msg =
-"Protein sequence is in conflict with the conceptual translation";
-
-static CharPtr no_protein_msg =
-"Coding region translates with internal stops";
-
-/**/
-/*  s_DisplayQVP () -- Displays the strings in a QVP structure.   */
-/*                     This is a debugging function only.         */
-/**/
-
-static void s_DisplayQVP(QualValPtr qvp, Uint1Ptr notetbl)
-{
-  Int2 j;
-  Int2 jdx;
-
-  fprintf(stderr,"\n");
-  for (j = 0, jdx = notetbl [j]; jdx != 0; j++, jdx = notetbl [j])
-    {
-      if (((int) qvp[jdx].str != 0x1000000) &&
-      ((int) qvp[jdx].str != 0x1) &&
-      ((int) qvp[jdx].str != 0xb) &&
-      (qvp[jdx].str != NULL))
-    fprintf(stderr, "%d\t%-25s %s\n", j, asn2gnbk_featur_quals[jdx].name,
-        qvp[jdx].str);
-      else
-    fprintf(stderr, "%d\t%-25s %s\n", j, asn2gnbk_featur_quals[jdx].name,
-        "NULL");
-    }
-}
-
-static Boolean NotInGeneSyn (
-  CharPtr str,
-  ValNodePtr gene_syn)
-
-{
-  CharPtr     syn;
-  ValNodePtr  vnp;
-
-  for (vnp = gene_syn; vnp != NULL; vnp = vnp->next) {
-    syn = (CharPtr) vnp->data.ptrvalue;
-    if (! StringHasNoText (syn)) {
-      if (StringICmp (str, syn) == 0) return FALSE;
-    }
-  }
-  return TRUE;
-}
-
-typedef struct valqualstruc {
-  Uint2       featdef;
-  FtQualType  ftqual;
-} ValQual, PNTR ValQualPtr;
-
-/*
-   WARNING - This list MUST be kept sorted in FEATDEF order as the primary
-   key, and within a FEATDEF group sorted by FTQUAL as the secondary key
-*/
-
-static ValQual legalGbqualList [] = {
-
-  { FEATDEF_GENE , FTQUAL_allele },
-  { FEATDEF_GENE , FTQUAL_function },
-  { FEATDEF_GENE , FTQUAL_label },
-  { FEATDEF_GENE , FTQUAL_map },
-  { FEATDEF_GENE , FTQUAL_operon },
-  { FEATDEF_GENE , FTQUAL_phenotype },
-  { FEATDEF_GENE , FTQUAL_product },
-  { FEATDEF_GENE , FTQUAL_standard_name },
-  { FEATDEF_GENE , FTQUAL_usedin },
-
-  { FEATDEF_CDS , FTQUAL_allele },
-  { FEATDEF_CDS , FTQUAL_codon },
-  { FEATDEF_CDS , FTQUAL_label },
-  { FEATDEF_CDS , FTQUAL_map },
-  { FEATDEF_CDS , FTQUAL_number },
-  { FEATDEF_CDS , FTQUAL_operon },
-  { FEATDEF_CDS , FTQUAL_standard_name },
-  { FEATDEF_CDS , FTQUAL_usedin },
-
-  { FEATDEF_PROT , FTQUAL_product },
-
-  { FEATDEF_preRNA , FTQUAL_allele },
-  { FEATDEF_preRNA , FTQUAL_function },
-  { FEATDEF_preRNA , FTQUAL_label },
-  { FEATDEF_preRNA , FTQUAL_map },
-  { FEATDEF_preRNA , FTQUAL_operon },
-  { FEATDEF_preRNA , FTQUAL_product },
-  { FEATDEF_preRNA , FTQUAL_standard_name },
-  { FEATDEF_preRNA , FTQUAL_usedin },
-
-  { FEATDEF_mRNA , FTQUAL_allele },
-  { FEATDEF_mRNA , FTQUAL_function },
-  { FEATDEF_mRNA , FTQUAL_label },
-  { FEATDEF_mRNA , FTQUAL_map },
-  { FEATDEF_mRNA , FTQUAL_operon },
-  { FEATDEF_mRNA , FTQUAL_product },
-  { FEATDEF_mRNA , FTQUAL_standard_name },
-  { FEATDEF_mRNA , FTQUAL_usedin },
-
-  { FEATDEF_tRNA , FTQUAL_allele },
-  { FEATDEF_tRNA , FTQUAL_function },
-  { FEATDEF_tRNA , FTQUAL_label },
-  { FEATDEF_tRNA , FTQUAL_map },
-  { FEATDEF_tRNA , FTQUAL_product },
-  { FEATDEF_tRNA , FTQUAL_standard_name },
-  { FEATDEF_tRNA , FTQUAL_usedin },
-
-  { FEATDEF_rRNA , FTQUAL_allele },
-  { FEATDEF_rRNA , FTQUAL_function },
-  { FEATDEF_rRNA , FTQUAL_label },
-  { FEATDEF_rRNA , FTQUAL_map },
-  { FEATDEF_rRNA , FTQUAL_product },
-  { FEATDEF_rRNA , FTQUAL_standard_name },
-  { FEATDEF_rRNA , FTQUAL_usedin },
-
-  { FEATDEF_snRNA , FTQUAL_allele },
-  { FEATDEF_snRNA , FTQUAL_function },
-  { FEATDEF_snRNA , FTQUAL_label },
-  { FEATDEF_snRNA , FTQUAL_map },
-  { FEATDEF_snRNA , FTQUAL_product },
-  { FEATDEF_snRNA , FTQUAL_standard_name },
-  { FEATDEF_snRNA , FTQUAL_usedin },
-
-  { FEATDEF_scRNA , FTQUAL_allele },
-  { FEATDEF_scRNA , FTQUAL_function },
-  { FEATDEF_scRNA , FTQUAL_label },
-  { FEATDEF_scRNA , FTQUAL_map },
-  { FEATDEF_scRNA , FTQUAL_product },
-  { FEATDEF_scRNA , FTQUAL_standard_name },
-  { FEATDEF_scRNA , FTQUAL_usedin },
-
-  { FEATDEF_otherRNA , FTQUAL_allele },
-  { FEATDEF_otherRNA , FTQUAL_function },
-  { FEATDEF_otherRNA , FTQUAL_label },
-  { FEATDEF_otherRNA , FTQUAL_map },
-  { FEATDEF_otherRNA , FTQUAL_operon },
-  { FEATDEF_otherRNA , FTQUAL_product },
-  { FEATDEF_otherRNA , FTQUAL_standard_name },
-  { FEATDEF_otherRNA , FTQUAL_usedin },
-
-  { FEATDEF_attenuator , FTQUAL_allele },
-  { FEATDEF_attenuator , FTQUAL_label },
-  { FEATDEF_attenuator , FTQUAL_map },
-  { FEATDEF_attenuator , FTQUAL_operon },
-  { FEATDEF_attenuator , FTQUAL_phenotype },
-  { FEATDEF_attenuator , FTQUAL_usedin },
-
-  { FEATDEF_C_region , FTQUAL_allele },
-  { FEATDEF_C_region , FTQUAL_label },
-  { FEATDEF_C_region , FTQUAL_map },
-  { FEATDEF_C_region , FTQUAL_product },
-  { FEATDEF_C_region , FTQUAL_standard_name },
-  { FEATDEF_C_region , FTQUAL_usedin },
-
-  { FEATDEF_CAAT_signal , FTQUAL_allele },
-  { FEATDEF_CAAT_signal , FTQUAL_label },
-  { FEATDEF_CAAT_signal , FTQUAL_map },
-  { FEATDEF_CAAT_signal , FTQUAL_usedin },
-
-  { FEATDEF_Imp_CDS , FTQUAL_codon },
-  { FEATDEF_Imp_CDS , FTQUAL_EC_number },
-  { FEATDEF_Imp_CDS , FTQUAL_function },
-  { FEATDEF_Imp_CDS , FTQUAL_label },
-  { FEATDEF_Imp_CDS , FTQUAL_map },
-  { FEATDEF_Imp_CDS , FTQUAL_number },
-  { FEATDEF_Imp_CDS , FTQUAL_operon },
-  { FEATDEF_Imp_CDS , FTQUAL_product },
-  { FEATDEF_Imp_CDS , FTQUAL_standard_name },
-  { FEATDEF_Imp_CDS , FTQUAL_usedin },
-
-  { FEATDEF_conflict , FTQUAL_allele },
-  { FEATDEF_conflict , FTQUAL_label },
-  { FEATDEF_conflict , FTQUAL_map },
-  { FEATDEF_conflict , FTQUAL_replace },
-  { FEATDEF_conflict , FTQUAL_usedin },
-
-  { FEATDEF_D_loop , FTQUAL_allele },
-  { FEATDEF_D_loop , FTQUAL_label },
-  { FEATDEF_D_loop , FTQUAL_map },
-  { FEATDEF_D_loop , FTQUAL_usedin },
-
-  { FEATDEF_D_segment , FTQUAL_allele },
-  { FEATDEF_D_segment , FTQUAL_label },
-  { FEATDEF_D_segment , FTQUAL_map },
-  { FEATDEF_D_segment , FTQUAL_product },
-  { FEATDEF_D_segment , FTQUAL_standard_name },
-  { FEATDEF_D_segment , FTQUAL_usedin },
-
-  { FEATDEF_enhancer , FTQUAL_allele },
-  { FEATDEF_enhancer , FTQUAL_label },
-  { FEATDEF_enhancer , FTQUAL_map },
-  { FEATDEF_enhancer , FTQUAL_standard_name },
-  { FEATDEF_enhancer , FTQUAL_usedin },
-
-  { FEATDEF_exon , FTQUAL_allele },
-  { FEATDEF_exon , FTQUAL_EC_number },
-  { FEATDEF_exon , FTQUAL_function },
-  { FEATDEF_exon , FTQUAL_label },
-  { FEATDEF_exon , FTQUAL_map },
-  { FEATDEF_exon , FTQUAL_number },
-  { FEATDEF_exon , FTQUAL_product },
-  { FEATDEF_exon , FTQUAL_standard_name },
-  { FEATDEF_exon , FTQUAL_usedin },
-
-  { FEATDEF_GC_signal , FTQUAL_allele },
-  { FEATDEF_GC_signal , FTQUAL_label },
-  { FEATDEF_GC_signal , FTQUAL_map },
-  { FEATDEF_GC_signal , FTQUAL_usedin },
-
-  { FEATDEF_iDNA , FTQUAL_allele },
-  { FEATDEF_iDNA , FTQUAL_function },
-  { FEATDEF_iDNA , FTQUAL_label },
-  { FEATDEF_iDNA , FTQUAL_map },
-  { FEATDEF_iDNA , FTQUAL_number },
-  { FEATDEF_iDNA , FTQUAL_standard_name },
-  { FEATDEF_iDNA , FTQUAL_usedin },
-
-  { FEATDEF_intron , FTQUAL_allele },
-  { FEATDEF_intron , FTQUAL_cons_splice },
-  { FEATDEF_intron , FTQUAL_function },
-  { FEATDEF_intron , FTQUAL_label },
-  { FEATDEF_intron , FTQUAL_map },
-  { FEATDEF_intron , FTQUAL_number },
-  { FEATDEF_intron , FTQUAL_standard_name },
-  { FEATDEF_intron , FTQUAL_usedin },
-
-  { FEATDEF_J_segment , FTQUAL_allele },
-  { FEATDEF_J_segment , FTQUAL_label },
-  { FEATDEF_J_segment , FTQUAL_map },
-  { FEATDEF_J_segment , FTQUAL_product },
-  { FEATDEF_J_segment , FTQUAL_standard_name },
-  { FEATDEF_J_segment , FTQUAL_usedin },
-
-  { FEATDEF_LTR , FTQUAL_allele },
-  { FEATDEF_LTR , FTQUAL_function },
-  { FEATDEF_LTR , FTQUAL_label },
-  { FEATDEF_LTR , FTQUAL_map },
-  { FEATDEF_LTR , FTQUAL_standard_name },
-  { FEATDEF_LTR , FTQUAL_usedin },
-
-  { FEATDEF_mat_peptide , FTQUAL_allele },
-  { FEATDEF_mat_peptide , FTQUAL_EC_number },
-  { FEATDEF_mat_peptide , FTQUAL_function },
-  { FEATDEF_mat_peptide , FTQUAL_label },
-  { FEATDEF_mat_peptide , FTQUAL_map },
-  { FEATDEF_mat_peptide , FTQUAL_product },
-  { FEATDEF_mat_peptide , FTQUAL_standard_name },
-  { FEATDEF_mat_peptide , FTQUAL_usedin },
-
-  { FEATDEF_misc_binding , FTQUAL_allele },
-  { FEATDEF_misc_binding , FTQUAL_bound_moiety },
-  { FEATDEF_misc_binding , FTQUAL_function },
-  { FEATDEF_misc_binding , FTQUAL_label },
-  { FEATDEF_misc_binding , FTQUAL_map },
-  { FEATDEF_misc_binding , FTQUAL_usedin },
-
-  { FEATDEF_misc_difference , FTQUAL_allele },
-  { FEATDEF_misc_difference , FTQUAL_clone },
-  { FEATDEF_misc_difference , FTQUAL_label },
-  { FEATDEF_misc_difference , FTQUAL_map },
-  { FEATDEF_misc_difference , FTQUAL_phenotype },
-  { FEATDEF_misc_difference , FTQUAL_replace },
-  { FEATDEF_misc_difference , FTQUAL_standard_name },
-  { FEATDEF_misc_difference , FTQUAL_usedin },
-
-  { FEATDEF_misc_feature , FTQUAL_allele },
-  { FEATDEF_misc_feature , FTQUAL_function },
-  { FEATDEF_misc_feature , FTQUAL_label },
-  { FEATDEF_misc_feature , FTQUAL_map },
-  { FEATDEF_misc_feature , FTQUAL_number },
-  { FEATDEF_misc_feature , FTQUAL_phenotype },
-  { FEATDEF_misc_feature , FTQUAL_product },
-  { FEATDEF_misc_feature , FTQUAL_standard_name },
-  { FEATDEF_misc_feature , FTQUAL_usedin },
-
-  { FEATDEF_misc_recomb , FTQUAL_allele },
-  { FEATDEF_misc_recomb , FTQUAL_label },
-  { FEATDEF_misc_recomb , FTQUAL_map },
-  { FEATDEF_misc_recomb , FTQUAL_organism },
-  { FEATDEF_misc_recomb , FTQUAL_standard_name },
-  { FEATDEF_misc_recomb , FTQUAL_usedin },
-
-  { FEATDEF_misc_signal , FTQUAL_allele },
-  { FEATDEF_misc_signal , FTQUAL_function },
-  { FEATDEF_misc_signal , FTQUAL_label },
-  { FEATDEF_misc_signal , FTQUAL_map },
-  { FEATDEF_misc_signal , FTQUAL_operon },
-  { FEATDEF_misc_signal , FTQUAL_phenotype },
-  { FEATDEF_misc_signal , FTQUAL_standard_name },
-  { FEATDEF_misc_signal , FTQUAL_usedin },
-
-  { FEATDEF_misc_structure , FTQUAL_allele },
-  { FEATDEF_misc_structure , FTQUAL_function },
-  { FEATDEF_misc_structure , FTQUAL_label },
-  { FEATDEF_misc_structure , FTQUAL_map },
-  { FEATDEF_misc_structure , FTQUAL_standard_name },
-  { FEATDEF_misc_structure , FTQUAL_usedin },
-
-  { FEATDEF_modified_base , FTQUAL_allele },
-  { FEATDEF_modified_base , FTQUAL_frequency },
-  { FEATDEF_modified_base , FTQUAL_label },
-  { FEATDEF_modified_base , FTQUAL_map },
-  { FEATDEF_modified_base , FTQUAL_mod_base },
-  { FEATDEF_modified_base , FTQUAL_usedin },
-
-  { FEATDEF_N_region , FTQUAL_allele },
-  { FEATDEF_N_region , FTQUAL_label },
-  { FEATDEF_N_region , FTQUAL_map },
-  { FEATDEF_N_region , FTQUAL_product },
-  { FEATDEF_N_region , FTQUAL_standard_name },
-  { FEATDEF_N_region , FTQUAL_usedin },
-
-  { FEATDEF_old_sequence , FTQUAL_allele },
-  { FEATDEF_old_sequence , FTQUAL_label },
-  { FEATDEF_old_sequence , FTQUAL_map },
-  { FEATDEF_old_sequence , FTQUAL_replace },
-  { FEATDEF_old_sequence , FTQUAL_usedin },
-
-  { FEATDEF_polyA_signal , FTQUAL_allele },
-  { FEATDEF_polyA_signal , FTQUAL_label },
-  { FEATDEF_polyA_signal , FTQUAL_map },
-  { FEATDEF_polyA_signal , FTQUAL_usedin },
-
-  { FEATDEF_polyA_site , FTQUAL_allele },
-  { FEATDEF_polyA_site , FTQUAL_label },
-  { FEATDEF_polyA_site , FTQUAL_map },
-  { FEATDEF_polyA_site , FTQUAL_usedin },
-
-  { FEATDEF_prim_transcript , FTQUAL_allele },
-  { FEATDEF_prim_transcript , FTQUAL_function },
-  { FEATDEF_prim_transcript , FTQUAL_label },
-  { FEATDEF_prim_transcript , FTQUAL_map },
-  { FEATDEF_prim_transcript , FTQUAL_operon },
-  { FEATDEF_prim_transcript , FTQUAL_standard_name },
-  { FEATDEF_prim_transcript , FTQUAL_usedin },
-
-  { FEATDEF_primer_bind , FTQUAL_allele },
-  { FEATDEF_primer_bind , FTQUAL_label },
-  { FEATDEF_primer_bind , FTQUAL_map },
-  { FEATDEF_primer_bind , FTQUAL_PCR_conditions },
-  { FEATDEF_primer_bind , FTQUAL_standard_name },
-  { FEATDEF_primer_bind , FTQUAL_usedin },
-
-  { FEATDEF_promoter , FTQUAL_allele },
-  { FEATDEF_promoter , FTQUAL_function },
-  { FEATDEF_promoter , FTQUAL_label },
-  { FEATDEF_promoter , FTQUAL_map },
-  { FEATDEF_promoter , FTQUAL_operon },
-  { FEATDEF_promoter , FTQUAL_phenotype },
-  { FEATDEF_promoter , FTQUAL_standard_name },
-  { FEATDEF_promoter , FTQUAL_usedin },
-
-  { FEATDEF_protein_bind , FTQUAL_allele },
-  { FEATDEF_protein_bind , FTQUAL_bound_moiety },
-  { FEATDEF_protein_bind , FTQUAL_function },
-  { FEATDEF_protein_bind , FTQUAL_label },
-  { FEATDEF_protein_bind , FTQUAL_map },
-  { FEATDEF_protein_bind , FTQUAL_standard_name },
-  { FEATDEF_protein_bind , FTQUAL_usedin },
-
-  { FEATDEF_RBS , FTQUAL_allele },
-  { FEATDEF_RBS , FTQUAL_label },
-  { FEATDEF_RBS , FTQUAL_map },
-  { FEATDEF_RBS , FTQUAL_standard_name },
-  { FEATDEF_RBS , FTQUAL_usedin },
-
-  { FEATDEF_repeat_region , FTQUAL_allele },
-  { FEATDEF_repeat_region , FTQUAL_function },
-  { FEATDEF_repeat_region , FTQUAL_insertion_seq },
-  { FEATDEF_repeat_region , FTQUAL_label },
-  { FEATDEF_repeat_region , FTQUAL_map },
-  { FEATDEF_repeat_region , FTQUAL_rpt_family },
-  { FEATDEF_repeat_region , FTQUAL_rpt_type },
-  { FEATDEF_repeat_region , FTQUAL_rpt_unit },
-  { FEATDEF_repeat_region , FTQUAL_standard_name },
-  { FEATDEF_repeat_region , FTQUAL_transposon },
-  { FEATDEF_repeat_region , FTQUAL_usedin },
-
-  { FEATDEF_repeat_unit , FTQUAL_allele },
-  { FEATDEF_repeat_unit , FTQUAL_function },
-  { FEATDEF_repeat_unit , FTQUAL_label },
-  { FEATDEF_repeat_unit , FTQUAL_map },
-  { FEATDEF_repeat_unit , FTQUAL_rpt_family },
-  { FEATDEF_repeat_unit , FTQUAL_rpt_type },
-  { FEATDEF_repeat_unit , FTQUAL_usedin },
-
-  { FEATDEF_rep_origin , FTQUAL_allele },
-  { FEATDEF_rep_origin , FTQUAL_direction },
-  { FEATDEF_rep_origin , FTQUAL_label },
-  { FEATDEF_rep_origin , FTQUAL_map },
-  { FEATDEF_rep_origin , FTQUAL_standard_name },
-  { FEATDEF_rep_origin , FTQUAL_usedin },
-
-  { FEATDEF_S_region , FTQUAL_allele },
-  { FEATDEF_S_region , FTQUAL_label },
-  { FEATDEF_S_region , FTQUAL_map },
-  { FEATDEF_S_region , FTQUAL_product },
-  { FEATDEF_S_region , FTQUAL_standard_name },
-  { FEATDEF_S_region , FTQUAL_usedin },
-
-  { FEATDEF_satellite , FTQUAL_allele },
-  { FEATDEF_satellite , FTQUAL_label },
-  { FEATDEF_satellite , FTQUAL_map },
-  { FEATDEF_satellite , FTQUAL_rpt_family },
-  { FEATDEF_satellite , FTQUAL_rpt_type },
-  { FEATDEF_satellite , FTQUAL_rpt_unit },
-  { FEATDEF_satellite , FTQUAL_standard_name },
-  { FEATDEF_satellite , FTQUAL_usedin },
-
-  { FEATDEF_sig_peptide , FTQUAL_allele },
-  { FEATDEF_sig_peptide , FTQUAL_function },
-  { FEATDEF_sig_peptide , FTQUAL_label },
-  { FEATDEF_sig_peptide , FTQUAL_map },
-  { FEATDEF_sig_peptide , FTQUAL_product },
-  { FEATDEF_sig_peptide , FTQUAL_standard_name },
-  { FEATDEF_sig_peptide , FTQUAL_usedin },
-
-  { FEATDEF_stem_loop , FTQUAL_allele },
-  { FEATDEF_stem_loop , FTQUAL_function },
-  { FEATDEF_stem_loop , FTQUAL_label },
-  { FEATDEF_stem_loop , FTQUAL_map },
-  { FEATDEF_stem_loop , FTQUAL_operon },
-  { FEATDEF_stem_loop , FTQUAL_standard_name },
-  { FEATDEF_stem_loop , FTQUAL_usedin },
-
-  { FEATDEF_STS , FTQUAL_allele },
-  { FEATDEF_STS , FTQUAL_label },
-  { FEATDEF_STS , FTQUAL_map },
-  { FEATDEF_STS , FTQUAL_standard_name },
-  { FEATDEF_STS , FTQUAL_usedin },
-
-  { FEATDEF_TATA_signal , FTQUAL_allele },
-  { FEATDEF_TATA_signal , FTQUAL_label },
-  { FEATDEF_TATA_signal , FTQUAL_map },
-  { FEATDEF_TATA_signal , FTQUAL_usedin },
-
-  { FEATDEF_terminator , FTQUAL_allele },
-  { FEATDEF_terminator , FTQUAL_label },
-  { FEATDEF_terminator , FTQUAL_map },
-  { FEATDEF_terminator , FTQUAL_operon },
-  { FEATDEF_terminator , FTQUAL_standard_name },
-  { FEATDEF_terminator , FTQUAL_usedin },
-
-  { FEATDEF_transit_peptide , FTQUAL_allele },
-  { FEATDEF_transit_peptide , FTQUAL_function },
-  { FEATDEF_transit_peptide , FTQUAL_label },
-  { FEATDEF_transit_peptide , FTQUAL_map },
-  { FEATDEF_transit_peptide , FTQUAL_product },
-  { FEATDEF_transit_peptide , FTQUAL_standard_name },
-  { FEATDEF_transit_peptide , FTQUAL_usedin },
-
-  { FEATDEF_unsure , FTQUAL_allele },
-  { FEATDEF_unsure , FTQUAL_label },
-  { FEATDEF_unsure , FTQUAL_map },
-  { FEATDEF_unsure , FTQUAL_replace },
-  { FEATDEF_unsure , FTQUAL_usedin },
-
-  { FEATDEF_V_region , FTQUAL_allele },
-  { FEATDEF_V_region , FTQUAL_label },
-  { FEATDEF_V_region , FTQUAL_map },
-  { FEATDEF_V_region , FTQUAL_product },
-  { FEATDEF_V_region , FTQUAL_standard_name },
-  { FEATDEF_V_region , FTQUAL_usedin },
-
-  { FEATDEF_V_segment , FTQUAL_allele },
-  { FEATDEF_V_segment , FTQUAL_label },
-  { FEATDEF_V_segment , FTQUAL_map },
-  { FEATDEF_V_segment , FTQUAL_product },
-  { FEATDEF_V_segment , FTQUAL_standard_name },
-  { FEATDEF_V_segment , FTQUAL_usedin },
-
-  { FEATDEF_variation , FTQUAL_allele },
-  { FEATDEF_variation , FTQUAL_frequency },
-  { FEATDEF_variation , FTQUAL_label },
-  { FEATDEF_variation , FTQUAL_map },
-  { FEATDEF_variation , FTQUAL_phenotype },
-  { FEATDEF_variation , FTQUAL_product },
-  { FEATDEF_variation , FTQUAL_replace },
-  { FEATDEF_variation , FTQUAL_standard_name },
-  { FEATDEF_variation , FTQUAL_usedin },
-
-  { FEATDEF_3clip , FTQUAL_allele },
-  { FEATDEF_3clip , FTQUAL_function },
-  { FEATDEF_3clip , FTQUAL_label },
-  { FEATDEF_3clip , FTQUAL_map },
-  { FEATDEF_3clip , FTQUAL_standard_name },
-  { FEATDEF_3clip , FTQUAL_usedin },
-
-  { FEATDEF_3UTR , FTQUAL_allele },
-  { FEATDEF_3UTR , FTQUAL_function },
-  { FEATDEF_3UTR , FTQUAL_label },
-  { FEATDEF_3UTR , FTQUAL_map },
-  { FEATDEF_3UTR , FTQUAL_standard_name },
-  { FEATDEF_3UTR , FTQUAL_usedin },
-
-  { FEATDEF_5clip , FTQUAL_allele },
-  { FEATDEF_5clip , FTQUAL_function },
-  { FEATDEF_5clip , FTQUAL_label },
-  { FEATDEF_5clip , FTQUAL_map },
-  { FEATDEF_5clip , FTQUAL_standard_name },
-  { FEATDEF_5clip , FTQUAL_usedin },
-
-  { FEATDEF_5UTR , FTQUAL_allele },
-  { FEATDEF_5UTR , FTQUAL_function },
-  { FEATDEF_5UTR , FTQUAL_label },
-  { FEATDEF_5UTR , FTQUAL_map },
-  { FEATDEF_5UTR , FTQUAL_standard_name },
-  { FEATDEF_5UTR , FTQUAL_usedin },
-
-  { FEATDEF_10_signal , FTQUAL_allele },
-  { FEATDEF_10_signal , FTQUAL_label },
-  { FEATDEF_10_signal , FTQUAL_map },
-  { FEATDEF_10_signal , FTQUAL_operon },
-  { FEATDEF_10_signal , FTQUAL_standard_name },
-  { FEATDEF_10_signal , FTQUAL_usedin },
-
-  { FEATDEF_35_signal , FTQUAL_allele },
-  { FEATDEF_35_signal , FTQUAL_label },
-  { FEATDEF_35_signal , FTQUAL_map },
-  { FEATDEF_35_signal , FTQUAL_operon },
-  { FEATDEF_35_signal , FTQUAL_standard_name },
-  { FEATDEF_35_signal , FTQUAL_usedin },
-
-  { FEATDEF_REGION , FTQUAL_function },
-  { FEATDEF_REGION , FTQUAL_label },
-  { FEATDEF_REGION , FTQUAL_map },
-  { FEATDEF_REGION , FTQUAL_number },
-  { FEATDEF_REGION , FTQUAL_phenotype },
-  { FEATDEF_REGION , FTQUAL_product },
-  { FEATDEF_REGION , FTQUAL_standard_name },
-  { FEATDEF_REGION , FTQUAL_usedin },
-
-  { FEATDEF_mat_peptide_aa , FTQUAL_allele },
-  { FEATDEF_mat_peptide_aa , FTQUAL_label },
-  { FEATDEF_mat_peptide_aa , FTQUAL_map },
-  { FEATDEF_mat_peptide_aa , FTQUAL_product },
-  { FEATDEF_mat_peptide_aa , FTQUAL_standard_name },
-  { FEATDEF_mat_peptide_aa , FTQUAL_usedin },
-
-  { FEATDEF_sig_peptide_aa , FTQUAL_allele },
-  { FEATDEF_sig_peptide_aa , FTQUAL_label },
-  { FEATDEF_sig_peptide_aa , FTQUAL_map },
-  { FEATDEF_sig_peptide_aa , FTQUAL_product },
-  { FEATDEF_sig_peptide_aa , FTQUAL_standard_name },
-  { FEATDEF_sig_peptide_aa , FTQUAL_usedin },
-
-  { FEATDEF_transit_peptide_aa , FTQUAL_allele },
-  { FEATDEF_transit_peptide_aa , FTQUAL_label },
-  { FEATDEF_transit_peptide_aa , FTQUAL_map },
-  { FEATDEF_transit_peptide_aa , FTQUAL_product },
-  { FEATDEF_transit_peptide_aa , FTQUAL_standard_name },
-  { FEATDEF_transit_peptide_aa , FTQUAL_usedin },
-
-  { FEATDEF_snoRNA , FTQUAL_allele },
-  { FEATDEF_snoRNA , FTQUAL_function },
-  { FEATDEF_snoRNA , FTQUAL_label },
-  { FEATDEF_snoRNA , FTQUAL_map },
-  { FEATDEF_snoRNA , FTQUAL_product },
-  { FEATDEF_snoRNA , FTQUAL_standard_name },
-  { FEATDEF_snoRNA , FTQUAL_usedin },
-
-  { FEATDEF_operon , FTQUAL_allele },
-  { FEATDEF_operon , FTQUAL_function },
-  { FEATDEF_operon , FTQUAL_label },
-  { FEATDEF_operon , FTQUAL_map },
-  { FEATDEF_operon , FTQUAL_operon },
-  { FEATDEF_operon , FTQUAL_phenotype },
-  { FEATDEF_operon , FTQUAL_standard_name },
-  { FEATDEF_operon , FTQUAL_usedin },
-
-  { FEATDEF_oriT , FTQUAL_allele },
-  { FEATDEF_oriT , FTQUAL_direction },
-  { FEATDEF_oriT , FTQUAL_label },
-  { FEATDEF_oriT , FTQUAL_map },
-  { FEATDEF_oriT , FTQUAL_rpt_type },
-  { FEATDEF_oriT , FTQUAL_rpt_type },
-  { FEATDEF_oriT , FTQUAL_rpt_unit },
-  { FEATDEF_oriT , FTQUAL_standard_name },
-  { FEATDEF_oriT , FTQUAL_usedin }
-};
-
-/* comparison of ValQual's -- first compare featdef then ftqual */
-
-/* macro did not work properly on linux machine, so using function instead */
-/* #define COMPARE_VALQUAL(av,aq,bv,bq) ( ((av)-(bv)) ? ((av)-(bv)) : ((aq)-(bq)) ) */
-
-static Int2 CompareValQual (Uint2 av, FtQualType aq, Uint2 bv, FtQualType bq)
-
-{
-  if (av == bv) return (aq - bq);
-  return (av - bv);
-}
-
-/* Returns TRUE if {featureKey, qualKey} exists in legalGbqualList */
-
-static Boolean AllowedValQual (Uint2 featureKey, FtQualType qualKey)
-
-{
-  Int2 L, R, mid;
-
-  L = 0;
-  R = sizeof (legalGbqualList) / sizeof (ValQual) - 1;
-  while (L < R) {
-    mid = (L + R) / 2;
-    if (CompareValQual (legalGbqualList [mid].featdef,
-       legalGbqualList [mid].ftqual,
-       featureKey, qualKey) < 0)
-      L = mid + 1;
-    else
-      R = mid;
-  }
-  if (CompareValQual (legalGbqualList [R].featdef,
-      legalGbqualList [R].ftqual,
-      featureKey, qualKey)) {
-    return 0;
-  }
-  return 1;
-}
-
-
-static CharPtr validRptString [] = {
-  "tandem", "inverted", "flanking", "terminal", "direct", "dispersed", "other", NULL
-};
-
-static CharPtr validLRBString [] = {
-  "LEFT", "RIGHT", "BOTH", NULL
-};
-
-static CharPtr validConsSpliceString [] = {
-  "(5'site:YES, 3'site:YES)",
-  "(5'site:YES, 3'site:NO)",
-  "(5'site:YES, 3'site:ABSENT)",
-  "(5'site:NO, 3'site:YES)",
-  "(5'site:NO, 3'site:NO)",
-  "(5'site:NO, 3'site:ABSENT)",
-  "(5'site:ABSENT, 3'site:YES)",
-  "(5'site:ABSENT, 3'site:NO)",
-  "(5'site:ABSENT, 3'site:ABSENT)",
-  NULL
-};
-
-static CharPtr validExceptionString [] = {
-  "RNA editing",
-  "reasons given in citation",
-  NULL
-};
-
-static CharPtr validRefSeqExceptionString [] = {
-  "RNA editing",
-  "reasons given in citation",
-  "ribosomal slippage",
-  "ribosome slippage",
-  "trans splicing",
-  "trans-splicing",
-  "alternative processing",
-  "alternate processing",
-  "artificial frameshift",
-  "non-consensus splice site",
-  "nonconsensus splice site",
-  "rearrangement required for product",
-  "unclassified transcription discrepancy",
-  "unclassified translation discrepancy",
-  NULL
-};
-
-static Boolean StringInStringList (CharPtr testString, CharPtr PNTR stringList) {
-  Int2 i;
-  i = 0;
-  while (stringList [i] != NULL) {
-    if (StringICmp (testString, stringList [i]) == 0)
-      return 1;
-    i++;
-  }
-  return 0;
-}
-
-/*
-Functions now public and prototyped in sequtil.h
-Return values are:
- 0: no problem - Accession is in proper format
--1: Accession did not start with a letter (or two letters)
--2: Accession did not contain five numbers (or six numbers after 2 letters)
--3: the original Accession number to be validated was NULL
--4: the original Accession number is too long (>16)
-*/
-
-NLM_EXTERN Int2 ValidateAccn (
-  CharPtr accession
-)
-
-{
-  Char     ch;
-  Int2     numAlpha = 0;
-  Int2     numDigits = 0;
-  Int2     numUndersc = 0;
-  CharPtr  str;
-
-  if (accession == NULL || accession [0] == '\0') return -3;
-
-  if (StringLen (accession) >= 16) return -4;
-
-  if (accession [0] < 'A' || accession [0] > 'Z') return -1;
-
-  str = accession;
-  if (StringNCmp (str, "NZ_", 3) == 0) {
-    str += 3;
-  }
-  ch = *str;
-  while (IS_ALPHA (ch)) {
-    numAlpha++;
-    str++;
-    ch = *str;
-  }
-  while (ch == '_') {
-    numUndersc++;
-    str++;
-    ch = *str;
-  }
-  while (IS_DIGIT (ch)) {
-    numDigits++;
-    str++;
-    ch = *str;
-  }
-  if (ch != '\0' && ch != ' ' && ch != '.') return -2;
-
-  if (numUndersc > 1) return -2;
-
-  if (numUndersc == 0) {
-    if (numAlpha == 1 && numDigits == 5) return 0;
-    if (numAlpha == 2 && numDigits == 6) return 0;
-    if (numAlpha == 3 && numDigits == 5) return 0;
-    if (numAlpha == 4 && numDigits == 8) return 0;
-  } else if (numUndersc == 1) {
-    if (numAlpha != 2 || (numDigits != 6 && numDigits != 8)) return -2;
-    if (accession [0] == 'N' || accession [0] == 'X' || accession [0] == 'Z') {
-      if (accession [1] == 'M' ||
-          accession [1] == 'C' ||
-          accession [1] == 'T' ||
-          accession [1] == 'P' ||
-          accession [1] == 'G' ||
-          accession [1] == 'R' ||
-          accession [1] == 'S' ||
-          accession [1] == 'Z') {
-        return 0;
-      }
-    }
-  }
-
-  return -2;
-}
-
-NLM_EXTERN Int2 ValidateSeqID (
-  SeqIdPtr sip
-)
-
-{
-  Char  buf [41];
-
-  if (sip == NULL) return -3;
-  SeqIdWrite (sip, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
-  return ValidateAccn (buf);
-}
-
-static CharPtr mrnaevtext1 = "Derived by automated computational analysis";
-static CharPtr mrnaevtext2 = "using gene prediction method:";
-static CharPtr mrnaevtext3 = "Supporting evidence includes similarity to:";
-
-static void GetStrFormRNAEvidence (
-  UserObjectPtr uop,
-  Pointer userdata
-)
-
-{
-  size_t        len;
-  CharPtr       method = NULL;
-  Int2          nm = 0;
-  ObjectIdPtr   oip;
-  CharPtr       str = NULL;
-  CharPtr PNTR  strp;
-  Char          tmp [20];
-  UserFieldPtr  u, ufp, uu;
-
-  if (uop == NULL) return;
-  oip = uop->type;
-  if (oip == NULL) return;
-  if (StringCmp (oip->str, "ModelEvidence") != 0) return;
-  strp = (CharPtr PNTR) userdata;
-
-  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-    oip = ufp->label;
-    if (oip == NULL || ufp->data.ptrvalue == NULL) continue;
-    if (StringCmp (oip->str, "Method") == 0) {
-      method = StringSaveNoNull ((CharPtr) ufp->data.ptrvalue);
-    }
-    if (StringCmp (oip->str, "mRNA") == 0) {
-      for (u = (UserFieldPtr) ufp->data.ptrvalue; u != NULL; u = u->next) {
-        if (u->data.ptrvalue == NULL) continue;
-        for (uu = (UserFieldPtr) u->data.ptrvalue; uu != NULL; uu = uu->next) {
-          oip = uu->label;
-          if (oip == NULL) continue;
-          if (StringCmp (oip->str, "accession") == 0) {
-            nm++;
-          }
-        }
-      }
-    }
-  }
-
-  len = StringLen (mrnaevtext1) + StringLen (mrnaevtext2) + StringLen (mrnaevtext3) + StringLen (method) + 30;
-  str = (CharPtr) MemNew (len);
-  if (str == NULL) return;
-
-  if (method != NULL) {
-    sprintf (str, "%s %s %s.", mrnaevtext1, mrnaevtext2, method);
-  } else {
-    sprintf (str, "%s.", mrnaevtext1);
-  }
-  if (nm > 0) {
-    StringCat (str, " ");
-    StringCat (str, mrnaevtext3);
-    if (nm > 1) {
-      sprintf (tmp, " %d mRNAs", (int) nm);
-    } else {
-      sprintf (tmp, " %d mRNA", (int) nm);
-    }
-    StringCat (str, tmp);
-  }
-
-  *strp = str;
-}
-
-static Boolean ValidateRptUnit (
-  CharPtr buf
-)
-
-{
-#if 0
-  CharPtr  str;
-  Char     tmp [255];
-
-  StringNCpy_0 (tmp, buf, sizeof (tmp));
-  TrimSpacesAroundString (tmp);
-
-  str = tmp;
-  /* first check for sequence letters with optional semicolons */
-  while (IS_ALPHA (*str) || *str == ';') str++;
-  if (*str == '\0') return TRUE;
-  /* next check for letters, digits, commas, parentheses, dashes, and underscores */
-  str = tmp;
-  while (IS_ALPHANUM (*str) || *str == '(' || *str == ')' || *str == ',' || *str == ';' || *str == '-' || *str == '_') str++;
-  if (*str == '\0') return TRUE;
-  /* now check for officially legal styles */
-  str = tmp;
-  while (IS_ALPHANUM (*str)) str++;
-  if (*str != '\0') { /* wasn't pure alphanumeric; now check for xxx..yyy */
-    str = buf;
-    while (IS_DIGIT (*str)) str++; /* xxx */
-    if (*str == '\0' /* must be something after the xxx */
-      || StringLen (str) < 3  /* need at least 2 '.'s and a digit*/
-      || str[0] != '.' || str[1] != '.') return FALSE;
-    str+=2;
-    while (IS_DIGIT (*str)) str++;
-    if (*str != '\0') return FALSE;  /* mustn't be anything after the yyy */
-  }
-#endif
-  return TRUE;
-}
-
-
-static CharPtr goQualType [] = {
-  "", "Process", "Component", "Function", NULL
-};
-
-static void RecordGoFieldsInQVP (
-  UserFieldPtr ufp,
-  Pointer userdata
-)
-
-{
-  UserFieldPtr  entry;
-  Int2          i;
-  ObjectIdPtr   oip;
-  QualValPtr    qvp;
-
-  qvp = (QualValPtr) userdata;
-
-  if (ufp == NULL || ufp->choice != 11) return;
-  oip = ufp->label;
-  if (oip == NULL) return;
-  for (i = 0; goQualType [i] != NULL; i++) {
-    if (StringICmp (oip->str, goQualType [i]) == 0) break;
-  }
-  if (goQualType [i] == NULL) return;
-
-  entry = ufp->data.ptrvalue;
-  if (entry == NULL || entry->choice != 11) return;
-
-  /* ufp = (UserFieldPtr)  entry->data.ptrvalue; */
-  switch (i) {
-    case 1 :
-      qvp [FTQUAL_go_process].ufp = entry;
-      break;
-    case 2 :
-      qvp [FTQUAL_go_component].ufp = entry;
-      break;
-    case 3 :
-      qvp [FTQUAL_go_function].ufp = entry;
-      break;
-    default :
-      break;
-  }
-}
-
-static void RecordUserObjectsInQVP (
-  UserObjectPtr uop,
-  Pointer userdata
-)
-
-{
-  ObjectIdPtr  oip;
-  QualValPtr   qvp;
-
-  if (uop == NULL || userdata == NULL) return;
-  qvp = (QualValPtr) userdata;
-  oip = uop->type;
-  if (oip == NULL) return;
-  if (StringCmp (oip->str, "ModelEvidence") == 0) {
-    qvp [FTQUAL_modelev].uop = uop;
-  } else if (StringCmp (oip->str, "GeneOntology") == 0) {
-    VisitUserFieldsInUop (uop, (Pointer) qvp, RecordGoFieldsInQVP);
-  }
-}
-
-static SeqIdPtr SeqLocIdForProduct (
-  SeqLocPtr product
-)
-
-{
-  SeqIdPtr   sip;
-  SeqLocPtr  slp;
-
-  /* in case product is a SEQLOC_EQUIV */
-
-  if (product == NULL) return NULL;
-  sip = SeqLocId (product);
-  if (sip != NULL) return sip;
-  slp = SeqLocFindNext (product, NULL);
-  while (slp != NULL) {
-    sip = SeqLocId (slp);
-    if (sip != NULL) return sip;
-    slp = SeqLocFindNext (product, slp);
-  }
-  return NULL;
-}
-
-static void AddIntervalsToGbfeat (
-  GBFeaturePtr gbfeat,
-  SeqLocPtr location,
-  BioseqPtr target
-)
-
-{
-  Char           accn [41];
-  SeqLocPtr      copy = NULL;
-  Int4           from;
-  GBIntervalPtr  gbint;
-  Int4           gi;
-  GBIntervalPtr  last = NULL;
-  Int4           point;
-  SeqIntPtr      sint;
-  SeqIdPtr       sip;
-  SeqLocPtr      slp;
-  SeqPntPtr      spp;
-  Int4           to;
-  Int4           swap;
-
-  if (gbfeat == NULL || location == NULL) return;
-  if (target != NULL) {
-    copy = SeqLocMerge (target, location, NULL, FALSE, TRUE, FALSE);
-    location = copy;
-  }
-
-  slp = SeqLocFindNext (location, NULL);
-  while (slp != NULL) {
-    from = 0;
-    to = 0;
-    point = 0;
-    sip = NULL;
-    switch (slp->choice) {
-      case SEQLOC_WHOLE :
-        sip = (SeqIdPtr) slp->data.ptrvalue;
-        if (sip != NULL) {
-          from = 1;
-          to = SeqLocLen (slp);
-          if (to < 0) {
-            sip = NULL;
-          }
-        }
-        break;
-      case SEQLOC_INT :
-        sint = (SeqIntPtr) slp->data.ptrvalue;
-        if (sint != NULL) {
-          from = sint->from + 1;
-          to = sint->to + 1;
-          sip = sint->id;
-          if (sint->strand == Seq_strand_minus && from < to) {
-            swap = from;
-            from = to;
-            to = swap;
-          }
-        }
-        break;
-      case SEQLOC_PNT :
-        spp = (SeqPntPtr) slp->data.ptrvalue;
-        if (spp != NULL) {
-          point = spp->point + 1;
-          sip = spp->id;
-        }
-        break;
-      default :
-        break;
-    }
-    if (sip != NULL) {
-      accn [0] = '\0';
-      if (sip->choice == SEQID_GI) {
-        gi = sip->data.intvalue;
-        if (! GetAccnVerFromServer (gi, accn)) {
-          accn [0] = '\0';
-        }
-        if (StringHasNoText (accn)) {
-          sip = GetSeqIdForGI (gi);
-          SeqIdWrite (sip, accn, PRINTID_TEXTID_ACC_VER, sizeof (accn));
-          SeqIdFree (sip);
-        }
-      } else {
-        SeqIdWrite (sip, accn, PRINTID_TEXTID_ACC_VER, sizeof (accn));
-      }
-      if (! StringHasNoText (accn)) {
-        gbint = GBIntervalNew ();
-        if (gbint != NULL) {
-          gbint->from = from;
-          gbint->to = to;
-          gbint->point = point;
-          gbint->accession = StringSave (accn);
-          if (gbfeat->intervals == NULL) {
-            gbfeat->intervals = gbint;
-          } else {
-            last->next = gbint;
-          }
-          last = gbint;
-        }
-      }
-    }
-    slp = SeqLocFindNext (location, slp);
-  }
-
-  SeqLocFree (copy);
-}
-
-static Boolean CountBasesByRead (
-  IntAsn2gbJobPtr ajp,
-  BioseqPtr bsp,
-  Int4Ptr base_count
-)
-
-{
-  Byte        bases [400];
-  Uint1       code = Seq_code_iupacna;
-  Int2        ctr;
-  Int2        i;
-  Int4        len;
-  Uint1       residue;
-  SeqPortPtr  spp = NULL;
-  Int4        total = 0;
-
-  if (ISA_aa (bsp->mol)) {
-    code = Seq_code_ncbieaa;
-  }
-
-  if (ajp->ajp.slp != NULL) {
-    spp = SeqPortNewByLoc (ajp->ajp.slp, code);
-    len = SeqLocLen (ajp->ajp.slp);
-  } else {
-    spp = SeqPortNew (bsp, 0, -1, 0, code);
-    len = bsp->length;
-  }
-  if (spp == NULL) return FALSE;
-  if (bsp->repr == Seq_repr_delta || bsp->repr == Seq_repr_virtual) {
-    SeqPortSet_do_virtual (spp, TRUE);
-  }
-
-  /* use SeqPortRead rather than SeqPortGetResidue for faster performance */
-
-  ctr = SeqPortRead (spp, bases, sizeof (bases));
-  i = 0;
-  residue = (Uint1) bases [i];
-  while (residue != SEQPORT_EOF) {
-    if (IS_residue (residue)) {
-      total++;
-      switch (residue) {
-        case 'A' :
-          (base_count [0])++;
-          break;
-        case 'C' :
-          (base_count [1])++;
-          break;
-        case 'G' :
-          (base_count [2])++;
-          break;
-        case 'T' :
-          (base_count [3])++;
-          break;
-        default :
-          (base_count [4])++;
-          break;
-      }
-    }
-    i++;
-    if (i >= ctr) {
-      i = 0;
-      ctr = SeqPortRead (spp, bases, sizeof (bases));
-      if (ctr < 0) {
-        bases [0] = -ctr;
-      } else if (ctr < 1) {
-        bases [0] = SEQPORT_EOF;
-      }
-    }
-    residue = (Uint1) bases [i];
-  }
-
-  SeqPortFree (spp);
-
-  return TRUE;
-}
-
-static void LIBCALLBACK CountBasesByStream (
-  CharPtr sequence,
-  Pointer userdata
-)
-
-{
-  Int4Ptr  base_count;
-  Char     ch;
-  CharPtr  ptr;
-
-  base_count = (Int4Ptr) userdata;
-
-  ptr = sequence;
-  ch = *ptr;
-  while (ch != '\0') {
-    ch = TO_UPPER (ch);
-    switch (ch) {
-      case 'A' :
-        (base_count [0])++;
-        break;
-      case 'C' :
-        (base_count [1])++;
-        break;
-      case 'G' :
-        (base_count [2])++;
-        break;
-      case 'T' :
-        (base_count [3])++;
-        break;
-      default :
-        (base_count [4])++;
-        break;
-    }
-    ptr++;
-    ch = *ptr;
-  }
-}
-
-static CharPtr FormatBasecountBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  IntAsn2gbJobPtr  ajp;
-  Asn2gbSectPtr    asp;
-  Int4             base_count [5];
-  BioseqPtr        bsp;
-  Char             buf [80];
-  Int2             i;
-  Int4             len;
-  StringItemPtr    ffstring;
-  CharPtr          str;
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-  bsp = (asp->bsp);
-  if (bsp == NULL) return NULL;
-
-  /* after first formatting, result is cached into bbp->string */
-
-  if (! StringHasNoText (bbp->string)) return StringSave (bbp->string);
-
-  for (i = 0; i < 5; i++) {
-    base_count [i] = 0;
-  }
-
-  if (ajp->ajp.slp != NULL) {
-    len = SeqLocLen (ajp->ajp.slp);
-    if (! CountBasesByRead (ajp, bsp, base_count)) return NULL;
-  } else {
-    len = bsp->length;
-    SeqPortStream (bsp, TRUE, (Pointer) base_count, CountBasesByStream);
-  }
-
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-
-    if (base_count [4] == 0) {
-      sprintf (buf, "%7ld a%7ld c%7ld g%7ld t",
-               (long) base_count [0], (long) base_count [1],
-               (long) base_count [2], (long) base_count [3]);
-    } else {
-      sprintf (buf, "%7ld a%7ld c%7ld g%7ld t%7ld others",
-               (long) base_count [0], (long) base_count [1],
-               (long) base_count [2], (long) base_count [3],
-               (long) base_count [4]);
-    }
-
-  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-
-    sprintf (buf, "Sequence %ld BP; %ld A; %ld C; %ld G; %ld T; %ld other;",
-             (long) len,
-             (long) base_count [0], (long) base_count [1],
-             (long) base_count [2], (long) base_count [3],
-             (long) base_count [4]);
-  }
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return NULL;
-
-  if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-    FFAddOneString(ffstring, "XX\n", FALSE, FALSE, TILDE_IGNORE);
-  }
-  FFStartPrint (ffstring, afp->format, 0, 0, "BASE COUNT", 12, 5, 5, "SQ", FALSE);
-  FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-  str = FFEndPrint(ajp, ffstring, afp->format, 12, 0, 5, 5, "SQ");
-  FFRecycleString(ajp, ffstring);
-
-  return str;
-}
-
-static void PrintSeqLine (
-  StringItemPtr ffstring,
-  FmtType format,
-  CharPtr buf,
-  Int4 start,
-  Int4 stop
-)
-
-{
-  size_t  len;
-  Char    pos [16];
-  Int4    pad;
-
-  len = StringLen (buf);
-  if (len > 0 && buf [len - 1] == ' ') {
-    buf [len - 1] = '\0';
-  }
-
-  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
-
-    sprintf (pos, "%9ld", (long) (start + 1));
-    FFAddOneString(ffstring, pos, FALSE, FALSE, TILDE_TO_SPACES);
-    FFAddOneChar(ffstring, ' ', FALSE);
-    FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-    FFAddOneChar(ffstring, '\n', FALSE);
-  } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-
-    sprintf (pos, "%8ld", (long) (stop));
-    FFAddNChar(ffstring, ' ', 5, FALSE);
-    FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-    pad = 72 - 5 - StringLen(buf);
-    FFAddNChar(ffstring, ' ', pad, FALSE);
-    FFAddOneString(ffstring, pos, FALSE, FALSE, TILDE_TO_SPACES);
-    FFAddOneChar(ffstring, '\n', FALSE);
-  }
-}
-
-static CharPtr CompressNonBases (CharPtr str)
-
-{
-  Char     ch;
-  CharPtr  dst;
-  CharPtr  ptr;
-
-  if (str == NULL || str [0] == '\0') return NULL;
-
-  dst = str;
-  ptr = str;
-  ch = *ptr;
-  while (ch != '\0') {
-    if (IS_ALPHA (ch)) {
-      *dst = ch;
-      dst++;
-    }
-    ptr++;
-    ch = *ptr;
-  }
-  *dst = '\0';
-
-  return str;
-}
-
-/*
-static void CatenateSequenceInGbseq (
-  GBSeqPtr gbseq,
-  CharPtr str
-)
-
-{
-  Char     ch;
-  CharPtr  tmp;
-
-  if (gbseq == NULL || StringHasNoText (str)) return;
-
-  if (gbseq->sequence == NULL) {
-    gbseq->sequence = StringSave (str);
-  } else {
-    tmp = (CharPtr) MemNew (StringLen (gbseq->sequence) + StringLen (str) + 2);
-    StringCpy (tmp, gbseq->sequence);
-    StringCat (tmp, str);
-    gbseq->sequence = MemFree (gbseq->sequence);
-    gbseq->sequence = tmp;
-  }
-
-  tmp = gbseq->sequence;
-  if (tmp == NULL) return;
-  ch = *tmp;
-  while (ch != '\0') {
-    if (ch == '\n' || ch == '\r' || ch == '\t') {
-      *tmp = ' ';
-    }
-    tmp++;
-    ch = *tmp;
-  }
-  TrimSpacesAroundString (gbseq->sequence);
-  CompressNonBases (gbseq->sequence);
-}
-*/
-
-  static Uint1 fasta_order [NUM_SEQID] = {
-    33, /* 0 = not set */
-    20, /* 1 = local Object-id */
-    15, /* 2 = gibbsq */
-    16, /* 3 = gibbmt */
-    30, /* 4 = giim Giimport-id */
-    10, /* 5 = genbank */
-    10, /* 6 = embl */
-    10, /* 7 = pir */
-    10, /* 8 = swissprot */
-    15, /* 9 = patent */
-    20, /* 10 = other TextSeqId */
-    20, /* 11 = general Dbtag */
-    255, /* 12 = gi */
-    10, /* 13 = ddbj */
-    10, /* 14 = prf */
-    12, /* 15 = pdb */
-    10, /* 16 = tpg */
-    10, /* 17 = tpe */
-    10  /* 18 = tpd */
-  };
-
-static void PrintGenome (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  SeqLocPtr slp_head, 
-  CharPtr prefix, 
-  Boolean segWithParts
-)
-{
-  Char         buf[40], val[166];
-  Boolean      first = TRUE;
-  SeqLocPtr    slp;
-  Int4         from, to, start, stop;
-  SeqIdPtr     sid, newid;
-  BioseqPtr    bsp = NULL;
-  Int2         p1=0, p2=0;
-
-  for (slp = slp_head; slp; slp = slp->next) {
-    from = to = 0;
-    sid = SeqLocId(slp);
-    if (slp->choice == SEQLOC_INT || slp->choice == SEQLOC_WHOLE) {
-      start = from = SeqLocStart(slp);
-      stop = to = SeqLocStop(slp);
-    } else if (slp->choice == SEQLOC_NULL){
-      sprintf(val, ",%s", "gap()");
-      FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
-      continue;
-    } else {
-      continue;
-    }
-    if (sid == NULL) {
-      continue;
-    }
-    newid = NULL;
-    buf [0] = '\0';
-    if (sid->choice == SEQID_GI) {
-      if (GetAccnVerFromServer (sid->data.intvalue, buf)) {
-        /* no need to call GetSeqIdForGI */
-      } else {
-        newid = GetSeqIdForGI (sid->data.intvalue);
-        if (newid != NULL && segWithParts) {
-          if (newid->choice == SEQID_GIBBSQ ||
-              newid->choice == SEQID_GIBBMT ||
-              newid->choice == SEQID_GIIM) {
-            bsp = BioseqFind (newid);
-            if (bsp != NULL && bsp->repr == Seq_repr_virtual) {
-              if (bsp->length > 0) {
-                sprintf (val, ",gap(%ld)", (long) bsp->length);
-              } else {
-                sprintf(val, ",%s", "gap()");
-              }
-              FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
-              continue;
-            }
-          }
-        }
-      }
-    } else if (sid->choice == SEQID_GENERAL) {
-      newid = sid;
-    } else {
-      newid = sid;
-    }
-    if (prefix != NULL) {
-      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    }
-    if (first) {
-      first = FALSE;
-    } else {
-      FFAddOneChar(ffstring, ',', FALSE);
-      /*ff_AddChar(',');*/
-    }
-    if (! StringHasNoText (buf)) {
-      /* filled in by GetAccnVerFromServer */
-    } else if (newid != NULL) {
-      SeqIdWrite (SeqIdSelect (newid, fasta_order, NUM_SEQID),
-                 buf, PRINTID_TEXTID_ACC_VER, sizeof(buf) -1 );
-    } else if (sid->choice == SEQID_GI) {
-      SeqIdWrite (sid, buf, PRINTID_FASTA_LONG, sizeof (buf) - 1);
-    }
-
-    if (SeqLocStrand (slp) == Seq_strand_minus) {
-      FFAddOneString(ffstring, "complement(", FALSE, FALSE, TILDE_IGNORE);
-    }
-    if ( GetWWW(ajp) ) {
-      if (newid == NULL) {
-        newid = sid;
-      }
-      if (newid->choice != SEQID_GENERAL) {
-        FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
-        FFAddTextToString(ffstring, "val=", buf, ">", FALSE, FALSE, TILDE_IGNORE);
-        FFAddTextToString(ffstring, NULL, buf, "</a>", FALSE, FALSE, TILDE_IGNORE);
-      }
-    } else {
-      FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
-    }
-
-    if (SeqLocStrand(slp) == Seq_strand_minus) {
-      sprintf (val,":%ld..%ld)", (long) start+1, (long) stop+1);
-    } else {
-      sprintf (val,":%ld..%ld", (long) start+1, (long) stop+1);
-    }
-    FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
-    p1 += StringLen (val);
-    p2 += StringLen (val);
-  }
-}
-
-static Boolean SegHasParts (
-  BioseqPtr bsp
-)
-
-{
-  BioseqSetPtr  bssp;
-  SeqEntryPtr   sep;
-
-  if (bsp == NULL || bsp->repr != Seq_repr_seg) return FALSE;
-  sep = bsp->seqentry;
-  if (sep == NULL) return FALSE;
-  sep = sep->next;
-  if (sep == NULL || (! IS_Bioseq_set (sep))) return FALSE;
-  bssp = (BioseqSetPtr) sep->data.ptrvalue;
-  if (bssp != NULL && bssp->_class == BioseqseqSet_class_parts) return TRUE;
-  return FALSE;
-}
-
-static Boolean DeltaLitOnly (
-  BioseqPtr bsp
-)
-
-{
-  ValNodePtr  vnp;
-
-  if (bsp == NULL || bsp->repr != Seq_repr_delta) return FALSE;
-  for (vnp = (ValNodePtr)(bsp->seq_ext); vnp != NULL; vnp = vnp->next) {
-    if (vnp->choice == 1) return FALSE;
-  }
-  return TRUE;
-}
-
-static CharPtr FormatContigBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  IntAsn2gbJobPtr  ajp;
-  Asn2gbSectPtr    asp;
-  BioseqPtr        bsp;
-  DeltaSeqPtr      dsp;
-  GBSeqPtr         gbseq;
-  SeqLitPtr        litp;
-  CharPtr          prefix = NULL;
-  Boolean          segWithParts = FALSE;
-  SeqLocPtr        slp_head = NULL;
-  CharPtr          str;
-  Char             val [20];
-  StringItemPtr    ffstring;
-  CharPtr          label;
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-  bsp = (asp->bsp);
-  if (bsp == NULL) return NULL;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return NULL;
-
-  if ( GetWWW(ajp) ) {
-    label = "CONTIG   ";
-  } else {
-    label = "CONTIG";
-  }
-  FFAddOneString(ffstring, label,  FALSE, FALSE, TILDE_IGNORE);  
-  FFAddNChar(ffstring, ' ', 12 - StringLen(label), FALSE);
-
-  FFAddOneString(ffstring, "join(", FALSE, FALSE, TILDE_IGNORE);
-
-  if (bsp->seq_ext_type == 1) {
-
-    if (bsp->repr == Seq_repr_seg && SegHasParts (bsp)) {
-      segWithParts = TRUE;
-    }
-
-    slp_head = (SeqLocPtr) bsp->seq_ext;
-    PrintGenome (ajp, ffstring, slp_head, prefix, segWithParts);
-
-  } else if (bsp->seq_ext_type == 4) {
-
-    for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp=dsp->next) {
-      if (dsp->choice == 1) {
-
-        slp_head = (SeqLocPtr) dsp->data.ptrvalue;
-        PrintGenome (ajp, ffstring, slp_head, prefix, FALSE);
-
-      } else {
-
-        litp = (SeqLitPtr) dsp->data.ptrvalue;
-        if (litp != NULL) {
-          if (litp->seq_data != NULL) {
-            if (litp->length == 0) {
-              sprintf (val, "gap(%ld)", (long) litp->length);
-              FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
-            } else {
-              /* don't know what to do here */
-            }
-          } else {
-            sprintf (val, ",gap(%ld)", (long) litp->length);
-            FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
-          }
-        }
-      }
-
-      prefix = ",";
-    }
-  }
-
-  FFAddOneChar(ffstring, ')', FALSE);
-
-  str = FFEndPrint(ajp, ffstring, afp->format, 12, 12, 12, 12, NULL);
-  FFRecycleString(ajp, ffstring);
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (gbseq != NULL) {
-    if (StringLen (str) > 12) {
-      gbseq->contig = StringSave (str + 12);
-    } else {
-      gbseq->contig = StringSave (str);
-    }
-
-    CleanQualValue (gbseq->contig);
-    Asn2gnbkCompressSpaces (gbseq->contig);
-    StripAllSpaces (gbseq->contig);
-  }
-
-  return str;
-}
-
-static CharPtr FormatSlashBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  GBFeaturePtr       currf, headf, nextf;
-  GBReferencePtr     currr, headr, nextr;
-  GBSeqPtr           gbseq;
-  IndxPtr            index;
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-
-  /* sort and unique indexes */
-
-  index = ajp->index;
-
-  if (index != NULL) {
-
-    MemCopy (index, &asp->index, sizeof (IndxBlock));
-    MemSet (&asp->index, 0, sizeof (IndxBlock));
-
-    index->authors = ValNodeSort (index->authors, SortVnpByString);
-    index->authors = UniqueValNode (index->authors);
-
-    index->genes = ValNodeSort (index->genes, SortVnpByString);
-    index->genes = UniqueValNode (index->genes);
-
-    index->journals = ValNodeSort (index->journals, SortVnpByString);
-    index->journals = UniqueValNode (index->journals);
-
-    index->keywords = ValNodeSort (index->keywords, SortVnpByString);
-    index->keywords = UniqueValNode (index->keywords);
-
-    index->secondaries = ValNodeSort (index->secondaries, SortVnpByString);
-    index->secondaries = UniqueValNode (index->secondaries);
-  }
-
-  /* adjust XML-ized GenBank format */
-
-  gbseq = ajp->gbseq;
-
-  if (gbseq != NULL) {
-
-    MemCopy (gbseq, &asp->gbseq, sizeof (GBSeq));
-    MemSet (&asp->gbseq, 0, sizeof (GBSeq));
-
-    /* reverse order of references */
-
-    headr = NULL;
-    for (currr = gbseq->references; currr != NULL; currr = nextr) {
-      nextr = currr->next;
-      currr->next = headr;
-      headr = currr;
-    }
-    gbseq->references = headr;
-
-    /* reverse order of features */
-
-    headf = NULL;
-    for (currf = gbseq->feature_table; currf != NULL; currf = nextf) {
-      nextf = currf->next;
-      currf->next = headf;
-      headf = currf;
-    }
-    gbseq->feature_table = headf;
-  }
-
-  /* slash always has string pre-allocated by add slash block function */
-
-  return StringSaveNoNull (bbp->string);
-}
-
-/* ********************************************************************** */
-
 /* functions to record sections or blocks in linked lists */
 
-static Asn2gbSectPtr Asn2gbAddSection (
-  Asn2gbWorkPtr awp
-)
-
-{
-  Asn2gbSectPtr  asp;
-  ValNodePtr     vnp;
-
-  if (awp == NULL) return NULL;
-
-  asp = (Asn2gbSectPtr) MemNew (sizeof (IntAsn2gbSect));
-  if (asp == NULL) return NULL;
-
-  vnp = ValNodeAddPointer (&(awp->lastsection), 0, asp);
-  if (vnp == NULL) return asp;
-
-  awp->lastsection = vnp;
-  if (awp->sectionList == NULL) {
-    awp->sectionList = vnp;
-  }
-
-  return asp;
-}
-
-static BaseBlockPtr Asn2gbAddBlock (
+NLM_EXTERN BaseBlockPtr Asn2gbAddBlock (
   Asn2gbWorkPtr awp,
   BlockType blocktype,
   size_t size
@@ -10856,8384 +1465,6 @@ static BaseBlockPtr Asn2gbAddBlock (
 }
 
 
-/* ********************************************************************** */
-
-/* add functions allocate specific blocks, populate with paragraph print info */
-
-static CharPtr strd [4] = {
-  "   ", "ss-", "ds-", "ms-"
-};
-
-static CharPtr gnbk_mol [14] = {
-  "    ", "DNA ", "RNA ", "mRNA", "rRNA", "tRNA", "snRNA", "scRNA", " AA ", "DNA ", "DNA ", "RNA ", "snoRNA", "RNA "
-};
-
-/* EMBL_FMT in RELEASE_MODE or ENTREZ_MODE, otherwise use gnbk_mol */
-
-static CharPtr embl_mol [14] = {
-  "xxx", "DNA", "RNA", "RNA", "RNA", "RNA", "RNA", "RNA", "AA ", "DNA", "DNA", "RNA", "RNA", "RNA"
-};
-
-static CharPtr embl_divs [18] = {
-  "FUN", "INV", "MAM", "ORG", "PHG", "PLN", "PRI", "PRO", "ROD"
-  "SYN", "UNA", "VRL", "VRT", "PAT", "EST", "STS", "HUM", "HTC"
-};
-
-static Uint1 imolToMoltype [14] = {
-  0, 1, 2, 5, 4, 3, 6, 7, 9, 1, 1, 2, 8, 2
-};
-
-static DatePtr GetBestDate (
-  DatePtr a,
-  DatePtr b
-)
-
-{
-  Int2  status;
-
-  if (a == NULL) return b;
-  if (b == NULL) return a;
-
-  status = DateMatch (a, b, FALSE);
-  if (status == 1) return a;
-
-  return b;
-}
-
-/*--------------------------------------------------------*/
-/*                                                        */
-/*  s_IsSeperatorNeeded()                                 */
-/*                                                        */
-/*--------------------------------------------------------*/
-
-static Boolean s_IsSeperatorNeeded(CharPtr baseString, Int4 baseLength, Int2 suffixLength)
-{
-  Char lastChar;
-  Char nextToLastChar;
-
-  lastChar = baseString[baseLength - 1];
-  nextToLastChar = baseString[baseLength - 2];
-
-  /* This first check put here to emulate what may be a  */
-  /* bug in the original code (in CheckLocusLength() )   */
-  /* which adds an 'S' segment seperator only if it      */
-  /* DOES make the string longer than the max.           */
-
-  if (baseLength + suffixLength < 16)
-    return FALSE;
-
-  /* If the last character is not a digit */
-  /* then don't use a seperator.          */
-
-  if (!IS_DIGIT(lastChar))
-    return FALSE;
-
-  /* If the last two characters are a non-digit   */
-  /* followed by a '0', then don't use seperator. */
-
-  if ((lastChar == '0') && (!IS_DIGIT(nextToLastChar)))
-    return FALSE;
-
-  /* If we made it to here, use a seperator */
-
-  return TRUE;
-}
-
-/*--------------------------------------------------------*/
-/*                                                        */
-/*  s_LocusAddSuffix() -                                  */
-/*                                                        */
-/*--------------------------------------------------------*/
-
-static Boolean s_LocusAddSuffix (CharPtr locus, Asn2gbWorkPtr awp)
-{
-  size_t  buflen;
-  Char    ch;
-  Char    segCountStr[6];
-  Int2    segCountStrLen;
-  Char    segSuffix[5];
-
-  buflen = StringLen (locus);
-
-  /* If there's one or less segments, */
-  /* no suffix is needed.             */
-
-  if (awp->numsegs <= 1)
-    return FALSE;
-
-  /* If the basestring has one or less */
-  /* characters, no suffix is needed.  */
-
-  if (buflen <=1)
-    return FALSE;
-
-  /* Add the suffix */
-
-  ch = locus[buflen-1];
-  sprintf(segCountStr,"%d",awp->numsegs);
-  segCountStrLen = StringLen(segCountStr);
-  segSuffix[0] = '\0';
-
-  if (s_IsSeperatorNeeded(locus,buflen,segCountStrLen) == TRUE)
-    sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg);
-  else
-    sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg);
-  StringCat(locus,segSuffix);
-
-  /* Return successfully */
-
-  return TRUE;
-}
-
-/*--------------------------------------------------------*/
-/*                                                        */
-/*  s_LocusAdjustLength() -                               */
-/*                                                        */
-/*--------------------------------------------------------*/
-
-static Boolean s_LocusAdjustLength(CharPtr locus, Int2 maxLength)
-{
-  Int2     trimCount;
-  Int2     buflen;
-  CharPtr  buftmp;
-
-  buflen = StringLen (locus);
-  if (buflen <= maxLength) return FALSE;
-
-  buftmp = MemNew(maxLength + 1);
-
-  /* If the sequence id is an NCBI locus of the */
-  /* form HSU00001, then make sure that if      */
-  /* there is trimming the HS gets trimmed off  */
-  /* as a unit, never just the 'H'.             */
-
-  trimCount = buflen - maxLength;
-  if (trimCount == 1)
-    if (IS_ALPHA(locus[0]) != 0 &&
-        IS_ALPHA(locus[1]) != 0 &&
-        IS_ALPHA(locus[2]) != 0 &&
-        IS_DIGIT(locus[3]) != 0 &&
-        IS_DIGIT(locus[4]) != 0 &&
-        IS_DIGIT(locus[5]) != 0 &&
-        IS_DIGIT(locus[6]) != 0 &&
-        IS_DIGIT(locus[7]) != 0 &&
-        locus[8] == 'S' &&
-        locus[9] == '\0')
-      trimCount++;
-
-  /* Left truncate the sequence id */
-
-  StringCpy(buftmp, &locus[trimCount]);
-  StringCpy(locus, buftmp);
-
-  MemFree(buftmp);
-  return TRUE;
-}
-
-/*--------------------------------------------------------*/
-/*                                                        */
-/*  AddLocusBlock() -                                     */
-/*                                                        */
-/*--------------------------------------------------------*/
-
-static DatePtr GetBestDateForBsp (
-  BioseqPtr bsp
-)
-
-{
-  DatePtr            best_date = NULL;
-  SeqMgrDescContext  dcontext;
-  DatePtr            dp;
-  EMBLBlockPtr       ebp;
-  GBBlockPtr         gbp;
-  PdbBlockPtr        pdp;
-  PdbRepPtr          prp;
-  SeqDescrPtr        sdp;
-  SPBlockPtr         spp;
-
-  if (bsp == NULL) return NULL;
-
-  dp = NULL;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_update_date, &dcontext);
-  if (sdp != NULL) {
-    dp = (DatePtr) sdp->data.ptrvalue;
-    best_date = GetBestDate (dp, best_date);
-  }
-
-  /* !!! temporarily also look at genbank block entry date !!! */
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
-  if (sdp != NULL) {
-    gbp = (GBBlockPtr) sdp->data.ptrvalue;
-    if (gbp != NULL) {
-      dp = gbp->entry_date;
-      best_date = GetBestDate (dp, best_date);
-    }
-  }
-
-  /* more complicated code for dates from various objects goes here */
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_embl, &dcontext);
-  if (sdp != NULL) {
-    ebp = (EMBLBlockPtr) sdp->data.ptrvalue;
-    if (ebp != NULL) {
-      dp = ebp->creation_date;
-      best_date = GetBestDate (dp, best_date);
-      dp = ebp->update_date;
-      best_date = GetBestDate (dp, best_date);
-    }
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_sp, &dcontext);
-  if (sdp != NULL) {
-    spp = (SPBlockPtr) sdp->data.ptrvalue;
-    if (spp != NULL) {
-      dp = spp->created;
-      if (dp != NULL && dp->data [0] == 1) {
-        best_date = GetBestDate (dp, best_date);
-      }
-      dp = spp->sequpd;
-      if (dp != NULL && dp->data [0] == 1) {
-        best_date = GetBestDate (dp, best_date);
-      }
-      dp = spp->annotupd;
-      if (dp != NULL && dp->data [0] == 1) {
-        best_date = GetBestDate (dp, best_date);
-      }
-    }
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pdb, &dcontext);
-  if (sdp != NULL) {
-    pdp = (PdbBlockPtr) sdp->data.ptrvalue;
-    if (pdp != NULL) {
-      dp = pdp->deposition;
-      if (dp != NULL && dp->data [0] == 1) {
-        best_date = GetBestDate (dp, best_date);
-      }
-      prp = pdp->replace;
-      if (prp != NULL) {
-        dp = prp->date;
-        if (dp != NULL && dp->data[0] == 1) {
-          best_date = GetBestDate (dp, best_date);
-        }
-      }
-    }
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_create_date, &dcontext);
-  if (sdp != NULL) {
-    dp = (DatePtr) sdp->data.ptrvalue;
-    if (dp != NULL) {
-      best_date = GetBestDate (dp, best_date);
-    }
-  }
-
-  return best_date;
-}
-
-static Boolean LocusHasBadChars (
-  CharPtr locus
-)
-
-{
-  Char     ch;
-  CharPtr  ptr;
-
-  ptr = locus;
-  ch = *ptr;
-  while (ch != '\0') {
-    if (! IS_ALPHANUM (ch)) {
-      return TRUE;
-    }
-    ptr++;
-    ch = *ptr;
-  }
-  return FALSE;
-}
-
-static void AddLocusBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  size_t             acclen;
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  BaseBlockPtr       bbp;
-  DatePtr            best_date = NULL;
-  BioSourcePtr       biop;
-  Int2               bmol = 0;
-  BioseqPtr          bsp;
-  SeqFeatPtr         cds;
-  Char               date [40];
-  SeqMgrDescContext  dcontext;
-  Char               div [10];
-  BioseqPtr          dna;
-  DatePtr            dp;
-  CharPtr            ebmol;
-  EMBLBlockPtr       ebp;
-  SeqMgrFeatContext  fcontext;
-  GBBlockPtr         gbp;
-  Char               gene [32];
-  Boolean            genome_view;
-  GBSeqPtr           gbseq;
-  Char               id [41];
-  Int2               imol = 0;
-  IndxPtr            index;
-  Int2               istrand;
-  Boolean            is_nm = FALSE;
-  Boolean            is_np = FALSE;
-  Boolean            is_nz = FALSE;
-  Boolean            is_transgenic = FALSE;
-  Char               len [32];
-  Int4               length;
-  size_t             loclen;
-  Char               locus [41];
-  MolInfoPtr         mip;
-  Char               mol [30];
-  BioseqPtr          nm = NULL;
-  OrgNamePtr         onp;
-  Uint1              origin;
-  OrgRefPtr          orp;
-  BioseqPtr          parent;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp;
-  SeqIdPtr           sip;
-  SubSourcePtr       ssp;
-  Uint1              tech;
-  Uint1              topology;
-  TextSeqIdPtr       tsip;
-  Boolean            wgsmaster = FALSE;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-  asp = awp->asp;
-  if (asp == NULL) return;
-
-  bbp = Asn2gbAddBlock (awp, LOCUS_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  mol [0] = '\0';
-  len [0] = '\0';
-  div [0] = '\0';
-  date [0] = '\0';
-  gene [0] = '\0';
-
-  genome_view = FALSE;
-  if (bsp->repr == Seq_repr_seg && (! SegHasParts (bsp))) {
-    genome_view = TRUE;
-  }
-  if (bsp->repr == Seq_repr_delta && (! DeltaLitOnly (bsp))) {
-    genome_view = TRUE;
-  }
-
-  /* locus id */
-
-  sip = NULL;
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_OTHER) {
-      tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-      if (tsip != NULL) {
-        if (StringNCmp (tsip->accession, "NM_", 3) == 0 ||
-            StringNCmp (tsip->accession, "NR_", 3) == 0 ||
-            StringNCmp (tsip->accession, "XM_", 3) == 0 ||
-            StringNCmp (tsip->accession, "XR_", 3) == 0) {
-          is_nm = TRUE;
-          nm = bsp;
-        } else if (StringNCmp (tsip->accession, "NP_", 3) == 0  ||
-                   StringNCmp (tsip->accession, "XP_", 3) == 0) {
-          is_np = TRUE;
-        } else if (StringNCmp (tsip->accession, "NZ_", 3) == 0) {
-          is_nz = TRUE;
-        }
-      }
-      break;
-    }
-    if (sip->choice == SEQID_GENBANK ||
-        sip->choice == SEQID_EMBL ||
-        sip->choice == SEQID_DDBJ) break;
-    if (sip->choice == SEQID_PIR ||
-        sip->choice == SEQID_SWISSPROT ||
-        sip->choice == SEQID_PRF ||
-        sip->choice == SEQID_PDB) break;
-    if (sip->choice == SEQID_TPG ||
-        sip->choice == SEQID_TPE ||
-        sip->choice == SEQID_TPD) break;
-  }
-  if (sip == NULL) {
-    sip = SeqIdFindBest (bsp->id, SEQID_GENBANK);
-  }
-
-  if (genome_view) {
-    SeqIdWrite (sip, locus, PRINTID_TEXTID_ACCESSION, sizeof (locus) - 1);
-  } else {
-    SeqIdWrite (sip, locus, PRINTID_TEXTID_LOCUS, sizeof (locus) - 1);
-    if (LocusHasBadChars (locus)) {
-      SeqIdWrite (sip, locus, PRINTID_TEXTID_ACCESSION, sizeof (locus) - 1);
-    }
-  }
-
-  if (is_np) {
-    sfp = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
-    if (sfp != NULL && fcontext.bsp != NULL) {
-      nm = fcontext.bsp;
-      for (sip = nm->id; sip != NULL; sip = sip->next) {
-        if (sip->choice == SEQID_OTHER) {
-          tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-          if (tsip != NULL) {
-            if (StringNCmp (tsip->accession, "NM_", 3) == 0 ||
-                StringNCmp (tsip->accession, "XM_", 3) == 0) {
-              is_nm = TRUE;
-            }
-          }
-        }
-      }
-      if (! is_nm) {
-        nm = NULL;
-      }
-    }
-  }
-  if (nm != NULL) {
-    /*
-    sfp = SeqMgrGetNextFeature (nm, NULL, SEQFEAT_GENE, 0, &fcontext);
-    if (sfp != NULL) {
-      StringNCpy_0 (gene, fcontext.label, sizeof (gene));
-      if (SeqMgrGetNextFeature (nm, sfp, SEQFEAT_GENE, 0, &fcontext) != NULL) {
-        gene [0] = '\0';
-      }
-      if (StringLen (gene) > 15) {
-        gene [0] = '\0';
-      }
-    }
-    */
-  }
-
-  /* more complicated code to get parent locus, if segmented, goes here */
-
-  if (awp->slp != NULL) {
-    length = SeqLocLen (awp->slp);
-  } else {
-    length = bsp->length;
-  }
-
-  mip = NULL;
-  tech = MI_TECH_standard;
-  origin = 0;
-  bmol = bsp->mol;
-  if (bmol > Seq_mol_aa) {
-    bmol = 0;
-  }
-  istrand = bsp->strand;
-  if (istrand > 3) {
-    istrand = 0;
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
-  if (sdp != NULL) {
-    bbp->entityID = dcontext.entityID;
-    bbp->itemID = dcontext.itemID;
-    bbp->itemtype = OBJ_SEQDESC;
-
-    mip = (MolInfoPtr) sdp->data.ptrvalue;
-    if (mip != NULL) {
-      if (mip->biomol <= MOLECULE_TYPE_TRANSCRIBED_RNA) {
-        imol = (Int2) mip->biomol;
-      }
-      tech = mip->tech;
-
-      if (tech == MI_TECH_wgs && bsp->repr == Seq_repr_virtual) {
-
-        /* check for WGS master record */
-
-        for (sip = bsp->id; sip != NULL; sip = sip->next) {
-          switch (sip->choice) {
-            case SEQID_GENBANK :
-            case SEQID_EMBL :
-            case SEQID_DDBJ :
-              tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-              if (tsip != NULL && tsip->accession != NULL) {
-                acclen = StringLen (tsip->accession);
-                if (acclen == 12) {
-                  if (StringCmp (tsip->accession + 6, "000000") == 0) {
-                    wgsmaster = TRUE;
-                  }
-                } else if (acclen == 13) {
-                  if (StringCmp (tsip->accession + 6, "0000000") == 0) {
-                    wgsmaster = TRUE;
-                  }
-                }
-              }
-              break;
-            case SEQID_OTHER :
-              tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-              if (tsip != NULL && tsip->accession != NULL) {
-                if (StringLen (tsip->accession) == 15) {
-                  if (StringCmp (tsip->accession + 9, "000000") == 0) {
-                    wgsmaster = TRUE;
-                  }
-                }
-              }
-              break;
-            default :
-              break;
-          }
-        }
-      }
-    }
-  }
-
-  /* check inst.mol if mol-type is not-set or genomic */
-
-  if (imol <= MOLECULE_TYPE_GENOMIC) {
-    if (bmol == Seq_mol_aa) {
-      imol = MOLECULE_TYPE_PEPTIDE;
-    } else if (bmol == Seq_mol_na) {
-      imol = 0;
-    } else if (bmol == Seq_mol_rna) {
-      imol = 2;
-    } else {
-      imol = 1;
-    }
-  } else if (imol == MOLECULE_TYPE_OTHER_GENETIC_MATERIAL) {
-    if (bmol == Seq_mol_rna) {
-      imol = 2;
-    }
-  }
-
-  /* if ds-DNA don't show ds */
-
-  if (bmol == Seq_mol_dna && istrand == 2) {
-    istrand = 0;
-  }
-
-  /* ss=any RNA don't show ss */
-
-  if ((bmol > Seq_mol_rna ||
-      (imol >= MOLECULE_TYPE_MRNA && imol <= MOLECULE_TYPE_PEPTIDE)) &&
-      istrand == 1) {
-    istrand = 0;
-  }
-
-  topology = bsp->topology;
-  if (awp->slp != NULL) {
-    topology = TOPOLOGY_LINEAR;
-  }
-
-  /* length, topology, and molecule type */
-
-  if (awp->format == GENBANK_FMT) {
-
-    if (awp->newLocusLine) {
-
-      if (wgsmaster && (! is_nz)) {
-        sprintf (len, "%ld rc", (long) length);
-      } else {
-        sprintf (len, "%ld bp", (long) length);
-      }
-      sprintf (mol, "%s%-4s", strd [istrand], gnbk_mol [imol]);
-
-    } else {
-
-      if (topology == TOPOLOGY_CIRCULAR) {
-        sprintf (len, "%7ld bp", (long) length);
-        sprintf (mol, "%s%-4s  circular", strd [istrand], gnbk_mol [imol]);
-      } else {
-        sprintf (len, "%7ld bp", (long) length);
-        sprintf (mol, "%s%-4s          ", strd [istrand], gnbk_mol [imol]);
-      }
-    }
-
-  } else if (awp->format == GENPEPT_FMT) {
-
-    if (awp->newLocusLine) {
-      sprintf (len, "%ld aa", (long) length);
-    } else {
-      sprintf (len, "%7ld aa", (long) length);
-    }
-
-  } else if (awp->format == EMBL_FMT) {
-
-    if (imol < MOLECULE_TYPE_PEPTIDE) {
-      if (ajp->flags.useEmblMolType) {
-        ebmol = embl_mol [imol];
-      } else {
-        ebmol = gnbk_mol [imol];
-      }
-
-      if (topology == TOPOLOGY_CIRCULAR) {
-        sprintf (mol, "circular %s", ebmol);
-        sprintf (len, "%ld BP.", (long) length);
-      } else {
-        sprintf (mol, "%s", ebmol);
-        sprintf (len, "%ld BP.", (long) length);
-      }
-    }
-  }
-
-  /* division */
-
-  biop = NULL;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
-  if (sdp != NULL) {
-    biop = (BioSourcePtr) sdp->data.ptrvalue;
-  } else {
-    sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
-    if (sfp != NULL) {
-      biop = (BioSourcePtr) sfp->data.value.ptrvalue;
-    } else if (ISA_aa (bsp->mol)) {
-
-      /* if protein with no sources, get sources applicable to DNA location of CDS */
-
-      cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
-      if (cds != NULL) {
-        sfp = SeqMgrGetOverlappingSource (cds->location, &fcontext);
-        if (sfp != NULL) {
-          biop = (BioSourcePtr) sfp->data.value.ptrvalue;
-        } else {
-          dna = BioseqFindFromSeqLoc (cds->location);
-          if (dna != NULL) {
-            sdp = SeqMgrGetNextDescriptor (dna, NULL, Seq_descr_source, &dcontext);
-            if (sdp != NULL) {
-              biop = (BioSourcePtr) sdp->data.ptrvalue;
-            }
-          }
-        }
-      }
-    }
-  }
-  if (biop != NULL) {
-    origin = biop->origin;
-    orp = biop->org;
-    if (orp != NULL) {
-      onp = orp->orgname;
-      if (onp != NULL) {
-        StringNCpy_0 (div, onp->div, sizeof (div));
-      }
-    }
-    for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
-      if (ssp->subtype == SUBSRC_transgenic) {
-        is_transgenic = TRUE;
-      }
-    }
-  }
-
-  switch (tech) {
-    case MI_TECH_est :
-      StringCpy (div, "EST");
-      break;
-    case MI_TECH_sts :
-      StringCpy (div, "STS");
-      break;
-    case MI_TECH_survey :
-      StringCpy (div, "GSS");
-      break;
-    case MI_TECH_htgs_0 :
-    case MI_TECH_htgs_1 :
-    case MI_TECH_htgs_2 :
-      StringCpy (div, "HTG");
-      break;
-    case MI_TECH_htc :
-      StringCpy (div, "HTC");
-      break;
-    default :
-      break;
-  }
-
-  if (origin == 5 || is_transgenic) {
-    StringCpy (div, "SYN");
-  }
-
-  sip = SeqIdFindBest (bsp->id, SEQID_PATENT);
-  if (sip != NULL && sip->choice == SEQID_PATENT) {
-    StringCpy (div, "PAT");
-  }
-
-  /* more complicated code for division, if necessary, goes here */
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
-  while (sdp != NULL) {
-    gbp = (GBBlockPtr) sdp->data.ptrvalue;
-    if (gbp != NULL) {
-      if (StringHasNoText (div) && gbp->div != NULL) {
-        StringCpy (div, gbp->div);
-      }
-      else if (StringCmp(gbp->div, "PAT") == 0 ||
-               StringCmp(gbp->div, "SYN") == 0 ) {
-        StringCpy (div, gbp->div);
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_genbank, &dcontext);
-  }
-
-  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
-
-    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_embl, &dcontext);
-    if (sdp != NULL) {
-      ebp = (EMBLBlockPtr) sdp->data.ptrvalue;
-      if (ebp != NULL) {
-        if (ebp->div == 255) {
-          if (mip == NULL) {
-            StringCpy (div, "HUM");
-          }
-        } else if (ebp->div < 18)  {
-          StringCpy (div, embl_divs [ebp->div]);
-        }
-      }
-    }
-
-    if (StringHasNoText (div)) {
-      StringCpy (div, "UNA");
-    }
-  }
-
-  /* empty division field if unable to find anything */
-
-  if (StringHasNoText (div)) {
-    StringCpy (div, "   ");
-  }
-
-  /* contig style (old genome_view flag) forces CON division */
-
-  if (awp->contig) {
-    StringCpy (div, "CON");
-  }
-
-  if (genome_view) {
-    StringCpy (div, "CON");
-  }
-
-  /* date */
-
-  best_date = GetBestDateForBsp (bsp);
-
-  if (best_date == NULL) {
-
-    /* if bsp is product of CDS or mRNA feature, get date from sfp->location bsp */
-
-    sfp = NULL;
-    if (ISA_na (bsp->mol)) {
-      sfp = SeqMgrGetRNAgivenProduct (bsp, NULL);
-    } else if (ISA_aa (bsp->mol)) {
-      sfp = SeqMgrGetCDSgivenProduct (bsp, NULL);
-    }
-    if (sfp != NULL) {
-      parent = BioseqFindFromSeqLoc (sfp->location);
-      if (parent != NULL) {
-        best_date = GetBestDateForBsp (parent);
-      }
-    }
-  }
-
-  /* convert best date */
-
-  if (best_date != NULL) {
-    DateToGB (date, best_date, FALSE);
-  }
-  if (StringHasNoText (date)) {
-    StringCpy (date, "01-JAN-1900");
-  }
-
-  if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) {
-
-    /* Create the proper locus name */
-
-    parent = awp->parent;
-    if (parent->repr == Seq_repr_seg) {
-
-      if (! StringHasNoText (awp->basename)) {
-        StringCpy (locus, awp->basename);
-        s_LocusAddSuffix (locus, awp);
-      }
-    }
-
-    /* Print the "LOCUS_NEW" line, if requested */
-
-    if (awp->newLocusLine) {
-      FFStartPrint (ffstring, awp->format, 0, 0, "LOCUS", 12, 0, 0, NULL, FALSE);
-      parent = awp->parent;
-
-      if (parent->repr == Seq_repr_seg)
-        s_LocusAdjustLength (locus,16);
-
-      if (is_nm && (! StringHasNoText (gene))) {
-        FFAddOneString (ffstring, gene, FALSE, FALSE, TILDE_IGNORE);
-      } else {
-        FFAddOneString (ffstring, locus, FALSE, FALSE, TILDE_IGNORE);
-      }
-      FFAddNChar(ffstring, ' ', 43 - StringLen(len)- ffstring->curr->pos, FALSE);
-      FFAddOneString (ffstring, len, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNChar(ffstring, ' ', 44 - ffstring->curr->pos, FALSE);
-      FFAddOneString (ffstring, mol, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNChar(ffstring, ' ', 55 - ffstring->curr->pos, FALSE);
-      if (topology == TOPOLOGY_CIRCULAR) {
-        FFAddOneString (ffstring, "circular", FALSE, FALSE, TILDE_IGNORE);
-      } else {
-        FFAddOneString (ffstring, "linear  ", FALSE, FALSE, TILDE_IGNORE);
-      }
-      FFAddNChar(ffstring, ' ', 64 - ffstring->curr->pos, FALSE);
-      FFAddOneString (ffstring, div, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNChar(ffstring, ' ', 68 - ffstring->curr->pos, FALSE);
-      FFAddOneString (ffstring, date, FALSE, FALSE, TILDE_IGNORE);
-    }
-
-    /* Else print the "LOCUS" line */
-
-    else {
-      FFStartPrint (ffstring, awp->format, 0, 0, "LOCUS", 12, 0, 0, NULL, FALSE);
-
-      if (parent->repr == Seq_repr_seg)
-        s_LocusAdjustLength (locus,16);
-
-      FFAddOneString (ffstring, locus, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNChar(ffstring, ' ', 32 - StringLen(len) - ffstring->curr->pos, FALSE);
-      FFAddOneString (ffstring, len, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNChar(ffstring, ' ', 33 - ffstring->curr->pos, FALSE);
-      FFAddOneString (ffstring, mol, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNChar(ffstring, ' ', 52 - ffstring->curr->pos, FALSE);
-      FFAddOneString (ffstring, div, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNChar(ffstring, ' ', 62 - ffstring->curr->pos, FALSE);
-      FFAddOneString (ffstring, date, FALSE, FALSE, TILDE_IGNORE);
-    }
-
-  } else if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
-    FFStartPrint (ffstring, awp->format, 0, 0, NULL, 0, 5, 0, "ID", FALSE);
-    FFAddOneString (ffstring, locus, FALSE, FALSE, TILDE_IGNORE);
-    loclen = StringLen(locus);
-    if (14 - 5 - loclen > 0) {
-      FFAddNChar(ffstring, ' ', 14 - 5 - loclen, FALSE);
-    }
-    if (awp->hup) {
-      FFAddOneString (ffstring, " confidential; ", FALSE, FALSE, TILDE_IGNORE);
-    } else {
-      FFAddOneString (ffstring, " standard; ", FALSE, FALSE, TILDE_IGNORE);
-    }
-    FFAddOneString (ffstring, mol, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, "; ", FALSE, FALSE, TILDE_IGNORE);
-
-    /* conditional code to make div "UNA" goes here */
-
-    FFAddOneString (ffstring, div, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, "; ", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, len, FALSE, FALSE, TILDE_IGNORE);
-  }
-
-  /* optionally populate indexes for NCBI internal database */
-
-  if (ajp->index) {
-    index = &asp->index;
-  } else {
-    index = NULL;
-  }
-
-  if (index != NULL) {
-    Char  tmp [20];
-    index->locus = StringSave (locus);
-    index->div = StringSave (div);
-    sprintf (tmp, "%ld", (long) length);
-    index->base_cnt = StringSave (tmp);
-  }
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (gbseq != NULL) {
-    gbseq->locus = StringSave (locus);
-    gbseq->length = length;
-    gbseq->division = StringSave (div);
-    gbseq->strandedness = bsp->strand;
-    gbseq->moltype = imolToMoltype [imol];
-    gbseq->topology = topology;
-
-    for (sip = bsp->id; sip != NULL; sip = sip->next) {
-      SeqIdWrite (sip, id, PRINTID_FASTA_SHORT, sizeof (id));
-      ValNodeCopyStr (&gbseq->other_seqids, 0, id);
-    }
-
-    date [0] = '\0';
-    dp = NULL;
-    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_create_date, &dcontext);
-    if (sdp != NULL) {
-      dp = (DatePtr) sdp->data.ptrvalue;
-    }
-    if (dp != NULL) {
-      DateToGB (date, dp, FALSE);
-    }
-    if (StringHasNoText (date)) {
-      StringCpy (date, "01-JAN-1900");
-    }
-    gbseq->create_date = StringSave (date);
-
-    date [0] = '\0';
-    dp = NULL;
-    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_update_date, &dcontext);
-    if (sdp != NULL) {
-      dp = (DatePtr) sdp->data.ptrvalue;
-    }
-    if (dp != NULL) {
-      DateToGB (date, dp, FALSE);
-    }
-    if (StringHasNoText (date)) {
-      StringCpy (date, "01-JAN-1900");
-    }
-    gbseq->update_date = StringSave (date);
-  }
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 0, 5, 0, "ID");
-  FFRecycleString(ajp, ffstring);
-}
-
-static void AddDeflineBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  Char               buf[4096]; 
-  /*CharPtr          buf;
-  size_t             buflen = 4096;*/ 
-  SeqMgrDescContext  dcontext;
-  GBSeqPtr           gbseq;
-  ItemInfo           ii;
-  MolInfoPtr         mip;
-  SeqDescrPtr        sdp;
-  Uint1              tech;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-  asp = awp->asp;
-  if (asp == NULL) return;
-
-  bbp = Asn2gbAddBlock (awp, DEFLINE_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  tech = 0;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
-  if (sdp != NULL) {
-    mip = (MolInfoPtr) sdp->data.ptrvalue;
-    if (mip != NULL) {
-      tech = mip->tech;
-    }
-  }
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  /*buf = MemNew (sizeof (Char) * (buflen + 1));*/
-  MemSet ((Pointer) (&ii), 0, sizeof (ItemInfo));
-  MemSet ((Pointer) buf, 0, sizeof (buf));
-
-  /* create default defline */
-
-  if ( CreateDefLine (&ii, bsp, buf, sizeof(buf), tech, NULL, NULL)) {
-    bbp->entityID = ii.entityID;
-    bbp->itemID = ii.itemID;
-    bbp->itemtype = ii.itemtype;
-
-    FFStartPrint (ffstring, awp->format, 0, 12, "DEFINITION", 12, 5, 5, "DE", TRUE);
-
-    if (StringHasNoText (buf)) {
-      FFAddOneChar (ffstring, '.', FALSE);
-    } else {
-      FFAddOneString (ffstring, buf, TRUE, TRUE, TILDE_IGNORE);
-    }
-
-    bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "DE");
-  }
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (gbseq != NULL) {
-    gbseq->definition = StringSave (buf);
-  }
-
-  FFRecycleString(ajp, ffstring);
-}
-
-/* !!! this definitely needs more work to support all classes, use proper SeqId !!! */
-
-static void AddAccessionBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  size_t             acclen;
-  SeqIdPtr           accn = NULL;
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  Char               buf [41];
-  SeqMgrDescContext  dcontext;
-  EMBLBlockPtr       ebp;
-  ValNodePtr         extra_access;
-  CharPtr            flatloc;
-  GBBlockPtr         gbp;
-  SeqIdPtr           gi = NULL;
-  GBSeqPtr           gbseq;
-  IndxPtr            index;
-  SeqIdPtr           lcl = NULL;
-  size_t             len = 0;
-  MolInfoPtr         mip;
-  SeqDescrPtr        sdp;
-  CharPtr            separator = " ";
-  SeqIdPtr           sip;
-  TextSeqIdPtr       tsip;
-  ValNodePtr         vnp;
-  CharPtr            wgsaccn = NULL;
-  CharPtr            xtra;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-  asp = awp->asp;
-  if (asp == NULL) return;
-  
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    switch (sip->choice) {
-      case SEQID_GI :
-        gi = sip;
-        break;
-      case SEQID_GENBANK :
-      case SEQID_EMBL :
-      case SEQID_DDBJ :
-        accn = sip;
-        tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-        if (tsip != NULL) {
-          acclen = StringLen (tsip->accession);
-          if (acclen == 12) {
-            wgsaccn = tsip->accession;
-            len = 12;
-          } else if (acclen == 13) {
-            wgsaccn = tsip->accession;
-            len = 13;
-          }
-        }
-        break;
-      case SEQID_OTHER :
-        accn = sip;
-        tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-        if (tsip != NULL) {
-          if (StringLen (tsip->accession) == 15) {
-            wgsaccn = tsip->accession;
-            len = 15;
-          }
-        }
-        break;
-      case SEQID_PIR :
-      case SEQID_SWISSPROT :
-      case SEQID_PRF :
-      case SEQID_PDB :
-        accn = sip;
-        break;
-      case SEQID_TPG :
-      case SEQID_TPE :
-      case SEQID_TPD :
-        accn = sip;
-        break;
-      case SEQID_GENERAL :
-        /* should not override better accession */
-        if (accn == NULL) {
-          accn = sip;
-        }
-        break;
-      case SEQID_LOCAL :
-        lcl = sip;
-        break;
-      default :
-        break;
-    }
-  }
-
-  sip = NULL;
-  if (accn != NULL) {
-    sip = accn;
-  } else if (lcl != NULL) {
-    sip = lcl;
-  } else if (gi != NULL) {
-    sip = gi;
-  }
-
-  if (sip == NULL) return;
-
-  SeqIdWrite (sip, buf, PRINTID_TEXTID_ACC_ONLY, sizeof (buf));
-
-  bbp = Asn2gbAddBlock (awp, ACCESSION_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  FFStartPrint (ffstring, awp->format, 0, 12, "ACCESSION", 12, 5, 5, "AC", TRUE);
-
-  if (awp->hup && accn != NULL) {
-    FFAddOneString (ffstring, ";", FALSE, FALSE, TILDE_TO_SPACES);
-
-  } else if (ajp->ajp.slp != NULL) {
-    FF_www_accession (ajp, ffstring, buf);
-    flatloc =  FlatLoc (ajp, bsp, ajp->ajp.slp, ajp->masterStyle);
-    FFAddTextToString (ffstring, " REGION: ", flatloc, NULL, FALSE, FALSE, TILDE_TO_SPACES);
-    MemFree (flatloc);
-  } else {
-    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-  }
-
-  /* optionally populate indexes for NCBI internal database */
-
-  if (ajp->index) {
-    index = &asp->index;
-  } else {
-    index = NULL;
-  }
-
-  if (index != NULL) {
-    index->accession = StringSave (buf);
-  }
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (gbseq != NULL) {
-    gbseq->primary_accession = StringSave (buf);
-  }
-
-  if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) {
-    separator = " ";
-  } else if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
-    separator = ";";
-  }
-
-  if (ajp->ajp.slp == NULL) {
-    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
-    if (sdp != NULL && wgsaccn != NULL) {
-      mip = (MolInfoPtr) sdp->data.ptrvalue;
-      if (mip != NULL && mip->tech == MI_TECH_wgs) {
-        StringNCpy_0 (buf, wgsaccn, sizeof (buf));
-        acclen = StringLen (buf);
-        if (acclen == 12 && StringCmp (buf + len - 6, "000000") != 0) {
-          StringCpy (buf + len - 6, "000000");
-        } else if (acclen == 13 && StringCmp (buf + len - 7, "0000000") != 0) {
-          StringCpy (buf + len - 7, "0000000");
-        } else if (acclen == 15 && StringCmp (buf + len - 8, "00000000") != 0) {
-          StringCpy (buf + len - 8, "00000000");
-        } else {
-          buf [0] = '\0';
-        }
-        if (! StringHasNoText (buf)) {
-          if ( GetWWW(ajp) ) {
-            FFAddTextToString(ffstring, separator, "<a href=", link_wgs, FALSE, FALSE, TILDE_IGNORE);
-            FFAddTextToString(ffstring, "db=Nucleotide&cmd=Search&term=", buf, ">", FALSE, FALSE, TILDE_IGNORE);
-            FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-            FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_TO_SPACES);
-          } else {
-            FFAddTextToString(ffstring, separator, buf, NULL, FALSE, FALSE, TILDE_TO_SPACES);
-          }
-        }
-      }
-    }
-
-    sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
-    while (sdp != NULL) {
-
-      extra_access = NULL;
-
-      switch (dcontext.seqdesctype) {
-        case Seq_descr_genbank :
-          gbp = (GBBlockPtr) sdp->data.ptrvalue;
-          if (gbp != NULL) {
-            extra_access = gbp->extra_accessions;
-          }
-          break;
-        case Seq_descr_embl :
-          ebp = (EMBLBlockPtr) sdp->data.ptrvalue;
-          if (ebp != NULL) {
-            extra_access = ebp->extra_acc;
-          }
-          break;
-        default :
-          break;
-      }
-
-      if (extra_access != NULL) {
-        bbp->entityID = dcontext.entityID;
-        bbp->itemID = dcontext.itemID;
-        bbp->itemtype = OBJ_SEQDESC;
-      }
-
-      for (vnp = extra_access; vnp != NULL; vnp = vnp->next) {
-        xtra = (CharPtr) vnp->data.ptrvalue;
-        if (ValidateAccn (xtra) == 0) {
-          FFAddTextToString(ffstring, separator, xtra, NULL, FALSE, FALSE, TILDE_TO_SPACES);
-
-          /* optionally populate indexes for NCBI internal database */
-
-          if (index != NULL) {
-            ValNodeCopyStrToHead (&(index->secondaries), 0, xtra);
-          }
-
-          /* optionally populate gbseq for XML-ized GenBank format */
-
-          if (gbseq != NULL) {
-            ValNodeCopyStr (&(gbseq->secondary_accessions), 0, xtra);
-          }
-        }
-      }
-
-      sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext);
-    }
-  }
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "AC");
-  FFRecycleString(ajp, ffstring);
-}
-
-static void AddVersionBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  SeqIdPtr         accn = NULL;
-  IntAsn2gbJobPtr  ajp;
-  Asn2gbSectPtr    asp;
-  BaseBlockPtr     bbp;
-  BioseqPtr        bsp;
-  Char             buf [41];
-  GBSeqPtr         gbseq;
-  Int4             gi = -1;
-  IndxPtr          index;
-  CharPtr          ptr;
-  SeqIdPtr         sip;
-  Char             tmp [41];
-  Char             version [64];
-  StringItemPtr    ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-  asp = awp->asp;
-  if (asp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    switch (sip->choice) {
-      case SEQID_GI :
-        gi = sip->data.intvalue;
-        break;
-      case SEQID_GENBANK :
-      case SEQID_EMBL :
-      case SEQID_DDBJ :
-      case SEQID_OTHER :
-        accn = sip;
-        break;
-      case SEQID_PIR :
-      case SEQID_SWISSPROT :
-      case SEQID_PRF :
-      case SEQID_PDB :
-        accn = sip;
-        break;
-      case SEQID_TPG :
-      case SEQID_TPE :
-      case SEQID_TPD :
-        accn = sip;
-        break;
-      default :
-        break;
-    }
-  }
-
-  /* if (gi < 1 && accn == NULL) return; */
-
-  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
-    if (gi < 1) return;
-  }
-
-  bbp = Asn2gbAddBlock (awp, VERSION_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  /* no longer displaying NID */
-
-  /*
-  if (gi > 0) {
-    sprintf (version, "g%ld", (long) gi);
-
-    gb_StartPrint (awp->format, needInitBuff, 0, 12, "NID", 13, 5, 5, "NI", TRUE);
-    needInitBuff = FALSE;
-
-    gb_AddString (NULL, version, NULL, FALSE, FALSE, TILDE_TO_SPACES);
-
-    ff_EndPrint();
-    needEndPrint = FALSE;
-  }
-  */
-
-  version [0] = '\0';
-
-  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
-    sprintf (version, "g%ld", (long) gi);
-
-    FFStartPrint (ffstring, awp->format, 0, 12, "VERSION", 12, 5, 5, "NI", TRUE);
-
-    FFAddOneString (ffstring, version, FALSE, FALSE, TILDE_TO_SPACES);
-
-    FFAddOneChar(ffstring, '\n', FALSE);
-
-    bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "NI");
-    FFRecycleString(ajp, ffstring);
-    return;
-  }
-
-  if (accn != NULL) {
-
-    buf [0] = '\0';
-    SeqIdWrite (accn, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
-
-    if (gi > 0) {
-      sprintf (version, "%s  GI:%ld", buf, (long) gi);
-    } else {
-      sprintf (version, "%s", buf);
-    }
-
-    FFStartPrint (ffstring, awp->format, 0, 12, "VERSION", 12, 5, 5, "SV", TRUE);
-
-    FFAddTextToString (ffstring, NULL, version, "\n", FALSE, FALSE, TILDE_TO_SPACES);
-    /* optionally populate indexes for NCBI internal database */
-
-    if (ajp->index) {
-      index = &asp->index;
-    } else {
-      index = NULL;
-    }
-
-    if (index != NULL) {
-      ptr = StringChr (buf, '.');
-      if (ptr != NULL) {
-        ptr++;
-        index->version = StringSave (ptr);
-      }
-      if (gi > 0) {
-        sprintf (tmp, "%ld", (long) gi);
-        index->gi = StringSave (tmp);
-      }
-    }
-
-    /* optionally populate gbseq for XML-ized GenBank format */
-
-    if (ajp->gbseq) {
-      gbseq = &asp->gbseq;
-    } else {
-      gbseq = NULL;
-    }
-
-    if (gbseq != NULL) {
-      ptr = StringChr (buf, '.');
-      if (ptr != NULL) {
-        gbseq->accession_version = StringSave (buf);
-      }
-    }
-
-  } else if (gi > 0) {
-
-    FFStartPrint (ffstring, awp->format, 0, 0, "VERSION", 12, 5, 5, "SV", TRUE);
-
-    sprintf (version, "  GI:%ld", (long) gi);
-
-    FFAddTextToString (ffstring, NULL, version, "\n", FALSE, FALSE, TILDE_TO_SPACES);
-
-  } else {
-
-    FFStartPrint (ffstring, awp->format, 0, 0, "VERSION", 0, 5, 5, "SV", TRUE);
-    FFAddOneChar(ffstring, '\n', FALSE);
-    bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "SV");
-  }
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "SV");
-  FFRecycleString(ajp, ffstring);
-}
-
-/* only displaying PID in GenPept format */
-
-static void AddPidBlock (Asn2gbWorkPtr awp)
-
-{
-  IntAsn2gbJobPtr  ajp;
-  BaseBlockPtr  bbp;
-  BioseqPtr     bsp;
-  Int4          gi = -1;
-  SeqIdPtr      sip;
-  Char          version [64];
-  StringItemPtr ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    switch (sip->choice) {
-      case SEQID_GI :
-        gi = sip->data.intvalue;
-        break;
-      default :
-        break;
-    }
-  }
-
-  if (gi < 1) return;
-
-  bbp = Asn2gbAddBlock (awp, PID_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  FFStartPrint (ffstring, awp->format, 0, 12, "PID", 12, 5, 5, NULL, TRUE);
-
-  sprintf (version, "g%ld", (long) gi);
-  FFAddOneString (ffstring, version, FALSE, FALSE, TILDE_TO_SPACES);
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, NULL);
-  FFRecycleString(ajp, ffstring);
-}
-
-static Uint1 dbsource_fasta_order [NUM_SEQID] = {
-  33, /* 0 = not set */
-  20, /* 1 = local Object-id */
-  15, /* 2 = gibbsq */
-  16, /* 3 = gibbmt */
-  30, /* 4 = giim Giimport-id */
-  10, /* 5 = genbank */
-  10, /* 6 = embl */
-  10, /* 7 = pir */
-  10, /* 8 = swissprot */
-  15, /* 9 = patent */
-  18, /* 10 = other TextSeqId */
-  20, /* 11 = general Dbtag */
-  31, /* 12 = gi */
-  10, /* 13 = ddbj */
-  10, /* 14 = prf */
-  12, /* 15 = pdb */
-  10, /* 16 = tpg */
-  10, /* 17 = tpe */
-  10  /* 18 = tpd */
-};
-
-static void AddToUniqueSipList (
-  ValNodePtr PNTR list,
-  SeqIdPtr sip
-)
-
-{
-  ValNodePtr  vnp;
-
-  if (list == NULL || sip == NULL) return;
-  for (vnp = *list; vnp != NULL; vnp = vnp->next) {
-    if (SeqIdMatch (sip, (SeqIdPtr) vnp->data.ptrvalue)) return;
-  }
-  ValNodeAddPointer (list, 0, (Pointer) sip);
-}
-
-static Boolean WriteDbsourceID (
-  SeqIdPtr sip,
-  CharPtr str
-)
-
-{
-  DbtagPtr      db;
-  CharPtr       dt;
-  Int4          gi;
-  ObjectIdPtr   oip;
-  CharPtr       pfx;
-  PDBSeqIdPtr   psip = NULL;
-  CharPtr       prefix;
-  Boolean       rsult = FALSE;
-  CharPtr       sfx;
-  CharPtr       suffix;
-  Char          tmp [32];
-  TextSeqIdPtr  tsip = NULL;
-
-  if (sip == NULL || str == NULL) return FALSE;
-  *str = '\0';
-  switch (sip->choice) {
-    case SEQID_LOCAL :
-      oip = (ObjectIdPtr) sip->data.ptrvalue;
-      if (oip == NULL) return FALSE;
-      if (! StringHasNoText (oip->str)) {
-        StringCat (str, oip->str);
-        return TRUE;
-      } else if (oip->id > 0) {
-        sprintf (tmp, "%ld", (long) oip->id);
-        StringCat (str, tmp);
-        return TRUE;
-      }
-      return FALSE;
-    case SEQID_GI :
-      gi = (Int4) sip->data.intvalue;
-      if (gi == 0) return FALSE;
-      sprintf (tmp, "gi: %ld", (long) gi);
-      StringCat (str, tmp);
-      return TRUE;
-    case SEQID_GENERAL :
-      db = (DbtagPtr) sip->data.ptrvalue;
-      if (db == NULL) return FALSE;
-      /* !!! still need to implement this !!! */
-      return FALSE;
-    case SEQID_GENBANK :
-    case SEQID_EMBL :
-    case SEQID_DDBJ :
-    case SEQID_OTHER :
-    case SEQID_PIR :
-    case SEQID_SWISSPROT :
-    case SEQID_PRF :
-    case SEQID_TPG :
-    case SEQID_TPE :
-    case SEQID_TPD :
-      tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-      if (tsip == NULL) return FALSE;
-      break;
-    case SEQID_PDB :
-      psip = (PDBSeqIdPtr) sip->data.ptrvalue;
-      if (psip == NULL) return FALSE;
-      break;
-    default :
-      break;
-  }
-  prefix = " ";
-  suffix = NULL;
-  switch (sip->choice) {
-    case SEQID_EMBL :
-      StringCat (str, "embl ");
-      suffix = ",";
-      break;
-    case SEQID_OTHER :
-      StringCat (str, "REFSEQ: ");
-      break;
-    case SEQID_SWISSPROT :
-      StringCat (str, "swissprot: ");
-      suffix = ",";
-      break;
-    case SEQID_PIR :
-      StringCat (str, "pir: ");
-      break;
-    case SEQID_PRF :
-      StringCat (str, "prf: ");
-      break;
-    case SEQID_PDB :
-      StringCat (str, "pdb: ");
-      suffix = ",";
-      break;
-    default :
-      break;
-  }
-  pfx = NULL;
-  sfx = NULL;
-  if (tsip != NULL) {
-    if (! StringHasNoText (tsip->name)) {
-      StringCat (str, sfx);
-      StringCat (str, pfx);
-      StringCat (str, "locus ");
-      StringCat (str, tsip->name);
-      sfx = suffix;
-      pfx = prefix;
-      rsult = TRUE;
-    }
-    if (! StringHasNoText (tsip->accession)) {
-      StringCat (str, sfx);
-      StringCat (str, pfx);
-      StringCat (str, "accession ");
-      StringCat (str, tsip->accession);
-      sfx = suffix;
-      pfx = prefix;
-      rsult = TRUE;
-    }
-    if (tsip->version > 0) {
-      sprintf (tmp, ".%d", (int) tsip->version);
-      StringCat (str, tmp);
-      sfx = suffix;
-      pfx = prefix;
-    }
-    if (! StringHasNoText (tsip->release)) {
-      StringCat (str, pfx);
-      StringCat (str, "release ");
-      StringCat (str, tsip->release);
-      sfx = suffix;
-      pfx = prefix;
-    }
-    if (sip->choice == SEQID_SWISSPROT || sip->choice == SEQID_PIR || sip->choice == SEQID_PRF) {
-      StringCat (str, ";");
-    }
-    return rsult;
-  }
-  if (psip != NULL) {
-    if (! StringHasNoText (psip->mol)) {
-      StringCat (str, "molecule ");
-      StringCat (str, psip->mol);
-      sfx = suffix;
-      pfx = prefix;
-      rsult = TRUE;
-    }
-    if (psip->chain > 0) {
-      StringCat (str, sfx);
-      StringCat (str, pfx);
-      sprintf (tmp, "chain %d", (int) psip->chain);
-      StringCat (str, tmp);
-      sfx = suffix;
-      pfx = prefix;
-      rsult = TRUE;
-    }
-    if (psip->rel != NULL) {
-      StringCat (str, sfx);
-      StringCat (str, pfx);
-      StringCat (str, "release ");
-      dt = asn2gb_PrintDate (psip->rel);
-      StringCat (str, dt);
-      MemFree (dt);
-      sfx = suffix;
-      pfx = prefix;
-      rsult = TRUE;
-    }
-    StringCat (str, ";");
-    return rsult;
-  }
-  return rsult;
-}
-
-
-static void AddSPBlock (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  BioseqPtr bsp
-)
-
-{
-  CharPtr            acc;
-  DbtagPtr           db;
-  SeqMgrDescContext  dcontext;
-  Boolean            first;
-  Boolean            has_link;
-  Char               id [41];
-  ObjectIdPtr        oip;
-  SeqDescrPtr        sdp;
-  SeqIdPtr           sid;
-  SPBlockPtr         spb;
-  CharPtr            string;
-  ValNodePtr         vnp;
-  CharPtr            str;
-  Char               numbuf[40];
-
-  if (bsp == NULL) return;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_sp, &dcontext);
-  if (sdp == NULL) return;
-  spb = (SPBlockPtr) sdp->data.ptrvalue;
-  if (spb == NULL) return;
-
-  if (spb->_class == 1) {
-    FFAddOneString (ffstring, "class: standard.", FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-  } else if (spb->_class == 2) {
-    FFAddOneString (ffstring, "class: preliminary.", FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-  }
-
-  if (spb->extra_acc) {
-    FFAddOneString (ffstring, "extra accessions:", FALSE, FALSE, TILDE_IGNORE);
-    for (vnp = spb->extra_acc; vnp != NULL; vnp = vnp->next) {
-      FFAddOneString (ffstring, (CharPtr) vnp->data.ptrvalue, FALSE, FALSE, TILDE_IGNORE);
-      FFAddOneChar (ffstring, ',', FALSE );
-    }
-  }
-
-  if (spb->imeth) {
-    FFAddOneString (ffstring, "seq starts with Met", FALSE, FALSE, TILDE_IGNORE);
-  }
-
-  if (spb->plasnm != NULL) {
-    FFAddOneString (ffstring, "plasmid:", FALSE, FALSE, TILDE_IGNORE);
-    for (vnp = spb->plasnm; vnp != NULL; vnp = vnp->next) {
-      FFAddOneString (ffstring, (CharPtr) vnp->data.ptrvalue, FALSE, FALSE, TILDE_IGNORE);
-      FFAddOneChar (ffstring, ',', FALSE );
-    }
-  }
-
-  if (spb->created) {
-    string = PrintDate (spb->created);
-    FFAddOneString (ffstring, "created: ", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, string, FALSE, FALSE, TILDE_IGNORE);
-
-    MemFree (string);
-  }
-
-  if (spb->sequpd) {
-    string = PrintDate (spb->sequpd);
-    FFAddOneString (ffstring, "sequence updated: ", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, string, FALSE, FALSE, TILDE_IGNORE);
-    MemFree (string);
-  }
-
-  if (spb->annotupd) {
-    string = PrintDate (spb->annotupd);
-    FFAddOneString (ffstring, "annotation updated: ", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, string, FALSE, FALSE, TILDE_IGNORE);
-    MemFree (string);
-  }
-
-  if (spb->seqref) {
-    FFAddOneString (ffstring, "xrefs: ", FALSE, FALSE, TILDE_IGNORE);
-    first = TRUE;
-    for (sid = spb->seqref; sid != NULL; sid = sid->next) {
-      acc = NULL;
-      has_link = FALSE;
-      if (first == FALSE) {
-        FFAddOneString (ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
-      }
-      first = FALSE;
-      SeqIdWrite (sid, id, PRINTID_TEXTID_ACC_VER, sizeof (id) - 1);
-      if (sid->choice == SEQID_GI) {
-        has_link = TRUE;
-      }
-      acc = id;
-      if (acc != NULL) {
-        switch (sid->choice) {
-          case SEQID_GENBANK:
-            FFAddOneString (ffstring, "genbank accession ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_EMBL:
-            FFAddOneString (ffstring, "embl accession ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_PIR:
-            FFAddOneString (ffstring, "pir locus ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_SWISSPROT:
-            FFAddOneString (ffstring, "swissprot accession ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_DDBJ:
-            FFAddOneString (ffstring, "ddbj accession ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_PRF:
-            FFAddOneString (ffstring, "prf accession ", FALSE, FALSE, TILDE_IGNORE);
-            break;
-          case SEQID_PDB:
-            FFAddOneString (ffstring, "pdb accession ", FALSE, FALSE, TILDE_IGNORE);
-            break;
-          case SEQID_GI:
-            FFAddOneString (ffstring, "gi: ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_TPG:
-            FFAddOneString (ffstring, "genbank third party accession ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_TPE:
-            FFAddOneString (ffstring, "embl third party accession ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_TPD:
-            FFAddOneString (ffstring, "ddbj third party accession ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          default:
-            acc = NULL;
-            break; 
-        }
-      }
-      if (acc != NULL) {
-        if ( GetWWW(ajp) && has_link ) {
-          sprintf(numbuf, "%ld", (long) sid->data.intvalue);
-          FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
-          FFAddTextToString(ffstring, "val=", numbuf, ">", FALSE, FALSE, TILDE_IGNORE);
-          FFAddOneString(ffstring, acc, FALSE, FALSE, TILDE_IGNORE);
-          FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-        } else {
-          FFAddOneString(ffstring, acc, FALSE, FALSE, TILDE_IGNORE);
-        }
-      }
-    }
-  }
-
-  first = TRUE;
-  for (vnp = spb->dbref; vnp != NULL; vnp = vnp->next) {
-    db = (DbtagPtr) vnp->data.ptrvalue;
-    if (db == NULL) continue;
-    oip = db->tag;
-    if (oip == NULL) continue;
-    has_link = FALSE;
-    if (first) {
-      FFAddNewLine(ffstring);
-      FFAddOneString (ffstring, "xrefs (non-sequence databases): ", FALSE, FALSE, TILDE_IGNORE);
-      first = FALSE;
-    } else {
-      FFAddOneString (ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
-    }
-    FFAddOneString (ffstring, db->db, FALSE, FALSE, TILDE_IGNORE);
-    if (StringCmp (db->db, "MIM") == 0) {
-      has_link = TRUE;
-    }
-
-    if ( oip->str != NULL ) {
-      str = oip->str;
-    } else if ( oip->id > 0 ) {
-      sprintf(numbuf, "%d", oip->id);
-      str = numbuf;
-    }
-
-    if ( !StringHasNoText(str) ) {
-      if ( GetWWW(ajp) && has_link) {
-        FFAddOneChar (ffstring, ' ', FALSE);
-        FFAddTextToString(ffstring, "<a href=", link_omim, str, FALSE, FALSE, TILDE_IGNORE);
-        FFAddTextToString(ffstring, ">", str, "</a>", FALSE, FALSE, TILDE_IGNORE);
-      } else {
-        FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
-      }
-    }
-  }
-}
-
-static void AddPIRBlock (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  BioseqPtr bsp
-)
-
-{
-  CharPtr            acc;
-  SeqMgrDescContext  dcontext;
-  Boolean            first;
-  Char               id [41];
-  CharPtr            prefix = NULL;
-  SeqDescrPtr        sdp;
-  SeqIdPtr           sid;
-  PirBlockPtr        pbp;
-
-  if (bsp == NULL) return;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pir, &dcontext);
-  if (sdp == NULL) return;
-  pbp = (PirBlockPtr) sdp->data.ptrvalue;
-  if (pbp == NULL) return;
-
-  if (pbp->host != NULL) {
-    FFAddTextToString (ffstring, "host:", pbp->host, "\n", FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->source != NULL) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString(ffstring, "source: ", pbp->source, "\n", FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->summary != NULL) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString(ffstring, "summary: ", pbp->summary, "\n", FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->genetic != NULL) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString(ffstring, "genetic: ", pbp->genetic, "\n", FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->includes != NULL) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString(ffstring, "includes: ", pbp->includes, "\n", FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->placement != NULL) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString(ffstring, "placement: ", pbp->placement, "\n", FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->superfamily != NULL) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString(ffstring, "superfamily: ", pbp->superfamily, "\n", FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->cross_reference != NULL) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString(ffstring, "xref: ", pbp->cross_reference, "\n", FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->date != NULL) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString (ffstring, "PIR dates: ", pbp->date, "\n", FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->had_punct) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddOneString (ffstring, "punctuation in sequence", FALSE, FALSE, TILDE_IGNORE);
-    prefix = ";";
-  }
-
-  if (pbp->seqref) {
-    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddOneString (ffstring, "xrefs: ", FALSE, FALSE, TILDE_IGNORE);
-    first = TRUE;
-    for (sid = pbp->seqref; sid != NULL; sid = sid->next) {
-      acc = NULL;
-      if (first == FALSE) {
-        FFAddOneString (ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
-      }
-      first = FALSE;
-      SeqIdWrite (sid, id, PRINTID_TEXTID_ACC_VER, sizeof (id) - 1);
-      acc = id;
-      if (acc != NULL) {
-        switch (sid->choice) {
-          case SEQID_GENBANK:
-            FFAddOneString (ffstring, "genbank ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_EMBL:
-            FFAddOneString (ffstring, "embl ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_PIR:
-            FFAddOneString (ffstring, "pir ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_SWISSPROT:
-            FFAddOneString (ffstring, "swissprot ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_DDBJ:
-            FFAddOneString (ffstring, "ddbj ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_PRF:
-            FFAddOneString (ffstring, "prf ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          case SEQID_GI:
-            FFAddOneString (ffstring, "gi: ", FALSE, FALSE, TILDE_IGNORE);
-            break; 
-          default:
-            acc = NULL;
-            break; 
-        }
-      }
-      if (acc != NULL) {
-        FFAddOneString (ffstring, acc, FALSE, FALSE, TILDE_IGNORE);
-      }
-    }
-  }
-  FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_IGNORE);
-}
-
-static void AddPRFBlock (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  BioseqPtr bsp
-)
-
-{
-  SeqMgrDescContext  dcontext;
-  PrfExtSrcPtr       extra;
-  CharPtr            prefix = NULL;
-  SeqDescrPtr        sdp;
-  PrfBlockPtr        prf;
-
-  if (bsp == NULL) return;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_prf, &dcontext);
-  if (sdp == NULL) return;
-  prf = (PrfBlockPtr) sdp->data.ptrvalue;
-  if (prf == NULL) return;
-  if ( ffstring == NULL ) return;
-
-  extra = prf->extra_src;
-  if (extra != NULL) {
-
-    if (extra->host != NULL) {
-      FFAddTextToString(ffstring, "host:", extra->host, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
-    }
-
-    if (extra->part != NULL) {
-      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
-      FFAddTextToString(ffstring, "part: ", extra->part, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
-    }
-    if (extra->state != NULL) {
-      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
-      FFAddTextToString(ffstring, "state: ", extra->state, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
-    }
-    if (extra->strain != NULL) {
-      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
-      FFAddTextToString(ffstring, "strain: ", extra->strain, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
-    }
-    if (extra->taxon != NULL) {
-      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
-      FFAddTextToString(ffstring, "taxonomy: ", extra->taxon, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
-    }
-
-    FFAddOneChar(ffstring, '.', FALSE);
-  }
-}
-
-static void AddPDBBlock (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  BioseqPtr bsp
-)
-
-{
-  SeqMgrDescContext  dcontext;
-  CharPtr            dt;
-  CharPtr            prefix = NULL;
-  SeqDescrPtr        sdp;
-  PdbBlockPtr        pdb;
-  PdbRepPtr          replace;
-  CharPtr            str;
-  ValNodePtr         vnp;
-
-  if (bsp == NULL) return;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pdb, &dcontext);
-  if (sdp == NULL) return;
-  pdb = (PdbBlockPtr) sdp->data.ptrvalue;
-  if (pdb == NULL) return;
-
-  if (pdb->deposition != NULL) {
-    dt = asn2gb_PrintDate (pdb->deposition);
-    FFAddTextToString (ffstring, "deposition: ", dt, NULL, FALSE, TRUE, TILDE_IGNORE);
-    MemFree (dt);
-    prefix = ";";
-  }
-  if (pdb->pdbclass != NULL) {
-    FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString(ffstring, "class: ", pdb->pdbclass, NULL, FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-  if (pdb->source != NULL) {
-    FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddOneString(ffstring, "source: ", FALSE, TRUE, TILDE_IGNORE);
-    prefix = NULL;
-    for (vnp = pdb->source; vnp != NULL; vnp = vnp->next) {
-      str = (CharPtr) vnp->data.ptrvalue;
-      if (StringHasNoText (str)) continue;
-      FFAddTextToString (ffstring, prefix, str, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ", ";
-    }
-    prefix = ";";
-  }
-  if (pdb->exp_method != NULL) {
-    FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-    FFAddNewLine(ffstring);
-    FFAddTextToString(ffstring, "Exp. method: ", pdb->exp_method, NULL, FALSE, TRUE, TILDE_IGNORE);
-    prefix = ";";
-  }
-  replace = pdb->replace;
-  if (replace != NULL) {
-    if (replace->ids != NULL) {
-      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
-      FFAddOneString(ffstring, "ids replaced: ", FALSE, TRUE, TILDE_IGNORE);
-
-      prefix = NULL;
-      for (vnp = replace->ids; vnp != NULL; vnp = vnp->next) {
-        str = (CharPtr) vnp->data.ptrvalue;
-        if (StringHasNoText (str)) continue;
-        FFAddTextToString (ffstring, prefix, str, NULL, FALSE, TRUE, TILDE_IGNORE);
-        prefix = ", ";
-      }
-      prefix = ";";
-    }
-    if (replace->date != NULL) {
-      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
-
-      dt = asn2gb_PrintDate (replace->date);
-      FFAddTextToString(ffstring, "replacement date: ", dt, NULL, FALSE, TRUE, TILDE_IGNORE);
-      MemFree (dt);
-      prefix = ";";
-    }
-  }
-
-  FFAddOneChar(ffstring, '.', FALSE);
-}
-
-static void AddDbsourceBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr  ajp;
-  Asn2gbSectPtr    asp;
-  BaseBlockPtr     bbp;
-  BioseqPtr        bsp;
-  Char             buf [256];
-  SeqFeatPtr       cds;
-  DbtagPtr         db;
-  GBSeqPtr         gbseq;
-  SeqIdPtr         id;
-  ValNodePtr       list = NULL;
-  BioseqPtr        nuc;
-  SeqIdPtr         sip;
-  SeqLocPtr        slp;
-  CharPtr          str;
-  Boolean          unknown = TRUE;
-  ValNodePtr       vnp;
-  StringItemPtr    ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  asp = awp->asp;
-  if (asp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  bbp = Asn2gbAddBlock (awp, DBSOURCE_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  FFStartPrint (ffstring, awp->format, 0, 12, "DBSOURCE", 12, 5, 5, NULL, TRUE);
-
-  sip = SeqIdSelect (bsp->id, dbsource_fasta_order, NUM_SEQID);
-
-  if (sip != NULL) {
-
-    switch (sip->choice) {
-      case SEQID_PIR :
-      case SEQID_SWISSPROT :
-      case SEQID_PRF :
-      case SEQID_PDB :
-        if (WriteDbsourceID (sip, buf)) {
-          FF_www_dbsource (ajp, ffstring, buf, TRUE, sip->choice);
-          FFAddNewLine(ffstring);
-          unknown = FALSE;
-        }
-        break;
-      case SEQID_GENERAL :
-        db = sip->data.ptrvalue;
-        if (db == NULL) {
-          break;
-        }
-        if (StringNCmp (db->db, "PIDe", 4) != 0 &&
-            StringNCmp (db->db, "PIDd", 4) != 0 &&
-            StringNCmp (db->db, "PID", 3) != 0) {
-          break;
-        }
-        /* if (ChoicePID) found, continue on to next set of cases */
-      case SEQID_EMBL :
-      case SEQID_GENBANK :
-      case SEQID_DDBJ :
-      case SEQID_GIBBSQ :
-      case SEQID_GIBBMT :
-      case SEQID_OTHER :
-      case SEQID_TPG :
-      case SEQID_TPE :
-      case SEQID_TPD :
-      case SEQID_GI :
-      case SEQID_GIIM :
-        cds = SeqMgrGetCDSgivenProduct (bsp, NULL);
-        if (cds == NULL) {
-          /* now may also be protein product of mature peptide feature */
-          cds = SeqMgrGetPROTgivenProduct (bsp, NULL);
-        }
-        if (cds != NULL) {
-          nuc = BioseqFindFromSeqLoc (cds->location);
-          if (nuc != NULL) {
-            slp = SeqLocFindNext (cds->location, NULL);
-            while (slp != NULL) {
-              sip = SeqLocId (slp);
-              AddToUniqueSipList (&list, sip);
-              slp = SeqLocFindNext (cds->location, slp);
-            }
-            for (vnp = list; vnp != NULL; vnp = vnp->next) {
-              id = (SeqIdPtr) vnp->data.ptrvalue;
-              nuc = BioseqFindCore (id);
-              sip = NULL;
-              if (nuc != NULL) {
-                sip = SeqIdSelect (nuc->id, dbsource_fasta_order, NUM_SEQID);
-              } else if (id != NULL && id->choice == SEQID_GI) {
-                sip = GetSeqIdForGI (id->data.intvalue);
-              }
-              if (sip == NULL) {
-                sip = id;
-              }
-              if (sip != NULL) {
-                if (WriteDbsourceID (sip, buf)) {
-                  FF_www_dbsource (ajp, ffstring, buf, TRUE, sip->choice);
-                  FFAddNewLine(ffstring);
-                  unknown = FALSE;
-                }
-              }
-            }
-            ValNodeFree (list);
-          }
-        } else {
-          if (WriteDbsourceID (sip, buf)) {
-            FF_www_dbsource (ajp, ffstring, buf, TRUE, sip->choice);
-            FFAddNewLine(ffstring);
-            unknown = FALSE;
-          }
-        }
-        break;
-      default :
-        break;
-    }
-
-    switch (sip->choice) {
-      case SEQID_PIR :
-        AddPIRBlock (ajp, ffstring, bsp);
-        break;
-      case SEQID_SWISSPROT :
-        AddSPBlock (ajp, ffstring, bsp);
-        break;
-      case SEQID_PRF :
-        AddPRFBlock (ajp, ffstring, bsp);
-        break;
-      case SEQID_PDB :
-        AddPDBBlock (ajp, ffstring, bsp);
-        break;
-      default :
-        break;
-    }
-  }
-
-  if (unknown) {
-    FFAddOneString (ffstring, "UNKNOWN", FALSE, FALSE, TILDE_TO_SPACES);
-  }
-
-  str = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, NULL);
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (gbseq != NULL) {
-    if (StringNCmp (str, "DBSOURCE    ", 12) == 0) {
-      gbseq->source_db = StringSave (str + 12);
-    } else {
-      gbseq->source_db = StringSave (str);
-    }
-    CleanQualValue (gbseq->source_db);
-    Asn2gnbkCompressSpaces (gbseq->source_db);
-  }
-
-  bbp->string = str;
-  FFRecycleString(ajp, ffstring);
-}
-
-static void AddDateBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  Char               date [40];
-  SeqMgrDescContext  dcontext;
-  DatePtr            dp;
-  SeqDescrPtr        sdp;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  bbp = Asn2gbAddBlock (awp, DATE_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  date [0] = '\0';
-
-  dp = NULL;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_create_date, &dcontext);
-  if (sdp != NULL) {
-    dp = (DatePtr) sdp->data.ptrvalue;
-  }
-  if (dp != NULL) {
-    DateToGB (date, dp, FALSE);
-  }
-  if (StringHasNoText (date)) {
-    StringCpy (date, "01-JAN-1900");
-  }
-
-  FFStartPrint (ffstring, awp->format, 0, 0, NULL, 0, 5, 5, "DT", TRUE);
-  FFAddOneString (ffstring, date, FALSE, FALSE, TILDE_IGNORE);
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 0, 0, 5, 5, "DT");
-  FFRecycleString(ajp, ffstring);
-
-  bbp = Asn2gbAddBlock (awp, DATE_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_update_date, &dcontext);
-  if (sdp != NULL) {
-    dp = (DatePtr) sdp->data.ptrvalue;
-  }
-  if (dp != NULL) {
-    DateToGB (date, dp, FALSE);
-  }
-
-  FFStartPrint (ffstring, awp->format, 0, 0, NULL, 0, 5, 5, "DT", FALSE);
-  FFAddOneString (ffstring, date, FALSE, FALSE, TILDE_IGNORE);
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 0, 0, 5, 5, "DT");
-  FFRecycleString(ajp, ffstring);
-}
-
-
-#define TOTAL_ESTKW 11
-#define TOTAL_STSKW 5
-#define TOTAL_GSSKW 2
-
-static CharPtr EST_kw_array[ TOTAL_ESTKW] = {
-  "EST", "EST PROTO((expressed sequence tag)", "expressed sequence tag",
-  "EST (expressed sequence tag)", "EST(expressed sequence tag)",
-  "partial cDNA sequence", "transcribed sequence fragment", "TSR",
-  "putatively transcribed partial sequence", "UK putts"
-};
-
-static CharPtr GSS_kw_array [TOTAL_GSSKW] = {
-  "GSS", "trapped exon"
-};
-static CharPtr STS_kw_array[TOTAL_STSKW] = {
-  "STS", "STS(sequence tagged site)", "STS (sequence tagged site)",
-  "STS sequence", "sequence tagged site"
-};
-
-static Int2 MatchArrayString (
-  CharPtr array_string [],
-  Int2 totalstr,
-  CharPtr text
-)
-
-{
-  Int2 i;
-
-  for (i = 0; i < totalstr && text != NULL; i++) {
-    if (StringCmp (array_string [i], text) == 0) {
-      return (i);
-    }
-  }
-
-  return (-1);
-}
-
-static Boolean CheckSpecialKeyword (
-  Boolean is_est,
-  Boolean is_sts,
-  Boolean is_gss,
-  CharPtr kwd
-)
-
-{
-  if (kwd == NULL) return FALSE;
-
-  if (is_est) {
-    if (MatchArrayString (STS_kw_array, TOTAL_STSKW, kwd) != -1) return FALSE;
-    if (MatchArrayString (GSS_kw_array, TOTAL_GSSKW, kwd) != -1) return FALSE;
-  }
-
-  if (is_sts) {
-    if (MatchArrayString (EST_kw_array, TOTAL_ESTKW, kwd) != -1) return FALSE;
-    if (MatchArrayString (GSS_kw_array, TOTAL_GSSKW, kwd) != -1) return FALSE;
-  }
-
-  if (is_gss) {
-    if (MatchArrayString (STS_kw_array, TOTAL_STSKW, kwd) != -1) return FALSE;
-    if (MatchArrayString (EST_kw_array, TOTAL_ESTKW, kwd) != -1) return FALSE;
-  }
-
-  return TRUE;
-}
-
-static Boolean KeywordAlreadyInList (
-  ValNodePtr head,
-  CharPtr kwd
-)
-
-{
-  ValNodePtr  vnp;
-
-  for (vnp = head; vnp != NULL; vnp = vnp->next) {
-    if (StringICmp ((CharPtr) vnp->data.ptrvalue, kwd) == 0) return TRUE;
-  }
-
-  return FALSE;
-}
-
-
-static void AddKeywordsBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  SeqMgrDescContext  dcontext;
-  EMBLBlockPtr       ebp;
-  GBBlockPtr         gbp;
-  GBSeqPtr           gbseq;
-  ValNodePtr         head = NULL;
-  IndxPtr            index;
-  Boolean            is_est = FALSE;
-  Boolean            is_gss = FALSE;
-  Boolean            is_sts = FALSE;
-  ValNodePtr         keywords;
-  CharPtr            kwd;
-  MolInfoPtr         mip;
-  PirBlockPtr        pir;
-  PrfBlockPtr        prf;
-  SeqDescrPtr        sdp;
-  SeqIdPtr           sip;
-  SPBlockPtr         sp;
-  CharPtr            str;
-  ValNodePtr         vnp;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-  asp = awp->asp;
-  if (asp == NULL) return;
-
-  bbp = (BaseBlockPtr) Asn2gbAddBlock (awp, KEYWORDS_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) {
-      ValNodeCopyStr (&head, 0, "Third Party Annotation");
-      ValNodeCopyStr (&head, 0, "; ");
-      ValNodeCopyStr (&head, 0, "TPA");
-    }
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
-  if (sdp != NULL) {
-    bbp->entityID = dcontext.entityID;
-    bbp->itemID = dcontext.itemID;
-    bbp->itemtype = OBJ_SEQDESC;
-
-    mip = (MolInfoPtr) sdp->data.ptrvalue;
-    if (mip != NULL) {
-      switch (mip->tech) {
-        case MI_TECH_htgs_1 :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          ValNodeCopyStr (&head, 0, "HTG");
-          ValNodeCopyStr (&head, 0, "; ");
-          ValNodeCopyStr (&head, 0, "HTGS_PHASE1");
-          break;
-        case MI_TECH_htgs_2 :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          ValNodeCopyStr (&head, 0, "HTG");
-          ValNodeCopyStr (&head, 0, "; ");
-          ValNodeCopyStr (&head, 0, "HTGS_PHASE2");
-          break;
-        case MI_TECH_htgs_3 :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          ValNodeCopyStr (&head, 0, "HTG");
-          break;
-        case MI_TECH_est :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          is_est = TRUE;
-          ValNodeCopyStr (&head, 0, "EST");
-          break;
-        case MI_TECH_sts :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          is_sts = TRUE;
-          ValNodeCopyStr (&head, 0, "STS");
-          break;
-        case MI_TECH_survey :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          is_gss = TRUE;
-          ValNodeCopyStr (&head, 0, "GSS");
-          break;
-        case MI_TECH_fli_cdna :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          ValNodeCopyStr (&head, 0, "FLI_CDNA");
-          break;
-        case MI_TECH_htgs_0 :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          ValNodeCopyStr (&head, 0, "HTG");
-          ValNodeCopyStr (&head, 0, "; ");
-          ValNodeCopyStr (&head, 0, "HTGS_PHASE0");
-          break;
-        case MI_TECH_htc :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          ValNodeCopyStr (&head, 0, "HTC");
-          break;
-        case MI_TECH_wgs :
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          ValNodeCopyStr (&head, 0, "WGS");
-          break;
-        default :
-          break;
-      }
-    }
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
-  while (sdp != NULL) {
-
-    keywords = NULL;
-
-    switch (dcontext.seqdesctype) {
-      case Seq_descr_genbank :
-        gbp = (GBBlockPtr) sdp->data.ptrvalue;
-        if (gbp != NULL) {
-          keywords = gbp->keywords;
-        }
-        break;
-      case Seq_descr_embl :
-        ebp = (EMBLBlockPtr) sdp->data.ptrvalue;
-        if (ebp != NULL) {
-          keywords = ebp->keywords;
-        }
-        break;
-      case Seq_descr_pir :
-        pir = (PirBlockPtr) sdp->data.ptrvalue;
-        if (pir != NULL) {
-          keywords = pir->keywords;
-        }
-        break;
-      case Seq_descr_prf :
-        prf = (PrfBlockPtr) sdp->data.ptrvalue;
-        if (prf != NULL) {
-          keywords = prf->keywords;
-        }
-        break;
-      case Seq_descr_sp :
-        sp = (SPBlockPtr) sdp->data.ptrvalue;
-        if (sp != NULL) {
-          keywords = sp->keywords;
-        }
-        break;
-      default :
-        break;
-    }
-
-    if (keywords != NULL) {
-      bbp->entityID = dcontext.entityID;
-      bbp->itemID = dcontext.itemID;
-      bbp->itemtype = OBJ_SEQDESC;
-    }
-
-    for (vnp = keywords; vnp != NULL; vnp = vnp->next) {
-      kwd = (CharPtr) vnp->data.ptrvalue;
-      if (CheckSpecialKeyword (is_est, is_sts, is_gss, kwd)) {
-        if (! KeywordAlreadyInList (head, kwd)) {
-          if (head != NULL) {
-            ValNodeCopyStr (&head, 0, "; ");
-          }
-          ValNodeCopyStr (&head, 0, kwd);
-        }
-      }
-    }
-
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext);
-  }
-
-  FFStartPrint( ffstring, awp->format, 0, 12, "KEYWORDS", 12, 5, 5, "KW", TRUE);
-  str = MergeValNodeStrings (head);
-  
-  /* if no keywords were found, period will still be added by this call */
-  if ( str != NULL ) {
-    FFAddOneString (ffstring, str, TRUE, FALSE, TILDE_TO_SPACES);
-  } else {
-    FFAddOneChar(ffstring, '.', FALSE);
-  }
-
-  MemFree (str);
-
-  /* optionally populate indexes for NCBI internal database */
-
-  if (ajp->index) {
-    index = &asp->index;
-  } else {
-    index = NULL;
-  }
-
-  if (index != NULL) {
-    for (vnp = head; vnp != NULL; vnp = vnp->next) {
-      kwd = (CharPtr) vnp->data.ptrvalue;
-      if (StringCmp (kwd, "; ") == 0) continue;
-      ValNodeCopyStrToHead (&(index->keywords), 0, kwd);
-    }
-  }
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (gbseq != NULL) {
-    for (vnp = head; vnp != NULL; vnp = vnp->next) {
-      kwd = (CharPtr) vnp->data.ptrvalue;
-      if (StringCmp (kwd, "; ") == 0) continue;
-      ValNodeCopyStr (&(gbseq->keywords), 0, kwd);
-    }
-  }
-
-  ValNodeFreeData (head);
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "KW");
-
-  FFRecycleString(ajp, ffstring);
-}
-
-static void AddSegmentBlock (
-  Asn2gbWorkPtr awp,
-  Boolean onePartOfSeg
-)
-
-{
-  Char             acc [41];
-  IntAsn2gbJobPtr  ajp;
-  Asn2gbSectPtr    asp;
-  BaseBlockPtr     bbp;
-  Char             buf [32];
-  GBSeqPtr         gbseq;
-  StringItemPtr    ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  asp = awp->asp;
-  if (asp == NULL) return;
-
-  if (awp->seg < 1 || awp->numsegs < 1) return;
-
-  bbp = Asn2gbAddBlock (awp, SEGMENT_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-
-  FFStartPrint (ffstring, awp->format, 0, 12, "SEGMENT", 12, 5, 5, "XX", FALSE);
-
-  if ( GetWWW(ajp) && awp->parent != NULL && onePartOfSeg) {
-    sprintf (buf, "%d of ", (int) awp->seg);
-    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
-    SeqIdWrite (awp->parent->id, acc, PRINTID_TEXTID_ACC_VER, sizeof (acc) - 1);
-
-    FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
-    FFAddTextToString(ffstring, "val=", acc, ">", FALSE, FALSE, TILDE_IGNORE);
-
-    sprintf (buf, "%ld", (long) awp->numsegs);
-    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-  } else {
-    sprintf (buf, "%d of %ld", (int) awp->seg, (long) awp->numsegs);
-    FFAddOneString (ffstring, buf, FALSE, TRUE, TILDE_TO_SPACES);
-  }
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (gbseq != NULL) {
-    sprintf (buf, "%d of %ld", (int) awp->seg, (long) awp->numsegs);
-    gbseq->segment = StringSave (buf);
-  }
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "XX");
-  FFRecycleString(ajp, ffstring);
-}
-
-static void AddSourceBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  SeqFeatPtr         cds;
-  SeqMgrDescContext  dcontext;
-  BioseqPtr          dna;
-  SeqMgrFeatContext  fcontext;
-  GBBlockPtr         gbp;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  bbp = Asn2gbAddBlock (awp, SOURCE_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
-  if (sdp != NULL && (! ajp->newSourceOrg)) {
-    gbp = (GBBlockPtr) sdp->data.ptrvalue;
-    if (gbp != NULL && (! StringHasNoText (gbp->source))) {
-      bbp->entityID = dcontext.entityID;
-      bbp->itemID = dcontext.itemID;
-      bbp->itemtype = OBJ_SEQDESC;
-      return;
-    }
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
-  if (sdp != NULL) {
-    bbp->entityID = dcontext.entityID;
-    bbp->itemID = dcontext.itemID;
-    bbp->itemtype = OBJ_SEQDESC;
-  } else {
-    sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
-    if (sfp != NULL) {
-      bbp->entityID = fcontext.entityID;
-      bbp->itemID = fcontext.itemID;
-      bbp->itemtype = OBJ_SEQFEAT;
-    } else if (ISA_aa (bsp->mol)) {
-
-      /* if protein with no sources, get sources applicable to DNA location of CDS */
-
-      cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
-      if (cds != NULL) {
-        sfp = SeqMgrGetOverlappingSource (cds->location, &fcontext);
-        if (sfp != NULL) {
-          bbp->entityID = fcontext.entityID;
-          bbp->itemID = fcontext.itemID;
-          bbp->itemtype = OBJ_SEQFEAT;
-        } else {
-          dna = BioseqFindFromSeqLoc (cds->location);
-          if (dna != NULL) {
-            sdp = SeqMgrGetNextDescriptor (dna, NULL, Seq_descr_source, &dcontext);
-            if (sdp != NULL) {
-              bbp->entityID = dcontext.entityID;
-              bbp->itemID = dcontext.itemID;
-              bbp->itemtype = OBJ_SEQDESC;
-            }
-          }
-        }
-      }
-    }
-  }
-}
-
-static void AddOrganismBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  SeqFeatPtr         cds;
-  SeqMgrDescContext  dcontext;
-  BioseqPtr          dna;
-  SeqMgrFeatContext  fcontext;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp;
-
-  if (awp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  bbp = Asn2gbAddBlock (awp, ORGANISM_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
-  if (sdp != NULL) {
-    bbp->entityID = dcontext.entityID;
-    bbp->itemID = dcontext.itemID;
-    bbp->itemtype = OBJ_SEQDESC;
-  } else {
-    sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
-    if (sfp != NULL) {
-      bbp->entityID = fcontext.entityID;
-      bbp->itemID = fcontext.itemID;
-      bbp->itemtype = OBJ_SEQFEAT;
-    } else if (ISA_aa (bsp->mol)) {
-
-      /* if protein with no sources, get sources applicable to DNA location of CDS */
-
-      cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
-      if (cds != NULL) {
-        sfp = SeqMgrGetOverlappingSource (cds->location, &fcontext);
-        if (sfp != NULL) {
-          bbp->entityID = fcontext.entityID;
-          bbp->itemID = fcontext.itemID;
-          bbp->itemtype = OBJ_SEQFEAT;
-        } else {
-          dna = BioseqFindFromSeqLoc (cds->location);
-          if (dna != NULL) {
-            sdp = SeqMgrGetNextDescriptor (dna, NULL, Seq_descr_source, &dcontext);
-            if (sdp != NULL) {
-              bbp->entityID = dcontext.entityID;
-              bbp->itemID = dcontext.itemID;
-              bbp->itemtype = OBJ_SEQDESC;
-            }
-          }
-        }
-      }
-    }
-  }
-}
-
-static RefBlockPtr AddPub (
-  Asn2gbWorkPtr awp,
-  ValNodePtr PNTR head,
-  PubdescPtr pdp
-)
-
-{
-  Char            buf [521]; /* increased for consortium in citsub */
-  CitArtPtr       cap;
-  CitBookPtr      cbp;
-  CitGenPtr       cgp;
-  CitJourPtr      cjp;
-  CitPatPtr       cpp;
-  CitSubPtr       csp;
-  DatePtr         dp = NULL;
-  Boolean         justuids = TRUE;
-  ImprintPtr      imp = NULL;
-  IntRefBlockPtr  irp;
-  RefBlockPtr     rbp;
-  ValNodePtr      vnp;
-
-  if (awp == NULL || head == NULL || pdp == NULL) return NULL;
-
-  if (awp->hideGeneRIFs) {
-    if (StringNICmp (pdp->comment, "GeneRIF", 7) == 0) return NULL;
-  } else if (awp->onlyGeneRIFs || awp->latestGeneRIFs) {
-    if (StringNICmp (pdp->comment, "GeneRIF", 7) != 0) return NULL;
-  }
-
-  rbp = (RefBlockPtr) MemNew (sizeof (IntRefBlock));
-  if (rbp == NULL) return NULL;
-  rbp->blocktype = REFERENCE_BLOCK;
-  rbp->section = awp->currsection;
-
-  rbp->serial = INT2_MAX;
-
-  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-    switch (vnp->choice) {
-      case PUB_Gen :
-        /* may be unpublished, or may be serial number of swiss-prot reference */
-        cgp = (CitGenPtr) vnp->data.ptrvalue;
-        if (cgp != NULL) {
-          if (StringNICmp ("BackBone id_pub", cgp->cit, 15) != 0) {
-            rbp->category = REF_CAT_UNP;
-            dp = cgp->date;
-            if (cgp->serial_number > 0) {
-              rbp->serial = cgp->serial_number;
-            }
-            if (cgp->cit != NULL) {
-              if (StringNICmp ("unpublished", cgp->cit, 11) != 0 &&
-                  StringNICmp ("submitted", cgp->cit, 8) != 0 &&
-                  StringNICmp ("to be published", cgp->cit, 15) != 0 &&
-                  StringNICmp ("in press", cgp->cit, 8) != 0 &&
-                  StringStr (cgp->cit, "Journal") == NULL) {
-                if (cgp->serial_number == 0) {
-                  MemFree (rbp);
-                  return NULL;
-                }
-              }
-            } else if (cgp->journal == NULL || cgp->date == NULL) {
-              if (cgp->serial_number == 0) {
-                MemFree (rbp);
-                return NULL;
-              }
-            }
-          }
-        }
-        break;
-      case PUB_Sub :
-        rbp->category = REF_CAT_SUB;
-        csp = (CitSubPtr) vnp->data.ptrvalue;
-        if (csp != NULL) {
-          imp = csp->imp;
-          if (imp != NULL) {
-            dp = imp->date;
-          }
-          if (csp->date != NULL) {
-            dp = csp->date;
-          }
-        }
-        break;
-      case PUB_Article:
-        cap = (CitArtPtr) vnp->data.ptrvalue;
-        if (cap != NULL) {
-          switch (cap->from) {
-            case 1:
-              cjp = (CitJourPtr) cap->fromptr;
-              if (cjp != NULL) {
-                imp = (ImprintPtr) cjp->imp;
-                if (imp != NULL) {
-                  dp = imp->date;
-                }
-              }
-              break;
-            case 2:
-              cbp = (CitBookPtr) cap->fromptr;
-              if (cbp != NULL) {
-                imp = (ImprintPtr) cbp->imp;
-                if (imp != NULL) {
-                  dp = imp->date;
-                }
-              }
-              break;
-            case 3:
-              cbp = (CitBookPtr) cap->fromptr;
-              if (cbp != NULL) {
-                imp = (ImprintPtr) cbp->imp;
-                if (imp != NULL) {
-                  dp = imp->date;
-                }
-              }
-              break;
-            default:
-              break;
-          }
-        }
-        break;
-      case PUB_Book:
-        cbp = (CitBookPtr) vnp->data.ptrvalue;
-        if (cbp != NULL) {
-          imp = (ImprintPtr) cbp->imp;
-          if (imp != NULL) {
-            dp = imp->date;
-          }
-        }
-        break;
-      case PUB_Proc:
-        cbp = (CitBookPtr) vnp->data.ptrvalue;
-        if (cbp != NULL) {
-          imp = (ImprintPtr) cbp->imp;
-          if (imp != NULL) {
-            dp = imp->date;
-          }
-        }
-        break;
-      case PUB_Patent :
-        rbp->category = REF_CAT_PUB;
-        cpp = (CitPatPtr) vnp->data.ptrvalue;
-        if (cpp != NULL) {
-          if (cpp->date_issue != NULL) {
-            dp = (DatePtr) cpp->date_issue;
-          } else if (cpp->app_date != NULL) {
-            dp = (DatePtr) cpp->app_date;
-          }
-        }
-        break;
-      case PUB_Man:
-        cbp = (CitBookPtr) vnp->data.ptrvalue;
-        if (cbp != NULL) {
-          imp = (ImprintPtr) cbp->imp;
-          if (imp != NULL) {
-            dp = imp->date;
-          }
-        }
-        break;
-      case PUB_Muid :
-        rbp->muid = vnp->data.intvalue;
-        rbp->category = REF_CAT_PUB;
-        break;
-      case PUB_PMid :
-        rbp->pmid = vnp->data.intvalue;
-        rbp->category = REF_CAT_PUB;
-        break;
-      default :
-        break;
-    }
-    if (vnp->choice != PUB_Muid && vnp->choice != PUB_PMid) {
-      justuids = FALSE;
-    }
-  }
-
-  /* check for submitted vs. in-press */
-
-  if (imp != NULL) {
-    rbp->category = REF_CAT_PUB;
-    switch (imp->prepub) {
-      case 1 :
-        rbp->category = REF_CAT_UNP;
-        break;
-      case 2 :
-        rbp->category = REF_CAT_PUB;
-        break;
-      default :
-        break;
-    }
-  }
-
-  /* check for sites reftype */
-
-  if (pdp->reftype != 0) {
-    rbp->sites = pdp->reftype;
-  }
-
-  if (rbp->muid == 0 && rbp->pmid == 0) {
-    vnp = pdp->pub;
-
-    /* skip over just serial number */
-
-    if (vnp != NULL && vnp->choice == PUB_Gen && vnp->next != NULL) {
-      cgp = (CitGenPtr) vnp->data.ptrvalue;
-      if (cgp != NULL) {
-        if (StringNICmp ("BackBone id_pub", cgp->cit, 15) != 0) {
-          if (cgp->cit == NULL && cgp->journal == NULL && cgp->date == NULL && cgp->serial_number) {
-            vnp = vnp->next;
-          }
-        }
-      }
-    }
-
-    if (PubLabelUnique (vnp, buf, sizeof (buf) - 1, OM_LABEL_CONTENT, TRUE) > 0) {
-      rbp->uniquestr = StringSaveNoNull (buf);
-    }
-  }
-
-  irp = (IntRefBlockPtr) rbp;
-  irp->date = DateDup (dp);
-  irp->justuids = justuids;
-  /* if (justuids) { */
-    irp->fig = StringSaveNoNull (pdp->fig);
-    irp->maploc = StringSaveNoNull (pdp->maploc);
-    irp->poly_a = pdp->poly_a;
-  /* } */
-
-  /* if not rejected by now, link in */
-
-  ValNodeAddPointer (head, 0, rbp);
-
-  return rbp;
-}
-
-static int LIBCALLBACK SortReferences (
-  VoidPtr ptr1,
-  VoidPtr ptr2,
-  Boolean serialFirst,
-  Boolean isRefSeq
-)
-
-{
-  int             compare;
-  IntRefBlockPtr  irp1;
-  IntRefBlockPtr  irp2;
-  RefBlockPtr     rbp1;
-  RefBlockPtr     rbp2;
-  Int2            status;
-  RefBlockPtr     temp;
-  ValNodePtr      vnp1;
-  ValNodePtr      vnp2;
-
-  if (ptr1 == NULL || ptr2 == NULL) return 0;
-  vnp1 = *((ValNodePtr PNTR) ptr1);
-  vnp2 = *((ValNodePtr PNTR) ptr2);
-  if (vnp1 == NULL || vnp2 == NULL) return 0;
-  rbp1 = (RefBlockPtr) vnp1->data.ptrvalue;
-  rbp2 = (RefBlockPtr) vnp2->data.ptrvalue;
-  if (rbp1 == NULL || rbp2 == NULL) return 0;
-
-  if (serialFirst) {
-    if (rbp1->serial > rbp2->serial) {
-      return 1;
-    } else if (rbp1->serial < rbp2->serial) {
-      return -1;
-    }
-  }
-
-  /* usual first sort by published, unpublished, and cit-subs */
-
-  if (rbp1->category > rbp2->category) {
-    return 1;
-  } else if (rbp1->category < rbp2->category) {
-    return -1;
-  }
-
-  /* for RefSeq, newer publications first, so temporarily swap pointers */
-
-  if (isRefSeq) {
-    temp = rbp1;
-    rbp1 = rbp2;
-    rbp2 = temp;
-  }
-
-  /* within class, sort by date, older publications first (except RefSeq) */
-
-  irp1 = (IntRefBlockPtr) rbp1;
-  irp2 = (IntRefBlockPtr) rbp2;
-  status = DateMatch (irp1->date, irp2->date, FALSE);
-  if (status == 1 || status == -1) return status;
-
-  /* if dates (e.g., years) match, try to distinguish by uids */
-
-  if (rbp1->pmid != 0 && rbp2->pmid != 0) {
-    if (rbp1->pmid > rbp2->pmid) {
-      return 1;
-    } else if (rbp1->pmid < rbp2->pmid) {
-      return -1;
-    }
-  }
-
-  if (rbp1->muid != 0 && rbp2->muid != 0) {
-    if (rbp1->muid > rbp2->muid) {
-      return 1;
-    } else if (rbp1->muid < rbp2->muid) {
-      return -1;
-    }
-  }
-
-  /* restore sort order after date and pmid/muid matching */
-
-  if (isRefSeq) {
-    temp = rbp1;
-    rbp1 = rbp2;
-    rbp2 = temp;
-  }
-
-  /* if same uid, one with just uids goes last to be excised but remembered */
-
-  if ((rbp1->pmid != 0 && rbp2->pmid != 0) || (rbp1->muid != 0 && rbp2->muid != 0)) {
-    if (irp1->justuids && (! irp2->justuids)) {
-      return 1;
-    } else if ((! irp1->justuids) && irp2->justuids) {
-      return -1;
-    }
-  }
-
-  /* put sites after pubs that refer to all or a range of bases */
-
-  if (rbp1->sites > 0) {
-    return 1;
-  } else if (rbp2->sites > 0) {
-    return -1;
-  }
-
-  /* for publication features, sort in explore index order */
-
-  if (irp1->index > irp2->index) {
-    return 1;
-  } else if (irp1->index < irp2->index) {
-    return -1;
-  }
-
-  /* next use author string */
-
-  if (irp1->authstr != NULL && irp2->authstr != NULL) {
-    compare = StringICmp (irp1->authstr, irp2->authstr);
-    if (compare > 0) {
-      return 1;
-    } else if (compare < 0) {
-      return -1;
-    }
-  }
-
-  /* use unique label string to determine sort order */
-
-  if (rbp1->uniquestr != NULL && rbp2->uniquestr != NULL) {
-    compare = StringICmp (rbp1->uniquestr, rbp2->uniquestr);
-    if (compare > 0) {
-      return 1;
-    } else if (compare < 0) {
-      return -1;
-    }
-  }
-
-  /* last resort for equivalent publication descriptors, sort in itemID order */
-
-  if (rbp1->itemtype == OBJ_SEQDESC && rbp2->itemtype == OBJ_SEQDESC) {
-    if (rbp1->itemID > rbp2->itemID) {
-      return 1;
-    } else if (rbp1->itemID < rbp2->itemID) {
-      return -1;
-    }
-  }
-
-  if (! serialFirst) {
-    if (rbp1->serial > rbp2->serial) {
-      return 1;
-    } else if (rbp1->serial < rbp2->serial) {
-      return -1;
-    }
-  }
-
-  return 0;
-}
-
-static int LIBCALLBACK SortReferencesA (
-  VoidPtr ptr1,
-  VoidPtr ptr2
-)
-
-{
-  return SortReferences (ptr1, ptr2, FALSE, FALSE);
-}
-
-static int LIBCALLBACK SortReferencesB (
-  VoidPtr ptr1,
-  VoidPtr ptr2
-)
-
-{
-  return SortReferences (ptr1, ptr2, TRUE, FALSE);
-}
-
-static int LIBCALLBACK SortReferencesAR (
-  VoidPtr ptr1,
-  VoidPtr ptr2
-)
-
-{
-  return SortReferences (ptr1, ptr2, FALSE, TRUE);
-}
-
-static int LIBCALLBACK SortReferencesBR (
-  VoidPtr ptr1,
-  VoidPtr ptr2
-)
-
-{
-  return SortReferences (ptr1, ptr2, TRUE, TRUE);
-}
-
-static CharPtr GetAuthorsPlusConsortium (
-  FmtType format,
-  AuthListPtr alp
-)
-
-{
-  CharPtr  consortium;
-  CharPtr  str;
-  CharPtr  tmp;
-
-  consortium = NULL;
-  str = GetAuthorsString (format, alp, &consortium, NULL, NULL);
-  if (str == NULL) return consortium;
-  if (consortium == NULL) return str;
-  tmp = MemNew (StringLen (str) + StringLen (consortium) + 5);
-  if (tmp == NULL) return NULL;
-  StringCpy (tmp, str);
-  StringCat (tmp, "; ");
-  StringCat (tmp, consortium);
-  MemFree (str);
-  MemFree (consortium);
-  return tmp;
-}
-
-static Boolean HasNoPmidOrMuid (
-  PubdescPtr pdp
-)
-
-{
-  ValNodePtr  vnp;
-
-  if (pdp == NULL) return TRUE;
-  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
-    if (vnp->choice == PUB_PMid || vnp->choice == PUB_Muid) return FALSE;
-  }
-  return TRUE;
-}
-
-typedef struct cdspubs {
-  Asn2gbWorkPtr  awp;
-  BioseqPtr      target;
-  ValNodePtr     vnp;
-} CdsPubs, PNTR CdsPubsPtr;
-
-static Boolean LIBCALLBACK GetRefsOnCDS (
-  SeqFeatPtr sfp,
-  SeqMgrFeatContextPtr context
-)
-
-{
-  AuthListPtr     alp;
-  Asn2gbWorkPtr   awp;
-  CdsPubsPtr      cpp;
-  IntRefBlockPtr  irp;
-  Boolean         okay;
-  PubdescPtr      pdp;
-  RefBlockPtr     rbp;
-
-  if (sfp == NULL || context == NULL) return TRUE;
-  cpp = (CdsPubsPtr) context->userdata;
-  awp = cpp->awp;
-  if (awp == NULL) return TRUE;
-
-  okay = TRUE;
-  pdp = (PubdescPtr) sfp->data.value.ptrvalue;
-  if (awp->format == FTABLE_FMT) {
-    if (HasNoPmidOrMuid (pdp)) {
-      okay = FALSE;
-    }
-  }
-
-  if (okay) {
-    rbp = AddPub (awp, &(awp->pubhead), pdp);
-    if (rbp != NULL) {
-
-      rbp->entityID = context->entityID;
-      rbp->itemID = context->itemID;
-      rbp->itemtype = OBJ_SEQFEAT;
-
-      irp = (IntRefBlockPtr) rbp;
-      irp->loc = SeqLocMerge (cpp->target, cpp->vnp, NULL, FALSE, TRUE, FALSE);
-      alp = GetAuthListPtr (pdp, NULL);
-      if (alp != NULL) {
-        irp->authstr = GetAuthorsPlusConsortium (awp->format, alp);
-      }
-      irp->index = 0;
-    }
-  }
-
-  return TRUE;
-}
-
-static void GetRefsOnBioseq (
-  Asn2gbWorkPtr awp,
-  BioseqPtr target,
-  BioseqPtr bsp,
-  Int4 from,
-  Int4 to,
-  SeqLocPtr cdsloc
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  AuthListPtr        alp;
-  CdsPubs            cp;
-  SeqMgrDescContext  dcontext;
-  SeqMgrFeatContext  fcontext;
-  Int2               i;
-  Int2               idx;
-  IntRefBlockPtr     irp;
-  Int4Ptr            ivals;
-  Int4               left;
-  SeqLocPtr          newloc;
-  Int2               numivals;
-  Boolean            okay;
-  PubdescPtr         pdp;
-  RefBlockPtr        rbp;
-  Int4               right;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp;
-  SeqInt             sint;
-  SeqIdPtr           sip;
-  Boolean            split;
-  Int4               start;
-  Int4               stop;
-  Uint1              strand;
-  Boolean            takeIt;
-  ValNode            vn;
-  ValNodePtr         vnp;
-
-  if (awp == NULL || target == NULL || bsp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-
-  /* full length loc for descriptors */
-
-  sint.from = 0;
-  if (ajp->ajp.slp != NULL) {
-    from = SeqLocStart (ajp->ajp.slp); /* other features use awp->slp for from and to */
-  }
-  if (ajp->ajp.slp != NULL) {
-    sint.to = SeqLocLen (ajp->ajp.slp) - 1;
-    to = SeqLocStop (ajp->ajp.slp); /* other features use awp->slp for from and to */
-  } else {
-    sint.to = bsp->length - 1;
-  }
-  sint.strand = Seq_strand_plus;
-  sint.id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0)));
-  sint.if_from = NULL;
-  sint.if_to = NULL;
-
-  vn.choice = SEQLOC_INT;
-  vn.data.ptrvalue = (Pointer) &sint;
-  vn.next = NULL;
-
-  sdp = SeqMgrGetNextDescriptor (target, NULL, Seq_descr_pub, &dcontext);
-  while (sdp != NULL) {
-
-    /* check if descriptor on part already added on segmented bioseq */
-
-    okay = TRUE;
-    for (vnp = awp->pubhead; vnp != NULL && okay; vnp = vnp->next) {
-      rbp = (RefBlockPtr) vnp->data.ptrvalue;
-      if (rbp != NULL) {
-        if (rbp->entityID == dcontext.entityID &&
-            rbp->itemID == dcontext.itemID &&
-            rbp->itemtype == OBJ_SEQDESC) {
-          okay = FALSE;
-        }
-      }
-    }
-    if (awp->format == FTABLE_FMT) {
-      pdp = (PubdescPtr) sdp->data.ptrvalue;
-      if (HasNoPmidOrMuid (pdp)) {
-        okay = FALSE;
-      }
-    }
-
-    if (okay) {
-      pdp = (PubdescPtr) sdp->data.ptrvalue;
-      rbp = AddPub (awp, &(awp->pubhead), pdp);
-      if (rbp != NULL) {
-
-        rbp->entityID = dcontext.entityID;
-        rbp->itemID = dcontext.itemID;
-        rbp->itemtype = OBJ_SEQDESC;
-
-        irp = (IntRefBlockPtr) rbp;
-        irp->loc = SeqLocMerge (target, &vn, NULL, FALSE, TRUE, FALSE);
-        alp = GetAuthListPtr (pdp, NULL);
-        if (alp != NULL) {
-          irp->authstr = GetAuthorsPlusConsortium (awp->format, alp);
-        }
-        irp->index = 0;
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (target, sdp, Seq_descr_pub, &dcontext);
-  }
-
-  /* if protein with no pubs, get pubs applicable to DNA location of CDS */
-
-  if (cdsloc != NULL) {
-    cp.awp = awp;
-    cp.target = target;
-    cp.vnp = &vn;
-    SeqMgrGetAllOverlappingFeatures (cdsloc, FEATDEF_PUB, NULL, 0, LOCATION_SUBSET, (Pointer) &cp, GetRefsOnCDS);
-  }
-
-  SeqIdFree (sint.id);
-
-  /* features are indexed on parent if segmented */
-
-  bsp = awp->parent;
-
-  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_PUB, 0, &fcontext);
-  while (sfp != NULL) {
-    ivals = fcontext.ivals;
-    numivals = fcontext.numivals;
-    if (ivals != NULL && numivals > 0) {
-
-      /*
-      idx = (numivals - 1) * 2;
-      start = ivals [idx];
-      stop = ivals [idx + 1];
-      */
-
-      takeIt = FALSE;
-      for (i = 0, idx = 0; i < numivals; i++, idx += 2) {
-        start = ivals [idx];
-        stop = ivals [idx + 1];
-        if ((start <= from && stop > from) ||
-            (start < to && stop >= to) ||
-            (start >= from && stop <= to)) {
-          takeIt = TRUE;
-        }
-      }
-      if (awp->format == FTABLE_FMT) {
-        pdp = (PubdescPtr) sdp->data.ptrvalue;
-        if (HasNoPmidOrMuid (pdp)) {
-          takeIt = FALSE;
-        }
-      }
-
-      if (takeIt /* stop >= from && stop <= to */) {
-
-        /*
-        start = ivals [0] + 1;
-        stop = ivals [idx + 1] + 1;
-        */
-        pdp = (PubdescPtr) sfp->data.value.ptrvalue;
-        rbp = AddPub (awp, &(awp->pubhead), pdp);
-        if (rbp != NULL) {
-
-          rbp->entityID = fcontext.entityID;
-          rbp->itemID = fcontext.itemID;
-          rbp->itemtype = OBJ_SEQFEAT;
-
-          irp = (IntRefBlockPtr) rbp;
-          irp->loc = SeqLocMerge (target, sfp->location, NULL, FALSE, TRUE, FALSE);
-          if (ajp->ajp.slp != NULL) {
-            sip = SeqIdParse ("lcl|dummy");
-            left = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_LEFT_END);
-            right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END);
-            strand = SeqLocStrand (ajp->ajp.slp);
-            split = FALSE;
-            newloc = SeqLocReMapEx (sip, ajp->ajp.slp, irp->loc, 0, FALSE, ajp->masterStyle);
-            /*
-            newloc = SeqLocCopyRegion (sip, irp->loc, bsp, left, right, strand, &split);
-            */
-            SeqIdFree (sip);
-            if (newloc != NULL) {
-              A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
-              irp->loc = SeqLocFree (irp->loc);
-              irp->loc = newloc;
-            }
-          }
-          alp = GetAuthListPtr (pdp, NULL);
-          if (alp != NULL) {
-            irp->authstr = GetAuthorsPlusConsortium (awp->format, alp);
-          }
-          irp->index = fcontext.index;
-        }
-      }
-    }
-
-    sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_PUB, 0, &fcontext);
-  }
-}
-
-static Boolean LIBCALLBACK GetRefsOnSeg (
-  SeqLocPtr slp,
-  SeqMgrSegmentContextPtr context
-)
-
-{
-  Asn2gbWorkPtr  awp;
-  BioseqPtr      bsp;
-  Int4           from;
-  SeqLocPtr      loc;
-  SeqEntryPtr    oldscope;
-  SeqEntryPtr    sep;
-  SeqIdPtr       sip;
-  Int4           to;
-
-  if (slp == NULL || context == NULL) return FALSE;
-  awp = (Asn2gbWorkPtr) context->userdata;
-
-  from = context->cumOffset;
-  to = from + context->to - context->from;
-
-  sip = SeqLocId (slp);
-  if (sip == NULL) {
-    loc = SeqLocFindNext (slp, NULL);
-    if (loc != NULL) {
-      sip = SeqLocId (loc);
-    }
-  }
-  if (sip == NULL) return TRUE;
-
-  /* reference descriptors only on parts within entity */
-
-  sep = GetTopSeqEntryForEntityID (awp->entityID);
-  oldscope = SeqEntrySetScope (sep);
-  bsp = BioseqFind (sip);
-  SeqEntrySetScope (oldscope);
-
-  if (bsp != NULL) {
-    GetRefsOnBioseq (awp, awp->refs, bsp, from, to, NULL);
-    return TRUE;
-  }
-
-  /* if we ever want to fetch remote references, code goes here */
-
-  return TRUE;
-}
-
-static Boolean AddReferenceBlock (
-  Asn2gbWorkPtr awp,
-  Boolean isRefSeq
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  AuthListPtr        alp;
-  Asn2gbSectPtr      asp;
-  BioseqPtr          bsp;
-  SeqFeatPtr         cds;
-  Boolean            combine;
-  SeqMgrFeatContext  context;
-  CitSubPtr          csp;
-  BioseqPtr          dna;
-  Boolean            excise;
-  ValNodePtr         head = NULL;
-  Int2               i;
-  IntRefBlockPtr     irp;
-  Boolean            is_aa;
-  Boolean            is_embl = FALSE;
-  Boolean            is_patent = FALSE;
-  IntRefBlockPtr     lastirp;
-  RefBlockPtr        lastrbp;
-  ValNodePtr         next;
-  Int2               numReferences;
-  ValNodePtr         PNTR prev;
-  RefBlockPtr        rbp;
-  RefBlockPtr        PNTR referenceArray;
-  BioseqPtr          refs;
-  SubmitBlockPtr     sbp;
-  SeqIdPtr           sip;
-  SeqLocPtr          slp;
-  BioseqPtr          target;
-  ValNodePtr         vnp;
-
-  if (awp == NULL) return FALSE;
-  ajp = awp->ajp;
-  if (ajp == NULL) return FALSE;
-  asp = awp->asp;
-  if (asp == NULL) return FALSE;
-  bsp = awp->bsp;
-  refs = awp->refs;
-  if (bsp == NULL || refs == NULL) return FALSE;
-
-  /* collect publications on bioseq */
-
-  awp->pubhead = NULL;
-  GetRefsOnBioseq (awp, bsp, refs, awp->from, awp->to, NULL);
-  target = bsp;
-
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_EMBL) {
-      is_embl = TRUE;
-    } else if (sip->choice == SEQID_PATENT) {
-      is_patent = TRUE;
-    }
-  }
-
-  is_aa = (Boolean) ISA_aa (bsp->mol);
-
-  if (bsp->repr == Seq_repr_seg) {
-
-    /* collect publication descriptors on local parts */
-
-    SeqMgrExploreSegments (bsp, (Pointer) awp, GetRefsOnSeg);
-    target = awp->refs;
-  }
-
-  if (awp->pubhead == NULL && ISA_aa (bsp->mol)) {
-
-    /* if protein with no pubs, get pubs applicable to DNA location of CDS */
-
-    cds = SeqMgrGetCDSgivenProduct (bsp, &context);
-    if (cds != NULL) {
-      dna = BioseqFindFromSeqLoc (cds->location);
-      if (dna != NULL) {
-        GetRefsOnBioseq (awp, dna, dna, context.left, context.right, cds->location);
-        target = dna;
-      }
-    }
-  }
-
-  head = awp->pubhead;
-  awp->pubhead = NULL;
-
-  if (head == NULL && awp->ssp == NULL) return FALSE;
-
-  /* sort by pub/unpub/sites/sub, then date, finally existing serial */
-
-  if (isRefSeq) {
-    head = SortValNode (head, SortReferencesAR);
-  } else {
-    head = SortValNode (head, SortReferencesA);
-  }
-
-  if (awp->ssp != NULL) {
-
-    /* add seq-submit citation */
-
-    rbp = (RefBlockPtr) MemNew (sizeof (IntRefBlock));
-    if (rbp != NULL) {
-      irp = (IntRefBlockPtr) rbp;
-
-      rbp->blocktype = REFERENCE_BLOCK;
-      rbp->section = awp->currsection;
-      rbp->serial = INT2_MAX;
-      rbp->category = REF_CAT_SUB;
-
-      rbp->entityID = ajp->ajp.entityID;
-      rbp->itemID = 1;
-      rbp->itemtype = OBJ_SEQSUB_CIT;
-
-      sbp = awp->ssp->sub;
-      if (sbp != NULL) {
-        csp = sbp->cit;
-        if (csp != NULL) {
-          alp = GetAuthListPtr (NULL, csp);
-          if (alp != NULL) {
-            irp->authstr = GetAuthorsPlusConsortium (awp->format, alp);
-          }
-        }
-      }
-
-      if (awp->citSubsFirst) {
-
-        /* for DDBJ, add seq-submit citation to beginning of list */
-
-        vnp = ValNodeNew (NULL);
-        if (vnp != NULL) {
-          vnp->choice = 0;
-          vnp->data.ptrvalue = (VoidPtr) rbp;
-          vnp->next = head;
-          head = vnp;
-        }
-
-      } else {
-
-        /* for GENBANK and EMBL add seq-submit citation to end of list */
-
-        ValNodeAddPointer (&head, 0, rbp);
-      }
-    }
-  }
-
-  /* unique references, excise duplicates from list */
-
-  prev = &(head);
-  vnp = head;
-  lastrbp = NULL;
-  while (vnp != NULL) {
-    excise = FALSE;
-    combine = TRUE;
-    next = vnp->next;
-    rbp = (RefBlockPtr) vnp->data.ptrvalue;
-    if (lastrbp != NULL) {
-      lastirp = (IntRefBlockPtr) lastrbp;
-      if (rbp != NULL) {
-        irp = (IntRefBlockPtr) rbp;
-        if (lastrbp->pmid != 0 && rbp->pmid != 0) {
-          if (lastrbp->pmid == rbp->pmid) {
-            excise = TRUE;
-          }
-        } else if (lastrbp->muid != 0 && rbp->muid != 0) {
-          if (lastrbp->muid == rbp->muid) {
-            excise = TRUE;
-          }
-        } else if (lastrbp->uniquestr != NULL && rbp->uniquestr != NULL) {
-          if (StringICmp (lastrbp->uniquestr, rbp->uniquestr) == 0) {
-            if (SeqLocCompare (irp->loc, lastirp->loc) == SLC_A_EQ_B) {
-              if (StringICmp (irp->authstr, lastirp->authstr) == 0) {
-
-                /* L76496.1 - removing duplicate submission pubs */
-                excise = TRUE;
-              }
-            }
-          }
-        }
-        if (excise && lastrbp->sites == 0 && rbp->sites > 0) {
-          /* real range trumps sites */
-          combine = FALSE;
-        }
-      }
-    }
-    if (rbp != NULL) {
-      irp = (IntRefBlockPtr) rbp;
-      if (irp->justuids) {
-        if (isRefSeq && is_aa) {
-          /* if allowing justuid in protein RefSeq, try to look up dynamically */
-          excise = TRUE; /* Back to old behavior, do not fetch */
-        } else {
-          /* do not allow justuids reference to appear by itself - S79174.1 */
-          excise = TRUE;
-          /* justuids should still combine, even if no authors - S67070.1 */
-        }
-      } else if (is_embl && is_patent) {
-        /* EMBL patent records do not need author or title - A29528.1 */
-      } else if (StringHasNoText (irp->authstr)) {
-        /* do not allow no author reference to appear by itself - U07000.1 */
-        excise = TRUE;
-        combine = FALSE;
-      }
-    }
-    if (excise) {
-      *prev = vnp->next;
-      vnp->next = NULL;
-
-      /* combine locations of duplicate references */
-
-      irp = (IntRefBlockPtr) rbp;
-      lastirp = (IntRefBlockPtr) lastrbp;
-      if (combine) {
-        if (lastirp != NULL) {
-          slp = SeqLocMerge (target, lastirp->loc, irp->loc, FALSE, TRUE, FALSE);
-          lastirp->loc = SeqLocFree (lastirp->loc);
-          lastirp->loc = slp;
-        }
-        if (irp != NULL && lastirp != NULL) {
-          if ((rbp->muid == lastrbp->muid && rbp->muid != 0) ||
-              (rbp->pmid == lastrbp->pmid && rbp->pmid != 0)) {
-            if (lastirp->fig == NULL) {
-              lastirp->fig = StringSaveNoNull (irp->fig);
-            }
-            if (lastirp->maploc == NULL) {
-              lastirp->maploc = StringSaveNoNull (irp->maploc);
-            }
-            lastirp->poly_a = irp->poly_a;
-          }
-        }
-      }
-
-      /* and remove duplicate reference */
-
-      MemFree (rbp->uniquestr);
-      DateFree (irp->date);
-      SeqLocFree (irp->loc);
-      MemFree (irp->authstr);
-      MemFree (irp->fig);
-      MemFree (irp->maploc);
-      MemFree (rbp);
-      ValNodeFree (vnp);
-
-    } else {
-
-      prev = &(vnp->next);
-      lastrbp = rbp;
-    }
-    vnp = next;
-  }
-
-  /* resort by existing serial, then pub/unpub/sites/sub, then date */
-
-  if (isRefSeq) {
-    head = SortValNode (head, SortReferencesBR);
-  } else {
-    head = SortValNode (head, SortReferencesB);
-  }
-
-  if (head == NULL) return FALSE;
-
-  /* if taking best GeneRIFs, free remainder */
-
-  if (awp->latestGeneRIFs) {
-    for (vnp = head, i = 0; vnp != NULL && i < 10; vnp = vnp->next, i++) continue;
-    if (vnp != NULL) {
-      next = vnp->next;
-      vnp->next = NULL;
-      for (vnp = next; vnp != NULL; vnp = vnp->next) {
-        rbp = (RefBlockPtr) vnp->data.ptrvalue;
-        MemFree (rbp->uniquestr);
-        irp = (IntRefBlockPtr) rbp;
-        DateFree (irp->date);
-        SeqLocFree (irp->loc);
-        MemFree (irp->authstr);
-        MemFree (irp->fig);
-        MemFree (irp->maploc);
-        MemFree (rbp);
-      }
-    }
-  }
-
-  /* assign serial numbers */
-
-  for (vnp = head, i = 1; vnp != NULL; vnp = vnp->next, i++) {
-    rbp = (RefBlockPtr) vnp->data.ptrvalue;
-    if (rbp != NULL) {
-      rbp->serial = i;
-    }
-  }
-
-  /* allocate reference array for this section */
-
-  numReferences = i - 1;
-  asp->numReferences = numReferences;
-
-  if (numReferences > 0) {
-    referenceArray = (RefBlockPtr PNTR) MemNew (sizeof (RefBlockPtr) * (numReferences + 1));
-    asp->referenceArray = referenceArray;
-
-    if (referenceArray != NULL) {
-
-      /* fill in reference array */
-
-      for (vnp = head, i = 0; vnp != NULL && i < numReferences; vnp = vnp->next, i++) {
-        referenceArray [i] = (RefBlockPtr) vnp->data.ptrvalue;
-      }
-    }
-  }
-
-  /* finally link into blocks for current section */
-
-  ValNodeLink (&(awp->lastblock), head);
-  vnp = awp->lastblock;
-  if (vnp == NULL) return FALSE;
-  while (vnp->next != NULL) {
-    vnp = vnp->next;
-  }
-
-  awp->lastblock = vnp;
-  if (awp->blockList == NULL) {
-    awp->blockList = vnp;
-  }
-
-  return TRUE;
-}
-
-static void AddHistCommentString (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  CharPtr prefix,
-  CharPtr suffix,
-  DatePtr dp,
-  SeqIdPtr ids
-)
-
-{
-  Int2      count = 0;
-  Char      buf [256];
-  Boolean   first;
-  Int4      gi = 0;
-  SeqIdPtr  sip;
-  CharPtr   strd;
-  
-  if (dp == NULL || ids == NULL || prefix == NULL || suffix == NULL || ffstring == NULL) return;
-
-  strd = asn2gb_PrintDate (dp);
-  if (strd == NULL) {
-    strd = StringSave ("?");
-  }
-
-  for (sip = ids; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_GI) {
-      gi = (long) sip->data.intvalue;
-      count++;
-    }
-  }
-
-  if (count > 1) {
-    sprintf (buf, "%s or before %s %s", prefix, strd, suffix);
-  } else {
-    sprintf (buf, "%s %s %s", prefix, strd, suffix);
-  }
-  FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
-
-  MemFree (strd);
-
-  if (gi == 0) {
-    FFAddOneString (ffstring, " gi:?", FALSE, FALSE, TILDE_EXPAND);
-    return;
-  }
-
-  first = TRUE;
-  for (sip = ids; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_GI) {
-      gi = (long) sip->data.intvalue;
-      if (! first) {
-        FFAddOneString (ffstring, ",", FALSE, FALSE, TILDE_IGNORE);
-      }
-      first = FALSE;
-      if ( GetWWW(ajp) ) {
-        FFAddOneString (ffstring, " gi:", FALSE, FALSE, TILDE_IGNORE);
-        FFAddTextToString (ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
-        sprintf (buf, "%ld", (long) gi);
-        FFAddTextToString (ffstring, "val=", buf, ">", FALSE, FALSE, TILDE_IGNORE);
-        FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
-        FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-      } else {
-        sprintf (buf, " gi:%ld", (long) gi);
-        FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
-      }
-    }
-  }
-
-  FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_EXPAND);
-}
-
-static void AddHTGSCommentString (
-  StringItemPtr ffstring,
-  BioseqPtr bsp,
-  MolInfoPtr mip
-)
-
-{
-  CharPtr      buf = NULL;
-  Char         buffer [256];
-  Int4         buflen = 0;
-  DeltaSeqPtr  dsp;
-  ValNodePtr   head = NULL;
-  Int4         num_s = 0;
-  Int4         num_g = 0;
-  CharPtr      str = NULL;
-
-  if (bsp == NULL || mip == NULL || mip->tech < 2) return;
-
-  if (bsp->repr == Seq_repr_delta) {
-    for (dsp = (DeltaSeqPtr) bsp->seq_ext, buflen = 0; dsp != NULL; dsp = dsp->next) {
-      buflen += 80;
-    }
-    if (buflen > 0) {
-      buf = MemNew ((size_t) (buflen + 1));
-      if (buf == NULL) return;
-      CountGapsInDeltaSeq (bsp, &num_s, &num_g, NULL, NULL, buf, buflen);
-    }
-  }
-
-  if (mip->tech == MI_TECH_htgs_0) {
-
-    if (num_s > 0) {
-      sprintf (buffer, "* NOTE: This record contains %ld individual~", (long) (num_g + 1));
-      ValNodeCopyStr (&head, 0, buffer);
-      ValNodeCopyStr (&head, 0, "* sequencing reads that have not been assembled into~");
-      ValNodeCopyStr (&head, 0, "* contigs. Runs of N are used to separate the reads~");
-      ValNodeCopyStr (&head, 0, "* and the order in which they appear is completely~");
-      ValNodeCopyStr (&head, 0, "* arbitrary. Low-pass sequence sampling is useful for~");
-      ValNodeCopyStr (&head, 0, "* identifying clones that may be gene-rich and allows~");
-      ValNodeCopyStr (&head, 0, "* overlap relationships among clones to be deduced.~");
-      ValNodeCopyStr (&head, 0, "* However, it should not be assumed that this clone~");
-      ValNodeCopyStr (&head, 0, "* will be sequenced to completion. In the event that~");
-      ValNodeCopyStr (&head, 0, "* the record is updated, the accession number will~");
-      ValNodeCopyStr (&head, 0, "* be preserved.");
-    }
-    ValNodeCopyStr (&head, 0, "~");
-    ValNodeCopyStr (&head, 0, buf);
-
-  } else if (mip->tech == MI_TECH_htgs_1) {
-
-    ValNodeCopyStr (&head, 0, "* NOTE: This is a \"working draft\" sequence.");
-    if (num_s > 0) {
-      sprintf (buffer, " It currently~* consists of %ld contigs. The true order of the pieces~", (long) (num_g + 1));
-      ValNodeCopyStr (&head, 0, buffer);
-      ValNodeCopyStr (&head, 0, "* is not known and their order in this sequence record is~");
-      ValNodeCopyStr (&head, 0, "* arbitrary. Gaps between the contigs are represented as~");
-      ValNodeCopyStr (&head, 0, "* runs of N, but the exact sizes of the gaps are unknown.");
-    }
-    ValNodeCopyStr (&head, 0, "~* This record will be updated with the finished sequence~");
-    ValNodeCopyStr (&head, 0, "* as soon as it is available and the accession number will~");
-    ValNodeCopyStr (&head, 0, "* be preserved.");
-    ValNodeCopyStr (&head, 0, "~");
-    ValNodeCopyStr (&head, 0, buf);
-
-  } else if (mip->tech == MI_TECH_htgs_2) {
-
-    ValNodeCopyStr (&head, 0, "* NOTE: This is a \"working draft\" sequence.");
-    if (num_s > 0) {
-      sprintf (buffer, " It currently~* consists of %ld contigs. Gaps between the contigs~", (long) (num_g + 1));
-      ValNodeCopyStr (&head, 0, buffer);
-      ValNodeCopyStr (&head, 0, "* are represented as runs of N. The order of the pieces~");
-      ValNodeCopyStr (&head, 0, "* is believed to be correct as given, however the sizes~");
-      ValNodeCopyStr (&head, 0, "* of the gaps between them are based on estimates that have~");
-      ValNodeCopyStr (&head, 0, "* provided by the submittor.");
-    }
-    ValNodeCopyStr (&head, 0, "~* This sequence will be replaced~");
-    ValNodeCopyStr (&head, 0, "* by the finished sequence as soon as it is available and~");
-    ValNodeCopyStr (&head, 0, "* the accession number will be preserved.");
-    ValNodeCopyStr (&head, 0, "~");
-    ValNodeCopyStr (&head, 0, buf);
-
-  } else if ((str = StringForSeqTech (mip->tech)) != NULL) {
-
-      sprintf (buffer, "Method: %s.", str);
-      ValNodeCopyStr (&head, 0, buffer);
-  }
-
-  MemFree (buf);
-
-  str = MergeValNodeStrings (head);
-
-  FFAddOneString (ffstring, str, TRUE, TRUE, TILDE_EXPAND);
-
-  MemFree (str);
-  ValNodeFreeData (head);
-}
-
-static void AddWGSMasterCommentString (
-  StringItemPtr ffstring,
-  BioseqPtr bsp,
-  CharPtr wgsaccn,
-  CharPtr wgsname
-)
-
-{
-  size_t             acclen;
-  BioSourcePtr       biop;
-  Char               buf [256];
-  SeqMgrDescContext  dcontext;
-  CharPtr            first = NULL;
-  ValNodePtr         head = NULL;
-  CharPtr            last = NULL;
-  ObjectIdPtr        oip;
-  OrgRefPtr          orp;
-  SeqDescrPtr        sdp;
-  CharPtr            taxname = NULL;
-  UserFieldPtr       ufp;
-  UserObjectPtr      uop;
-  Char               ver [16];
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
-  if (sdp != NULL) {
-    biop = (BioSourcePtr) sdp->data.ptrvalue;
-    if (biop != NULL) {
-      orp = biop->org;
-      if (orp != NULL) {
-        taxname = orp->taxname;
-      }
-    }
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
-  while (sdp != NULL) {
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    if (uop != NULL) {
-      oip = uop->type;
-      if (oip != NULL && StringICmp (oip->str, "WGSProjects") == 0) {
-        for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-          oip = ufp->label;
-          if (oip == NULL || oip->str == NULL || ufp->choice != 1) continue;
-          if (StringICmp (oip->str, "WGS_accession_first") == 0) {
-            first = (CharPtr) ufp->data.ptrvalue;
-          } else if (StringICmp (oip->str, "WGS_accession_last") == 0) {
-            last = (CharPtr) ufp->data.ptrvalue;
-          }
-        }
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
-  }
-
-  if (StringHasNoText (taxname)) {
-    taxname = "?";
-  }
-  if (StringHasNoText (first)) {
-    first = "?";
-  }
-  if (StringHasNoText (last)) {
-    last = "?";
-  }
-  ver [0] = '\0';
-  acclen = StringLen (wgsname);
-  if (acclen == 12) {
-    StringCpy (ver, wgsname + 4);
-    ver [2] = '\0';
-  } else if (acclen == 13) {
-    StringCpy (ver, wgsname + 4);
-    ver [2] = '\0';
-  } else if (acclen == 15) {
-    StringCpy (ver, wgsname + 7);
-    ver [2] = '\0';
-  }
-
-  sprintf (buf, "The %s whole genome shotgun (WGS) project has the project accession %s.", taxname, wgsaccn);
-  FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND);
-
-  sprintf (buf, "  This version of the project (%s) has the accession number %s,", ver, wgsname);
-  FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
-
-  if (StringCmp (first, last) != 0) {
-    sprintf (buf, " and consists of sequences %s-%s.", first, last);
-    FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND);
-  } else {
-    sprintf (buf, " and consists of sequence %s.", first);
-    FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND);
-  }
-}
-
-
-static CharPtr GetMolInfoCommentString (
-  BioseqPtr bsp,
-  MolInfoPtr mip
-)
-
-{
-  Boolean  is_aa;
-  CharPtr  str = NULL;
-
-  if (bsp == NULL || mip == NULL) return NULL;
-
-  is_aa = ISA_aa (bsp->mol);
-  switch (mip->completeness) {
-    case 1 :
-      str = "COMPLETENESS: full length";
-      break;
-    case 2 :
-      str = "COMPLETENESS: not full length";
-      break;
-    case 3 :
-      if (is_aa) {
-        str = "COMPLETENESS: incomplete on the amino end";
-      } else {
-        str = "COMPLETENESS: incomplete on the 5' end";
-      }
-      break;
-    case 4 :
-      if (is_aa) {
-        str = "COMPLETENESS: incomplete on the carboxy end";
-      } else {
-        str = "COMPLETENESS: incomplete on the 3' end";
-      }
-      break;
-    case 5 :
-      str = "COMPLETENESS: incomplete on both ends";
-      break;
-    case 6 :
-      if (is_aa) {
-        str = "COMPLETENESS: complete on the amino end";
-      } else {
-        str = "COMPLETENESS: complete on the 5' end";
-      }
-      break;
-    case 7 :
-      if (is_aa) {
-        str = "COMPLETENESS: complete on the carboxy end";
-      } else {
-        str = "COMPLETENESS: complete on the 3' end";
-      }
-      break;
-    default :
-      str = "COMPLETENESS: unknown";
-      break;
-  }
-
-  return str;
-}
-
-static CharPtr GetStrForBankit (
-  UserObjectPtr uop
-)
-
-{
-  CharPtr       bic = NULL, uvc = NULL, ptr;
-  ObjectIdPtr   oip;
-  UserFieldPtr  ufp;
-
-  if (uop == NULL) return NULL;
-  if ((oip = uop->type) == NULL) return NULL;
-  if (StringCmp (oip->str, "Submission") != 0) return NULL;
-
-  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-    oip = ufp->label;
-    if (StringCmp(oip->str, "UniVecComment") == 0) {
-      uvc = ufp->data.ptrvalue;
-    } else if (StringCmp(oip->str, "AdditionalComment") == 0) {
-      bic = ufp->data.ptrvalue;
-    }
-  }
-
-  if (uvc == NULL && bic == NULL) return NULL;
-
-  ptr = (CharPtr) MemNew (StringLen (uvc) + StringLen (bic) + 45);
-  if (uvc != NULL && bic != NULL) {
-    sprintf (ptr, "Vector Explanation: %s~Bankit Comment: %s", uvc, bic);
-  } else if (uvc != NULL) {
-    sprintf (ptr, "Vector Explanation: %s", uvc);
-  } else if (bic != NULL) {
-    sprintf (ptr, "Bankit Comment: %s", bic);
-  }
-
-  return ptr;
-}
-
-static CharPtr reftxt0 = " The reference sequence was derived from ";
-static CharPtr reftxt1 = " This record is predicted by genome sequence analysis and is not yet supported by experimental evidence.";
-static CharPtr reftxt2 = " This record has not yet been subject to final NCBI review.";
-static CharPtr reftxt3 = " The mRNA record is supported by experimental evidence; however, the coding sequence is predicted.";
-static CharPtr reftxt4 = " This record has undergone preliminary review of the sequence, but has not yet been subject to final review.";
-static CharPtr reftxt5 = " This record has been curated by ";
-static CharPtr reftxt6 = " This record is predicted by automated computational analysis.";
-static CharPtr reftxt7 = " This record is provided to represent a collection of whole genome shotgun sequences.";
-static CharPtr reftxt8 = " This record is derived from an annotated genomic sequence (";
-
-static CharPtr GetStatusForRefTrack (
-  UserObjectPtr uop
-)
-
-{
-  CharPtr       st;
-  ObjectIdPtr   oip;
-  UserFieldPtr  ufp, urf = NULL;
-
-  if (uop == NULL) return NULL;
-  if ((oip = uop->type) == NULL) return NULL;
-  if (StringCmp (oip->str, "RefGeneTracking") != 0) return NULL;
-  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-    oip = ufp->label;
-    if (StringCmp(oip->str, "Assembly") == 0) {
-      urf = ufp;
-    }
-  }
-  /* if (urf == NULL || urf->choice != 11) return NULL; */
-  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-    oip = ufp->label;
-    if (StringCmp (oip->str, "Status") == 0) {
-      st = (CharPtr) ufp->data.ptrvalue;
-      if (StringICmp (st, "Inferred") == 0) {
-        return "INFERRED ";
-      } else if (StringICmp (st, "Provisional") == 0) {
-        return "PROVISIONAL ";
-      } else if (StringICmp (st, "Predicted") == 0) {
-        return "PREDICTED ";
-      } else if (StringICmp (st, "Validated") == 0) {
-        return "VALIDATED ";
-      } else if (StringICmp (st, "Reviewed") == 0) {
-        return "REVIEWED ";
-      } else if (StringICmp (st, "Model") == 0) {
-        return "MODEL ";
-      } else if (StringICmp (st, "WGS") == 0) {
-        return "WGS ";
-      }
-    }
-  }
-  return NULL;
-}
-
-
-static void AddStrForRefTrack (
-  IntAsn2gbJobPtr ajp,
-  StringItemPtr ffstring,
-  UserObjectPtr uop
-)
-
-{
-  CharPtr       accn, curator = NULL, source = NULL, st;
-  ObjectIdPtr   oip;
-  UserFieldPtr  ufp, tmp, u, urf = NULL;
-  Int2          i = 0;
-  Int2          review = 0,len;
-  Boolean       is_accn;
-
-  if ( uop == NULL || ffstring == NULL ) return;
-  if ((oip = uop->type) == NULL) return;
-  if (StringCmp (oip->str, "RefGeneTracking") != 0) return;
-
-  len = StringLen (reftxt0);
-  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-    oip = ufp->label;
-    if (StringCmp(oip->str, "Assembly") == 0) {
-      urf = ufp;
-    }
-    if (StringCmp (oip->str, "Status") == 0) {
-      st = (CharPtr) ufp->data.ptrvalue;
-      if (StringICmp (st, "Inferred") == 0) {
-        review = 1;
-      } else if (StringICmp (st, "Provisional") == 0) {
-        review = 2;
-      } else if (StringICmp (st, "Predicted") == 0) {
-        review = 3;
-      } else if (StringICmp (st, "Validated") == 0) {
-        review = 4;
-      } else if (StringICmp (st, "Reviewed") == 0) {
-        review = 5;
-      } else if (StringICmp (st, "Model") == 0) {
-        review = 6;
-      } else if (StringICmp (st, "WGS") == 0) {
-        review = 7;
-      }
-    } else if (StringCmp (oip->str, "Collaborator") == 0) {
-      st = (CharPtr) ufp->data.ptrvalue;
-      if (! StringHasNoText (st)) {
-        curator = st;
-      }
-    } else if (StringCmp (oip->str, "GenomicSource") == 0) {
-      st = (CharPtr) ufp->data.ptrvalue;
-      if (! StringHasNoText (st)) {
-        source = st;
-      }
-    }
-  }
-  if (urf != NULL && urf->choice == 11) {
-    for (tmp = urf->data.ptrvalue; tmp != NULL; tmp = tmp->next) {
-      for (u = tmp->data.ptrvalue; u != NULL; u = u->next) {
-        oip = u->label;
-        if (StringCmp (oip->str, "accession") == 0 ||
-            StringCmp (oip->str, "name") == 0) {
-          i++;
-        }
-      }
-    }
-  }
-  if ( GetWWW(ajp) ) {
-    FFAddTextToString(ffstring, "<a href=", ref_link, ">", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-  } else {
-    FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
-  }
-  FFAddOneString (ffstring, ":", FALSE, FALSE, TILDE_IGNORE);
-  if (review == 1) {
-    FFAddOneString (ffstring, reftxt1, FALSE, FALSE, TILDE_IGNORE);
-  } else if (review == 2) {
-    FFAddOneString (ffstring, reftxt2, FALSE, FALSE, TILDE_IGNORE);
-  } else if (review == 3) {
-    FFAddOneString (ffstring, reftxt3, FALSE, FALSE, TILDE_IGNORE);
-  } else if (review == 4) {
-    FFAddOneString (ffstring, reftxt4, FALSE, FALSE, TILDE_IGNORE);
-  } else if (review == 5) {
-    if (curator == NULL) {
-      curator = "NCBI staff";
-    }
-    FFAddOneString (ffstring, reftxt5, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, curator, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_IGNORE);
-  } else if (review == 6) {
-    FFAddOneString (ffstring, reftxt6, FALSE, FALSE, TILDE_IGNORE);
-  } else if (review == 7) {
-    FFAddOneString (ffstring, reftxt7, FALSE, FALSE, TILDE_IGNORE);
-  }
-  if (review != 5 && curator != NULL) {
-    FFAddOneString (ffstring, reftxt5, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, curator, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_IGNORE);
-  }
-  if (source != NULL) {
-    FFAddOneString (ffstring, reftxt8, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, source, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, ").", FALSE, FALSE, TILDE_IGNORE);
-  }
-  if (i > 0) {
-    FFAddOneString (ffstring, reftxt0, FALSE, FALSE, TILDE_IGNORE);
-
-    for (tmp = urf->data.ptrvalue; tmp != NULL; tmp = tmp->next) {
-      is_accn = TRUE;
-      for (u = tmp->data.ptrvalue; u != NULL; u = u->next) {
-        oip = u->label;
-        if (StringCmp (oip->str, "accession") == 0) break;
-        if (StringCmp (oip->str, "name") == 0) {
-          is_accn = FALSE;
-          break;
-        }
-      }
-      if (u == NULL) continue;
-      accn = (CharPtr) u->data.ptrvalue;
-      if (StringHasNoText (accn)) continue;
-      if (is_accn && GetWWW(ajp) ) {
-        FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
-        FFAddTextToString(ffstring, "val=", accn, ">", FALSE, FALSE, TILDE_IGNORE);
-        FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
-        FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-      } else {
-        FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
-      }
-      if (tmp->next != NULL) {
-        ufp = tmp->next;
-        if (ufp->next != NULL) {
-          FFAddOneString (ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
-        } else {
-          FFAddOneString (ffstring, " and ", FALSE, FALSE, TILDE_IGNORE);
-        }
-      }
-    }
-    FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_EXPAND);
-  }
-}
-
-static CharPtr GetGenomeBuildNumber (
-  UserObjectPtr uop
-)
-
-{
-  ObjectIdPtr   oip;
-  CharPtr       str;
-  UserFieldPtr  ufp;
-
-  if (uop == NULL) return NULL;
-  if ((oip = uop->type) == NULL) return NULL;
-  if (StringCmp (oip->str, "GenomeBuild") != 0) return NULL;
-  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-    oip = ufp->label;
-    if (StringCmp(oip->str, "NcbiAnnotation") == 0) {
-      if (ufp->choice == 1) { /* string */
-        str = ufp->data.ptrvalue;
-        if (! StringHasNoText (str)) return str;
-      }
-    } else if (StringCmp (oip->str, "Annotation") == 0) {
-      if (ufp->choice == 1) { /* string */
-        str = ufp->data.ptrvalue;
-        if (! StringHasNoText (str)) {
-          if (StringNICmp (str, "NCBI build ", 11) == 0) {
-            if (! StringHasNoText (str + 11)) {
-              return (str + 11);
-            }
-          }
-        }
-      }
-    }
-  }
-  return NULL;
-}
-
-
-static CharPtr reftxt11 = "This record is predicted by automated computational analysis. This record is derived from an annotated genomic sequence";
-static CharPtr reftxt12 = "using gene prediction method:";
-
-static void FindModelEvidenceUop (
-  UserObjectPtr uop,
-  Pointer userdata
-)
-
-{
-  ObjectIdPtr         oip;
-  UserObjectPtr PNTR  uopp;
-
-  if (uop == NULL || userdata == NULL) return;
-  uopp = (UserObjectPtr PNTR) userdata;
-  oip = uop->type;
-  if (oip == NULL) return;
-  if (StringCmp (oip->str, "ModelEvidence") == 0) {
-    *uopp = uop;
-  }
-}
-
-static Boolean DoGetAnnotationComment (
-   BioseqPtr bsp,
-   CharPtr PNTR namep,
-   CharPtr PNTR methodp,
-   BoolPtr mrnaEv,
-   BoolPtr estEv
-)
-
-{
-  SeqMgrDescContext  dcontext;
-  CharPtr            method = NULL;
-  UserObjectPtr      moduop;
-  CharPtr            name = NULL;
-  ObjectIdPtr        oip;
-  SeqDescrPtr        sdp;
-  UserFieldPtr       ufp;
-  UserObjectPtr      uop;
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
-  while (sdp != NULL) {
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    if (uop != NULL) {
-      moduop = NULL;
-      VisitUserObjectsInUop (uop, (Pointer) &moduop, FindModelEvidenceUop);
-      if (moduop != NULL) {
-        oip = moduop->type;
-        if (oip != NULL && StringCmp(oip->str, "ModelEvidence") == 0) {
-          for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-            oip = ufp->label;
-            if (oip == NULL) continue;
-            if (StringCmp(oip->str, "Contig Name") == 0) {
-              name = (CharPtr) ufp->data.ptrvalue;
-            } else if (StringCmp(oip->str, "Method") == 0) {
-              method = (CharPtr) ufp->data.ptrvalue;
-            } else if (StringCmp(oip->str, "mRNA") == 0) {
-              *mrnaEv = TRUE;
-            } else if (StringCmp(oip->str, "EST") == 0) {
-              *estEv = TRUE;
-            }
-          }
-        }
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
-  }
-  if (StringHasNoText (name)) return FALSE;
-  *namep = name;
-  if (! StringHasNoText (method)) {
-    *methodp = method;
-  }
-  return TRUE;
-}
-
-static Boolean GetAnnotationComment (
-   BioseqPtr bsp,
-   CharPtr PNTR namep,
-   CharPtr PNTR methodp,
-   BoolPtr mrnaEv,
-   BoolPtr estEv
-)
-
-{
-  SeqFeatPtr  cds;
-
-  if (DoGetAnnotationComment (bsp, namep, methodp, mrnaEv, estEv)) return TRUE;
-  if (ISA_aa (bsp->mol)) {
-    cds = SeqMgrGetCDSgivenProduct (bsp, NULL);
-    if (cds != NULL) {
-      bsp = BioseqFindFromSeqLoc (cds->location);
-      if (bsp != NULL) {
-        return DoGetAnnotationComment (bsp, namep, methodp, mrnaEv, estEv);
-      }
-    }
-  }
-  return FALSE;
-}
-
-static void FindGeneFeat (
-  SeqFeatPtr sfp,
-  Pointer userdata
-)
-
-{
-  SeqFeatPtr PNTR  sfpp;
-
-  if (sfp->data.choice != SEQFEAT_GENE) return;
-  sfpp = (SeqFeatPtr PNTR) userdata;
-  *sfpp = sfp;
-}
-
-static void FindLocusId (
-  ValNodePtr dbxref,
-  CharPtr locusIDp
-)
-
-{
-  DbtagPtr     dbt;
-  ObjectIdPtr  oip;
-  ValNodePtr   vnp;
-
-  for (vnp = dbxref; vnp != NULL; vnp = vnp->next) {
-    dbt = (DbtagPtr) vnp->data.ptrvalue;
-    if (dbt == NULL) continue;
-    if (StringICmp (dbt->db, "LocusID") != 0 && StringICmp (dbt->db, "InterimID") != 0) continue;
-    oip = dbt->tag;
-    if (oip == NULL) continue;
-    if (oip->str != NULL) {
-      StringCpy (locusIDp, oip->str);
-    } else if (oip->id > 0) {
-      sprintf (locusIDp, "%ld", (long) oip->id);
-    }
-  }
-}
-
-static Boolean GetGeneAndLocus (
-  BioseqPtr bsp,
-  CharPtr PNTR genep,
-  CharPtr locusIDp,
-  CharPtr taxIDp
-)
-
-{
-  BioSourcePtr       biop;
-  DbtagPtr           dbt;
-  SeqMgrDescContext  dcontext;
-  SeqFeatPtr         gene = NULL;
-  GeneRefPtr         grp;
-  ObjectIdPtr        oip;
-  OrgRefPtr          orp;
-  SeqDescrPtr        sdp;
-  SeqEntryPtr        sep;
-  CharPtr            str;
-  ValNodePtr         syn;
-  ValNodePtr         vnp;
-
-  sep = GetTopSeqEntryForEntityID (bsp->idx.entityID);
-  if (sep == NULL) return FALSE;
-  VisitFeaturesInSep (sep, (Pointer) &gene, FindGeneFeat);
-  if (gene == NULL) return FALSE;
-
-  grp = (GeneRefPtr) gene->data.value.ptrvalue;
-  if (grp == NULL) return FALSE;
-  if (! StringHasNoText (grp->locus)) {
-    *genep = grp->locus;
-  } else {
-    syn = grp->syn;
-    if (syn != NULL) {
-      str = (CharPtr) syn->data.ptrvalue;
-      if (! StringHasNoText (str)) {
-        *genep = str;
-      }
-    }
-  }
-  FindLocusId (gene->dbxref, locusIDp);
-  FindLocusId (grp->db, locusIDp);
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
-  if (sdp != NULL) {
-    biop = (BioSourcePtr) sdp->data.ptrvalue;
-    if (biop != NULL) {
-      orp = biop->org;
-      if (orp != NULL) {
-        for (vnp = orp->db; vnp != NULL; vnp = vnp->next) {
-          dbt = (DbtagPtr) vnp->data.ptrvalue;
-          if (dbt == NULL) continue;
-          if (StringCmp (dbt->db, "taxon") == 0) {
-            oip = dbt->tag;
-            if (oip == NULL) continue;
-            if (oip->str != NULL) {
-              StringCpy (taxIDp, oip->str);
-            } else if (oip->id > 0) {
-              sprintf (taxIDp, "%ld", (long) oip->id);
-            }
-          }
-        }
-      }
-    }
-  }
-
-  if (genep == NULL || StringHasNoText (locusIDp)) return FALSE;
-
-  return TRUE;
-}
-
-static CharPtr reftxt21 = "NCBI contigs are derived from assembled genomic sequence data.";
-
-static CharPtr reftxt22 = "Features on this sequence have been produced for build ";
-static CharPtr reftxt23 = " of the NCBI's genome annotation";
-
-static CharPtr nsAreGapsString = "The strings of n's in this record represent gaps between contigs, and the length of each string corresponds to the length of the gap.";
-
-static Boolean IsTpa (
-  BioseqPtr bsp,
-  Boolean has_tpa_assembly,
-  BoolPtr isRefSeqP
-)
-
-{
-  DbtagPtr  dbt;
-  Boolean   has_bankit = FALSE;
-  Boolean   has_genbank = FALSE;
-  Boolean   has_gi = FALSE;
-  Boolean   has_local = FALSE;
-  Boolean   has_refseq = FALSE;
-  Boolean   has_smart = FALSE;
-  Boolean   has_tpa = FALSE;
-  SeqIdPtr  sip;
-
-  if (bsp == NULL || bsp->id == NULL) return FALSE;
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    switch (sip->choice) {
-      case SEQID_LOCAL :
-        has_local = TRUE;
-        break;
-      case SEQID_GENBANK :
-      case SEQID_EMBL :
-      case SEQID_DDBJ :
-        has_genbank = TRUE;
-        break;
-      case SEQID_OTHER :
-        has_refseq = TRUE;
-        if (isRefSeqP != NULL) {
-          *isRefSeqP = TRUE;
-        }
-        break;
-      case SEQID_GI :
-        has_gi = TRUE;
-        break;
-      case SEQID_TPG :
-      case SEQID_TPE :
-      case SEQID_TPD :
-        has_tpa = TRUE;
-        break;
-      case SEQID_GENERAL :
-        dbt = (DbtagPtr) sip->data.ptrvalue;
-        if (dbt != NULL) {
-          if (StringICmp (dbt->db, "BankIt") == 0) {
-            has_bankit = TRUE;
-          }
-          if (StringICmp (dbt->db, "TMSMART") == 0) {
-            has_smart = TRUE;
-          }
-        }
-        break;
-      default :
-        break;
-    }
-  }
-
-  if (has_genbank) return FALSE;
-  if (has_tpa) return TRUE;
-  if (has_refseq) return FALSE;
-  if (has_bankit && has_tpa_assembly) return TRUE;
-  if (has_smart && has_tpa_assembly) return TRUE;
-  if (has_gi) return FALSE;
-  if (has_local && has_tpa_assembly) return TRUE;
-
-  return FALSE;
-}
-
-static CharPtr GetStrForTpaOrRefSeqHist (
-  BioseqPtr bsp
-)
-
-{
-  Boolean      accn;
-  Char         buf [64];
-  DbtagPtr     dbt;
-  Int4         gi;
-  ValNodePtr   head = NULL;
-  SeqHistPtr   hist;
-  SeqIdPtr     id;
-  Boolean      isRefSeq = FALSE;
-  Boolean      minus1;
-  Boolean      minus2;
-  SeqAlignPtr  salp;
-  SeqAlignPtr  salptmp;
-  SeqIdPtr     sip;
-  Int4         start;
-  Int4         stop;
-  CharPtr      str;
-  Char         tmp [80];
-
-  hist = bsp->hist;
-  if (hist != NULL && hist->assembly != NULL) {
-    salp = SeqAlignListDup (hist->assembly);
-    AlnMgr2IndexLite (salp);
-    AlnMgr2SortAlnSetByNthRowPos (salp, 1);
-    salptmp = (SeqAlignPtr) (salp->segs);
-    while (salptmp != NULL) {
-      AlnMgr2GetNthSeqRangeInSA (salptmp, 1, &start, &stop);
-      sip = AlnMgr2GetNthSeqIdPtr (salptmp, 2);
-      if (sip != NULL) {
-        id = NULL;
-        accn = FALSE;
-        if (sip->choice == SEQID_GI) {
-          gi = (Int4) sip->data.intvalue;
-          if (GetAccnVerFromServer (gi, buf)) {
-            accn = TRUE;
-          } else {
-            id = GetSeqIdForGI (gi);
-          }
-        } else {
-          id = SeqIdDup (sip);
-        }
-        if (id != NULL || accn) {
-          if (head == NULL) {
-            if (isRefSeq) {
-              ValNodeCopyStr (&head, 0, "REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP");
-            } else {
-              ValNodeCopyStr (&head, 0, "TPA_SPAN            PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP");
-            }
-          }
-          if (id != NULL) {
-            SeqIdWrite (id, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
-            if (id->choice == SEQID_GENERAL) {
-              dbt = (DbtagPtr) id->data.ptrvalue;
-              if (dbt != NULL && StringICmp (dbt->db, "ti") == 0) {
-                StringCpy (buf, "TI");
-                SeqIdWrite (id, buf + 2, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 3);
-              }
-            }
-          }
-          sprintf (tmp, "~%ld-%ld                                        ",
-                   (long) (start + 1), (long) (stop + 1));
-          /*
-          i = 39 - StringLen (buf);
-          if (i > 0) {
-            tmp [i] = '\0';
-          } else {
-            tmp [21] = '\0';
-          }
-          */
-          tmp [21] = '\0';
-          StringCat (buf, "                                        ");
-          buf [18] = '\0';
-          StringCat (tmp, buf);
-          AlnMgr2GetNthSeqRangeInSA (salptmp, 2, &start, &stop);
-          sprintf (buf, " %ld-%ld                                        ",
-                   (long) (start + 1), (long) (stop + 1));
-          buf [21] = '\0';
-          StringCat (tmp, buf);
-          minus1 = (Boolean) (AlnMgr2GetNthStrand (salptmp, 1) == Seq_strand_minus);
-          minus2 = (Boolean) (AlnMgr2GetNthStrand (salptmp, 2) == Seq_strand_minus);
-          if (minus1 || minus2) {
-            if (! (minus1 && minus2)) {
-              StringCat (tmp, "c");
-            }
-          }
-          ValNodeCopyStr (&head, 0, tmp);
-        }
-        SeqIdFree (id);
-      }
-      SeqIdFree (sip);
-      salptmp = salptmp->next;
-    }
-    SeqAlignFree (salp);
-  }
-
-  if (head == NULL) return NULL;
-
-  str = MergeValNodeStrings (head);
-  ValNodeFreeData (head);
-
-  return str;
-}
-
-static CharPtr tpaString = "THIRD PARTY ANNOTATION DATABASE: This TPA record uses data from DDBJ/EMBL/GenBank ";
-
-static CharPtr GetStrForTPA (
-  UserObjectPtr uop,
-  BioseqPtr bsp
-)
-
-{
-  Char          ch;
-  UserFieldPtr  curr;
-  SeqHistPtr    hist;
-  Int2          i;
-  Char          id [41];
-  Boolean       isRefSeq = FALSE;
-  Int2          j;
-  size_t        len;
-  ObjectIdPtr   oip;
-  CharPtr       ptr;
-  CharPtr       str;
-  CharPtr       tmp;
-  UserFieldPtr  ufp;
-
-  if (uop == NULL) return NULL;
-  if ((oip = uop->type) == NULL) return NULL;
-  if (StringCmp (oip->str, "TpaAssembly") != 0) return NULL;
-  if (bsp == NULL) return NULL;
-  hist = bsp->hist;
-  if (hist != NULL && hist->assembly != NULL) return NULL;
-  if (! IsTpa (bsp, TRUE, &isRefSeq)) return NULL;
-  if (isRefSeq) return NULL;
-
-  len = StringLen (tpaString) + StringLen ("entries ") + StringLen ("and ") + 5;
-  i = 0;
-  for (curr = uop->data; curr != NULL; curr = curr->next) {
-    if (curr->choice != 11) continue;
-    for (ufp = curr->data.ptrvalue; ufp != NULL; ufp = ufp->next) {
-      if (ufp->choice != 1) continue;
-      oip = ufp->label;
-      if (oip == NULL || StringICmp (oip->str, "accession") != 0) continue;
-      str = (CharPtr) ufp->data.ptrvalue;
-      if (StringHasNoText (str)) continue;
-      len += StringLen (str) + 2;
-      i++;
-    }
-  }
-  if (i == 0) return NULL;
-
-  ptr = (CharPtr) MemNew (len);
-  if (ptr == NULL) return NULL;
-  StringCpy (ptr, tpaString);
-  if (i > 1) {
-    StringCat (ptr, "entries ");
-  } else {
-    StringCat (ptr, "entry ");
-  }
-
-  j = 0;
-  for (curr = uop->data; curr != NULL; curr = curr->next) {
-    if (curr->choice != 11) continue;
-    for (ufp = curr->data.ptrvalue; ufp != NULL; ufp = ufp->next) {
-      if (ufp->choice != 1) continue;
-      oip = ufp->label;
-      if (oip == NULL || StringICmp (oip->str, "accession") != 0) continue;
-      str = (CharPtr) ufp->data.ptrvalue;
-      if (StringHasNoText (str)) continue;
-      StringNCpy_0 (id, str, sizeof (id));
-      tmp = id;
-      ch = *tmp;
-      while (ch != '\0') {
-        if (IS_LOWER (ch)) {
-          *tmp = TO_UPPER (ch);
-        }
-        tmp++;
-        ch = *tmp;
-      }
-      if (j == i - 1 && i > 1) {
-        StringCat (ptr, " and ");
-      } else if (j > 0) {
-        StringCat (ptr, ", ");
-      }
-      StringCat (ptr, id);
-      j++;
-    }
-  }
-
-  return ptr;
-}
-
-static CharPtr GetStrForGenome (
-  UserObjectPtr uop,
-  BioseqPtr bsp
-)
-
-{
-  ObjectIdPtr  oip;
-
-  if (uop == NULL) return NULL;
-  if ((oip = uop->type) == NULL) return NULL;
-  if (StringCmp (oip->str, "GenomeInfo") != 0) return NULL;
-
-  /* !!! need to implement !!! */
-
-  return NULL;
-}
-
-static void AddPrimaryBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  BaseBlockPtr       bbp = NULL;
-  BioseqPtr          bsp;
-  SeqMgrDescContext  dcontext;
-  GBSeqPtr           gbseq;
-  Boolean            has_tpa_assembly = FALSE;
-  SeqHistPtr         hist;
-  Boolean            isRefSeq = FALSE;
-  ObjectIdPtr        oip;
-  SeqDescrPtr        sdp;
-  CharPtr            str;
-  UserObjectPtr      uop;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-  asp = awp->asp;
-  if (asp == NULL) return;
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
-  while (sdp != NULL) {
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    if (uop != NULL) {
-      oip = uop->type;
-      if (oip != NULL) {
-        if (StringCmp (oip->str, "TpaAssembly") == 0) {
-          has_tpa_assembly = TRUE;
-        }
-      }
-    }
-    if (has_tpa_assembly) {
-      sdp = NULL;
-    } else {
-      sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
-    }
-  }
-
-  if (! IsTpa (bsp, has_tpa_assembly, &isRefSeq)) return;
-  hist = bsp->hist;
-  if (hist == NULL || hist->assembly == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  str = GetStrForTpaOrRefSeqHist (bsp);
-  if (str != NULL) {
-
-    bbp = (BaseBlockPtr) Asn2gbAddBlock (awp, PRIMARY_BLOCK, sizeof (BaseBlock));
-    if (bbp != NULL) {
-
-      if (has_tpa_assembly) {
-        bbp->entityID = dcontext.entityID;
-        bbp->itemID = dcontext.itemID;
-        bbp->itemtype = OBJ_SEQDESC;
-      }
-
-      FFStartPrint (ffstring, awp->format, 0, 12, "PRIMARY", 12, 5, 5, "PR", TRUE);
-
-      FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
-
-      bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "PR");
-
-      /* optionally populate gbseq for XML-ized GenBank format */
-
-      if (ajp->gbseq) {
-        gbseq = &asp->gbseq;
-      } else {
-        gbseq = NULL;
-      }
-
-      if (gbseq != NULL) {
-        gbseq->primary = StringSave (str);
-      }
-    }
-    MemFree (str);
-  }
-
-  FFRecycleString(ajp, ffstring);
-}
-
-static void AddCommentBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  size_t             acclen;
-  IntAsn2gbJobPtr    ajp;
-  BioseqPtr          bsp;
-  Char               buf [128];
-  CommentBlockPtr    cbp = NULL;
-  Char               ch;
-  Boolean            didGenome = FALSE;
-  Boolean            didRefTrack = FALSE;
-  Boolean            didTPA = FALSE;
-  DbtagPtr           dbt;
-  SeqMgrDescContext  dcontext;
-  DeltaSeqPtr        dsp;
-  Boolean            estEv = FALSE;
-  SeqMgrFeatContext  fcontext;
-  Boolean            first = TRUE;
-  GBBlockPtr         gbp;
-  CharPtr            geneName = NULL;
-  CharPtr            genomeBuildNumber = NULL;
-  Int4               gi = 0;
-  CommentBlockPtr    gsdbcbp = NULL;
-  Int4               gsdbid = 0;
-  Boolean            has_gaps = FALSE;
-  Boolean            hasRefTrackStatus = FALSE;
-  SeqHistPtr         hist;
-  Boolean            is_collab = FALSE;
-  Boolean            is_other = FALSE;
-  Boolean            is_tpa = FALSE;
-  Boolean            is_wgs = FALSE;
-  SeqLitPtr          litp;
-  ObjectIdPtr        localID = NULL;
-  Char               locusID [32];
-  CharPtr            method = NULL;
-  MolInfoPtr         mip;
-  Boolean            mrnaEv = FALSE;
-  CharPtr            name = NULL;
-  Boolean            okay;
-  BioseqPtr          parent;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp;
-  Boolean            showGBBSource = FALSE;
-  SeqIdPtr           sip;
-  CharPtr            str;
-  Char               taxID [32];
-  TextSeqIdPtr       tsip;
-  UserObjectPtr      uop;
-  CharPtr            wgsaccn = NULL;
-  CharPtr            wgsname = NULL;
-  StringItemPtr      ffstring = NULL;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring ==  NULL ) return;
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
-  while (sdp != NULL) {
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    if (uop != NULL) {
-      str = GetStatusForRefTrack (uop);
-      if (str != NULL) {
-        hasRefTrackStatus = TRUE;
-      }
-      if (genomeBuildNumber == NULL) {
-        genomeBuildNumber = GetGenomeBuildNumber (uop);
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
-  }
-
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_OTHER) {
-      tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-
-      if (tsip != NULL) {
-        is_other = TRUE;
-        if (StringNCmp (tsip->accession, "NC_", 3) == 0) {
-          if (! StringHasNoText (genomeBuildNumber)) {
-            cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-            if (cbp != NULL) {
-
-              cbp->first = first;
-              first = FALSE;
-
-              if (cbp->first) {
-                FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-              } else {
-                FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-              }
-
-              FFAddOneString (ffstring, "GENOME ANNOTATION ", FALSE, FALSE, TILDE_IGNORE);
-
-              if ( GetWWW(ajp) ) {
-                FFAddTextToString (ffstring, "<a href=", ref_link, ">", FALSE, FALSE, TILDE_IGNORE);
-              }
-              FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
-              if ( GetWWW(ajp) ) {
-                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-              }
-              FFAddOneString (ffstring, ":  ", FALSE, FALSE, TILDE_IGNORE);
-
-              FFAddOneString (ffstring, reftxt22, FALSE, FALSE, TILDE_EXPAND);
-              FFAddOneString (ffstring, genomeBuildNumber, FALSE, FALSE, TILDE_EXPAND);
-              FFAddOneString (ffstring, reftxt23, FALSE, FALSE, TILDE_EXPAND);
-
-              FFAddOneString (ffstring, " [see ", FALSE, FALSE, TILDE_EXPAND);
-
-              if ( GetWWW(ajp) ) {
-                FFAddTextToString (ffstring, "<a href=", doc_link, ">", FALSE, FALSE, TILDE_IGNORE);
-              }
-              FFAddOneString (ffstring, "documentation", FALSE, FALSE, TILDE_IGNORE);
-              if ( GetWWW(ajp) ) {
-                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-              }
-
-              FFAddOneString (ffstring, "].", FALSE, FALSE, TILDE_EXPAND);
-
-              cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-              FFRecycleString(ajp, ffstring);
-              ffstring = FFGetString(ajp);
-            }
-          }
-
-        } else if (StringNCmp(tsip->accession, "NT_", 3) == 0 || StringNCmp(tsip->accession, "NW_", 3) == 0) {
-
-          if (! hasRefTrackStatus) {
-            cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-            if (cbp != NULL) {
-
-              cbp->first = first;
-              first = FALSE;
-
-              if (cbp->first) {
-                FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-              } else {
-                FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-              }
-
-              FFAddOneString (ffstring, "GENOME ANNOTATION ", FALSE, FALSE, TILDE_IGNORE);
-
-              if ( GetWWW(ajp) ) {
-                FFAddTextToString (ffstring, "<a href=", ref_link, ">", FALSE, FALSE, TILDE_IGNORE);
-              }
-              FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
-              if ( GetWWW(ajp) ) {
-                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-              }
-              FFAddOneString (ffstring, ":  ", FALSE, FALSE, TILDE_IGNORE);
-
-              if (! StringHasNoText (genomeBuildNumber)) {
-                FFAddOneString (ffstring, reftxt22, FALSE, FALSE, TILDE_EXPAND);
-                FFAddOneString (ffstring, genomeBuildNumber, FALSE, FALSE, TILDE_EXPAND);
-                FFAddOneString (ffstring, reftxt23, FALSE, FALSE, TILDE_EXPAND);
-
-                FFAddOneString (ffstring, " [see ", FALSE, FALSE, TILDE_EXPAND);
-
-                if ( GetWWW(ajp) ) {
-                  FFAddTextToString (ffstring, "<a href=", doc_link, ">", FALSE, FALSE, TILDE_IGNORE);
-                }
-                FFAddOneString (ffstring, "documentation", FALSE, FALSE, TILDE_IGNORE);
-                if ( GetWWW(ajp) ) {
-                  FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-                }
-
-                FFAddOneString (ffstring, "].", FALSE, FALSE, TILDE_EXPAND);
-              } else {
-
-                FFAddOneString (ffstring, reftxt21, TRUE, FALSE, TILDE_EXPAND);
-
-                FFAddOneString (ffstring, "~Also see:~    ", FALSE, FALSE, TILDE_EXPAND);
-
-                if ( GetWWW(ajp) ) {
-                  FFAddTextToString (ffstring, "<a href=", doc_link, ">", FALSE, FALSE, TILDE_IGNORE);
-                }
-                FFAddOneString (ffstring, "Documentation", FALSE, FALSE, TILDE_IGNORE);
-                if ( GetWWW(ajp) ) {
-                  FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-                }
-
-                FFAddOneString (ffstring, " of NCBI's Annotation Process~    ", FALSE, FALSE, TILDE_EXPAND);
-              }
-
-              cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-              FFRecycleString(ajp, ffstring);
-              ffstring = FFGetString(ajp);
-            }
-          }
-
-        } else if (StringNCmp(tsip->accession, "XP_", 3) == 0 ||
-                   StringNCmp(tsip->accession, "XM_", 3) == 0 ||
-                   StringNCmp(tsip->accession, "XR_", 3) == 0 ||
-                   StringNCmp(tsip->accession, "ZP_", 3) == 0) {
-
-          name = NULL;
-          method = NULL;
-          mrnaEv = FALSE;
-          estEv = FALSE;
-          if (GetAnnotationComment (bsp, &name, &method, &mrnaEv, &estEv)) {
-
-            cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-            if (cbp != NULL) {
-
-              cbp->first = first;
-              first = FALSE;
-
-              if (cbp->first) {
-                FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-              } else {
-                FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-              }
-
-              FFAddOneString (ffstring, "MODEL ", FALSE, FALSE, TILDE_IGNORE);
-
-              if ( GetWWW(ajp) ) {
-                FFAddTextToString (ffstring, "<a href=", ref_link, ">", FALSE, FALSE, TILDE_IGNORE);
-              }
-              FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
-              if ( GetWWW(ajp) ) {
-                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-              }
-              FFAddOneString (ffstring, ":  ", FALSE, FALSE, TILDE_IGNORE);
-
-              FFAddTextToString (ffstring, NULL, reftxt11, " (", FALSE, FALSE, TILDE_IGNORE);
-
-              if ( GetWWW(ajp) ) {
-                FFAddTextToString (ffstring, "<a href=", nt_link, name, FALSE, FALSE, TILDE_IGNORE);
-                FFAddOneString (ffstring, ">", FALSE, FALSE, TILDE_IGNORE);
-              }
-              FFAddOneString (ffstring, name, FALSE, FALSE, TILDE_IGNORE);
-              if ( GetWWW(ajp) ) {
-                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-              }
-
-              FFAddOneString (ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
- 
-              if (method != NULL) {
-                FFAddOneString (ffstring, " ", FALSE, FALSE, TILDE_IGNORE);
-                FFAddOneString (ffstring, reftxt12, FALSE, FALSE, TILDE_IGNORE);
-                FFAddOneString (ffstring, " ", FALSE, FALSE, TILDE_IGNORE);
-                FFAddOneString (ffstring, method, FALSE, FALSE, TILDE_IGNORE);
-              }
-
-              if (mrnaEv || estEv) {
-                FFAddOneString (ffstring, ", supported by ", FALSE, FALSE, TILDE_IGNORE);
-                if (mrnaEv && estEv) {
-                  FFAddOneString (ffstring, "mRNA and EST ", FALSE, FALSE, TILDE_IGNORE);
-                } else if (mrnaEv) {
-                  FFAddOneString (ffstring, "mRNA ", FALSE, FALSE, TILDE_IGNORE);
-                } else {
-                  FFAddOneString (ffstring, "EST ", FALSE, FALSE, TILDE_IGNORE);
-                }
-                geneName = NULL;
-                locusID [0] = '\0';
-                taxID [0] = '\0';
-                if ( GetWWW(ajp) && GetGeneAndLocus (bsp, &geneName, locusID, taxID)) {
-                  FFAddTextToString (ffstring, "<a href=", ev_link, NULL, FALSE, FALSE, TILDE_IGNORE);
-                  FFAddTextToString (ffstring, "contig=", name, NULL, FALSE, FALSE, TILDE_IGNORE);
-                  FFAddTextToString (ffstring, "&gene=", geneName, NULL, FALSE, FALSE, TILDE_IGNORE);
-                  FFAddTextToString (ffstring, "&lid=", locusID, NULL, FALSE, FALSE, TILDE_IGNORE);
-                  if (! StringHasNoText (taxID)) {
-                    FFAddTextToString (ffstring, "&taxid=", taxID, NULL, FALSE, FALSE, TILDE_IGNORE);
-                  }
-                  FFAddOneString (ffstring, ">", FALSE, FALSE, TILDE_IGNORE);
-                  FFAddOneString (ffstring, "evidence", FALSE, FALSE, TILDE_IGNORE);
-                  FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-                } else {
-                  FFAddOneString (ffstring, "evidence", FALSE, FALSE, TILDE_IGNORE);
-                }
-              }
-
-              FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_IGNORE);
-
-              FFAddOneString (ffstring, "~Also see:~    ", FALSE, FALSE, TILDE_EXPAND);
-
-              if ( GetWWW(ajp) ) {
-                FFAddTextToString (ffstring, "<a href=", doc_link, ">", FALSE, FALSE, TILDE_IGNORE);
-              }
-              FFAddOneString (ffstring, "Documentation", FALSE, FALSE, TILDE_IGNORE);
-              if ( GetWWW(ajp) ) {
-                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-              }
-
-              FFAddOneString (ffstring, " of NCBI's Annotation Process~    ", FALSE, FALSE, TILDE_EXPAND);
-
-              cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-              FFRecycleString(ajp, ffstring);
-              ffstring = FFGetString(ajp);
-            }
-          }
-        } else {
-          if (StringLen (tsip->accession) == 15) {
-            is_wgs = TRUE;
-            if (StringCmp (tsip->accession + 9, "000000") == 0) {
-              wgsaccn = tsip->accession;
-              wgsname = tsip->name; /* master accession has 8 zeroes, name has project version plus 6 zeroes */
-            }
-          }
-        }
-      }
-
-    } else if (sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) {
-
-      is_tpa = TRUE;
-
-    } else if (sip->choice == SEQID_GENBANK || sip->choice == SEQID_EMBL || sip->choice == SEQID_DDBJ) {
-
-      is_collab = TRUE;
-
-      tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-      if (tsip != NULL && tsip->accession != NULL) {
-        acclen = StringLen (tsip->accession);
-        if (acclen == 12) {
-          is_wgs = TRUE;
-          if (StringCmp (tsip->accession + 6, "000000") == 0) {
-            wgsaccn = tsip->accession;
-            wgsname = tsip->name; /* master accession has 8 zeroes, name has project version plus 6 zeroes */
-          }
-        } else if (acclen == 13) {
-          is_wgs = TRUE;
-          if (StringCmp (tsip->accession + 6, "0000000") == 0) {
-            wgsaccn = tsip->accession;
-            wgsname = tsip->name; /* master accession has 9 zeroes, name has project version plus 7 zeroes */
-          }
-        } else if (ajp->newSourceOrg && StringLen (tsip->accession) == 6) {
-          ch = tsip->accession [0];
-          if (ch == 'J' || ch == 'K' || ch == 'L' || ch == 'M') {
-            showGBBSource = TRUE;
-          }
-        }
-      }
-
-    } else if (sip->choice == SEQID_GENERAL) {
-      dbt = (DbtagPtr) sip->data.ptrvalue;
-
-      /* show GSDB sequence identifier */
-
-      if (dbt != NULL && StringCmp (dbt->db, "GSDB") == 0 && dbt->tag != NULL) {
-        gsdbcbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-        if (gsdbcbp != NULL) {
-          gsdbcbp->first = first;
-
-          /* string will be created after we know if there are additional comments */
-
-          gsdbid = dbt->tag->id;
-          first = FALSE;
-        }
-      }
-
-    } else if (sip->choice == SEQID_GI) {
-      gi = (Int4) sip->data.intvalue;
-
-    } else if (sip->choice == SEQID_LOCAL) {
-      localID = (ObjectIdPtr) sip->data.ptrvalue;
-    }
-  }
-
-  if (localID != NULL) {
-    if (is_tpa || is_collab) {
-      if (awp->mode == SEQUIN_MODE || awp->mode == DUMP_MODE) {
-        buf [0] = '\0';
-        if (! StringHasNoText (localID->str)) {
-          if (StringLen (localID->str) < 100) {
-            sprintf (buf, "LocalID: %s", localID->str);
-          } else {
-            sprintf (buf, "LocalID string too large");
-          }
-        } else {
-          sprintf (buf, "LocalID: %ld", (long) localID->id);
-        }
-
-        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-        if (cbp != NULL) {
-
-          cbp->first = first;
-          first = FALSE;
-
-          if (cbp->first) {
-            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-          } else {
-            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-          }
-
-          FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
-
-          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12,5, 5, "CC");
-          FFRecycleString(ajp, ffstring);
-          ffstring = FFGetString(ajp);
-        }
-      }
-    }
-  }
-
-  /* RefSeq results in allocated comment string */
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
-  while (sdp != NULL) {
-
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    if (uop != NULL) {
-
-      if (! didTPA) {
-        str = GetStrForTPA (uop, bsp);
-        if (str != NULL) {
-
-          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-          if (cbp != NULL) {
-
-            cbp->entityID = dcontext.entityID;
-            cbp->itemID = dcontext.itemID;
-            cbp->itemtype = OBJ_SEQDESC;
-            cbp->first = first;
-            first = FALSE;
-
-            if (cbp->first) {
-              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-            } else {
-              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-            }
-
-            FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
-
-            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12,5, 5, "CC");
-            FFRecycleString(ajp, ffstring);
-            ffstring = FFGetString(ajp);
-          }
-          MemFree (str);
-          didTPA = TRUE;
-        }
-      }
-
-      if (! ajp->flags.hideBankItComment) {
-        str = GetStrForBankit (uop);
-        if (str != NULL) {
-
-          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-          if (cbp != NULL) {
-
-            cbp->entityID = dcontext.entityID;
-            cbp->itemID = dcontext.itemID;
-            cbp->itemtype = OBJ_SEQDESC;
-            cbp->first = first;
-            first = FALSE;
-
-            if (cbp->first) {
-              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-            } else {
-              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-            }
-
-            FFAddOneString (ffstring, str, TRUE, FALSE, TILDE_EXPAND);
-
-            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12,5, 5, "CC");
-            FFRecycleString(ajp, ffstring);
-            ffstring = FFGetString(ajp);
-          }
-          MemFree (str);
-        }
-      }
-
-      if (! didRefTrack) {
-        str = GetStatusForRefTrack (uop);
-        if (str != NULL) {
-
-          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-          if (cbp != NULL) {
-
-            cbp->entityID = dcontext.entityID;
-            cbp->itemID = dcontext.itemID;
-            cbp->itemtype = OBJ_SEQDESC;
-            cbp->first = first;
-            first = FALSE;
-
-            if (cbp->first) {
-              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-            } else {
-              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-            }
-
-            FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
-
-            AddStrForRefTrack (ajp, ffstring, uop);
-
-            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12,5, 5, "CC");
-            FFRecycleString(ajp, ffstring);
-            ffstring = FFGetString(ajp);
-          }
-          /* do not free static str from GetStatusForRefTrack */
-          didRefTrack = TRUE;
-        }
-      }
-
-      if (! didGenome) {
-        str = GetStrForGenome (uop, bsp);
-        if (str != NULL) {
-
-          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-          if (cbp != NULL) {
-
-            cbp->entityID = dcontext.entityID;
-            cbp->itemID = dcontext.itemID;
-            cbp->itemtype = OBJ_SEQDESC;
-            cbp->first = first;
-            first = FALSE;
-
-            if (cbp->first) {
-              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-            } else {
-              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-            }
-
-            FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
-
-            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-            FFRecycleString(ajp, ffstring);
-            ffstring = FFGetString(ajp);
-          }
-          MemFree (str);
-          didGenome = TRUE;
-        }
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
-  }
-
-  if (bsp->repr == Seq_repr_delta && bsp->seq_ext_type == 4 && is_wgs) {
-    has_gaps = FALSE;
-    for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp; dsp=dsp->next) {
-      if (dsp->choice == 2) {
-        litp = (SeqLitPtr) dsp->data.ptrvalue;
-        if (litp != NULL) {
-          if (litp->seq_data == NULL && litp->length > 0) {
-            has_gaps = TRUE;
-          }
-        }
-      }
-    }
-    if (has_gaps) {
-      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-      if (cbp != NULL) {
-
-        cbp->first = first;
-        first = FALSE;
-
-        if (cbp->first) {
-          FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-        } else {
-          FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-        }
-
-        FFAddOneString (ffstring, nsAreGapsString, TRUE, FALSE, TILDE_EXPAND);
-
-        cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-        FFRecycleString(ajp, ffstring);
-        ffstring = FFGetString(ajp);
-      }
-    }
-  }
-
-  /* Seq-hist results in allocated comment string */
-
-  hist = bsp->hist;
-  if (hist != NULL) {
-
-    if (hist->replaced_by_ids != NULL && hist->replaced_by_date != NULL) {
-
-      okay = TRUE;
-      for (sip = hist->replaced_by_ids; sip != NULL; sip = sip->next) {
-        if (sip->choice == SEQID_GI) {
-          if (gi == (Int4) sip->data.intvalue) {
-            okay = FALSE;
-          }
-        }
-      }
-
-      if (okay) {
-        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-        if (cbp != NULL) {
-          cbp->first = first;
-          first = FALSE;
-
-          if (cbp->first) {
-            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-          } else {
-            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-          }
-
-          AddHistCommentString (ajp, ffstring, "[WARNING] On", "this sequence was replaced by a newer version",
-                                hist->replaced_by_date, hist->replaced_by_ids);
-
-          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-          FFRecycleString(ajp, ffstring);
-          ffstring = FFGetString(ajp);
-        }
-      }
-    }
-
-    if (hist->replace_ids != NULL && hist->replace_date != NULL && awp->mode != SEQUIN_MODE) {
-
-      okay = TRUE;
-      for (sip = hist->replace_ids; sip != NULL; sip = sip->next) {
-        if (sip->choice == SEQID_GI) {
-          if (gi == (Int4) sip->data.intvalue) {
-            okay = FALSE;
-          }
-        }
-      }
-
-      if (okay) {
-        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-        if (cbp != NULL) {
-          cbp->first = first;
-          first = FALSE;
-
-          if (cbp->first) {
-            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-          } else {
-            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-          }
-
-          AddHistCommentString (ajp, ffstring, "On", "this sequence version replaced",
-                                hist->replace_date, hist->replace_ids);
-
-          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-          FFRecycleString(ajp, ffstring);
-          ffstring = FFGetString(ajp);
-        }
-      }
-    }
-
-  }
-
-  /* just save IDs for comment, maploc, and region descriptors */
-
-  /*
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_comment, &dcontext);
-  while (sdp != NULL) {
-    if (sdp->data.ptrvalue != NULL) {
-      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-      if (cbp != NULL) {
-        cbp->entityID = dcontext.entityID;
-        cbp->itemID = dcontext.itemID;
-        cbp->itemtype = OBJ_SEQDESC;
-        cbp->first = first;
-        first = FALSE;
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_comment, &dcontext);
-  }
-  */
-
-  /* WGS master comment goes before comment descriptors */
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
-  if (sdp != NULL) {
-
-    mip = (MolInfoPtr) sdp->data.ptrvalue;
-    if (mip != NULL) {
-      if (mip->tech == MI_TECH_wgs) {
-
-        if (wgsname != NULL) {
-
-          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-          if (cbp != NULL) {
-
-            /*
-            cbp->entityID = dcontext.entityID;
-            cbp->itemID = dcontext.itemID;
-            cbp->itemtype = OBJ_SEQDESC;
-            */
-            cbp->first = first;
-            first = FALSE;
-
-            if (cbp->first) {
-              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-            } else {
-              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-            }
-
-            AddWGSMasterCommentString (ffstring,bsp, wgsaccn, wgsname);
-
-            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-            FFRecycleString(ajp, ffstring);
-            ffstring = FFGetString(ajp);
-          }
-        }
-      }
-    }
-  }
-
-  if (showGBBSource) {
-    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
-    if (sdp != NULL) {
-      gbp = (GBBlockPtr) sdp->data.ptrvalue;
-      if (gbp != NULL && (! StringHasNoText (gbp->source))) {
-        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-        if (cbp != NULL) {
-          cbp->entityID = dcontext.entityID;
-          cbp->itemID = dcontext.itemID;
-          cbp->itemtype = OBJ_SEQDESC;
-          cbp->first = first;
-          first = FALSE;
-
-          if (cbp->first) {
-            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-          } else {
-            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-          }
-
-          FFAddOneString (ffstring, "Original source text: ", FALSE, FALSE, TILDE_EXPAND);
-          FFAddOneString (ffstring, gbp->source, TRUE, TRUE, TILDE_EXPAND);
-
-          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-          FFRecycleString(ajp, ffstring);
-          ffstring = FFGetString(ajp);
-        }
-      }
-    }
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_comment, &dcontext);
-  while (sdp != NULL) {
-    if (sdp->data.ptrvalue != NULL) {
-      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-      if (cbp != NULL) {
-        cbp->entityID = dcontext.entityID;
-        cbp->itemID = dcontext.itemID;
-        cbp->itemtype = OBJ_SEQDESC;
-        cbp->first = first;
-        first = FALSE;
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_comment, &dcontext);
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_maploc, &dcontext);
-  while (sdp != NULL) {
-    cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-    if (cbp != NULL) {
-      cbp->entityID = dcontext.entityID;
-      cbp->itemID = dcontext.itemID;
-      cbp->itemtype = OBJ_SEQDESC;
-      cbp->first = first;
-      first = FALSE;
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_maploc, &dcontext);
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_region, &dcontext);
-  while (sdp != NULL) {
-    if (sdp->data.ptrvalue != NULL) {
-      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-      if (cbp != NULL) {
-        cbp->entityID = dcontext.entityID;
-        cbp->itemID = dcontext.itemID;
-        cbp->itemtype = OBJ_SEQDESC;
-        cbp->first = first;
-        first = FALSE;
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_region, &dcontext);
-  }
-
-  /* HTGS results in allocated comment string */
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
-  if (sdp != NULL) {
-
-    mip = (MolInfoPtr) sdp->data.ptrvalue;
-    if (mip != NULL) {
-      if (mip->completeness != 0 && is_other) {
-
-        str = GetMolInfoCommentString (bsp, mip);
-
-        if (str != NULL) {
-          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-          if (cbp != NULL) {
-
-            cbp->entityID = dcontext.entityID;
-            cbp->itemID = dcontext.itemID;
-            cbp->itemtype = OBJ_SEQDESC;
-            cbp->first = first;
-            first = FALSE;
-
-            if (cbp->first) {
-              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-            } else {
-              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-            }
-
-            FFAddOneString (ffstring, str, TRUE, FALSE, TILDE_EXPAND);
-
-            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-            FFRecycleString(ajp, ffstring);
-            ffstring = FFGetString(ajp);
-          }
-        }
-
-      }
-      if (mip->tech == MI_TECH_htgs_0 ||
-          mip->tech == MI_TECH_htgs_1 ||
-          mip->tech == MI_TECH_htgs_2) {
-
-        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-        if (cbp != NULL) {
-
-          /*
-          cbp->entityID = dcontext.entityID;
-          cbp->itemID = dcontext.itemID;
-          cbp->itemtype = OBJ_SEQDESC;
-          */
-          cbp->first = first;
-          first = FALSE;
-
-          if (cbp->first) {
-            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-          } else {
-            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-          }
-          
-          AddHTGSCommentString (ffstring, bsp, mip);
-
-          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-          FFRecycleString(ajp, ffstring);
-          ffstring = FFGetString(ajp);
-        }
-
-      } else {
-        str = StringForSeqTech (mip->tech);
-        if (! StringHasNoText (str)) {
-
-          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-          if (cbp != NULL) {
-
-            /*
-            cbp->entityID = dcontext.entityID;
-            cbp->itemID = dcontext.itemID;
-            cbp->itemtype = OBJ_SEQDESC;
-            */
-            cbp->first = first;
-            first = FALSE;
-
-            if (cbp->first) {
-              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-            } else {
-              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-            }
-
-            FFAddTextToString (ffstring, "Method: ", str, NULL, TRUE, FALSE, TILDE_EXPAND);
-
-            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-            FFRecycleString(ajp, ffstring);
-            ffstring = FFGetString(ajp);
-          }
-        }
-      }
-    }
-  }
-
-  /* add comment features that are full length on appropriate segment */
-
-  parent = awp->parent;
-  if (parent == NULL) return;
-
-  sfp = SeqMgrGetNextFeature (parent, NULL, SEQFEAT_COMMENT, 0, &fcontext);
-  while (sfp != NULL) {
-    if (fcontext.left == awp->from && fcontext.right == awp->to) {
-      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-      if (cbp != NULL) {
-        cbp->entityID = fcontext.entityID;
-        cbp->itemID = fcontext.itemID;
-        cbp->itemtype = OBJ_SEQFEAT;
-        cbp->first = first;
-        first = FALSE;
-      }
-    }
-    sfp = SeqMgrGetNextFeature (parent, sfp, SEQFEAT_COMMENT, 0, &fcontext);
-  }
-
-  if (gsdbcbp != NULL) {
-
-    /* if there were no subsequent comments, do not add period after GSDB id */
-
-    if (cbp == NULL) {
-      sprintf (buf, "GSDB:S:%ld", (long) gsdbid);
-    } else {
-      sprintf (buf, "GSDB:S:%ld.", (long) gsdbid);
-    }
-
-    if (gsdbcbp->first) {
-      FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
-    } else {
-      FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
-    }
-
-    /* CheckEndPunctuation, ConvertDoubleQuotes, and ExpandTildes already taken into account */
-
-    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
-
-    gsdbcbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-    FFRecycleString(ajp, ffstring);
-    ffstring = FFGetString(ajp);
-  }
-
-  FFRecycleString(ajp, ffstring);
-}
-
-static void AddFeatHeaderBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr ajp;
-  BaseBlockPtr    bbp;
-  StringItemPtr   ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-
-  bbp = Asn2gbAddBlock (awp, FEATHEADER_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  if (awp->format == FTABLE_FMT) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  FFStartPrint (ffstring, awp->format, 0, 12, "FEATURES", 21, 5, 0, "FH", TRUE);
-
-  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
-    FFAddOneString (ffstring, "Key", FALSE, FALSE, TILDE_IGNORE);
-    FFAddNChar(ffstring, ' ', 13 , FALSE);
-  }
-
-  FFAddOneString (ffstring, "Location/Qualifiers", FALSE, FALSE, TILDE_TO_SPACES);
-
-  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
-    FFAddNewLine(ffstring);
-    FFAddNewLine(ffstring);
-  }
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 21, 5, 0, "FH");
-  FFRecycleString(ajp, ffstring);
-}
-
-static Uint2 ComputeSourceHash (
-  CharPtr key,
-  Uint2 start
-)
-
-{
-  Uint4  h;
-  Uint2  M;
-  Uint2  S;
-
-  if (key == NULL) return start;
-
-  M = 101; /* prime key */
-  S = 256; /* size of alphabet */
-
-  for (h = start; *key != '\0'; key++) {
-    h = (S * h + *key) % M;
-  }
-
-  return (Uint2) h;
-}
-
-static BaseBlockPtr AddSource (
-  Asn2gbWorkPtr awp,
-  ValNodePtr PNTR head,
-  BioSourcePtr biop,
-  CharPtr comment
-)
-
-{
-  BaseBlockPtr    bbp;
-  DbtagPtr        dbt;
-  Uint2           hash;
-  Int2            idx;
-  IntSrcBlockPtr  isp;
-  ObjectIdPtr     oip;
-  OrgModPtr       omp;
-  OrgNamePtr      onp;
-  OrgRefPtr       orp;
-  SubSourcePtr    ssp;
-  CharPtr         str;
-  Uint1           subtype;
-  Char            tmp [16];
-  ValNodePtr      vnp;
-
-  if (awp == NULL || head == NULL || biop == NULL) return NULL;
-
-  bbp = (BaseBlockPtr) MemNew (sizeof (IntSrcBlock));
-  if (bbp == NULL) return NULL;
-  bbp->blocktype = SOURCEFEAT_BLOCK;
-  bbp->section = awp->currsection;
-
-  ValNodeAddPointer (head, 0, bbp);
-
-  isp = (IntSrcBlockPtr) bbp;
-  isp->biop = biop;
-  isp->is_focus = biop->is_focus;
-  if (biop->origin == 5) {
-    isp->is_synthetic = TRUE;
-  }
-
-  orp = biop->org;
-  if (orp == NULL) return bbp;
-
-  isp->orghash = ComputeSourceHash (orp->taxname, 0);
-  isp->taxname = orp->taxname;
-
-  hash = 0;
-  onp = orp->orgname;
-  if (onp != NULL) {
-    if (StringICmp (onp->div, "SYN") == 0) {
-      isp->is_synthetic = TRUE;
-    }
-    isp->omp = onp->mod;
-    for (omp = onp->mod; omp != NULL; omp = omp->next) {
-      subtype = omp->subtype;
-      if (subtype == 253) {
-        subtype = 35;
-      } else if (subtype == 254) {
-        subtype = 36;
-      } else if (subtype == 255) {
-        subtype = 37;
-      }
-      if (subtype < 38) {
-        idx = orgModToSourceIdx [subtype];
-        if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) {
-          str = asn2gnbk_source_quals [idx].name;
-          hash = ComputeSourceHash (str, hash);
-          hash = ComputeSourceHash (omp->subname, hash);
-        }
-      }
-    }
-  }
-  if (comment != NULL) {
-    hash = ComputeSourceHash ("note", hash);
-    hash = ComputeSourceHash (comment, hash);
-  }
-  isp->modhash = hash;
-
-  hash = 0;
-  for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
-    subtype = ssp->subtype;
-    if (subtype == 255) {
-      subtype = 29;
-    }
-    if (subtype < 30) {
-      idx = subSourceToSourceIdx [subtype];
-      if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) {
-        str = asn2gnbk_source_quals [idx].name;
-        hash = ComputeSourceHash (str, hash);
-        hash = ComputeSourceHash (ssp->name, hash);
-      }
-    }
-  }
-  isp->subhash = hash;
-  isp->ssp = biop->subtype;
-
-  hash = 0;
-  for (vnp = orp->db; vnp != NULL; vnp = vnp->next) {
-    dbt = (DbtagPtr) vnp->data.ptrvalue;
-    if (dbt != NULL) {
-      hash = ComputeSourceHash (dbt->db, hash);
-      oip = dbt->tag;
-      if (oip != NULL) {
-        if (oip->str != NULL) {
-          hash = ComputeSourceHash (oip->str, hash);
-        } else {
-          sprintf (tmp, "%ld", (long) oip->id);
-          hash = ComputeSourceHash (tmp, hash);
-        }
-      }
-    }
-  }
-  isp->xrfhash = hash;
-  isp->vnp = orp->db;
-
-  return bbp;
-}
-
-static int LIBCALLBACK SortSourcesByHash (
-  VoidPtr ptr1,
-  VoidPtr ptr2
-)
-
-{
-  Int4            diff;
-  IntSrcBlockPtr  isp1;
-  IntSrcBlockPtr  isp2;
-  ValNodePtr      vnp1;
-  ValNodePtr      vnp2;
-
-  if (ptr1 == NULL || ptr2 == NULL) return 0;
-  vnp1 = *((ValNodePtr PNTR) ptr1);
-  vnp2 = *((ValNodePtr PNTR) ptr2);
-  if (vnp1 == NULL || vnp2 == NULL) return 0;
-  isp1 = (IntSrcBlockPtr) vnp1->data.ptrvalue;
-  isp2 = (IntSrcBlockPtr) vnp2->data.ptrvalue;
-  if (isp1 == NULL || isp2 == NULL) return 0;
-
-  if (isp1->is_focus && (! isp2->is_focus)) return -1;
-  if (isp2->is_focus && (! isp1->is_focus)) return 1;
-
-  diff = isp1->orghash - isp2->orghash;
-  if (diff > 0) return -1;
-  if (diff < 0) return 1;
-
-  diff = isp1->xrfhash - isp2->xrfhash;
-  if (diff > 0) return -1;
-  if (diff < 0) return 1;
-
-  /* sort so that sources with modifiers come first */
-
-  diff = isp1->modhash - isp2->modhash;
-  if (diff > 0) return -1;
-  if (diff < 0) return 1;
-
-  diff = isp1->subhash - isp2->subhash;
-  if (diff > 0) return -1;
-  if (diff < 0) return 1;
-
-  /* if all hashes are equal, descriptor comes first */
-
-  if (isp1->is_descriptor && (! isp2->is_descriptor)) {
-    return -1;
-  } else if (isp2->is_descriptor && (! isp1->is_descriptor)) {
-    return 1;
-  }
-
-  return 0;
-}
-
-static int LIBCALLBACK SortSourcesByPos (
-  VoidPtr ptr1,
-  VoidPtr ptr2
-)
-
-{
-  IntSrcBlockPtr  isp1;
-  IntSrcBlockPtr  isp2;
-  ValNodePtr      vnp1;
-  ValNodePtr      vnp2;
-
-  if (ptr1 == NULL || ptr2 == NULL) return 0;
-  vnp1 = *((ValNodePtr PNTR) ptr1);
-  vnp2 = *((ValNodePtr PNTR) ptr2);
-  if (vnp1 == NULL || vnp2 == NULL) return 0;
-  isp1 = (IntSrcBlockPtr) vnp1->data.ptrvalue;
-  isp2 = (IntSrcBlockPtr) vnp2->data.ptrvalue;
-  if (isp1 == NULL || isp2 == NULL) return 0;
-
-  /* descriptor always goes first */
-
-  if (isp1->is_descriptor && (! isp2->is_descriptor)) {
-    return -1;
-  } else if (isp2->is_descriptor && (! isp1->is_descriptor)) {
-    return 1;
-  }
-
-  /* feature with smallest left extreme is first */
-
-  if (isp1->left > isp2->left) {
-    return 1;
-  } else if (isp1->left < isp2->left) {
-    return -1;
-  }
-
-  /* if same left extreme, shortest source feature is first just for flatfile */
-
-  if (isp1->right > isp2->right) {
-    return 1;
-  } else if (isp1->right < isp2->right) {
-    return -1;
-  }
-
-  return 0;
-}
-
-/*                                                                   */
-/* s_isFuzzyLoc () -- Determines is a location has fuzzy coordinates */
-/*                                                                   */
-
-static Boolean s_isFuzzyLoc ( SeqLocPtr pLocation )
-{
-  SeqIntPtr pIntLocation;
-
-  if (pLocation == NULL)
-    return FALSE;
-
-  if (pLocation->choice != SEQLOC_INT)
-    return FALSE;
-
-  if (pLocation->data.ptrvalue == NULL)
-    return FALSE;
-
-  pIntLocation = (SeqIntPtr) pLocation->data.ptrvalue;
-
-  if ((pIntLocation->if_from != NULL) && (pIntLocation->if_from->choice == 2))
-    return TRUE;
-
-  if ((pIntLocation->if_to != NULL) && (pIntLocation->if_to->choice == 2))
-    return TRUE;
-
-  return FALSE;
-}
-
-static void GetSourcesOnBioseq (
-  Asn2gbWorkPtr awp,
-  BioseqPtr target,
-  BioseqPtr bsp,
-  Int4 from,
-  Int4 to
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  BaseBlockPtr       bbp;
-  BioSourcePtr       biop;
-  SeqMgrDescContext  dcontext;
-  SeqMgrFeatContext  fcontext;
-  Boolean            hasNulls;
-  Int4               left;
-  Boolean            loop = FALSE;
-  Int2               idx;
-  IntSrcBlockPtr     isp;
-  Int4Ptr            ivals;
-  SeqLocPtr          newloc;
-  Boolean            noLeft;
-  Boolean            noRight;
-  Int2               numivals;
-  Boolean            okay;
-  Int4               right;
-  SeqDescrPtr        sdp;
-  SeqFeatPtr         sfp;
-  SeqInt             sint;
-  SeqIdPtr           sip;
-  Boolean            split;
-  Int4               start;
-  Int4               stop;
-  Uint1              strand;
-  ValNode            vn;
-  ValNodePtr         vnp;
-
-  if (awp == NULL || target == NULL || bsp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-
-  /* full length loc for descriptors */
-
-  sint.from = 0;
-  if (ajp->ajp.slp != NULL) {
-    sint.to = SeqLocLen (ajp->ajp.slp) - 1;
-  } else {
-    sint.to = bsp->length - 1;
-  }
-  sint.strand = Seq_strand_plus;
-  sint.id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0)));
-  sint.if_from = NULL;
-  sint.if_to = NULL;
-
-  vn.choice = SEQLOC_INT;
-  vn.data.ptrvalue = (Pointer) &sint;
-  vn.next = NULL;
-
-  /* if SWISS-PROT, may have multiple source descriptors */
-
-  if (ISA_aa (bsp->mol)) {
-    for (sip = bsp->id; sip != NULL; sip = sip->next) {
-      if (sip->choice == SEQID_SWISSPROT) {
-        loop = TRUE;
-      }
-    }
-  }
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
-  while (sdp != NULL) {
-
-    /* check if descriptor on part already added on segmented bioseq */
-
-    okay = TRUE;
-    for (vnp = awp->srchead; vnp != NULL && okay; vnp = vnp->next) {
-      bbp = (BaseBlockPtr) vnp->data.ptrvalue;
-      if (bbp != NULL) {
-        if (bbp->entityID == dcontext.entityID &&
-            bbp->itemID == dcontext.itemID &&
-            bbp->itemtype == OBJ_SEQDESC) {
-          okay = FALSE;
-        }
-      }
-    }
-
-    if (okay) {
-      biop = (BioSourcePtr) sdp->data.ptrvalue;
-      bbp = AddSource (awp, &(awp->srchead), biop, NULL);
-      if (bbp != NULL) {
-
-        bbp->entityID = dcontext.entityID;
-        bbp->itemID = dcontext.itemID;
-        bbp->itemtype = OBJ_SEQDESC;
-
-        isp = (IntSrcBlockPtr) bbp;
-        isp->loc = SeqLocMerge (target, &vn, NULL, FALSE, TRUE, FALSE);
-        isp->left = 0;
-        isp->right = bsp->length - 1;
-        isp->is_descriptor = TRUE;
-      }
-    }
-
-    /* if SWISS-PROT, loop through multiple source descriptors */
-
-    if (loop) {
-      sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext);
-    } else {
-      sdp = NULL;
-    }
-  }
-
-  SeqIdFree (sint.id);
-
-  if ((! awp->contig) || awp->showconsource) {
-
-    /* features are indexed on parent if segmented */
-
-    bsp = awp->parent;
-
-    sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
-    while (sfp != NULL) {
-      ivals = fcontext.ivals;
-      numivals = fcontext.numivals;
-      if (ivals != NULL && numivals > 0) {
-
-        idx = (numivals - 1) * 2;
-        start = ivals [idx];
-        stop = ivals [idx + 1];
-        if (stop >= from && stop <= to && (ajp->ajp.slp == NULL || SeqLocCompare (sfp->location, ajp->ajp.slp) > 0)) {
-
-          biop = (BioSourcePtr) sfp->data.value.ptrvalue;
-          bbp = AddSource (awp, &(awp->srchead), biop, sfp->comment);
-          if (bbp != NULL) {
-
-            bbp->entityID = fcontext.entityID;
-            bbp->itemID = fcontext.itemID;
-            bbp->itemtype = OBJ_SEQFEAT;
-
-            isp = (IntSrcBlockPtr) bbp;
-            if (sfp->location != NULL && sfp->location->choice == SEQLOC_PNT) {
-              isp->loc = AsnIoMemCopy ((Pointer) sfp->location,
-                                       (AsnReadFunc) SeqLocAsnRead,
-                                       (AsnWriteFunc) SeqLocAsnWrite);
-            } else if (s_isFuzzyLoc (sfp->location)) {
-              isp->loc = AsnIoMemCopy ((Pointer) sfp->location,
-                                      (AsnReadFunc) SeqLocAsnRead,
-                                      (AsnWriteFunc) SeqLocAsnWrite);
-            } else if (SeqLocId(sfp->location) == NULL) {
-              isp->loc = AsnIoMemCopy ((Pointer) sfp->location,
-                                       (AsnReadFunc) SeqLocAsnRead,
-                                       (AsnWriteFunc) SeqLocAsnWrite);
-            } else {
-              CheckSeqLocForPartial (sfp->location, &noLeft, &noRight);
-              hasNulls = LocationHasNullsBetween (sfp->location);
-              isp->loc = SeqLocMerge (target, sfp->location, NULL, FALSE, TRUE, hasNulls);
-              SetSeqLocPartial (isp->loc, noLeft, noRight);
-            }
-            isp->left = fcontext.left;
-            isp->right = fcontext.right;
-            isp->comment = sfp->comment;
-            if (ajp->ajp.slp != NULL) {
-              sip = SeqIdParse ("lcl|dummy");
-              left = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_LEFT_END);
-              right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END);
-              strand = SeqLocStrand (ajp->ajp.slp);
-              split = FALSE;
-              newloc = SeqLocReMapEx (sip, ajp->ajp.slp, isp->loc, 0, FALSE, ajp->masterStyle);
-              /*
-              newloc = SeqLocCopyRegion (sip, isp->loc, bsp, left, right, strand, &split);
-              */
-              SeqIdFree (sip);
-              if (newloc != NULL) {
-                A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
-                isp->loc = SeqLocFree (isp->loc);
-                isp->loc = newloc;
-                isp->left = left;
-                isp->right = right;
-              }
-            }
-          }
-        }
-      }
-
-      sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext);
-    }
-  }
-}
-
-static Boolean LIBCALLBACK GetSourcesOnSeg (
-  SeqLocPtr slp,
-  SeqMgrSegmentContextPtr context
-)
-
-{
-  Asn2gbWorkPtr  awp;
-  BioseqPtr      bsp;
-  Int4           from;
-  SeqLocPtr      loc;
-  SeqEntryPtr    oldscope;
-  SeqEntryPtr    sep;
-  SeqIdPtr       sip;
-  Int4           to;
-
-  if (slp == NULL || context == NULL) return FALSE;
-  awp = (Asn2gbWorkPtr) context->userdata;
-
-  from = context->cumOffset;
-  to = from + context->to - context->from;
-
-  sip = SeqLocId (slp);
-  if (sip == NULL) {
-    loc = SeqLocFindNext (slp, NULL);
-    if (loc != NULL) {
-      sip = SeqLocId (loc);
-    }
-  }
-  if (sip == NULL) return TRUE;
-
-  /* biosource descriptors only on parts within entity */
-
-  sep = GetTopSeqEntryForEntityID (awp->entityID);
-  oldscope = SeqEntrySetScope (sep);
-  bsp = BioseqFind (sip);
-  SeqEntrySetScope (oldscope);
-
-  if (bsp != NULL) {
-    GetSourcesOnBioseq (awp, awp->target, bsp, from, to);
-    return TRUE;
-  }
-
-  /* if we ever want to fetch remote sources, code goes here */
-
-#if 0
-  Uint2          entityID;
-
-  /* may remote fetch genome component if not already in memory */
-
-  bsp = BioseqLockById (sip);
-
-  if (bsp == NULL) return TRUE;
-
-  entityID = ObjMgrGetEntityIDForPointer (bsp);
-
-  if (entityID != awp->entityID) {
-
-    /* if segment not packaged in record, may need to feature index it */
-
-    if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
-      SeqMgrIndexFeatures (entityID, NULL);
-    }
-
-    /* collect features indexed on the remote bioseq */
-
-    from = 0;
-    to = bsp->length - 1;
-  }
-
-  GetSourcesOnBioseq (awp, awp->target, bsp, from, to);
-
-  BioseqUnlock (bsp);
-#endif
-
-  return TRUE;
-}
-
-/* isIdenticalSource() -- Checks to see if two sources are identical */
-/*                        by comparing the actual values in the      */
-/*                        fields.  This only gets called if the two  */
-/*                        sources hashed the same -- it's a double-  */
-/*                        check since two non-identical things will  */
-/*                        occassionally hash to the same value.      */
-
-static Boolean isIdenticalSource (IntSrcBlockPtr isp1, IntSrcBlockPtr isp2)
-{
-  OrgModPtr     omp1;
-  OrgModPtr     omp2;
-  SubSourcePtr  ssp1;
-  SubSourcePtr  ssp2;
-  ValNodePtr    vnp1;
-  ValNodePtr    vnp2;
-  ObjectIdPtr   oip1;
-  ObjectIdPtr   oip2;
-  DbtagPtr      dbt1;
-  DbtagPtr      dbt2;
-
-  if (isp1->is_focus != isp2->is_focus)
-    return FALSE;
-
-  /* Compare the taxonomy names */
-
-  if (StringICmp(isp1->taxname,isp2->taxname) != 0)
-    return FALSE;
-
-  /* Compare the comment */
-
-  if (StringICmp(isp1->comment,isp2->comment) != 0)
-    return FALSE;
-
-  /* Compare the org mods */
-
-  omp1 = isp1->omp;
-  omp2 = isp2->omp;
-  while (omp1 != NULL && omp2 != NULL)
-    {
-      if (omp1->subtype != omp2->subtype)
-        return FALSE;
-      if (StringICmp (omp1->subname, omp2->subname) != 0)
-        return FALSE;
-      omp1 = omp1->next;
-      omp2 = omp2->next;
-    }
-
-  if (omp1 != NULL || omp2 != NULL)
-    return FALSE;
-
-  /* Compare the subtypes */
-
-  ssp1 = isp1->ssp;
-  ssp2 = isp2->ssp;
-
-  while (ssp1 != NULL && ssp2 != NULL)
-    {
-      if (ssp1->subtype != ssp2->subtype)
-        return FALSE;
-      if (StringICmp(ssp1->name,ssp2->name) != 0)
-        return FALSE;
-      ssp1 = ssp1->next;
-      ssp2 = ssp2->next;
-    }
-
-  if (ssp1 != NULL || ssp2 != NULL)
-    return FALSE;
-
-  /* Compare the DB tags */
-
-  vnp1 = isp1->vnp;
-  vnp2 = isp2->vnp;
-
-  while (vnp1 != NULL && vnp2 != NULL)
-    {
-      dbt1 = (DbtagPtr) vnp1->data.ptrvalue;
-      dbt2 = (DbtagPtr) vnp2->data.ptrvalue;
-
-      if ((dbt1 != NULL) && (dbt2 != NULL)) {
-        if (dbt1->db != dbt2->db)
-          return FALSE;
-
-        oip1 = dbt1->tag;
-        oip2 = dbt2->tag;
-        if ((oip1 != NULL) && (oip2 != NULL)) {
-          if (oip1->str != NULL) {
-            if (StringICmp(oip1->str, oip2->str) != 0)
-              return FALSE;
-          } else  {
-            if (oip1->id != oip2->id)
-              return FALSE;
-          }
-        }
-        else if (oip1 != NULL)
-          return FALSE;
-        else if (oip2 != NULL)
-          return FALSE;
-      }
-      else if (dbt1 != NULL)
-        return FALSE;
-      else if (dbt2 != NULL)
-        return FALSE;
-
-      vnp1 = vnp1->next;
-      vnp2 = vnp2->next;
-    }
-
-  if (vnp1 != NULL || vnp2 != NULL)
-    return FALSE;
-
-  /* If it passed all checks, then they */
-  /* are the same, so return true.      */
-
-  return TRUE;
-}
-
-static void CleanupPackedSeqInt (SeqLocPtr location)
-
-{
-  SeqLocPtr  head = NULL;
-  SeqIntPtr  loc;
-  SeqIntPtr  sintp;
-  SeqLocPtr  slp;
-
-  if (location == NULL || location->choice != SEQLOC_PACKED_INT || location->data.ptrvalue == NULL) return;
-
-  slp = SeqLocFindNext (location, NULL);
-  while (slp != NULL) {
-    if (slp->choice == SEQLOC_INT) {
-      sintp = (SeqIntPtr) slp->data.ptrvalue;
-      if (sintp != NULL) {
-        loc = AsnIoMemCopy (sintp, (AsnReadFunc) SeqIntAsnRead,
-                            (AsnWriteFunc) SeqIntAsnWrite);
-        ValNodeAddPointer (&head, SEQLOC_INT, loc);
-      }
-    }
-    slp = SeqLocFindNext (location, slp);
-  }
-  if (head == NULL) return;
-
-  location->data.ptrvalue = SeqLocFree (location->data.ptrvalue);
-  location->data.ptrvalue = head;
-
-  slp = location->data.ptrvalue;
-  if (slp == NULL || slp->next != NULL) return;
-    /* here seqloc_packed_int points to a single location element, so no need for seqloc_packed_int parent */
-    location->choice = slp->choice;
-    location->data.ptrvalue = (Pointer) slp->data.ptrvalue;
-    MemFree (slp);
-}
-
-
-static void AddSourceFeatBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  SeqFeatPtr         cds;
-  SeqMgrFeatContext  context;
-  BioseqPtr          dna;
-  SeqLocPtr          duploc;
-  Boolean            excise;
-  ValNodePtr         head = NULL;
-  IntSrcBlockPtr     isp;
-  IntSrcBlockPtr     lastisp;
-  IntSrcBlockPtr     descrIsp;
-  ValNodePtr         next;
-  ValNodePtr         PNTR prev;
-  SeqInt             sint;
-  SeqLocPtr          slp;
-  CharPtr            str;
-  BioseqPtr          target;
-  ValNode            vn;
-  ValNodePtr         vnp;
-  Boolean            descHasFocus = FALSE;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  /* collect biosources on bioseq */
-
-  awp->srchead = NULL;
-  GetSourcesOnBioseq (awp, bsp, bsp, awp->from, awp->to);
-  target = bsp;
-
-  if (bsp->repr == Seq_repr_seg) {
-
-    /* collect biosource descriptors on local parts */
-
-    SeqMgrExploreSegments (bsp, (Pointer) awp, GetSourcesOnSeg);
-    target = awp->target;
-  }
-
-  if (awp->srchead == NULL && ISA_aa (bsp->mol)) {
-
-    /* if protein with no sources, get sources applicable to DNA location of CDS */
-
-    cds = SeqMgrGetCDSgivenProduct (bsp, &context);
-    if (cds != NULL) {
-      dna = BioseqFindFromSeqLoc (cds->location);
-      if (dna != NULL) {
-        GetSourcesOnBioseq (awp, dna, dna, context.left, context.right);
-        target = dna;
-      }
-    }
-  }
-
-  head = awp->srchead;
-  awp->srchead = NULL;
-
-  if (head == NULL) {
-    sint.from = 0;
-    sint.to = bsp->length - 1;
-    sint.strand = Seq_strand_plus;
-    sint.id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0)));
-    sint.if_from = NULL;
-    sint.if_to = NULL;
-
-    vn.choice = SEQLOC_INT;
-    vn.data.ptrvalue = (Pointer) &sint;
-    vn.next = NULL;
-
-    FFStartPrint (ffstring, awp->format, 5, 21, NULL, 0, 5, 21, "FT", FALSE);
-    FFAddOneString(ffstring, "source", FALSE, FALSE, TILDE_IGNORE);
-    FFAddNChar(ffstring, ' ', 21 - 5 - StringLen("source"), FALSE);
-
-    str = FlatLoc (ajp, bsp, &vn, (Boolean) (awp->style == MASTER_STYLE));
-    if ( GetWWW(ajp) ) {
-      FF_www_featloc (ffstring, str);
-    } else {
-      FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_IGNORE);
-    }
-    MemFree (str);
-
-    if (ajp->flags.needOrganismQual) {
-      FFAddNewLine(ffstring);
-      FFAddTextToString (ffstring, "/organism=\"", "unknown", "\"", FALSE, TRUE, TILDE_TO_SPACES);
-#ifdef ASN2GNBK_PRINT_UNKNOWN_ORG
-    } else {
-      FFAddNewLine(ffstring);
-      FFAddTextToString (ffstring, "/organism=\"", "unknown", "\"", FALSE, TRUE, TILDE_TO_SPACES);
-#endif
-    }
-
-    str = GetMolTypeQual (bsp);
-    if (str == NULL) {
-      switch (bsp->mol) {
-        case Seq_mol_dna :
-          str = "unassigned DNA";
-          break;
-        case Seq_mol_rna :
-          str = "unassigned RNA";
-          break;
-        case Seq_mol_aa :
-          break;
-        default :
-          str = "unassigned DNA";
-          break;
-      }
-    }
-    if (str != NULL) {
-      FFAddNewLine(ffstring);
-      FFAddTextToString (ffstring, "/mol_type=\"", str, "\"", FALSE, TRUE, TILDE_TO_SPACES);
-    }
-
-    str = FFEndPrint(ajp, ffstring, awp->format, 5, 21, 5, 21, "FT");
-
-    bbp = (BaseBlockPtr) Asn2gbAddBlock (awp, SOURCEFEAT_BLOCK, sizeof (IntSrcBlock));
-    if (bbp != NULL) {
-      bbp->section = awp->currsection;
-      bbp->string = str;
-    } else {
-      MemFree(str);
-    }
-    FFRecycleString(ajp, ffstring);
-    return;
-  }
-
-  /* sort by hash values */
-
-  head = SortValNode (head, SortSourcesByHash);
-
-  /* unique sources, excise duplicates from list */
-
-  prev = &(head);
-  vnp = head;
-  lastisp = NULL;
-  while (vnp != NULL) {
-    excise = FALSE;
-    next = vnp->next;
-    isp = (IntSrcBlockPtr) vnp->data.ptrvalue;
-    if (isp->is_descriptor && isp->is_focus)
-      descHasFocus = TRUE;
-    if (lastisp != NULL) {
-      if (isp != NULL) {
-        if (lastisp->is_focus == isp->is_focus &&
-            lastisp->orghash == isp->orghash &&
-            lastisp->xrfhash == isp->xrfhash) {
-
-          /* check for identical modifiers */
-
-          if (lastisp->modhash == isp->modhash &&
-              lastisp->subhash == isp->subhash) {
-
-            excise = isIdenticalSource (isp, lastisp);
-
-          /* or modifiers only in lastisp (e.g., on part bioseq) */
-
-          } else if (isp->modhash == 0 && isp->subhash == 0) {
-            excise = isIdenticalSource (isp, lastisp);
-          }
-        }
-      }
-    }
-    if (excise) {
-      *prev = vnp->next;
-      vnp->next = NULL;
-
-      /* combine locations of duplicate sources */
-
-      if (lastisp != NULL) {
-        slp = SeqLocMerge (target, lastisp->loc, isp->loc, FALSE, TRUE, FALSE);
-        lastisp->loc = SeqLocFree (lastisp->loc);
-        lastisp->loc = slp;
-        lastisp->left = MIN (lastisp->left,isp->left);
-        lastisp->right = MAX (lastisp->right, isp->right);
-      }
-
-      /* and remove duplicate source */
-
-      SeqLocFree (isp->loc);
-      MemFree (isp);
-      ValNodeFree (vnp);
-
-    } else {
-
-      prev = &(vnp->next);
-      lastisp = isp;
-    }
-    vnp = next;
-  }
-
-  /* Sort again, by location this time */
-
-  head = SortValNode (head, SortSourcesByPos);
-
-  /* If the descriptor has a focus, then subtract */
-  /* out all the other source locations.          */
-
-  descrIsp = (IntSrcBlockPtr) head->data.ptrvalue; /* Sorted 1st by now */
-
-  if ((descHasFocus) && (! descrIsp->is_synthetic)) {
-
-    vnp = head;
-    duploc = AsnIoMemCopy ((Pointer) descrIsp->loc,
-                           (AsnReadFunc) SeqLocAsnRead,
-                           (AsnWriteFunc) SeqLocAsnWrite);
-    vnp = vnp->next;
-    while (vnp != NULL) {
-      isp = (IntSrcBlockPtr) vnp->data.ptrvalue;
-      if (SeqLocAinB (descrIsp->loc, isp->loc) >= 0) {
-        vnp = NULL; /* break the chain */
-        descrIsp->loc = SeqLocFree (descrIsp->loc);
-        descrIsp->loc = duploc;
-        duploc = NULL;
-      } else {
-        descrIsp->loc = SeqLocSubtract (descrIsp->loc, isp->loc);
-        vnp = vnp->next;
-      }
-    }
-    CleanupPackedSeqInt (descrIsp->loc);
-    descrIsp->left  = SeqLocStart (descrIsp->loc);
-    descrIsp->right = SeqLocStop (descrIsp->loc);
-    SeqLocFree (duploc);
-  }
-
-  /* if features completely subtracted descriptor
-     intervals, suppress in release, entrez modes */
-
-  if (descrIsp->loc == NULL && ajp->flags.hideEmptySource && head->next != NULL) {
-    vnp = head->next;
-    head->next = NULL;
-    ValNodeFreeData (head);
-    head = vnp;
-  }
-
-  /* finally link into blocks for current section */
-
-  ValNodeLink (&(awp->lastblock), head);
-  vnp = awp->lastblock;
-  if (vnp == NULL) return;
-  while (vnp->next != NULL) {
-    vnp = vnp->next;
-  }
-
-  awp->lastblock = vnp;
-  if (awp->blockList == NULL) {
-    awp->blockList = vnp;
-  }
-  FFRecycleString(ajp, ffstring);
-}
-
-static Boolean IsCDD (
-  SeqFeatPtr sfp
-)
-
-{
-  DbtagPtr    dbt;
-  ValNodePtr  vnp;
-
-  for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next) {
-    dbt = (DbtagPtr) vnp->data.ptrvalue;
-    if (dbt != NULL && StringCmp (dbt->db, "CDD") == 0) return TRUE;
-  }
-
-  return FALSE;
-}
-
-static void GetFeatsOnCdsProduct (
-  SeqFeatPtr cds,
-  BioseqPtr nbsp,
-  BioseqPtr pbsp,
-  IntAsn2gbJobPtr ajp,
-  Asn2gbWorkPtr awp
-)
-
-{
-  FeatBlockPtr       fbp;
-  IntFeatBlockPtr    ifp;
-  Boolean            isRefSeq;
-  Int4               lastleft;
-  Int4               lastright;
-  SeqAnnotPtr        lastsap;
-  SeqFeatPtr         lastsfp;
-  SeqLocPtr          location;
-  SeqLocPtr          newloc;
-  SeqMgrFeatContext  pcontext;
-  SeqFeatPtr         prt;
-  SeqIdPtr           sip;
-  SeqLocPtr          slp;
-  Boolean            suppress;
-
-  if (cds == NULL || ajp == NULL || awp == NULL) return;
-  if (nbsp == NULL || pbsp == NULL || (! ISA_aa (pbsp->mol))) return;
-
-  if (awp->hideCdsProdFeats) return;
-
-  isRefSeq = FALSE;
-  for (sip = nbsp->id; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_OTHER) {
-      isRefSeq = TRUE;
-    }
-  }
-
-  /* explore mat_peptides, sites, etc. */
-
-  lastsfp = NULL;
-  lastsap = NULL;
-  lastleft = 0;
-  lastright = 0;
-
-  prt = SeqMgrGetNextFeature (pbsp, NULL, 0, 0, &pcontext);
-  while (prt != NULL) {
-
-    if (pcontext.featdeftype == FEATDEF_REGION ||
-        pcontext.featdeftype == FEATDEF_SITE ||
-        pcontext.featdeftype == FEATDEF_BOND ||
-        pcontext.featdeftype == FEATDEF_mat_peptide_aa ||
-        pcontext.featdeftype == FEATDEF_sig_peptide_aa ||
-        pcontext.featdeftype == FEATDEF_transit_peptide_aa ||
-        (pcontext.featdeftype == FEATDEF_preprotein && isRefSeq)) {
-
-      if (awp->hideCddFeats && pcontext.featdeftype == FEATDEF_REGION && IsCDD (prt)) {
-
-        /* passing this test prevents mapping of COG CDD region features */
-
-      } else if (pcontext.dnaStop >= awp->from && pcontext.dnaStop <= awp->to) {
-
-        /* suppress duplicate features (on protein) */
-
-        suppress = FALSE;
-        if (lastsfp != NULL && lastsap != NULL) {
-          if (lastsfp->idx.subtype == prt->idx.subtype &&
-              lastleft == pcontext.left &&
-              lastright == pcontext.right) {
-              if (lastsap == pcontext.sap ||
-                  (lastsap->desc == NULL && pcontext.sap->desc == NULL)) {
-              if (AsnIoMemComp (lastsfp, prt, (AsnWriteFunc) SeqFeatAsnWrite)) {
-                suppress = TRUE;
-              }
-            }
-          }
-        }
-
-        /* make sure feature maps within nucleotide sublocation */
-
-        if (! suppress) {
-          if (ajp->ajp.slp != NULL) {
-            location = aaFeatLoc_to_dnaFeatLoc (cds, prt->location);
-            slp = SeqLocMerge (nbsp, location, NULL, FALSE, TRUE, FALSE);
-            if (slp != NULL) {
-              sip = SeqIdParse ("lcl|dummy");
-              newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
-              SeqIdFree (sip);
-              SeqLocFree (slp);
-              if (newloc == NULL) {
-                suppress = TRUE;
-              }
-              SeqLocFree (newloc);
-            } else {
-              suppress = TRUE;
-            }
-            SeqLocFree (location);
-          }
-        }
-
-        if (! suppress) {
-
-          fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntFeatBlock));
-          if (fbp != NULL) {
-
-            fbp->entityID = pcontext.entityID;
-            fbp->itemID = pcontext.itemID;
-            fbp->itemtype = OBJ_SEQFEAT;
-            fbp->featdeftype = pcontext.featdeftype;
-            ifp = (IntFeatBlockPtr) fbp;
-            ifp->mapToNuc = TRUE;
-            ifp->mapToProt = FALSE;
-            ifp->mapToGen = FALSE;
-            ifp->mapToMrna = FALSE;
-            ifp->mapToPep = FALSE;
-            ifp->firstfeat = awp->firstfeat;
-            awp->firstfeat = FALSE;
-          }
-        }
-
-        lastsfp = prt;
-        lastsap = pcontext.sap;
-        lastleft = pcontext.left;
-        lastright = pcontext.right;
-
-      }
-    }
-    prt = SeqMgrGetNextFeature (pbsp, prt, 0, 0, &pcontext);
-  }
-}
-
-static Boolean NotEMBLorDDBJ (
-  BioseqPtr bsp
-)
-
-{
-  SeqIdPtr  sip;
-
-  if (bsp == NULL) return TRUE;
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_EMBL) return FALSE;
-    if (sip->choice == SEQID_DDBJ) return FALSE;
-  }
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK GetFeatsOnBioseq (
-  SeqFeatPtr sfp,
-  SeqMgrFeatContextPtr fcontext
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  Asn2gbWorkPtr      awp;
-  BioseqPtr          bsp;
-  Char               buf [41];
-  SeqFeatPtr         cds;
-  SeqMgrFeatContext  cdscontext;
-  SeqMgrDescContext  dcontext;
-  FeatBlockPtr       fbp;
-  SeqLocPtr          firstslp;
-  GBQualPtr          gbq;
-  SeqFeatPtr         gene;
-  Int4               gi;
-  GeneRefPtr         grp;
-  Boolean            juststop = FALSE;
-  IntCdsBlockPtr     icp;
-  Int2               idx;
-  IntFeatBlockPtr    ifp;
-  Int4Ptr            ivals;
-  Int2               j;
-  SeqAnnotPtr        lastsap;
-  SeqFeatPtr         lastsfp;
-  SeqLocPtr          lastslp;
-  SeqLocPtr          newloc;
-  Int2               numivals;
-  Boolean            okay;
-  SeqEntryPtr        oldscope;
-  BioseqPtr          parent;
-  Boolean            partial5;
-  Boolean            partial3;
-  ValNodePtr         ppr;
-  PubdescPtr         pdp;
-  BioseqPtr          prod;
-  Boolean            pseudo = FALSE;
-  SeqDescrPtr        sdp;
-  SeqEntryPtr        sep;
-  SeqIdPtr           sip;
-  SeqLocPtr          slp;
-  Int4               start;
-  Int4               stop;
-  TextSeqIdPtr       tsip;
-  ValNodePtr         vnp;
-
-  if (sfp == NULL || fcontext == NULL) return FALSE;
-  awp = (Asn2gbWorkPtr) fcontext->userdata;
-  if (awp == NULL) return FALSE;
-  ajp = awp->ajp;
-  if (ajp == NULL) return FALSE;
-  asp = awp->asp;
-  if (asp == NULL) return FALSE;
-  bsp = asp->bsp;
-  if (bsp == NULL) return FALSE;
-
-  if (fcontext->featdeftype == FEATDEF_PUB ||
-      fcontext->featdeftype == FEATDEF_NON_STD_RESIDUE ||
-      fcontext->featdeftype == FEATDEF_BIOSRC ||
-      fcontext->featdeftype == FEATDEF_RSITE ||
-      fcontext->featdeftype == FEATDEF_SEQ) return TRUE;
-
-  if (ajp->flags.validateFeats &&
-      (fcontext->featdeftype == FEATDEF_BAD ||
-       fcontext->featdeftype == FEATDEF_virion)) {
-    return TRUE;
-  }
-
-  if (ISA_na (bsp->mol) && fcontext->featdeftype == FEATDEF_HET) return TRUE;
-
-  /* check feature customization flags */
-
-  if (awp->hideImpFeats && sfp->data.choice == SEQFEAT_IMP) return TRUE;
-  if (awp->hideSnpFeats && fcontext->featdeftype == FEATDEF_variation) return TRUE;
-  if (awp->hideExonFeats && fcontext->featdeftype == FEATDEF_exon) return TRUE;
-  if (awp->hideIntronFeats && fcontext->featdeftype == FEATDEF_intron) return TRUE;
-  if (awp->hideMiscFeats && fcontext->featdeftype == FEATDEF_misc_feature) return TRUE;
-  if (awp->hideRemImpFeats && sfp->data.choice == SEQFEAT_IMP) {
-    if (fcontext->featdeftype != FEATDEF_variation &&
-        fcontext->featdeftype != FEATDEF_exon &&
-        fcontext->featdeftype != FEATDEF_intron &&
-        fcontext->featdeftype != FEATDEF_misc_feature) return TRUE;
-  }
-  if (ISA_aa (bsp->mol) && fcontext->featdeftype == FEATDEF_REGION &&
-      awp->hideCddFeats && IsCDD (sfp)) return TRUE;
-
-  /* DDBJ does not want to show gene features */
-
-  if (fcontext->seqfeattype == SEQFEAT_GENE && awp->hideGeneFeats) return TRUE;
-
-  /* suppress comment features that are full length */
-
-  if (fcontext->seqfeattype == SEQFEAT_COMMENT &&
-      fcontext->left == awp->from && fcontext->right == awp->to) return TRUE;
-
-  ivals = fcontext->ivals;
-  numivals = fcontext->numivals;
-
-  /* check to see if last interval is on this awp->from - awp->to range */
-
-  if (ivals != NULL && numivals > 0) {
-    idx = (numivals - 1) * 2;
-    start = ivals [idx];
-    stop = ivals [idx + 1];
-    if (stop < awp->from || stop > awp->to) {
-
-      /* may need to map sig_peptide on a different segment */
-
-      if (fcontext->seqfeattype == SEQFEAT_CDREGION) {
-        sip = SeqLocIdForProduct (sfp->product);
-        bsp = BioseqFind (sip);
-        GetFeatsOnCdsProduct (sfp, asp->bsp, bsp, ajp, awp);
-      }
-
-      if (! awp->showAllFeats) return TRUE;
-
-      /* if showing one segment, only show features covering this segment */
-
-      if (fcontext->right < awp->from || fcontext->left > awp->to) return TRUE;
-
-    } else if (fcontext->farloc && NotEMBLorDDBJ (awp->bsp)) {
-
-      /* last interval may not have been mapped to bioseq if far */
-
-      firstslp = NULL;
-      lastslp = NULL;
-
-      slp = SeqLocFindNext (sfp->location, NULL);
-      while (slp != NULL) {
-        if (slp->choice != SEQLOC_NULL) {
-          lastslp = slp;
-          if (firstslp == NULL) {
-            firstslp = slp;
-          }
-        }
-        slp = SeqLocFindNext (sfp->location, slp);
-      }
-
-      /* !!! EMBL may have different desired behavior on where to map !!! */
-
-      if (firstslp != NULL && SeqLocStrand (firstslp) == Seq_strand_minus) {
-        slp = firstslp;
-      } else {
-        slp = lastslp;
-      }
-
-      if (slp != NULL) {
-        sip = SeqLocId (slp);
-        if (sip != NULL) {
-          bsp = BioseqFindCore (sip);
-          if (bsp == NULL || (bsp != awp->parent && bsp != awp->bsp)) {
-
-            return TRUE;
-          }
-        }
-      }
-    }
-  }
-
-  /* make sure feature is within sublocation */
-
-  if (ajp->ajp.slp != NULL) {
-    if (SeqLocCompare (sfp->location, ajp->ajp.slp) == SLC_NO_MATCH) {
-      slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, TRUE, FALSE);
-      if (slp == NULL) return TRUE;
-      sip = SeqIdParse ("lcl|dummy");
-      newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
-      SeqIdFree (sip);
-      SeqLocFree (slp);
-      if (newloc == NULL) return TRUE;
-      SeqLocFree (newloc);
-    }
-  }
-
-  /* suppress duplicate features (on nucleotide) */
-
-  lastsfp = awp->lastsfp;
-  lastsap = awp->lastsap;
-  if (lastsfp != NULL && lastsap != NULL) {
-    if (lastsfp->idx.subtype == sfp->idx.subtype &&
-        awp->lastleft == fcontext->left &&
-        awp->lastright == fcontext->right) {
-        if (lastsap == fcontext->sap ||
-            (lastsap->desc == NULL && fcontext->sap->desc == NULL)) {
-        if (AsnIoMemComp (lastsfp, sfp, (AsnWriteFunc) SeqFeatAsnWrite)) {
-          return TRUE;
-        }
-      }
-    }
-  }
-
-  /* if RELEASE_MODE, verify that features have all mandatory qualifiers */
-
-  if (ajp->flags.needRequiredQuals) {
-    okay = FALSE;
-
-    switch (fcontext->featdeftype) {
-
-    case FEATDEF_CDS:
-      if (ajp->flags.checkCDSproductID) {
-        /* non-pseudo CDS must have /product */
-        if (sfp->pseudo) {
-          pseudo = TRUE;
-        }
-        grp = SeqMgrGetGeneXref (sfp);
-        if (grp == NULL) {
-          sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
-          oldscope = SeqEntrySetScope (sep);
-          gene = SeqMgrGetOverlappingGene (sfp->location, NULL);
-          SeqEntrySetScope (oldscope);
-          if (gene != NULL) {
-            grp = (GeneRefPtr) gene->data.value.ptrvalue;
-            if (gene->pseudo) {
-              pseudo = TRUE;
-            }
-          }
-        }
-        if (grp != NULL && grp->pseudo) {
-          pseudo = TRUE;
-        }
-        if (sfp->location != NULL) {
-          if (CheckSeqLocForPartial (sfp->location, &partial5, &partial3)) {
-            if (partial5 && (! partial3)) {
-              if (SeqLocLen (sfp->location) <= 5) {
-                juststop = TRUE;
-              }
-            }
-          }
-        }
-        if (pseudo || juststop) {
-          okay = TRUE;
-        } else if (sfp->product != NULL) {
-          sip = SeqLocIdForProduct (sfp->product);
-          if (sip != NULL) {
-            if ((sip->choice == SEQID_GI && sip->data.intvalue > 0) ||
-                sip->choice == SEQID_LOCAL) {
-              sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
-              oldscope = SeqEntrySetScope (sep);
-              prod = BioseqFind (sip);
-              SeqEntrySetScope (oldscope);
-              if (prod != NULL) {
-                for (sip = prod->id; sip != NULL; sip = sip->next) {
-                  if (sip->choice == SEQID_GENBANK ||
-                     sip->choice == SEQID_EMBL ||
-                      sip->choice == SEQID_DDBJ ||
-                      sip->choice == SEQID_OTHER ||
-                      sip->choice == SEQID_PATENT ||
-                      sip->choice == SEQID_TPG ||
-                      sip->choice == SEQID_TPE ||
-                      sip->choice == SEQID_TPD) {
-                    tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-                    if (tsip != NULL && (! StringHasNoText (tsip->accession))) {
-                      if (ValidateAccn (tsip->accession) == 0)
-                      okay = TRUE;
-                    }
-                  }
-                }
-              } else if (sip->choice == SEQID_GI && sip->data.intvalue > 0) {
-                /* RELEASE_MODE requires that /protein_id is an accession */
-                gi = sip->data.intvalue;
-                if (GetAccnVerFromServer (gi, buf)) {
-                  okay = TRUE;
-                } else {
-                  sip = GetSeqIdForGI (gi);
-                  if (sip != NULL) {
-                    okay = TRUE;
-                  }
-                }
-              }
-            } else if (sip->choice == SEQID_GENBANK ||
-                       sip->choice == SEQID_EMBL ||
-                       sip->choice == SEQID_DDBJ ||
-                       sip->choice == SEQID_OTHER ||
-                       sip->choice == SEQID_PATENT ||
-                       sip->choice == SEQID_TPG ||
-                       sip->choice == SEQID_TPE ||
-                       sip->choice == SEQID_TPD) {
-              tsip = (TextSeqIdPtr) sip->data.ptrvalue;
-              if (tsip != NULL && (! StringHasNoText (tsip->accession))) {
-                if (ValidateAccn (tsip->accession) == 0)
-                okay = TRUE;
-              }
-            }
-          }
-        } else {
-          if (sfp->excpt && (! StringHasNoText (sfp->except_text))) {
-            if (StringStr (sfp->except_text, "rearrangement required for product") != NULL) {
-              okay = TRUE;
-            }
-          }
-        }
-      } else {
-        okay = TRUE;
-      }
-      if (! okay) {
-        ajp->relModeError = TRUE;
-      }
-      break;
-
-    case FEATDEF_conflict:
-      if (sfp->cit == NULL) {
-        /* RefSeq allows conflict with accession in comment instead of sfp->cit */
-        for (sip = bsp->id; sip != NULL; sip = sip->next) {
-          if (sip->choice == SEQID_OTHER) {
-            if (! StringHasNoText (sfp->comment)) {
-              okay = TRUE;
-            }
-          }
-        }
-      }
-      /* continue on to old_sequence */
-    case FEATDEF_old_sequence:
-      /* conflict and old_sequence require a publication printable on the segment */
-      vnp = sfp->cit;
-
-      if (vnp != NULL && asp->referenceArray != NULL) {
-        for (ppr = vnp->data.ptrvalue; ppr != NULL; ppr = ppr->next) {
-          j = MatchRef (ppr, asp->referenceArray, asp->numReferences);
-          if (j > 0) {
-            okay = TRUE;
-            break;
-          }
-        }
-      }
-      break;
-
-    case FEATDEF_GENE:
-      /* gene requires /gene or /locus_tag, but desc or syn can be mapped to /gene */
-      grp = (GeneRefPtr) sfp->data.value.ptrvalue;
-      if (grp != NULL) {
-        if (! StringHasNoText (grp->locus)) {
-          okay = TRUE;
-        }  else if (! StringHasNoText (grp->locus_tag)) {
-          okay = TRUE;
-        } else if (! StringHasNoText (grp->desc)) {
-          okay = TRUE;
-        } else {
-          vnp = grp->syn;
-          if (vnp != NULL) {
-            if (! StringHasNoText (vnp->data.ptrvalue)) {
-              okay = TRUE;
-            }
-          }
-        }
-      }
-      break;
-
-    case FEATDEF_protein_bind:
-    case FEATDEF_misc_binding:
-      /* protein_bind or misc_binding require FTQUAL_bound_moiety */
-      gbq = sfp->qual;
-      while (gbq != NULL) {
-        if (StringICmp (gbq->qual, "bound_moiety") == 0 && (! StringHasNoText (gbq->val))) {
-          okay = TRUE;
-          break;
-        }
-        gbq = gbq->next;
-      }
-      break;
-
-    case FEATDEF_modified_base:
-      /* modified_base requires FTQUAL_mod_base */
-      gbq = sfp->qual;
-      while (gbq != NULL) {
-        if (StringICmp (gbq->qual, "mod_base") == 0 && (! StringHasNoText (gbq->val))) {
-          okay = TRUE;
-          break;
-        }
-        gbq = gbq->next;
-      }
-      break;
-
-    default:
-      if (fcontext->featdeftype >= FEATDEF_GENE && fcontext->featdeftype < FEATDEF_MAX) {
-        okay = TRUE;
-      }
-      break;
-    }
-
-    if (okay == FALSE) return TRUE;
-  }
-
-  /* if RELEASE_MODE, suppress features with location on segmented Bioseq */
-
-  if (ajp->flags.suppressSegLoc) {
-    bsp = awp->parent;
-    if (bsp != NULL && bsp->repr == Seq_repr_seg) {
-      slp = SeqLocFindNext (sfp->location, NULL);
-      while (slp != NULL) {
-        sip = SeqLocId (slp);
-        if (sip != NULL) {
-          if (SeqIdIn (sip, bsp->id)) return TRUE;
-        }
-        slp = SeqLocFindNext (sfp->location, slp);
-      }
-    }
-  }
-
-  awp->lastsfp = sfp;
-  awp->lastsap = fcontext->sap;
-  awp->lastleft = fcontext->left;
-  awp->lastright = fcontext->right;
-
-  if (fcontext->seqfeattype == SEQFEAT_CDREGION) {
-    fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
-  } else {
-    fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntFeatBlock));
-  }
-  if (fbp == NULL) return TRUE;
-
-  fbp->entityID = fcontext->entityID;
-  fbp->itemID = fcontext->itemID;
-  fbp->itemtype = OBJ_SEQFEAT;
-  fbp->featdeftype = fcontext->featdeftype;
-  ifp = (IntFeatBlockPtr) fbp;
-  ifp->mapToNuc = FALSE;
-  ifp->mapToProt = FALSE;
-  ifp->mapToGen = FALSE;
-  ifp->mapToMrna = FALSE;
-  ifp->mapToPep = FALSE;
-  ifp->firstfeat = awp->firstfeat;
-  awp->firstfeat = FALSE;
-  awp->featseen = TRUE;
-
-  /* optionally map CDS from cDNA onto genomic */
-
-  if (awp->isGPS && ISA_na (bsp->mol) && awp->copyGpsCdsUp &&
-      fcontext->featdeftype == FEATDEF_mRNA) {
-    sip = SeqLocIdForProduct (sfp->product);
-    bsp = BioseqFind (sip);
-    if (bsp != NULL && ISA_na (bsp->mol)) {
-      cds = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &cdscontext);
-      if (cds != NULL) {
-        fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
-        if (fbp != NULL) {
-
-          fbp->entityID = cdscontext.entityID;
-          fbp->itemID = cdscontext.itemID;
-          fbp->itemtype = OBJ_SEQFEAT;
-          fbp->featdeftype = cdscontext.featdeftype;
-          ifp = (IntFeatBlockPtr) fbp;
-          ifp->mapToNuc = FALSE;
-          ifp->mapToProt = FALSE;
-          ifp->mapToGen = TRUE;
-          ifp->mapToMrna = FALSE;
-          ifp->mapToPep = FALSE;
-          ifp->firstfeat = awp->firstfeat;
-          awp->firstfeat = FALSE;
-        }
-      }
-    }
-  }
-
-  if (fcontext->seqfeattype != SEQFEAT_CDREGION) return TRUE;
-
-  /* if feature table format, do not get features from protein product */
-
-  if (awp->format == FTABLE_FMT) return TRUE;
-
-  /* if CDS, collect more information from product protein bioseq - may be part */
-
-  sip = SeqLocIdForProduct (sfp->product);
-  bsp = BioseqFind (sip);
-  if (bsp == NULL || (! ISA_aa (bsp->mol))) return TRUE;
-
-  ifp->isCDS = TRUE;
-  icp = (IntCdsBlockPtr) ifp;
-
-  /* first explore pubs to pick up figure and maploc */
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pub, &dcontext);
-  while (sdp != NULL) {
-    pdp = (PubdescPtr) sdp->data.ptrvalue;
-    if (pdp != NULL) {
-      if (icp->fig == NULL) {
-        icp->fig = StringSaveNoNull (pdp->fig);
-      }
-      if (icp->maploc == NULL) {
-        icp->maploc = StringSaveNoNull (pdp->maploc);
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_pub, &dcontext);
-  }
-
-  /* product may be segmented part, and remaining features are indexed on parent */
-
-  parent = SeqMgrGetParentOfPart (bsp, NULL);
-  if (parent != NULL) {
-    bsp = parent;
-  }
-
-  /* then explore mat_peptides, sites, etc. */
-
-  GetFeatsOnCdsProduct (sfp, asp->bsp, bsp, ajp, awp);
-
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK GetFeatsOnSeg (
-  SeqLocPtr slp,
-  SeqMgrSegmentContextPtr context
-)
-
-{
-  IntAsn2gbJobPtr  ajp;
-  Asn2gbWorkPtr    awp;
-  BioseqPtr        bsp;
-  Uint2            entityID;
-  Int4             from;
-  Int4             left;
-  SeqLocPtr        loc;
-  Int4             right;
-  SeqIdPtr         sip;
-  Int4             to;
-
-  if (slp == NULL || context == NULL) return FALSE;
-  awp = (Asn2gbWorkPtr) context->userdata;
-  if (awp == NULL) return FALSE;
-  ajp = awp->ajp;
-  if (ajp == NULL) return FALSE;
-
-  /* do not fetch outside of desired component */
-
-  if (ajp->ajp.slp != NULL) {
-    left = GetOffsetInBioseq (ajp->ajp.slp, awp->parent, SEQLOC_LEFT_END);
-    right = GetOffsetInBioseq (ajp->ajp.slp, awp->parent, SEQLOC_RIGHT_END);
-
-    from = context->cumOffset;
-    to = from + context->to - context->from;
-
-    if (left > to) return TRUE;
-    if (right < from) return TRUE;
-  }
- 
-  from = awp->from;
-  to = awp->to;
-
-  sip = SeqLocId (slp);
-  if (sip == NULL) {
-    loc = SeqLocFindNext (slp, NULL);
-    if (loc != NULL) {
-      sip = SeqLocId (loc);
-    }
-  }
-  if (sip == NULL) return TRUE;
-
-  /* may want to remote fetch genome component if not already in memory */
-
-  bsp = BioseqLockById (sip);
-
-  if (bsp == NULL) return TRUE;
-
-  entityID = ObjMgrGetEntityIDForPointer (bsp);
-
-  if (entityID != awp->entityID) {
-
-    /* if segment not packaged in record, may need to feature index it */
-
-    if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
-      SeqMgrIndexFeatures (entityID, NULL);
-    }
-
-    /* collect features indexed on the remote bioseq */
-
-    awp->from = 0;
-    awp->to = bsp->length - 1;
-  }
-
-  awp->lastsfp = NULL;
-  awp->lastsap = NULL;
-  awp->lastleft = 0;
-  awp->lastright = 0;
-
-  if (context->strand == Seq_strand_minus) {
-    SeqMgrExploreFeaturesRev (bsp, (Pointer) awp, GetFeatsOnBioseq, /* awp->slp */ slp, NULL, NULL);
-  } else {
-    SeqMgrExploreFeatures (bsp, (Pointer) awp, GetFeatsOnBioseq, /* awp->slp */ slp, NULL, NULL);
-  }
-
-  /* restore original from and to */
-
-  awp->from = from;
-  awp->to = to;
-
-  BioseqUnlock (bsp);
-
-  return TRUE;
-}
-
-static void AddFeatureBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  BioseqPtr          bsp;
-  SeqFeatPtr         cds;
-  SeqMgrDescContext  dcontext;
-  SeqMgrFeatContext  fcontext;
-  FeatBlockPtr       fbp;
-  SeqFeatPtr         gene;
-  IntFeatBlockPtr    ifp;
-  Boolean            is_other;
-  MolInfoPtr         mip;
-  SeqFeatPtr         mrna;
-  SeqFeatPtr         prot;
-  SeqDescrPtr        sdp;
-  SeqIdPtr           sip;
-  SeqLocPtr          slp;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->parent;
-  if (bsp == NULL) return;
-
-  awp->lastsfp = NULL;
-  awp->lastsap = NULL;
-  awp->lastleft = 0;
-  awp->lastright = 0;
-
-  /* optionally map gene from genomic onto cDNA */
-
-  if (awp->isGPS && ISA_na (bsp->mol) && awp->copyGpsGeneDown) {
-    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
-    if (sdp != NULL && sdp->choice == Seq_descr_molinfo) {
-      mip = (MolInfoPtr) sdp->data.ptrvalue;
-      if (mip != NULL) {
-        if (mip->biomol == MOLECULE_TYPE_MRNA) {
-          mrna = SeqMgrGetRNAgivenProduct (bsp, NULL);
-          if (mrna != NULL) {
-            gene = SeqMgrGetOverlappingGene (mrna->location, &fcontext);
-            if (gene != NULL && gene->data.choice == SEQFEAT_GENE) {
-
-              fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
-              if (fbp != NULL) {
-
-                fbp->entityID = fcontext.entityID;
-                fbp->itemID = fcontext.itemID;
-                fbp->itemtype = OBJ_SEQFEAT;
-                fbp->featdeftype = fcontext.featdeftype;
-                ifp = (IntFeatBlockPtr) fbp;
-                ifp->mapToNuc = FALSE;
-                ifp->mapToProt = FALSE;
-                ifp->mapToGen = FALSE;
-                ifp->mapToMrna = TRUE;
-                ifp->mapToPep = FALSE;
-                ifp->isCDS = TRUE;
-                ifp->firstfeat = awp->firstfeat;
-                awp->firstfeat = FALSE;
-              }
-            }
-          }
-        }
-      }
-    }
-  }
-
-  if (awp->farFeatsSuppress) {
-
-    if (bsp->repr == Seq_repr_seg || bsp->repr == Seq_repr_delta) {
-
-      /* if farFeatsSuppress first collect features on remote segments in MASTER_STYLE */
-
-      SeqMgrExploreSegments (bsp, (Pointer) awp, GetFeatsOnSeg);
-    }
-  }
-
-  if ((! awp->farFeatsSuppress) || (! awp->featseen)) {
-
-    /* reminder - features on near parts are indexed on segmented Bioseq */
-
-    slp = ajp->ajp.slp;
-    if (slp != NULL && SeqLocStrand (slp) == Seq_strand_minus) {
-      SeqMgrExploreFeaturesRev (bsp, (Pointer) awp, GetFeatsOnBioseq, awp->slp, NULL, NULL);
-    } else {
-      SeqMgrExploreFeatures (bsp, (Pointer) awp, GetFeatsOnBioseq, awp->slp, NULL, NULL);
-    }
-  }
-
-  if (awp->format == GENPEPT_FMT && ISA_aa (bsp->mol)) {
-    cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
-    if (cds != NULL && cds->data.choice == SEQFEAT_CDREGION) {
-
-      fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
-      if (fbp != NULL) {
-
-        fbp->entityID = fcontext.entityID;
-        fbp->itemID = fcontext.itemID;
-        fbp->itemtype = OBJ_SEQFEAT;
-        fbp->featdeftype = fcontext.featdeftype;
-        ifp = (IntFeatBlockPtr) fbp;
-        ifp->mapToNuc = FALSE;
-        ifp->mapToProt = TRUE;
-        ifp->mapToGen = FALSE;
-        ifp->mapToMrna = FALSE;
-        ifp->mapToPep = FALSE;
-        ifp->isCDS = TRUE;
-        ifp->firstfeat = awp->firstfeat;
-        awp->firstfeat = FALSE;
-      }
-    }
-    prot = SeqMgrGetPROTgivenProduct (bsp, &fcontext);
-    if (prot != NULL && prot->data.choice == SEQFEAT_PROT) {
-
-      is_other = FALSE;
-      for (sip = bsp->id; sip != NULL; sip = sip->next) {
-        if (sip->choice == SEQID_OTHER) {
-          is_other = TRUE;
-        }
-      }
-
-      /* for RefSeq records or GenBank not release_mode */
-      if (is_other || (! ajp->flags.forGbRelease)) {
-
-        fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
-        if (fbp != NULL) {
-
-          fbp->entityID = fcontext.entityID;
-          fbp->itemID = fcontext.itemID;
-          fbp->itemtype = OBJ_SEQFEAT;
-          fbp->featdeftype = fcontext.featdeftype;
-          ifp = (IntFeatBlockPtr) fbp;
-          ifp->mapToNuc = FALSE;
-          ifp->mapToProt = FALSE;
-          ifp->mapToGen = FALSE;
-          ifp->mapToMrna = FALSE;
-          ifp->mapToPep = TRUE;
-          ifp->firstfeat = awp->firstfeat;
-          awp->firstfeat = FALSE;
-        }
-      }
-    }
-  }
-
-  if (awp->onlyNearFeats) return;
-  if (awp->nearFeatsSuppress && awp->featseen) return;
-
-  if (! awp->farFeatsSuppress) {
-
-    if (bsp->repr == Seq_repr_seg || bsp->repr == Seq_repr_delta) {
-
-      /* if not farFeatsSuppress now collect features on remote segments in MASTER_STYLE */
-
-      SeqMgrExploreSegments (bsp, (Pointer) awp, GetFeatsOnSeg);
-    }
-  }
-}
-
-static void AddWGSBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  Char               buf [80];
-  SeqMgrDescContext  dcontext;
-  CharPtr            first = NULL;
-  CharPtr            last = NULL;
-  ObjectIdPtr        oip;
-  SeqDescrPtr        sdp;
-  UserFieldPtr       ufp;
-  UserObjectPtr      uop;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if ( ajp == NULL ) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) return;
-
-  bbp = Asn2gbAddBlock (awp, WGS_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
-  while (sdp != NULL) {
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    if (uop != NULL) {
-      oip = uop->type;
-      if (oip != NULL && StringICmp (oip->str, "WGSProjects") == 0) {
-        for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-          oip = ufp->label;
-          if (oip == NULL || oip->str == NULL || ufp->choice != 1) continue;
-          if (StringICmp (oip->str, "WGS_accession_first") == 0) {
-            first = (CharPtr) ufp->data.ptrvalue;
-          } else if (StringICmp (oip->str, "WGS_accession_last") == 0) {
-            last = (CharPtr) ufp->data.ptrvalue;
-          }
-        }
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
-  }
-
-  FFStartPrint (ffstring, awp->format, 0, 12, "WGS", 12, 0, 0, NULL, FALSE);
-
-  if (first != NULL && last != NULL) {
-
-    if ( GetWWW(ajp) ) {
-      if (StringCmp (first, last) != 0) {
-        FFAddTextToString(ffstring, "<a href=", link_wgs, NULL, FALSE, FALSE, TILDE_IGNORE);
-        FFAddTextToString(ffstring, "db=Nucleotide&cmd=Search&term=", first, NULL, FALSE, FALSE, TILDE_IGNORE);
-        FFAddTextToString(ffstring, ":", last, "[ACCN]>", FALSE, FALSE, TILDE_IGNORE);
-        sprintf (buf, "%s-%s", first, last);
-        FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-        FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_TO_SPACES);
-      } else {
-        FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
-        FFAddTextToString(ffstring, "val=", first, ">", FALSE, FALSE, TILDE_IGNORE);
-        sprintf (buf, "%s", first);
-        FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-        FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_TO_SPACES);
-      }
-    } else {
-      if (StringCmp (first, last) != 0) {
-        sprintf (buf, "%s-%s", first, last);
-        FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-      } else {
-        sprintf (buf, "%s", first);
-        FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-      }
-    }
-  }
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 0, 0, NULL);
-  FFRecycleString(ajp, ffstring);
-}
-
-static void AddGenomeBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  CharPtr            accn;
-  IntAsn2gbJobPtr    ajp;
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  SeqMgrDescContext  dcontext;
-  Boolean            first = TRUE;
-  CharPtr            moltype;
-  ObjectIdPtr        oip;
-  SeqDescrPtr        sdp;
-  UserFieldPtr       ufp;
-  UserObjectPtr      uop;
-  UserFieldPtr       urf;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if ( ajp == NULL ) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) return;
-
-  bbp = Asn2gbAddBlock (awp, GENOME_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  FFStartPrint (ffstring, awp->format, 0, 12, "GENOME", 12, 0, 0, NULL, FALSE);
-
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
-  while (sdp != NULL) {
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    if (uop != NULL) {
-      oip = uop->type;
-      if (oip != NULL && StringICmp (oip->str, "GenomeProject") == 0) {
-        for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
-          oip = ufp->label;
-          if (oip == NULL || oip->str == NULL || ufp->choice != 11) continue;
-          if (StringICmp (oip->str, "Chromosome") != 0) continue;
-          accn = NULL;
-          moltype = NULL;
-          for (urf = (UserFieldPtr) ufp->data.ptrvalue; urf != NULL; urf = urf->next) {
-            oip = urf->label;
-            if (oip == NULL || oip->str == NULL || urf->choice != 1) continue;
-            if (StringICmp (oip->str, "accession") == 0) {
-              accn = (CharPtr) urf->data.ptrvalue;
-            } else if (StringICmp (oip->str, "Moltype") == 0) {
-              moltype = (CharPtr) urf->data.ptrvalue;
-            }
-          }
-          if (! StringHasNoText (accn)) {
-            if (! first) {
-              FFAddNewLine(ffstring);
-            }
-            first = FALSE;
-            FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
-            if (! StringHasNoText (moltype)) {
-              FFAddTextToString (ffstring, " (", moltype, ")", FALSE, FALSE, TILDE_TO_SPACES);
-            }
-          }
-        }
-      }
-    }
-    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
-  }
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 0, 0, NULL);
-  FFRecycleString(ajp, ffstring);
-}
-
-static void AddBasecountBlock (
-  Asn2gbWorkPtr awp,
-  CharPtr bases
-)
-
-{
-  IntAsn2gbJobPtr  ajp;
-  Int4             base_count [5];
-  BaseBlockPtr     bbp;
-  BioseqPtr        bsp;
-  Char             buf [80];
-  Char             ch;
-  Int2             i;
-  Int4             len;
-  StringItemPtr    ffstring;
-  CharPtr          ptr;
-  CharPtr          str;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  bbp = Asn2gbAddBlock (awp, BASECOUNT_BLOCK, sizeof (BaseBlock));
-
-  if (bases == NULL || ajp->ajp.slp != NULL) return;
-  len = bsp->length;
-  for (i = 0; i < 5; i++) {
-    base_count [i] = 0;
-  }
-
-  ptr = bases;
-  ch = *ptr;
-  while (ch != '\0') {
-    ch = TO_UPPER (ch);
-    switch (ch) {
-      case 'A' :
-        (base_count [0])++;
-        break;
-      case 'C' :
-        (base_count [1])++;
-        break;
-      case 'G' :
-        (base_count [2])++;
-        break;
-      case 'T' :
-        (base_count [3])++;
-        break;
-      default :
-        (base_count [4])++;
-        break;
-    }
-    ptr++;
-    ch = *ptr;
-  }
-
-  if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) {
-
-    if (base_count [4] == 0) {
-      sprintf (buf, "%7ld a%7ld c%7ld g%7ld t",
-               (long) base_count [0], (long) base_count [1],
-               (long) base_count [2], (long) base_count [3]);
-    } else {
-      sprintf (buf, "%7ld a%7ld c%7ld g%7ld t%7ld others",
-               (long) base_count [0], (long) base_count [1],
-               (long) base_count [2], (long) base_count [3],
-               (long) base_count [4]);
-    }
-
-  } else if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
-
-    sprintf (buf, "Sequence %ld BP; %ld A; %ld C; %ld G; %ld T; %ld other;",
-             (long) len,
-             (long) base_count [0], (long) base_count [1],
-             (long) base_count [2], (long) base_count [3],
-             (long) base_count [4]);
-  }
-
-  ffstring = FFGetString (ajp);
-  if ( ffstring == NULL ) return;
-
-  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
-    FFAddOneString(ffstring, "XX\n", FALSE, FALSE, TILDE_IGNORE);
-  }
-  FFStartPrint (ffstring, awp->format, 0, 0, "BASE COUNT", 12, 5, 5, "SQ", FALSE);
-  FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
-  str = FFEndPrint(ajp, ffstring, awp->format, 12, 0, 5, 5, "SQ");
-  FFRecycleString(ajp, ffstring);
-
-  bbp->string = StringSave (str);
-}
-
-static void AddOriginBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  IntAsn2gbJobPtr    ajp;
-  BaseBlockPtr       bbp;
-  BioseqPtr          bsp;
-  Char               buf [67];
-  SeqMgrDescContext  dcontext;
-  GBBlockPtr         gbp;
-  SeqDescrPtr        sdp;
-  StringItemPtr      ffstring;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) return;
-  
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return;
-
-  bbp = Asn2gbAddBlock (awp, ORIGIN_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) {
-
-    buf [0] = '\0';
-
-    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
-    if (sdp != NULL) {
-      gbp = (GBBlockPtr) sdp->data.ptrvalue;
-      if (gbp != NULL && (! StringHasNoText (gbp->origin))) {
-        StringNCpy_0 (buf, gbp->origin, sizeof (buf));
-        bbp->entityID = dcontext.entityID;
-        bbp->itemID = dcontext.itemID;
-        bbp->itemtype = OBJ_SEQDESC;
-      }
-    }
-
-    FFStartPrint (ffstring, awp->format, 0, 12, "ORIGIN", 12, 0, 0, NULL, FALSE);
-
-    if (! StringHasNoText (buf)) {
-      FFAddOneString (ffstring, buf, TRUE, FALSE, TILDE_TO_SPACES);
-    }
-  }
-
-  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 0, 12, 0, 0, NULL);
-  FFRecycleString(ajp, ffstring);
-}
-
-#define BASES_PER_BLOCK 1200
-
-static void AddSequenceBlock (
-  Asn2gbWorkPtr awp,
-  CharPtr bases
-)
-
-{
-  IntAsn2gbJobPtr  ajp;
-  BioseqPtr        bsp;
-  Int4             i;
-  Int4             j;
-  Int4             len;
-  CharPtr          ptr;
-  SeqBlockPtr      sbp;
-  Int4             start;
-  Int4             stop;
-  CharPtr          str;
-
-  if (awp == NULL) return;
-  ajp = awp->ajp;
-  if (ajp == NULL) return;
-  bsp = awp->bsp;
-  if (bsp == NULL) return;
-
-  if (awp->slp != NULL) {
-    len = SeqLocLen (awp->slp);
-  } else {
-    len = bsp->length;
-  }
-
-  /* if generating GBSeq XML, populate single sequence block */
-
-  if (ajp->gbseq) {
-    sbp = (SeqBlockPtr) Asn2gbAddBlock (awp, SEQUENCE_BLOCK, sizeof (SeqBlock));
-    if (sbp == NULL) return;
-
-    sbp->entityID = bsp->idx.entityID;
-    sbp->itemID = bsp->idx.itemID;
-    sbp->itemtype = OBJ_BIOSEQ;
-
-    sbp->start = 0;
-    sbp->stop = len;
-    return;
-  }
-
-  /* otherwise populate individual sequence blocks for given range */
-
-  ptr = bases;
-
-  for (start = 0; start < len; start += BASES_PER_BLOCK) {
-    sbp = (SeqBlockPtr) Asn2gbAddBlock (awp, SEQUENCE_BLOCK, sizeof (SeqBlock));
-    if (sbp == NULL) continue;
-
-    sbp->entityID = bsp->idx.entityID;
-    sbp->itemID = bsp->idx.itemID;
-    sbp->itemtype = OBJ_BIOSEQ;
-
-    stop = start + BASES_PER_BLOCK;
-    if (stop >= len) {
-      stop = len;
-    }
-
-    sbp->start = start;
-    sbp->stop = stop;
-
-    if (ptr != NULL) {
-      str = MemNew (sizeof (Char) * (BASES_PER_BLOCK + 2));
-      if (str != NULL) {
-        sbp->bases = str;
-        j = stop - start;
-        for (i = 0; i < j; i++) {
-          *str = *ptr;
-          ptr++;
-          str++;
-        }
-      }
-    }
-  }
-}
-
-static void AddContigBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  BaseBlockPtr  bbp;
-
-  if (awp == NULL) return;
-
-  bbp = Asn2gbAddBlock (awp, CONTIG_BLOCK, sizeof (BaseBlock));
-}
-
-static void AddSlashBlock (
-  Asn2gbWorkPtr awp
-)
-
-{
-  BaseBlockPtr  bbp;
-  CharPtr str;
-
-  if (awp == NULL) return;
-
-  bbp = Asn2gbAddBlock (awp, SLASH_BLOCK, sizeof (BaseBlock));
-  if (bbp == NULL) return;
-
-  str = MemNew(sizeof(Char) * 4);
-  StringNCpy(str, "//\n", 4);
-
-  bbp->string = str;
-}
-
 /*--------------------------------------------------------*/
 /*                                                        */
 /*  s_LocusGetBaseName() -                                */
@@ -19341,6 +1572,54 @@ static Boolean s_LocusGetBaseName (BioseqPtr parent, BioseqPtr segment, CharPtr
 
 /* ********************************************************************** */
 
+  static Uint1 fasta_order [NUM_SEQID] = {
+    33, /* 0 = not set */
+    20, /* 1 = local Object-id */
+    15, /* 2 = gibbsq */
+    16, /* 3 = gibbmt */
+    30, /* 4 = giim Giimport-id */
+    10, /* 5 = genbank */
+    10, /* 6 = embl */
+    10, /* 7 = pir */
+    10, /* 8 = swissprot */
+    15, /* 9 = patent */
+    20, /* 10 = other TextSeqId */
+    20, /* 11 = general Dbtag */
+    255, /* 12 = gi */
+    10, /* 13 = ddbj */
+    10, /* 14 = prf */
+    12, /* 15 = pdb */
+    10, /* 16 = tpg */
+    10, /* 17 = tpe */
+    10  /* 18 = tpd */
+  };
+
+/* DoOneSection builds a single report for one bioseq or segment */
+
+static Asn2gbSectPtr Asn2gbAddSection (
+  Asn2gbWorkPtr awp
+)
+
+{
+  Asn2gbSectPtr  asp;
+  ValNodePtr     vnp;
+
+  if (awp == NULL) return NULL;
+
+  asp = (Asn2gbSectPtr) MemNew (sizeof (IntAsn2gbSect));
+  if (asp == NULL) return NULL;
+
+  vnp = ValNodeAddPointer (&(awp->lastsection), 0, asp);
+  if (vnp == NULL) return asp;
+
+  awp->lastsection = vnp;
+  if (awp->sectionList == NULL) {
+    awp->sectionList = vnp;
+  }
+
+  return asp;
+}
+
 static void LIBCALLBACK SaveGBSeqSequence (
   CharPtr sequence,
   Pointer userdata
@@ -19358,6 +1637,31 @@ static void LIBCALLBACK SaveGBSeqSequence (
   *tmpp = tmp;
 }
 
+static CharPtr CompressNonBases (CharPtr str)
+
+{
+  Char     ch;
+  CharPtr  dst;
+  CharPtr  ptr;
+
+  if (str == NULL || str [0] == '\0') return NULL;
+
+  dst = str;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    if (IS_ALPHA (ch)) {
+      *dst = ch;
+      dst++;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+  *dst = '\0';
+
+  return str;
+}
+
 static CharPtr DoSeqPortStream (
   BioseqPtr bsp
 )
@@ -19391,9 +1695,39 @@ static CharPtr DoSeqPortStream (
   return str;
 }
 
-/* DoOneSection builds a single report for one bioseq or segment */
+static Boolean DeltaLitOnly (
+  BioseqPtr bsp
+)
+
+{
+  ValNodePtr  vnp;
+
+  if (bsp == NULL || bsp->repr != Seq_repr_delta) return FALSE;
+  for (vnp = (ValNodePtr)(bsp->seq_ext); vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == 1) return FALSE;
+  }
+  return TRUE;
+}
+
+static Boolean SegHasParts (
+  BioseqPtr bsp
+)
+
+{
+  BioseqSetPtr  bssp;
+  SeqEntryPtr   sep;
+
+  if (bsp == NULL || bsp->repr != Seq_repr_seg) return FALSE;
+  sep = bsp->seqentry;
+  if (sep == NULL) return FALSE;
+  sep = sep->next;
+  if (sep == NULL || (! IS_Bioseq_set (sep))) return FALSE;
+  bssp = (BioseqSetPtr) sep->data.ptrvalue;
+  if (bssp != NULL && bssp->_class == BioseqseqSet_class_parts) return TRUE;
+  return FALSE;
+}
 
-static void DoOneSection (
+NLM_EXTERN void DoOneSection (
   BioseqPtr target,
   BioseqPtr parent,
   BioseqPtr bsp,
@@ -19557,11 +1891,11 @@ static void DoOneSection (
   /* start exploring and populating paragraphs */
 
   if (awp->format == FTABLE_FMT) {
-
     AddFeatHeaderBlock (awp);
     if (awp->showRefs) {
       AddReferenceBlock (awp, isRefSeq);
     }
+    AddSourceFeatBlock (awp);
     AddFeatureBlock (awp);
 
   } else {
@@ -19714,6 +2048,7 @@ static void DoOneSection (
   (awp->currsection)++;
 }
 
+/* ********************************************************************** */
 
 /*
 the following functions handle various kinds of input, all calling
@@ -19855,7 +2190,7 @@ static Boolean LIBCALLBACK FindSegForPart (
   return FALSE;
 }
 
-static void DoOneBioseq (
+NLM_EXTERN void DoOneBioseq (
   BioseqPtr bsp,
   Pointer userdata
 )
@@ -20081,3261 +2416,6 @@ static void DoOneBioseqSet (
 
 
 
-static CharPtr goFieldType [] = {
-  "", "text string", "go id", "pubmed id", "evidence", NULL
-};
-
-static CharPtr GetGOtext (
-  UserFieldPtr topufp
-)
-
-{
-  CharPtr       evidence = NULL;
-  Char          gid [32];
-  CharPtr       goid = NULL;
-  Int2          j;
-  ObjectIdPtr   oip;
-  Int4          pmid = 0;
-  CharPtr       str;
-  CharPtr       textstr = NULL;
-  Char          tmp [32];
-  UserFieldPtr  ufp;
-
-  for (ufp = topufp; ufp != NULL; ufp = ufp->next) {
-    oip = ufp->label;
-    if (oip == NULL) continue;
-    for (j = 0; goFieldType [j] != NULL; j++) {
-      if (StringICmp (oip->str, goFieldType [j]) == 0) break;
-    }
-    if (goFieldType [j] == NULL) continue;
-    switch (j) {
-      case 1 :
-        if (ufp->choice == 1) {
-          textstr = (CharPtr) ufp->data.ptrvalue;
-        }
-        break;
-      case 2 :
-        if (ufp->choice == 1) {
-          goid = (CharPtr) ufp->data.ptrvalue;
-        } else if (ufp->choice == 2) {
-          sprintf (gid, "%ld", (long) (Int4) ufp->data.intvalue);
-          goid = (CharPtr) gid;
-        }
-        break;
-      case 3 :
-        if (ufp->choice == 2) {
-          pmid = (Int4) ufp->data.intvalue;
-        }
-        break;
-      case 4 :
-        if (ufp->choice == 1) {
-          evidence = (CharPtr) ufp->data.ptrvalue;
-        }
-        break;
-      default :
-        break;
-    }
-  }
-  /* if (StringHasNoText (textstr)) return NULL; */
-
-  str = (CharPtr) MemNew (StringLen (textstr) + StringLen (goid) + StringLen (evidence) + 50);
-  if (str == NULL) return NULL;
-
-  StringCpy (str, textstr);
-  if (! StringHasNoText (goid)) {
-    StringCat (str, " [goid ");
-    StringCat (str, goid);
-    StringCat (str, "]");
-  }
-  if (! StringHasNoText (evidence)) {
-    StringCat (str, " [evidence ");
-    StringCat (str, evidence);
-    StringCat (str, "]");
-  }
-  if (pmid != 0) {
-    sprintf (tmp, " [pmid %ld", (long) pmid);
-    StringCat (str, tmp);
-    StringCat (str, "]");
-  }
-  TrimSpacesAroundString (str);
-
-  return str;
-}
-
-static Boolean DbxrefAlreadyInGeneXref (
-  DbtagPtr dbt,
-  ValNodePtr dbxref
-)
-
-{
-  DbtagPtr    gdbt;
-  ValNodePtr  vnp;
-
-  if (dbt == NULL) return FALSE;
-
-  for (vnp = dbxref; vnp != NULL; vnp = vnp->next) {
-    gdbt = (DbtagPtr) vnp->data.ptrvalue;
-    if (gdbt == NULL) continue;
-    if (DbtagMatch (dbt, gdbt)) return TRUE;
-  }
-
-  return FALSE;
-}
-
-/* FormatFeatureblockQuals should not be called directly,
-   except from FormatFeatureBlock.  It performs no input
-   validation.  (perhaps it should?) */
-
-static void FormatFeatureBlockQuals (
-  StringItemPtr    ffstring,
-  IntAsn2gbJobPtr  ajp,
-  Asn2gbFormatPtr  afp,
-  Asn2gbSectPtr    asp,
-  BioseqPtr        bsp,
-  Uint1            featdeftype,
-  ValNodePtr       gene_syn,
-  CharPtr          lasttype,
-  SeqLocPtr        location,
-  BioseqPtr        prod,
-  CharPtr          protein_pid_g,
-  QualValPtr       qvp,
-  Int4             left,
-  Int4             right,
-  Uint1            strand,
-  SeqFeatPtr       sfp,
-  BioseqPtr        target,
-  Boolean          is_other,
-  Boolean          is_journalscan,
-  Boolean          is_gps
-)
-
-{
-  Boolean            add_period;
-  CharPtr            ascii;
-  Int2               ascii_len;
-  Boolean            at_end = FALSE;
-  ByteStorePtr       bs;
-  Char               buf[80];
-  Choice             cbaa;
-  CodeBreakPtr       cbp;
-  Char               ch;
-  Uint1              choice;
-  Uint1              code = Seq_code_ncbieaa;
-  Int4               gi;
-  Boolean            hadProtDesc = FALSE;
-  DbtagPtr           dbt;
-  UserFieldPtr       entry;
-  Int4               exp_ev;
-  GBQualPtr          gbq;
-  Int2               i;
-  Uint1              idx;
-  Boolean            isTRNA;
-  Int2               j;
-  Uint1              jdx;
-  Int4               len;
-  SeqLocPtr          newloc;
-  CharPtr            notestr;
-  Char               numbuf [32];
-  Int2               numcodons;
-  Int2               numsyns;
-  ObjectIdPtr        oip;
-  Boolean            okay;
-  Boolean            only_digits;
-  BioseqPtr          pbsp;
-  ValNodePtr         ppr;
-  CharPtr            prefix;
-  CharPtr            protein_seq = NULL;
-  size_t             prtlen;
-  CharPtr            ptr;
-  Uint1              residue;
-  SeqCodeTablePtr    sctp;
-  Int4               sec_str;
-  Uint1              seqcode;
-  Char               seqid [50];
-  SeqIntPtr          sintp;
-  SeqIdPtr           sip;
-  SeqLocPtr          slp;
-  Boolean            split;
-  SeqPortPtr         spp;
-  CharPtr            start;
-  CharPtr            str;
-  Boolean            suppress_period;
-  CharPtr            tmp;
-  tRNAPtr            trna;
-  UserFieldPtr       ufp;
-  UserObjectPtr      uop;
-  ValNodePtr         vnp;
-  StringItemPtr      unique;
-
-  unique = FFGetString(ajp);
-  if ( unique == NULL ) return;
-
-  for (i = 0, idx = feat_qual_order [i]; idx != 0; i++, idx = feat_qual_order [i]) {
-
-    lasttype = NULL;
-    switch (asn2gnbk_featur_quals [idx].qualclass) {
-
-      case Qual_class_ignore :
-        break;
-
-      case Qual_class_string :
-        if (! StringHasNoText (qvp [idx].str)) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-            FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"",
-            FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_locus_tag :
-        if (! StringHasNoText (qvp [idx].str)) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-            FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"",
-            FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_tilde :
-        if (! StringHasNoText (qvp [idx].str)) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-            FALSE, TRUE, TILDE_EXPAND);
-          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"",
-            FALSE, TRUE, TILDE_EXPAND);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_product :
-        if (StringHasNoText (qvp [idx].str) ||
-            (ajp->flags.dropIllegalQuals &&
-             (! AllowedValQual (featdeftype, FTQUAL_product)))) break;
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-            FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"",
-            FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        break;
-
-      case Qual_class_sgml :
-        if (! StringHasNoText (qvp [idx].str)) {
-          if (is_journalscan) {
-            ascii_len = Sgml2AsciiLen (qvp [idx].str);
-            start = ascii = MemNew ((size_t) (10 + ascii_len));
-            if (start != NULL) {
-              ascii = Sgml2Ascii (qvp [idx].str, ascii, ascii_len + 1);
-
-              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-                FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddTextToString(ffstring, "\"", start, "\"",
-                FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddOneChar(ffstring, '\n', FALSE);
-
-              MemFree (start);
-            }
-          } else {
-              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-                FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddTextToString(ffstring, "\"", qvp[idx].str, "\"",
-                FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddOneChar(ffstring, '\n', FALSE);
-          }
-        }
-        break;
-
-      case Qual_class_boolean :
-        if (qvp [idx].ble) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "\n",
-                            FALSE, TRUE, TILDE_IGNORE);
-        }
-        break;
-
-      case Qual_class_int :
-        if (qvp [idx].num > 0) {
-          if (idx == FTQUAL_transl_table) {
-            sprintf (numbuf, "%ld", (long) qvp [idx].num);
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-              FALSE, TRUE, TILDE_IGNORE);
-            FF_www_gcode (ajp, ffstring, numbuf);
-          } else {
-            sprintf (numbuf, "%ld", (long) qvp [idx].num);
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-              FALSE, TRUE, TILDE_IGNORE);
-            FFAddTextToString(ffstring, NULL, numbuf, NULL,
-              FALSE, TRUE, TILDE_IGNORE);
-          }
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_evidence :
-        exp_ev = qvp [idx].num;
-        if (exp_ev > 0 && exp_ev <= 2) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-              FALSE, TRUE, TILDE_IGNORE);
-          FFAddOneString(ffstring, evidenceText [exp_ev], FALSE, TRUE, TILDE_IGNORE);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_valnode :
-        for (vnp = qvp[idx].vnp; vnp != NULL; vnp = vnp->next) {
-          str = (CharPtr) vnp->data.ptrvalue;
-          if (str != NULL) {
-              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-                  FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddTextToString(ffstring, "\"", str, "\"",
-                  FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddOneChar(ffstring, '\n', FALSE);
-          }
-        }
-        break;
-
-      case Qual_class_gene_syn :
-        /*
-        for (vnp = qvp[idx].vnp; vnp != NULL; vnp = vnp->next) {
-          str = (CharPtr) vnp->data.ptrvalue;
-          if (str != NULL) {
-              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-                  FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddTextToString(ffstring, "\"", str, "\"",
-                  FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddOneChar(ffstring, '\n', FALSE);
-          }
-        }
-        */
-        numsyns = 0;
-        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
-          str = (CharPtr) vnp->data.ptrvalue;
-          if (! StringHasNoText (str)) {
-            numsyns++;
-          }
-        }
-        if (numsyns > 0) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
-                FALSE, TRUE, TILDE_TO_SPACES);
-          prefix = NULL;
-          for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
-            str = (CharPtr) vnp->data.ptrvalue;
-            if (! StringHasNoText (str)) {
-              FFAddTextToString (ffstring, prefix, str, NULL, FALSE, FALSE, TILDE_IGNORE);
-              prefix = ", ";
-            }
-          }
-          FFAddOneChar(ffstring, '\"', FALSE);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_EC_valnode :
-        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
-          str = (CharPtr) vnp->data.ptrvalue;
-          okay = TRUE;
-
-          if (str == NULL) continue;
-
-          if (ajp->flags.dropIllegalQuals) {
-            tmp = str;
-            while (*tmp != '\0' && *tmp == '\"')
-              tmp++;
-            for (; *tmp != '\0' && *tmp != '\"'; tmp++) {
-              if (!IS_DIGIT(*tmp) && *tmp != '.' && *tmp != '-') {
-                okay = FALSE;
-              }
-            }
-          }
-          if (!okay) continue;
-
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-                FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddOneChar(ffstring, '\"', FALSE);
-          FF_AddECnumber(ajp, ffstring, str);
-          FFAddOneChar(ffstring, '\"', FALSE);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_EC_quote :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          okay = TRUE;
-          if (gbq->val == NULL) {
-            okay = FALSE;
-          }
-
-          if (ajp->flags.dropIllegalQuals && okay) {
-            tmp = gbq->val;
-            while (*tmp != '\0' && *tmp == '\"')
-              tmp++;
-            for (; *tmp != '\0' && *tmp != '\"'; tmp++) {
-              if (!IS_DIGIT(*tmp) && *tmp != '.' && *tmp != '-') {
-                okay = FALSE;
-              }
-            }
-          }
-
-          if (StringHasNoText (gbq->val)) {
-            okay = FALSE;
-          }
-
-          if (okay) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-                  FALSE, TRUE, TILDE_TO_SPACES);
-            FFAddOneChar(ffstring, '\"', FALSE);
-            if (!StringIsJustQuotes (gbq->val)) {
-              FF_AddECnumber (ajp, ffstring, gbq->val);
-            }
-            FFAddOneChar(ffstring, '\"', FALSE);
-            FFAddOneChar(ffstring, '\n', FALSE);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_quote :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
-                  FALSE, TRUE, TILDE_IGNORE);
-            if (!StringIsJustQuotes (gbq->val)) {
-              FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_IGNORE);
-            }
-            FFAddOneChar(ffstring, '\"', FALSE);
-            FFAddOneChar(ffstring, '\n', FALSE);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_noquote :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
-                  FALSE, TRUE, TILDE_IGNORE);
-            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
-            FFAddOneChar(ffstring, '\n', FALSE);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_label :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            if (ajp->flags.checkQualSyntax) { /* single token, not just numeric */
-              str = gbq->val;
-              ch = *str;
-              only_digits = TRUE;
-              while (ch != '\0') {
-                if (IS_WHITESP (ch)) break; /* only single token allowed */
-                if (! IS_DIGIT (ch)) {
-                  only_digits = FALSE;
-                }
-                str++;
-                ch = *str;
-              }
-              if (only_digits) break; /* must not be just numeric */
-            }
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                  FALSE, TRUE, TILDE_IGNORE);
-            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
-            FFAddOneChar(ffstring, '\n', FALSE);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_number :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-
-        if (ajp->flags.checkQualSyntax) {
-          str = gbq->val;
-
-          if ( StringHasNoText (str) )
-            break;
-          while (!IS_WHITESP (*str) && *str != '\0')
-            str++;
-          if (! StringHasNoText (str) )
-            break;
-        }
-
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                  FALSE, TRUE, TILDE_IGNORE);
-            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
-            FFAddOneChar(ffstring, '\n', FALSE);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_paren :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            tmp = StringSave (gbq->val);
-            str = tmp;
-            len = StringLen (str);
-            if (len > 1 && *str == '(' && str [len - 1] == ')' &&
-                StringChr (str, ',') != NULL) {
-              str++;
-              while (! StringHasNoText (str)) {
-                ptr = StringChr (str, ',');
-                if (ptr == NULL) {
-                  ptr = StringChr (str, ')');
-                }
-                if (ptr != NULL) {
-                  *ptr = '\0';
-                  ptr++;
-                }
-                FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                  FALSE, TRUE, TILDE_IGNORE);
-                FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
-                FFAddOneChar(ffstring, '\n', FALSE);
-                str = ptr;
-              }
-            } else {
-              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                  FALSE, TRUE, TILDE_IGNORE);
-              FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddOneChar(ffstring, '\n', FALSE);
-            }
-            MemFree (tmp);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_rpt :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            tmp = StringSave (gbq->val);
-            str = tmp;
-            len = StringLen (str);
-            if (len > 1 && *str == '(' && str [len - 1] == ')' &&
-                StringChr (str, ',') != NULL) {
-              str++;
-              while (! StringHasNoText (str)) {
-                ptr = StringChr (str, ',');
-                if (ptr == NULL) {
-                  ptr = StringChr (str, ')');
-                }
-                if (ptr != NULL) {
-                  *ptr = '\0';
-                  ptr++;
-                }
-                if ((! ajp->flags.checkQualSyntax) || (StringInStringList (str, validRptString))) {
-                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                                    FALSE, TRUE, TILDE_IGNORE);
-                  FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
-                  FFAddOneChar(ffstring, '\n', FALSE);
-                }
-                str = ptr;
-              }
-            } else {
-              if ((! ajp->flags.checkQualSyntax) || (StringInStringList (str, validRptString))) {
-                FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                                  FALSE, TRUE, TILDE_IGNORE);
-                FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
-                FFAddOneChar(ffstring, '\n', FALSE);
-              }
-            }
-            MemFree (tmp);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_rpt_unit :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-
-        /* in release_mode, must be of the form 123..4567 or a single-token label,
-           or (technically illegal but common) letters and semicolons - NO LONGER CHECKED */
-
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            tmp = StringSave (gbq->val);
-            str = tmp;
-            len = StringLen (str);
-            if (len > 1 && *str == '(' && str [len - 1] == ')' /* && StringChr (str, ',') != NULL */) {
-              str++;
-              while (! StringHasNoText (str)) {
-                ptr = StringChr (str, ',');
-                if (ptr == NULL) {
-                  ptr = StringChr (str, ')');
-                }
-                if (ptr != NULL) {
-                  *ptr = '\0';
-                  ptr++;
-                }
-                if ((! ajp->flags.checkQualSyntax) || (ValidateRptUnit (str))) {
-                  TrimSpacesAroundString (str);
-                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=\"",
-                                    FALSE, TRUE, TILDE_IGNORE);
-                  FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
-                  FFAddOneChar(ffstring, '\"', FALSE);
-                  FFAddOneChar(ffstring, '\n', FALSE);
-                }
-                str = ptr;
-              }
-            } else {
-              if ((! ajp->flags.checkQualSyntax) || (ValidateRptUnit (str))) {
-                TrimSpacesAroundString (str);
-                FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=\"",
-                                  FALSE, TRUE, TILDE_IGNORE);
-                FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
-                FFAddOneChar(ffstring, '\"', FALSE);
-                FFAddOneChar(ffstring, '\n', FALSE);
-              }
-            }
-            MemFree (tmp);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_replace :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                            FALSE, TRUE, TILDE_IGNORE);
-          FFAddOneChar(ffstring, '\"', FALSE);
-          if (!StringHasNoText (gbq->val)) {
-            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
-          }
-          FFAddOneChar(ffstring, '\"', FALSE);
-          FFAddOneChar(ffstring, '\n', FALSE);
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_consplice :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-
-        if (ajp->flags.checkQualSyntax && (! StringInStringList (gbq->val, validConsSpliceString)) ) {
-          break;
-        }
-
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                              FALSE, TRUE, TILDE_IGNORE);
-            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
-            FFAddOneChar(ffstring, '\n', FALSE);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_site :
-        if (! StringHasNoText (qvp [idx].str)) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                            FALSE, TRUE, TILDE_IGNORE);
-          FFAddTextToString(ffstring, "\"", qvp[idx].str, "\"", FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_bond :
-        if (! StringHasNoText (qvp [idx].str)) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                            FALSE, TRUE, TILDE_IGNORE);
-          FFAddTextToString(ffstring, "\"", qvp[idx].str, "\"", FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_L_R_B :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-
-        if (ajp->flags.checkQualSyntax && (! StringInStringList (gbq->val, validLRBString)) ) {
-          break;
-        }
-
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                              FALSE, TRUE, TILDE_IGNORE);
-            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
-            FFAddOneChar(ffstring, '\n', FALSE);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_sec_str :
-        sec_str = qvp [idx].num;
-        if (sec_str > 0 && sec_str <= 3) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                            FALSE, TRUE, TILDE_IGNORE);
-          FFAddTextToString(ffstring, "\"", secStrText[sec_str], "\"", 
-                            FALSE, FALSE, TILDE_IGNORE);
-          FFAddOneChar(ffstring, '\n', FALSE);
-        }
-        break;
-
-      case Qual_class_seq_loc :
-        slp = qvp [idx].slp;
-        if (slp != NULL) {
-          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                            FALSE, TRUE, TILDE_IGNORE);
-          str = FlatLoc (ajp, target, slp, /* ajp->masterStyle */ FALSE);
-          FFAddTextToString(ffstring, "\"", str, "\"", 
-                            FALSE, TRUE, TILDE_TO_SPACES);
-          FFAddOneChar(ffstring, '\n', FALSE);
-          MemFree (str);
-        }
-        break;
-
-      case Qual_class_code_break :
-        cbp = qvp [idx].cbp;
-        seqcode = 0;
-        sctp = NULL;
-        while (cbp != NULL) {
-          cbaa = cbp->aa;
-          switch (cbaa.choice) {
-            case 1 :
-              seqcode = Seq_code_ncbieaa;
-              break;
-            case 2 :
-              seqcode = Seq_code_ncbi8aa;
-              break;
-            case 3 :
-              seqcode = Seq_code_ncbistdaa;
-              break;
-            default :
-              break;
-          }
-          if (seqcode != 0) {
-            sctp = SeqCodeTableFind (seqcode);
-            if (sctp != NULL) {
-              slp = NULL;
-              while ((slp = SeqLocFindNext (cbp->loc, slp)) != NULL) {
-                str = NULL;
-                if (ajp->ajp.slp != NULL) {
-                  sip = SeqIdParse ("lcl|dummy");
-                  split = FALSE;
-                  newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
- 
-                  SeqIdFree (sip);
-                  if (newloc != NULL) {
-                    A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
-                    str = FlatLoc (ajp, target, newloc, ajp->masterStyle);
-                    SeqLocFree (newloc);
-                  }
-                } else {
-                  str = FlatLoc (ajp, target, slp, ajp->masterStyle);
-                }
-                if (str != NULL) {
-                  residue = cbaa.value.intvalue;
-                  ptr = Get3LetterSymbol (ajp, seqcode, sctp, residue);
-                  if (ptr == NULL) {
-                    ptr = "OTHER";
-                  }
-                  FFAddOneString(ffstring, "/transl_except=", FALSE, FALSE, TILDE_IGNORE);
-                  FFAddTextToString(ffstring, "(pos:", str, ",", FALSE, FALSE, TILDE_IGNORE);
-                  FFAddTextToString(ffstring, "aa:", ptr, ")", FALSE, FALSE, TILDE_IGNORE);
-                  FFAddOneChar(ffstring, '\n', FALSE);
-                }
-                MemFree (str);
-              }
-            }
-          }
-          cbp = cbp->next;
-        }
-        break;
-
-      case Qual_class_anti_codon :
-        slp = qvp [FTQUAL_anticodon].slp;
-        newloc = NULL;
-        if (slp != NULL && ajp->ajp.slp != NULL) {
-          sip = SeqIdParse ("lcl|dummy");
-          split = FALSE;
-          newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
-          /*
-          newloc = SeqLocCopyRegion (sip, slp, bsp, left, right, strand, &split);
-          */
-          SeqIdFree (sip);
-          slp = newloc;
-          if (newloc != NULL) {
-            A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
-          }
-        }
-        if (slp != NULL && slp->choice == SEQLOC_INT) {
-          sintp = (SeqIntPtr) slp->data.ptrvalue;
-          if (sintp != NULL) {
-            str = qvp [FTQUAL_trna_aa].str;
-            if (! StringHasNoText (str)) {
-              sprintf(numbuf, "%ld", (long) sintp->from + 1);
-              FFAddTextToString(ffstring, "/anticodon=(pos:", numbuf, "..",
-                                FALSE, FALSE, TILDE_IGNORE);
-              sprintf(numbuf, "%ld", (long) sintp->to + 1);
-              FFAddTextToString(ffstring, NULL, numbuf, ",",
-                                FALSE, FALSE, TILDE_IGNORE);
-              FFAddTextToString(ffstring, "aa:", str, ")",
-                                FALSE, FALSE, TILDE_IGNORE);
-              FFAddOneChar(ffstring, '\n', FALSE);
-            }
-          }
-        }
-        if (newloc != NULL) {
-          SeqLocFree (newloc);
-        }
-        break;
-
-      case Qual_class_codon :
-        gbq = qvp [idx].gbq;
-        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
-        if (lasttype == NULL) {
-          lasttype = gbq->qual;
-        }
-        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-          if (! StringHasNoText (gbq->val)) {
-            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
-                              FALSE, FALSE, TILDE_IGNORE);
-            FFAddOneString(ffstring, gbq->val, FALSE, FALSE, TILDE_TO_SPACES);
-            FFAddOneChar(ffstring, '\n', FALSE);
-          }
-          gbq = gbq->next;
-        }
-        break;
-
-      case Qual_class_pubset :
-        vnp = qvp [idx].vnp;
-        if (vnp != NULL && asp->referenceArray != NULL) {
-          for (ppr = vnp->data.ptrvalue; ppr != NULL; ppr = ppr->next) {
-            j = MatchRef (ppr, asp->referenceArray, asp->numReferences);
-            if (j > 0) {
-              sprintf (numbuf, "%d", (int) j);
-              FFAddTextToString(ffstring, "/citation=[", numbuf, "]",
-                                FALSE, TRUE, TILDE_TO_SPACES);
-              FFAddOneChar(ffstring, '\n', FALSE);
-            }
-          }
-        }
-        break;
-
-      case Qual_class_db_xref :
-        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
-          buf [0] = '\0';
-          dbt = (DbtagPtr) vnp->data.ptrvalue;
-          if (dbt != NULL && (! StringHasNoText (dbt->db))) {
-            oip = dbt->tag;
-            if (oip != NULL) {
-
-              okay = TRUE;
-              if (StringCmp (dbt->db, "PID") == 0 || StringCmp (dbt->db, "GI") == 0) {
-                okay = FALSE;
-              }
-              if (ajp->flags.dropBadDbxref) {
-                /* if RELEASE_MODE, drop unknown dbtag */
-                okay = FALSE;
-                for (j = 0; legalDbXrefs [j] != NULL; j++) {
-                  if (StringCmp (dbt->db, legalDbXrefs [j]) == 0) {
-                    okay = TRUE;
-                  }
-                }
-                if (! okay) {
-                  if (is_gps || is_other) {
-                    for (j = 0; legalRefSeqDbXrefs [j] != NULL; j++) {
-                      if (StringCmp (dbt->db, legalRefSeqDbXrefs [j]) == 0) {
-                        okay = TRUE;
-                      }
-                    }
-                  }
-                }
-              }
-              if (okay && idx == FTQUAL_db_xref && qvp [FTQUAL_gene_xref].vnp != NULL) {
-                if (DbxrefAlreadyInGeneXref (dbt, qvp [FTQUAL_gene_xref].vnp)) {
-                  okay = FALSE;
-                }
-              }
-
-              if (okay) {
-                if (! StringHasNoText (oip->str)) {
-                  if (StringLen (oip->str) < 80) {
-                    sprintf (buf, "%s", oip->str);
-                  }
-                } else {
-                  sprintf (buf, "%ld", (long) oip->id);
-                }
-              }
-            }
-          }
-          if (! StringHasNoText (buf)) {
-            if (StringICmp (buf, protein_pid_g) != 0) {
-              /* already sorted and uniqued by BasicSeqEntryCleanup, per feature */
-              if (StringICmp (dbt->db, "LocusID") == 0 || StringICmp (dbt->db, "InterimID") == 0) {
-                if (FFStringSearch (ffstring, dbt->db, 0) >= 0) {
-                  okay = FALSE;
-                }
-              }
-              if (okay) {
-                FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-                FF_www_db_xref(ajp, ffstring, dbt->db, buf);
-                FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-              }
-            }
-          }
-        }
-        break;
-
-      
-      case Qual_class_seq_id :
-        sip = qvp [idx].sip;
-        if (sip != NULL) {
-          /* should always be found above for protein_id or transcript_id
-          prod = BioseqFind (sip);
-          */
-          if (prod != NULL) {
-            choice = 0;
-            for (sip = prod->id; sip != NULL; sip = sip->next) {
-              if (sip->choice == SEQID_GENBANK ||
-                  sip->choice == SEQID_EMBL ||
-                  sip->choice == SEQID_DDBJ ||
-                  sip->choice == SEQID_OTHER ||
-                  sip->choice == SEQID_TPG ||
-                  sip->choice == SEQID_TPE ||
-                  sip->choice == SEQID_TPD) {
-                choice = sip->choice;
-                if (SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
-                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
-                                    FALSE, FALSE, TILDE_IGNORE);
-                  FF_www_protein_id(ajp, ffstring, seqid);
-                  FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-                }
-              } else if (sip->choice == SEQID_GI) {
-                if (choice == 0) {
-                  sprintf (seqid, "%ld", (long) sip->data.intvalue);
-                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
-                                    FALSE, FALSE, TILDE_IGNORE);
-                  FF_www_protein_id(ajp, ffstring, seqid);
-                  FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-                }
-                sprintf (seqid, "%ld", (long) sip->data.intvalue);
-                FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-                FF_www_db_xref(ajp, ffstring, "GI", seqid);
-                FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-              } else if (sip->choice == SEQID_GENERAL) {
-                dbt = (DbtagPtr) sip->data.ptrvalue;
-                if (dbt != NULL && StringCmp (dbt->db, "PID") == 0) {
-                  /*
-                  oip = dbt->tag;
-                  if (oip != NULL) {
-                    if (! StringHasNoText (oip->str)) {
-                      sprintf (seqid, "PID:%s", oip->str);
-                      NewContLine ();
-                      gb_AddString ("/db_xref=\"", seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES);
-                    }
-                  }
-                  */
-                } else if (dbt != NULL) {
-                  pbsp = BioseqFind (sip);
-                  if (pbsp != NULL && pbsp->id != NULL && pbsp->id->next == NULL) {
-                    if (SeqIdWrite (sip, seqid, PRINTID_REPORT, sizeof (seqid)) != NULL) {
-                      FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
-                                        FALSE, FALSE, TILDE_IGNORE);
-                      FF_www_protein_id(ajp, ffstring, seqid);
-                      FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-                    }
-                  }
-                }
-              }
-            }
-          } else {
-            if (sip->choice == SEQID_GI) {
-              gi = sip->data.intvalue;
-              if (GetAccnVerFromServer (gi, seqid)) {
-                if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
-                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
-                                    FALSE, FALSE, TILDE_IGNORE);
-                  FF_www_protein_id(ajp, ffstring, seqid);
-                  FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-                } else {
-                  ajp->relModeError = TRUE;
-                }
-              } else {
-                sip = GetSeqIdForGI(gi);
-                if (sip != NULL && SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
-                  if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
-                    FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
-                                    FALSE, FALSE, TILDE_IGNORE);
-                    FF_www_protein_id(ajp, ffstring, seqid);
-                    FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-                  } else {
-                    ajp->relModeError = TRUE;
-                  }
-                } else if (! ajp->flags.dropIllegalQuals) {
-                  sprintf (seqid, "%ld", (long) gi);
-                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
-                                    FALSE, FALSE, TILDE_IGNORE);
-                  FF_www_protein_id(ajp, ffstring, seqid);
-                  FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-                } else {
-                  ajp->relModeError = TRUE;
-                }
-              }
-
-              sprintf (seqid, "%ld", (long) gi);
-              FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-              FF_www_db_xref(ajp, ffstring, "GI", seqid);
-              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) {
-                FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
-                                  FALSE, FALSE, TILDE_IGNORE);
-                FF_www_protein_id(ajp, ffstring, seqid);
-                FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-              } else {
-                ajp->relModeError = TRUE;
-              }
-
-              gi = GetGIForSeqId (sip);
-              if (gi > 0) {
-                sprintf (seqid, "%ld", (long) gi);
-                FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-                FF_www_db_xref(ajp, ffstring, "GI", seqid);
-                FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-              }
-            }
-          }
-        }
-        break;
-
-      case Qual_class_translation :
-        if (qvp [idx].ble) {
-          if ((prod == NULL && ajp->transIfNoProd) || ajp->alwaysTranslCds) {
-            bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
-            if (bs != NULL) {
-              str = BSMerge (bs, NULL);
-              bs = BSFree (bs);
-              if (str != NULL) {
-                ptr = str;
-                ch = *ptr;
-                while (ch != '\0') {
-                  *ptr = TO_UPPER (ch);
-                  ptr++;
-                  ch = *ptr;
-                }
-                prtlen = StringLen (str);
-                if (prtlen > 1) {
-                   if (str [prtlen - 1] == '*') {
-                     str [prtlen - 1] = '\0';
-                   }
-                }
-                if (! StringHasNoText (str)) {
-                  FFAddTextToString(ffstring, "/translation=\"", str, "\"", 
-                                    FALSE, TRUE, TILDE_TO_SPACES);
-                  FFAddOneChar(ffstring, '\n', FALSE);
-                }
-                MemFree (str);
-              }
-            } else {
-              ajp->relModeError = TRUE;
-            }
-          } else if (prod != NULL) {
-            len = SeqLocLen (sfp->product);
-            if (len > 0) {
-              if (SeqLocStart (location) == 0 || SeqLocStop (location) == bsp->length - 1) {
-                at_end = TRUE;
-              }
-              str = (CharPtr) MemNew ((size_t) (len + 1) * sizeof (Char));
-              protein_seq = str;
-              if (ajp->flags.iupacaaOnly) {
-                code = Seq_code_iupacaa;
-              } else {
-                code = Seq_code_ncbieaa;
-              }
-              spp = SeqPortNewByLoc (sfp->product, code);
-              if (spp != NULL) {
-                SeqPortSet_do_virtual (spp, TRUE);
-                while ((residue = SeqPortGetResidue (spp)) != SEQPORT_EOF) {
-                  if (! (IS_residue (residue))) continue;
-                  if (residue == INVALID_RESIDUE) {
-                    residue = (Uint1) 'X';
-                  }
-                  *protein_seq = residue;
-                  protein_seq++;
-                }
-                /*
-                if (at_end && StringLen (str) < GENPEPT_MIN) {
-                  str = MemFree (str);
-                }
-                */
-                if (! StringHasNoText (str)) {
-                  FFAddTextToString(ffstring, "/translation=\"", str, "\"", 
-                                    FALSE, TRUE, TILDE_TO_SPACES);
-                  FFAddOneChar(ffstring, '\n', FALSE);
-                }
-                MemFree (str);
-              } else {
-                ajp->relModeError = TRUE;
-              }
-              SeqPortFree (spp);
-            } else {
-              ajp->relModeError = TRUE;
-            }
-          }
-        }
-        break;
-      
-      case Qual_class_transcription :
-        if (qvp [idx].ble) {
-          if (ajp->showTranscript) {
-            str = GetSequenceByFeature (sfp);
-            if (str != NULL) {
-              ptr = str;
-              ch = *ptr;
-              while (ch != '\0') {
-                *ptr = TO_UPPER (ch);
-                ptr++;
-                ch = *ptr;
-              }
-              if (! StringHasNoText (str)) {
-                FFAddTextToString(ffstring, "/transcription=\"", str, "\"", 
-                                  FALSE, TRUE, TILDE_TO_SPACES);
-                FFAddOneChar(ffstring, '\n', FALSE);
-              }
-              MemFree (str);
-            }
-          }
-        }
-        break;
-      
-      case Qual_class_peptide :
-        if (qvp [idx].ble) {
-          if (ajp->showPeptide) {
-            str = GetSequenceByFeature (sfp);
-            if (str != NULL) {
-              ptr = str;
-              ch = *ptr;
-              while (ch != '\0') {
-                *ptr = TO_UPPER (ch);
-                ptr++;
-                ch = *ptr;
-              }
-              if (! StringHasNoText (str)) {
-                FFAddTextToString(ffstring, "/peptide=\"", str, "\"", 
-                                  FALSE, TRUE, TILDE_TO_SPACES);
-                FFAddOneChar(ffstring, '\n', FALSE);
-              }
-              MemFree (str);
-            }
-          }
-        }
-        break;
-      
-      case Qual_class_illegal :
-        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
-          str = (CharPtr) vnp->data.ptrvalue;
-          if (str != NULL) {
-            FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_TO_SPACES);
-            FFAddNewLine(ffstring);
-          }
-        }
-        break;
-
-      case Qual_class_note :
-        if (! ajp->flags.goQualsToNote) {
-
-          /* in sequin_mode and dump_mode in RefSeq, GO terms show up as separate /qualifiers */
-
-          for (j = 0, jdx = feat_note_order [j]; jdx != 0; j++, jdx = feat_note_order [j]) {
-            switch (asn2gnbk_featur_quals [jdx].qualclass) {
-
-              case Qual_class_go :
-                if (qvp [jdx].ufp != NULL) {
-                  for (entry = qvp [jdx].ufp; entry != NULL; entry = entry->next) {
-                    if (entry == NULL || entry->choice != 11) break;
-                    ufp = (UserFieldPtr)  entry->data.ptrvalue;
-                    str = GetGOtext (ufp);
-                    if (! StringHasNoText (str)) {
-                      FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[jdx].name, "=",
-                                        FALSE, TRUE, TILDE_IGNORE);
-                      FFAddTextToString(ffstring, "\"", str, "\"", 
-                                        FALSE, FALSE, TILDE_IGNORE);
-                      FFAddOneChar(ffstring, '\n', FALSE);
-                    }
-                    MemFree (str);
-                  }
-                }
-                break;
-
-              default :
-                break;
-            }
-          }
-        }
-
-        /*head = NULL;*/
-        notestr = NULL;
-        prefix = NULL;
-        add_period = FALSE;
-        suppress_period = FALSE;
-        lasttype = NULL;
-        isTRNA = TRUE;
-        
-
-#ifdef DISPLAY_STRINGS
-        s_DisplayQVP (qvp, feat_note_order);
-#endif
-        for (j = 0, jdx = feat_note_order [j]; jdx != 0; j++, jdx = feat_note_order [j]) {
-          switch (asn2gnbk_featur_quals [jdx].qualclass) {
-
-            case Qual_class_string :
-              if (! StringHasNoText (qvp [jdx].str)) {
-                if (jdx == FTQUAL_figure) {
-                  if (!IsEllipsis (qvp [jdx].str))
-                    s_RemovePeriodFromEnd (qvp [jdx].str);
-                  sprintf (buf, "This sequence comes from %s", qvp [jdx].str);
-                  FFAddString_NoRedund (unique, prefix, buf, NULL);
-                  add_period = FALSE;
-                } else if (jdx == FTQUAL_maploc) {
-                  if (!IsEllipsis (qvp [jdx].str))
-                    s_RemovePeriodFromEnd (qvp [jdx].str);
-                  sprintf (buf, "Map location %s", qvp [jdx].str);
-                  FFAddString_NoRedund (unique, prefix, buf, NULL);
-                  add_period = FALSE;
-                } else if (jdx == FTQUAL_seqfeat_note) {
-                  str = StringSave (qvp [jdx].str);
-                  TrimSpacesAndJunkFromEnds (str, TRUE);
-                  if (! IsEllipsis (str))
-                    add_period = s_RemovePeriodFromEnd (str);
-                  /*  NOTE -- The following function call cleans up some strings
-                      (i.e., U34661 & U31565) but should be commented back
-                      in only if the problem can't be fixed upstream of here
-
-                  s_StringCleanup(str);
-
-                  */
-                  FFAddString_NoRedund (unique, prefix, str, NULL);
-                  MemFree (str);
-                  if (hadProtDesc) {
-                    suppress_period = TRUE;
-                  }
-                } else if (jdx == FTQUAL_prot_note) {
-                  str = StringSave (qvp [jdx].str);
-                  TrimSpacesAndJunkFromEnds (str, TRUE);
-                  if (! IsEllipsis (str))
-                    s_RemovePeriodFromEnd (str);
-                  FFAddString_NoRedund (unique, prefix, str, NULL);
-                  MemFree (str);
-                  add_period = FALSE;
-                } else if (jdx == FTQUAL_prot_desc) {
-                  str = StringSave (qvp [jdx].str);
-                  TrimSpacesAndJunkFromEnds (str, TRUE);
-                  if (! IsEllipsis (str))
-                    add_period = s_RemovePeriodFromEnd (str);
-                  FFAddString_NoRedund (unique, prefix, str, NULL);
-                  MemFree (str);
-                  hadProtDesc = TRUE; /* gi|347886|gb|M96268.1|ECOUBIA */
-                } else {
-                  if (! IsEllipsis (qvp [jdx].str)) {
-                    s_RemovePeriodFromEnd (qvp [jdx].str);
-                  }
-                  FFAddString_NoRedund (unique, prefix, qvp [jdx].str, NULL);
-                  add_period = FALSE;
-                }
-                prefix = "; ";
-              }
-              break;
-
-            case Qual_class_locus_tag :
-              if (! StringHasNoText (qvp [jdx].str)) {
-                if (! IsEllipsis (qvp [jdx].str)) {
-                  s_RemovePeriodFromEnd (qvp [jdx].str);
-                }
-                FFAddTextToString (unique, prefix, "locus_tag: ", NULL, FALSE, FALSE, TILDE_IGNORE);
-                FFAddString_NoRedund (unique, NULL, qvp [jdx].str, NULL);
-                prefix = "; ";
-                add_period = FALSE;
-              }
-              break;
-
-            case Qual_class_go :
-              if (ajp->flags.goQualsToNote && qvp [jdx].ufp != NULL) {
-                for (entry = qvp [jdx].ufp; entry != NULL; entry = entry->next) {
-                  if (entry == NULL || entry->choice != 11) break;
-                  ufp = (UserFieldPtr)  entry->data.ptrvalue;
-                  str = GetGOtext (ufp);
-                  if (! StringHasNoText (str)) {
-                    if (StringCmp (prefix, "; ") == 0) {
-                      prefix = ";\n";
-                    }
-                    FFAddTextToString (unique, prefix, asn2gnbk_featur_quals[jdx].name, ": ", FALSE, FALSE, TILDE_IGNORE);
-                    FFAddTextToString(unique, NULL, str, NULL, FALSE, FALSE, TILDE_IGNORE);
-                  }
-                  MemFree (str);
-                  prefix = "; ";
-                  add_period = FALSE;
-                }
-              }
-              break;
-
-            case Qual_class_method :
-              if (! StringHasNoText (qvp [jdx].str)) {
-                if ( FFEmpty(unique) ) {
-                  prefix = "Method: ";
-                } else {
-                  prefix = "; Method: ";
-                }
-                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, NULL);
-                prefix = "; ";
-                add_period = FALSE;
-              }
-              break;
-
-            case Qual_class_valnode :
-              for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
-                str = (CharPtr) vnp->data.ptrvalue;
-                if (! StringHasNoText (str)) {
-                  FFAddString_NoRedund (unique, prefix, str, NULL);
-                  prefix = "; ";
-                  add_period = FALSE;
-                }
-              }
-              break;
-
-            case Qual_class_gene_syn :
-              numsyns = 0;
-              for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
-                str = (CharPtr) vnp->data.ptrvalue;
-                if (! StringHasNoText (str)) {
-                  numsyns++;
-                }
-              }
-              if (numsyns > 0) {
-                if (numsyns > 1) {
-                  FFAddTextToString (unique, prefix, "synonyms: ", NULL, FALSE, FALSE, TILDE_IGNORE);
-                } else {
-                  FFAddTextToString (unique, prefix, "synonym: ", NULL, FALSE, FALSE, TILDE_IGNORE);
-                }
-                prefix = NULL;
-                for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
-                  str = (CharPtr) vnp->data.ptrvalue;
-                  if (! StringHasNoText (str)) {
-                    FFAddTextToString (unique, prefix, str, NULL, FALSE, FALSE, TILDE_IGNORE);
-                    prefix = ", ";
-                  }
-                }
-                prefix = "; ";
-                add_period = FALSE;
-              }
-              break;
-
-            case Qual_class_region :
-              if (! StringHasNoText (qvp [jdx].str)) {
-                if ( FFEmpty(unique) ) {
-                  prefix = "Region: ";
-                } else {
-                  prefix = "; Region: ";
-                }
-#ifdef ASN2GNBK_STRIP_NOTE_PERIODS
-                FFAddTextToString(unique, prefix, qvp [jdx].str, NULL, FALSE, FALSE, TILDE_IGNORE);
-#else
-                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, NULL);
-#endif
-                prefix = "; ";
-                add_period = FALSE;
-              }
-              break;
-
-            case Qual_class_site :
-              if (! StringHasNoText (qvp [jdx].str)) {
-                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, " site");
-                add_period = FALSE;
-                prefix = "\n";
-              }
-              break;
-
-            case Qual_class_bond :
-              if (! StringHasNoText (qvp [jdx].str)) {
-                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, " bond");
-                add_period = FALSE;
-                prefix = "\n";
-              }
-              break;
-
-            case Qual_class_protnames :
-              /* process gene sgml for check against subsequent protein names */
-              start = NULL;
-              if (! StringHasNoText (qvp [FTQUAL_gene].str)) {
-                if (is_journalscan) {
-                  ascii_len = Sgml2AsciiLen (qvp [FTQUAL_gene].str);
-                  start = ascii = MemNew ((size_t) (10 + ascii_len));
-                  if (start != NULL) {
-                    ascii = Sgml2Ascii (qvp [FTQUAL_gene].str, ascii, ascii_len + 1);
-                  }
-                } else {
-                  start = StringSaveNoNull (qvp [FTQUAL_gene].str);
-                }
-              }
-              for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
-                str = (CharPtr) vnp->data.ptrvalue;
-                if (! StringHasNoText (str)) {
-                  /* case sensitive - gi|4973426|gb|AF148501.1|AF148501 */
-                  /* check with and without sgml conversion */
-                  if (StringCmp (start, str) != 0 &&
-                      StringCmp (qvp [FTQUAL_gene].str, str) != 0) {
-                    if (! StringStr (qvp [FTQUAL_prot_desc].str, str)) {
-                      /* if (NotInGeneSyn (str, gene_syn)) { */
-                        FFAddString_NoRedund (unique, prefix, str, NULL);
-                        prefix = "; ";
-                        add_period = FALSE;
-                      /* } */
-                    }
-                  }
-                }
-              }
-              MemFree (start);
-              break;
-
-            case Qual_class_xtraprds :
-              gbq = qvp [jdx].gbq;
-              if (lasttype == NULL && gbq != NULL) {
-                lasttype = gbq->qual;
-              }
-              while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-                if (! StringHasNoText (gbq->val)) {
-                  if (StringCmp(gbq->val,qvp[FTQUAL_gene].str) != 0 &&
-                      StringCmp(gbq->val,qvp[FTQUAL_product].str) != 0) {
-                    if (!isTRNA || !StringStr (gbq->val, "RNA")) {
-                      FFAddString_NoRedund (unique, prefix, gbq->val, NULL);
-                      prefix = "; ";
-                      add_period = FALSE;
-                    }
-                  }
-                }
-                gbq = gbq->next;
-              }
-              break;
-
-            case Qual_class_its :
-              str = qvp [jdx].str;
-              if (! StringHasNoText (str)) {
-                if (sfp->comment == NULL || StringStr (sfp->comment, str) == NULL) {
-                  FFAddString_NoRedund (unique, prefix, str, NULL);
-                  prefix = "; ";
-                  add_period = FALSE;
-                }
-              }
-              break;
-
-            case Qual_class_trna_codons :
-              trna = qvp [jdx].trp;
-              if (trna) {
-                numcodons = ComposeCodonsRecognizedString (trna, numbuf, sizeof (numbuf));
-                if (numcodons < 1 || StringHasNoText (numbuf)) {
-                } else if (numcodons == 1) {
-                  isTRNA = TRUE;
-                  sprintf (buf, "codon recognized: %s", numbuf);
-                  if (StringStr (qvp [FTQUAL_seqfeat_note].str, buf) == NULL) {
-                    FFAddString_NoRedund (unique, prefix, "codon recognized: ", numbuf);
-                    prefix = "; ";
-                  }
-                } else {
-                  isTRNA = TRUE;
-                  FFAddString_NoRedund (unique, prefix, "codons recognized: ", numbuf);
-                  prefix = "; ";
-                  add_period = FALSE;
-                }
-              }
-              break;
-
-            case Qual_class_model_ev :
-              uop = qvp [jdx].uop;
-              if (uop != NULL) {
-                str = NULL;
-                VisitUserObjectsInUop (sfp->ext, (Pointer) &str, GetStrFormRNAEvidence);
-                if (! StringHasNoText (str)) {
-                  FFAddString_NoRedund (unique, prefix, str, NULL);
-                  prefix = "; ";
-                  add_period = FALSE;
-                }
-              }
-              break;
-
-            case Qual_class_seq_id :
-              sip = qvp [jdx].sip;
-              if (sip != NULL) {
-                /* should always be found above for protein_id or transcript_id
-                prod = BioseqFind (sip);
-                */
-                if (prod != NULL) {
-                  choice = 0;
-                  for (sip = prod->id; sip != NULL; sip = sip->next) {
-                    if (sip->choice == SEQID_GENBANK ||
-                        sip->choice == SEQID_EMBL ||
-                        sip->choice == SEQID_DDBJ ||
-                        sip->choice == SEQID_OTHER ||
-                        sip->choice == SEQID_TPG ||
-                        sip->choice == SEQID_TPE ||
-                        sip->choice == SEQID_TPD) {
-                      choice = sip->choice;
-                      if (SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
-                        FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
-                                          FALSE, FALSE, TILDE_IGNORE);
-                      }
-                    } else if (sip->choice == SEQID_GI) {
-                      if (choice == 0) {
-                        sprintf (seqid, "%ld", (long) sip->data.intvalue);
-                        FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
-                                          FALSE, FALSE, TILDE_IGNORE);
-                      }
-                    }
-                  }
-                } else {
-                  if (sip->choice == SEQID_GI) {
-                    gi = sip->data.intvalue;
-                    if (GetAccnVerFromServer (gi, seqid)) {
-                      if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
-                        FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
-                                          FALSE, FALSE, TILDE_IGNORE);
-                      }
-                    } else {
-                      sip = GetSeqIdForGI(gi);
-                      if (sip != NULL && SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
-                        if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
-                          FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
-                                          FALSE, FALSE, TILDE_IGNORE);
-                        }
-                      } else if (! ajp->flags.dropIllegalQuals) {
-                        sprintf (seqid, "%ld", (long) gi);
-                          FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
-                                          FALSE, FALSE, TILDE_IGNORE);
-                      }
-                    }
-                  } else if (SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
-                    if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
-                          FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
-                                          FALSE, FALSE, TILDE_IGNORE);
-                    }
-                  }
-                }
-                prefix = "; ";
-                add_period = FALSE;
-              }
-              break;
-
-            default :
-              break;
-          }
-        }
-
-        if ( !FFEmpty(unique) ) {
-          notestr = FFToCharPtr(unique);
-          TrimSpacesAroundString (notestr);
-          if (add_period) {
-            if (! suppress_period) {
-              s_AddPeriodToEnd (notestr);
-            }
-          }
-
-#ifdef ASN2GNBK_STRIP_NOTE_PERIODS
-          if (! IsEllipsis (notestr))
-            s_RemovePeriodFromEnd (notestr);
-#endif
-    
-          FFAddOneString(ffstring, "/note=\"", FALSE, FALSE, TILDE_IGNORE);
-          FFAddOneString(ffstring, notestr, FALSE, TRUE, TILDE_EXPAND);
-          FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
-
-          MemFree (notestr);
-          /*ValNodeFreeData (head);*/
-        }
-        break;
-
-      default:
-        break;
-
-    }
-  }
-  FFRecycleString(ajp, unique);
-}
-
-
-
-static void FF_asn2gb_www_featkey (
-  StringItemPtr ffstring,
-  CharPtr key,
-  SeqLocPtr slp,
-  Int4 from,
-  Int4 to,
-  Uint1 strand,
-  Uint4 itemID
-)
-
-{
-  BioseqPtr  bsp;
-  Int4       gi = 0;
-  SeqIdPtr   sip;
-  Boolean    is_aa = FALSE;
-  Char gi_buf[16];
-  Char itemID_buf[16];
-
-  bsp = BioseqFindFromSeqLoc (slp);
-  if (bsp != NULL) {
-    is_aa = ISA_aa (bsp->mol);
-    for (sip = bsp->id; sip != NULL; sip = sip->next) {
-      if (sip->choice == SEQID_GI) {
-        gi = (Int4) sip->data.intvalue;
-      }
-    }
-  }
-
-  sprintf(gi_buf, "%ld", (long)gi);
-  sprintf(itemID_buf, "%ld", (long)itemID);
-
-
-  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);
-  FFAddOneString(ffstring, "&itemID=", FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, itemID_buf, FALSE, FALSE, TILDE_IGNORE);
-  
-
-  if ( is_aa ) {
-    FFAddOneString(ffstring, "&view=gpwithparts>", FALSE, FALSE, TILDE_IGNORE);
-  } else {
-    FFAddOneString(ffstring, "&view=gbwithparts>", FALSE, FALSE, TILDE_IGNORE);
-  }
-
-  FFAddOneString(ffstring, key, FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-}
-
-
-
-static CharPtr FormatFeatureBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  Uint1              aa;
-  IntAsn2gbJobPtr    ajp;
-  Asn2gbSectPtr      asp;
-  Int2               bondidx;
-  BioseqPtr          bsp;
-  BioseqSetPtr       bssp;
-  Choice             cbaa;
-  CodeBreakPtr       cbp;
-  BioseqPtr          cdna;
-  SeqFeatPtr         cds;
-  Char               ch;
-  Uint1              code = Seq_code_ncbieaa;
-  CdRegionPtr        crp;
-  SeqMgrDescContext  dcontext;
-  SeqMgrFeatContext  fcontext;
-  Uint1              featdeftype;
-  Uint1              from;
-  GBQualPtr          gbq;
-  GBFeaturePtr       gbfeat = NULL;
-  GBSeqPtr           gbseq;
-  SeqMgrFeatContext  gcontext;
-  ValNodePtr         gcp;
-  SeqFeatPtr         gene = NULL;
-  ValNodePtr         gene_syn = NULL;
-  GeneRefPtr         grp;
-  IntCdsBlockPtr     icp;
-  Uint2              idx;
-  IntFeatBlockPtr    ifp;
-  ValNodePtr         illegal = NULL;
-  ImpFeatPtr         imp = NULL;
-  IndxPtr            index;
-  Boolean            is_gps = FALSE;
-  Boolean            is_journalscan = FALSE;
-  Boolean            is_other = FALSE;
-  CharPtr            key;
-  CharPtr            lasttype = NULL;
-  Int4               left = -1;
-  SeqLocPtr          loc = NULL;
-  SeqLocPtr          location = NULL;
-  SeqLocPtr          locforgene = NULL;
-  SeqMgrFeatContext  mcontext;
-  MolInfoPtr         mip;
-  SeqFeatPtr         mrna;
-  SeqLocPtr          newloc;
-  Boolean            noLeft;
-  Boolean            noRight;
-  SeqMgrFeatContext  ocontext;
-  SeqEntryPtr        oldscope;
-  SeqFeatPtr         operon = NULL;
-  Uint2              partial;
-  SeqMgrFeatContext  pcontext;
-  BioseqPtr          prd;
-  CharPtr            precursor_comment = NULL;
-  BioseqPtr          prod = NULL;
-  SeqFeatPtr         prot;
-  Boolean            protein = FALSE;
-  Char               protein_pid_g [32];
-  ProtRefPtr         prp;
-  ProtRefPtr         prpxref;
-  Boolean            pseudo = FALSE;
-  CharPtr            ptr;
-  Int2               qualclass;
-  QualValPtr         qvp;
-  Uint1              residue;
-  Int4               right = -1;
-  RnaRefPtr          rrp;
-  SeqCodeTablePtr    sctp;
-  SeqDescrPtr        sdp;
-  SeqEntryPtr        sep;
-  Uint1              seqcode;
-  SeqFeatPtr         sfp;
-  Uint1              shift;
-  SeqIdPtr           sip;
-  Int2               siteidx;
-  SeqMapTablePtr     smtp;
-  Boolean            split;
-  CharPtr            str;
-  Uint1              strand = Seq_strand_unknown;
-  BioseqPtr          target;
-  CharPtr            tmp;
-  tRNAPtr            trna;
-  BioseqPtr          unlockme = NULL;
-  ValNodePtr         vnp;
-  StringItemPtr      ffstring;
-
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-  target = asp->target;
-  bsp = asp->bsp;
-  if (target == NULL || bsp == NULL) return NULL;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-  qvp = afp->qvp;
-  if (qvp == NULL) return NULL;
-
-  ffstring = FFGetString(ajp);
-  if ( ffstring == NULL ) return NULL;
-
-  if (ajp->index) {
-    index = &asp->index;
-  } else {
-    index = NULL;
-  }
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-  
-  protein_pid_g [0] = '\0';
-
-  /* all features in this list are known to be valid for the designated mode */
-
-  sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
-  if (sfp == NULL) return NULL;
-
-  /* may need to map location between aa and dna */
-
-  ifp = (IntFeatBlockPtr) bbp;
-  if (ifp->mapToNuc) {
-
-    /* map mat_peptide, etc., to nucleotide coordinates */
-
-    sip = SeqLocId (sfp->location);
-    prd = BioseqFind (sip);
-    cds = SeqMgrGetCDSgivenProduct (prd, NULL);
-    CheckSeqLocForPartial (sfp->location, &noLeft, &noRight);
-    location = aaFeatLoc_to_dnaFeatLoc (cds, sfp->location);
-    SetSeqLocPartial (location, noLeft, noRight);
-    locforgene = location;
-    loc = location;
-
-  } else if (ifp->mapToProt) {
-
-    /* map CDS to protein product coordinates */
-
-    sip = SeqLocIdForProduct (sfp->product);
-    prd = BioseqFind (sip);
-    cds = SeqMgrGetCDSgivenProduct (prd, NULL);
-    location = dnaLoc_to_aaLoc (cds, sfp->location, TRUE, NULL, FALSE);
-    SetSeqLocPartial (location, FALSE, FALSE);
-    locforgene = sfp->location;
-    loc = location;
-
-  } else if (ifp->mapToGen) {
-
-    /* map CDS from cDNA to genomic Bioseq */
-
-    cdna = BioseqFindFromSeqLoc (sfp->location);
-    mrna = SeqMgrGetRNAgivenProduct (cdna, &mcontext);
-    CheckSeqLocForPartial (sfp->location, &noLeft, &noRight);
-    location = productLoc_to_locationLoc (mrna, sfp->location);
-    SetSeqLocPartial (location, noLeft, noRight);
-    locforgene = location;
-    loc = location;
-
-  } else if (ifp->mapToMrna) {
-
-    /* map gene from genomic to cDNA Bioseq */
-
-    sep = SeqMgrGetSeqEntryForData (bsp);
-    location = CreateWholeInterval (sep);
-    SetSeqLocPartial (location, FALSE, FALSE);
-    locforgene = location;
-    loc = location;
-
-  } else if (ifp->mapToPep) {
-
-    /* map protein processing from precursor to subpeptide Bioseq */
-
-    sep = SeqMgrGetSeqEntryForData (bsp);
-    location = CreateWholeInterval (sep);
-    SetSeqLocPartial (location, FALSE, FALSE);
-    locforgene = location;
-    loc = location;
-
-  } else {
-
-    /* no aa-dna or dna-aa mapping, just use location */
-
-    location = sfp->location;
-    locforgene = sfp->location;
-  }
-  if (location == NULL) return NULL;
-
-  sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
-  if (sep == NULL && IS_Bioseq_set (sep)) {
-    bssp = (BioseqSetPtr) sep->data.ptrvalue;
-    if (bssp != NULL && bssp->_class == BioseqseqSet_class_gen_prod_set) {
-      is_gps = TRUE;
-    }
-  }
-
-  for (sip = bsp->id; sip != NULL; sip = sip->next) {
-    if (sip->choice == SEQID_OTHER) {
-      is_other = TRUE;
-    } else if (sip->choice == SEQID_GIBBSQ ||
-               sip->choice == SEQID_GIBBMT ||
-               sip->choice == SEQID_GIIM) {
-      is_journalscan = TRUE;
-    }
-  }
-
-  featdeftype = fcontext.featdeftype;
-  if (featdeftype < FEATDEF_GENE || featdeftype >= FEATDEF_MAX) {
-    featdeftype = FEATDEF_BAD;
-  }
-  key = FindKeyFromFeatDefType (featdeftype, TRUE);
-
-  if (afp->format == GENPEPT_FMT && ISA_aa (bsp->mol)) {
-    if (featdeftype == FEATDEF_REGION) {
-      key = "Region";
-    } else if (featdeftype == FEATDEF_BOND) {
-      key = "Bond";
-    } else if (featdeftype == FEATDEF_SITE) {
-      key = "Site";
-    }
-    if (ifp->mapToPep) {
-      if (featdeftype >= FEATDEF_preprotein && featdeftype <= FEATDEF_transit_peptide_aa) {
-        key = "Precursor";
-      }
-    }
-  }
-
-  /* deal with unmappable impfeats */
-
-  if (featdeftype == FEATDEF_BAD && fcontext.seqfeattype == SEQFEAT_IMP) {
-    imp = (ImpFeatPtr) sfp->data.value.ptrvalue;
-    if (imp != NULL) {
-      key = imp->key;
-    }
-  }
-
-  FFStartPrint(ffstring, afp->format, 5, 21, NULL, 0, 5, 21, "FT", /* ifp->firstfeat */ FALSE);
-  if (ajp->ajp.slp != NULL) {
-    FFAddOneString(ffstring, key, FALSE, FALSE, TILDE_IGNORE);
-  } else if ( GetWWW(ajp) /* && SeqMgrGetParentOfPart (bsp, NULL) == NULL */ ) {
-    FF_asn2gb_www_featkey (ffstring, key, sfp->location, fcontext.left + 1, fcontext.right + 1, fcontext.strand, fcontext.itemID);
-  } else {
-    FFAddOneString(ffstring, key, FALSE, FALSE, TILDE_IGNORE);
-  }
-  FFAddNChar(ffstring, ' ', 21 - 5 - StringLen(key), FALSE);
-
-  if (gbseq != NULL) {
-    gbfeat = GBFeatureNew ();
-    if (gbfeat != NULL) {
-      gbfeat->key = StringSave (key);
-    }
-  }
-
-  if (imp == NULL || StringHasNoText (imp->loc)) {
-
-    
-    if (ajp->ajp.slp != NULL) {
-      sip = SeqIdParse ("lcl|dummy");
-      left = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_LEFT_END);
-      right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END);
-      strand = SeqLocStrand (ajp->ajp.slp);
-      split = FALSE;
-      newloc = SeqLocReMapEx (sip, ajp->ajp.slp, location, 0, FALSE, ajp->masterStyle);
-      /*
-      newloc = SeqLocCopyRegion (sip, location, bsp, left, right, strand, &split);
-      */
-      SeqIdFree (sip);
-      if (newloc == NULL) return NULL;
-      A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
-      str = FlatLoc (ajp, target, newloc, ajp->masterStyle);
-      SeqLocFree (newloc);
-    } else {
-      str = FlatLoc (ajp, target, location, ajp->masterStyle);
-    }
-  } else {
-    str = StringSave (imp->loc);
-  }
-  if ( GetWWW(ajp) ) {
-    FF_www_featloc (ffstring, str);
-  } else {
-    FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
-  }
-
-  if (gbseq != NULL) {
-    if (gbfeat != NULL) {
-      gbfeat->location = StringSave (str);
-      if (ajp->masterStyle) {
-        AddIntervalsToGbfeat (gbfeat, location, target);
-      } else {
-        AddIntervalsToGbfeat (gbfeat, location, NULL);
-      }
-    }
-  }
-
-  MemFree (str);
-
-  /* populate qualifier table from feature fields */
-
-  /*
-  if (sfp->partial == TRUE)
-    sfp->partial = FlatAnnotPartial(sfp, use_product);
-  */
-
-  if (sfp->partial) {
-    partial = SeqLocPartialCheck (location);
-    if (partial == SLP_COMPLETE /* || partial > SLP_OTHER */ ) {
-      qvp [FTQUAL_partial].ble = TRUE;
-    }
-    if (LookForFuzz (location)) {
-      qvp [FTQUAL_partial].ble = FALSE;
-    }
-    if (imp != NULL) {
-      if (StringChr (imp->loc, '<') != NULL || StringChr (imp->loc, '>') != NULL) {
-        qvp [FTQUAL_partial].ble = FALSE;
-      }
-    }
-
-    /* hide unclassified /partial in RELEASE_MODE and ENTREZ_MODE */
-
-    if (ajp->mode == RELEASE_MODE || ajp->mode == ENTREZ_MODE) {
-      qvp [FTQUAL_partial].ble = FALSE;
-    }
-    /*
-    if (ajp->flags.checkQualSyntax) {
-      switch (featdeftype) {
-      case FEATDEF_conflict:
-      case FEATDEF_mutation:
-      case FEATDEF_N_region:
-      case FEATDEF_polyA_site:
-        qvp [FTQUAL_partial].ble = FALSE;
-        break;
-      default:
-        break;
-      }
-    }
-    */
-  }
-  if (ifp->mapToProt) {
-    qvp [FTQUAL_partial].ble = FALSE;
-  }
-
-  if (sfp->pseudo) {
-    pseudo = TRUE;
-  }
-
-  if (fcontext.seqfeattype == SEQFEAT_GENE) {
-    grp = (GeneRefPtr) sfp->data.value.ptrvalue;
-    if (grp != NULL) {
-      if (! StringHasNoText (grp->locus)) {
-        qvp [FTQUAL_gene].str = grp->locus;
-        qvp [FTQUAL_locus_tag].str = grp->locus_tag;
-        qvp [FTQUAL_gene_desc].str = grp->desc;
-        qvp [FTQUAL_gene_syn].vnp = grp->syn;
-      } else if (grp->locus_tag != NULL) {
-        qvp [FTQUAL_locus_tag].str = grp->locus_tag;
-        qvp [FTQUAL_gene_desc].str = grp->desc;
-        qvp [FTQUAL_gene_syn].vnp = grp->syn;
-      } else if (! StringHasNoText (grp->desc)) {
-        qvp [FTQUAL_gene].str = grp->desc;
-        qvp [FTQUAL_gene_syn].vnp = grp->syn;
-      } else if (grp->syn != NULL) {
-        vnp = grp->syn;
-        qvp [FTQUAL_gene].str = (CharPtr) vnp->data.ptrvalue;
-        vnp = vnp->next;
-        qvp [FTQUAL_gene_syn].vnp = vnp;
-      }
-      qvp [FTQUAL_gene_map].str = grp->maploc;
-      qvp [FTQUAL_gene_allele].str = grp->allele;
-      qvp [FTQUAL_gene_xref].vnp = grp->db;
-      if (grp->pseudo) {
-        pseudo = TRUE;
-      }
-    }
-    if (! ajp->flags.geneSynsToNote) {
-      qvp [FTQUAL_gene_syn_refseq].vnp = qvp [FTQUAL_gene_syn].vnp;
-      qvp [FTQUAL_gene_syn].vnp = NULL;
-    }
-    operon = SeqMgrGetOverlappingOperon (locforgene, &ocontext);
-    if (operon != NULL) {
-      for (gbq = operon->qual; gbq != NULL; gbq = gbq->next) {
-        if (StringCmp (gbq->qual, "operon") == 0) {
-          qvp [FTQUAL_operon].gbq = gbq;
-        }
-      }
-    }
-
-  } else {
-
-    grp = SeqMgrGetGeneXref (sfp);
-    if (grp != NULL) {
-      qvp [FTQUAL_gene_xref].vnp = grp->db;
-    }
-    if (grp == NULL) {
-      sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
-      oldscope = SeqEntrySetScope (sep);
-      gene = SeqMgrGetOverlappingGene (locforgene, &gcontext);
-      SeqEntrySetScope (oldscope);
-      if (gene != NULL) {
-        qvp [FTQUAL_gene_note].str = gene->comment;
-        grp = (GeneRefPtr) gene->data.value.ptrvalue;
-        if (gene->pseudo) {
-          pseudo = TRUE;
-        }
-        if (grp != NULL && grp->db != NULL) {
-          qvp [FTQUAL_gene_xref].vnp = grp->db;
-        } else {
-          qvp [FTQUAL_gene_xref].vnp = gene->dbxref;
-        }
-      }
-    }
-    if (grp != NULL && grp->pseudo) {
-      pseudo = TRUE;
-    }
-    if (grp != NULL && (! SeqMgrGeneIsSuppressed (grp)) &&
-        (fcontext.featdeftype != FEATDEF_repeat_region || gene == NULL)) {
-      if (! StringHasNoText (grp->locus)) {
-        qvp [FTQUAL_gene].str = grp->locus;
-        qvp [FTQUAL_locus_tag].str = grp->locus_tag;
-        gene_syn = grp->syn;
-      } else if (! StringHasNoText (grp->locus_tag)) {
-        qvp [FTQUAL_locus_tag].str = grp->locus_tag;
-        gene_syn = grp->syn;
-      } else if (! StringHasNoText (grp->desc)) {
-        qvp [FTQUAL_gene].str = grp->desc;
-        gene_syn = grp->syn;
-      } else if (grp->syn != NULL) {
-        vnp = grp->syn;
-        qvp [FTQUAL_gene].str = (CharPtr) vnp->data.ptrvalue;
-        vnp = vnp->next;
-        gene_syn = vnp;
-      }
-    }
-    if (grp != NULL && fcontext.featdeftype != FEATDEF_variation) {
-      qvp [FTQUAL_gene_allele].str = grp->allele; /* now propagating /allele */
-    }
-    if (fcontext.seqfeattype != SEQFEAT_CDREGION &&
-        fcontext.seqfeattype != SEQFEAT_RNA) {
-      qvp [FTQUAL_gene_xref].vnp = NULL;
-    }
-    if (fcontext.featdeftype != FEATDEF_operon) {
-      grp = SeqMgrGetGeneXref (sfp);
-      if (grp == NULL || (! SeqMgrGeneIsSuppressed (grp))) {
-        operon = SeqMgrGetOverlappingOperon (locforgene, &ocontext);
-        if (operon != NULL) {
-          for (gbq = operon->qual; gbq != NULL; gbq = gbq->next) {
-            if (StringCmp (gbq->qual, "operon") == 0) {
-              qvp [FTQUAL_operon].gbq = gbq;
-            }
-          }
-        }
-      }
-    }
-
-    /* specific fields set here */
-
-    switch (fcontext.seqfeattype) {
-      case SEQFEAT_CDREGION :
-        if (! ifp->mapToProt) {
-          crp = (CdRegionPtr) sfp->data.value.ptrvalue;
-          if (crp != NULL) {
-
-            qvp [FTQUAL_codon_start].num = crp->frame;
-            if (qvp [FTQUAL_codon_start].num == 0) {
-              qvp [FTQUAL_codon_start].num = 1;
-            }
-            qvp [FTQUAL_transl_except].cbp = crp->code_break;
-            for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
-              seqcode = 0;
-              sctp = NULL;
-              cbaa = cbp->aa;
-              switch (cbaa.choice) {
-                case 1 :
-                  seqcode = Seq_code_ncbieaa;
-                  break;
-                case 2 :
-                  seqcode = Seq_code_ncbi8aa;
-                  break;
-                case 3 :
-                  seqcode = Seq_code_ncbistdaa;
-                  break;
-                default :
-                  break;
-              }
-              if (seqcode != 0) {
-                sctp = SeqCodeTableFind (seqcode);
-                if (sctp != NULL) {
-                  residue = cbaa.value.intvalue;
-                  if (residue != 42) {
-                    if (seqcode != Seq_code_ncbieaa) {
-                      smtp = SeqMapTableFind (seqcode, Seq_code_ncbieaa);
-                      residue = SeqMapTableConvert (smtp, residue);
-                    }
-                    if (residue == 'U') {
-                      if (ajp->flags.selenocysteineToNote) {
-                        qvp [FTQUAL_selenocysteine_note].str = "selenocysteine";
-                      } else {
-                        qvp [FTQUAL_selenocysteine].ble = TRUE;
-                      }
-                    }
-                  }
-                }
-              }
-            }
-
-            gcp = crp->genetic_code;
-            if (gcp != NULL) {
-              for (vnp = gcp->data.ptrvalue; vnp != NULL; vnp = vnp->next) {
-                if (vnp->choice == 2 && vnp->data.intvalue != 0) {
-                  qvp [FTQUAL_transl_table].num = vnp->data.intvalue;
-                }
-              }
-
-              /* suppress table 1, but always show it in GBSeqXML */
-
-              if (qvp [FTQUAL_transl_table].num == 1 && ajp->gbseq == NULL) {
-                qvp [FTQUAL_transl_table].num = 0;
-              }
-            }
-
-            if (sfp->product != NULL && SeqLocLen (sfp->product) != 0) {
-              protein = TRUE;
-            }
-            if (crp->conflict && (protein || (! sfp->excpt))) {
-              if (protein) {
-                qvp [FTQUAL_prot_conflict].str = conflict_msg;
-              } else {
-                /*
-                qvp [FTQUAL_prot_missing].str = no_protein_msg;
-                */
-              }
-            }
-          }
-
-          sip = SeqLocIdForProduct (sfp->product);
-          qvp [FTQUAL_protein_id].sip = sip;
-
-          sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
-
-          if (! ajp->alwaysTranslCds) {
-
-            /* by default only show /translation if product bioseq is within entity */
-
-            oldscope = SeqEntrySetScope (sep);
-            prod = BioseqFind (sip);
-            SeqEntrySetScope (oldscope);
-
-            if (prod == NULL && ajp->showFarTransl) {
-
-              /* but flag can override and force far /translation */
-
-              prod = BioseqLockById (sip);
-              unlockme = prod;
-            }
-          }
-
-          prp = NULL;
-
-          if (prod != NULL) {
-            for (sip = prod->id; sip != NULL; sip = sip->next) {
-              if (sip->choice == SEQID_GI) {
-                sprintf (protein_pid_g, "PID:g%ld", (long) sip->data.intvalue);
-              }
-            }
-            sdp = SeqMgrGetNextDescriptor (prod, NULL, Seq_descr_comment, &dcontext);
-            if (sdp != NULL && dcontext.level == 0) {
-              if (! StringHasNoText ((CharPtr) sdp->data.ptrvalue)) {
-                qvp [FTQUAL_prot_comment].str = (CharPtr) sdp->data.ptrvalue;
-              }
-            }
-            sdp = SeqMgrGetNextDescriptor (prod, NULL, Seq_descr_molinfo, &dcontext);
-            if (sdp != NULL && dcontext.level == 0) {
-              mip = (MolInfoPtr) sdp->data.ptrvalue;
-              if (mip != NULL && mip->tech > 1 &&
-                  mip->tech != MI_TECH_concept_trans &&
-                  mip->tech != MI_TECH_concept_trans_a) {
-                str = StringForSeqTech (mip->tech);
-                if (! StringHasNoText (str)) {
-                  qvp [FTQUAL_prot_method].str = str;
-                }
-              }
-            }
-            prot = SeqMgrGetBestProteinFeature (prod, &pcontext);
-            if (prot != NULL) {
-              prp = (ProtRefPtr) prot->data.value.ptrvalue;
-              if (prp != NULL && prp->processed < 2) {
-                qvp [FTQUAL_prot_note].str = prot->comment;
-              }
-            }
-          }
-
-          /* protein xref overrides names, but should not prevent /protein_id, etc. */
-
-          prpxref = SeqMgrGetProtXref (sfp);
-          if (prpxref != NULL) {
-            prp = prpxref;
-          }
-          if (prp != NULL) {
-            vnp = prp->name;
-            if (vnp != NULL && (! StringHasNoText ((CharPtr) vnp->data.ptrvalue))) {
-              qvp [FTQUAL_cds_product].str = (CharPtr) vnp->data.ptrvalue;
-              vnp = vnp->next;
-              qvp [FTQUAL_prot_names].vnp = vnp;
-            }
-            qvp [FTQUAL_prot_desc].str = prp->desc;
-            qvp [FTQUAL_prot_activity].vnp = prp->activity;
-            qvp [FTQUAL_prot_EC_number].vnp = prp->ec;
-          }
-
-          if (! pseudo) {
-            if (prod != NULL || ajp->transIfNoProd || ajp->alwaysTranslCds) {
-              qvp [FTQUAL_translation].ble = TRUE;
-            }
-          }
-
-          if (ifp->isCDS) {
-            icp = (IntCdsBlockPtr) ifp;
-            qvp [FTQUAL_figure].str = icp->fig;
-            qvp [FTQUAL_maploc].str = icp->maploc;
-          }
-        } else {
-          qvp [FTQUAL_coded_by].slp = sfp->location;
-
-          crp = (CdRegionPtr) sfp->data.value.ptrvalue;
-          if (crp != NULL) {
-            gcp = crp->genetic_code;
-            if (gcp != NULL) {
-              for (vnp = gcp->data.ptrvalue; vnp != NULL; vnp = vnp->next) {
-                if (vnp->choice == 2 && vnp->data.intvalue != 0) {
-                  qvp [FTQUAL_transl_table].num = vnp->data.intvalue;
-                }
-              }
-
-              /* suppress table 1 */
-
-              if (qvp [FTQUAL_transl_table].num == 1) {
-                qvp [FTQUAL_transl_table].num = 0;
-              }
-            }
-            for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
-              seqcode = 0;
-              sctp = NULL;
-              cbaa = cbp->aa;
-              switch (cbaa.choice) {
-                case 1 :
-                  seqcode = Seq_code_ncbieaa;
-                  break;
-                case 2 :
-                  seqcode = Seq_code_ncbi8aa;
-                  break;
-                case 3 :
-                  seqcode = Seq_code_ncbistdaa;
-                  break;
-                default :
-                  break;
-              }
-              if (seqcode != 0) {
-                sctp = SeqCodeTableFind (seqcode);
-                if (sctp != NULL) {
-                  residue = cbaa.value.intvalue;
-                  if (residue != 42) {
-                    if (seqcode != Seq_code_ncbieaa) {
-                      smtp = SeqMapTableFind (seqcode, Seq_code_ncbieaa);
-                      residue = SeqMapTableConvert (smtp, residue);
-                    }
-                    if (residue == 'U') {
-                      if (ajp->flags.selenocysteineToNote) {
-                        qvp [FTQUAL_selenocysteine_note].str = "selenocysteine";
-                      } else {
-                        qvp [FTQUAL_selenocysteine].ble = TRUE;
-                      }
-                    }
-                  }
-                }
-              }
-            }
-          }
-        }
-        break;
-      case SEQFEAT_PROT :
-        if (! ifp->mapToPep) {
-          prp = (ProtRefPtr) sfp->data.value.ptrvalue;
-          if (prp != NULL) {
-            vnp = prp->name;
-            if (vnp != NULL && (! StringHasNoText ((CharPtr) vnp->data.ptrvalue))) {
-              qvp [FTQUAL_product].str = (CharPtr) vnp->data.ptrvalue;
-              vnp = vnp->next;
-              qvp [FTQUAL_prot_names].vnp = vnp;
-            }
-            if (afp->format != GENPEPT_FMT) {
-              qvp [FTQUAL_prot_desc].str = prp->desc;
-            } else {
-              qvp [FTQUAL_prot_name].str = prp->desc;
-            }
-            if (afp->format != GENPEPT_FMT || prp->processed != 2) {
-              qvp [FTQUAL_prot_activity].vnp = prp->activity;
-            }
-            qvp [FTQUAL_prot_EC_number].vnp = prp->ec;
-          }
-          sip = SeqLocIdForProduct (sfp->product);
-          if (sip != NULL) {
-            /* for RefSeq records or GenBank not release_mode */
-            if (is_other || (! ajp->flags.forGbRelease)) {
-              qvp [FTQUAL_protein_id].sip = sip;
-            }
-            prod = BioseqFind (sip);
-          }
-        } else {
-          qvp [FTQUAL_derived_from].slp = sfp->location;
-          sip = SeqLocIdForProduct (sfp->product);
-          if (sip != NULL) {
-            prod = BioseqFind (sip);
-            if (prod != NULL) {
-              prot = SeqMgrGetBestProteinFeature (prod, NULL);
-              if (prot != NULL) {
-                precursor_comment = prot->comment;
-              }
-            }
-          }
-        }
-        prp = (ProtRefPtr) sfp->data.value.ptrvalue;
-        if (prp != NULL) {
-          if (! pseudo) {
-            if (ajp->showPeptide) {
-              if (prp->processed == 2 || prp->processed == 3 || prp->processed == 4) {
-                qvp [FTQUAL_peptide].ble = TRUE;
-              }
-            }
-          }
-          if (prp->processed == 3 || prp->processed == 4) {
-            if (! is_other) {
-              /* Only RefSeq allows product on signal or transit peptide */
-              qvp [FTQUAL_product].str = NULL;
-            }
-          }
-        }
-        break;
-      case SEQFEAT_RNA :
-        rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
-        if (rrp != NULL) {
-          if (rrp->pseudo) {
-            pseudo = TRUE;
-          }
-          if (rrp->type == 2) {
-            sip = SeqLocIdForProduct (sfp->product);
-            if (sip != NULL) {
-              /* for RefSeq records or GenBank not release_mode or entrez_mode */
-              if (is_other || (ajp->mode == SEQUIN_MODE || ajp->mode == DUMP_MODE)) {
-                qvp [FTQUAL_transcript_id].sip = sip;
-              } else {
-                /* otherwise now goes in note */
-                qvp [FTQUAL_transcript_id_note].sip = sip; /* !!! remove October 15, 2003 !!! */
-              }
-              prod = BioseqFind (sip);
-            }
-            if (! pseudo) {
-              if (ajp->showTranscript) {
-                qvp [FTQUAL_transcription].ble = TRUE;
-              }
-            }
-          }
-          if (rrp->type == 3) {
-            if (rrp->ext.choice == 1) {
-              /* amino acid could not be parsed into structured form */
-              if (! ajp->flags.dropIllegalQuals) {
-                str = (CharPtr) rrp->ext.value.ptrvalue;
-                qvp [FTQUAL_product].str = str;
-              } else {
-                qvp [FTQUAL_product].str = "tRNA-OTHER";
-              }
-            } else if (rrp->ext.choice == 2) {
-              trna = (tRNAPtr) rrp->ext.value.ptrvalue;
-              if (trna != NULL) {
-                aa = 0;
-                if (trna->aatype == 2) {
-                  aa = trna->aa;
-                } else {
-                  from = 0;
-                  switch (trna->aatype) {
-                    case 0 :
-                      from = 0;
-                      break;
-                    case 1 :
-                      from = Seq_code_iupacaa;
-                      break;
-                    case 2 :
-                      from = Seq_code_ncbieaa;
-                      break;
-                    case 3 :
-                      from = Seq_code_ncbi8aa;
-                      break;
-                    case 4 :
-                      from = Seq_code_ncbistdaa;
-                      break;
-                    default:
-                      break;
-                  }
-                  if (ajp->flags.iupacaaOnly) {
-                    code = Seq_code_iupacaa;
-                  } else {
-                    code = Seq_code_ncbieaa;
-                  }
-                  smtp = SeqMapTableFind (code, from);
-                  if (smtp != NULL) {
-                    aa = SeqMapTableConvert (smtp, trna->aa);
-                    if (aa == 255 && from == Seq_code_iupacaa && trna->aa == 'U') {
-                      aa = 'U';
-                    }
-                  }
-                }
-                if (ajp->flags.iupacaaOnly) {
-                  smtp = SeqMapTableFind (Seq_code_iupacaa, Seq_code_ncbieaa);
-                  if (smtp != NULL) {
-                    aa = SeqMapTableConvert (smtp, trna->aa);
-                  } else {
-                    aa = 'X';
-                  }
-                }
-                if (aa > 0 && aa != 255) {
-                  if (aa <= 74) {
-                    shift = 0;
-                  } else if (aa > 79) {
-                    shift = 2;
-                  } else {
-                    shift = 1;
-                  }
-                  if (aa != '*') {
-                    idx = aa - (64 + shift);
-                  } else {
-                    idx = 25;
-                  }
-                  if (idx > 0 && idx < 26) {
-                    str = trnaList [idx];
-                    qvp [FTQUAL_product].str = str;
-                    if (StringNICmp (str, "tRNA-", 5) == 0) {
-                      qvp [FTQUAL_trna_aa].str = str + 5;
-                    }
-                  }
-                }
-                qvp [FTQUAL_anticodon].slp = trna->anticodon;
-                qvp [FTQUAL_trna_codons].trp = trna;
-              }
-            }
-          } else {
-            if (rrp->ext.choice == 1) {
-              str = (CharPtr) rrp->ext.value.ptrvalue;
-              qvp [FTQUAL_product].str = str;
-
-              /*
-              if (rrp->type == 255 && (! StringHasNoText (str))) {
-                if        (StringICmp (str, "internal transcribed spacer 1") == 0 ||
-                           StringICmp (str, "internal transcribed spacer ITS1") == 0 ||
-                           StringICmp (str, "ITS1") == 0) {
-                  qvp [FTQUAL_rrna_its].str = "ITS1";
-                } else if (StringICmp (str, "internal transcribed spacer 2") == 0 ||
-                           StringICmp (str, "internal transcribed spacer ITS2") == 0 ||
-                           StringICmp (str, "ITS2") == 0) {
-                  qvp [FTQUAL_rrna_its].str = "ITS2";
-                } else if (StringICmp (str, "internal transcribed spacer 3") == 0 ||
-                           StringICmp (str, "internal transcribed spacer ITS3") == 0 ||
-                           StringICmp (str, "ITS3") == 0) {
-                  qvp [FTQUAL_rrna_its].str = "ITS3";
-                }
-              }
-              */
-            }
-          }
-        }
-        break;
-      case SEQFEAT_REGION :
-        if (afp->format == GENPEPT_FMT && featdeftype == FEATDEF_REGION && ISA_aa (bsp->mol)) {
-          qvp [FTQUAL_region_name].str = (CharPtr) sfp->data.value.ptrvalue;
-        } else {
-          qvp [FTQUAL_region].str = (CharPtr) sfp->data.value.ptrvalue;
-        }
-        break;
-      case SEQFEAT_COMMENT :
-        break;
-      case SEQFEAT_BOND :
-        bondidx = (Int2) sfp->data.value.intvalue;
-        if (bondidx == 255) {
-          bondidx = 5;
-        }
-        if (bondidx > 0 && bondidx < 6) {
-          if (afp->format == GENPEPT_FMT && ISA_aa (bsp->mol)) {
-            qvp [FTQUAL_bond_type].str = bondList [bondidx];
-          } else {
-            qvp [FTQUAL_bond].str = bondList [bondidx];
-          }
-        }
-        break;
-      case SEQFEAT_SITE :
-        siteidx = (Int2) sfp->data.value.intvalue;
-        if (siteidx == 255) {
-          siteidx = 26;
-        }
-        if (siteidx > 0 && siteidx < 27) {
-          if (afp->format == GENPEPT_FMT && ISA_aa (bsp->mol)) {
-            qvp [FTQUAL_site_type].str = siteList [siteidx];
-          } else {
-            qvp [FTQUAL_site].str = siteList [siteidx];
-          }
-        }
-        break;
-      case SEQFEAT_PSEC_STR :
-        qvp [FTQUAL_sec_str_type].num = sfp->data.value.intvalue;
-        break;
-      case SEQFEAT_HET :
-        qvp [FTQUAL_heterogen].str = (CharPtr) sfp->data.value.ptrvalue;
-        break;
-      default :
-        break;
-    }
-  }
-
-  /* common fields set here */
-
-  VisitUserObjectsInUop (sfp->ext, (Pointer) qvp, RecordUserObjectsInQVP);
-
-  if (fcontext.featdeftype == FEATDEF_repeat_region) {
-    pseudo = FALSE;
-  }
-
-  qvp [FTQUAL_pseudo].ble = pseudo;
-
-  qvp [FTQUAL_seqfeat_note].str = sfp->comment;
-
-  /* if RELEASE_MODE, check list of features that can have /pseudo */
-
-  if (ajp->flags.dropIllegalQuals && pseudo  &&
-      (fcontext.seqfeattype == SEQFEAT_RNA || fcontext.seqfeattype == SEQFEAT_IMP) ) {
-    switch (featdeftype) {
-
-    case  FEATDEF_allele:
-    case  FEATDEF_attenuator:
-    case  FEATDEF_CAAT_signal:
-    case  FEATDEF_conflict:
-    case  FEATDEF_D_loop:
-    case  FEATDEF_enhancer:
-    case  FEATDEF_GC_signal:
-    case  FEATDEF_iDNA:
-    case  FEATDEF_intron:
-    case  FEATDEF_LTR:
-    case  FEATDEF_misc_binding:
-    case  FEATDEF_misc_difference:
-    case  FEATDEF_misc_recomb:
-    case  FEATDEF_misc_RNA:
-    case  FEATDEF_misc_signal:
-    case  FEATDEF_misc_structure:
-    case  FEATDEF_modified_base:
-    case  FEATDEF_mutation:
-    case  FEATDEF_old_sequence:
-    case  FEATDEF_polyA_signal:
-    case  FEATDEF_polyA_site:
-    case  FEATDEF_precursor_RNA:
-    case  FEATDEF_prim_transcript:
-    case  FEATDEF_primer_bind:
-    case  FEATDEF_protein_bind:
-    case  FEATDEF_RBS:
-    case  FEATDEF_repeat_region:
-    case  FEATDEF_repeat_unit:
-    case  FEATDEF_rep_origin:
-    case  FEATDEF_satellite:
-    case  FEATDEF_stem_loop:
-    case  FEATDEF_STS:
-    case  FEATDEF_TATA_signal:
-    case  FEATDEF_terminator:
-    case  FEATDEF_unsure:
-    case  FEATDEF_variation:
-    case  FEATDEF_3clip:
-    case  FEATDEF_3UTR:
-    case  FEATDEF_5clip:
-    case  FEATDEF_5UTR:
-    case  FEATDEF_10_signal:
-    case  FEATDEF_35_signal:
-      qvp [FTQUAL_pseudo].ble = FALSE;
-        break;
-    default:
-        break;
-    }
-  }
-
-  if (afp->format != GENPEPT_FMT) {
-    qvp [FTQUAL_evidence].num = sfp->exp_ev;
-  }
-
-  /* exception currently legal only on CDS */
-
-  if ((! ajp->flags.dropIllegalQuals) || fcontext.seqfeattype == SEQFEAT_CDREGION) {
-    qvp [FTQUAL_exception].str = sfp->except_text;
-
-    if (sfp->excpt && qvp [FTQUAL_exception].str == NULL) {
-      if (qvp [FTQUAL_seqfeat_note].str != NULL) {
-        if (ajp->flags.dropIllegalQuals &&
-            (! StringInStringList (qvp [FTQUAL_seqfeat_note].str, validExceptionString))) {
-        /* !!! if ajp->flags.dropIllegalQuals, check CDS list to avoid losing note !!! */
-          qvp [FTQUAL_exception].str = NULL;
-        } else {
-          /* if no /exception text, use text in comment, remove from /note */
-
-          qvp [FTQUAL_exception].str = qvp [FTQUAL_seqfeat_note].str;
-          qvp [FTQUAL_seqfeat_note].str = NULL;
-        }
-      } else {
-        qvp [FTQUAL_exception].str = "No explanation supplied";
-      }
-
-      /* !!! if ajp->flags.dropIllegalQuals, check CDS list here as well !!! */
-      if (ajp->flags.dropIllegalQuals &&
-          (! StringInStringList (qvp [FTQUAL_seqfeat_note].str, validExceptionString))) {
-        qvp [FTQUAL_exception].str = NULL;
-      }
-    }
-    if (ajp->flags.dropIllegalQuals) {
-      if (is_other) {
-        if (! StringInStringList (qvp [FTQUAL_exception].str, validRefSeqExceptionString)) {
-          qvp [FTQUAL_exception_note].str = qvp [FTQUAL_exception].str;
-          qvp [FTQUAL_exception].str = NULL;
-        }
-      } else {
-        if (! StringInStringList (qvp [FTQUAL_exception].str, validExceptionString)) {
-          qvp [FTQUAL_exception_note].str = qvp [FTQUAL_exception].str;
-          qvp [FTQUAL_exception].str = NULL;
-        }
-      }
-    }
-  } else {
-    qvp [FTQUAL_exception_note].str = sfp->except_text;
-  }
-  if (StringHasNoText (qvp [FTQUAL_exception].str)) {
-    qvp [FTQUAL_exception].str = NULL;
-  }
-  if (StringHasNoText (qvp [FTQUAL_exception_note].str)) {
-    qvp [FTQUAL_exception_note].str = NULL;
-  }
-
-  qvp [FTQUAL_db_xref].vnp = sfp->dbxref;
-  qvp [FTQUAL_citation].vnp = sfp->cit;
-
-  /* /product same as sfp->comment will suppress /note */
-
-  if (! StringHasNoText (qvp [FTQUAL_product].str) &&
-      StringICmp (sfp->comment, qvp [FTQUAL_product].str) == 0) {
-    qvp [FTQUAL_seqfeat_note].str = NULL;
-  }
-  /* case sensitive AJ011317.1 */
-  if (! StringHasNoText (qvp [FTQUAL_cds_product].str) &&
-      StringCmp (sfp->comment, qvp [FTQUAL_cds_product].str) == 0) {
-    qvp [FTQUAL_seqfeat_note].str = NULL;
-  }
-
-  /* /gene same as sfp->comment will suppress /note */
-  /* case sensitive -gi|6572973|gb|AF195052.1|AF195052 */
-
-  if (! StringHasNoText (qvp [FTQUAL_gene].str) &&
-      StringCmp (sfp->comment, qvp [FTQUAL_gene].str) == 0) {
-    qvp [FTQUAL_seqfeat_note].str = NULL;
-  }
-
-  /* gene /note same as sfp->comment will suppress /note - U92435.1 says do not do this */
-
-  /*
-  if (! StringHasNoText (qvp [FTQUAL_gene_note].str) &&
-      StringICmp (sfp->comment, qvp [FTQUAL_gene_note].str) == 0) {
-    qvp [FTQUAL_seqfeat_note].str = NULL;
-  }
-  */
-
-  /* if site sfp->comment contains site name, suppress site in /note */
-
-  if (! StringHasNoText (qvp [FTQUAL_site].str) &&
-      StringStr (sfp->comment, qvp [FTQUAL_site].str) != NULL) {
-    qvp [FTQUAL_site].str = NULL;
-  }
-
-  /* /EC_number same as sfp->comment will suppress /note */
-
-  for (vnp = qvp [FTQUAL_prot_EC_number].vnp; vnp != NULL; vnp = vnp->next) {
-    str = (CharPtr) vnp->data.ptrvalue;
-    if ((! StringHasNoText (str)) &&
-        StringICmp (sfp->comment, str) == 0) {
-      qvp [FTQUAL_seqfeat_note].str = NULL;
-    }
-  }
-
-  /* mat_peptide precursor same as sfp->comment will suppress /note in GenPept */
-
-  if (precursor_comment != NULL && StringCmp (precursor_comment, sfp->comment) == 0) {
-    qvp [FTQUAL_seqfeat_note].str = NULL;
-  }
-
-
-  /* now go through gbqual list */
-
-  for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
-    idx = GbqualToFeaturIndex (gbq->qual);
-    if (idx > 0 && idx < ASN2GNBK_TOTAL_FEATUR) {
-      if (qvp [idx].gbq == NULL) {
-        if (idx == FTQUAL_product_quals) {
-          if (qvp [FTQUAL_product].str == NULL) {
-            qvp [FTQUAL_product].str = gbq->val;
-          } else if (qvp [FTQUAL_xtra_prod_quals].gbq == NULL) {
-            /* chain will include remaining product gbquals */
-            qvp [FTQUAL_xtra_prod_quals].gbq = gbq;
-          }
-        } else {
-          qvp [idx].gbq = gbq;
-        }
-      }
-
-    } else if (idx == 0) {
-
-      qualclass = IllegalGbqualToClass (gbq->qual);
-      if (qualclass == 0) {
-        qualclass = Qual_class_quote;
-      }
-      tmp = StringSave (gbq->val);
-      if (tmp != NULL) {
-        str = MemNew (sizeof (Char) * (StringLen (gbq->qual) + StringLen (tmp) + 10));
-        if (str != NULL) {
-          if (qualclass == Qual_class_quote) {
-            if (StringIsJustQuotes (tmp)) {
-              sprintf (str, "/%s", gbq->qual);
-            } else {
-              ptr = tmp;
-              ch = *ptr;
-              while (ch != '\0') {
-                if (ch == '"') {
-                  *ptr = '\'';
-                }
-                ptr++;
-                ch = *ptr;
-              }
-              sprintf (str, "/%s=\"%s\"", gbq->qual, tmp);
-            }
-            ValNodeCopyStr (&illegal, 0, str);
-          } else if (qualclass == Qual_class_noquote || qualclass == Qual_class_label) {
-            if (StringIsJustQuotes (tmp)) {
-              sprintf (str, "/%s", gbq->qual);
-            } else {
-              sprintf (str, "/%s=%s", gbq->qual, tmp);
-            }
-            ValNodeCopyStr (&illegal, 0, str);
-          }
-          MemFree (str);
-        }
-        MemFree (tmp);
-      }
-    }
-  }
-
-  /* illegal qualifiers are copied and formatted in valnode chain */
-
-  if (! ajp->flags.dropIllegalQuals) {
-    qvp [FTQUAL_illegal_qual].vnp = illegal;
-  }
-
-  /* remove protein description that equals the gene name, case sensitive */
-
-  if (StringCmp (qvp [FTQUAL_gene].str, qvp [FTQUAL_prot_desc].str) == 0) {
-    qvp [FTQUAL_prot_desc].str = NULL;
-  }
-
-  /* remove protein description that equals the cds product, case sensitive */
-
-  if (StringCmp (qvp [FTQUAL_cds_product].str, qvp [FTQUAL_prot_desc].str) == 0) {
-    qvp [FTQUAL_prot_desc].str = NULL;
-  }
-
-  /* remove comment contained in prot_desc - gi|4530123|gb|AF071539.1|AF071539 */
-
-  if (StringStr (qvp [FTQUAL_prot_desc].str, qvp [FTQUAL_seqfeat_note].str) != NULL) {
-    qvp [FTQUAL_seqfeat_note].str = NULL;
-  }
-
-  /* remove protein description that equals the standard name */
-
-  if (qvp [FTQUAL_standard_name].gbq != NULL && qvp [FTQUAL_prot_desc].str != NULL) {
-    gbq = qvp [FTQUAL_standard_name].gbq;
-    lasttype = gbq->qual;
-    while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
-      if (StringICmp (gbq->val, qvp [FTQUAL_prot_desc].str) == 0) {
-        qvp [FTQUAL_prot_desc].str = NULL;
-      }
-      gbq = gbq->next;
-    }
-  }
-
-  /* remove protein description that equals a gene synonym - case insensitive AF109216.1 */
-
-  for (vnp = gene_syn; vnp != NULL; vnp = vnp->next) {
-    str = (CharPtr) vnp->data.ptrvalue;
-    if ((! StringHasNoText (str)) &&
-        StringCmp (str, qvp [FTQUAL_prot_desc].str) == 0) {
-      /* NC_001823 leave in prot_desc if no cds_product */
-      if (qvp [FTQUAL_cds_product].str != NULL) {
-        qvp [FTQUAL_prot_desc].str = NULL;
-      }
-    }
-  }
-
-  /* remove comment that equals a gene synonym */
-
-  if (afp->format != GENPEPT_FMT && (! ifp->mapToProt)) {
-    for (vnp = gene_syn; vnp != NULL; vnp = vnp->next) {
-      str = (CharPtr) vnp->data.ptrvalue;
-      if ((! StringHasNoText (str)) &&
-          StringICmp (str, qvp [FTQUAL_seqfeat_note].str) == 0) {
-        qvp [FTQUAL_seqfeat_note].str = NULL;
-      }
-    }
-  }
-
-  /* remove protein comment descriptor that equals the protein note */
-
-  if (StringCmp (qvp [FTQUAL_prot_note].str, qvp [FTQUAL_prot_comment].str) == 0) {
-    qvp [FTQUAL_prot_comment].str = NULL;
-  }
-
-  /* suppress cds comment if a subset of protein note - AF002218.1 */
-
-  if (StringStr (qvp [FTQUAL_prot_note].str, qvp [FTQUAL_seqfeat_note].str) != NULL) {
-    qvp [FTQUAL_seqfeat_note].str = NULL;
-  }
-
-  /* suppress selenocysteine note if already in comment */
-
-  if (StringStr (sfp->comment, "selenocysteine") != NULL) {
-    qvp [FTQUAL_selenocysteine_note].str = NULL;
-  }
-
-  /* if /allele inherited from gene, suppress allele gbqual on feature */
-
-  if (qvp [FTQUAL_gene_allele].str != NULL) {
-    qvp [FTQUAL_allele].gbq = NULL;
-  }
-
-  /* now print qualifiers from table */
-
-#ifdef DISPLAY_STRINGS
-  s_DisplayQVP(qvp, feat_note_order);
-#endif
-
-  /* Strip duplicate notes */
-
-  if ((StringCmp(qvp[FTQUAL_product].str,
-         qvp[FTQUAL_seqfeat_note].str) == 0)) {
-    qvp[FTQUAL_seqfeat_note].str = NULL;
-  }
-
-  if ((qvp[FTQUAL_standard_name].gbq != NULL) &&
-      (qvp[FTQUAL_standard_name].gbq->val != NULL)) {
-    if ((StringCmp(qvp[FTQUAL_seqfeat_note].str,
-           qvp[FTQUAL_standard_name].gbq->val) == 0)) {
-      qvp[FTQUAL_seqfeat_note].str = NULL;
-    }
-  }
-
-  /* Display strings for debugging purposes */
-
-#ifdef DISPLAY_STRINGS
-  s_DisplayQVP(qvp, feat_qual_order);
-#endif
-
-  /* optionally populate indexes for NCBI internal database */
-
-  if (index != NULL) {
-    if (! StringHasNoText (qvp [FTQUAL_gene].str)) {
-      ValNodeCopyStrToHead (&(index->genes), 0, qvp [FTQUAL_gene].str);
-    }
-  }
-
-  FFAddOneChar(ffstring, '\n', FALSE);
-
-  /* Build the flat file */
-  FormatFeatureBlockQuals (ffstring, ajp, afp, asp, bsp, featdeftype, gene_syn,
-                           lasttype, location, prod,
-                           protein_pid_g, qvp,
-                           left, right, strand,
-                           sfp, target, is_other,
-                           is_journalscan, is_gps);
-
-  /* ??? and then deal with the various note types separately (not in order table) ??? */
-
-  /* free aa-dna or dna-aa mapped location */
-
-  SeqLocFree (loc);
-
-  ValNodeFreeData (illegal);
-
-  BioseqUnlock (unlockme);
-
-  str = FFEndPrint (ajp, ffstring, afp->format, 21, 21, 21, 21, "FT");
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  if (gbseq != NULL) {
-    if (gbfeat != NULL) {
-      AddFeatureToGbseq (gbseq, gbfeat, str, sfp);
-    }
-  }
-
-  FFRecycleString(ajp, ffstring);
-  return str;
-}
-
-
-static CharPtr FormatSequenceBlock (
-  Asn2gbFormatPtr afp,
-  BaseBlockPtr bbp
-)
-
-{
-  IntAsn2gbJobPtr   ajp;
-  Asn2gbSectPtr     asp;
-  Byte              bases [400];
-  Int2              blk;
-  BioseqPtr         bsp;
-  Char              buf [80];
-  Char              ch;
-  Int2              cnt;
-  Uint1             code = Seq_code_iupacna;
-  Int2              count;
-  Int2              ctr;
-  GBSeqPtr          gbseq;
-  Int2              i;
-  IntAsn2gbSectPtr  iasp;
-  Boolean           is_na;
-  Int2              lin;
-  Int4              pos;
-  CharPtr           ptr;
-  Uint1             residue;
-  SeqBlockPtr       sbp;
-  SeqPortPtr        spp;
-  Int4              start;
-  Int4              stop;
-  CharPtr           str;
-  CharPtr           tmp;
-  StringItemPtr     ffstring;
-
-  if (afp == NULL || bbp == NULL) return NULL;
-  sbp = (SeqBlockPtr) bbp;
-  ajp = afp->ajp;
-  if (ajp == NULL) return NULL;
-  asp = afp->asp;
-  if (asp == NULL) return NULL;
-  iasp = (IntAsn2gbSectPtr) asp;
-  bsp = (asp->bsp);
-  if (bsp == NULL) return NULL;
-
-  /* if GBSeq XML, use SeqPortStream on single block */
-
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-
-    str = MemNew (sizeof (Char) * (bsp->length + 10));
-    if (str == NULL) return NULL;
-
-    tmp = str;
-    SeqPortStream (bsp, TRUE, (Pointer) &tmp, SaveGBSeqSequence);
-    gbseq->sequence = StringSave (str);
-
-    tmp = gbseq->sequence;
-    if (tmp == NULL) return NULL;
-    ch = *tmp;
-    while (ch != '\0') {
-      if (ch == '\n' || ch == '\r' || ch == '\t') {
-        *tmp = ' ';
-      }
-      tmp++;
-      ch = *tmp;
-    }
-    TrimSpacesAroundString (gbseq->sequence);
-    CompressNonBases (gbseq->sequence);
-
-    return str;
-  }
-
-  /* if subsequence cached with SeqPortStream, use it */
-
-  if (sbp->bases != NULL) {
-    ffstring = FFGetString (ajp);
-
-    start = sbp->start;
-    stop = sbp->stop;
-
-    count = 0;
-    blk = 0;
-    lin = 0;
-
-    ptr = sbp->bases;
-    ch = *ptr;
-
-    while (ch != '\0') {
-      buf [count] = (Char) (TO_LOWER (ch));
-      count++;
-      ptr++;
-      ch = *ptr;
-
-      blk++;
-      lin++;
-      if (lin >= 60) {
-
-        buf [count] = '\0';
-        PrintSeqLine (ffstring, afp->format, buf, start, start + cnt);
-        count = 0;
-        cnt = 0;
-        blk = 0;
-        lin = 0;
-        start += 60;
-
-      } else if (blk >= 10) {
-
-        buf [count] = ' ';
-        count++;
-        blk = 0;
-
-      }
-    }
-
-    buf [count] = '\0';
-    if (count > 0) {
-      PrintSeqLine (ffstring, afp->format, buf, start, start + cnt);
-    }
-
-    str = FFToCharPtr(ffstring);
-
-    FFRecycleString (ajp, ffstring);
-    return str;
-  }
-
-  /* otherwise split into smaller blocks */
-
-  spp = iasp->spp;
-  if (spp == NULL) {
-
-    /* if first time, create SeqPort for this section */
-
-    if (ISA_aa (bsp->mol)) {
-      if (ajp->flags.iupacaaOnly) {
-        code = Seq_code_iupacaa;
-      } else {
-        code = Seq_code_ncbieaa;
-      }
-    }
-
-    if (ajp->ajp.slp != NULL) {
-      spp = SeqPortNewByLoc (ajp->ajp.slp, code);
-    } else {
-      spp = SeqPortNew (bsp, 0, -1, 0, code);
-    }
-    if (spp == NULL) return NULL;
-    if (bsp->repr == Seq_repr_delta || bsp->repr == Seq_repr_virtual) {
-      SeqPortSet_do_virtual (spp, TRUE);
-    }
-
-    iasp->spp = spp;
-  }
-
-  start = sbp->start;
-  stop = sbp->stop;
-
-  if (start != spp->curpos) {
-    SeqPortSeek (spp, start, SEEK_SET);
-  }
-
-  pos = start;
-
-  count = 0;
-  cnt = 0;
-  blk = 0;
-  lin = 0;
-
-  is_na = ISA_na (bsp->mol);
-
-  ctr = (Int2) MIN ((Int4) (stop - pos), (Int4) sizeof (bases));
-  ctr = SeqPortRead (spp, bases, ctr);
-
-  i = 0;
-
-  if (ctr < 0) {
-    residue = -ctr;
-  } else if (ctr < 1) {
-    residue = SEQPORT_EOF;
-  } else {
-    residue = (Uint1) bases [i];
-  }
-
-
-  ffstring = FFGetString(ajp);
-  while (pos < stop && residue != SEQPORT_EOF) {
-
-    if (residue == INVALID_RESIDUE) {
-      if (is_na) {
-        residue = 'N';
-      } else {
-        residue = 'X';
-      }
-    }
-
-    if (IS_residue (residue)) {
-
-      buf [count] = (Char) (TO_LOWER (residue));
-      count++;
-      cnt++;
-      pos++;
-
-      blk++;
-      lin++;
-      if (lin >= 60) {
-
-        buf [count] = '\0';
-        PrintSeqLine (ffstring, afp->format, buf, start, start + cnt);
-        count = 0;
-        cnt = 0;
-        blk = 0;
-        lin = 0;
-        start += 60;
-
-      } else if (blk >= 10) {
-
-        buf [count] = ' ';
-        count++;
-        blk = 0;
-
-      }
-    }
-
-    i++;
-    if (i >= ctr) {
-      i = 0;
-      ctr = (Int2) MIN ((Int4) (stop - pos), (Int4) sizeof (bases));
-      ctr = SeqPortRead (spp, bases, ctr);
-      if (ctr < 0) {
-        bases [0] = -ctr;
-      } else if (ctr < 1) {
-        bases [0] = SEQPORT_EOF;
-      }
-    }
-    residue = (Uint1) bases [i];
-  }
-
-  buf [count] = '\0';
-  if (count > 0) {
-    PrintSeqLine (ffstring, afp->format, buf, start, start + cnt);
-  }
-
-  if (ajp->transientSeqPort) {
-    iasp->spp = SeqPortFree (iasp->spp);
-  }
-
-  str = FFToCharPtr(ffstring);
-
-  /* optionally populate gbseq for XML-ized GenBank format */
-
-  /*
-  if (ajp->gbseq) {
-    gbseq = &asp->gbseq;
-  } else {
-    gbseq = NULL;
-  }
-
-  if (gbseq != NULL) {
-    CatenateSequenceInGbseq (gbseq, str);
-  }
-  */
-
-  FFRecycleString(ajp, ffstring);
-  return str;
-}
-
-
 
 /* ********************************************************************** */
 
@@ -23552,6 +2632,7 @@ typedef struct lookforids {
   Boolean isNTorNW;
   Boolean isNC;
   Boolean isTPA;
+  Boolean isAEorCH;
   Boolean isNuc;
   Boolean isProt;
 } LookForIDs, PNTR LookForIDsPtr;
@@ -23576,6 +2657,14 @@ static void LookForSeqIDs (BioseqPtr bsp, Pointer userdata)
       case SEQID_EMBL :
       case SEQID_DDBJ :
         lfip->isGED = TRUE;
+        tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+        if (tsip != NULL) {
+          if (StringNCmp (tsip->accession, "AE", 2) == 0) {
+            lfip->isAEorCH = TRUE;
+          } else if (StringNCmp (tsip->accession, "CH", 2) == 0) {
+            lfip->isAEorCH = TRUE;
+          }
+        }
         break;
       case SEQID_TPG :
       case SEQID_TPE :
@@ -23606,6 +2695,7 @@ static void LookForGEDetc (
   BoolPtr isNTorNW,
   BoolPtr isNC,
   BoolPtr isTPA,
+  BoolPtr isAEorCH,
   BoolPtr isNuc,
   BoolPtr isProt
 )
@@ -23619,6 +2709,7 @@ static void LookForGEDetc (
   *isNTorNW = lfi.isNTorNW;
   *isNC = lfi.isNC;
   *isTPA = lfi.isTPA;
+  *isAEorCH = lfi.isAEorCH;
   *isNuc = lfi.isNuc;
   *isProt = lfi.isProt;
 }
@@ -23650,6 +2741,7 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   GBSeqPtr         gbseq = NULL;
   Int4             i;
   IndxPtr          index = NULL;
+  Boolean          isAEorCH;
   Boolean          isGED;
   Boolean          isNTorNW;
   Boolean          isNC;
@@ -23684,6 +2776,16 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   ValNodePtr       vnp;
   Boolean          is_html = FALSE;
 
+  if (format == 0) {
+    format = GENBANK_FMT;
+  }
+  if (mode == 0) {
+    mode = SEQUIN_MODE;
+  }
+  if (style == 0) {
+    style = NORMAL_STYLE;
+  }
+
   if (extra != NULL) {
     index = extra->index;
     gbseq = extra->gbseq;
@@ -23840,7 +2942,7 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   aw.onlyNearFeats = FALSE;
   aw.farFeatsSuppress = FALSE;
   aw.nearFeatsSuppress = FALSE;
-  LookForGEDetc (sep, &isGED, &isNTorNW, &isNC, &isTPA, &isNuc, &isProt);
+  LookForGEDetc (sep, &isGED, &isNTorNW, &isNC, &isTPA, &isAEorCH, &isNuc, &isProt);
   if (ajp->ajp.slp != NULL) {
     /* specified location obeys fetching parameters, for now */
     aw.onlyNearFeats = (Boolean) ((flags & FEAT_FETCH_MASK) == ONLY_NEAR_FEATURES);
@@ -23852,6 +2954,13 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
     aw.showconfeats = TRUE;
   } else if (isNTorNW || isTPA) {
     aw.onlyNearFeats = TRUE;
+  } else if (isAEorCH) {
+    /* AE or CH are special cases in CON division */
+    if ((Boolean) ((flags & FEAT_FETCH_MASK) == ONLY_NEAR_FEATURES)) {
+      aw.onlyNearFeats = TRUE;
+    } else {
+      aw.nearFeatsSuppress = TRUE;
+    }
   } else if (isNC) {
     if ((Boolean) ((flags & FEAT_FETCH_MASK) == ONLY_NEAR_FEATURES)) {
       aw.onlyNearFeats = TRUE;
@@ -24024,6 +3133,23 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   return (Asn2gbJobPtr) ajp;
 }
 
+/* ********************************************************************** */
+
+/* format functions allocate printable string for given paragraph */
+
+NLM_EXTERN CharPtr DefaultFormatBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  if (afp == NULL || bbp == NULL) return NULL;
+
+  /* default format function assumes string pre-allocated by add block function */
+
+  return StringSaveNoNull (bbp->string);
+}
+
 typedef CharPtr (*FormatProc) (Asn2gbFormatPtr afp, BaseBlockPtr bbp);
 
 static FormatProc asn2gnbk_fmt_functions [27] = {
@@ -24277,7 +3403,7 @@ static void PrintFTCodeBreak (
 
   slp = SeqLocFindNext (cbp->loc, NULL);
   while (slp != NULL) {
-    str = FlatLoc (&iaj, target, slp, FALSE);
+    str = FFFlatLoc (&iaj, target, slp, FALSE);
     if (str != NULL) {
       residue = cbaa.value.intvalue;
       ptr = Get3LetterSymbol (&iaj, seqcode, sctp, residue);
@@ -24321,6 +3447,253 @@ static SeqIdPtr SeqIdFindForTable (SeqIdPtr sip)
 
 /* #define MAKE_MRNA_GPS_FEAT */
 
+static void PrintBioSourceFtableEntry (
+  ValNodePtr PNTR head,
+  BioSourcePtr    biop
+)
+{
+  OrgModPtr    mod;
+  SubSourcePtr ssp;
+  Char         str [256];
+
+  if (head == NULL || biop == NULL) return;
+
+  if (biop->org != NULL && ! StringHasNoText (biop->org->taxname))
+  {
+    sprintf (str, "\t\t\torganism\t%s\n", biop->org->taxname);
+    ValNodeCopyStr (head, 0, str);
+  }
+
+  /* add OrgMods */
+  if (biop->org != NULL && biop->org->orgname != NULL)
+  {
+    for (mod = biop->org->orgname->mod;
+         mod != NULL;
+         mod = mod->next)
+    {
+      switch (mod->subtype)
+      {
+        case ORGMOD_strain :
+          sprintf (str, "\t\t\tstrain\t");
+          break;
+        case ORGMOD_substrain :
+          sprintf (str, "\t\t\tsubstrain\t");
+          break;
+        case ORGMOD_type :
+          sprintf (str, "\t\t\ttype\t");
+          break;
+        case ORGMOD_subtype :
+          sprintf (str, "\t\t\tsubtype\t");
+          break;
+        case ORGMOD_variety :
+          sprintf (str, "\t\t\tvariety\t");
+          break;
+        case ORGMOD_serotype :
+          sprintf (str, "\t\t\tserotype\t");
+          break;
+        case ORGMOD_serogroup :
+          sprintf (str, "\t\t\tserogroup\t");
+          break;
+        case ORGMOD_serovar :
+          sprintf (str, "\t\t\tserovar\t");
+          break;
+        case ORGMOD_cultivar :
+          sprintf (str, "\t\t\tcultivar\t");
+          break;
+        case ORGMOD_pathovar :
+          sprintf (str, "\t\t\tpathovar\t");
+          break;
+        case ORGMOD_chemovar :
+          sprintf (str, "\t\t\tchemovar\t");
+          break;
+        case ORGMOD_biovar :
+          sprintf (str, "\t\t\tbiovar\t");
+          break;
+        case ORGMOD_biotype :
+          sprintf (str, "\t\t\tbiotype\t");
+          break;
+        case ORGMOD_group :
+          sprintf (str, "\t\t\tgroup\t");
+          break;
+        case ORGMOD_subgroup :
+          sprintf (str, "\t\t\tsubgroup\t");
+          break;
+        case ORGMOD_isolate :
+          sprintf (str, "\t\t\tisolate\t");
+          break;
+        case ORGMOD_common :
+          sprintf (str, "\t\t\tcommon\t");
+          break;
+        case ORGMOD_acronym :
+          sprintf (str, "\t\t\tacronym\t");
+          break;
+        case ORGMOD_dosage :
+          sprintf (str, "\t\t\tdosage\t");
+          break;
+        case ORGMOD_nat_host :
+          sprintf (str, "\t\t\tnat_host\t");
+          break;
+        case ORGMOD_sub_species :
+          sprintf (str, "\t\t\tsub_species\t");
+          break;
+        case ORGMOD_specimen_voucher :
+          sprintf (str, "\t\t\tspecimen_voucher\t");
+          break;
+        case ORGMOD_authority :
+          sprintf (str, "\t\t\tauthority\t");
+          break;
+        case ORGMOD_forma :
+          sprintf (str, "\t\t\tforma\t");
+          break;
+        case ORGMOD_forma_specialis :
+          sprintf (str, "\t\t\tforma_specialis\t");
+          break;
+        case ORGMOD_ecotype :
+          sprintf (str, "\t\t\tecotype\t");
+          break;
+        case ORGMOD_synonym :
+          sprintf (str, "\t\t\tsynonym\t");
+          break;
+        case ORGMOD_anamorph :
+          sprintf (str, "\t\t\tanamorph\t");
+          break;
+        case ORGMOD_teleomorph :
+          sprintf (str, "\t\t\tteleomorph\t");
+          break;
+        case ORGMOD_breed :
+          sprintf (str, "\t\t\tbreed\t");
+          break;
+        case ORGMOD_gb_acronym :
+          sprintf (str, "\t\t\tgb_acronym\t");
+          break;
+        case ORGMOD_gb_anamorph :
+          sprintf (str, "\t\t\tgb_anamorph\t");
+          break;
+        case ORGMOD_old_lineage :
+          sprintf (str, "\t\t\told_lineage\t");
+          break;
+        case ORGMOD_old_name :
+          sprintf (str, "\t\t\told_name\t");
+          break;
+        case ORGMOD_other :
+          sprintf (str, "\t\t\tnote\t");
+          break;
+        default :
+          str [0] = 0;
+      }
+      if ( str [0] == 0) continue;
+      if (! StringHasNoText (mod->subname))
+      {
+        StringNCat (str, mod->subname, sizeof (str) - StringLen (str) - 2);
+        str [sizeof (str) - 2] = 0;
+      }
+      StringCat (str, "\n");
+      ValNodeCopyStr (head, 0, str);
+    }
+  }
+   
+  for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next)
+  {
+    switch (ssp->subtype)
+    {
+      case SUBSRC_chromosome :
+        sprintf (str, "\t\t\tchromosome\t");
+        break;
+      case SUBSRC_map :
+        sprintf (str, "\t\t\tmap\t");
+        break;
+      case SUBSRC_clone :
+        sprintf (str, "\t\t\tclone\t");
+        break;
+      case SUBSRC_haplotype :
+        sprintf (str, "\t\t\thaplotype\t");
+        break;
+      case SUBSRC_genotype :
+        sprintf (str, "\t\t\tgenotype\t");
+        break;
+      case SUBSRC_sex :
+        sprintf (str, "\t\t\tsex\t");
+        break;
+      case SUBSRC_cell_line :
+        sprintf (str, "\t\t\tcell_line\t");
+        break;
+      case SUBSRC_cell_type :
+        sprintf (str, "\t\t\tcell_type\t");
+        break;
+      case SUBSRC_tissue_type :
+        sprintf (str, "\t\t\ttissue_type\t");
+        break;
+      case SUBSRC_clone_lib :
+        sprintf (str, "\t\t\tclone_lib\t");
+        break;
+      case SUBSRC_dev_stage :
+        sprintf (str, "\t\t\tdev_stage\t");
+        break;
+      case SUBSRC_frequency :
+        sprintf (str, "\t\t\tfrequency\t");
+        break;
+      case SUBSRC_germline :
+        sprintf (str, "\t\t\tgermline\t");
+        break;
+      case SUBSRC_rearranged :
+        sprintf (str, "\t\t\trearranged\t");
+        break;
+      case SUBSRC_lab_host :
+        sprintf (str, "\t\t\tlab_host\t");
+        break;
+      case SUBSRC_pop_variant :
+        sprintf (str, "\t\t\tpop_variant\t");
+        break;
+      case SUBSRC_tissue_lib :
+        sprintf (str, "\t\t\ttissue_lib\t");
+        break;
+      case SUBSRC_plasmid_name :
+        sprintf (str, "\t\t\tplasmid_name\t");
+        break;
+      case SUBSRC_transposon_name :
+        sprintf (str, "\t\t\ttransposon_name\t");
+        break;
+      case SUBSRC_insertion_seq_name :
+        sprintf (str, "\t\t\tinsertion_seq_name\t");
+        break;
+      case SUBSRC_plastid_name :
+        sprintf (str, "\t\t\tplastid_name\t");
+        break;
+      case SUBSRC_country :
+        sprintf (str, "\t\t\tcountry\t");
+        break;
+      case SUBSRC_segment :
+        sprintf (str, "\t\t\tsegment\t");
+        break;
+      case SUBSRC_endogenous_virus_name :
+        sprintf (str, "\t\t\tendogenous_virus_name\t");
+        break;
+      case SUBSRC_transgenic :
+        sprintf (str, "\t\t\ttransgenic\t");
+        break;
+      case SUBSRC_environmental_sample :
+        sprintf (str, "\t\t\tenvironmental_sample\t");
+        break;
+      case SUBSRC_isolation_source :
+        sprintf (str, "\t\t\tisolation_source\t");
+        break;
+      case SUBSRC_other :
+          sprintf (str, "\t\t\tnote\t");
+          break;
+      default :
+        str [0] = 0;
+    }
+    if ( str [0] == 0) continue;
+    if (! StringHasNoText (ssp->name))
+    {
+      StringNCat (str, ssp->name, sizeof (str) - StringLen (str) - 2);
+      str [sizeof (str) - 2] = 0;
+    }
+    StringCat (str, "\n");
+    ValNodeCopyStr (head, 0, str);
+  }  
+}
+
 static void PrintFtableLocAndQuals (
   IntAsn2gbJobPtr ajp,
   ValNodePtr PNTR head,
@@ -24371,6 +3744,9 @@ static void PrintFtableLocAndQuals (
   if (StringCmp (label, "Gene") == 0) {
     label = "gene";
   }
+  else if (StringCmp (label, "Src") == 0) {
+    label = "source";
+  }
   if (StringHasNoText (label)) {
     label = "???";
   }
@@ -24813,6 +4189,9 @@ static void PrintFtableLocAndQuals (
         ValNodeCopyStr (head, 0, tmp);
       }
       break;
+    case SEQFEAT_BIOSRC :
+      PrintBioSourceFtableEntry (head, sfp->data.value.ptrvalue);
+      break;
     default :
       break;
   }
@@ -24953,6 +4332,46 @@ static BioseqPtr BioseqLockAndIndexByEntity (Uint2 entityID)
   return bsp;
 }
 
+static CharPtr FormatFtableSourceFeatBlock (
+  BaseBlockPtr bbp,
+  BioseqPtr target
+)
+{
+  SeqFeatPtr        sfp;
+  SeqDescPtr        sdp;
+  SeqMgrDescContext dcontext;
+  SeqMgrFeatContext fcontext;
+  BioSourcePtr      biop;
+  ValNodePtr        head;
+  IntSrcBlockPtr    isp;
+  CharPtr           str;
+
+  if (bbp == NULL) return NULL;
+
+  isp = (IntSrcBlockPtr) bbp;
+  head = NULL;
+  biop = NULL;
+
+  if (bbp->itemtype == OBJ_SEQDESC) {
+    sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID,
+                                      0, NULL, &dcontext);
+    if (sdp == NULL) return NULL;
+    biop = sdp->data.ptrvalue;
+  } else if (bbp->itemtype == OBJ_SEQFEAT) {
+    sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
+    if (sfp == NULL) return NULL;
+    biop = sfp->data.value.ptrvalue;
+  }
+  if (biop == NULL) return NULL;
+  PrintFtableIntervals (&head, target, isp->loc, "source");
+  PrintBioSourceFtableEntry (&head, biop);
+
+  str = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  return str;
+}
+
 NLM_EXTERN CharPtr asn2gnbk_format (
   Asn2gbJobPtr ajp,
   Int4 paragraph
@@ -25059,7 +4478,7 @@ NLM_EXTERN CharPtr asn2gnbk_format (
               sprintf (tmp, "\t\t\tmuid\t%ld\n", (long) irp->rb.muid);
               ValNodeCopyStr (&head, 0, tmp);
             }
-            str = MergeValNodeStrings (head);
+            str = MergeFFValNodeStrs (head);
             ValNodeFreeData (head);
           }
         }
@@ -25070,9 +4489,11 @@ NLM_EXTERN CharPtr asn2gnbk_format (
         if (sfp != NULL) {
           head = NULL;
           PrintFtableLocAndQuals (af.ajp, &head, target, sfp, &fcontext);
-          str = MergeValNodeStrings (head);
+          str = MergeFFValNodeStrs (head);
           ValNodeFreeData (head);
         }
+      } else if (blocktype == SOURCEFEAT_BLOCK) {
+        str = FormatFtableSourceFeatBlock (bbp, target);
       }
 
       SeqEntrySetScope (oldscope);
@@ -25380,7 +4801,7 @@ NLM_EXTERN Boolean SeqEntryToGnbk (
 
     for (i = 0; i < numParagraphs; i++) {
       str = asn2gnbk_format (ajp, i);
-      block = 0;
+      block = (BlockType) 0;
       if (paragraphArray != NULL) {
         bbp = paragraphArray [i];
         if (bbp != NULL) {
diff --git a/api/asn2gnb2.c b/api/asn2gnb2.c
new file mode 100644
index 00000000..3310cbbb
--- /dev/null
+++ b/api/asn2gnb2.c
@@ -0,0 +1,4778 @@
+/*   asn2gnb2.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  asn2gnb2.c
+*
+* Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans,
+*          Mati Shomrat
+*
+* Version Creation Date:   10/21/98
+*
+* $Revision: 1.1 $
+*
+* File Description:  New GenBank flatfile generator - work in progress
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <objall.h>
+#include <objsset.h>
+#include <objsub.h>
+#include <objfdef.h>
+#include <objpubme.h>
+#include <seqport.h>
+#include <sequtil.h>
+#include <sqnutils.h>
+#include <subutil.h>
+#include <tofasta.h>
+#include <explore.h>
+#include <gbfeat.h>
+#include <gbftdef.h>
+#include <edutil.h>
+#include <alignmgr2.h>
+#include <asn2gnbi.h>
+
+#ifdef WIN_MAC
+#if __profile__
+#include <Profiler.h>
+#endif
+#endif
+
+/* ********************************************************************** */
+
+static Boolean DeltaLitOnly (
+  BioseqPtr bsp
+)
+
+{
+  ValNodePtr  vnp;
+
+  if (bsp == NULL || bsp->repr != Seq_repr_delta) return FALSE;
+  for (vnp = (ValNodePtr)(bsp->seq_ext); vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == 1) return FALSE;
+  }
+  return TRUE;
+}
+
+static Boolean SegHasParts (
+  BioseqPtr bsp
+)
+
+{
+  BioseqSetPtr  bssp;
+  SeqEntryPtr   sep;
+
+  if (bsp == NULL || bsp->repr != Seq_repr_seg) return FALSE;
+  sep = bsp->seqentry;
+  if (sep == NULL) return FALSE;
+  sep = sep->next;
+  if (sep == NULL || (! IS_Bioseq_set (sep))) return FALSE;
+  bssp = (BioseqSetPtr) sep->data.ptrvalue;
+  if (bssp != NULL && bssp->_class == BioseqseqSet_class_parts) return TRUE;
+  return FALSE;
+}
+
+/* add functions allocate specific blocks, populate with paragraph print info */
+
+static CharPtr strd [4] = {
+  "   ", "ss-", "ds-", "ms-"
+};
+
+static CharPtr gnbk_mol [14] = {
+  "    ", "DNA ", "RNA ", "mRNA", "rRNA", "tRNA", "snRNA", "scRNA", " AA ", "DNA ", "DNA ", "RNA ", "snoRNA", "RNA "
+};
+
+/* EMBL_FMT in RELEASE_MODE or ENTREZ_MODE, otherwise use gnbk_mol */
+
+static CharPtr embl_mol [14] = {
+  "xxx", "DNA", "RNA", "RNA", "RNA", "RNA", "RNA", "RNA", "AA ", "DNA", "DNA", "RNA", "RNA", "RNA"
+};
+
+static CharPtr embl_divs [18] = {
+  "FUN", "INV", "MAM", "ORG", "PHG", "PLN", "PRI", "PRO", "ROD"
+  "SYN", "UNA", "VRL", "VRT", "PAT", "EST", "STS", "HUM", "HTC"
+};
+
+static Uint1 imolToMoltype [14] = {
+  0, 1, 2, 5, 4, 3, 6, 7, 9, 1, 1, 2, 8, 2
+};
+
+static DatePtr GetBestDate (
+  DatePtr a,
+  DatePtr b
+)
+
+{
+  Int2  status;
+
+  if (a == NULL) return b;
+  if (b == NULL) return a;
+
+  status = DateMatch (a, b, FALSE);
+  if (status == 1) return a;
+
+  return b;
+}
+
+/*--------------------------------------------------------*/
+/*                                                        */
+/*  s_IsSeperatorNeeded()                                 */
+/*                                                        */
+/*--------------------------------------------------------*/
+
+static Boolean s_IsSeperatorNeeded(CharPtr baseString, Int4 baseLength, Int2 suffixLength)
+{
+  Char lastChar;
+  Char nextToLastChar;
+
+  lastChar = baseString[baseLength - 1];
+  nextToLastChar = baseString[baseLength - 2];
+
+  /* This first check put here to emulate what may be a  */
+  /* bug in the original code (in CheckLocusLength() )   */
+  /* which adds an 'S' segment seperator only if it      */
+  /* DOES make the string longer than the max.           */
+
+  if (baseLength + suffixLength < 16)
+    return FALSE;
+
+  /* If the last character is not a digit */
+  /* then don't use a seperator.          */
+
+  if (!IS_DIGIT(lastChar))
+    return FALSE;
+
+  /* If the last two characters are a non-digit   */
+  /* followed by a '0', then don't use seperator. */
+
+  if ((lastChar == '0') && (!IS_DIGIT(nextToLastChar)))
+    return FALSE;
+
+  /* If we made it to here, use a seperator */
+
+  return TRUE;
+}
+
+/*--------------------------------------------------------*/
+/*                                                        */
+/*  s_LocusAddSuffix() -                                  */
+/*                                                        */
+/*--------------------------------------------------------*/
+
+static Boolean s_LocusAddSuffix (CharPtr locus, Asn2gbWorkPtr awp)
+{
+  size_t  buflen;
+  Char    ch;
+  Char    segCountStr[6];
+  Int2    segCountStrLen;
+  Char    segSuffix[5];
+
+  buflen = StringLen (locus);
+
+  /* If there's one or less segments, */
+  /* no suffix is needed.             */
+
+  if (awp->numsegs <= 1)
+    return FALSE;
+
+  /* If the basestring has one or less */
+  /* characters, no suffix is needed.  */
+
+  if (buflen <=1)
+    return FALSE;
+
+  /* Add the suffix */
+
+  ch = locus[buflen-1];
+  sprintf(segCountStr,"%d",awp->numsegs);
+  segCountStrLen = StringLen(segCountStr);
+  segSuffix[0] = '\0';
+
+  if (s_IsSeperatorNeeded(locus,buflen,segCountStrLen) == TRUE)
+    sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg);
+  else
+    sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg);
+  StringCat(locus,segSuffix);
+
+  /* Return successfully */
+
+  return TRUE;
+}
+
+/*--------------------------------------------------------*/
+/*                                                        */
+/*  s_LocusAdjustLength() -                               */
+/*                                                        */
+/*--------------------------------------------------------*/
+
+static Boolean s_LocusAdjustLength(CharPtr locus, Int2 maxLength)
+{
+  Int2     trimCount;
+  Int2     buflen;
+  CharPtr  buftmp;
+
+  buflen = StringLen (locus);
+  if (buflen <= maxLength) return FALSE;
+
+  buftmp = MemNew(maxLength + 1);
+
+  /* If the sequence id is an NCBI locus of the */
+  /* form HSU00001, then make sure that if      */
+  /* there is trimming the HS gets trimmed off  */
+  /* as a unit, never just the 'H'.             */
+
+  trimCount = buflen - maxLength;
+  if (trimCount == 1)
+    if (IS_ALPHA(locus[0]) != 0 &&
+        IS_ALPHA(locus[1]) != 0 &&
+        IS_ALPHA(locus[2]) != 0 &&
+        IS_DIGIT(locus[3]) != 0 &&
+        IS_DIGIT(locus[4]) != 0 &&
+        IS_DIGIT(locus[5]) != 0 &&
+        IS_DIGIT(locus[6]) != 0 &&
+        IS_DIGIT(locus[7]) != 0 &&
+        locus[8] == 'S' &&
+        locus[9] == '\0')
+      trimCount++;
+
+  /* Left truncate the sequence id */
+
+  StringCpy(buftmp, &locus[trimCount]);
+  StringCpy(locus, buftmp);
+
+  MemFree(buftmp);
+  return TRUE;
+}
+
+/*--------------------------------------------------------*/
+/*                                                        */
+/*  AddLocusBlock() -                                     */
+/*                                                        */
+/*--------------------------------------------------------*/
+
+static DatePtr GetBestDateForBsp (
+  BioseqPtr bsp
+)
+
+{
+  DatePtr            best_date = NULL;
+  SeqMgrDescContext  dcontext;
+  DatePtr            dp;
+  EMBLBlockPtr       ebp;
+  GBBlockPtr         gbp;
+  PdbBlockPtr        pdp;
+  PdbRepPtr          prp;
+  SeqDescrPtr        sdp;
+  SPBlockPtr         spp;
+
+  if (bsp == NULL) return NULL;
+
+  dp = NULL;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_update_date, &dcontext);
+  if (sdp != NULL) {
+    dp = (DatePtr) sdp->data.ptrvalue;
+    best_date = GetBestDate (dp, best_date);
+  }
+
+  /* !!! temporarily also look at genbank block entry date !!! */
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
+  if (sdp != NULL) {
+    gbp = (GBBlockPtr) sdp->data.ptrvalue;
+    if (gbp != NULL) {
+      dp = gbp->entry_date;
+      best_date = GetBestDate (dp, best_date);
+    }
+  }
+
+  /* more complicated code for dates from various objects goes here */
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_embl, &dcontext);
+  if (sdp != NULL) {
+    ebp = (EMBLBlockPtr) sdp->data.ptrvalue;
+    if (ebp != NULL) {
+      dp = ebp->creation_date;
+      best_date = GetBestDate (dp, best_date);
+      dp = ebp->update_date;
+      best_date = GetBestDate (dp, best_date);
+    }
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_sp, &dcontext);
+  if (sdp != NULL) {
+    spp = (SPBlockPtr) sdp->data.ptrvalue;
+    if (spp != NULL) {
+      dp = spp->created;
+      if (dp != NULL && dp->data [0] == 1) {
+        best_date = GetBestDate (dp, best_date);
+      }
+      dp = spp->sequpd;
+      if (dp != NULL && dp->data [0] == 1) {
+        best_date = GetBestDate (dp, best_date);
+      }
+      dp = spp->annotupd;
+      if (dp != NULL && dp->data [0] == 1) {
+        best_date = GetBestDate (dp, best_date);
+      }
+    }
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pdb, &dcontext);
+  if (sdp != NULL) {
+    pdp = (PdbBlockPtr) sdp->data.ptrvalue;
+    if (pdp != NULL) {
+      dp = pdp->deposition;
+      if (dp != NULL && dp->data [0] == 1) {
+        best_date = GetBestDate (dp, best_date);
+      }
+      prp = pdp->replace;
+      if (prp != NULL) {
+        dp = prp->date;
+        if (dp != NULL && dp->data[0] == 1) {
+          best_date = GetBestDate (dp, best_date);
+        }
+      }
+    }
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_create_date, &dcontext);
+  if (sdp != NULL) {
+    dp = (DatePtr) sdp->data.ptrvalue;
+    if (dp != NULL) {
+      best_date = GetBestDate (dp, best_date);
+    }
+  }
+
+  return best_date;
+}
+
+static Boolean LocusHasBadChars (
+  CharPtr locus
+)
+
+{
+  Char     ch;
+  CharPtr  ptr;
+
+  ptr = locus;
+  ch = *ptr;
+  while (ch != '\0') {
+    if (! IS_ALPHANUM (ch)) {
+      return TRUE;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+  return FALSE;
+}
+
+NLM_EXTERN void AddLocusBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  size_t             acclen;
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  BaseBlockPtr       bbp;
+  DatePtr            best_date = NULL;
+  BioSourcePtr       biop;
+  Int2               bmol = 0;
+  BioseqPtr          bsp;
+  SeqFeatPtr         cds;
+  Char               date [40];
+  SeqMgrDescContext  dcontext;
+  Char               div [10];
+  BioseqPtr          dna;
+  DatePtr            dp;
+  CharPtr            ebmol;
+  EMBLBlockPtr       ebp;
+  SeqMgrFeatContext  fcontext;
+  GBBlockPtr         gbp;
+  Char               gene [32];
+  Boolean            genome_view;
+  GBSeqPtr           gbseq;
+  Char               id [41];
+  Int2               imol = 0;
+  IndxPtr            index;
+  Int2               istrand;
+  Boolean            is_nm = FALSE;
+  Boolean            is_np = FALSE;
+  Boolean            is_nz = FALSE;
+  Boolean            is_transgenic = FALSE;
+  Char               len [32];
+  Int4               length;
+  size_t             loclen;
+  Char               locus [41];
+  MolInfoPtr         mip;
+  Char               mol [30];
+  BioseqPtr          nm = NULL;
+  OrgNamePtr         onp;
+  Uint1              origin;
+  OrgRefPtr          orp;
+  BioseqPtr          parent;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  SeqIdPtr           sip;
+  SubSourcePtr       ssp;
+  Uint1              tech;
+  Uint1              topology;
+  TextSeqIdPtr       tsip;
+  Boolean            wgsmaster = FALSE;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+
+  bbp = Asn2gbAddBlock (awp, LOCUS_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  mol [0] = '\0';
+  len [0] = '\0';
+  div [0] = '\0';
+  date [0] = '\0';
+  gene [0] = '\0';
+
+  genome_view = FALSE;
+  if (bsp->repr == Seq_repr_seg && (! SegHasParts (bsp))) {
+    genome_view = TRUE;
+  }
+  if (bsp->repr == Seq_repr_delta && (! DeltaLitOnly (bsp))) {
+    genome_view = TRUE;
+  }
+
+  /* locus id */
+
+  sip = NULL;
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_OTHER) {
+      tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+      if (tsip != NULL) {
+        if (StringNCmp (tsip->accession, "NM_", 3) == 0 ||
+            StringNCmp (tsip->accession, "NR_", 3) == 0 ||
+            StringNCmp (tsip->accession, "XM_", 3) == 0 ||
+            StringNCmp (tsip->accession, "XR_", 3) == 0) {
+          is_nm = TRUE;
+          nm = bsp;
+        } else if (StringNCmp (tsip->accession, "NP_", 3) == 0  ||
+                   StringNCmp (tsip->accession, "XP_", 3) == 0) {
+          is_np = TRUE;
+        } else if (StringNCmp (tsip->accession, "NZ_", 3) == 0) {
+          is_nz = TRUE;
+        }
+      }
+      break;
+    }
+    if (sip->choice == SEQID_GENBANK ||
+        sip->choice == SEQID_EMBL ||
+        sip->choice == SEQID_DDBJ) break;
+    if (sip->choice == SEQID_PIR ||
+        sip->choice == SEQID_SWISSPROT ||
+        sip->choice == SEQID_PRF ||
+        sip->choice == SEQID_PDB) break;
+    if (sip->choice == SEQID_TPG ||
+        sip->choice == SEQID_TPE ||
+        sip->choice == SEQID_TPD) break;
+  }
+  if (sip == NULL) {
+    sip = SeqIdFindBest (bsp->id, SEQID_GENBANK);
+  }
+
+  if (genome_view) {
+    SeqIdWrite (sip, locus, PRINTID_TEXTID_ACCESSION, sizeof (locus) - 1);
+  } else {
+    SeqIdWrite (sip, locus, PRINTID_TEXTID_LOCUS, sizeof (locus) - 1);
+    if (LocusHasBadChars (locus)) {
+      SeqIdWrite (sip, locus, PRINTID_TEXTID_ACCESSION, sizeof (locus) - 1);
+    }
+  }
+
+  if (is_np) {
+    sfp = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
+    if (sfp != NULL && fcontext.bsp != NULL) {
+      nm = fcontext.bsp;
+      for (sip = nm->id; sip != NULL; sip = sip->next) {
+        if (sip->choice == SEQID_OTHER) {
+          tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+          if (tsip != NULL) {
+            if (StringNCmp (tsip->accession, "NM_", 3) == 0 ||
+                StringNCmp (tsip->accession, "XM_", 3) == 0) {
+              is_nm = TRUE;
+            }
+          }
+        }
+      }
+      if (! is_nm) {
+        nm = NULL;
+      }
+    }
+  }
+  if (nm != NULL) {
+    /*
+    sfp = SeqMgrGetNextFeature (nm, NULL, SEQFEAT_GENE, 0, &fcontext);
+    if (sfp != NULL) {
+      StringNCpy_0 (gene, fcontext.label, sizeof (gene));
+      if (SeqMgrGetNextFeature (nm, sfp, SEQFEAT_GENE, 0, &fcontext) != NULL) {
+        gene [0] = '\0';
+      }
+      if (StringLen (gene) > 15) {
+        gene [0] = '\0';
+      }
+    }
+    */
+  }
+
+  /* more complicated code to get parent locus, if segmented, goes here */
+
+  if (awp->slp != NULL) {
+    length = SeqLocLen (awp->slp);
+  } else {
+    length = bsp->length;
+  }
+
+  mip = NULL;
+  tech = MI_TECH_standard;
+  origin = 0;
+  bmol = bsp->mol;
+  if (bmol > Seq_mol_aa) {
+    bmol = 0;
+  }
+  istrand = bsp->strand;
+  if (istrand > 3) {
+    istrand = 0;
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp != NULL) {
+    bbp->entityID = dcontext.entityID;
+    bbp->itemID = dcontext.itemID;
+    bbp->itemtype = OBJ_SEQDESC;
+
+    mip = (MolInfoPtr) sdp->data.ptrvalue;
+    if (mip != NULL) {
+      if (mip->biomol <= MOLECULE_TYPE_TRANSCRIBED_RNA) {
+        imol = (Int2) mip->biomol;
+      }
+      tech = mip->tech;
+
+      if (tech == MI_TECH_wgs && bsp->repr == Seq_repr_virtual) {
+
+        /* check for WGS master record */
+
+        for (sip = bsp->id; sip != NULL; sip = sip->next) {
+          switch (sip->choice) {
+            case SEQID_GENBANK :
+            case SEQID_EMBL :
+            case SEQID_DDBJ :
+              tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+              if (tsip != NULL && tsip->accession != NULL) {
+                acclen = StringLen (tsip->accession);
+                if (acclen == 12) {
+                  if (StringCmp (tsip->accession + 6, "000000") == 0) {
+                    wgsmaster = TRUE;
+                  }
+                } else if (acclen == 13) {
+                  if (StringCmp (tsip->accession + 6, "0000000") == 0) {
+                    wgsmaster = TRUE;
+                  }
+                }
+              }
+              break;
+            case SEQID_OTHER :
+              tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+              if (tsip != NULL && tsip->accession != NULL) {
+                if (StringLen (tsip->accession) == 15) {
+                  if (StringCmp (tsip->accession + 9, "000000") == 0) {
+                    wgsmaster = TRUE;
+                  }
+                }
+              }
+              break;
+            default :
+              break;
+          }
+        }
+      }
+    }
+  }
+
+  /* check inst.mol if mol-type is not-set or genomic */
+
+  if (imol <= MOLECULE_TYPE_GENOMIC) {
+    if (bmol == Seq_mol_aa) {
+      imol = MOLECULE_TYPE_PEPTIDE;
+    } else if (bmol == Seq_mol_na) {
+      imol = 0;
+    } else if (bmol == Seq_mol_rna) {
+      imol = 2;
+    } else {
+      imol = 1;
+    }
+  } else if (imol == MOLECULE_TYPE_OTHER_GENETIC_MATERIAL) {
+    if (bmol == Seq_mol_rna) {
+      imol = 2;
+    }
+  }
+
+  /* if ds-DNA don't show ds */
+
+  if (bmol == Seq_mol_dna && istrand == 2) {
+    istrand = 0;
+  }
+
+  /* ss=any RNA don't show ss */
+
+  if ((bmol > Seq_mol_rna ||
+      (imol >= MOLECULE_TYPE_MRNA && imol <= MOLECULE_TYPE_PEPTIDE)) &&
+      istrand == 1) {
+    istrand = 0;
+  }
+
+  topology = bsp->topology;
+  if (awp->slp != NULL) {
+    topology = TOPOLOGY_LINEAR;
+  }
+
+  /* length, topology, and molecule type */
+
+  if (awp->format == GENBANK_FMT) {
+
+    if (awp->newLocusLine) {
+
+      if (wgsmaster && (! is_nz)) {
+        sprintf (len, "%ld rc", (long) length);
+      } else {
+        sprintf (len, "%ld bp", (long) length);
+      }
+      sprintf (mol, "%s%-4s", strd [istrand], gnbk_mol [imol]);
+
+    } else {
+
+      if (topology == TOPOLOGY_CIRCULAR) {
+        sprintf (len, "%7ld bp", (long) length);
+        sprintf (mol, "%s%-4s  circular", strd [istrand], gnbk_mol [imol]);
+      } else {
+        sprintf (len, "%7ld bp", (long) length);
+        sprintf (mol, "%s%-4s          ", strd [istrand], gnbk_mol [imol]);
+      }
+    }
+
+  } else if (awp->format == GENPEPT_FMT) {
+
+    if (awp->newLocusLine) {
+      sprintf (len, "%ld aa", (long) length);
+    } else {
+      sprintf (len, "%7ld aa", (long) length);
+    }
+
+  } else if (awp->format == EMBL_FMT) {
+
+    if (imol < MOLECULE_TYPE_PEPTIDE) {
+      if (ajp->flags.useEmblMolType) {
+        ebmol = embl_mol [imol];
+      } else {
+        ebmol = gnbk_mol [imol];
+      }
+
+      if (topology == TOPOLOGY_CIRCULAR) {
+        sprintf (mol, "circular %s", ebmol);
+        sprintf (len, "%ld BP.", (long) length);
+      } else {
+        sprintf (mol, "%s", ebmol);
+        sprintf (len, "%ld BP.", (long) length);
+      }
+    }
+  }
+
+  /* division */
+
+  biop = NULL;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  if (sdp != NULL) {
+    biop = (BioSourcePtr) sdp->data.ptrvalue;
+  } else {
+    sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
+    if (sfp != NULL) {
+      biop = (BioSourcePtr) sfp->data.value.ptrvalue;
+    } else if (ISA_aa (bsp->mol)) {
+
+      /* if protein with no sources, get sources applicable to DNA location of CDS */
+
+      cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
+      if (cds != NULL) {
+        sfp = SeqMgrGetOverlappingSource (cds->location, &fcontext);
+        if (sfp != NULL) {
+          biop = (BioSourcePtr) sfp->data.value.ptrvalue;
+        } else {
+          dna = BioseqFindFromSeqLoc (cds->location);
+          if (dna != NULL) {
+            sdp = SeqMgrGetNextDescriptor (dna, NULL, Seq_descr_source, &dcontext);
+            if (sdp != NULL) {
+              biop = (BioSourcePtr) sdp->data.ptrvalue;
+            }
+          }
+        }
+      }
+    }
+  }
+  if (biop != NULL) {
+    origin = biop->origin;
+    orp = biop->org;
+    if (orp != NULL) {
+      onp = orp->orgname;
+      if (onp != NULL) {
+        StringNCpy_0 (div, onp->div, sizeof (div));
+      }
+    }
+    for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
+      if (ssp->subtype == SUBSRC_transgenic) {
+        is_transgenic = TRUE;
+      }
+    }
+  }
+
+  switch (tech) {
+    case MI_TECH_est :
+      StringCpy (div, "EST");
+      break;
+    case MI_TECH_sts :
+      StringCpy (div, "STS");
+      break;
+    case MI_TECH_survey :
+      StringCpy (div, "GSS");
+      break;
+    case MI_TECH_htgs_0 :
+    case MI_TECH_htgs_1 :
+    case MI_TECH_htgs_2 :
+      StringCpy (div, "HTG");
+      break;
+    case MI_TECH_htc :
+      StringCpy (div, "HTC");
+      break;
+    default :
+      break;
+  }
+
+  if (origin == ORG_MUT || origin == ORG_ARTIFICIAL || origin == ORG_SYNTHETIC || is_transgenic) {
+    StringCpy (div, "SYN");
+  }
+
+  sip = SeqIdFindBest (bsp->id, SEQID_PATENT);
+  if (sip != NULL && sip->choice == SEQID_PATENT) {
+    StringCpy (div, "PAT");
+  }
+
+  /* more complicated code for division, if necessary, goes here */
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
+  while (sdp != NULL) {
+    gbp = (GBBlockPtr) sdp->data.ptrvalue;
+    if (gbp != NULL) {
+      if (StringHasNoText (div) && gbp->div != NULL) {
+        StringCpy (div, gbp->div);
+      }
+      else if (StringCmp(gbp->div, "PAT") == 0 ||
+               StringCmp(gbp->div, "SYN") == 0 ) {
+        StringCpy (div, gbp->div);
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_genbank, &dcontext);
+  }
+
+  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_embl, &dcontext);
+    if (sdp != NULL) {
+      ebp = (EMBLBlockPtr) sdp->data.ptrvalue;
+      if (ebp != NULL) {
+        if (ebp->div == 255) {
+          if (mip == NULL) {
+            StringCpy (div, "HUM");
+          }
+        } else if (ebp->div < 18)  {
+          StringCpy (div, embl_divs [ebp->div]);
+        }
+      }
+    }
+
+    if (StringHasNoText (div)) {
+      StringCpy (div, "UNA");
+    }
+  }
+
+  /* empty division field if unable to find anything */
+
+  if (StringHasNoText (div)) {
+    StringCpy (div, "   ");
+  }
+
+  /* contig style (old genome_view flag) forces CON division */
+
+  if (awp->contig) {
+    StringCpy (div, "CON");
+  }
+
+  if (genome_view) {
+    StringCpy (div, "CON");
+  }
+
+  /* date */
+
+  best_date = GetBestDateForBsp (bsp);
+
+  if (best_date == NULL) {
+
+    /* if bsp is product of CDS or mRNA feature, get date from sfp->location bsp */
+
+    sfp = NULL;
+    if (ISA_na (bsp->mol)) {
+      sfp = SeqMgrGetRNAgivenProduct (bsp, NULL);
+    } else if (ISA_aa (bsp->mol)) {
+      sfp = SeqMgrGetCDSgivenProduct (bsp, NULL);
+    }
+    if (sfp != NULL) {
+      parent = BioseqFindFromSeqLoc (sfp->location);
+      if (parent != NULL) {
+        best_date = GetBestDateForBsp (parent);
+      }
+    }
+  }
+
+  /* convert best date */
+
+  if (best_date != NULL) {
+    DateToFF (date, best_date, FALSE);
+  }
+  if (StringHasNoText (date)) {
+    StringCpy (date, "01-JAN-1900");
+  }
+
+  if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) {
+
+    /* Create the proper locus name */
+
+    parent = awp->parent;
+    if (parent->repr == Seq_repr_seg) {
+
+      if (! StringHasNoText (awp->basename)) {
+        StringCpy (locus, awp->basename);
+        s_LocusAddSuffix (locus, awp);
+      }
+    }
+
+    /* Print the "LOCUS_NEW" line, if requested */
+
+    if (awp->newLocusLine) {
+      FFStartPrint (ffstring, awp->format, 0, 0, "LOCUS", 12, 0, 0, NULL, FALSE);
+      parent = awp->parent;
+
+      if (parent->repr == Seq_repr_seg)
+        s_LocusAdjustLength (locus,16);
+
+      if (is_nm && (! StringHasNoText (gene))) {
+        FFAddOneString (ffstring, gene, FALSE, FALSE, TILDE_IGNORE);
+      } else {
+        FFAddOneString (ffstring, locus, FALSE, FALSE, TILDE_IGNORE);
+      }
+      FFAddNChar(ffstring, ' ', 43 - StringLen(len)- ffstring->curr->pos, FALSE);
+      FFAddOneString (ffstring, len, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNChar(ffstring, ' ', 44 - ffstring->curr->pos, FALSE);
+      FFAddOneString (ffstring, mol, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNChar(ffstring, ' ', 55 - ffstring->curr->pos, FALSE);
+      if (topology == TOPOLOGY_CIRCULAR) {
+        FFAddOneString (ffstring, "circular", FALSE, FALSE, TILDE_IGNORE);
+      } else {
+        FFAddOneString (ffstring, "linear  ", FALSE, FALSE, TILDE_IGNORE);
+      }
+      FFAddNChar(ffstring, ' ', 64 - ffstring->curr->pos, FALSE);
+      FFAddOneString (ffstring, div, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNChar(ffstring, ' ', 68 - ffstring->curr->pos, FALSE);
+      FFAddOneString (ffstring, date, FALSE, FALSE, TILDE_IGNORE);
+    }
+
+    /* Else print the "LOCUS" line */
+
+    else {
+      FFStartPrint (ffstring, awp->format, 0, 0, "LOCUS", 12, 0, 0, NULL, FALSE);
+
+      if (parent->repr == Seq_repr_seg)
+        s_LocusAdjustLength (locus,16);
+
+      FFAddOneString (ffstring, locus, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNChar(ffstring, ' ', 32 - StringLen(len) - ffstring->curr->pos, FALSE);
+      FFAddOneString (ffstring, len, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNChar(ffstring, ' ', 33 - ffstring->curr->pos, FALSE);
+      FFAddOneString (ffstring, mol, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNChar(ffstring, ' ', 52 - ffstring->curr->pos, FALSE);
+      FFAddOneString (ffstring, div, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNChar(ffstring, ' ', 62 - ffstring->curr->pos, FALSE);
+      FFAddOneString (ffstring, date, FALSE, FALSE, TILDE_IGNORE);
+    }
+
+  } else if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+    FFStartPrint (ffstring, awp->format, 0, 0, NULL, 0, 5, 0, "ID", FALSE);
+    FFAddOneString (ffstring, locus, FALSE, FALSE, TILDE_IGNORE);
+    loclen = StringLen(locus);
+    if (14 - 5 - loclen > 0) {
+      FFAddNChar(ffstring, ' ', 14 - 5 - loclen, FALSE);
+    }
+    if (awp->hup) {
+      FFAddOneString (ffstring, " confidential; ", FALSE, FALSE, TILDE_IGNORE);
+    } else {
+      FFAddOneString (ffstring, " standard; ", FALSE, FALSE, TILDE_IGNORE);
+    }
+    FFAddOneString (ffstring, mol, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, "; ", FALSE, FALSE, TILDE_IGNORE);
+
+    /* conditional code to make div "UNA" goes here */
+
+    FFAddOneString (ffstring, div, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, "; ", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, len, FALSE, FALSE, TILDE_IGNORE);
+  }
+
+  /* optionally populate indexes for NCBI internal database */
+
+  if (ajp->index) {
+    index = &asp->index;
+  } else {
+    index = NULL;
+  }
+
+  if (index != NULL) {
+    Char  tmp [20];
+    index->locus = StringSave (locus);
+    index->div = StringSave (div);
+    sprintf (tmp, "%ld", (long) length);
+    index->base_cnt = StringSave (tmp);
+  }
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (gbseq != NULL) {
+    gbseq->locus = StringSave (locus);
+    gbseq->length = length;
+    gbseq->division = StringSave (div);
+    gbseq->strandedness = bsp->strand;
+    gbseq->moltype = imolToMoltype [imol];
+    gbseq->topology = topology;
+
+    for (sip = bsp->id; sip != NULL; sip = sip->next) {
+      SeqIdWrite (sip, id, PRINTID_FASTA_SHORT, sizeof (id));
+      ValNodeCopyStr (&gbseq->other_seqids, 0, id);
+    }
+
+    date [0] = '\0';
+    dp = NULL;
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_create_date, &dcontext);
+    if (sdp != NULL) {
+      dp = (DatePtr) sdp->data.ptrvalue;
+    }
+    if (dp != NULL) {
+      DateToFF (date, dp, FALSE);
+    }
+    if (StringHasNoText (date)) {
+      StringCpy (date, "01-JAN-1900");
+    }
+    gbseq->create_date = StringSave (date);
+
+    date [0] = '\0';
+    dp = NULL;
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_update_date, &dcontext);
+    if (sdp != NULL) {
+      dp = (DatePtr) sdp->data.ptrvalue;
+    }
+    if (dp != NULL) {
+      DateToFF (date, dp, FALSE);
+    }
+    if (StringHasNoText (date)) {
+      StringCpy (date, "01-JAN-1900");
+    }
+    gbseq->update_date = StringSave (date);
+  }
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 0, 5, 0, "ID");
+  FFRecycleString(ajp, ffstring);
+}
+
+NLM_EXTERN void AddDeflineBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  Char               buf[4096]; 
+  /*CharPtr          buf;
+  size_t             buflen = 4096;*/ 
+  SeqMgrDescContext  dcontext;
+  GBSeqPtr           gbseq;
+  ItemInfo           ii;
+  MolInfoPtr         mip;
+  SeqDescrPtr        sdp;
+  Uint1              tech;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+
+  bbp = Asn2gbAddBlock (awp, DEFLINE_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  tech = 0;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp != NULL) {
+    mip = (MolInfoPtr) sdp->data.ptrvalue;
+    if (mip != NULL) {
+      tech = mip->tech;
+    }
+  }
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  /*buf = MemNew (sizeof (Char) * (buflen + 1));*/
+  MemSet ((Pointer) (&ii), 0, sizeof (ItemInfo));
+  MemSet ((Pointer) buf, 0, sizeof (buf));
+
+  /* create default defline */
+
+  if ( CreateDefLine (&ii, bsp, buf, sizeof(buf), tech, NULL, NULL)) {
+    bbp->entityID = ii.entityID;
+    bbp->itemID = ii.itemID;
+    bbp->itemtype = ii.itemtype;
+
+    FFStartPrint (ffstring, awp->format, 0, 12, "DEFINITION", 12, 5, 5, "DE", TRUE);
+
+    if (StringHasNoText (buf)) {
+      FFAddOneChar (ffstring, '.', FALSE);
+    } else {
+      FFAddOneString (ffstring, buf, TRUE, TRUE, TILDE_IGNORE);
+    }
+
+    bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "DE");
+  }
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (gbseq != NULL) {
+    gbseq->definition = StringSave (buf);
+  }
+
+  FFRecycleString(ajp, ffstring);
+}
+
+static void FF_www_accession (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr cstring
+)
+{
+  if (cstring == NULL || ffstring == NULL) return;
+
+  if ( GetWWW(ajp) ) {
+    FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
+    FFAddTextToString(ffstring, "val=", cstring, ">", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, cstring, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+  } else {
+    FFAddOneString(ffstring, cstring, FALSE, FALSE, TILDE_IGNORE);
+  }
+  return;
+}
+
+/* !!! this definitely needs more work to support all classes, use proper SeqId !!! */
+
+NLM_EXTERN void AddAccessionBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  size_t             acclen;
+  SeqIdPtr           accn = NULL;
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  Char               buf [41];
+  SeqMgrDescContext  dcontext;
+  EMBLBlockPtr       ebp;
+  ValNodePtr         extra_access;
+  CharPtr            flatloc;
+  GBBlockPtr         gbp;
+  SeqIdPtr           gi = NULL;
+  GBSeqPtr           gbseq;
+  IndxPtr            index;
+  SeqIdPtr           lcl = NULL;
+  size_t             len = 0;
+  MolInfoPtr         mip;
+  SeqDescrPtr        sdp;
+  CharPtr            separator = " ";
+  SeqIdPtr           sip;
+  TextSeqIdPtr       tsip;
+  ValNodePtr         vnp;
+  CharPtr            wgsaccn = NULL;
+  CharPtr            xtra;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+  
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    switch (sip->choice) {
+      case SEQID_GI :
+        gi = sip;
+        break;
+      case SEQID_GENBANK :
+      case SEQID_EMBL :
+      case SEQID_DDBJ :
+        accn = sip;
+        tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+        if (tsip != NULL) {
+          acclen = StringLen (tsip->accession);
+          if (acclen == 12) {
+            wgsaccn = tsip->accession;
+            len = 12;
+          } else if (acclen == 13) {
+            wgsaccn = tsip->accession;
+            len = 13;
+          }
+        }
+        break;
+      case SEQID_OTHER :
+        accn = sip;
+        tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+        if (tsip != NULL) {
+          if (StringLen (tsip->accession) == 15) {
+            wgsaccn = tsip->accession;
+            len = 15;
+          }
+        }
+        break;
+      case SEQID_PIR :
+      case SEQID_SWISSPROT :
+      case SEQID_PRF :
+      case SEQID_PDB :
+        accn = sip;
+        break;
+      case SEQID_TPG :
+      case SEQID_TPE :
+      case SEQID_TPD :
+        accn = sip;
+        break;
+      case SEQID_GENERAL :
+        /* should not override better accession */
+        if (accn == NULL) {
+          accn = sip;
+        }
+        break;
+      case SEQID_LOCAL :
+        lcl = sip;
+        break;
+      default :
+        break;
+    }
+  }
+
+  sip = NULL;
+  if (accn != NULL) {
+    sip = accn;
+  } else if (lcl != NULL) {
+    sip = lcl;
+  } else if (gi != NULL) {
+    sip = gi;
+  }
+
+  if (sip == NULL) return;
+
+  SeqIdWrite (sip, buf, PRINTID_TEXTID_ACC_ONLY, sizeof (buf));
+
+  bbp = Asn2gbAddBlock (awp, ACCESSION_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  FFStartPrint (ffstring, awp->format, 0, 12, "ACCESSION", 12, 5, 5, "AC", TRUE);
+
+  if (awp->hup && accn != NULL) {
+    FFAddOneString (ffstring, ";", FALSE, FALSE, TILDE_TO_SPACES);
+
+  } else if (ajp->ajp.slp != NULL) {
+    FF_www_accession (ajp, ffstring, buf);
+    flatloc =  FFFlatLoc (ajp, bsp, ajp->ajp.slp, ajp->masterStyle);
+    FFAddTextToString (ffstring, " REGION: ", flatloc, NULL, FALSE, FALSE, TILDE_TO_SPACES);
+    MemFree (flatloc);
+  } else {
+    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+    if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+        FFAddOneChar(ffstring, ';', FALSE);
+    }
+  }
+
+  /* optionally populate indexes for NCBI internal database */
+
+  if (ajp->index) {
+    index = &asp->index;
+  } else {
+    index = NULL;
+  }
+
+  if (index != NULL) {
+    index->accession = StringSave (buf);
+  }
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (gbseq != NULL) {
+    gbseq->primary_accession = StringSave (buf);
+  }
+
+  if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) {
+    separator = " ";
+  } else if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+    separator = " ";
+  }
+
+  if (ajp->ajp.slp == NULL) {
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+    if (sdp != NULL && wgsaccn != NULL) {
+      mip = (MolInfoPtr) sdp->data.ptrvalue;
+      if (mip != NULL && mip->tech == MI_TECH_wgs) {
+        StringNCpy_0 (buf, wgsaccn, sizeof (buf));
+        acclen = StringLen (buf);
+        if (acclen == 12 && StringCmp (buf + len - 6, "000000") != 0) {
+          StringCpy (buf + len - 6, "000000");
+        } else if (acclen == 13 && StringCmp (buf + len - 7, "0000000") != 0) {
+          StringCpy (buf + len - 7, "0000000");
+        } else if (acclen == 15 && StringCmp (buf + len - 8, "00000000") != 0) {
+          StringCpy (buf + len - 8, "00000000");
+        } else {
+          buf [0] = '\0';
+        }
+        if (! StringHasNoText (buf)) {
+          if ( GetWWW(ajp) ) {
+            FFAddTextToString(ffstring, separator, "<a href=", link_wgs, FALSE, FALSE, TILDE_IGNORE);
+            FFAddTextToString(ffstring, "db=Nucleotide&cmd=Search&term=", buf, ">", FALSE, FALSE, TILDE_IGNORE);
+            FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+            FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_TO_SPACES);
+          } else {
+            FFAddTextToString(ffstring, separator, buf, NULL, FALSE, FALSE, TILDE_TO_SPACES);
+          }
+          if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+              FFAddOneChar(ffstring, ';', FALSE);
+          }
+        }
+      }
+    }
+
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
+    while (sdp != NULL) {
+
+      extra_access = NULL;
+
+      switch (dcontext.seqdesctype) {
+        case Seq_descr_genbank :
+          gbp = (GBBlockPtr) sdp->data.ptrvalue;
+          if (gbp != NULL) {
+            extra_access = gbp->extra_accessions;
+          }
+          break;
+        case Seq_descr_embl :
+          ebp = (EMBLBlockPtr) sdp->data.ptrvalue;
+          if (ebp != NULL) {
+            extra_access = ebp->extra_acc;
+          }
+          break;
+        default :
+          break;
+      }
+
+      if (extra_access != NULL) {
+        bbp->entityID = dcontext.entityID;
+        bbp->itemID = dcontext.itemID;
+        bbp->itemtype = OBJ_SEQDESC;
+      }
+
+      for (vnp = extra_access; vnp != NULL; vnp = vnp->next) {
+        xtra = (CharPtr) vnp->data.ptrvalue;
+        if (ValidateAccn (xtra) == 0) {
+          FFAddTextToString(ffstring, separator, xtra, NULL, FALSE, FALSE, TILDE_TO_SPACES);
+          if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+              FFAddOneChar(ffstring, ';', FALSE);
+          }
+
+          /* optionally populate indexes for NCBI internal database */
+
+          if (index != NULL) {
+            ValNodeCopyStrToHead (&(index->secondaries), 0, xtra);
+          }
+
+          /* optionally populate gbseq for XML-ized GenBank format */
+
+          if (gbseq != NULL) {
+            ValNodeCopyStr (&(gbseq->secondary_accessions), 0, xtra);
+          }
+        }
+      }
+
+      sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext);
+    }
+  }
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "AC");
+  FFRecycleString(ajp, ffstring);
+}
+
+NLM_EXTERN void AddVersionBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  SeqIdPtr         accn = NULL;
+  IntAsn2gbJobPtr  ajp;
+  Asn2gbSectPtr    asp;
+  BaseBlockPtr     bbp;
+  BioseqPtr        bsp;
+  Char             buf [41];
+  GBSeqPtr         gbseq;
+  Int4             gi = -1;
+  IndxPtr          index;
+  CharPtr          ptr;
+  SeqIdPtr         sip;
+  Char             tmp [41];
+  Char             version [64];
+  StringItemPtr    ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    switch (sip->choice) {
+      case SEQID_GI :
+        gi = sip->data.intvalue;
+        break;
+      case SEQID_GENBANK :
+      case SEQID_EMBL :
+      case SEQID_DDBJ :
+      case SEQID_OTHER :
+        accn = sip;
+        break;
+      case SEQID_PIR :
+      case SEQID_SWISSPROT :
+      case SEQID_PRF :
+      case SEQID_PDB :
+        accn = sip;
+        break;
+      case SEQID_TPG :
+      case SEQID_TPE :
+      case SEQID_TPD :
+        accn = sip;
+        break;
+      default :
+        break;
+    }
+  }
+
+  /* if (gi < 1 && accn == NULL) return; */
+
+  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+    if ( accn == NULL ) return;
+  }
+
+  bbp = Asn2gbAddBlock (awp, VERSION_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  /* no longer displaying NID */
+
+  /*
+  if (gi > 0) {
+    sprintf (version, "g%ld", (long) gi);
+
+    gb_StartPrint (awp->format, needInitBuff, 0, 12, "NID", 13, 5, 5, "NI", TRUE);
+    needInitBuff = FALSE;
+
+    gb_AddString (NULL, version, NULL, FALSE, FALSE, TILDE_TO_SPACES);
+
+    ff_EndPrint();
+    needEndPrint = FALSE;
+  }
+  */
+
+  version [0] = '\0';
+
+  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+    SeqIdWrite (accn, version, PRINTID_TEXTID_ACC_VER, sizeof (version) - 1);
+
+    FFStartPrint (ffstring, awp->format, 0, 12, "VERSION", 12, 5, 5, "SV", TRUE);
+
+    FFAddOneString (ffstring, version, FALSE, FALSE, TILDE_TO_SPACES);
+
+    FFAddOneChar(ffstring, '\n', FALSE);
+
+    bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "SV");
+    FFRecycleString(ajp, ffstring);
+    return;
+  }
+
+  if (accn != NULL) {
+
+    buf [0] = '\0';
+    SeqIdWrite (accn, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
+
+    if (gi > 0) {
+      sprintf (version, "%s  GI:%ld", buf, (long) gi);
+    } else {
+      sprintf (version, "%s", buf);
+    }
+
+    FFStartPrint (ffstring, awp->format, 0, 12, "VERSION", 12, 5, 5, "SV", TRUE);
+
+    FFAddTextToString (ffstring, NULL, version, "\n", FALSE, FALSE, TILDE_TO_SPACES);
+    /* optionally populate indexes for NCBI internal database */
+
+    if (ajp->index) {
+      index = &asp->index;
+    } else {
+      index = NULL;
+    }
+
+    if (index != NULL) {
+      ptr = StringChr (buf, '.');
+      if (ptr != NULL) {
+        ptr++;
+        index->version = StringSave (ptr);
+      }
+      if (gi > 0) {
+        sprintf (tmp, "%ld", (long) gi);
+        index->gi = StringSave (tmp);
+      }
+    }
+
+    /* optionally populate gbseq for XML-ized GenBank format */
+
+    if (ajp->gbseq) {
+      gbseq = &asp->gbseq;
+    } else {
+      gbseq = NULL;
+    }
+
+    if (gbseq != NULL) {
+      ptr = StringChr (buf, '.');
+      if (ptr != NULL) {
+        gbseq->accession_version = StringSave (buf);
+      }
+    }
+
+  } else if (gi > 0) {
+
+    FFStartPrint (ffstring, awp->format, 0, 0, "VERSION", 12, 5, 5, "SV", TRUE);
+
+    sprintf (version, "  GI:%ld", (long) gi);
+
+    FFAddTextToString (ffstring, NULL, version, "\n", FALSE, FALSE, TILDE_TO_SPACES);
+
+  } else {
+
+    FFStartPrint (ffstring, awp->format, 0, 0, "VERSION", 0, 5, 5, "SV", TRUE);
+    FFAddOneChar(ffstring, '\n', FALSE);
+    bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "SV");
+  }
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "SV");
+  FFRecycleString(ajp, ffstring);
+}
+
+/* only displaying PID in GenPept format */
+
+static void AddPidBlock (Asn2gbWorkPtr awp)
+
+{
+  IntAsn2gbJobPtr  ajp;
+  BaseBlockPtr  bbp;
+  BioseqPtr     bsp;
+  Int4          gi = -1;
+  SeqIdPtr      sip;
+  Char          version [64];
+  StringItemPtr ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    switch (sip->choice) {
+      case SEQID_GI :
+        gi = sip->data.intvalue;
+        break;
+      default :
+        break;
+    }
+  }
+
+  if (gi < 1) return;
+
+  bbp = Asn2gbAddBlock (awp, PID_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  FFStartPrint (ffstring, awp->format, 0, 12, "PID", 12, 5, 5, NULL, TRUE);
+
+  sprintf (version, "g%ld", (long) gi);
+  FFAddOneString (ffstring, version, FALSE, FALSE, TILDE_TO_SPACES);
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, NULL);
+  FFRecycleString(ajp, ffstring);
+}
+
+static Uint1 dbsource_fasta_order [NUM_SEQID] = {
+  33, /* 0 = not set */
+  20, /* 1 = local Object-id */
+  15, /* 2 = gibbsq */
+  16, /* 3 = gibbmt */
+  30, /* 4 = giim Giimport-id */
+  10, /* 5 = genbank */
+  10, /* 6 = embl */
+  10, /* 7 = pir */
+  10, /* 8 = swissprot */
+  15, /* 9 = patent */
+  18, /* 10 = other TextSeqId */
+  20, /* 11 = general Dbtag */
+  31, /* 12 = gi */
+  10, /* 13 = ddbj */
+  10, /* 14 = prf */
+  12, /* 15 = pdb */
+  10, /* 16 = tpg */
+  10, /* 17 = tpe */
+  10  /* 18 = tpd */
+};
+
+static void AddToUniqueSipList (
+  ValNodePtr PNTR list,
+  SeqIdPtr sip
+)
+
+{
+  ValNodePtr  vnp;
+
+  if (list == NULL || sip == NULL) return;
+  for (vnp = *list; vnp != NULL; vnp = vnp->next) {
+    if (SeqIdMatch (sip, (SeqIdPtr) vnp->data.ptrvalue)) return;
+  }
+  ValNodeAddPointer (list, 0, (Pointer) sip);
+}
+
+static Boolean WriteDbsourceID (
+  SeqIdPtr sip,
+  CharPtr str
+)
+
+{
+  DbtagPtr      db;
+  CharPtr       dt;
+  Int4          gi;
+  ObjectIdPtr   oip;
+  CharPtr       pfx;
+  PDBSeqIdPtr   psip = NULL;
+  CharPtr       prefix;
+  Boolean       rsult = FALSE;
+  CharPtr       sfx;
+  CharPtr       suffix;
+  Char          tmp [32];
+  TextSeqIdPtr  tsip = NULL;
+
+  if (sip == NULL || str == NULL) return FALSE;
+  *str = '\0';
+  switch (sip->choice) {
+    case SEQID_LOCAL :
+      oip = (ObjectIdPtr) sip->data.ptrvalue;
+      if (oip == NULL) return FALSE;
+      if (! StringHasNoText (oip->str)) {
+        StringCat (str, oip->str);
+        return TRUE;
+      } else if (oip->id > 0) {
+        sprintf (tmp, "%ld", (long) oip->id);
+        StringCat (str, tmp);
+        return TRUE;
+      }
+      return FALSE;
+    case SEQID_GI :
+      gi = (Int4) sip->data.intvalue;
+      if (gi == 0) return FALSE;
+      sprintf (tmp, "gi: %ld", (long) gi);
+      StringCat (str, tmp);
+      return TRUE;
+    case SEQID_GENERAL :
+      db = (DbtagPtr) sip->data.ptrvalue;
+      if (db == NULL) return FALSE;
+      /* !!! still need to implement this !!! */
+      return FALSE;
+    case SEQID_GENBANK :
+    case SEQID_EMBL :
+    case SEQID_DDBJ :
+    case SEQID_OTHER :
+    case SEQID_PIR :
+    case SEQID_SWISSPROT :
+    case SEQID_PRF :
+    case SEQID_TPG :
+    case SEQID_TPE :
+    case SEQID_TPD :
+      tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+      if (tsip == NULL) return FALSE;
+      break;
+    case SEQID_PDB :
+      psip = (PDBSeqIdPtr) sip->data.ptrvalue;
+      if (psip == NULL) return FALSE;
+      break;
+    default :
+      break;
+  }
+  prefix = " ";
+  suffix = NULL;
+  switch (sip->choice) {
+    case SEQID_EMBL :
+      StringCat (str, "embl ");
+      suffix = ",";
+      break;
+    case SEQID_OTHER :
+      StringCat (str, "REFSEQ: ");
+      break;
+    case SEQID_SWISSPROT :
+      StringCat (str, "swissprot: ");
+      suffix = ",";
+      break;
+    case SEQID_PIR :
+      StringCat (str, "pir: ");
+      break;
+    case SEQID_PRF :
+      StringCat (str, "prf: ");
+      break;
+    case SEQID_PDB :
+      StringCat (str, "pdb: ");
+      suffix = ",";
+      break;
+    default :
+      break;
+  }
+  pfx = NULL;
+  sfx = NULL;
+  if (tsip != NULL) {
+    if (! StringHasNoText (tsip->name)) {
+      StringCat (str, sfx);
+      StringCat (str, pfx);
+      StringCat (str, "locus ");
+      StringCat (str, tsip->name);
+      sfx = suffix;
+      pfx = prefix;
+      rsult = TRUE;
+    }
+    if (! StringHasNoText (tsip->accession)) {
+      StringCat (str, sfx);
+      StringCat (str, pfx);
+      StringCat (str, "accession ");
+      StringCat (str, tsip->accession);
+      sfx = suffix;
+      pfx = prefix;
+      rsult = TRUE;
+    }
+    if (tsip->version > 0) {
+      sprintf (tmp, ".%d", (int) tsip->version);
+      StringCat (str, tmp);
+      sfx = suffix;
+      pfx = prefix;
+    }
+    if (! StringHasNoText (tsip->release)) {
+      StringCat (str, pfx);
+      StringCat (str, "release ");
+      StringCat (str, tsip->release);
+      sfx = suffix;
+      pfx = prefix;
+    }
+    if (sip->choice == SEQID_SWISSPROT || sip->choice == SEQID_PIR || sip->choice == SEQID_PRF) {
+      StringCat (str, ";");
+    }
+    return rsult;
+  }
+  if (psip != NULL) {
+    if (! StringHasNoText (psip->mol)) {
+      StringCat (str, "molecule ");
+      StringCat (str, psip->mol);
+      sfx = suffix;
+      pfx = prefix;
+      rsult = TRUE;
+    }
+    if (psip->chain > 0) {
+      StringCat (str, sfx);
+      StringCat (str, pfx);
+      sprintf (tmp, "chain %d", (int) psip->chain);
+      StringCat (str, tmp);
+      sfx = suffix;
+      pfx = prefix;
+      rsult = TRUE;
+    }
+    if (psip->rel != NULL) {
+      StringCat (str, sfx);
+      StringCat (str, pfx);
+      StringCat (str, "release ");
+      dt = asn2gb_PrintDate (psip->rel);
+      StringCat (str, dt);
+      MemFree (dt);
+      sfx = suffix;
+      pfx = prefix;
+      rsult = TRUE;
+    }
+    StringCat (str, ";");
+    return rsult;
+  }
+  return rsult;
+}
+
+
+static void AddSPBlock (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  BioseqPtr bsp
+)
+
+{
+  CharPtr            acc;
+  DbtagPtr           db;
+  SeqMgrDescContext  dcontext;
+  Boolean            first;
+  Boolean            has_link;
+  Char               id [41];
+  ObjectIdPtr        oip;
+  SeqDescrPtr        sdp;
+  SeqIdPtr           sid;
+  SPBlockPtr         spb;
+  CharPtr            string;
+  ValNodePtr         vnp;
+  CharPtr            str;
+  Char               numbuf[40];
+
+  if (bsp == NULL) return;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_sp, &dcontext);
+  if (sdp == NULL) return;
+  spb = (SPBlockPtr) sdp->data.ptrvalue;
+  if (spb == NULL) return;
+
+  if (spb->_class == 1) {
+    FFAddOneString (ffstring, "class: standard.", FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+  } else if (spb->_class == 2) {
+    FFAddOneString (ffstring, "class: preliminary.", FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+  }
+
+  if (spb->extra_acc) {
+    FFAddOneString (ffstring, "extra accessions:", FALSE, FALSE, TILDE_IGNORE);
+    for (vnp = spb->extra_acc; vnp != NULL; vnp = vnp->next) {
+      FFAddOneString (ffstring, (CharPtr) vnp->data.ptrvalue, FALSE, FALSE, TILDE_IGNORE);
+      FFAddOneChar (ffstring, ',', FALSE );
+    }
+  }
+
+  if (spb->imeth) {
+    FFAddOneString (ffstring, "seq starts with Met", FALSE, FALSE, TILDE_IGNORE);
+  }
+
+  if (spb->plasnm != NULL) {
+    FFAddOneString (ffstring, "plasmid:", FALSE, FALSE, TILDE_IGNORE);
+    for (vnp = spb->plasnm; vnp != NULL; vnp = vnp->next) {
+      FFAddOneString (ffstring, (CharPtr) vnp->data.ptrvalue, FALSE, FALSE, TILDE_IGNORE);
+      FFAddOneChar (ffstring, ',', FALSE );
+    }
+  }
+
+  if (spb->created) {
+    string = PrintDate (spb->created);
+    FFAddOneString (ffstring, "created: ", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, string, FALSE, FALSE, TILDE_IGNORE);
+
+    MemFree (string);
+  }
+
+  if (spb->sequpd) {
+    string = PrintDate (spb->sequpd);
+    FFAddOneString (ffstring, "sequence updated: ", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, string, FALSE, FALSE, TILDE_IGNORE);
+    MemFree (string);
+  }
+
+  if (spb->annotupd) {
+    string = PrintDate (spb->annotupd);
+    FFAddOneString (ffstring, "annotation updated: ", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, string, FALSE, FALSE, TILDE_IGNORE);
+    MemFree (string);
+  }
+
+  if (spb->seqref) {
+    FFAddOneString (ffstring, "xrefs: ", FALSE, FALSE, TILDE_IGNORE);
+    first = TRUE;
+    for (sid = spb->seqref; sid != NULL; sid = sid->next) {
+      acc = NULL;
+      has_link = FALSE;
+      if (first == FALSE) {
+        FFAddOneString (ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
+      }
+      first = FALSE;
+      SeqIdWrite (sid, id, PRINTID_TEXTID_ACC_VER, sizeof (id) - 1);
+      if (sid->choice == SEQID_GI) {
+        has_link = TRUE;
+      }
+      acc = id;
+      if (acc != NULL) {
+        switch (sid->choice) {
+          case SEQID_GENBANK:
+            FFAddOneString (ffstring, "genbank accession ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_EMBL:
+            FFAddOneString (ffstring, "embl accession ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_PIR:
+            FFAddOneString (ffstring, "pir locus ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_SWISSPROT:
+            FFAddOneString (ffstring, "swissprot accession ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_DDBJ:
+            FFAddOneString (ffstring, "ddbj accession ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_PRF:
+            FFAddOneString (ffstring, "prf accession ", FALSE, FALSE, TILDE_IGNORE);
+            break;
+          case SEQID_PDB:
+            FFAddOneString (ffstring, "pdb accession ", FALSE, FALSE, TILDE_IGNORE);
+            break;
+          case SEQID_GI:
+            FFAddOneString (ffstring, "gi: ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_TPG:
+            FFAddOneString (ffstring, "genbank third party accession ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_TPE:
+            FFAddOneString (ffstring, "embl third party accession ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_TPD:
+            FFAddOneString (ffstring, "ddbj third party accession ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          default:
+            acc = NULL;
+            break; 
+        }
+      }
+      if (acc != NULL) {
+        if ( GetWWW(ajp) && has_link ) {
+          sprintf(numbuf, "%ld", (long) sid->data.intvalue);
+          FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
+          FFAddTextToString(ffstring, "val=", numbuf, ">", FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString(ffstring, acc, FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+        } else {
+          FFAddOneString(ffstring, acc, FALSE, FALSE, TILDE_IGNORE);
+        }
+      }
+    }
+  }
+
+  first = TRUE;
+  for (vnp = spb->dbref; vnp != NULL; vnp = vnp->next) {
+    db = (DbtagPtr) vnp->data.ptrvalue;
+    if (db == NULL) continue;
+    oip = db->tag;
+    if (oip == NULL) continue;
+    has_link = FALSE;
+    if (first) {
+      FFAddNewLine(ffstring);
+      FFAddOneString (ffstring, "xrefs (non-sequence databases): ", FALSE, FALSE, TILDE_IGNORE);
+      first = FALSE;
+    } else {
+      FFAddOneString (ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
+    }
+    if (StringCmp (db->db, "MGD") == 0 || StringCmp (db->db, "MGI") == 0) {
+      FFAddOneString (ffstring, "MGI", FALSE, FALSE, TILDE_IGNORE);
+    } else {
+      FFAddOneString (ffstring, db->db, FALSE, FALSE, TILDE_IGNORE);
+    }
+    if (StringCmp (db->db, "MIM") == 0) {
+      has_link = TRUE;
+    }
+
+    str = NULL;
+    if ( oip->str != NULL ) {
+      str = oip->str;
+      if (StringNCmp (str, "GO:", 3) == 0) {
+        str += 3;
+      } else if (StringNCmp (str, "MGI:", 4) == 0) {
+        str += 4;
+      }
+    } else if ( oip->id > 0 ) {
+      sprintf(numbuf, "%d", oip->id);
+      str = numbuf;
+    }
+
+    if ( !StringHasNoText(str) ) {
+      if ( GetWWW(ajp) && has_link) {
+        FFAddOneChar (ffstring, ' ', FALSE);
+        FFAddTextToString(ffstring, "<a href=", link_omim, str, FALSE, FALSE, TILDE_IGNORE);
+        FFAddTextToString(ffstring, ">", str, "</a>", FALSE, FALSE, TILDE_IGNORE);
+      } else {
+        FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
+      }
+    }
+  }
+}
+
+static void AddPIRBlock (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  BioseqPtr bsp
+)
+
+{
+  CharPtr            acc;
+  SeqMgrDescContext  dcontext;
+  Boolean            first;
+  Char               id [41];
+  CharPtr            prefix = NULL;
+  SeqDescrPtr        sdp;
+  SeqIdPtr           sid;
+  PirBlockPtr        pbp;
+
+  if (bsp == NULL) return;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pir, &dcontext);
+  if (sdp == NULL) return;
+  pbp = (PirBlockPtr) sdp->data.ptrvalue;
+  if (pbp == NULL) return;
+
+  if (pbp->host != NULL) {
+    FFAddTextToString (ffstring, "host:", pbp->host, "\n", FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->source != NULL) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString(ffstring, "source: ", pbp->source, "\n", FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->summary != NULL) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString(ffstring, "summary: ", pbp->summary, "\n", FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->genetic != NULL) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString(ffstring, "genetic: ", pbp->genetic, "\n", FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->includes != NULL) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString(ffstring, "includes: ", pbp->includes, "\n", FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->placement != NULL) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString(ffstring, "placement: ", pbp->placement, "\n", FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->superfamily != NULL) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString(ffstring, "superfamily: ", pbp->superfamily, "\n", FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->cross_reference != NULL) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString(ffstring, "xref: ", pbp->cross_reference, "\n", FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->date != NULL) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString (ffstring, "PIR dates: ", pbp->date, "\n", FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->had_punct) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddOneString (ffstring, "punctuation in sequence", FALSE, FALSE, TILDE_IGNORE);
+    prefix = ";";
+  }
+
+  if (pbp->seqref) {
+    FFAddOneString (ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddOneString (ffstring, "xrefs: ", FALSE, FALSE, TILDE_IGNORE);
+    first = TRUE;
+    for (sid = pbp->seqref; sid != NULL; sid = sid->next) {
+      acc = NULL;
+      if (first == FALSE) {
+        FFAddOneString (ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
+      }
+      first = FALSE;
+      SeqIdWrite (sid, id, PRINTID_TEXTID_ACC_VER, sizeof (id) - 1);
+      acc = id;
+      if (acc != NULL) {
+        switch (sid->choice) {
+          case SEQID_GENBANK:
+            FFAddOneString (ffstring, "genbank ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_EMBL:
+            FFAddOneString (ffstring, "embl ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_PIR:
+            FFAddOneString (ffstring, "pir ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_SWISSPROT:
+            FFAddOneString (ffstring, "swissprot ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_DDBJ:
+            FFAddOneString (ffstring, "ddbj ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_PRF:
+            FFAddOneString (ffstring, "prf ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          case SEQID_GI:
+            FFAddOneString (ffstring, "gi: ", FALSE, FALSE, TILDE_IGNORE);
+            break; 
+          default:
+            acc = NULL;
+            break; 
+        }
+      }
+      if (acc != NULL) {
+        FFAddOneString (ffstring, acc, FALSE, FALSE, TILDE_IGNORE);
+      }
+    }
+  }
+  FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_IGNORE);
+}
+
+static void AddPRFBlock (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  BioseqPtr bsp
+)
+
+{
+  SeqMgrDescContext  dcontext;
+  PrfExtSrcPtr       extra;
+  CharPtr            prefix = NULL;
+  SeqDescrPtr        sdp;
+  PrfBlockPtr        prf;
+
+  if (bsp == NULL) return;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_prf, &dcontext);
+  if (sdp == NULL) return;
+  prf = (PrfBlockPtr) sdp->data.ptrvalue;
+  if (prf == NULL) return;
+  if ( ffstring == NULL ) return;
+
+  extra = prf->extra_src;
+  if (extra != NULL) {
+
+    if (extra->host != NULL) {
+      FFAddTextToString(ffstring, "host:", extra->host, NULL, FALSE, TRUE, TILDE_IGNORE);
+      prefix = ";";
+    }
+
+    if (extra->part != NULL) {
+      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNewLine(ffstring);
+      FFAddTextToString(ffstring, "part: ", extra->part, NULL, FALSE, TRUE, TILDE_IGNORE);
+      prefix = ";";
+    }
+    if (extra->state != NULL) {
+      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNewLine(ffstring);
+      FFAddTextToString(ffstring, "state: ", extra->state, NULL, FALSE, TRUE, TILDE_IGNORE);
+      prefix = ";";
+    }
+    if (extra->strain != NULL) {
+      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNewLine(ffstring);
+      FFAddTextToString(ffstring, "strain: ", extra->strain, NULL, FALSE, TRUE, TILDE_IGNORE);
+      prefix = ";";
+    }
+    if (extra->taxon != NULL) {
+      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNewLine(ffstring);
+      FFAddTextToString(ffstring, "taxonomy: ", extra->taxon, NULL, FALSE, TRUE, TILDE_IGNORE);
+      prefix = ";";
+    }
+
+    FFAddOneChar(ffstring, '.', FALSE);
+  }
+}
+
+static void AddPDBBlock (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  BioseqPtr bsp
+)
+
+{
+  SeqMgrDescContext  dcontext;
+  CharPtr            dt;
+  CharPtr            prefix = NULL;
+  SeqDescrPtr        sdp;
+  PdbBlockPtr        pdb;
+  PdbRepPtr          replace;
+  CharPtr            str;
+  ValNodePtr         vnp;
+
+  if (bsp == NULL) return;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pdb, &dcontext);
+  if (sdp == NULL) return;
+  pdb = (PdbBlockPtr) sdp->data.ptrvalue;
+  if (pdb == NULL) return;
+
+  if (pdb->deposition != NULL) {
+    dt = asn2gb_PrintDate (pdb->deposition);
+    FFAddTextToString (ffstring, "deposition: ", dt, NULL, FALSE, TRUE, TILDE_IGNORE);
+    MemFree (dt);
+    prefix = ";";
+  }
+  if (pdb->pdbclass != NULL) {
+    FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString(ffstring, "class: ", pdb->pdbclass, NULL, FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+  if (pdb->source != NULL) {
+    FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddOneString(ffstring, "source: ", FALSE, TRUE, TILDE_IGNORE);
+    prefix = NULL;
+    for (vnp = pdb->source; vnp != NULL; vnp = vnp->next) {
+      str = (CharPtr) vnp->data.ptrvalue;
+      if (StringHasNoText (str)) continue;
+      FFAddTextToString (ffstring, prefix, str, NULL, FALSE, TRUE, TILDE_IGNORE);
+      prefix = ", ";
+    }
+    prefix = ";";
+  }
+  if (pdb->exp_method != NULL) {
+    FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    FFAddNewLine(ffstring);
+    FFAddTextToString(ffstring, "Exp. method: ", pdb->exp_method, NULL, FALSE, TRUE, TILDE_IGNORE);
+    prefix = ";";
+  }
+  replace = pdb->replace;
+  if (replace != NULL) {
+    if (replace->ids != NULL) {
+      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNewLine(ffstring);
+      FFAddOneString(ffstring, "ids replaced: ", FALSE, TRUE, TILDE_IGNORE);
+
+      prefix = NULL;
+      for (vnp = replace->ids; vnp != NULL; vnp = vnp->next) {
+        str = (CharPtr) vnp->data.ptrvalue;
+        if (StringHasNoText (str)) continue;
+        FFAddTextToString (ffstring, prefix, str, NULL, FALSE, TRUE, TILDE_IGNORE);
+        prefix = ", ";
+      }
+      prefix = ";";
+    }
+    if (replace->date != NULL) {
+      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+      FFAddNewLine(ffstring);
+
+      dt = asn2gb_PrintDate (replace->date);
+      FFAddTextToString(ffstring, "replacement date: ", dt, NULL, FALSE, TRUE, TILDE_IGNORE);
+      MemFree (dt);
+      prefix = ";";
+    }
+  }
+
+  FFAddOneChar(ffstring, '.', FALSE);
+}
+
+static CharPtr TxtSave (CharPtr text, size_t len)
+
+{
+   CharPtr str = NULL;
+
+   if ((text == NULL) || (len == 0))
+      return str;
+
+   str = MemNew((size_t)(len + 1));
+   MemCopy(str, text, (size_t)len);
+
+   return (str);
+}
+
+static Boolean FF_www_dbsource(
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr str,
+  Boolean first,
+  Uint1 choice
+)
+{
+  CharPtr  temp, end, text, loc, link=NULL;
+  Int2 j;
+
+  if( GetWWW(ajp) ) {
+    if (choice == SEQID_PIR /*|| choice == SEQID_SWISSPROT */) {
+      link = link_seq;
+    } else if (choice == SEQID_PDB || choice == SEQID_PRF) {
+      link = link_seq;
+    } else if (choice == SEQID_EMBL || choice == SEQID_GENBANK || 
+        choice == SEQID_DDBJ || choice == SEQID_GIBBSQ || 
+        choice == SEQID_GIBBMT || choice == SEQID_GI || 
+        choice == SEQID_GIIM || choice == SEQID_OTHER ||
+        choice == SEQID_TPG || choice == SEQID_TPE || choice == SEQID_TPD)  {
+      link = link_seq;
+    } else {
+      AddStringWithTildes(ffstring, str);
+      return TRUE;
+    }
+  
+    if ((text = StringStr(str, "accession")) != NULL) {
+      end = text + 9;
+      j = 9;
+      while (*end == ' ') {
+        ++end;
+        j++;
+      }
+      if (first == FALSE) {
+        FFAddOneString(ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
+      }
+      loc = TxtSave (str, end-str - j);
+      FFAddOneString(ffstring, loc, FALSE, FALSE, TILDE_IGNORE);
+      MemFree (loc);
+      for (; text != end; ++text ) {
+        FFAddOneChar(ffstring, *text, FALSE);
+      }
+
+      temp = text;
+      end += StringLen(text) - 1;
+      if ( *end != ';' ) {
+        ++end;
+      }
+
+      FFAddTextToString(ffstring, "<a href=", link, "val=", FALSE, FALSE, TILDE_IGNORE);
+      for (text = temp; text != end; ++text ) {
+        FFAddOneChar(ffstring, *text, FALSE);
+      }
+      FFAddOneString(ffstring, ">", FALSE, FALSE, TILDE_IGNORE);
+
+      text = temp;
+      FFAddOneString(ffstring, text, FALSE, FALSE, TILDE_IGNORE);
+      FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+    } else {
+      if (first == FALSE) {
+        FFAddOneString(ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
+      }
+      FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
+    }
+  } else {
+    AddStringWithTildes(ffstring, str);
+  }
+  return TRUE;
+}
+
+static CharPtr CleanQualValue (
+  CharPtr str
+)
+
+{
+  Char     ch;
+  CharPtr  dst;
+  CharPtr  ptr;
+
+  if (str == NULL || str [0] == '\0') return NULL;
+
+  dst = str;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    if (ch == '\n' || ch == '\r' || ch == '\t' || ch == '"') {
+      *dst = ' ';
+      dst++;
+    } else {
+      *dst = ch;
+      dst++;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+  *dst = '\0';
+
+  return str;
+}
+
+static CharPtr Asn2gnbkCompressSpaces (CharPtr str)
+
+{
+  Char     ch;
+  CharPtr  dst;
+  Char     last;
+  CharPtr  ptr;
+
+  if (str != NULL && str [0] != '\0') {
+    dst = str;
+    ptr = str;
+    ch = *ptr;
+    while (ch != '\0' && ch <= ' ') {
+      ptr++;
+      ch = *ptr;
+    }
+    while (ch != '\0') {
+      *dst = ch;
+      dst++;
+      ptr++;
+      last = ch;
+      ch = *ptr;
+      if (ch != '\0' && ch < ' ') {
+        *ptr = ' ';
+        ch = *ptr;
+      }
+      while (ch != '\0' && last <= ' ' && ch <= ' ') {
+        ptr++;
+        ch = *ptr;
+      }
+    }
+    *dst = '\0';
+    dst = NULL;
+    ptr = str;
+    ch = *ptr;
+    while (ch != '\0') {
+      if (ch != ' ') {
+        dst = NULL;
+      } else if (dst == NULL) {
+        dst = ptr;
+      }
+      ptr++;
+      ch = *ptr;
+    }
+    if (dst != NULL) {
+      *dst = '\0';
+    }
+  }
+  return str;
+}
+
+static CharPtr StripAllSpaces (
+  CharPtr str
+)
+
+{
+  Char     ch;
+  CharPtr  dst;
+  CharPtr  ptr;
+
+  if (str == NULL || str [0] == '\0') return NULL;
+
+  dst = str;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    if (ch == ' ' || ch == '\t') {
+    } else {
+      *dst = ch;
+      dst++;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+  *dst = '\0';
+
+  return str;
+}
+
+NLM_EXTERN void AddDbsourceBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr  ajp;
+  Asn2gbSectPtr    asp;
+  BaseBlockPtr     bbp;
+  BioseqPtr        bsp;
+  Char             buf [256];
+  SeqFeatPtr       cds;
+  DbtagPtr         db;
+  GBSeqPtr         gbseq;
+  SeqIdPtr         id;
+  ValNodePtr       list = NULL;
+  BioseqPtr        nuc;
+  SeqIdPtr         sip;
+  SeqLocPtr        slp;
+  CharPtr          str;
+  Boolean          unknown = TRUE;
+  ValNodePtr       vnp;
+  StringItemPtr    ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  bbp = Asn2gbAddBlock (awp, DBSOURCE_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  FFStartPrint (ffstring, awp->format, 0, 12, "DBSOURCE", 12, 5, 5, NULL, TRUE);
+
+  sip = SeqIdSelect (bsp->id, dbsource_fasta_order, NUM_SEQID);
+
+  if (sip != NULL) {
+
+    switch (sip->choice) {
+      case SEQID_PIR :
+      case SEQID_SWISSPROT :
+      case SEQID_PRF :
+      case SEQID_PDB :
+        if (WriteDbsourceID (sip, buf)) {
+          FF_www_dbsource (ajp, ffstring, buf, TRUE, sip->choice);
+          FFAddNewLine(ffstring);
+          unknown = FALSE;
+        }
+        break;
+      case SEQID_GENERAL :
+        db = sip->data.ptrvalue;
+        if (db == NULL) {
+          break;
+        }
+        if (StringNCmp (db->db, "PIDe", 4) != 0 &&
+            StringNCmp (db->db, "PIDd", 4) != 0 &&
+            StringNCmp (db->db, "PID", 3) != 0) {
+          break;
+        }
+        /* if (ChoicePID) found, continue on to next set of cases */
+      case SEQID_EMBL :
+      case SEQID_GENBANK :
+      case SEQID_DDBJ :
+      case SEQID_GIBBSQ :
+      case SEQID_GIBBMT :
+      case SEQID_OTHER :
+      case SEQID_TPG :
+      case SEQID_TPE :
+      case SEQID_TPD :
+      case SEQID_GI :
+      case SEQID_GIIM :
+        cds = SeqMgrGetCDSgivenProduct (bsp, NULL);
+        if (cds == NULL) {
+          /* now may also be protein product of mature peptide feature */
+          cds = SeqMgrGetPROTgivenProduct (bsp, NULL);
+        }
+        if (cds != NULL) {
+          nuc = BioseqFindFromSeqLoc (cds->location);
+          if (nuc != NULL) {
+            slp = SeqLocFindNext (cds->location, NULL);
+            while (slp != NULL) {
+              sip = SeqLocId (slp);
+              AddToUniqueSipList (&list, sip);
+              slp = SeqLocFindNext (cds->location, slp);
+            }
+            for (vnp = list; vnp != NULL; vnp = vnp->next) {
+              id = (SeqIdPtr) vnp->data.ptrvalue;
+              nuc = BioseqFindCore (id);
+              sip = NULL;
+              if (nuc != NULL) {
+                sip = SeqIdSelect (nuc->id, dbsource_fasta_order, NUM_SEQID);
+              } else if (id != NULL && id->choice == SEQID_GI) {
+                sip = GetSeqIdForGI (id->data.intvalue);
+              }
+              if (sip == NULL) {
+                sip = id;
+              }
+              if (sip != NULL) {
+                if (WriteDbsourceID (sip, buf)) {
+                  FF_www_dbsource (ajp, ffstring, buf, TRUE, sip->choice);
+                  FFAddNewLine(ffstring);
+                  unknown = FALSE;
+                }
+              }
+            }
+            ValNodeFree (list);
+          }
+        } else {
+          if (WriteDbsourceID (sip, buf)) {
+            FF_www_dbsource (ajp, ffstring, buf, TRUE, sip->choice);
+            FFAddNewLine(ffstring);
+            unknown = FALSE;
+          }
+        }
+        break;
+      default :
+        break;
+    }
+
+    switch (sip->choice) {
+      case SEQID_PIR :
+        AddPIRBlock (ajp, ffstring, bsp);
+        break;
+      case SEQID_SWISSPROT :
+        AddSPBlock (ajp, ffstring, bsp);
+        break;
+      case SEQID_PRF :
+        AddPRFBlock (ajp, ffstring, bsp);
+        break;
+      case SEQID_PDB :
+        AddPDBBlock (ajp, ffstring, bsp);
+        break;
+      default :
+        break;
+    }
+  }
+
+  if (unknown) {
+    FFAddOneString (ffstring, "UNKNOWN", FALSE, FALSE, TILDE_TO_SPACES);
+  }
+
+  str = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, NULL);
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (gbseq != NULL) {
+    if (StringNCmp (str, "DBSOURCE    ", 12) == 0) {
+      gbseq->source_db = StringSave (str + 12);
+    } else {
+      gbseq->source_db = StringSave (str);
+    }
+    CleanQualValue (gbseq->source_db);
+    Asn2gnbkCompressSpaces (gbseq->source_db);
+  }
+
+  bbp->string = str;
+  FFRecycleString(ajp, ffstring);
+}
+
+NLM_EXTERN void AddDateBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  Char               date [40];
+  SeqMgrDescContext  dcontext;
+  DatePtr            dp;
+  SeqDescrPtr        sdp;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  bbp = Asn2gbAddBlock (awp, DATE_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  date [0] = '\0';
+
+  dp = NULL;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_create_date, &dcontext);
+  if (sdp != NULL) {
+    dp = (DatePtr) sdp->data.ptrvalue;
+  }
+  if (dp != NULL) {
+    DateToFF (date, dp, FALSE);
+  }
+  if (StringHasNoText (date)) {
+    StringCpy (date, "01-JAN-1900");
+  }
+
+  FFStartPrint (ffstring, awp->format, 0, 0, NULL, 0, 5, 5, "DT", TRUE);
+  FFAddOneString (ffstring, date, FALSE, FALSE, TILDE_IGNORE);
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 0, 0, 5, 5, "DT");
+  FFRecycleString(ajp, ffstring);
+
+  bbp = Asn2gbAddBlock (awp, DATE_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_update_date, &dcontext);
+  if (sdp != NULL) {
+    dp = (DatePtr) sdp->data.ptrvalue;
+  }
+  if (dp != NULL) {
+    DateToFF (date, dp, FALSE);
+  }
+
+  FFStartPrint (ffstring, awp->format, 0, 0, NULL, 0, 5, 5, "DT", FALSE);
+  FFAddOneString (ffstring, date, FALSE, FALSE, TILDE_IGNORE);
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 0, 0, 5, 5, "DT");
+  FFRecycleString(ajp, ffstring);
+}
+
+
+#define TOTAL_ESTKW 11
+#define TOTAL_STSKW 5
+#define TOTAL_GSSKW 2
+
+static CharPtr EST_kw_array[ TOTAL_ESTKW] = {
+  "EST", "EST PROTO((expressed sequence tag)", "expressed sequence tag",
+  "EST (expressed sequence tag)", "EST(expressed sequence tag)",
+  "partial cDNA sequence", "transcribed sequence fragment", "TSR",
+  "putatively transcribed partial sequence", "UK putts"
+};
+
+static CharPtr GSS_kw_array [TOTAL_GSSKW] = {
+  "GSS", "trapped exon"
+};
+static CharPtr STS_kw_array[TOTAL_STSKW] = {
+  "STS", "STS(sequence tagged site)", "STS (sequence tagged site)",
+  "STS sequence", "sequence tagged site"
+};
+
+static Int2 MatchArrayString (
+  CharPtr array_string [],
+  Int2 totalstr,
+  CharPtr text
+)
+
+{
+  Int2 i;
+
+  for (i = 0; i < totalstr && text != NULL; i++) {
+    if (StringCmp (array_string [i], text) == 0) {
+      return (i);
+    }
+  }
+
+  return (-1);
+}
+
+static Boolean CheckSpecialKeyword (
+  Boolean is_est,
+  Boolean is_sts,
+  Boolean is_gss,
+  CharPtr kwd
+)
+
+{
+  if (kwd == NULL) return FALSE;
+
+  if (is_est) {
+    if (MatchArrayString (STS_kw_array, TOTAL_STSKW, kwd) != -1) return FALSE;
+    if (MatchArrayString (GSS_kw_array, TOTAL_GSSKW, kwd) != -1) return FALSE;
+  }
+
+  if (is_sts) {
+    if (MatchArrayString (EST_kw_array, TOTAL_ESTKW, kwd) != -1) return FALSE;
+    if (MatchArrayString (GSS_kw_array, TOTAL_GSSKW, kwd) != -1) return FALSE;
+  }
+
+  if (is_gss) {
+    if (MatchArrayString (STS_kw_array, TOTAL_STSKW, kwd) != -1) return FALSE;
+    if (MatchArrayString (EST_kw_array, TOTAL_ESTKW, kwd) != -1) return FALSE;
+  }
+
+  return TRUE;
+}
+
+static Boolean KeywordAlreadyInList (
+  ValNodePtr head,
+  CharPtr kwd
+)
+
+{
+  ValNodePtr  vnp;
+
+  for (vnp = head; vnp != NULL; vnp = vnp->next) {
+    if (StringICmp ((CharPtr) vnp->data.ptrvalue, kwd) == 0) return TRUE;
+  }
+
+  return FALSE;
+}
+
+
+NLM_EXTERN void AddKeywordsBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  Boolean            add_encode = FALSE;
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  SeqMgrDescContext  dcontext;
+  EMBLBlockPtr       ebp;
+  GBBlockPtr         gbp;
+  GBSeqPtr           gbseq;
+  ValNodePtr         head = NULL;
+  IndxPtr            index;
+  Boolean            is_est = FALSE;
+  Boolean            is_gss = FALSE;
+  Boolean            is_sts = FALSE;
+  ValNodePtr         keywords;
+  CharPtr            kwd;
+  MolInfoPtr         mip;
+  ObjectIdPtr        oip;
+  PirBlockPtr        pir;
+  PrfBlockPtr        prf;
+  SeqDescrPtr        sdp;
+  SeqIdPtr           sip;
+  SPBlockPtr         sp;
+  CharPtr            str;
+  UserObjectPtr      uop;
+  ValNodePtr         vnp;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+
+  bbp = (BaseBlockPtr) Asn2gbAddBlock (awp, KEYWORDS_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) {
+      ValNodeCopyStr (&head, 0, "Third Party Annotation");
+      ValNodeCopyStr (&head, 0, "; ");
+      ValNodeCopyStr (&head, 0, "TPA");
+    }
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp != NULL) {
+    bbp->entityID = dcontext.entityID;
+    bbp->itemID = dcontext.itemID;
+    bbp->itemtype = OBJ_SEQDESC;
+
+    mip = (MolInfoPtr) sdp->data.ptrvalue;
+    if (mip != NULL) {
+      switch (mip->tech) {
+        case MI_TECH_htgs_1 :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          ValNodeCopyStr (&head, 0, "HTG");
+          ValNodeCopyStr (&head, 0, "; ");
+          ValNodeCopyStr (&head, 0, "HTGS_PHASE1");
+          break;
+        case MI_TECH_htgs_2 :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          ValNodeCopyStr (&head, 0, "HTG");
+          ValNodeCopyStr (&head, 0, "; ");
+          ValNodeCopyStr (&head, 0, "HTGS_PHASE2");
+          break;
+        case MI_TECH_htgs_3 :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          ValNodeCopyStr (&head, 0, "HTG");
+          break;
+        case MI_TECH_est :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          is_est = TRUE;
+          ValNodeCopyStr (&head, 0, "EST");
+          break;
+        case MI_TECH_sts :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          is_sts = TRUE;
+          ValNodeCopyStr (&head, 0, "STS");
+          break;
+        case MI_TECH_survey :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          is_gss = TRUE;
+          ValNodeCopyStr (&head, 0, "GSS");
+          break;
+        case MI_TECH_fli_cdna :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          ValNodeCopyStr (&head, 0, "FLI_CDNA");
+          break;
+        case MI_TECH_htgs_0 :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          ValNodeCopyStr (&head, 0, "HTG");
+          ValNodeCopyStr (&head, 0, "; ");
+          ValNodeCopyStr (&head, 0, "HTGS_PHASE0");
+          break;
+        case MI_TECH_htc :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          ValNodeCopyStr (&head, 0, "HTC");
+          break;
+        case MI_TECH_wgs :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          ValNodeCopyStr (&head, 0, "WGS");
+          break;
+        default :
+          break;
+      }
+    }
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {
+    uop = (UserObjectPtr) sdp->data.ptrvalue;
+    if (uop != NULL) {
+      oip = uop->type;
+      if (oip != NULL && StringICmp (oip->str, "ENCODE") == 0) {
+        add_encode = TRUE;
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+  }
+  if (add_encode) {
+    if (head != NULL) {
+      ValNodeCopyStr (&head, 0, "; ");
+    }
+    ValNodeCopyStr (&head, 0, "ENCODE");
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
+  while (sdp != NULL) {
+
+    keywords = NULL;
+
+    switch (dcontext.seqdesctype) {
+      case Seq_descr_genbank :
+        gbp = (GBBlockPtr) sdp->data.ptrvalue;
+        if (gbp != NULL) {
+          keywords = gbp->keywords;
+        }
+        break;
+      case Seq_descr_embl :
+        ebp = (EMBLBlockPtr) sdp->data.ptrvalue;
+        if (ebp != NULL) {
+          keywords = ebp->keywords;
+        }
+        break;
+      case Seq_descr_pir :
+        pir = (PirBlockPtr) sdp->data.ptrvalue;
+        if (pir != NULL) {
+          keywords = pir->keywords;
+        }
+        break;
+      case Seq_descr_prf :
+        prf = (PrfBlockPtr) sdp->data.ptrvalue;
+        if (prf != NULL) {
+          keywords = prf->keywords;
+        }
+        break;
+      case Seq_descr_sp :
+        sp = (SPBlockPtr) sdp->data.ptrvalue;
+        if (sp != NULL) {
+          keywords = sp->keywords;
+        }
+        break;
+      default :
+        break;
+    }
+
+    if (keywords != NULL) {
+      bbp->entityID = dcontext.entityID;
+      bbp->itemID = dcontext.itemID;
+      bbp->itemtype = OBJ_SEQDESC;
+    }
+
+    for (vnp = keywords; vnp != NULL; vnp = vnp->next) {
+      kwd = (CharPtr) vnp->data.ptrvalue;
+      if (CheckSpecialKeyword (is_est, is_sts, is_gss, kwd)) {
+        if (! KeywordAlreadyInList (head, kwd)) {
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          ValNodeCopyStr (&head, 0, kwd);
+        }
+      }
+    }
+
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext);
+  }
+
+  FFStartPrint( ffstring, awp->format, 0, 12, "KEYWORDS", 12, 5, 5, "KW", TRUE);
+  str = MergeFFValNodeStrs (head);
+  
+  /* if no keywords were found, period will still be added by this call */
+  if ( str != NULL ) {
+    FFAddOneString (ffstring, str, TRUE, FALSE, TILDE_TO_SPACES);
+  } else {
+    FFAddOneChar(ffstring, '.', FALSE);
+  }
+
+  MemFree (str);
+
+  /* optionally populate indexes for NCBI internal database */
+
+  if (ajp->index) {
+    index = &asp->index;
+  } else {
+    index = NULL;
+  }
+
+  if (index != NULL) {
+    for (vnp = head; vnp != NULL; vnp = vnp->next) {
+      kwd = (CharPtr) vnp->data.ptrvalue;
+      if (StringCmp (kwd, "; ") == 0) continue;
+      ValNodeCopyStrToHead (&(index->keywords), 0, kwd);
+    }
+  }
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (gbseq != NULL) {
+    for (vnp = head; vnp != NULL; vnp = vnp->next) {
+      kwd = (CharPtr) vnp->data.ptrvalue;
+      if (StringCmp (kwd, "; ") == 0) continue;
+      ValNodeCopyStr (&(gbseq->keywords), 0, kwd);
+    }
+  }
+
+  ValNodeFreeData (head);
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "KW");
+
+  FFRecycleString(ajp, ffstring);
+}
+
+NLM_EXTERN void AddSegmentBlock (
+  Asn2gbWorkPtr awp,
+  Boolean onePartOfSeg
+)
+
+{
+  Char             acc [41];
+  IntAsn2gbJobPtr  ajp;
+  Asn2gbSectPtr    asp;
+  BaseBlockPtr     bbp;
+  Char             buf [32];
+  GBSeqPtr         gbseq;
+  StringItemPtr    ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+
+  if (awp->seg < 1 || awp->numsegs < 1) return;
+
+  bbp = Asn2gbAddBlock (awp, SEGMENT_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+
+  FFStartPrint (ffstring, awp->format, 0, 12, "SEGMENT", 12, 5, 5, "XX", FALSE);
+
+  if ( GetWWW(ajp) && awp->parent != NULL && onePartOfSeg) {
+    sprintf (buf, "%d of ", (int) awp->seg);
+    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+    SeqIdWrite (awp->parent->id, acc, PRINTID_TEXTID_ACC_VER, sizeof (acc) - 1);
+
+    FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
+    FFAddTextToString(ffstring, "val=", acc, ">", FALSE, FALSE, TILDE_IGNORE);
+
+    sprintf (buf, "%ld", (long) awp->numsegs);
+    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+  } else {
+    sprintf (buf, "%d of %ld", (int) awp->seg, (long) awp->numsegs);
+    FFAddOneString (ffstring, buf, FALSE, TRUE, TILDE_TO_SPACES);
+  }
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (gbseq != NULL) {
+    sprintf (buf, "%d of %ld", (int) awp->seg, (long) awp->numsegs);
+    gbseq->segment = StringSave (buf);
+  }
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "XX");
+  FFRecycleString(ajp, ffstring);
+}
+
+NLM_EXTERN void AddSourceBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  SeqFeatPtr         cds;
+  SeqMgrDescContext  dcontext;
+  BioseqPtr          dna;
+  SeqMgrFeatContext  fcontext;
+  GBBlockPtr         gbp;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  bbp = Asn2gbAddBlock (awp, SOURCE_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
+  if (sdp != NULL && (! ajp->newSourceOrg)) {
+    gbp = (GBBlockPtr) sdp->data.ptrvalue;
+    if (gbp != NULL && (! StringHasNoText (gbp->source))) {
+      bbp->entityID = dcontext.entityID;
+      bbp->itemID = dcontext.itemID;
+      bbp->itemtype = OBJ_SEQDESC;
+      return;
+    }
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  if (sdp != NULL) {
+    bbp->entityID = dcontext.entityID;
+    bbp->itemID = dcontext.itemID;
+    bbp->itemtype = OBJ_SEQDESC;
+  } else {
+    sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
+    if (sfp != NULL) {
+      bbp->entityID = fcontext.entityID;
+      bbp->itemID = fcontext.itemID;
+      bbp->itemtype = OBJ_SEQFEAT;
+    } else if (ISA_aa (bsp->mol)) {
+
+      /* if protein with no sources, get sources applicable to DNA location of CDS */
+
+      cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
+      if (cds != NULL) {
+        sfp = SeqMgrGetOverlappingSource (cds->location, &fcontext);
+        if (sfp != NULL) {
+          bbp->entityID = fcontext.entityID;
+          bbp->itemID = fcontext.itemID;
+          bbp->itemtype = OBJ_SEQFEAT;
+        } else {
+          dna = BioseqFindFromSeqLoc (cds->location);
+          if (dna != NULL) {
+            sdp = SeqMgrGetNextDescriptor (dna, NULL, Seq_descr_source, &dcontext);
+            if (sdp != NULL) {
+              bbp->entityID = dcontext.entityID;
+              bbp->itemID = dcontext.itemID;
+              bbp->itemtype = OBJ_SEQDESC;
+            }
+          }
+        }
+      }
+    }
+  }
+}
+
+NLM_EXTERN void AddOrganismBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  SeqFeatPtr         cds;
+  SeqMgrDescContext  dcontext;
+  BioseqPtr          dna;
+  SeqMgrFeatContext  fcontext;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+
+  if (awp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  bbp = Asn2gbAddBlock (awp, ORGANISM_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  if (sdp != NULL) {
+    bbp->entityID = dcontext.entityID;
+    bbp->itemID = dcontext.itemID;
+    bbp->itemtype = OBJ_SEQDESC;
+  } else {
+    sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
+    if (sfp != NULL) {
+      bbp->entityID = fcontext.entityID;
+      bbp->itemID = fcontext.itemID;
+      bbp->itemtype = OBJ_SEQFEAT;
+    } else if (ISA_aa (bsp->mol)) {
+
+      /* if protein with no sources, get sources applicable to DNA location of CDS */
+
+      cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
+      if (cds != NULL) {
+        sfp = SeqMgrGetOverlappingSource (cds->location, &fcontext);
+        if (sfp != NULL) {
+          bbp->entityID = fcontext.entityID;
+          bbp->itemID = fcontext.itemID;
+          bbp->itemtype = OBJ_SEQFEAT;
+        } else {
+          dna = BioseqFindFromSeqLoc (cds->location);
+          if (dna != NULL) {
+            sdp = SeqMgrGetNextDescriptor (dna, NULL, Seq_descr_source, &dcontext);
+            if (sdp != NULL) {
+              bbp->entityID = dcontext.entityID;
+              bbp->itemID = dcontext.itemID;
+              bbp->itemtype = OBJ_SEQDESC;
+            }
+          }
+        }
+      }
+    }
+  }
+}
+
+static RefBlockPtr AddPub (
+  Asn2gbWorkPtr awp,
+  ValNodePtr PNTR head,
+  PubdescPtr pdp
+)
+
+{
+  Char            buf [521]; /* increased for consortium in citsub */
+  CitArtPtr       cap;
+  CitBookPtr      cbp;
+  CitGenPtr       cgp;
+  CitJourPtr      cjp;
+  CitPatPtr       cpp;
+  CitSubPtr       csp;
+  DatePtr         dp = NULL;
+  Boolean         justuids = TRUE;
+  ImprintPtr      imp = NULL;
+  IntRefBlockPtr  irp;
+  RefBlockPtr     rbp;
+  ValNodePtr      vnp;
+
+  if (awp == NULL || head == NULL || pdp == NULL) return NULL;
+
+  if (awp->hideGeneRIFs) {
+    if (StringNICmp (pdp->comment, "GeneRIF", 7) == 0) return NULL;
+  } else if (awp->onlyGeneRIFs || awp->latestGeneRIFs) {
+    if (StringNICmp (pdp->comment, "GeneRIF", 7) != 0) return NULL;
+  }
+
+  rbp = (RefBlockPtr) MemNew (sizeof (IntRefBlock));
+  if (rbp == NULL) return NULL;
+  rbp->blocktype = REFERENCE_BLOCK;
+  rbp->section = awp->currsection;
+
+  rbp->serial = INT2_MAX;
+
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    switch (vnp->choice) {
+      case PUB_Gen :
+        /* may be unpublished, or may be serial number of swiss-prot reference */
+        cgp = (CitGenPtr) vnp->data.ptrvalue;
+        if (cgp != NULL) {
+          if (StringNICmp ("BackBone id_pub", cgp->cit, 15) != 0) {
+            rbp->category = REF_CAT_UNP;
+            dp = cgp->date;
+            if (cgp->serial_number > 0) {
+              rbp->serial = cgp->serial_number;
+            }
+            if (cgp->cit != NULL) {
+              if (StringNICmp ("unpublished", cgp->cit, 11) != 0 &&
+                  StringNICmp ("submitted", cgp->cit, 8) != 0 &&
+                  StringNICmp ("to be published", cgp->cit, 15) != 0 &&
+                  StringNICmp ("in press", cgp->cit, 8) != 0 &&
+                  StringStr (cgp->cit, "Journal") == NULL) {
+                if (cgp->serial_number == 0) {
+                  MemFree (rbp);
+                  return NULL;
+                }
+              }
+            } else if (cgp->journal == NULL || cgp->date == NULL) {
+              if (cgp->serial_number == 0) {
+                MemFree (rbp);
+                return NULL;
+              }
+            }
+          }
+        }
+        break;
+      case PUB_Sub :
+        rbp->category = REF_CAT_SUB;
+        csp = (CitSubPtr) vnp->data.ptrvalue;
+        if (csp != NULL) {
+          imp = csp->imp;
+          if (imp != NULL) {
+            dp = imp->date;
+          }
+          if (csp->date != NULL) {
+            dp = csp->date;
+          }
+        }
+        break;
+      case PUB_Article:
+        cap = (CitArtPtr) vnp->data.ptrvalue;
+        if (cap != NULL) {
+          switch (cap->from) {
+            case 1:
+              cjp = (CitJourPtr) cap->fromptr;
+              if (cjp != NULL) {
+                imp = (ImprintPtr) cjp->imp;
+                if (imp != NULL) {
+                  dp = imp->date;
+                }
+              }
+              break;
+            case 2:
+              cbp = (CitBookPtr) cap->fromptr;
+              if (cbp != NULL) {
+                imp = (ImprintPtr) cbp->imp;
+                if (imp != NULL) {
+                  dp = imp->date;
+                }
+              }
+              break;
+            case 3:
+              cbp = (CitBookPtr) cap->fromptr;
+              if (cbp != NULL) {
+                imp = (ImprintPtr) cbp->imp;
+                if (imp != NULL) {
+                  dp = imp->date;
+                }
+              }
+              break;
+            default:
+              break;
+          }
+        }
+        break;
+      case PUB_Book:
+        cbp = (CitBookPtr) vnp->data.ptrvalue;
+        if (cbp != NULL) {
+          imp = (ImprintPtr) cbp->imp;
+          if (imp != NULL) {
+            dp = imp->date;
+          }
+        }
+        break;
+      case PUB_Proc:
+        cbp = (CitBookPtr) vnp->data.ptrvalue;
+        if (cbp != NULL) {
+          imp = (ImprintPtr) cbp->imp;
+          if (imp != NULL) {
+            dp = imp->date;
+          }
+        }
+        break;
+      case PUB_Patent :
+        rbp->category = REF_CAT_PUB;
+        cpp = (CitPatPtr) vnp->data.ptrvalue;
+        if (cpp != NULL) {
+          if (cpp->date_issue != NULL) {
+            dp = (DatePtr) cpp->date_issue;
+          } else if (cpp->app_date != NULL) {
+            dp = (DatePtr) cpp->app_date;
+          }
+        }
+        break;
+      case PUB_Man:
+        cbp = (CitBookPtr) vnp->data.ptrvalue;
+        if (cbp != NULL) {
+          imp = (ImprintPtr) cbp->imp;
+          if (imp != NULL) {
+            dp = imp->date;
+          }
+        }
+        break;
+      case PUB_Muid :
+        rbp->muid = vnp->data.intvalue;
+        rbp->category = REF_CAT_PUB;
+        break;
+      case PUB_PMid :
+        rbp->pmid = vnp->data.intvalue;
+        rbp->category = REF_CAT_PUB;
+        break;
+      default :
+        break;
+    }
+    if (vnp->choice != PUB_Muid && vnp->choice != PUB_PMid) {
+      justuids = FALSE;
+    }
+  }
+
+  /* check for submitted vs. in-press */
+
+  if (imp != NULL) {
+    rbp->category = REF_CAT_PUB;
+    switch (imp->prepub) {
+      case 1 :
+        rbp->category = REF_CAT_UNP;
+        break;
+      case 2 :
+        rbp->category = REF_CAT_PUB;
+        break;
+      default :
+        break;
+    }
+  }
+
+  /* check for sites reftype */
+
+  if (pdp->reftype != 0) {
+    rbp->sites = pdp->reftype;
+  }
+
+  if (rbp->muid == 0 && rbp->pmid == 0) {
+    vnp = pdp->pub;
+
+    /* skip over just serial number */
+
+    if (vnp != NULL && vnp->choice == PUB_Gen && vnp->next != NULL) {
+      cgp = (CitGenPtr) vnp->data.ptrvalue;
+      if (cgp != NULL) {
+        if (StringNICmp ("BackBone id_pub", cgp->cit, 15) != 0) {
+          if (cgp->cit == NULL && cgp->journal == NULL && cgp->date == NULL && cgp->serial_number) {
+            vnp = vnp->next;
+          }
+        }
+      }
+    }
+
+    if (PubLabelUnique (vnp, buf, sizeof (buf) - 1, OM_LABEL_CONTENT, TRUE) > 0) {
+      rbp->uniquestr = StringSaveNoNull (buf);
+    }
+  }
+
+  irp = (IntRefBlockPtr) rbp;
+  irp->date = DateDup (dp);
+  irp->justuids = justuids;
+  /* if (justuids) { */
+    irp->fig = StringSaveNoNull (pdp->fig);
+    irp->maploc = StringSaveNoNull (pdp->maploc);
+    irp->poly_a = pdp->poly_a;
+  /* } */
+
+  /* if not rejected by now, link in */
+
+  ValNodeAddPointer (head, 0, rbp);
+
+  return rbp;
+}
+
+static int LIBCALLBACK SortReferences (
+  VoidPtr ptr1,
+  VoidPtr ptr2,
+  Boolean serialFirst,
+  Boolean isRefSeq
+)
+
+{
+  int             compare;
+  IntRefBlockPtr  irp1;
+  IntRefBlockPtr  irp2;
+  RefBlockPtr     rbp1;
+  RefBlockPtr     rbp2;
+  Int2            status;
+  RefBlockPtr     temp;
+  ValNodePtr      vnp1;
+  ValNodePtr      vnp2;
+
+  if (ptr1 == NULL || ptr2 == NULL) return 0;
+  vnp1 = *((ValNodePtr PNTR) ptr1);
+  vnp2 = *((ValNodePtr PNTR) ptr2);
+  if (vnp1 == NULL || vnp2 == NULL) return 0;
+  rbp1 = (RefBlockPtr) vnp1->data.ptrvalue;
+  rbp2 = (RefBlockPtr) vnp2->data.ptrvalue;
+  if (rbp1 == NULL || rbp2 == NULL) return 0;
+
+  if (serialFirst) {
+    if (rbp1->serial > rbp2->serial) {
+      return 1;
+    } else if (rbp1->serial < rbp2->serial) {
+      return -1;
+    }
+  }
+
+  /* usual first sort by published, unpublished, and cit-subs */
+
+  if (rbp1->category > rbp2->category) {
+    return 1;
+  } else if (rbp1->category < rbp2->category) {
+    return -1;
+  }
+
+  /* for RefSeq, newer publications first, so temporarily swap pointers */
+
+  if (isRefSeq) {
+    temp = rbp1;
+    rbp1 = rbp2;
+    rbp2 = temp;
+  }
+
+  /* within class, sort by date, older publications first (except RefSeq) */
+
+  irp1 = (IntRefBlockPtr) rbp1;
+  irp2 = (IntRefBlockPtr) rbp2;
+  status = DateMatch (irp1->date, irp2->date, FALSE);
+  if (status == 1 || status == -1) return status;
+
+  /* if dates (e.g., years) match, try to distinguish by uids */
+
+  if (rbp1->pmid != 0 && rbp2->pmid != 0) {
+    if (rbp1->pmid > rbp2->pmid) {
+      return 1;
+    } else if (rbp1->pmid < rbp2->pmid) {
+      return -1;
+    }
+  }
+
+  if (rbp1->muid != 0 && rbp2->muid != 0) {
+    if (rbp1->muid > rbp2->muid) {
+      return 1;
+    } else if (rbp1->muid < rbp2->muid) {
+      return -1;
+    }
+  }
+
+  /* restore sort order after date and pmid/muid matching */
+
+  if (isRefSeq) {
+    temp = rbp1;
+    rbp1 = rbp2;
+    rbp2 = temp;
+  }
+
+  /* if same uid, one with just uids goes last to be excised but remembered */
+
+  if ((rbp1->pmid != 0 && rbp2->pmid != 0) || (rbp1->muid != 0 && rbp2->muid != 0)) {
+    if (irp1->justuids && (! irp2->justuids)) {
+      return 1;
+    } else if ((! irp1->justuids) && irp2->justuids) {
+      return -1;
+    }
+  }
+
+  /* put sites after pubs that refer to all or a range of bases */
+
+  if (rbp1->sites > 0) {
+    return 1;
+  } else if (rbp2->sites > 0) {
+    return -1;
+  }
+
+  /* for publication features, sort in explore index order */
+
+  if (irp1->index > irp2->index) {
+    return 1;
+  } else if (irp1->index < irp2->index) {
+    return -1;
+  }
+
+  /* next use author string */
+
+  if (irp1->authstr != NULL && irp2->authstr != NULL) {
+    compare = StringICmp (irp1->authstr, irp2->authstr);
+    if (compare > 0) {
+      return 1;
+    } else if (compare < 0) {
+      return -1;
+    }
+  }
+
+  /* use unique label string to determine sort order */
+
+  if (rbp1->uniquestr != NULL && rbp2->uniquestr != NULL) {
+    compare = StringICmp (rbp1->uniquestr, rbp2->uniquestr);
+    if (compare > 0) {
+      return 1;
+    } else if (compare < 0) {
+      return -1;
+    }
+  }
+
+  /* last resort for equivalent publication descriptors, sort in itemID order */
+
+  if (rbp1->itemtype == OBJ_SEQDESC && rbp2->itemtype == OBJ_SEQDESC) {
+    if (rbp1->itemID > rbp2->itemID) {
+      return 1;
+    } else if (rbp1->itemID < rbp2->itemID) {
+      return -1;
+    }
+  }
+
+  if (! serialFirst) {
+    if (rbp1->serial > rbp2->serial) {
+      return 1;
+    } else if (rbp1->serial < rbp2->serial) {
+      return -1;
+    }
+  }
+
+  return 0;
+}
+
+static int LIBCALLBACK SortReferencesA (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+
+{
+  return SortReferences (ptr1, ptr2, FALSE, FALSE);
+}
+
+static int LIBCALLBACK SortReferencesB (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+
+{
+  return SortReferences (ptr1, ptr2, TRUE, FALSE);
+}
+
+static int LIBCALLBACK SortReferencesAR (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+
+{
+  return SortReferences (ptr1, ptr2, FALSE, TRUE);
+}
+
+static int LIBCALLBACK SortReferencesBR (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+
+{
+  return SortReferences (ptr1, ptr2, TRUE, TRUE);
+}
+
+static CharPtr GetAuthorsPlusConsortium (
+  FmtType format,
+  AuthListPtr alp
+)
+
+{
+  CharPtr  consortium;
+  CharPtr  str;
+  CharPtr  tmp;
+
+  consortium = NULL;
+  str = GetAuthorsString (format, alp, &consortium, NULL, NULL);
+  if (str == NULL) return consortium;
+  if (consortium == NULL) return str;
+  tmp = MemNew (StringLen (str) + StringLen (consortium) + 5);
+  if (tmp == NULL) return NULL;
+  StringCpy (tmp, str);
+  StringCat (tmp, "; ");
+  StringCat (tmp, consortium);
+  MemFree (str);
+  MemFree (consortium);
+  return tmp;
+}
+
+static Boolean HasNoPmidOrMuid (
+  PubdescPtr pdp
+)
+
+{
+  ValNodePtr  vnp;
+
+  if (pdp == NULL) return TRUE;
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == PUB_PMid || vnp->choice == PUB_Muid) return FALSE;
+  }
+  return TRUE;
+}
+
+typedef struct cdspubs {
+  Asn2gbWorkPtr  awp;
+  BioseqPtr      target;
+  ValNodePtr     vnp;
+} CdsPubs, PNTR CdsPubsPtr;
+
+static Boolean LIBCALLBACK GetRefsOnCDS (
+  SeqFeatPtr sfp,
+  SeqMgrFeatContextPtr context
+)
+
+{
+  AuthListPtr     alp;
+  Asn2gbWorkPtr   awp;
+  CdsPubsPtr      cpp;
+  IntRefBlockPtr  irp;
+  Boolean         okay;
+  PubdescPtr      pdp;
+  RefBlockPtr     rbp;
+
+  if (sfp == NULL || context == NULL) return TRUE;
+  cpp = (CdsPubsPtr) context->userdata;
+  awp = cpp->awp;
+  if (awp == NULL) return TRUE;
+
+  okay = TRUE;
+  pdp = (PubdescPtr) sfp->data.value.ptrvalue;
+  if (awp->format == FTABLE_FMT) {
+    if (HasNoPmidOrMuid (pdp)) {
+      okay = FALSE;
+    }
+  }
+
+  if (okay) {
+    rbp = AddPub (awp, &(awp->pubhead), pdp);
+    if (rbp != NULL) {
+
+      rbp->entityID = context->entityID;
+      rbp->itemID = context->itemID;
+      rbp->itemtype = OBJ_SEQFEAT;
+
+      irp = (IntRefBlockPtr) rbp;
+      irp->loc = SeqLocMerge (cpp->target, cpp->vnp, NULL, FALSE, TRUE, FALSE);
+      alp = GetAuthListPtr (pdp, NULL);
+      if (alp != NULL) {
+        irp->authstr = GetAuthorsPlusConsortium (awp->format, alp);
+      }
+      irp->index = 0;
+    }
+  }
+
+  return TRUE;
+}
+
+static void GetRefsOnBioseq (
+  Asn2gbWorkPtr awp,
+  BioseqPtr target,
+  BioseqPtr bsp,
+  Int4 from,
+  Int4 to,
+  SeqLocPtr cdsloc
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  AuthListPtr        alp;
+  CdsPubs            cp;
+  SeqMgrDescContext  dcontext;
+  SeqMgrFeatContext  fcontext;
+  Int2               i;
+  Int2               idx;
+  IntRefBlockPtr     irp;
+  Int4Ptr            ivals;
+  Int4               left;
+  SeqLocPtr          newloc;
+  Int2               numivals;
+  Boolean            okay;
+  PubdescPtr         pdp;
+  RefBlockPtr        rbp;
+  Int4               right;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  SeqInt             sint;
+  SeqIdPtr           sip;
+  Boolean            split;
+  Int4               start;
+  Int4               stop;
+  Uint1              strand;
+  Boolean            takeIt;
+  ValNode            vn;
+  ValNodePtr         vnp;
+
+  if (awp == NULL || target == NULL || bsp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+
+  /* full length loc for descriptors */
+
+  sint.from = 0;
+  if (ajp->ajp.slp != NULL) {
+    from = SeqLocStart (ajp->ajp.slp); /* other features use awp->slp for from and to */
+  }
+  if (ajp->ajp.slp != NULL) {
+    sint.to = SeqLocLen (ajp->ajp.slp) - 1;
+    to = SeqLocStop (ajp->ajp.slp); /* other features use awp->slp for from and to */
+  } else {
+    sint.to = bsp->length - 1;
+  }
+  sint.strand = Seq_strand_plus;
+  sint.id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0)));
+  sint.if_from = NULL;
+  sint.if_to = NULL;
+
+  vn.choice = SEQLOC_INT;
+  vn.data.ptrvalue = (Pointer) &sint;
+  vn.next = NULL;
+
+  sdp = SeqMgrGetNextDescriptor (target, NULL, Seq_descr_pub, &dcontext);
+  while (sdp != NULL) {
+
+    /* check if descriptor on part already added on segmented bioseq */
+
+    okay = TRUE;
+    for (vnp = awp->pubhead; vnp != NULL && okay; vnp = vnp->next) {
+      rbp = (RefBlockPtr) vnp->data.ptrvalue;
+      if (rbp != NULL) {
+        if (rbp->entityID == dcontext.entityID &&
+            rbp->itemID == dcontext.itemID &&
+            rbp->itemtype == OBJ_SEQDESC) {
+          okay = FALSE;
+        }
+      }
+    }
+    if (awp->format == FTABLE_FMT) {
+      pdp = (PubdescPtr) sdp->data.ptrvalue;
+      if (HasNoPmidOrMuid (pdp)) {
+        okay = FALSE;
+      }
+    }
+
+    if (okay) {
+      pdp = (PubdescPtr) sdp->data.ptrvalue;
+      rbp = AddPub (awp, &(awp->pubhead), pdp);
+      if (rbp != NULL) {
+
+        rbp->entityID = dcontext.entityID;
+        rbp->itemID = dcontext.itemID;
+        rbp->itemtype = OBJ_SEQDESC;
+
+        irp = (IntRefBlockPtr) rbp;
+        irp->loc = SeqLocMerge (target, &vn, NULL, FALSE, TRUE, FALSE);
+        alp = GetAuthListPtr (pdp, NULL);
+        if (alp != NULL) {
+          irp->authstr = GetAuthorsPlusConsortium (awp->format, alp);
+        }
+        irp->index = 0;
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (target, sdp, Seq_descr_pub, &dcontext);
+  }
+
+  /* if protein with no pubs, get pubs applicable to DNA location of CDS */
+
+  if (cdsloc != NULL) {
+    cp.awp = awp;
+    cp.target = target;
+    cp.vnp = &vn;
+    SeqMgrGetAllOverlappingFeatures (cdsloc, FEATDEF_PUB, NULL, 0, LOCATION_SUBSET, (Pointer) &cp, GetRefsOnCDS);
+  }
+
+  SeqIdFree (sint.id);
+
+  /* features are indexed on parent if segmented */
+
+  bsp = awp->parent;
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_PUB, 0, &fcontext);
+  while (sfp != NULL) {
+    ivals = fcontext.ivals;
+    numivals = fcontext.numivals;
+    if (ivals != NULL && numivals > 0) {
+
+      /*
+      idx = (numivals - 1) * 2;
+      start = ivals [idx];
+      stop = ivals [idx + 1];
+      */
+
+      takeIt = FALSE;
+      for (i = 0, idx = 0; i < numivals; i++, idx += 2) {
+        start = ivals [idx];
+        stop = ivals [idx + 1];
+        if ((start <= from && stop > from) ||
+            (start < to && stop >= to) ||
+            (start >= from && stop <= to)) {
+          takeIt = TRUE;
+        }
+      }
+      if (awp->format == FTABLE_FMT) {
+        pdp = (PubdescPtr) sdp->data.ptrvalue;
+        if (HasNoPmidOrMuid (pdp)) {
+          takeIt = FALSE;
+        }
+      }
+
+      if (takeIt /* stop >= from && stop <= to */) {
+
+        /*
+        start = ivals [0] + 1;
+        stop = ivals [idx + 1] + 1;
+        */
+        pdp = (PubdescPtr) sfp->data.value.ptrvalue;
+        rbp = AddPub (awp, &(awp->pubhead), pdp);
+        if (rbp != NULL) {
+
+          rbp->entityID = fcontext.entityID;
+          rbp->itemID = fcontext.itemID;
+          rbp->itemtype = OBJ_SEQFEAT;
+
+          irp = (IntRefBlockPtr) rbp;
+          irp->loc = SeqLocMerge (target, sfp->location, NULL, FALSE, TRUE, FALSE);
+          if (ajp->ajp.slp != NULL) {
+            sip = SeqIdParse ("lcl|dummy");
+            left = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_LEFT_END);
+            right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END);
+            strand = SeqLocStrand (ajp->ajp.slp);
+            split = FALSE;
+            newloc = SeqLocReMapEx (sip, ajp->ajp.slp, irp->loc, 0, FALSE, ajp->masterStyle);
+            /*
+            newloc = SeqLocCopyRegion (sip, irp->loc, bsp, left, right, strand, &split);
+            */
+            SeqIdFree (sip);
+            if (newloc != NULL) {
+              A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
+              irp->loc = SeqLocFree (irp->loc);
+              irp->loc = newloc;
+            }
+          }
+          alp = GetAuthListPtr (pdp, NULL);
+          if (alp != NULL) {
+            irp->authstr = GetAuthorsPlusConsortium (awp->format, alp);
+          }
+          irp->index = fcontext.index;
+        }
+      }
+    }
+
+    sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_PUB, 0, &fcontext);
+  }
+}
+
+static Boolean LIBCALLBACK GetRefsOnSeg (
+  SeqLocPtr slp,
+  SeqMgrSegmentContextPtr context
+)
+
+{
+  Asn2gbWorkPtr  awp;
+  BioseqPtr      bsp;
+  Int4           from;
+  SeqLocPtr      loc;
+  SeqEntryPtr    oldscope;
+  SeqEntryPtr    sep;
+  SeqIdPtr       sip;
+  Int4           to;
+
+  if (slp == NULL || context == NULL) return FALSE;
+  awp = (Asn2gbWorkPtr) context->userdata;
+
+  from = context->cumOffset;
+  to = from + context->to - context->from;
+
+  sip = SeqLocId (slp);
+  if (sip == NULL) {
+    loc = SeqLocFindNext (slp, NULL);
+    if (loc != NULL) {
+      sip = SeqLocId (loc);
+    }
+  }
+  if (sip == NULL) return TRUE;
+
+  /* reference descriptors only on parts within entity */
+
+  sep = GetTopSeqEntryForEntityID (awp->entityID);
+  oldscope = SeqEntrySetScope (sep);
+  bsp = BioseqFind (sip);
+  SeqEntrySetScope (oldscope);
+
+  if (bsp != NULL) {
+    GetRefsOnBioseq (awp, awp->refs, bsp, from, to, NULL);
+    return TRUE;
+  }
+
+  /* if we ever want to fetch remote references, code goes here */
+
+  return TRUE;
+}
+
+NLM_EXTERN Boolean AddReferenceBlock (
+  Asn2gbWorkPtr awp,
+  Boolean isRefSeq
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  AuthListPtr        alp;
+  Asn2gbSectPtr      asp;
+  BioseqPtr          bsp;
+  SeqFeatPtr         cds;
+  Boolean            combine;
+  SeqMgrFeatContext  context;
+  CitSubPtr          csp;
+  BioseqPtr          dna;
+  Boolean            excise;
+  ValNodePtr         head = NULL;
+  Int2               i;
+  IntRefBlockPtr     irp;
+  Boolean            is_aa;
+  Boolean            is_embl = FALSE;
+  Boolean            is_patent = FALSE;
+  IntRefBlockPtr     lastirp;
+  RefBlockPtr        lastrbp;
+  ValNodePtr         next;
+  Int2               numReferences;
+  ValNodePtr         PNTR prev;
+  RefBlockPtr        rbp;
+  RefBlockPtr        PNTR referenceArray;
+  BioseqPtr          refs;
+  SubmitBlockPtr     sbp;
+  SeqIdPtr           sip;
+  SeqLocPtr          slp;
+  BioseqPtr          target;
+  ValNodePtr         vnp;
+
+  if (awp == NULL) return FALSE;
+  ajp = awp->ajp;
+  if (ajp == NULL) return FALSE;
+  asp = awp->asp;
+  if (asp == NULL) return FALSE;
+  bsp = awp->bsp;
+  refs = awp->refs;
+  if (bsp == NULL || refs == NULL) return FALSE;
+
+  /* collect publications on bioseq */
+
+  awp->pubhead = NULL;
+  GetRefsOnBioseq (awp, bsp, refs, awp->from, awp->to, NULL);
+  target = bsp;
+
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_EMBL) {
+      is_embl = TRUE;
+    } else if (sip->choice == SEQID_PATENT) {
+      is_patent = TRUE;
+    }
+  }
+
+  is_aa = (Boolean) ISA_aa (bsp->mol);
+
+  if (bsp->repr == Seq_repr_seg) {
+
+    /* collect publication descriptors on local parts */
+
+    SeqMgrExploreSegments (bsp, (Pointer) awp, GetRefsOnSeg);
+    target = awp->refs;
+  }
+
+  if (awp->pubhead == NULL && ISA_aa (bsp->mol)) {
+
+    /* if protein with no pubs, get pubs applicable to DNA location of CDS */
+
+    cds = SeqMgrGetCDSgivenProduct (bsp, &context);
+    if (cds != NULL) {
+      dna = BioseqFindFromSeqLoc (cds->location);
+      if (dna != NULL) {
+        GetRefsOnBioseq (awp, dna, dna, context.left, context.right, cds->location);
+        target = dna;
+      }
+    }
+  }
+
+  head = awp->pubhead;
+  awp->pubhead = NULL;
+
+  if (head == NULL && awp->ssp == NULL) return FALSE;
+
+  /* sort by pub/unpub/sites/sub, then date, finally existing serial */
+
+  if (isRefSeq) {
+    head = SortValNode (head, SortReferencesAR);
+  } else {
+    head = SortValNode (head, SortReferencesA);
+  }
+
+  if (awp->ssp != NULL) {
+
+    /* add seq-submit citation */
+
+    rbp = (RefBlockPtr) MemNew (sizeof (IntRefBlock));
+    if (rbp != NULL) {
+      irp = (IntRefBlockPtr) rbp;
+
+      rbp->blocktype = REFERENCE_BLOCK;
+      rbp->section = awp->currsection;
+      rbp->serial = INT2_MAX;
+      rbp->category = REF_CAT_SUB;
+
+      rbp->entityID = ajp->ajp.entityID;
+      rbp->itemID = 1;
+      rbp->itemtype = OBJ_SEQSUB_CIT;
+
+      sbp = awp->ssp->sub;
+      if (sbp != NULL) {
+        csp = sbp->cit;
+        if (csp != NULL) {
+          alp = GetAuthListPtr (NULL, csp);
+          if (alp != NULL) {
+            irp->authstr = GetAuthorsPlusConsortium (awp->format, alp);
+          }
+        }
+      }
+
+      if (awp->citSubsFirst) {
+
+        /* for DDBJ, add seq-submit citation to beginning of list */
+
+        vnp = ValNodeNew (NULL);
+        if (vnp != NULL) {
+          vnp->choice = 0;
+          vnp->data.ptrvalue = (VoidPtr) rbp;
+          vnp->next = head;
+          head = vnp;
+        }
+
+      } else {
+
+        /* for GENBANK and EMBL add seq-submit citation to end of list */
+
+        ValNodeAddPointer (&head, 0, rbp);
+      }
+    }
+  }
+
+  /* unique references, excise duplicates from list */
+
+  prev = &(head);
+  vnp = head;
+  lastrbp = NULL;
+  while (vnp != NULL) {
+    excise = FALSE;
+    combine = TRUE;
+    next = vnp->next;
+    rbp = (RefBlockPtr) vnp->data.ptrvalue;
+    if (lastrbp != NULL) {
+      lastirp = (IntRefBlockPtr) lastrbp;
+      if (rbp != NULL) {
+        irp = (IntRefBlockPtr) rbp;
+        if (lastrbp->pmid != 0 && rbp->pmid != 0) {
+          if (lastrbp->pmid == rbp->pmid) {
+            excise = TRUE;
+          }
+        } else if (lastrbp->muid != 0 && rbp->muid != 0) {
+          if (lastrbp->muid == rbp->muid) {
+            excise = TRUE;
+          }
+        } else if (lastrbp->uniquestr != NULL && rbp->uniquestr != NULL) {
+          if (StringICmp (lastrbp->uniquestr, rbp->uniquestr) == 0) {
+            if (SeqLocCompare (irp->loc, lastirp->loc) == SLC_A_EQ_B) {
+              if (StringICmp (irp->authstr, lastirp->authstr) == 0) {
+
+                /* L76496.1 - removing duplicate submission pubs */
+                excise = TRUE;
+              }
+            }
+          }
+        }
+        if (excise && lastrbp->sites == 0 && rbp->sites > 0) {
+          /* real range trumps sites */
+          combine = FALSE;
+        }
+      }
+    }
+    if (rbp != NULL) {
+      irp = (IntRefBlockPtr) rbp;
+      if (irp->justuids) {
+        if (isRefSeq && is_aa) {
+          /* if allowing justuid in protein RefSeq, try to look up dynamically */
+          excise = TRUE; /* Back to old behavior, do not fetch */
+        } else {
+          /* do not allow justuids reference to appear by itself - S79174.1 */
+          excise = TRUE;
+          /* justuids should still combine, even if no authors - S67070.1 */
+        }
+      } else if (is_embl && is_patent) {
+        /* EMBL patent records do not need author or title - A29528.1 */
+      } else if (StringHasNoText (irp->authstr)) {
+        /* do not allow no author reference to appear by itself - U07000.1 */
+        excise = TRUE;
+        combine = FALSE;
+      }
+    }
+    if (excise) {
+      *prev = vnp->next;
+      vnp->next = NULL;
+
+      /* combine locations of duplicate references */
+
+      irp = (IntRefBlockPtr) rbp;
+      lastirp = (IntRefBlockPtr) lastrbp;
+      if (combine) {
+        if (lastirp != NULL) {
+          slp = SeqLocMerge (target, lastirp->loc, irp->loc, FALSE, TRUE, FALSE);
+          lastirp->loc = SeqLocFree (lastirp->loc);
+          lastirp->loc = slp;
+        }
+        if (irp != NULL && lastirp != NULL) {
+          if ((rbp->muid == lastrbp->muid && rbp->muid != 0) ||
+              (rbp->pmid == lastrbp->pmid && rbp->pmid != 0)) {
+            if (lastirp->fig == NULL) {
+              lastirp->fig = StringSaveNoNull (irp->fig);
+            }
+            if (lastirp->maploc == NULL) {
+              lastirp->maploc = StringSaveNoNull (irp->maploc);
+            }
+            lastirp->poly_a = irp->poly_a;
+          }
+        }
+      }
+
+      /* and remove duplicate reference */
+
+      MemFree (rbp->uniquestr);
+      DateFree (irp->date);
+      SeqLocFree (irp->loc);
+      MemFree (irp->authstr);
+      MemFree (irp->fig);
+      MemFree (irp->maploc);
+      MemFree (rbp);
+      ValNodeFree (vnp);
+
+    } else {
+
+      prev = &(vnp->next);
+      lastrbp = rbp;
+    }
+    vnp = next;
+  }
+
+  /* resort by existing serial, then pub/unpub/sites/sub, then date */
+
+  if (isRefSeq) {
+    head = SortValNode (head, SortReferencesBR);
+  } else {
+    head = SortValNode (head, SortReferencesB);
+  }
+
+  if (head == NULL) return FALSE;
+
+  /* if taking best GeneRIFs, free remainder */
+
+  if (awp->latestGeneRIFs) {
+    for (vnp = head, i = 0; vnp != NULL && i < 10; vnp = vnp->next, i++) continue;
+    if (vnp != NULL) {
+      next = vnp->next;
+      vnp->next = NULL;
+      for (vnp = next; vnp != NULL; vnp = vnp->next) {
+        rbp = (RefBlockPtr) vnp->data.ptrvalue;
+        MemFree (rbp->uniquestr);
+        irp = (IntRefBlockPtr) rbp;
+        DateFree (irp->date);
+        SeqLocFree (irp->loc);
+        MemFree (irp->authstr);
+        MemFree (irp->fig);
+        MemFree (irp->maploc);
+        MemFree (rbp);
+      }
+    }
+  }
+
+  /* assign serial numbers */
+
+  for (vnp = head, i = 1; vnp != NULL; vnp = vnp->next, i++) {
+    rbp = (RefBlockPtr) vnp->data.ptrvalue;
+    if (rbp != NULL) {
+      rbp->serial = i;
+    }
+  }
+
+  /* allocate reference array for this section */
+
+  numReferences = i - 1;
+  asp->numReferences = numReferences;
+
+  if (numReferences > 0) {
+    referenceArray = (RefBlockPtr PNTR) MemNew (sizeof (RefBlockPtr) * (numReferences + 1));
+    asp->referenceArray = referenceArray;
+
+    if (referenceArray != NULL) {
+
+      /* fill in reference array */
+
+      for (vnp = head, i = 0; vnp != NULL && i < numReferences; vnp = vnp->next, i++) {
+        referenceArray [i] = (RefBlockPtr) vnp->data.ptrvalue;
+      }
+    }
+  }
+
+  /* finally link into blocks for current section */
+
+  ValNodeLink (&(awp->lastblock), head);
+  vnp = awp->lastblock;
+  if (vnp == NULL) return FALSE;
+  while (vnp->next != NULL) {
+    vnp = vnp->next;
+  }
+
+  awp->lastblock = vnp;
+  if (awp->blockList == NULL) {
+    awp->blockList = vnp;
+  }
+
+  return TRUE;
+}
+
+NLM_EXTERN void AddWGSBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  Char               buf [80];
+  SeqMgrDescContext  dcontext;
+  CharPtr            first;
+  CharPtr            last;
+  ObjectIdPtr        oip;
+  SeqDescrPtr        sdp;
+  UserFieldPtr       ufp;
+  UserObjectPtr      uop;
+  Int2               wgstype;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if ( ajp == NULL ) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) return;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {
+    uop = (UserObjectPtr) sdp->data.ptrvalue;
+    if (uop != NULL) {
+      oip = uop->type;
+      first = NULL;
+      last = NULL;
+      wgstype = 0;
+      if (oip != NULL) {
+        if (StringICmp (oip->str, "WGSProjects") == 0) {
+          wgstype = 1;
+        } else if (StringICmp (oip->str, "WGS-Scaffold-List") == 0) {
+          wgstype = 2;
+        } else if (StringICmp (oip->str, "WGS-Contig-List") == 0) {
+          wgstype = 3;
+        }
+        if (wgstype != 0) {
+          for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+            oip = ufp->label;
+            if (oip == NULL || oip->str == NULL || ufp->choice != 1) continue;
+            if (StringICmp (oip->str, "WGS_accession_first") == 0) {
+              first = (CharPtr) ufp->data.ptrvalue;
+            } else if (StringICmp (oip->str, "WGS_accession_last") == 0) {
+              last = (CharPtr) ufp->data.ptrvalue;
+            } else if (StringICmp (oip->str, "Accession_first") == 0) {
+              first = (CharPtr) ufp->data.ptrvalue;
+            } else if (StringICmp (oip->str, "Accession_last") == 0) {
+              last = (CharPtr) ufp->data.ptrvalue;
+            }
+          }
+          if (first != NULL && last != NULL) {
+            bbp = Asn2gbAddBlock (awp, WGS_BLOCK, sizeof (BaseBlock));
+            if (bbp != NULL) {
+              ffstring = FFGetString (ajp);
+              if (ffstring != NULL) {
+                if (wgstype == 1) {
+                  FFStartPrint (ffstring, awp->format, 0, 12, "WGS", 12, 0, 0, NULL, FALSE);
+                } else if (wgstype == 2) {
+                  FFStartPrint (ffstring, awp->format, 0, 12, "WGS_SCAFLD", 12, 0, 0, NULL, FALSE);
+                } else if (wgstype == 3) {
+                  FFStartPrint (ffstring, awp->format, 0, 12, "WGS_CONTIG", 12, 0, 0, NULL, FALSE);
+                }
+              
+                if ( GetWWW(ajp) ) {
+                  if (StringCmp (first, last) != 0) {
+                    FFAddTextToString(ffstring, "<a href=", link_wgs, NULL, FALSE, FALSE, TILDE_IGNORE);
+                    FFAddTextToString(ffstring, "db=Nucleotide&cmd=Search&term=", first, NULL, FALSE, FALSE, TILDE_IGNORE);
+                    FFAddTextToString(ffstring, ":", last, "[ACCN]>", FALSE, FALSE, TILDE_IGNORE);
+                    sprintf (buf, "%s-%s", first, last);
+                    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+                    FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_TO_SPACES);
+                  } else {
+                    FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
+                    FFAddTextToString(ffstring, "val=", first, ">", FALSE, FALSE, TILDE_IGNORE);
+                    sprintf (buf, "%s", first);
+                    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+                    FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_TO_SPACES);
+                  }
+                } else {
+                  if (StringCmp (first, last) != 0) {
+                    sprintf (buf, "%s-%s", first, last);
+                    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+                  } else {
+                    sprintf (buf, "%s", first);
+                    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+                  }
+                }
+
+                bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 0, 0, NULL);
+                FFRecycleString(ajp, ffstring);
+              }
+            }
+          }
+        }
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+  }
+}
+
+NLM_EXTERN void AddGenomeBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  CharPtr            accn;
+  IntAsn2gbJobPtr    ajp;
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  SeqMgrDescContext  dcontext;
+  Boolean            first = TRUE;
+  CharPtr            moltype;
+  ObjectIdPtr        oip;
+  SeqDescrPtr        sdp;
+  UserFieldPtr       ufp;
+  UserObjectPtr      uop;
+  UserFieldPtr       urf;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if ( ajp == NULL ) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) return;
+
+  bbp = Asn2gbAddBlock (awp, GENOME_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  FFStartPrint (ffstring, awp->format, 0, 12, "GENOME", 12, 0, 0, NULL, FALSE);
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {
+    uop = (UserObjectPtr) sdp->data.ptrvalue;
+    if (uop != NULL) {
+      oip = uop->type;
+      if (oip != NULL && StringICmp (oip->str, "GenomeProject") == 0) {
+        for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+          oip = ufp->label;
+          if (oip == NULL || oip->str == NULL || ufp->choice != 11) continue;
+          if (StringICmp (oip->str, "Chromosome") != 0) continue;
+          accn = NULL;
+          moltype = NULL;
+          for (urf = (UserFieldPtr) ufp->data.ptrvalue; urf != NULL; urf = urf->next) {
+            oip = urf->label;
+            if (oip == NULL || oip->str == NULL || urf->choice != 1) continue;
+            if (StringICmp (oip->str, "accession") == 0) {
+              accn = (CharPtr) urf->data.ptrvalue;
+            } else if (StringICmp (oip->str, "Moltype") == 0) {
+              moltype = (CharPtr) urf->data.ptrvalue;
+            }
+          }
+          if (! StringHasNoText (accn)) {
+            if (! first) {
+              FFAddNewLine(ffstring);
+            }
+            first = FALSE;
+            FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
+            if (! StringHasNoText (moltype)) {
+              FFAddTextToString (ffstring, " (", moltype, ")", FALSE, FALSE, TILDE_TO_SPACES);
+            }
+          }
+        }
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+  }
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 0, 0, NULL);
+  FFRecycleString(ajp, ffstring);
+}
+
+NLM_EXTERN void AddBasecountBlock (
+  Asn2gbWorkPtr awp,
+  CharPtr bases
+)
+
+{
+  IntAsn2gbJobPtr  ajp;
+  Int4             base_count [5];
+  BaseBlockPtr     bbp;
+  BioseqPtr        bsp;
+  Char             buf [80];
+  Char             ch;
+  Int2             i;
+  Int4             len;
+  StringItemPtr    ffstring;
+  CharPtr          ptr;
+  CharPtr          str;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  bbp = Asn2gbAddBlock (awp, BASECOUNT_BLOCK, sizeof (BaseBlock));
+
+  if (bases == NULL || ajp->ajp.slp != NULL) return;
+  len = bsp->length;
+  for (i = 0; i < 5; i++) {
+    base_count [i] = 0;
+  }
+
+  ptr = bases;
+  ch = *ptr;
+  while (ch != '\0') {
+    ch = TO_UPPER (ch);
+    switch (ch) {
+      case 'A' :
+        (base_count [0])++;
+        break;
+      case 'C' :
+        (base_count [1])++;
+        break;
+      case 'G' :
+        (base_count [2])++;
+        break;
+      case 'T' :
+        (base_count [3])++;
+        break;
+      default :
+        (base_count [4])++;
+        break;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+
+  if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) {
+
+    if (base_count [4] == 0) {
+      sprintf (buf, "%7ld a%7ld c%7ld g%7ld t",
+               (long) base_count [0], (long) base_count [1],
+               (long) base_count [2], (long) base_count [3]);
+    } else {
+      sprintf (buf, "%7ld a%7ld c%7ld g%7ld t%7ld others",
+               (long) base_count [0], (long) base_count [1],
+               (long) base_count [2], (long) base_count [3],
+               (long) base_count [4]);
+    }
+
+  } else if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+
+    sprintf (buf, "Sequence %ld BP; %ld A; %ld C; %ld G; %ld T; %ld other;",
+             (long) len,
+             (long) base_count [0], (long) base_count [1],
+             (long) base_count [2], (long) base_count [3],
+             (long) base_count [4]);
+  }
+
+  ffstring = FFGetString (ajp);
+  if ( ffstring == NULL ) return;
+
+  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+    FFAddOneString(ffstring, "XX\n", FALSE, FALSE, TILDE_IGNORE);
+  }
+  FFStartPrint (ffstring, awp->format, 0, 0, "BASE COUNT", 12, 5, 5, "SQ", FALSE);
+  FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+  str = FFEndPrint(ajp, ffstring, awp->format, 12, 0, 5, 5, "SQ");
+  FFRecycleString(ajp, ffstring);
+
+  bbp->string = StringSave (str);
+}
+
+NLM_EXTERN void AddOriginBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  Char               buf [67];
+  SeqMgrDescContext  dcontext;
+  GBBlockPtr         gbp;
+  SeqDescrPtr        sdp;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) return;
+  
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  bbp = Asn2gbAddBlock (awp, ORIGIN_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) {
+
+    buf [0] = '\0';
+
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
+    if (sdp != NULL) {
+      gbp = (GBBlockPtr) sdp->data.ptrvalue;
+      if (gbp != NULL && (! StringHasNoText (gbp->origin))) {
+        StringNCpy_0 (buf, gbp->origin, sizeof (buf));
+        bbp->entityID = dcontext.entityID;
+        bbp->itemID = dcontext.itemID;
+        bbp->itemtype = OBJ_SEQDESC;
+      }
+    }
+
+    FFStartPrint (ffstring, awp->format, 0, 12, "ORIGIN", 12, 0, 0, NULL, FALSE);
+
+    if (! StringHasNoText (buf)) {
+      FFAddOneString (ffstring, buf, TRUE, FALSE, TILDE_TO_SPACES);
+    }
+  }
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 0, 12, 0, 0, NULL);
+  FFRecycleString(ajp, ffstring);
+}
+
+#define BASES_PER_BLOCK 1200
+
+NLM_EXTERN void AddSequenceBlock (
+  Asn2gbWorkPtr awp,
+  CharPtr bases
+)
+
+{
+  IntAsn2gbJobPtr  ajp;
+  BioseqPtr        bsp;
+  Int4             i;
+  Int4             j;
+  Int4             len;
+  CharPtr          ptr;
+  SeqBlockPtr      sbp;
+  Int4             start;
+  Int4             stop;
+  CharPtr          str;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  if (awp->slp != NULL) {
+    len = SeqLocLen (awp->slp);
+  } else {
+    len = bsp->length;
+  }
+
+  /* if generating GBSeq XML, populate single sequence block */
+
+  if (ajp->gbseq) {
+    sbp = (SeqBlockPtr) Asn2gbAddBlock (awp, SEQUENCE_BLOCK, sizeof (SeqBlock));
+    if (sbp == NULL) return;
+
+    sbp->entityID = bsp->idx.entityID;
+    sbp->itemID = bsp->idx.itemID;
+    sbp->itemtype = OBJ_BIOSEQ;
+
+    sbp->start = 0;
+    sbp->stop = len;
+    return;
+  }
+
+  /* otherwise populate individual sequence blocks for given range */
+
+  ptr = bases;
+
+  for (start = 0; start < len; start += BASES_PER_BLOCK) {
+    sbp = (SeqBlockPtr) Asn2gbAddBlock (awp, SEQUENCE_BLOCK, sizeof (SeqBlock));
+    if (sbp == NULL) continue;
+
+    sbp->entityID = bsp->idx.entityID;
+    sbp->itemID = bsp->idx.itemID;
+    sbp->itemtype = OBJ_BIOSEQ;
+
+    stop = start + BASES_PER_BLOCK;
+    if (stop >= len) {
+      stop = len;
+    }
+
+    sbp->start = start;
+    sbp->stop = stop;
+
+    if (ptr != NULL) {
+      str = MemNew (sizeof (Char) * (BASES_PER_BLOCK + 2));
+      if (str != NULL) {
+        sbp->bases = str;
+        j = stop - start;
+        for (i = 0; i < j; i++) {
+          *str = *ptr;
+          ptr++;
+          str++;
+        }
+      }
+    }
+  }
+}
+
+NLM_EXTERN void AddContigBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  BaseBlockPtr  bbp;
+
+  if (awp == NULL) return;
+
+  bbp = Asn2gbAddBlock (awp, CONTIG_BLOCK, sizeof (BaseBlock));
+}
+
+NLM_EXTERN void AddSlashBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  BaseBlockPtr  bbp;
+  CharPtr str;
+
+  if (awp == NULL) return;
+
+  bbp = Asn2gbAddBlock (awp, SLASH_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  str = MemNew(sizeof(Char) * 4);
+  StringNCpy(str, "//\n", 4);
+
+  bbp->string = str;
+}
+
diff --git a/api/asn2gnb3.c b/api/asn2gnb3.c
new file mode 100644
index 00000000..9506e54a
--- /dev/null
+++ b/api/asn2gnb3.c
@@ -0,0 +1,4312 @@
+/*   asn2gnb3.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  asn2gnb3.c
+*
+* Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans,
+*          Mati Shomrat
+*
+* Version Creation Date:   10/21/98
+*
+* $Revision: 1.4 $
+*
+* File Description:  New GenBank flatfile generator - work in progress
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <objall.h>
+#include <objsset.h>
+#include <objsub.h>
+#include <objfdef.h>
+#include <objpubme.h>
+#include <seqport.h>
+#include <sequtil.h>
+#include <sqnutils.h>
+#include <subutil.h>
+#include <tofasta.h>
+#include <explore.h>
+#include <gbfeat.h>
+#include <gbftdef.h>
+#include <edutil.h>
+#include <alignmgr2.h>
+#include <asn2gnbi.h>
+
+#ifdef WIN_MAC
+#if __profile__
+#include <Profiler.h>
+#endif
+#endif
+
+/* ********************************************************************** */
+
+static void AddHistCommentString (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr prefix,
+  CharPtr suffix,
+  DatePtr dp,
+  SeqIdPtr ids
+)
+
+{
+  Int2      count = 0;
+  Char      buf [256];
+  Boolean   first;
+  Int4      gi = 0;
+  SeqIdPtr  sip;
+  CharPtr   strd;
+  
+  if (dp == NULL || ids == NULL || prefix == NULL || suffix == NULL || ffstring == NULL) return;
+
+  strd = asn2gb_PrintDate (dp);
+  if (strd == NULL) {
+    strd = StringSave ("?");
+  }
+
+  for (sip = ids; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_GI) {
+      gi = (long) sip->data.intvalue;
+      count++;
+    }
+  }
+
+  if (count > 1) {
+    sprintf (buf, "%s or before %s %s", prefix, strd, suffix);
+  } else {
+    sprintf (buf, "%s %s %s", prefix, strd, suffix);
+  }
+  FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
+
+  MemFree (strd);
+
+  if (gi == 0) {
+    FFAddOneString (ffstring, " gi:?", FALSE, FALSE, TILDE_EXPAND);
+    return;
+  }
+
+  first = TRUE;
+  for (sip = ids; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_GI) {
+      gi = (long) sip->data.intvalue;
+      if (! first) {
+        FFAddOneString (ffstring, ",", FALSE, FALSE, TILDE_IGNORE);
+      }
+      first = FALSE;
+      if ( GetWWW(ajp) ) {
+        FFAddOneString (ffstring, " gi:", FALSE, FALSE, TILDE_IGNORE);
+        FFAddTextToString (ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
+        sprintf (buf, "%ld", (long) gi);
+        FFAddTextToString (ffstring, "val=", buf, ">", FALSE, FALSE, TILDE_IGNORE);
+        FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
+        FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+      } else {
+        sprintf (buf, " gi:%ld", (long) gi);
+        FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
+      }
+    }
+  }
+
+  FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_EXPAND);
+}
+
+static void AddHTGSCommentString (
+  StringItemPtr ffstring,
+  BioseqPtr bsp,
+  MolInfoPtr mip
+)
+
+{
+  CharPtr      buf = NULL;
+  Char         buffer [256];
+  Int4         buflen = 0;
+  DeltaSeqPtr  dsp;
+  ValNodePtr   head = NULL;
+  Int4         num_s = 0;
+  Int4         num_g = 0;
+  CharPtr      str = NULL;
+
+  if (bsp == NULL || mip == NULL || mip->tech < 2) return;
+
+  if (bsp->repr == Seq_repr_delta) {
+    for (dsp = (DeltaSeqPtr) bsp->seq_ext, buflen = 0; dsp != NULL; dsp = dsp->next) {
+      buflen += 80;
+    }
+    if (buflen > 0) {
+      buf = MemNew ((size_t) (buflen + 1));
+      if (buf == NULL) return;
+      CountGapsInDeltaSeq (bsp, &num_s, &num_g, NULL, NULL, buf, buflen);
+    }
+  }
+
+  if (mip->tech == MI_TECH_htgs_0) {
+
+    if (num_s > 0) {
+      sprintf (buffer, "* NOTE: This record contains %ld individual~", (long) (num_g + 1));
+      ValNodeCopyStr (&head, 0, buffer);
+      ValNodeCopyStr (&head, 0, "* sequencing reads that have not been assembled into~");
+      ValNodeCopyStr (&head, 0, "* contigs. Runs of N are used to separate the reads~");
+      ValNodeCopyStr (&head, 0, "* and the order in which they appear is completely~");
+      ValNodeCopyStr (&head, 0, "* arbitrary. Low-pass sequence sampling is useful for~");
+      ValNodeCopyStr (&head, 0, "* identifying clones that may be gene-rich and allows~");
+      ValNodeCopyStr (&head, 0, "* overlap relationships among clones to be deduced.~");
+      ValNodeCopyStr (&head, 0, "* However, it should not be assumed that this clone~");
+      ValNodeCopyStr (&head, 0, "* will be sequenced to completion. In the event that~");
+      ValNodeCopyStr (&head, 0, "* the record is updated, the accession number will~");
+      ValNodeCopyStr (&head, 0, "* be preserved.");
+    }
+    ValNodeCopyStr (&head, 0, "~");
+    ValNodeCopyStr (&head, 0, buf);
+
+  } else if (mip->tech == MI_TECH_htgs_1) {
+
+    ValNodeCopyStr (&head, 0, "* NOTE: This is a \"working draft\" sequence.");
+    if (num_s > 0) {
+      sprintf (buffer, " It currently~* consists of %ld contigs. The true order of the pieces~", (long) (num_g + 1));
+      ValNodeCopyStr (&head, 0, buffer);
+      ValNodeCopyStr (&head, 0, "* is not known and their order in this sequence record is~");
+      ValNodeCopyStr (&head, 0, "* arbitrary. Gaps between the contigs are represented as~");
+      ValNodeCopyStr (&head, 0, "* runs of N, but the exact sizes of the gaps are unknown.");
+    }
+    ValNodeCopyStr (&head, 0, "~* This record will be updated with the finished sequence~");
+    ValNodeCopyStr (&head, 0, "* as soon as it is available and the accession number will~");
+    ValNodeCopyStr (&head, 0, "* be preserved.");
+    ValNodeCopyStr (&head, 0, "~");
+    ValNodeCopyStr (&head, 0, buf);
+
+  } else if (mip->tech == MI_TECH_htgs_2) {
+
+    ValNodeCopyStr (&head, 0, "* NOTE: This is a \"working draft\" sequence.");
+    if (num_s > 0) {
+      sprintf (buffer, " It currently~* consists of %ld contigs. Gaps between the contigs~", (long) (num_g + 1));
+      ValNodeCopyStr (&head, 0, buffer);
+      ValNodeCopyStr (&head, 0, "* are represented as runs of N. The order of the pieces~");
+      ValNodeCopyStr (&head, 0, "* is believed to be correct as given, however the sizes~");
+      ValNodeCopyStr (&head, 0, "* of the gaps between them are based on estimates that have~");
+      ValNodeCopyStr (&head, 0, "* provided by the submittor.");
+    }
+    ValNodeCopyStr (&head, 0, "~* This sequence will be replaced~");
+    ValNodeCopyStr (&head, 0, "* by the finished sequence as soon as it is available and~");
+    ValNodeCopyStr (&head, 0, "* the accession number will be preserved.");
+    ValNodeCopyStr (&head, 0, "~");
+    ValNodeCopyStr (&head, 0, buf);
+
+  } else if ((str = StringForSeqTech (mip->tech)) != NULL) {
+
+      sprintf (buffer, "Method: %s.", str);
+      ValNodeCopyStr (&head, 0, buffer);
+  }
+
+  MemFree (buf);
+
+  str = MergeFFValNodeStrs (head);
+
+  FFAddOneString (ffstring, str, TRUE, TRUE, TILDE_EXPAND);
+
+  MemFree (str);
+  ValNodeFreeData (head);
+}
+
+static void AddWGSMasterCommentString (
+  StringItemPtr ffstring,
+  BioseqPtr bsp,
+  CharPtr wgsaccn,
+  CharPtr wgsname
+)
+
+{
+  size_t             acclen;
+  BioSourcePtr       biop;
+  Char               buf [256];
+  SeqMgrDescContext  dcontext;
+  CharPtr            first = NULL;
+  CharPtr            last = NULL;
+  ObjectIdPtr        oip;
+  OrgRefPtr          orp;
+  SeqDescrPtr        sdp;
+  CharPtr            taxname = NULL;
+  UserFieldPtr       ufp;
+  UserObjectPtr      uop;
+  Char               ver [16];
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  if (sdp != NULL) {
+    biop = (BioSourcePtr) sdp->data.ptrvalue;
+    if (biop != NULL) {
+      orp = biop->org;
+      if (orp != NULL) {
+        taxname = orp->taxname;
+      }
+    }
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {
+    uop = (UserObjectPtr) sdp->data.ptrvalue;
+    if (uop != NULL) {
+      oip = uop->type;
+      if (oip != NULL && StringICmp (oip->str, "WGSProjects") == 0) {
+        for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+          oip = ufp->label;
+          if (oip == NULL || oip->str == NULL || ufp->choice != 1) continue;
+          if (StringICmp (oip->str, "WGS_accession_first") == 0) {
+            first = (CharPtr) ufp->data.ptrvalue;
+          } else if (StringICmp (oip->str, "WGS_accession_last") == 0) {
+            last = (CharPtr) ufp->data.ptrvalue;
+          }
+        }
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+  }
+
+  if (StringHasNoText (taxname)) {
+    taxname = "?";
+  }
+  if (StringHasNoText (first)) {
+    first = "?";
+  }
+  if (StringHasNoText (last)) {
+    last = "?";
+  }
+  ver [0] = '\0';
+  acclen = StringLen (wgsname);
+  if (acclen == 12) {
+    StringCpy (ver, wgsname + 4);
+    ver [2] = '\0';
+  } else if (acclen == 13) {
+    StringCpy (ver, wgsname + 4);
+    ver [2] = '\0';
+  } else if (acclen == 15) {
+    StringCpy (ver, wgsname + 7);
+    ver [2] = '\0';
+  }
+
+  sprintf (buf, "The %s whole genome shotgun (WGS) project has the project accession %s.", taxname, wgsaccn);
+  FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND);
+
+  sprintf (buf, "  This version of the project (%s) has the accession number %s,", ver, wgsname);
+  FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
+
+  if (StringCmp (first, last) != 0) {
+    sprintf (buf, " and consists of sequences %s-%s.", first, last);
+    FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND);
+  } else {
+    sprintf (buf, " and consists of sequence %s.", first);
+    FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND);
+  }
+}
+
+
+static CharPtr GetMolInfoCommentString (
+  BioseqPtr bsp,
+  MolInfoPtr mip
+)
+
+{
+  Boolean  is_aa;
+  CharPtr  str = NULL;
+
+  if (bsp == NULL || mip == NULL) return NULL;
+
+  is_aa = ISA_aa (bsp->mol);
+  switch (mip->completeness) {
+    case 1 :
+      str = "COMPLETENESS: full length";
+      break;
+    case 2 :
+      str = "COMPLETENESS: not full length";
+      break;
+    case 3 :
+      if (is_aa) {
+        str = "COMPLETENESS: incomplete on the amino end";
+      } else {
+        str = "COMPLETENESS: incomplete on the 5' end";
+      }
+      break;
+    case 4 :
+      if (is_aa) {
+        str = "COMPLETENESS: incomplete on the carboxy end";
+      } else {
+        str = "COMPLETENESS: incomplete on the 3' end";
+      }
+      break;
+    case 5 :
+      str = "COMPLETENESS: incomplete on both ends";
+      break;
+    case 6 :
+      if (is_aa) {
+        str = "COMPLETENESS: complete on the amino end";
+      } else {
+        str = "COMPLETENESS: complete on the 5' end";
+      }
+      break;
+    case 7 :
+      if (is_aa) {
+        str = "COMPLETENESS: complete on the carboxy end";
+      } else {
+        str = "COMPLETENESS: complete on the 3' end";
+      }
+      break;
+    default :
+      str = "COMPLETENESS: unknown";
+      break;
+  }
+
+  return str;
+}
+
+static CharPtr GetStrForBankit (
+  UserObjectPtr uop
+)
+
+{
+  CharPtr       bic = NULL, uvc = NULL, ptr;
+  ObjectIdPtr   oip;
+  UserFieldPtr  ufp;
+
+  if (uop == NULL) return NULL;
+  if ((oip = uop->type) == NULL) return NULL;
+  if (StringCmp (oip->str, "Submission") != 0) return NULL;
+
+  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+    oip = ufp->label;
+    if (StringCmp(oip->str, "UniVecComment") == 0) {
+      uvc = ufp->data.ptrvalue;
+    } else if (StringCmp(oip->str, "AdditionalComment") == 0) {
+      bic = ufp->data.ptrvalue;
+    }
+  }
+
+  if (uvc == NULL && bic == NULL) return NULL;
+
+  ptr = (CharPtr) MemNew (StringLen (uvc) + StringLen (bic) + 45);
+  if (uvc != NULL && bic != NULL) {
+    sprintf (ptr, "Vector Explanation: %s~Bankit Comment: %s", uvc, bic);
+  } else if (uvc != NULL) {
+    sprintf (ptr, "Vector Explanation: %s", uvc);
+  } else if (bic != NULL) {
+    sprintf (ptr, "Bankit Comment: %s", bic);
+  }
+
+  return ptr;
+}
+
+static CharPtr reftxt0 = " The reference sequence was derived from ";
+static CharPtr reftxt1 = " This record is predicted by genome sequence analysis and is not yet supported by experimental evidence.";
+static CharPtr reftxt2 = " This record has not yet been subject to final NCBI review.";
+static CharPtr reftxt3 = " The mRNA record is supported by experimental evidence; however, the coding sequence is predicted.";
+static CharPtr reftxt4 = " This record has undergone preliminary review of the sequence, but has not yet been subject to final review.";
+static CharPtr reftxt5 = " This record has been curated by ";
+static CharPtr reftxt6 = " This record is predicted by automated computational analysis.";
+static CharPtr reftxt7 = " This record is provided to represent a collection of whole genome shotgun sequences.";
+static CharPtr reftxt8 = " This record is derived from an annotated genomic sequence (";
+
+static CharPtr GetStatusForRefTrack (
+  UserObjectPtr uop
+)
+
+{
+  CharPtr       st;
+  ObjectIdPtr   oip;
+  UserFieldPtr  ufp, urf = NULL;
+
+  if (uop == NULL) return NULL;
+  if ((oip = uop->type) == NULL) return NULL;
+  if (StringCmp (oip->str, "RefGeneTracking") != 0) return NULL;
+  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+    oip = ufp->label;
+    if (StringCmp(oip->str, "Assembly") == 0) {
+      urf = ufp;
+    }
+  }
+  /* if (urf == NULL || urf->choice != 11) return NULL; */
+  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+    oip = ufp->label;
+    if (StringCmp (oip->str, "Status") == 0) {
+      st = (CharPtr) ufp->data.ptrvalue;
+      if (StringICmp (st, "Inferred") == 0) {
+        return "INFERRED ";
+      } else if (StringICmp (st, "Provisional") == 0) {
+        return "PROVISIONAL ";
+      } else if (StringICmp (st, "Predicted") == 0) {
+        return "PREDICTED ";
+      } else if (StringICmp (st, "Validated") == 0) {
+        return "VALIDATED ";
+      } else if (StringICmp (st, "Reviewed") == 0) {
+        return "REVIEWED ";
+      } else if (StringICmp (st, "Model") == 0) {
+        return "MODEL ";
+      } else if (StringICmp (st, "WGS") == 0) {
+        return "WGS ";
+      }
+    }
+  }
+  return NULL;
+}
+
+
+static void AddStrForRefTrack (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  UserObjectPtr uop
+)
+
+{
+  CharPtr       accn, curator = NULL, source = NULL, st;
+  ObjectIdPtr   oip;
+  UserFieldPtr  ufp, tmp, u, urf = NULL;
+  Int2          i = 0;
+  Int2          review = 0,len;
+  Boolean       is_accn;
+
+  if ( uop == NULL || ffstring == NULL ) return;
+  if ((oip = uop->type) == NULL) return;
+  if (StringCmp (oip->str, "RefGeneTracking") != 0) return;
+
+  len = StringLen (reftxt0);
+  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+    oip = ufp->label;
+    if (StringCmp(oip->str, "Assembly") == 0) {
+      urf = ufp;
+    }
+    if (StringCmp (oip->str, "Status") == 0) {
+      st = (CharPtr) ufp->data.ptrvalue;
+      if (StringICmp (st, "Inferred") == 0) {
+        review = 1;
+      } else if (StringICmp (st, "Provisional") == 0) {
+        review = 2;
+      } else if (StringICmp (st, "Predicted") == 0) {
+        review = 3;
+      } else if (StringICmp (st, "Validated") == 0) {
+        review = 4;
+      } else if (StringICmp (st, "Reviewed") == 0) {
+        review = 5;
+      } else if (StringICmp (st, "Model") == 0) {
+        review = 6;
+      } else if (StringICmp (st, "WGS") == 0) {
+        review = 7;
+      }
+    } else if (StringCmp (oip->str, "Collaborator") == 0) {
+      st = (CharPtr) ufp->data.ptrvalue;
+      if (! StringHasNoText (st)) {
+        curator = st;
+      }
+    } else if (StringCmp (oip->str, "GenomicSource") == 0) {
+      st = (CharPtr) ufp->data.ptrvalue;
+      if (! StringHasNoText (st)) {
+        source = st;
+      }
+    }
+  }
+  if (urf != NULL && urf->choice == 11) {
+    for (tmp = urf->data.ptrvalue; tmp != NULL; tmp = tmp->next) {
+      for (u = tmp->data.ptrvalue; u != NULL; u = u->next) {
+        oip = u->label;
+        if (StringCmp (oip->str, "accession") == 0 ||
+            StringCmp (oip->str, "name") == 0) {
+          i++;
+        }
+      }
+    }
+  }
+  if ( GetWWW(ajp) ) {
+    FFAddTextToString(ffstring, "<a href=", ref_link, ">", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+  } else {
+    FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
+  }
+  FFAddOneString (ffstring, ":", FALSE, FALSE, TILDE_IGNORE);
+  if (review == 1) {
+    FFAddOneString (ffstring, reftxt1, FALSE, FALSE, TILDE_IGNORE);
+  } else if (review == 2) {
+    FFAddOneString (ffstring, reftxt2, FALSE, FALSE, TILDE_IGNORE);
+  } else if (review == 3) {
+    FFAddOneString (ffstring, reftxt3, FALSE, FALSE, TILDE_IGNORE);
+  } else if (review == 4) {
+    FFAddOneString (ffstring, reftxt4, FALSE, FALSE, TILDE_IGNORE);
+  } else if (review == 5) {
+    if (curator == NULL) {
+      curator = "NCBI staff";
+    }
+    FFAddOneString (ffstring, reftxt5, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, curator, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_IGNORE);
+  } else if (review == 6) {
+    FFAddOneString (ffstring, reftxt6, FALSE, FALSE, TILDE_IGNORE);
+  } else if (review == 7) {
+    FFAddOneString (ffstring, reftxt7, FALSE, FALSE, TILDE_IGNORE);
+  }
+  if (review != 5 && curator != NULL) {
+    FFAddOneString (ffstring, reftxt5, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, curator, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_IGNORE);
+  }
+  if (source != NULL) {
+    FFAddOneString (ffstring, reftxt8, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, source, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString (ffstring, ").", FALSE, FALSE, TILDE_IGNORE);
+  }
+  if (i > 0) {
+    FFAddOneString (ffstring, reftxt0, FALSE, FALSE, TILDE_IGNORE);
+
+    for (tmp = urf->data.ptrvalue; tmp != NULL; tmp = tmp->next) {
+      is_accn = TRUE;
+      for (u = tmp->data.ptrvalue; u != NULL; u = u->next) {
+        oip = u->label;
+        if (StringCmp (oip->str, "accession") == 0) break;
+        if (StringCmp (oip->str, "name") == 0) {
+          is_accn = FALSE;
+          break;
+        }
+      }
+      if (u == NULL) continue;
+      accn = (CharPtr) u->data.ptrvalue;
+      if (StringHasNoText (accn)) continue;
+      if (is_accn && GetWWW(ajp) ) {
+        FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
+        FFAddTextToString(ffstring, "val=", accn, ">", FALSE, FALSE, TILDE_IGNORE);
+        FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
+        FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+      } else {
+        FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
+      }
+      if (tmp->next != NULL) {
+        ufp = tmp->next;
+        if (ufp->next != NULL) {
+          FFAddOneString (ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
+        } else {
+          FFAddOneString (ffstring, " and ", FALSE, FALSE, TILDE_IGNORE);
+        }
+      }
+    }
+    FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_EXPAND);
+  }
+}
+
+static CharPtr GetGenomeBuildNumber (
+  UserObjectPtr uop
+)
+
+{
+  ObjectIdPtr   oip;
+  CharPtr       str;
+  UserFieldPtr  ufp;
+
+  if (uop == NULL) return NULL;
+  if ((oip = uop->type) == NULL) return NULL;
+  if (StringCmp (oip->str, "GenomeBuild") != 0) return NULL;
+  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+    oip = ufp->label;
+    if (StringCmp(oip->str, "NcbiAnnotation") == 0) {
+      if (ufp->choice == 1) { /* string */
+        str = ufp->data.ptrvalue;
+        if (! StringHasNoText (str)) return str;
+      }
+    } else if (StringCmp (oip->str, "Annotation") == 0) {
+      if (ufp->choice == 1) { /* string */
+        str = ufp->data.ptrvalue;
+        if (! StringHasNoText (str)) {
+          if (StringNICmp (str, "NCBI build ", 11) == 0) {
+            if (! StringHasNoText (str + 11)) {
+              return (str + 11);
+            }
+          }
+        }
+      }
+    }
+  }
+  return NULL;
+}
+
+static CharPtr GetGenomeVersionNumber (
+  UserObjectPtr uop
+)
+
+{
+  ObjectIdPtr   oip;
+  CharPtr       str;
+  UserFieldPtr  ufp;
+
+  if (uop == NULL) return NULL;
+  if ((oip = uop->type) == NULL) return NULL;
+  if (StringCmp (oip->str, "GenomeBuild") != 0) return NULL;
+  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+    oip = ufp->label;
+    if (StringCmp(oip->str, "NcbiVersion") == 0) {
+      if (ufp->choice == 1) { /* string */
+        str = ufp->data.ptrvalue;
+        if (! StringHasNoText (str)) return str;
+      }
+    }
+  }
+  return NULL;
+}
+
+
+static CharPtr reftxt11 = "This record is predicted by automated computational analysis. This record is derived from an annotated genomic sequence";
+static CharPtr reftxt12 = "using gene prediction method:";
+
+static void FindModelEvidenceUop (
+  UserObjectPtr uop,
+  Pointer userdata
+)
+
+{
+  ObjectIdPtr         oip;
+  UserObjectPtr PNTR  uopp;
+
+  if (uop == NULL || userdata == NULL) return;
+  uopp = (UserObjectPtr PNTR) userdata;
+  oip = uop->type;
+  if (oip == NULL) return;
+  if (StringCmp (oip->str, "ModelEvidence") == 0) {
+    *uopp = uop;
+  }
+}
+
+static Boolean DoGetAnnotationComment (
+   BioseqPtr bsp,
+   CharPtr PNTR namep,
+   CharPtr PNTR methodp,
+   BoolPtr mrnaEv,
+   BoolPtr estEv
+)
+
+{
+  SeqMgrDescContext  dcontext;
+  CharPtr            method = NULL;
+  UserObjectPtr      moduop;
+  CharPtr            name = NULL;
+  ObjectIdPtr        oip;
+  SeqDescrPtr        sdp;
+  UserFieldPtr       ufp;
+  UserObjectPtr      uop;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {
+    uop = (UserObjectPtr) sdp->data.ptrvalue;
+    if (uop != NULL) {
+      moduop = NULL;
+      VisitUserObjectsInUop (uop, (Pointer) &moduop, FindModelEvidenceUop);
+      if (moduop != NULL) {
+        oip = moduop->type;
+        if (oip != NULL && StringCmp(oip->str, "ModelEvidence") == 0) {
+          for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+            oip = ufp->label;
+            if (oip == NULL) continue;
+            if (StringCmp(oip->str, "Contig Name") == 0) {
+              name = (CharPtr) ufp->data.ptrvalue;
+            } else if (StringCmp(oip->str, "Method") == 0) {
+              method = (CharPtr) ufp->data.ptrvalue;
+            } else if (StringCmp(oip->str, "mRNA") == 0) {
+              *mrnaEv = TRUE;
+            } else if (StringCmp(oip->str, "EST") == 0) {
+              *estEv = TRUE;
+            }
+          }
+        }
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+  }
+  if (StringHasNoText (name)) return FALSE;
+  *namep = name;
+  if (! StringHasNoText (method)) {
+    *methodp = method;
+  }
+  return TRUE;
+}
+
+static Boolean GetAnnotationComment (
+   BioseqPtr bsp,
+   CharPtr PNTR namep,
+   CharPtr PNTR methodp,
+   BoolPtr mrnaEv,
+   BoolPtr estEv
+)
+
+{
+  SeqFeatPtr  cds;
+
+  if (DoGetAnnotationComment (bsp, namep, methodp, mrnaEv, estEv)) return TRUE;
+  if (ISA_aa (bsp->mol)) {
+    cds = SeqMgrGetCDSgivenProduct (bsp, NULL);
+    if (cds != NULL) {
+      bsp = BioseqFindFromSeqLoc (cds->location);
+      if (bsp != NULL) {
+        return DoGetAnnotationComment (bsp, namep, methodp, mrnaEv, estEv);
+      }
+    }
+  }
+  return FALSE;
+}
+
+static void FindGeneFeat (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  SeqFeatPtr PNTR  sfpp;
+
+  if (sfp->data.choice != SEQFEAT_GENE) return;
+  sfpp = (SeqFeatPtr PNTR) userdata;
+  *sfpp = sfp;
+}
+
+static void FindLocusId (
+  ValNodePtr dbxref,
+  CharPtr locusIDp
+)
+
+{
+  DbtagPtr     dbt;
+  ObjectIdPtr  oip;
+  ValNodePtr   vnp;
+
+  for (vnp = dbxref; vnp != NULL; vnp = vnp->next) {
+    dbt = (DbtagPtr) vnp->data.ptrvalue;
+    if (dbt == NULL) continue;
+    if (StringICmp (dbt->db, "LocusID") != 0 && StringICmp (dbt->db, "InterimID") != 0) continue;
+    oip = dbt->tag;
+    if (oip == NULL) continue;
+    if (oip->str != NULL) {
+      StringCpy (locusIDp, oip->str);
+    } else if (oip->id > 0) {
+      sprintf (locusIDp, "%ld", (long) oip->id);
+    }
+  }
+}
+
+static Boolean GetGeneAndLocus (
+  BioseqPtr bsp,
+  CharPtr PNTR genep,
+  CharPtr locusIDp,
+  CharPtr taxIDp
+)
+
+{
+  BioSourcePtr       biop;
+  DbtagPtr           dbt;
+  SeqMgrDescContext  dcontext;
+  SeqFeatPtr         gene = NULL;
+  GeneRefPtr         grp;
+  ObjectIdPtr        oip;
+  OrgRefPtr          orp;
+  SeqDescrPtr        sdp;
+  SeqEntryPtr        sep;
+  CharPtr            str;
+  ValNodePtr         syn;
+  ValNodePtr         vnp;
+
+  sep = GetTopSeqEntryForEntityID (bsp->idx.entityID);
+  if (sep == NULL) return FALSE;
+  VisitFeaturesInSep (sep, (Pointer) &gene, FindGeneFeat);
+  if (gene == NULL) return FALSE;
+
+  grp = (GeneRefPtr) gene->data.value.ptrvalue;
+  if (grp == NULL) return FALSE;
+  if (! StringHasNoText (grp->locus)) {
+    *genep = grp->locus;
+  } else {
+    syn = grp->syn;
+    if (syn != NULL) {
+      str = (CharPtr) syn->data.ptrvalue;
+      if (! StringHasNoText (str)) {
+        *genep = str;
+      }
+    }
+  }
+  FindLocusId (gene->dbxref, locusIDp);
+  FindLocusId (grp->db, locusIDp);
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  if (sdp != NULL) {
+    biop = (BioSourcePtr) sdp->data.ptrvalue;
+    if (biop != NULL) {
+      orp = biop->org;
+      if (orp != NULL) {
+        for (vnp = orp->db; vnp != NULL; vnp = vnp->next) {
+          dbt = (DbtagPtr) vnp->data.ptrvalue;
+          if (dbt == NULL) continue;
+          if (StringCmp (dbt->db, "taxon") == 0) {
+            oip = dbt->tag;
+            if (oip == NULL) continue;
+            if (oip->str != NULL) {
+              StringCpy (taxIDp, oip->str);
+            } else if (oip->id > 0) {
+              sprintf (taxIDp, "%ld", (long) oip->id);
+            }
+          }
+        }
+      }
+    }
+  }
+
+  if (genep == NULL || StringHasNoText (locusIDp)) return FALSE;
+
+  return TRUE;
+}
+
+static CharPtr reftxt21 = "NCBI contigs are derived from assembled genomic sequence data.";
+
+static CharPtr reftxt22 = "Features on this sequence have been produced for build ";
+static CharPtr reftxt23 = " of the NCBI's genome annotation";
+
+static CharPtr nsAreGapsString = "The strings of n's in this record represent gaps between contigs, and the length of each string corresponds to the length of the gap.";
+
+static Boolean IsTpa (
+  BioseqPtr bsp,
+  Boolean has_tpa_assembly,
+  BoolPtr isRefSeqP
+)
+
+{
+  DbtagPtr  dbt;
+  Boolean   has_bankit = FALSE;
+  Boolean   has_genbank = FALSE;
+  Boolean   has_gi = FALSE;
+  Boolean   has_local = FALSE;
+  Boolean   has_refseq = FALSE;
+  Boolean   has_smart = FALSE;
+  Boolean   has_tpa = FALSE;
+  SeqIdPtr  sip;
+
+  if (bsp == NULL || bsp->id == NULL) return FALSE;
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    switch (sip->choice) {
+      case SEQID_LOCAL :
+        has_local = TRUE;
+        break;
+      case SEQID_GENBANK :
+      case SEQID_EMBL :
+      case SEQID_DDBJ :
+        has_genbank = TRUE;
+        break;
+      case SEQID_OTHER :
+        has_refseq = TRUE;
+        if (isRefSeqP != NULL) {
+          *isRefSeqP = TRUE;
+        }
+        break;
+      case SEQID_GI :
+        has_gi = TRUE;
+        break;
+      case SEQID_TPG :
+      case SEQID_TPE :
+      case SEQID_TPD :
+        has_tpa = TRUE;
+        break;
+      case SEQID_GENERAL :
+        dbt = (DbtagPtr) sip->data.ptrvalue;
+        if (dbt != NULL) {
+          if (StringICmp (dbt->db, "BankIt") == 0) {
+            has_bankit = TRUE;
+          }
+          if (StringICmp (dbt->db, "TMSMART") == 0) {
+            has_smart = TRUE;
+          }
+        }
+        break;
+      default :
+        break;
+    }
+  }
+
+  if (has_genbank) return FALSE;
+  if (has_tpa) return TRUE;
+  if (has_refseq) return FALSE;
+  if (has_bankit && has_tpa_assembly) return TRUE;
+  if (has_smart && has_tpa_assembly) return TRUE;
+  if (has_gi) return FALSE;
+  if (has_local && has_tpa_assembly) return TRUE;
+
+  return FALSE;
+}
+
+static Boolean GetAccnVerFromServer (Int4 gi, CharPtr buf)
+
+{
+  AccnVerLookupFunc  func;
+  SeqMgrPtr          smp;
+  CharPtr            str;
+
+  if (buf == NULL) return FALSE;
+  *buf = '\0';
+  smp = SeqMgrWriteLock ();
+  if (smp == NULL) return FALSE;
+  func = smp->accn_ver_lookup_func;
+  SeqMgrUnlock ();
+  if (func == NULL) return FALSE;
+  str = (*func) (gi);
+  if (str == NULL) return FALSE;
+  if (StringLen (str) < 40) {
+    StringCpy (buf, str);
+  }
+  MemFree (str);
+  return TRUE;
+}
+
+static CharPtr GetStrForTpaOrRefSeqHist (
+  BioseqPtr bsp
+)
+
+{
+  Boolean      accn;
+  Char         buf [64];
+  DbtagPtr     dbt;
+  Int4         gi;
+  ValNodePtr   head = NULL;
+  SeqHistPtr   hist;
+  SeqIdPtr     id;
+  Boolean      isRefSeq = FALSE;
+  Boolean      minus1;
+  Boolean      minus2;
+  SeqAlignPtr  salp;
+  SeqAlignPtr  salptmp;
+  SeqIdPtr     sip;
+  Int4         start;
+  Int4         stop;
+  CharPtr      str;
+  Char         tmp [80];
+
+  hist = bsp->hist;
+  if (hist != NULL && hist->assembly != NULL) {
+    salp = SeqAlignListDup (hist->assembly);
+    AlnMgr2IndexLite (salp);
+    AlnMgr2SortAlnSetByNthRowPos (salp, 1);
+    salptmp = (SeqAlignPtr) (salp->segs);
+    while (salptmp != NULL) {
+      AlnMgr2GetNthSeqRangeInSA (salptmp, 1, &start, &stop);
+      sip = AlnMgr2GetNthSeqIdPtr (salptmp, 2);
+      if (sip != NULL) {
+        id = NULL;
+        accn = FALSE;
+        if (sip->choice == SEQID_GI) {
+          gi = (Int4) sip->data.intvalue;
+          if (GetAccnVerFromServer (gi, buf)) {
+            accn = TRUE;
+          } else {
+            id = GetSeqIdForGI (gi);
+          }
+        } else {
+          id = SeqIdDup (sip);
+        }
+        if (id != NULL || accn) {
+          if (head == NULL) {
+            if (isRefSeq) {
+              ValNodeCopyStr (&head, 0, "REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP");
+            } else {
+              ValNodeCopyStr (&head, 0, "TPA_SPAN            PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP");
+            }
+          }
+          if (id != NULL) {
+            SeqIdWrite (id, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
+            if (id->choice == SEQID_GENERAL) {
+              dbt = (DbtagPtr) id->data.ptrvalue;
+              if (dbt != NULL && StringICmp (dbt->db, "ti") == 0) {
+                StringCpy (buf, "TI");
+                SeqIdWrite (id, buf + 2, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 3);
+              }
+            }
+          }
+          sprintf (tmp, "~%ld-%ld                                        ",
+                   (long) (start + 1), (long) (stop + 1));
+          /*
+          i = 39 - StringLen (buf);
+          if (i > 0) {
+            tmp [i] = '\0';
+          } else {
+            tmp [21] = '\0';
+          }
+          */
+          tmp [21] = '\0';
+          StringCat (buf, "                                        ");
+          buf [18] = '\0';
+          StringCat (tmp, buf);
+          AlnMgr2GetNthSeqRangeInSA (salptmp, 2, &start, &stop);
+          sprintf (buf, " %ld-%ld                                        ",
+                   (long) (start + 1), (long) (stop + 1));
+          buf [21] = '\0';
+          StringCat (tmp, buf);
+          minus1 = (Boolean) (AlnMgr2GetNthStrand (salptmp, 1) == Seq_strand_minus);
+          minus2 = (Boolean) (AlnMgr2GetNthStrand (salptmp, 2) == Seq_strand_minus);
+          if (minus1 || minus2) {
+            if (! (minus1 && minus2)) {
+              StringCat (tmp, "c");
+            }
+          }
+          ValNodeCopyStr (&head, 0, tmp);
+        }
+        SeqIdFree (id);
+      }
+      SeqIdFree (sip);
+      salptmp = salptmp->next;
+    }
+    SeqAlignFree (salp);
+  }
+
+  if (head == NULL) return NULL;
+
+  str = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  return str;
+}
+
+static CharPtr tpaString = "THIRD PARTY ANNOTATION DATABASE: This TPA record uses data from DDBJ/EMBL/GenBank ";
+
+static CharPtr GetStrForTPA (
+  UserObjectPtr uop,
+  BioseqPtr bsp
+)
+
+{
+  Char          ch;
+  UserFieldPtr  curr;
+  SeqHistPtr    hist;
+  Int2          i;
+  Char          id [41];
+  Boolean       isRefSeq = FALSE;
+  Int2          j;
+  size_t        len;
+  ObjectIdPtr   oip;
+  CharPtr       ptr;
+  CharPtr       str;
+  CharPtr       tmp;
+  UserFieldPtr  ufp;
+
+  if (uop == NULL) return NULL;
+  if ((oip = uop->type) == NULL) return NULL;
+  if (StringCmp (oip->str, "TpaAssembly") != 0) return NULL;
+  if (bsp == NULL) return NULL;
+  hist = bsp->hist;
+  if (hist != NULL && hist->assembly != NULL) return NULL;
+  if (! IsTpa (bsp, TRUE, &isRefSeq)) return NULL;
+  if (isRefSeq) return NULL;
+
+  len = StringLen (tpaString) + StringLen ("entries ") + StringLen ("and ") + 5;
+  i = 0;
+  for (curr = uop->data; curr != NULL; curr = curr->next) {
+    if (curr->choice != 11) continue;
+    for (ufp = curr->data.ptrvalue; ufp != NULL; ufp = ufp->next) {
+      if (ufp->choice != 1) continue;
+      oip = ufp->label;
+      if (oip == NULL || StringICmp (oip->str, "accession") != 0) continue;
+      str = (CharPtr) ufp->data.ptrvalue;
+      if (StringHasNoText (str)) continue;
+      len += StringLen (str) + 2;
+      i++;
+    }
+  }
+  if (i == 0) return NULL;
+
+  ptr = (CharPtr) MemNew (len);
+  if (ptr == NULL) return NULL;
+  StringCpy (ptr, tpaString);
+  if (i > 1) {
+    StringCat (ptr, "entries ");
+  } else {
+    StringCat (ptr, "entry ");
+  }
+
+  j = 0;
+  for (curr = uop->data; curr != NULL; curr = curr->next) {
+    if (curr->choice != 11) continue;
+    for (ufp = curr->data.ptrvalue; ufp != NULL; ufp = ufp->next) {
+      if (ufp->choice != 1) continue;
+      oip = ufp->label;
+      if (oip == NULL || StringICmp (oip->str, "accession") != 0) continue;
+      str = (CharPtr) ufp->data.ptrvalue;
+      if (StringHasNoText (str)) continue;
+      StringNCpy_0 (id, str, sizeof (id));
+      tmp = id;
+      ch = *tmp;
+      while (ch != '\0') {
+        if (IS_LOWER (ch)) {
+          *tmp = TO_UPPER (ch);
+        }
+        tmp++;
+        ch = *tmp;
+      }
+      if (j == i - 1 && i > 1) {
+        StringCat (ptr, " and ");
+      } else if (j > 0) {
+        StringCat (ptr, ", ");
+      }
+      StringCat (ptr, id);
+      j++;
+    }
+  }
+
+  return ptr;
+}
+
+static CharPtr GetStrForGenome (
+  UserObjectPtr uop,
+  BioseqPtr bsp
+)
+
+{
+  ObjectIdPtr  oip;
+
+  if (uop == NULL) return NULL;
+  if ((oip = uop->type) == NULL) return NULL;
+  if (StringCmp (oip->str, "GenomeInfo") != 0) return NULL;
+
+  /* !!! need to implement !!! */
+
+  return NULL;
+}
+
+NLM_EXTERN void AddPrimaryBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  BaseBlockPtr       bbp = NULL;
+  BioseqPtr          bsp;
+  SeqMgrDescContext  dcontext;
+  GBSeqPtr           gbseq;
+  Boolean            has_tpa_assembly = FALSE;
+  SeqHistPtr         hist;
+  Boolean            isRefSeq = FALSE;
+  ObjectIdPtr        oip;
+  SeqDescrPtr        sdp;
+  CharPtr            str;
+  UserObjectPtr      uop;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {
+    uop = (UserObjectPtr) sdp->data.ptrvalue;
+    if (uop != NULL) {
+      oip = uop->type;
+      if (oip != NULL) {
+        if (StringCmp (oip->str, "TpaAssembly") == 0) {
+          has_tpa_assembly = TRUE;
+        }
+      }
+    }
+    if (has_tpa_assembly) {
+      sdp = NULL;
+    } else {
+      sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+    }
+  }
+
+  if (! IsTpa (bsp, has_tpa_assembly, &isRefSeq)) return;
+  hist = bsp->hist;
+  if (hist == NULL || hist->assembly == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  str = GetStrForTpaOrRefSeqHist (bsp);
+  if (str != NULL) {
+
+    bbp = (BaseBlockPtr) Asn2gbAddBlock (awp, PRIMARY_BLOCK, sizeof (BaseBlock));
+    if (bbp != NULL) {
+
+      if (has_tpa_assembly) {
+        bbp->entityID = dcontext.entityID;
+        bbp->itemID = dcontext.itemID;
+        bbp->itemtype = OBJ_SEQDESC;
+      }
+
+      FFStartPrint (ffstring, awp->format, 0, 12, "PRIMARY", 12, 5, 5, "PR", TRUE);
+
+      FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
+
+      bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "PR");
+
+      /* optionally populate gbseq for XML-ized GenBank format */
+
+      if (ajp->gbseq) {
+        gbseq = &asp->gbseq;
+      } else {
+        gbseq = NULL;
+      }
+
+      if (gbseq != NULL) {
+        gbseq->primary = StringSave (str);
+      }
+    }
+    MemFree (str);
+  }
+
+  FFRecycleString(ajp, ffstring);
+}
+
+static CharPtr reftxt32 = "It is defined by coordinates on the sequence of chromosome";
+static CharPtr reftxt33 = "from the";
+static CharPtr reftxt34 = "assembly of the human genome (NCBI build";
+static CharPtr reftxt35 = ").";
+
+static CharPtr GetEncodeString (
+  UserObjectPtr uop,
+  BioseqPtr bsp
+)
+
+{
+  CharPtr            assembly_date = NULL;
+  BioSourcePtr       biop;
+  CharPtr            chromosome = NULL;
+  SeqMgrDescContext  dcontext;
+  size_t             len;
+  CharPtr            ncbi_annotation = NULL;
+  ObjectIdPtr        oip;
+  SeqDescrPtr        sdp;
+  SubSourcePtr       ssp;
+  CharPtr            str;
+  UserFieldPtr       ufp;
+
+  if (uop == NULL || bsp == NULL) return NULL;
+
+  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+    oip = ufp->label;
+    if (oip == NULL || oip->str == NULL || ufp->choice != 1) continue;
+    if (StringICmp (oip->str, "AssemblyDate") == 0) {
+      assembly_date = (CharPtr) ufp->data.ptrvalue;
+    } else if (StringICmp (oip->str, "NcbiAnnotation") == 0) {
+      ncbi_annotation = (CharPtr) ufp->data.ptrvalue;
+    }
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  if (sdp != NULL) {
+    biop = (BioSourcePtr) sdp->data.ptrvalue;
+    if (biop != NULL) {
+      for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
+        if (ssp->subtype == SUBSRC_chromosome) {
+          chromosome = ssp->name;
+        }
+      }
+    }
+  }
+
+  if (StringHasNoText (chromosome)) {
+    chromosome = "?";
+  }
+  if (StringHasNoText (assembly_date)) {
+    assembly_date = "?";
+  }
+  if (StringHasNoText (ncbi_annotation)) {
+    ncbi_annotation = "?";
+  }
+
+  len = StringLen (reftxt32) + StringLen (reftxt33) +
+        StringLen (reftxt34) + StringLen (reftxt35) +
+        StringLen (chromosome) +
+        StringLen (assembly_date) +
+        StringLen (ncbi_annotation);
+
+  str = (CharPtr) MemNew (sizeof (Char) * (len + 10));
+  if (str == NULL) return NULL;
+
+  sprintf (str, "%s %s %s %s %s %s%s", reftxt32, chromosome, reftxt33,
+           assembly_date, reftxt34, ncbi_annotation, reftxt35);
+
+  return str;
+}
+
+static void GetAnnotComments (
+  SeqAnnotPtr sap,
+  Pointer userdata
+)
+
+{
+  AnnotDescrPtr    desc;
+  ValNodePtr PNTR  head;
+  CharPtr          str;
+
+  head = (ValNodePtr PNTR) userdata;
+  if (sap == NULL || head == NULL) return;
+
+  for (desc = sap->desc; desc != NULL; desc = desc->next) {
+    str = NULL;
+    if (desc->choice == Annot_descr_comment) {
+      str = (CharPtr) desc->data.ptrvalue;
+    }
+    if (StringHasNoText (str)) continue;
+    ValNodeCopyStr (head, 0, str);
+  }
+}
+
+NLM_EXTERN void AddCommentBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  size_t             acclen;
+  IntAsn2gbJobPtr    ajp;
+  BioseqPtr          bsp;
+  Char               buf [128];
+  CommentBlockPtr    cbp = NULL;
+  Char               ch;
+  Boolean            didGenome = FALSE;
+  Boolean            didRefTrack = FALSE;
+  Boolean            didTPA = FALSE;
+  DbtagPtr           dbt;
+  SeqMgrDescContext  dcontext;
+  DeltaSeqPtr        dsp;
+  Boolean            estEv = FALSE;
+  SeqMgrFeatContext  fcontext;
+  Boolean            first = TRUE;
+  GBBlockPtr         gbp;
+  CharPtr            geneName = NULL;
+  CharPtr            genomeBuildNumber = NULL;
+  CharPtr            genomeVersionNumber = NULL;
+  Int4               gi = 0;
+  CommentBlockPtr    gsdbcbp = NULL;
+  Int4               gsdbid = 0;
+  Boolean            has_gaps = FALSE;
+  Boolean            hasRefTrackStatus = FALSE;
+  ValNodePtr         head;
+  SeqHistPtr         hist;
+  Boolean            is_collab = FALSE;
+  Boolean            is_encode = FALSE;
+  Boolean            is_other = FALSE;
+  Boolean            is_tpa = FALSE;
+  Boolean            is_wgs = FALSE;
+  SeqLitPtr          litp;
+  ObjectIdPtr        localID = NULL;
+  Char               locusID [32];
+  CharPtr            method = NULL;
+  MolInfoPtr         mip;
+  Boolean            mrnaEv = FALSE;
+  CharPtr            name = NULL;
+  ObjectIdPtr        oip;
+  Boolean            okay;
+  BioseqPtr          parent;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  Boolean            showGBBSource = FALSE;
+  SeqIdPtr           sip;
+  CharPtr            str;
+  Char               taxID [32];
+  TextSeqIdPtr       tsip;
+  UserObjectPtr      uop;
+  ValNodePtr         vnp;
+  CharPtr            wgsaccn = NULL;
+  CharPtr            wgsname = NULL;
+  StringItemPtr      ffstring = NULL;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring ==  NULL ) return;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {
+    uop = (UserObjectPtr) sdp->data.ptrvalue;
+    if (uop != NULL) {
+      str = GetStatusForRefTrack (uop);
+      if (str != NULL) {
+        hasRefTrackStatus = TRUE;
+      }
+      if (genomeBuildNumber == NULL) {
+        genomeBuildNumber = GetGenomeBuildNumber (uop);
+      }
+      if (genomeVersionNumber == NULL) {
+        genomeVersionNumber = GetGenomeVersionNumber (uop);
+      }
+      oip = uop->type;
+      if (oip != NULL && StringICmp (oip->str, "ENCODE") == 0) {
+        is_encode = TRUE;
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+  }
+
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_OTHER) {
+      tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+
+      if (tsip != NULL) {
+        is_other = TRUE;
+        if (StringNCmp (tsip->accession, "NC_", 3) == 0) {
+          if (! StringHasNoText (genomeBuildNumber)) {
+            cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+            if (cbp != NULL) {
+
+              cbp->first = first;
+              first = FALSE;
+
+              if (cbp->first) {
+                FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+              } else {
+                FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+              }
+
+              FFAddOneString (ffstring, "GENOME ANNOTATION ", FALSE, FALSE, TILDE_IGNORE);
+
+              if ( GetWWW(ajp) ) {
+                FFAddTextToString (ffstring, "<a href=", ref_link, ">", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
+              if ( GetWWW(ajp) ) {
+                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, ":  ", FALSE, FALSE, TILDE_IGNORE);
+
+              FFAddOneString (ffstring, reftxt22, FALSE, FALSE, TILDE_EXPAND);
+              FFAddOneString (ffstring, genomeBuildNumber, FALSE, FALSE, TILDE_EXPAND);
+              if (StringHasNoText (genomeVersionNumber)) {
+                genomeVersionNumber = "1";
+              }
+              FFAddOneString (ffstring, " version ", FALSE, FALSE, TILDE_EXPAND);
+              FFAddOneString (ffstring, genomeVersionNumber, FALSE, FALSE, TILDE_EXPAND);
+              FFAddOneString (ffstring, reftxt23, FALSE, FALSE, TILDE_EXPAND);
+
+              FFAddOneString (ffstring, " [see ", FALSE, FALSE, TILDE_EXPAND);
+
+              if ( GetWWW(ajp) ) {
+                FFAddTextToString (ffstring, "<a href=", doc_link, ">", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, "documentation", FALSE, FALSE, TILDE_IGNORE);
+              if ( GetWWW(ajp) ) {
+                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+              }
+
+              FFAddOneString (ffstring, "].", FALSE, FALSE, TILDE_EXPAND);
+
+              cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+              FFRecycleString(ajp, ffstring);
+              ffstring = FFGetString(ajp);
+            }
+          }
+
+        } else if (StringNCmp(tsip->accession, "NT_", 3) == 0 || StringNCmp(tsip->accession, "NW_", 3) == 0) {
+
+          if (is_encode) {
+            cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+            if (cbp != NULL) {
+
+              cbp->first = first;
+              first = FALSE;
+
+              if (cbp->first) {
+                FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+              } else {
+                FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+              }
+
+              FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
+              FFAddOneString (ffstring, ":  ", FALSE, FALSE, TILDE_IGNORE);
+
+              FFAddOneString (ffstring, "This record was provided by the ", FALSE, FALSE, TILDE_EXPAND);
+              if ( GetWWW(ajp) ) {
+                FFAddTextToString (ffstring, "<a href=", link_encode, ">", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, "ENCODE", FALSE, FALSE, TILDE_EXPAND);
+              if ( GetWWW(ajp) ) {
+                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, " project.", FALSE, FALSE, TILDE_EXPAND);
+
+              str = GetEncodeString (uop, bsp);
+              if (str != NULL) {
+                FFAddOneString (ffstring, "  ", FALSE, FALSE, TILDE_EXPAND);
+                FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
+              }
+              MemFree (str);
+
+              cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+              FFRecycleString(ajp, ffstring);
+              ffstring = FFGetString(ajp);
+            }
+
+          } else if (! hasRefTrackStatus) {
+
+            cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+            if (cbp != NULL) {
+
+              cbp->first = first;
+              first = FALSE;
+
+              if (cbp->first) {
+                FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+              } else {
+                FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+              }
+
+              FFAddOneString (ffstring, "GENOME ANNOTATION ", FALSE, FALSE, TILDE_IGNORE);
+
+              if ( GetWWW(ajp) ) {
+                FFAddTextToString (ffstring, "<a href=", ref_link, ">", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
+              if ( GetWWW(ajp) ) {
+                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, ":  ", FALSE, FALSE, TILDE_IGNORE);
+
+              if (! StringHasNoText (genomeBuildNumber)) {
+                FFAddOneString (ffstring, reftxt22, FALSE, FALSE, TILDE_EXPAND);
+                FFAddOneString (ffstring, genomeBuildNumber, FALSE, FALSE, TILDE_EXPAND);
+                if (StringHasNoText (genomeVersionNumber)) {
+                  genomeVersionNumber = "1";
+                }
+                FFAddOneString (ffstring, " version ", FALSE, FALSE, TILDE_EXPAND);
+                FFAddOneString (ffstring, genomeVersionNumber, FALSE, FALSE, TILDE_EXPAND);
+                FFAddOneString (ffstring, reftxt23, FALSE, FALSE, TILDE_EXPAND);
+
+                FFAddOneString (ffstring, " [see ", FALSE, FALSE, TILDE_EXPAND);
+
+                if ( GetWWW(ajp) ) {
+                  FFAddTextToString (ffstring, "<a href=", doc_link, ">", FALSE, FALSE, TILDE_IGNORE);
+                }
+                FFAddOneString (ffstring, "documentation", FALSE, FALSE, TILDE_IGNORE);
+                if ( GetWWW(ajp) ) {
+                  FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+                }
+
+                FFAddOneString (ffstring, "].", FALSE, FALSE, TILDE_EXPAND);
+              } else {
+
+                FFAddOneString (ffstring, reftxt21, TRUE, FALSE, TILDE_EXPAND);
+
+                FFAddOneString (ffstring, "~Also see:~    ", FALSE, FALSE, TILDE_EXPAND);
+
+                if ( GetWWW(ajp) ) {
+                  FFAddTextToString (ffstring, "<a href=", doc_link, ">", FALSE, FALSE, TILDE_IGNORE);
+                }
+                FFAddOneString (ffstring, "Documentation", FALSE, FALSE, TILDE_IGNORE);
+                if ( GetWWW(ajp) ) {
+                  FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+                }
+
+                FFAddOneString (ffstring, " of NCBI's Annotation Process~    ", FALSE, FALSE, TILDE_EXPAND);
+              }
+
+              cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+              FFRecycleString(ajp, ffstring);
+              ffstring = FFGetString(ajp);
+            }
+          }
+
+        } else if (StringNCmp(tsip->accession, "XP_", 3) == 0 ||
+                   StringNCmp(tsip->accession, "XM_", 3) == 0 ||
+                   StringNCmp(tsip->accession, "XR_", 3) == 0 ||
+                   StringNCmp(tsip->accession, "ZP_", 3) == 0) {
+
+          name = NULL;
+          method = NULL;
+          mrnaEv = FALSE;
+          estEv = FALSE;
+          if (GetAnnotationComment (bsp, &name, &method, &mrnaEv, &estEv)) {
+
+            cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+            if (cbp != NULL) {
+
+              cbp->first = first;
+              first = FALSE;
+
+              if (cbp->first) {
+                FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+              } else {
+                FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+              }
+
+              FFAddOneString (ffstring, "MODEL ", FALSE, FALSE, TILDE_IGNORE);
+
+              if ( GetWWW(ajp) ) {
+                FFAddTextToString (ffstring, "<a href=", ref_link, ">", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, "REFSEQ", FALSE, FALSE, TILDE_IGNORE);
+              if ( GetWWW(ajp) ) {
+                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, ":  ", FALSE, FALSE, TILDE_IGNORE);
+
+              FFAddTextToString (ffstring, NULL, reftxt11, " (", FALSE, FALSE, TILDE_IGNORE);
+
+              if ( GetWWW(ajp) ) {
+                FFAddTextToString (ffstring, "<a href=", nt_link, name, FALSE, FALSE, TILDE_IGNORE);
+                FFAddOneString (ffstring, ">", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, name, FALSE, FALSE, TILDE_IGNORE);
+              if ( GetWWW(ajp) ) {
+                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+              }
+
+              FFAddOneString (ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
+ 
+              if (method != NULL) {
+                FFAddOneString (ffstring, " ", FALSE, FALSE, TILDE_IGNORE);
+                FFAddOneString (ffstring, reftxt12, FALSE, FALSE, TILDE_IGNORE);
+                FFAddOneString (ffstring, " ", FALSE, FALSE, TILDE_IGNORE);
+                FFAddOneString (ffstring, method, FALSE, FALSE, TILDE_IGNORE);
+              }
+
+              if (mrnaEv || estEv) {
+                FFAddOneString (ffstring, ", supported by ", FALSE, FALSE, TILDE_IGNORE);
+                if (mrnaEv && estEv) {
+                  FFAddOneString (ffstring, "mRNA and EST ", FALSE, FALSE, TILDE_IGNORE);
+                } else if (mrnaEv) {
+                  FFAddOneString (ffstring, "mRNA ", FALSE, FALSE, TILDE_IGNORE);
+                } else {
+                  FFAddOneString (ffstring, "EST ", FALSE, FALSE, TILDE_IGNORE);
+                }
+                geneName = NULL;
+                locusID [0] = '\0';
+                taxID [0] = '\0';
+                if ( GetWWW(ajp) && GetGeneAndLocus (bsp, &geneName, locusID, taxID)) {
+                  FFAddTextToString (ffstring, "<a href=", ev_link, NULL, FALSE, FALSE, TILDE_IGNORE);
+                  FFAddTextToString (ffstring, "contig=", name, NULL, FALSE, FALSE, TILDE_IGNORE);
+                  FFAddTextToString (ffstring, "&gene=", geneName, NULL, FALSE, FALSE, TILDE_IGNORE);
+                  FFAddTextToString (ffstring, "&lid=", locusID, NULL, FALSE, FALSE, TILDE_IGNORE);
+                  if (! StringHasNoText (taxID)) {
+                    FFAddTextToString (ffstring, "&taxid=", taxID, NULL, FALSE, FALSE, TILDE_IGNORE);
+                  }
+                  FFAddOneString (ffstring, ">", FALSE, FALSE, TILDE_IGNORE);
+                  FFAddOneString (ffstring, "evidence", FALSE, FALSE, TILDE_IGNORE);
+                  FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+                } else {
+                  FFAddOneString (ffstring, "evidence", FALSE, FALSE, TILDE_IGNORE);
+                }
+              }
+
+              FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_IGNORE);
+
+              FFAddOneString (ffstring, "~Also see:~    ", FALSE, FALSE, TILDE_EXPAND);
+
+              if ( GetWWW(ajp) ) {
+                FFAddTextToString (ffstring, "<a href=", doc_link, ">", FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString (ffstring, "Documentation", FALSE, FALSE, TILDE_IGNORE);
+              if ( GetWWW(ajp) ) {
+                FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+              }
+
+              FFAddOneString (ffstring, " of NCBI's Annotation Process~    ", FALSE, FALSE, TILDE_EXPAND);
+
+              cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+              FFRecycleString(ajp, ffstring);
+              ffstring = FFGetString(ajp);
+            }
+          }
+        } else {
+          if (StringLen (tsip->accession) == 15) {
+            is_wgs = TRUE;
+            if (StringCmp (tsip->accession + 9, "000000") == 0) {
+              wgsaccn = tsip->accession;
+              wgsname = tsip->name; /* master accession has 8 zeroes, name has project version plus 6 zeroes */
+            }
+          }
+        }
+      }
+
+    } else if (sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) {
+
+      is_tpa = TRUE;
+
+    } else if (sip->choice == SEQID_GENBANK || sip->choice == SEQID_EMBL || sip->choice == SEQID_DDBJ) {
+
+      is_collab = TRUE;
+
+      tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+      if (tsip != NULL && tsip->accession != NULL) {
+        acclen = StringLen (tsip->accession);
+        if (acclen == 12) {
+          is_wgs = TRUE;
+          if (StringCmp (tsip->accession + 6, "000000") == 0) {
+            wgsaccn = tsip->accession;
+            wgsname = tsip->name; /* master accession has 8 zeroes, name has project version plus 6 zeroes */
+          }
+        } else if (acclen == 13) {
+          is_wgs = TRUE;
+          if (StringCmp (tsip->accession + 6, "0000000") == 0) {
+            wgsaccn = tsip->accession;
+            wgsname = tsip->name; /* master accession has 9 zeroes, name has project version plus 7 zeroes */
+          }
+        } else if (ajp->newSourceOrg && StringLen (tsip->accession) == 6) {
+          ch = tsip->accession [0];
+          if (ch == 'J' || ch == 'K' || ch == 'L' || ch == 'M') {
+            showGBBSource = TRUE;
+          }
+        }
+      }
+
+    } else if (sip->choice == SEQID_GENERAL) {
+      dbt = (DbtagPtr) sip->data.ptrvalue;
+
+      /* show GSDB sequence identifier */
+
+      if (dbt != NULL && StringCmp (dbt->db, "GSDB") == 0 && dbt->tag != NULL) {
+        gsdbcbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+        if (gsdbcbp != NULL) {
+          gsdbcbp->first = first;
+
+          /* string will be created after we know if there are additional comments */
+
+          gsdbid = dbt->tag->id;
+          first = FALSE;
+        }
+      }
+
+    } else if (sip->choice == SEQID_GI) {
+      gi = (Int4) sip->data.intvalue;
+
+    } else if (sip->choice == SEQID_LOCAL) {
+      localID = (ObjectIdPtr) sip->data.ptrvalue;
+    }
+  }
+
+  if (localID != NULL) {
+    if (is_tpa || is_collab) {
+      if (awp->mode == SEQUIN_MODE || awp->mode == DUMP_MODE) {
+        buf [0] = '\0';
+        if (! StringHasNoText (localID->str)) {
+          if (StringLen (localID->str) < 100) {
+            sprintf (buf, "LocalID: %s", localID->str);
+          } else {
+            sprintf (buf, "LocalID string too large");
+          }
+        } else {
+          sprintf (buf, "LocalID: %ld", (long) localID->id);
+        }
+
+        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+        if (cbp != NULL) {
+
+          cbp->first = first;
+          first = FALSE;
+
+          if (cbp->first) {
+            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+          } else {
+            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+          }
+
+          FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
+
+          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12,5, 5, "CC");
+          FFRecycleString(ajp, ffstring);
+          ffstring = FFGetString(ajp);
+        }
+      }
+    }
+  }
+
+  /* RefSeq results in allocated comment string */
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {
+
+    uop = (UserObjectPtr) sdp->data.ptrvalue;
+    if (uop != NULL) {
+
+      if (! didTPA) {
+        str = GetStrForTPA (uop, bsp);
+        if (str != NULL) {
+
+          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+          if (cbp != NULL) {
+
+            cbp->entityID = dcontext.entityID;
+            cbp->itemID = dcontext.itemID;
+            cbp->itemtype = OBJ_SEQDESC;
+            cbp->first = first;
+            first = FALSE;
+
+            if (cbp->first) {
+              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+            } else {
+              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+            }
+
+            FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
+
+            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12,5, 5, "CC");
+            FFRecycleString(ajp, ffstring);
+            ffstring = FFGetString(ajp);
+          }
+          MemFree (str);
+          didTPA = TRUE;
+        }
+      }
+
+      if (! ajp->flags.hideBankItComment) {
+        str = GetStrForBankit (uop);
+        if (str != NULL) {
+
+          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+          if (cbp != NULL) {
+
+            cbp->entityID = dcontext.entityID;
+            cbp->itemID = dcontext.itemID;
+            cbp->itemtype = OBJ_SEQDESC;
+            cbp->first = first;
+            first = FALSE;
+
+            if (cbp->first) {
+              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+            } else {
+              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+            }
+
+            FFAddOneString (ffstring, str, TRUE, FALSE, TILDE_EXPAND);
+
+            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12,5, 5, "CC");
+            FFRecycleString(ajp, ffstring);
+            ffstring = FFGetString(ajp);
+          }
+          MemFree (str);
+        }
+      }
+
+      if (! didRefTrack) {
+        str = GetStatusForRefTrack (uop);
+        if (str != NULL) {
+
+          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+          if (cbp != NULL) {
+
+            cbp->entityID = dcontext.entityID;
+            cbp->itemID = dcontext.itemID;
+            cbp->itemtype = OBJ_SEQDESC;
+            cbp->first = first;
+            first = FALSE;
+
+            if (cbp->first) {
+              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+            } else {
+              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+            }
+
+            FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
+
+            AddStrForRefTrack (ajp, ffstring, uop);
+
+            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12,5, 5, "CC");
+            FFRecycleString(ajp, ffstring);
+            ffstring = FFGetString(ajp);
+          }
+          /* do not free static str from GetStatusForRefTrack */
+          didRefTrack = TRUE;
+        }
+      }
+
+      if (! didGenome) {
+        str = GetStrForGenome (uop, bsp);
+        if (str != NULL) {
+
+          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+          if (cbp != NULL) {
+
+            cbp->entityID = dcontext.entityID;
+            cbp->itemID = dcontext.itemID;
+            cbp->itemtype = OBJ_SEQDESC;
+            cbp->first = first;
+            first = FALSE;
+
+            if (cbp->first) {
+              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+            } else {
+              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+            }
+
+            FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
+
+            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+            FFRecycleString(ajp, ffstring);
+            ffstring = FFGetString(ajp);
+          }
+          MemFree (str);
+          didGenome = TRUE;
+        }
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+  }
+
+  if (bsp->repr == Seq_repr_delta && bsp->seq_ext_type == 4 && is_wgs) {
+    has_gaps = FALSE;
+    for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp; dsp=dsp->next) {
+      if (dsp->choice == 2) {
+        litp = (SeqLitPtr) dsp->data.ptrvalue;
+        if (litp != NULL) {
+          if (litp->seq_data == NULL && litp->length > 0) {
+            has_gaps = TRUE;
+          }
+        }
+      }
+    }
+    if (has_gaps) {
+      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+      if (cbp != NULL) {
+
+        cbp->first = first;
+        first = FALSE;
+
+        if (cbp->first) {
+          FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+        } else {
+          FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+        }
+
+        FFAddOneString (ffstring, nsAreGapsString, TRUE, FALSE, TILDE_EXPAND);
+
+        cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+        FFRecycleString(ajp, ffstring);
+        ffstring = FFGetString(ajp);
+      }
+    }
+  }
+
+  /* Seq-hist results in allocated comment string */
+
+  hist = bsp->hist;
+  if (hist != NULL) {
+
+    if (hist->replaced_by_ids != NULL && hist->replaced_by_date != NULL) {
+
+      okay = TRUE;
+      for (sip = hist->replaced_by_ids; sip != NULL; sip = sip->next) {
+        if (sip->choice == SEQID_GI) {
+          if (gi == (Int4) sip->data.intvalue) {
+            okay = FALSE;
+          }
+        }
+      }
+
+      if (okay) {
+        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+        if (cbp != NULL) {
+          cbp->first = first;
+          first = FALSE;
+
+          if (cbp->first) {
+            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+          } else {
+            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+          }
+
+          AddHistCommentString (ajp, ffstring, "[WARNING] On", "this sequence was replaced by a newer version",
+                                hist->replaced_by_date, hist->replaced_by_ids);
+
+          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+          FFRecycleString(ajp, ffstring);
+          ffstring = FFGetString(ajp);
+        }
+      }
+    }
+
+    if (hist->replace_ids != NULL && hist->replace_date != NULL && awp->mode != SEQUIN_MODE) {
+
+      okay = TRUE;
+      for (sip = hist->replace_ids; sip != NULL; sip = sip->next) {
+        if (sip->choice == SEQID_GI) {
+          if (gi == (Int4) sip->data.intvalue) {
+            okay = FALSE;
+          }
+        }
+      }
+
+      if (okay) {
+        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+        if (cbp != NULL) {
+          cbp->first = first;
+          first = FALSE;
+
+          if (cbp->first) {
+            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+          } else {
+            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+          }
+
+          AddHistCommentString (ajp, ffstring, "On", "this sequence version replaced",
+                                hist->replace_date, hist->replace_ids);
+
+          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+          FFRecycleString(ajp, ffstring);
+          ffstring = FFGetString(ajp);
+        }
+      }
+    }
+
+  }
+
+  /* just save IDs for comment, maploc, and region descriptors */
+
+  /*
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_comment, &dcontext);
+  while (sdp != NULL) {
+    if (sdp->data.ptrvalue != NULL) {
+      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+      if (cbp != NULL) {
+        cbp->entityID = dcontext.entityID;
+        cbp->itemID = dcontext.itemID;
+        cbp->itemtype = OBJ_SEQDESC;
+        cbp->first = first;
+        first = FALSE;
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_comment, &dcontext);
+  }
+  */
+
+  /* WGS master comment goes before comment descriptors */
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp != NULL) {
+
+    mip = (MolInfoPtr) sdp->data.ptrvalue;
+    if (mip != NULL) {
+      if (mip->tech == MI_TECH_wgs) {
+
+        if (wgsname != NULL) {
+
+          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+          if (cbp != NULL) {
+
+            /*
+            cbp->entityID = dcontext.entityID;
+            cbp->itemID = dcontext.itemID;
+            cbp->itemtype = OBJ_SEQDESC;
+            */
+            cbp->first = first;
+            first = FALSE;
+
+            if (cbp->first) {
+              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+            } else {
+              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+            }
+
+            AddWGSMasterCommentString (ffstring,bsp, wgsaccn, wgsname);
+
+            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+            FFRecycleString(ajp, ffstring);
+            ffstring = FFGetString(ajp);
+          }
+        }
+      }
+    }
+  }
+
+  if (showGBBSource) {
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
+    if (sdp != NULL) {
+      gbp = (GBBlockPtr) sdp->data.ptrvalue;
+      if (gbp != NULL && (! StringHasNoText (gbp->source))) {
+        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+        if (cbp != NULL) {
+          cbp->entityID = dcontext.entityID;
+          cbp->itemID = dcontext.itemID;
+          cbp->itemtype = OBJ_SEQDESC;
+          cbp->first = first;
+          first = FALSE;
+
+          if (cbp->first) {
+            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+          } else {
+            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+          }
+
+          FFAddOneString (ffstring, "Original source text: ", FALSE, FALSE, TILDE_EXPAND);
+          FFAddOneString (ffstring, gbp->source, TRUE, TRUE, TILDE_EXPAND);
+
+          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+          FFRecycleString(ajp, ffstring);
+          ffstring = FFGetString(ajp);
+        }
+      }
+    }
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_comment, &dcontext);
+  while (sdp != NULL) {
+    if (sdp->data.ptrvalue != NULL) {
+      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+      if (cbp != NULL) {
+        cbp->entityID = dcontext.entityID;
+        cbp->itemID = dcontext.itemID;
+        cbp->itemtype = OBJ_SEQDESC;
+        cbp->first = first;
+        first = FALSE;
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_comment, &dcontext);
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_maploc, &dcontext);
+  while (sdp != NULL) {
+    cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+    if (cbp != NULL) {
+      cbp->entityID = dcontext.entityID;
+      cbp->itemID = dcontext.itemID;
+      cbp->itemtype = OBJ_SEQDESC;
+      cbp->first = first;
+      first = FALSE;
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_maploc, &dcontext);
+  }
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_region, &dcontext);
+  while (sdp != NULL) {
+    if (sdp->data.ptrvalue != NULL) {
+      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+      if (cbp != NULL) {
+        cbp->entityID = dcontext.entityID;
+        cbp->itemID = dcontext.itemID;
+        cbp->itemtype = OBJ_SEQDESC;
+        cbp->first = first;
+        first = FALSE;
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_region, &dcontext);
+  }
+
+  /* HTGS results in allocated comment string */
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp != NULL) {
+
+    mip = (MolInfoPtr) sdp->data.ptrvalue;
+    if (mip != NULL) {
+      if (mip->completeness != 0 && is_other) {
+
+        str = GetMolInfoCommentString (bsp, mip);
+
+        if (str != NULL) {
+          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+          if (cbp != NULL) {
+
+            cbp->entityID = dcontext.entityID;
+            cbp->itemID = dcontext.itemID;
+            cbp->itemtype = OBJ_SEQDESC;
+            cbp->first = first;
+            first = FALSE;
+
+            if (cbp->first) {
+              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+            } else {
+              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+            }
+
+            FFAddOneString (ffstring, str, TRUE, FALSE, TILDE_EXPAND);
+
+            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+            FFRecycleString(ajp, ffstring);
+            ffstring = FFGetString(ajp);
+          }
+        }
+
+      }
+      if (mip->tech == MI_TECH_htgs_0 ||
+          mip->tech == MI_TECH_htgs_1 ||
+          mip->tech == MI_TECH_htgs_2) {
+
+        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+        if (cbp != NULL) {
+
+          /*
+          cbp->entityID = dcontext.entityID;
+          cbp->itemID = dcontext.itemID;
+          cbp->itemtype = OBJ_SEQDESC;
+          */
+          cbp->first = first;
+          first = FALSE;
+
+          if (cbp->first) {
+            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+          } else {
+            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+          }
+          
+          AddHTGSCommentString (ffstring, bsp, mip);
+
+          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+          FFRecycleString(ajp, ffstring);
+          ffstring = FFGetString(ajp);
+        }
+
+      } else {
+        str = StringForSeqTech (mip->tech);
+        if (! StringHasNoText (str)) {
+
+          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+          if (cbp != NULL) {
+
+            /*
+            cbp->entityID = dcontext.entityID;
+            cbp->itemID = dcontext.itemID;
+            cbp->itemtype = OBJ_SEQDESC;
+            */
+            cbp->first = first;
+            first = FALSE;
+
+            if (cbp->first) {
+              FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+            } else {
+              FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+            }
+
+            FFAddTextToString (ffstring, "Method: ", str, NULL, TRUE, FALSE, TILDE_EXPAND);
+
+            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+            FFRecycleString(ajp, ffstring);
+            ffstring = FFGetString(ajp);
+          }
+        }
+      }
+    }
+  }
+
+  /* add comment features that are full length on appropriate segment */
+
+  parent = awp->parent;
+  if (parent == NULL) return;
+
+  sfp = SeqMgrGetNextFeature (parent, NULL, SEQFEAT_COMMENT, 0, &fcontext);
+  while (sfp != NULL) {
+    if (fcontext.left == awp->from && fcontext.right == awp->to) {
+      cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+      if (cbp != NULL) {
+        cbp->entityID = fcontext.entityID;
+        cbp->itemID = fcontext.itemID;
+        cbp->itemtype = OBJ_SEQFEAT;
+        cbp->first = first;
+        first = FALSE;
+      }
+    }
+    sfp = SeqMgrGetNextFeature (parent, sfp, SEQFEAT_COMMENT, 0, &fcontext);
+  }
+
+  /* look for Seq-annot.desc.comment on annots packaged on current bioseq */
+
+  head = NULL;
+  VisitAnnotsOnBsp (bsp, (Pointer) &head, GetAnnotComments);
+  for (vnp = head; vnp != NULL; vnp = vnp->next) {
+    str = (CharPtr) vnp->data.ptrvalue;
+    if (StringHasNoText (str)) continue;
+    cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+    if (cbp != NULL) {
+
+      cbp->first = first;
+      first = FALSE;
+
+      if (cbp->first) {
+        FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+      } else {
+        FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+      }
+
+      FFAddOneString (ffstring, str, TRUE, FALSE, TILDE_EXPAND);
+
+      cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+      FFRecycleString(ajp, ffstring);
+      ffstring = FFGetString(ajp);
+    }
+  }
+  ValNodeFreeData (head);
+
+  if (gsdbcbp != NULL) {
+
+    /* if there were no subsequent comments, do not add period after GSDB id */
+
+    if (cbp == NULL) {
+      sprintf (buf, "GSDB:S:%ld", (long) gsdbid);
+    } else {
+      sprintf (buf, "GSDB:S:%ld.", (long) gsdbid);
+    }
+
+    if (gsdbcbp->first) {
+      FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+    } else {
+      FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+    }
+
+    /* CheckEndPunctuation, ConvertDoubleQuotes, and ExpandTildes already taken into account */
+
+    FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+
+    gsdbcbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
+    FFRecycleString(ajp, ffstring);
+    ffstring = FFGetString(ajp);
+  }
+
+  FFRecycleString(ajp, ffstring);
+}
+
+NLM_EXTERN void AddFeatHeaderBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr ajp;
+  BaseBlockPtr    bbp;
+  StringItemPtr   ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+
+  bbp = Asn2gbAddBlock (awp, FEATHEADER_BLOCK, sizeof (BaseBlock));
+  if (bbp == NULL) return;
+
+  if (awp->format == FTABLE_FMT) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  FFStartPrint (ffstring, awp->format, 0, 12, "FEATURES", 21, 5, 0, "FH", TRUE);
+
+  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+    FFAddOneString (ffstring, "Key", FALSE, FALSE, TILDE_IGNORE);
+    FFAddNChar(ffstring, ' ', 13 , FALSE);
+  }
+
+  FFAddOneString (ffstring, "Location/Qualifiers", FALSE, FALSE, TILDE_TO_SPACES);
+
+  if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) {
+    FFAddNewLine(ffstring);
+    FFAddNewLine(ffstring);
+  }
+
+  bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 21, 5, 0, "FH");
+  FFRecycleString(ajp, ffstring);
+}
+
+static Uint2 ComputeSourceHash (
+  CharPtr key,
+  Uint2 start
+)
+
+{
+  Uint4  h;
+  Uint2  M;
+  Uint2  S;
+
+  if (key == NULL) return start;
+
+  M = 101; /* prime key */
+  S = 256; /* size of alphabet */
+
+  for (h = start; *key != '\0'; key++) {
+    h = (S * h + *key) % M;
+  }
+
+  return (Uint2) h;
+}
+
+static BaseBlockPtr AddSource (
+  Asn2gbWorkPtr awp,
+  ValNodePtr PNTR head,
+  BioSourcePtr biop,
+  CharPtr comment
+)
+
+{
+  BaseBlockPtr    bbp;
+  DbtagPtr        dbt;
+  Uint2           hash;
+  SourceType      idx;
+  IntSrcBlockPtr  isp;
+  ObjectIdPtr     oip;
+  OrgModPtr       omp;
+  OrgNamePtr      onp;
+  OrgRefPtr       orp;
+  SubSourcePtr    ssp;
+  CharPtr         str;
+  Uint1           subtype;
+  Char            tmp [16];
+  ValNodePtr      vnp;
+
+  if (awp == NULL || head == NULL || biop == NULL) return NULL;
+
+  bbp = (BaseBlockPtr) MemNew (sizeof (IntSrcBlock));
+  if (bbp == NULL) return NULL;
+  bbp->blocktype = SOURCEFEAT_BLOCK;
+  bbp->section = awp->currsection;
+
+  ValNodeAddPointer (head, 0, bbp);
+
+  isp = (IntSrcBlockPtr) bbp;
+  isp->biop = biop;
+  isp->is_focus = biop->is_focus;
+  if (biop->origin == 5) {
+    isp->is_synthetic = TRUE;
+  }
+
+  orp = biop->org;
+  if (orp == NULL) return bbp;
+
+  isp->orghash = ComputeSourceHash (orp->taxname, 0);
+  isp->taxname = orp->taxname;
+
+  hash = 0;
+  onp = orp->orgname;
+  if (onp != NULL) {
+    if (StringICmp (onp->div, "SYN") == 0) {
+      isp->is_synthetic = TRUE;
+    }
+    isp->omp = onp->mod;
+    for (omp = onp->mod; omp != NULL; omp = omp->next) {
+      subtype = omp->subtype;
+      if (subtype == 253) {
+        subtype = 35;
+      } else if (subtype == 254) {
+        subtype = 36;
+      } else if (subtype == 255) {
+        subtype = 37;
+      }
+      if (subtype < 38) {
+        idx = orgModToSourceIdx [subtype];
+        if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) {
+          str = asn2gnbk_source_quals [idx].name;
+          hash = ComputeSourceHash (str, hash);
+          hash = ComputeSourceHash (omp->subname, hash);
+        }
+      }
+    }
+  }
+  if (comment != NULL) {
+    hash = ComputeSourceHash ("note", hash);
+    hash = ComputeSourceHash (comment, hash);
+  }
+  isp->modhash = hash;
+
+  hash = 0;
+  for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
+    subtype = ssp->subtype;
+    if (subtype == 255) {
+      subtype = 29;
+    }
+    if (subtype < 30) {
+      idx = subSourceToSourceIdx [subtype];
+      if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) {
+        str = asn2gnbk_source_quals [idx].name;
+        hash = ComputeSourceHash (str, hash);
+        hash = ComputeSourceHash (ssp->name, hash);
+      }
+    }
+  }
+  isp->subhash = hash;
+  isp->ssp = biop->subtype;
+
+  hash = 0;
+  for (vnp = orp->db; vnp != NULL; vnp = vnp->next) {
+    dbt = (DbtagPtr) vnp->data.ptrvalue;
+    if (dbt != NULL) {
+      hash = ComputeSourceHash (dbt->db, hash);
+      oip = dbt->tag;
+      if (oip != NULL) {
+        if (oip->str != NULL) {
+          hash = ComputeSourceHash (oip->str, hash);
+        } else {
+          sprintf (tmp, "%ld", (long) oip->id);
+          hash = ComputeSourceHash (tmp, hash);
+        }
+      }
+    }
+  }
+  isp->xrfhash = hash;
+  isp->vnp = orp->db;
+
+  return bbp;
+}
+
+static int LIBCALLBACK SortSourcesByHash (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+
+{
+  Int4            diff;
+  IntSrcBlockPtr  isp1;
+  IntSrcBlockPtr  isp2;
+  ValNodePtr      vnp1;
+  ValNodePtr      vnp2;
+
+  if (ptr1 == NULL || ptr2 == NULL) return 0;
+  vnp1 = *((ValNodePtr PNTR) ptr1);
+  vnp2 = *((ValNodePtr PNTR) ptr2);
+  if (vnp1 == NULL || vnp2 == NULL) return 0;
+  isp1 = (IntSrcBlockPtr) vnp1->data.ptrvalue;
+  isp2 = (IntSrcBlockPtr) vnp2->data.ptrvalue;
+  if (isp1 == NULL || isp2 == NULL) return 0;
+
+  if (isp1->is_focus && (! isp2->is_focus)) return -1;
+  if (isp2->is_focus && (! isp1->is_focus)) return 1;
+
+  diff = isp1->orghash - isp2->orghash;
+  if (diff > 0) return -1;
+  if (diff < 0) return 1;
+
+  diff = isp1->xrfhash - isp2->xrfhash;
+  if (diff > 0) return -1;
+  if (diff < 0) return 1;
+
+  /* sort so that sources with modifiers come first */
+
+  diff = isp1->modhash - isp2->modhash;
+  if (diff > 0) return -1;
+  if (diff < 0) return 1;
+
+  diff = isp1->subhash - isp2->subhash;
+  if (diff > 0) return -1;
+  if (diff < 0) return 1;
+
+  /* if all hashes are equal, descriptor comes first */
+
+  if (isp1->is_descriptor && (! isp2->is_descriptor)) {
+    return -1;
+  } else if (isp2->is_descriptor && (! isp1->is_descriptor)) {
+    return 1;
+  }
+
+  return 0;
+}
+
+static int LIBCALLBACK SortSourcesByPos (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+
+{
+  IntSrcBlockPtr  isp1;
+  IntSrcBlockPtr  isp2;
+  ValNodePtr      vnp1;
+  ValNodePtr      vnp2;
+
+  if (ptr1 == NULL || ptr2 == NULL) return 0;
+  vnp1 = *((ValNodePtr PNTR) ptr1);
+  vnp2 = *((ValNodePtr PNTR) ptr2);
+  if (vnp1 == NULL || vnp2 == NULL) return 0;
+  isp1 = (IntSrcBlockPtr) vnp1->data.ptrvalue;
+  isp2 = (IntSrcBlockPtr) vnp2->data.ptrvalue;
+  if (isp1 == NULL || isp2 == NULL) return 0;
+
+  /* descriptor always goes first */
+
+  if (isp1->is_descriptor && (! isp2->is_descriptor)) {
+    return -1;
+  } else if (isp2->is_descriptor && (! isp1->is_descriptor)) {
+    return 1;
+  }
+
+  /* feature with smallest left extreme is first */
+
+  if (isp1->left > isp2->left) {
+    return 1;
+  } else if (isp1->left < isp2->left) {
+    return -1;
+  }
+
+  /* if same left extreme, shortest source feature is first just for flatfile */
+
+  if (isp1->right > isp2->right) {
+    return 1;
+  } else if (isp1->right < isp2->right) {
+    return -1;
+  }
+
+  return 0;
+}
+
+/*                                                                   */
+/* s_isFuzzyLoc () -- Determines is a location has fuzzy coordinates */
+/*                                                                   */
+
+static Boolean s_isFuzzyLoc ( SeqLocPtr pLocation )
+{
+  SeqIntPtr pIntLocation;
+
+  if (pLocation == NULL)
+    return FALSE;
+
+  if (pLocation->choice != SEQLOC_INT)
+    return FALSE;
+
+  if (pLocation->data.ptrvalue == NULL)
+    return FALSE;
+
+  pIntLocation = (SeqIntPtr) pLocation->data.ptrvalue;
+
+  if ((pIntLocation->if_from != NULL) && (pIntLocation->if_from->choice == 2))
+    return TRUE;
+
+  if ((pIntLocation->if_to != NULL) && (pIntLocation->if_to->choice == 2))
+    return TRUE;
+
+  return FALSE;
+}
+
+static void GetSourcesOnBioseq (
+  Asn2gbWorkPtr awp,
+  BioseqPtr target,
+  BioseqPtr bsp,
+  Int4 from,
+  Int4 to
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  BaseBlockPtr       bbp;
+  BioSourcePtr       biop;
+  SeqMgrDescContext  dcontext;
+  SeqMgrFeatContext  fcontext;
+  Boolean            hasNulls;
+  Int4               left;
+  Boolean            loop = FALSE;
+  Int2               idx;
+  IntSrcBlockPtr     isp;
+  Int4Ptr            ivals;
+  SeqLocPtr          newloc;
+  Boolean            noLeft;
+  Boolean            noRight;
+  Int2               numivals;
+  Boolean            okay;
+  Int4               right;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  SeqInt             sint;
+  SeqIdPtr           sip;
+  Boolean            split;
+  Int4               start;
+  Int4               stop;
+  Uint1              strand;
+  ValNode            vn;
+  ValNodePtr         vnp;
+
+  if (awp == NULL || target == NULL || bsp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+
+  if (awp->format != FTABLE_FMT || awp->mode == DUMP_MODE) {
+
+	/* full length loc for descriptors */
+  
+	sint.from = 0;
+	if (ajp->ajp.slp != NULL) {
+	  sint.to = SeqLocLen (ajp->ajp.slp) - 1;
+	} else {
+	  sint.to = bsp->length - 1;
+	}
+	sint.strand = Seq_strand_plus;
+	sint.id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0)));
+	sint.if_from = NULL;
+	sint.if_to = NULL;
+  
+	vn.choice = SEQLOC_INT;
+	vn.data.ptrvalue = (Pointer) &sint;
+	vn.next = NULL;
+  
+	/* if SWISS-PROT, may have multiple source descriptors */
+  
+	if (ISA_aa (bsp->mol)) {
+	  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+		if (sip->choice == SEQID_SWISSPROT) {
+		  loop = TRUE;
+		}
+	  }
+	}
+  
+	sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+	while (sdp != NULL) {
+  
+	  /* check if descriptor on part already added on segmented bioseq */
+  
+	  okay = TRUE;
+	  for (vnp = awp->srchead; vnp != NULL && okay; vnp = vnp->next) {
+		bbp = (BaseBlockPtr) vnp->data.ptrvalue;
+		if (bbp != NULL) {
+		  if (bbp->entityID == dcontext.entityID &&
+			  bbp->itemID == dcontext.itemID &&
+			  bbp->itemtype == OBJ_SEQDESC) {
+			okay = FALSE;
+		  }
+		}
+	  }
+  
+	  if (okay) {
+		biop = (BioSourcePtr) sdp->data.ptrvalue;
+		bbp = AddSource (awp, &(awp->srchead), biop, NULL);
+		if (bbp != NULL) {
+  
+		  bbp->entityID = dcontext.entityID;
+		  bbp->itemID = dcontext.itemID;
+		  bbp->itemtype = OBJ_SEQDESC;
+  
+		  isp = (IntSrcBlockPtr) bbp;
+		  isp->loc = SeqLocMerge (target, &vn, NULL, FALSE, TRUE, FALSE);
+		  isp->left = 0;
+		  isp->right = bsp->length - 1;
+		  isp->is_descriptor = TRUE;
+		}
+	  }
+  
+	  /* if SWISS-PROT, loop through multiple source descriptors */
+  
+	  if (loop) {
+		sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext);
+	  } else {
+		sdp = NULL;
+	  }
+	}
+  
+	SeqIdFree (sint.id);
+  }
+
+  if ((! awp->contig) || awp->showconsource) {
+
+    /* features are indexed on parent if segmented */
+
+    bsp = awp->parent;
+
+    sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
+    while (sfp != NULL) {
+      ivals = fcontext.ivals;
+      numivals = fcontext.numivals;
+      if (ivals != NULL && numivals > 0) {
+
+        idx = (numivals - 1) * 2;
+        start = ivals [idx];
+        stop = ivals [idx + 1];
+        if (stop >= from && stop <= to && (ajp->ajp.slp == NULL || SeqLocCompare (sfp->location, ajp->ajp.slp) > 0)) {
+
+          biop = (BioSourcePtr) sfp->data.value.ptrvalue;
+          bbp = AddSource (awp, &(awp->srchead), biop, sfp->comment);
+          if (bbp != NULL) {
+
+            bbp->entityID = fcontext.entityID;
+            bbp->itemID = fcontext.itemID;
+            bbp->itemtype = OBJ_SEQFEAT;
+
+            isp = (IntSrcBlockPtr) bbp;
+            if (sfp->location != NULL && sfp->location->choice == SEQLOC_PNT) {
+              isp->loc = AsnIoMemCopy ((Pointer) sfp->location,
+                                       (AsnReadFunc) SeqLocAsnRead,
+                                       (AsnWriteFunc) SeqLocAsnWrite);
+            } else if (s_isFuzzyLoc (sfp->location)) {
+              isp->loc = AsnIoMemCopy ((Pointer) sfp->location,
+                                      (AsnReadFunc) SeqLocAsnRead,
+                                      (AsnWriteFunc) SeqLocAsnWrite);
+            } else if (SeqLocId(sfp->location) == NULL) {
+              isp->loc = AsnIoMemCopy ((Pointer) sfp->location,
+                                       (AsnReadFunc) SeqLocAsnRead,
+                                       (AsnWriteFunc) SeqLocAsnWrite);
+            } else {
+              CheckSeqLocForPartial (sfp->location, &noLeft, &noRight);
+              hasNulls = LocationHasNullsBetween (sfp->location);
+              isp->loc = SeqLocMerge (target, sfp->location, NULL, FALSE, TRUE, hasNulls);
+              SetSeqLocPartial (isp->loc, noLeft, noRight);
+            }
+            isp->left = fcontext.left;
+            isp->right = fcontext.right;
+            isp->comment = sfp->comment;
+            if (ajp->ajp.slp != NULL) {
+              sip = SeqIdParse ("lcl|dummy");
+              left = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_LEFT_END);
+              right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END);
+              strand = SeqLocStrand (ajp->ajp.slp);
+              split = FALSE;
+              newloc = SeqLocReMapEx (sip, ajp->ajp.slp, isp->loc, 0, FALSE, ajp->masterStyle);
+              /*
+              newloc = SeqLocCopyRegion (sip, isp->loc, bsp, left, right, strand, &split);
+              */
+              SeqIdFree (sip);
+              if (newloc != NULL) {
+                A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
+                isp->loc = SeqLocFree (isp->loc);
+                isp->loc = newloc;
+                isp->left = left;
+                isp->right = right;
+              }
+            }
+          }
+        }
+      }
+
+      sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext);
+    }
+  }
+}
+
+static Boolean LIBCALLBACK GetSourcesOnSeg (
+  SeqLocPtr slp,
+  SeqMgrSegmentContextPtr context
+)
+
+{
+  Asn2gbWorkPtr  awp;
+  BioseqPtr      bsp;
+  Int4           from;
+  SeqLocPtr      loc;
+  SeqEntryPtr    oldscope;
+  SeqEntryPtr    sep;
+  SeqIdPtr       sip;
+  Int4           to;
+
+  if (slp == NULL || context == NULL) return FALSE;
+  awp = (Asn2gbWorkPtr) context->userdata;
+
+  from = context->cumOffset;
+  to = from + context->to - context->from;
+
+  sip = SeqLocId (slp);
+  if (sip == NULL) {
+    loc = SeqLocFindNext (slp, NULL);
+    if (loc != NULL) {
+      sip = SeqLocId (loc);
+    }
+  }
+  if (sip == NULL) return TRUE;
+
+  /* biosource descriptors only on parts within entity */
+
+  sep = GetTopSeqEntryForEntityID (awp->entityID);
+  oldscope = SeqEntrySetScope (sep);
+  bsp = BioseqFind (sip);
+  SeqEntrySetScope (oldscope);
+
+  if (bsp != NULL) {
+    GetSourcesOnBioseq (awp, awp->target, bsp, from, to);
+    return TRUE;
+  }
+
+  /* if we ever want to fetch remote sources, code goes here */
+
+#if 0
+  Uint2          entityID;
+
+  /* may remote fetch genome component if not already in memory */
+
+  bsp = BioseqLockById (sip);
+
+  if (bsp == NULL) return TRUE;
+
+  entityID = ObjMgrGetEntityIDForPointer (bsp);
+
+  if (entityID != awp->entityID) {
+
+    /* if segment not packaged in record, may need to feature index it */
+
+    if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
+      SeqMgrIndexFeatures (entityID, NULL);
+    }
+
+    /* collect features indexed on the remote bioseq */
+
+    from = 0;
+    to = bsp->length - 1;
+  }
+
+  GetSourcesOnBioseq (awp, awp->target, bsp, from, to);
+
+  BioseqUnlock (bsp);
+#endif
+
+  return TRUE;
+}
+
+/* isIdenticalSource() -- Checks to see if two sources are identical */
+/*                        by comparing the actual values in the      */
+/*                        fields.  This only gets called if the two  */
+/*                        sources hashed the same -- it's a double-  */
+/*                        check since two non-identical things will  */
+/*                        occassionally hash to the same value.      */
+
+static Boolean isIdenticalSource (IntSrcBlockPtr isp1, IntSrcBlockPtr isp2)
+{
+  OrgModPtr     omp1;
+  OrgModPtr     omp2;
+  SubSourcePtr  ssp1;
+  SubSourcePtr  ssp2;
+  ValNodePtr    vnp1;
+  ValNodePtr    vnp2;
+  ObjectIdPtr   oip1;
+  ObjectIdPtr   oip2;
+  DbtagPtr      dbt1;
+  DbtagPtr      dbt2;
+
+  if (isp1->is_focus != isp2->is_focus)
+    return FALSE;
+
+  /* Compare the taxonomy names */
+
+  if (StringICmp(isp1->taxname,isp2->taxname) != 0)
+    return FALSE;
+
+  /* Compare the comment */
+
+  if (StringICmp(isp1->comment,isp2->comment) != 0)
+    return FALSE;
+
+  /* Compare the org mods */
+
+  omp1 = isp1->omp;
+  omp2 = isp2->omp;
+  while (omp1 != NULL && omp2 != NULL)
+    {
+      if (omp1->subtype != omp2->subtype)
+        return FALSE;
+      if (StringICmp (omp1->subname, omp2->subname) != 0)
+        return FALSE;
+      omp1 = omp1->next;
+      omp2 = omp2->next;
+    }
+
+  if (omp1 != NULL || omp2 != NULL)
+    return FALSE;
+
+  /* Compare the subtypes */
+
+  ssp1 = isp1->ssp;
+  ssp2 = isp2->ssp;
+
+  while (ssp1 != NULL && ssp2 != NULL)
+    {
+      if (ssp1->subtype != ssp2->subtype)
+        return FALSE;
+      if (StringICmp(ssp1->name,ssp2->name) != 0)
+        return FALSE;
+      ssp1 = ssp1->next;
+      ssp2 = ssp2->next;
+    }
+
+  if (ssp1 != NULL || ssp2 != NULL)
+    return FALSE;
+
+  /* Compare the DB tags */
+
+  vnp1 = isp1->vnp;
+  vnp2 = isp2->vnp;
+
+  while (vnp1 != NULL && vnp2 != NULL)
+    {
+      dbt1 = (DbtagPtr) vnp1->data.ptrvalue;
+      dbt2 = (DbtagPtr) vnp2->data.ptrvalue;
+
+      if ((dbt1 != NULL) && (dbt2 != NULL)) {
+        if (dbt1->db != dbt2->db)
+          return FALSE;
+
+        oip1 = dbt1->tag;
+        oip2 = dbt2->tag;
+        if ((oip1 != NULL) && (oip2 != NULL)) {
+          if (oip1->str != NULL) {
+            if (StringICmp(oip1->str, oip2->str) != 0)
+              return FALSE;
+          } else  {
+            if (oip1->id != oip2->id)
+              return FALSE;
+          }
+        }
+        else if (oip1 != NULL)
+          return FALSE;
+        else if (oip2 != NULL)
+          return FALSE;
+      }
+      else if (dbt1 != NULL)
+        return FALSE;
+      else if (dbt2 != NULL)
+        return FALSE;
+
+      vnp1 = vnp1->next;
+      vnp2 = vnp2->next;
+    }
+
+  if (vnp1 != NULL || vnp2 != NULL)
+    return FALSE;
+
+  /* If it passed all checks, then they */
+  /* are the same, so return true.      */
+
+  return TRUE;
+}
+
+static void CleanupPackedSeqInt (SeqLocPtr location)
+
+{
+  SeqLocPtr  head = NULL;
+  SeqIntPtr  loc;
+  SeqIntPtr  sintp;
+  SeqLocPtr  slp;
+
+  if (location == NULL || location->choice != SEQLOC_PACKED_INT || location->data.ptrvalue == NULL) return;
+
+  slp = SeqLocFindNext (location, NULL);
+  while (slp != NULL) {
+    if (slp->choice == SEQLOC_INT) {
+      sintp = (SeqIntPtr) slp->data.ptrvalue;
+      if (sintp != NULL) {
+        loc = AsnIoMemCopy (sintp, (AsnReadFunc) SeqIntAsnRead,
+                            (AsnWriteFunc) SeqIntAsnWrite);
+        ValNodeAddPointer (&head, SEQLOC_INT, loc);
+      }
+    }
+    slp = SeqLocFindNext (location, slp);
+  }
+  if (head == NULL) return;
+
+  location->data.ptrvalue = SeqLocFree (location->data.ptrvalue);
+  location->data.ptrvalue = head;
+
+  slp = location->data.ptrvalue;
+  if (slp == NULL || slp->next != NULL) return;
+    /* here seqloc_packed_int points to a single location element, so no need for seqloc_packed_int parent */
+    location->choice = slp->choice;
+    location->data.ptrvalue = (Pointer) slp->data.ptrvalue;
+    MemFree (slp);
+}
+
+
+NLM_EXTERN void AddSourceFeatBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  BaseBlockPtr       bbp;
+  BioseqPtr          bsp;
+  SeqFeatPtr         cds;
+  SeqMgrFeatContext  context;
+  BioseqPtr          dna;
+  SeqLocPtr          duploc;
+  Boolean            excise;
+  GBFeaturePtr       gbfeat = NULL;
+  GBSeqPtr           gbseq;
+  ValNodePtr         head = NULL;
+  IntSrcBlockPtr     isp;
+  IntSrcBlockPtr     lastisp;
+  IntSrcBlockPtr     descrIsp;
+  ValNodePtr         next;
+  ValNodePtr         PNTR prev;
+  SeqInt             sint;
+  SeqLocPtr          slp;
+  CharPtr            str;
+  BioseqPtr          target;
+  ValNode            vn;
+  ValNodePtr         vnp;
+  Boolean            descHasFocus = FALSE;
+  StringItemPtr      ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+
+  /* collect biosources on bioseq */
+
+  awp->srchead = NULL;
+  GetSourcesOnBioseq (awp, bsp, bsp, awp->from, awp->to);
+  target = bsp;
+
+  if (bsp->repr == Seq_repr_seg) {
+
+    /* collect biosource descriptors on local parts */
+
+    SeqMgrExploreSegments (bsp, (Pointer) awp, GetSourcesOnSeg);
+    target = awp->target;
+  }
+
+  if (awp->srchead == NULL && ISA_aa (bsp->mol)) {
+
+    /* if protein with no sources, get sources applicable to DNA location of CDS */
+
+    cds = SeqMgrGetCDSgivenProduct (bsp, &context);
+    if (cds != NULL) {
+      dna = BioseqFindFromSeqLoc (cds->location);
+      if (dna != NULL) {
+        GetSourcesOnBioseq (awp, dna, dna, context.left, context.right);
+        target = dna;
+      }
+    }
+  }
+
+  head = awp->srchead;
+  awp->srchead = NULL;
+
+  if (head == NULL && (awp->format != FTABLE_FMT || awp->mode == DUMP_MODE)) {
+
+    if (ajp->gbseq) {
+      gbseq = &asp->gbseq;
+    } else {
+      gbseq = NULL;
+    }
+
+    sint.from = 0;
+    sint.to = bsp->length - 1;
+    sint.strand = Seq_strand_plus;
+    sint.id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0)));
+    sint.if_from = NULL;
+    sint.if_to = NULL;
+
+    vn.choice = SEQLOC_INT;
+    vn.data.ptrvalue = (Pointer) &sint;
+    vn.next = NULL;
+
+    FFStartPrint (ffstring, awp->format, 5, 21, NULL, 0, 5, 21, "FT", FALSE);
+    FFAddOneString(ffstring, "source", FALSE, FALSE, TILDE_IGNORE);
+    FFAddNChar(ffstring, ' ', 21 - 5 - StringLen("source"), FALSE);
+
+    if (gbseq != NULL) {
+      gbfeat = GBFeatureNew ();
+      if (gbfeat != NULL) {
+        gbfeat->key = StringSave ("source");
+      }
+    }
+
+    str = FFFlatLoc (ajp, bsp, &vn, (Boolean) (awp->style == MASTER_STYLE));
+    if ( GetWWW(ajp) ) {
+      FF_www_featloc (ffstring, str);
+    } else {
+      FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_IGNORE);
+    }
+
+    if (gbseq != NULL) {
+      if (gbfeat != NULL) {
+        if (! StringHasNoText (str)) {
+          gbfeat->location = StringSave (str);
+        } else {
+          gbfeat->location = StringSave ("");
+        }
+      }
+    }
+
+    MemFree (str);
+
+    if (ajp->flags.needOrganismQual) {
+      FFAddNewLine(ffstring);
+      FFAddTextToString (ffstring, "/organism=\"", "unknown", "\"", FALSE, TRUE, TILDE_TO_SPACES);
+#ifdef ASN2GNBK_PRINT_UNKNOWN_ORG
+    } else {
+      FFAddNewLine(ffstring);
+      FFAddTextToString (ffstring, "/organism=\"", "unknown", "\"", FALSE, TRUE, TILDE_TO_SPACES);
+#endif
+    }
+
+    str = GetMolTypeQual (bsp);
+    if (str == NULL) {
+      switch (bsp->mol) {
+        case Seq_mol_dna :
+          str = "unassigned DNA";
+          break;
+        case Seq_mol_rna :
+          str = "unassigned RNA";
+          break;
+        case Seq_mol_aa :
+          break;
+        default :
+          str = "unassigned DNA";
+          break;
+      }
+    }
+    if (str != NULL) {
+      FFAddNewLine(ffstring);
+      FFAddTextToString (ffstring, "/mol_type=\"", str, "\"", FALSE, TRUE, TILDE_TO_SPACES);
+    }
+
+    str = FFEndPrint(ajp, ffstring, awp->format, 5, 21, 5, 21, "FT");
+
+    bbp = (BaseBlockPtr) Asn2gbAddBlock (awp, SOURCEFEAT_BLOCK, sizeof (IntSrcBlock));
+    if (bbp != NULL) {
+      bbp->section = awp->currsection;
+      bbp->string = str;
+    } else {
+      MemFree(str);
+    }
+    FFRecycleString(ajp, ffstring);
+
+    /* optionally populate gbseq for XML-ized GenBank format */
+
+    if (gbseq != NULL) {
+      if (gbfeat != NULL) {
+        AddFeatureToGbseq (gbseq, gbfeat, str, NULL);
+      }
+    }
+  }
+
+  if (head == NULL) return;
+
+  /* sort by hash values */
+
+  head = SortValNode (head, SortSourcesByHash);
+
+  /* unique sources, excise duplicates from list */
+
+  prev = &(head);
+  vnp = head;
+  lastisp = NULL;
+  while (vnp != NULL) {
+    excise = FALSE;
+    next = vnp->next;
+    isp = (IntSrcBlockPtr) vnp->data.ptrvalue;
+    if (isp->is_descriptor && isp->is_focus)
+      descHasFocus = TRUE;
+    if (lastisp != NULL) {
+      if (isp != NULL) {
+        if (lastisp->is_focus == isp->is_focus &&
+            lastisp->orghash == isp->orghash &&
+            lastisp->xrfhash == isp->xrfhash) {
+
+          /* check for identical modifiers */
+
+          if (lastisp->modhash == isp->modhash &&
+              lastisp->subhash == isp->subhash) {
+
+            excise = isIdenticalSource (isp, lastisp);
+
+          /* or modifiers only in lastisp (e.g., on part bioseq) */
+
+          } else if (isp->modhash == 0 && isp->subhash == 0) {
+            excise = isIdenticalSource (isp, lastisp);
+          }
+        }
+      }
+    }
+    if (excise) {
+      *prev = vnp->next;
+      vnp->next = NULL;
+
+      /* combine locations of duplicate sources */
+
+      if (lastisp != NULL) {
+        slp = SeqLocMerge (target, lastisp->loc, isp->loc, FALSE, TRUE, FALSE);
+        lastisp->loc = SeqLocFree (lastisp->loc);
+        lastisp->loc = slp;
+        lastisp->left = MIN (lastisp->left,isp->left);
+        lastisp->right = MAX (lastisp->right, isp->right);
+      }
+
+      /* and remove duplicate source */
+
+      SeqLocFree (isp->loc);
+      MemFree (isp);
+      ValNodeFree (vnp);
+
+    } else {
+
+      prev = &(vnp->next);
+      lastisp = isp;
+    }
+    vnp = next;
+  }
+
+  /* Sort again, by location this time */
+
+  head = SortValNode (head, SortSourcesByPos);
+
+  /* If the descriptor has a focus, then subtract */
+  /* out all the other source locations.          */
+
+  descrIsp = (IntSrcBlockPtr) head->data.ptrvalue; /* Sorted 1st by now */
+
+  if ((descHasFocus) && (! descrIsp->is_synthetic)) {
+
+    vnp = head;
+    duploc = AsnIoMemCopy ((Pointer) descrIsp->loc,
+                           (AsnReadFunc) SeqLocAsnRead,
+                           (AsnWriteFunc) SeqLocAsnWrite);
+    vnp = vnp->next;
+    while (vnp != NULL) {
+      isp = (IntSrcBlockPtr) vnp->data.ptrvalue;
+      if (SeqLocAinB (descrIsp->loc, isp->loc) >= 0) {
+        vnp = NULL; /* break the chain */
+        descrIsp->loc = SeqLocFree (descrIsp->loc);
+        descrIsp->loc = duploc;
+        duploc = NULL;
+      } else {
+        descrIsp->loc = SeqLocSubtract (descrIsp->loc, isp->loc);
+        vnp = vnp->next;
+      }
+    }
+    CleanupPackedSeqInt (descrIsp->loc);
+    descrIsp->left  = SeqLocStart (descrIsp->loc);
+    descrIsp->right = SeqLocStop (descrIsp->loc);
+    SeqLocFree (duploc);
+  }
+
+  /* if features completely subtracted descriptor
+     intervals, suppress in release, entrez modes */
+
+  if (descrIsp->loc == NULL && ajp->flags.hideEmptySource && head->next != NULL) {
+    vnp = head->next;
+    head->next = NULL;
+    ValNodeFreeData (head);
+    head = vnp;
+  }
+
+  /* finally link into blocks for current section */
+
+  ValNodeLink (&(awp->lastblock), head);
+  vnp = awp->lastblock;
+  if (vnp == NULL) return;
+  while (vnp->next != NULL) {
+    vnp = vnp->next;
+  }
+
+  awp->lastblock = vnp;
+  if (awp->blockList == NULL) {
+    awp->blockList = vnp;
+  }
+  FFRecycleString(ajp, ffstring);
+}
+
+static Boolean IsCDD (
+  SeqFeatPtr sfp
+)
+
+{
+  DbtagPtr    dbt;
+  ValNodePtr  vnp;
+
+  for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next) {
+    dbt = (DbtagPtr) vnp->data.ptrvalue;
+    if (dbt != NULL && StringCmp (dbt->db, "CDD") == 0) return TRUE;
+  }
+
+  return FALSE;
+}
+
+static void GetFeatsOnCdsProduct (
+  SeqFeatPtr cds,
+  BioseqPtr nbsp,
+  BioseqPtr pbsp,
+  IntAsn2gbJobPtr ajp,
+  Asn2gbWorkPtr awp
+)
+
+{
+  FeatBlockPtr       fbp;
+  IntFeatBlockPtr    ifp;
+  Boolean            isRefSeq;
+  Int4               lastleft;
+  Int4               lastright;
+  SeqAnnotPtr        lastsap;
+  SeqFeatPtr         lastsfp;
+  SeqLocPtr          location;
+  SeqLocPtr          newloc;
+  SeqMgrFeatContext  pcontext;
+  SeqFeatPtr         prt;
+  SeqIdPtr           sip;
+  SeqLocPtr          slp;
+  Boolean            suppress;
+
+  if (cds == NULL || ajp == NULL || awp == NULL) return;
+  if (nbsp == NULL || pbsp == NULL || (! ISA_aa (pbsp->mol))) return;
+
+  if (awp->hideCdsProdFeats) return;
+
+  isRefSeq = FALSE;
+  for (sip = nbsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_OTHER) {
+      isRefSeq = TRUE;
+    }
+  }
+
+  /* explore mat_peptides, sites, etc. */
+
+  lastsfp = NULL;
+  lastsap = NULL;
+  lastleft = 0;
+  lastright = 0;
+
+  prt = SeqMgrGetNextFeature (pbsp, NULL, 0, 0, &pcontext);
+  while (prt != NULL) {
+
+    if (pcontext.featdeftype == FEATDEF_REGION ||
+        pcontext.featdeftype == FEATDEF_SITE ||
+        pcontext.featdeftype == FEATDEF_BOND ||
+        pcontext.featdeftype == FEATDEF_mat_peptide_aa ||
+        pcontext.featdeftype == FEATDEF_sig_peptide_aa ||
+        pcontext.featdeftype == FEATDEF_transit_peptide_aa ||
+        (pcontext.featdeftype == FEATDEF_preprotein /* && isRefSeq */)) {
+
+      if (awp->hideCddFeats && pcontext.featdeftype == FEATDEF_REGION && IsCDD (prt)) {
+
+        /* passing this test prevents mapping of COG CDD region features */
+
+      } else if (pcontext.dnaStop >= awp->from && pcontext.dnaStop <= awp->to) {
+
+        /* suppress duplicate features (on protein) */
+
+        suppress = FALSE;
+        if (lastsfp != NULL && lastsap != NULL) {
+          if (lastsfp->idx.subtype == prt->idx.subtype &&
+              lastleft == pcontext.left &&
+              lastright == pcontext.right) {
+              if (lastsap == pcontext.sap ||
+                  (lastsap->desc == NULL && pcontext.sap->desc == NULL)) {
+              if (AsnIoMemComp (lastsfp, prt, (AsnWriteFunc) SeqFeatAsnWrite)) {
+                suppress = TRUE;
+              }
+            }
+          }
+        }
+
+        /* make sure feature maps within nucleotide sublocation */
+
+        if (! suppress) {
+          if (ajp->ajp.slp != NULL) {
+            location = aaFeatLoc_to_dnaFeatLoc (cds, prt->location);
+            slp = SeqLocMerge (nbsp, location, NULL, FALSE, TRUE, FALSE);
+            if (slp != NULL) {
+              sip = SeqIdParse ("lcl|dummy");
+              newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
+              SeqIdFree (sip);
+              SeqLocFree (slp);
+              if (newloc == NULL) {
+                suppress = TRUE;
+              }
+              SeqLocFree (newloc);
+            } else {
+              suppress = TRUE;
+            }
+            SeqLocFree (location);
+          }
+        }
+
+        if (! suppress) {
+
+          fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntFeatBlock));
+          if (fbp != NULL) {
+
+            fbp->entityID = pcontext.entityID;
+            fbp->itemID = pcontext.itemID;
+            fbp->itemtype = OBJ_SEQFEAT;
+            fbp->featdeftype = pcontext.featdeftype;
+            ifp = (IntFeatBlockPtr) fbp;
+            ifp->mapToNuc = TRUE;
+            ifp->mapToProt = FALSE;
+            ifp->mapToGen = FALSE;
+            ifp->mapToMrna = FALSE;
+            ifp->mapToPep = FALSE;
+            ifp->firstfeat = awp->firstfeat;
+            awp->firstfeat = FALSE;
+          }
+        }
+
+        lastsfp = prt;
+        lastsap = pcontext.sap;
+        lastleft = pcontext.left;
+        lastright = pcontext.right;
+
+      }
+    }
+    prt = SeqMgrGetNextFeature (pbsp, prt, 0, 0, &pcontext);
+  }
+}
+
+static Boolean NotEMBLorDDBJ (
+  BioseqPtr bsp
+)
+
+{
+  SeqIdPtr  sip;
+
+  if (bsp == NULL) return TRUE;
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_EMBL) return FALSE;
+    if (sip->choice == SEQID_DDBJ) return FALSE;
+  }
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK GetFeatsOnBioseq (
+  SeqFeatPtr sfp,
+  SeqMgrFeatContextPtr fcontext
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  Asn2gbWorkPtr      awp;
+  BioseqPtr          bsp;
+  Char               buf [41];
+  SeqFeatPtr         cds;
+  SeqMgrFeatContext  cdscontext;
+  SeqMgrDescContext  dcontext;
+  FeatBlockPtr       fbp;
+  SeqLocPtr          firstslp;
+  GBQualPtr          gbq;
+  SeqFeatPtr         gene;
+  Int4               gi;
+  GeneRefPtr         grp;
+  Boolean            juststop = FALSE;
+  IntCdsBlockPtr     icp;
+  Int2               idx;
+  IntFeatBlockPtr    ifp;
+  Int4Ptr            ivals;
+  Int2               j;
+  SeqAnnotPtr        lastsap;
+  SeqFeatPtr         lastsfp;
+  SeqLocPtr          lastslp;
+  SeqLocPtr          newloc;
+  Int2               numivals;
+  Boolean            okay;
+  SeqEntryPtr        oldscope;
+  BioseqPtr          parent;
+  Boolean            partial5;
+  Boolean            partial3;
+  ValNodePtr         ppr;
+  PubdescPtr         pdp;
+  BioseqPtr          prod;
+  Boolean            pseudo = FALSE;
+  SeqDescrPtr        sdp;
+  SeqEntryPtr        sep;
+  SeqIdPtr           sip;
+  SeqLocPtr          slp;
+  Int4               start;
+  Int4               stop;
+  TextSeqIdPtr       tsip;
+  ValNodePtr         vnp;
+
+  if (sfp == NULL || fcontext == NULL) return FALSE;
+  awp = (Asn2gbWorkPtr) fcontext->userdata;
+  if (awp == NULL) return FALSE;
+  ajp = awp->ajp;
+  if (ajp == NULL) return FALSE;
+  asp = awp->asp;
+  if (asp == NULL) return FALSE;
+  bsp = asp->bsp;
+  if (bsp == NULL) return FALSE;
+
+  if (fcontext->featdeftype == FEATDEF_PUB ||
+      fcontext->featdeftype == FEATDEF_NON_STD_RESIDUE ||
+      fcontext->featdeftype == FEATDEF_RSITE ||
+      fcontext->featdeftype == FEATDEF_SEQ) return TRUE;
+
+  if (fcontext->featdeftype == FEATDEF_BIOSRC) return TRUE;
+
+  if (ajp->flags.validateFeats &&
+      (fcontext->featdeftype == FEATDEF_BAD ||
+       fcontext->featdeftype == FEATDEF_virion)) {
+    return TRUE;
+  }
+
+  if (ISA_na (bsp->mol) && fcontext->featdeftype == FEATDEF_HET) return TRUE;
+
+  /* check feature customization flags */
+
+  if (awp->hideImpFeats && sfp->data.choice == SEQFEAT_IMP) return TRUE;
+  if (awp->hideSnpFeats && fcontext->featdeftype == FEATDEF_variation) return TRUE;
+  if (awp->hideExonFeats && fcontext->featdeftype == FEATDEF_exon) return TRUE;
+  if (awp->hideIntronFeats && fcontext->featdeftype == FEATDEF_intron) return TRUE;
+  if (awp->hideMiscFeats && fcontext->featdeftype == FEATDEF_misc_feature) return TRUE;
+  if (awp->hideRemImpFeats && sfp->data.choice == SEQFEAT_IMP) {
+    if (fcontext->featdeftype != FEATDEF_variation &&
+        fcontext->featdeftype != FEATDEF_exon &&
+        fcontext->featdeftype != FEATDEF_intron &&
+        fcontext->featdeftype != FEATDEF_misc_feature) return TRUE;
+  }
+  if (ISA_aa (bsp->mol) && fcontext->featdeftype == FEATDEF_REGION &&
+      awp->hideCddFeats && IsCDD (sfp)) return TRUE;
+
+  /* DDBJ does not want to show gene features */
+
+  if (fcontext->seqfeattype == SEQFEAT_GENE && awp->hideGeneFeats) return TRUE;
+
+  /* suppress comment features that are full length */
+
+  if (fcontext->seqfeattype == SEQFEAT_COMMENT &&
+      fcontext->left == awp->from && fcontext->right == awp->to) return TRUE;
+
+  ivals = fcontext->ivals;
+  numivals = fcontext->numivals;
+
+  /* check to see if last interval is on this awp->from - awp->to range */
+
+  if (ivals != NULL && numivals > 0) {
+    idx = (numivals - 1) * 2;
+    start = ivals [idx];
+    stop = ivals [idx + 1];
+    if (stop < awp->from || stop > awp->to) {
+
+      /* may need to map sig_peptide on a different segment */
+
+      if (fcontext->seqfeattype == SEQFEAT_CDREGION) {
+        sip = SeqLocIdForProduct (sfp->product);
+        bsp = BioseqFind (sip);
+        GetFeatsOnCdsProduct (sfp, asp->bsp, bsp, ajp, awp);
+      }
+
+      if (! awp->showAllFeats) return TRUE;
+
+      /* if showing one segment, only show features covering this segment */
+
+      if (fcontext->right < awp->from || fcontext->left > awp->to) return TRUE;
+
+    } else if (fcontext->farloc && NotEMBLorDDBJ (awp->bsp)) {
+
+      /* last interval may not have been mapped to bioseq if far */
+
+      firstslp = NULL;
+      lastslp = NULL;
+
+      slp = SeqLocFindNext (sfp->location, NULL);
+      while (slp != NULL) {
+        if (slp->choice != SEQLOC_NULL) {
+          lastslp = slp;
+          if (firstslp == NULL) {
+            firstslp = slp;
+          }
+        }
+        slp = SeqLocFindNext (sfp->location, slp);
+      }
+
+      /* !!! EMBL may have different desired behavior on where to map !!! */
+
+      if (firstslp != NULL && SeqLocStrand (firstslp) == Seq_strand_minus) {
+        slp = firstslp;
+      } else {
+        slp = lastslp;
+      }
+
+      if (slp != NULL) {
+        sip = SeqLocId (slp);
+        if (sip != NULL) {
+          bsp = BioseqFindCore (sip);
+          if (bsp == NULL || (bsp != awp->parent && bsp != awp->bsp)) {
+
+            return TRUE;
+          }
+        }
+      }
+    }
+  }
+
+  /* make sure feature is within sublocation */
+
+  if (ajp->ajp.slp != NULL) {
+    if (SeqLocCompare (sfp->location, ajp->ajp.slp) == SLC_NO_MATCH) {
+      slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, TRUE, FALSE);
+      if (slp == NULL) return TRUE;
+      sip = SeqIdParse ("lcl|dummy");
+      newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
+      SeqIdFree (sip);
+      SeqLocFree (slp);
+      if (newloc == NULL) return TRUE;
+      SeqLocFree (newloc);
+    }
+  }
+
+  /* suppress duplicate features (on nucleotide) */
+
+  lastsfp = awp->lastsfp;
+  lastsap = awp->lastsap;
+  if (lastsfp != NULL && lastsap != NULL) {
+    if (lastsfp->idx.subtype == sfp->idx.subtype &&
+        awp->lastleft == fcontext->left &&
+        awp->lastright == fcontext->right) {
+        if (lastsap == fcontext->sap ||
+            (lastsap->desc == NULL && fcontext->sap->desc == NULL)) {
+        if (AsnIoMemComp (lastsfp, sfp, (AsnWriteFunc) SeqFeatAsnWrite)) {
+          return TRUE;
+        }
+      }
+    }
+  }
+
+  /* if RELEASE_MODE, verify that features have all mandatory qualifiers */
+
+  if (ajp->flags.needRequiredQuals) {
+    okay = FALSE;
+
+    switch (fcontext->featdeftype) {
+
+    case FEATDEF_CDS:
+      if (ajp->flags.checkCDSproductID) {
+        /* non-pseudo CDS must have /product */
+        if (sfp->pseudo) {
+          pseudo = TRUE;
+        }
+        grp = SeqMgrGetGeneXref (sfp);
+        if (grp == NULL) {
+          sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
+          oldscope = SeqEntrySetScope (sep);
+          gene = SeqMgrGetOverlappingGene (sfp->location, NULL);
+          SeqEntrySetScope (oldscope);
+          if (gene != NULL) {
+            grp = (GeneRefPtr) gene->data.value.ptrvalue;
+            if (gene->pseudo) {
+              pseudo = TRUE;
+            }
+          }
+        }
+        if (grp != NULL && grp->pseudo) {
+          pseudo = TRUE;
+        }
+        if (sfp->location != NULL) {
+          if (CheckSeqLocForPartial (sfp->location, &partial5, &partial3)) {
+            if (partial5 && (! partial3)) {
+              if (SeqLocLen (sfp->location) <= 5) {
+                juststop = TRUE;
+              }
+            }
+          }
+        }
+        if (pseudo || juststop) {
+          okay = TRUE;
+        } else if (sfp->product != NULL) {
+          sip = SeqLocIdForProduct (sfp->product);
+          if (sip != NULL) {
+            if ((sip->choice == SEQID_GI && sip->data.intvalue > 0) ||
+                sip->choice == SEQID_LOCAL) {
+              sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
+              oldscope = SeqEntrySetScope (sep);
+              prod = BioseqFind (sip);
+              SeqEntrySetScope (oldscope);
+              if (prod != NULL) {
+                for (sip = prod->id; sip != NULL; sip = sip->next) {
+                  if (sip->choice == SEQID_GENBANK ||
+                     sip->choice == SEQID_EMBL ||
+                      sip->choice == SEQID_DDBJ ||
+                      sip->choice == SEQID_OTHER ||
+                      sip->choice == SEQID_PATENT ||
+                      sip->choice == SEQID_TPG ||
+                      sip->choice == SEQID_TPE ||
+                      sip->choice == SEQID_TPD) {
+                    tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+                    if (tsip != NULL && (! StringHasNoText (tsip->accession))) {
+                      if (ValidateAccn (tsip->accession) == 0)
+                      okay = TRUE;
+                    }
+                  }
+                }
+              } else if (sip->choice == SEQID_GI && sip->data.intvalue > 0) {
+                /* RELEASE_MODE requires that /protein_id is an accession */
+                gi = sip->data.intvalue;
+                if (GetAccnVerFromServer (gi, buf)) {
+                  okay = TRUE;
+                } else {
+                  sip = GetSeqIdForGI (gi);
+                  if (sip != NULL) {
+                    okay = TRUE;
+                  }
+                }
+              }
+            } else if (sip->choice == SEQID_GENBANK ||
+                       sip->choice == SEQID_EMBL ||
+                       sip->choice == SEQID_DDBJ ||
+                       sip->choice == SEQID_OTHER ||
+                       sip->choice == SEQID_PATENT ||
+                       sip->choice == SEQID_TPG ||
+                       sip->choice == SEQID_TPE ||
+                       sip->choice == SEQID_TPD) {
+              tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+              if (tsip != NULL && (! StringHasNoText (tsip->accession))) {
+                if (ValidateAccn (tsip->accession) == 0)
+                okay = TRUE;
+              }
+            }
+          }
+        } else {
+          if (sfp->excpt && (! StringHasNoText (sfp->except_text))) {
+            if (StringStr (sfp->except_text, "rearrangement required for product") != NULL) {
+              okay = TRUE;
+            }
+          }
+        }
+      } else {
+        okay = TRUE;
+      }
+      if (! okay) {
+        ajp->relModeError = TRUE;
+      }
+      break;
+
+    case FEATDEF_conflict:
+      if (sfp->cit == NULL) {
+        /* RefSeq allows conflict with accession in comment instead of sfp->cit */
+        for (sip = bsp->id; sip != NULL; sip = sip->next) {
+          if (sip->choice == SEQID_OTHER) {
+            if (! StringHasNoText (sfp->comment)) {
+              okay = TRUE;
+            }
+          }
+        }
+      }
+      /* continue on to old_sequence */
+    case FEATDEF_old_sequence:
+      /* conflict and old_sequence require a publication printable on the segment */
+      vnp = sfp->cit;
+
+      if (vnp != NULL && asp->referenceArray != NULL) {
+        for (ppr = vnp->data.ptrvalue; ppr != NULL; ppr = ppr->next) {
+          j = MatchRef (ppr, asp->referenceArray, asp->numReferences);
+          if (j > 0) {
+            okay = TRUE;
+            break;
+          }
+        }
+      }
+      break;
+
+    case FEATDEF_GENE:
+      /* gene requires /gene or /locus_tag, but desc or syn can be mapped to /gene */
+      grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+      if (grp != NULL) {
+        if (! StringHasNoText (grp->locus)) {
+          okay = TRUE;
+        }  else if (! StringHasNoText (grp->locus_tag)) {
+          okay = TRUE;
+        } else if (! StringHasNoText (grp->desc)) {
+          okay = TRUE;
+        } else {
+          vnp = grp->syn;
+          if (vnp != NULL) {
+            if (! StringHasNoText (vnp->data.ptrvalue)) {
+              okay = TRUE;
+            }
+          }
+        }
+      }
+      break;
+
+    case FEATDEF_protein_bind:
+    case FEATDEF_misc_binding:
+      /* protein_bind or misc_binding require FTQUAL_bound_moiety */
+      gbq = sfp->qual;
+      while (gbq != NULL) {
+        if (StringICmp (gbq->qual, "bound_moiety") == 0 && (! StringHasNoText (gbq->val))) {
+          okay = TRUE;
+          break;
+        }
+        gbq = gbq->next;
+      }
+      break;
+
+    case FEATDEF_modified_base:
+      /* modified_base requires FTQUAL_mod_base */
+      gbq = sfp->qual;
+      while (gbq != NULL) {
+        if (StringICmp (gbq->qual, "mod_base") == 0 && (! StringHasNoText (gbq->val))) {
+          okay = TRUE;
+          break;
+        }
+        gbq = gbq->next;
+      }
+      break;
+
+    default:
+      if (fcontext->featdeftype >= FEATDEF_GENE && fcontext->featdeftype < FEATDEF_MAX) {
+        okay = TRUE;
+      }
+      break;
+    }
+
+    if (okay == FALSE) return TRUE;
+  }
+
+  /* if RELEASE_MODE, suppress features with location on segmented Bioseq */
+
+  if (ajp->flags.suppressSegLoc) {
+    bsp = awp->parent;
+    if (bsp != NULL && bsp->repr == Seq_repr_seg) {
+      slp = SeqLocFindNext (sfp->location, NULL);
+      while (slp != NULL) {
+        sip = SeqLocId (slp);
+        if (sip != NULL) {
+          if (SeqIdIn (sip, bsp->id)) return TRUE;
+        }
+        slp = SeqLocFindNext (sfp->location, slp);
+      }
+    }
+  }
+
+  awp->lastsfp = sfp;
+  awp->lastsap = fcontext->sap;
+  awp->lastleft = fcontext->left;
+  awp->lastright = fcontext->right;
+
+  if (fcontext->seqfeattype == SEQFEAT_CDREGION) {
+    fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
+  } else {
+    fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntFeatBlock));
+  }
+  if (fbp == NULL) return TRUE;
+
+  fbp->entityID = fcontext->entityID;
+  fbp->itemID = fcontext->itemID;
+  fbp->itemtype = OBJ_SEQFEAT;
+  fbp->featdeftype = fcontext->featdeftype;
+  ifp = (IntFeatBlockPtr) fbp;
+  ifp->mapToNuc = FALSE;
+  ifp->mapToProt = FALSE;
+  ifp->mapToGen = FALSE;
+  ifp->mapToMrna = FALSE;
+  ifp->mapToPep = FALSE;
+  ifp->firstfeat = awp->firstfeat;
+  awp->firstfeat = FALSE;
+  awp->featseen = TRUE;
+
+  /* optionally map CDS from cDNA onto genomic */
+
+  if (awp->isGPS && ISA_na (bsp->mol) && awp->copyGpsCdsUp &&
+      fcontext->featdeftype == FEATDEF_mRNA) {
+    sip = SeqLocIdForProduct (sfp->product);
+    bsp = BioseqFind (sip);
+    if (bsp != NULL && ISA_na (bsp->mol)) {
+      cds = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &cdscontext);
+      if (cds != NULL) {
+        fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
+        if (fbp != NULL) {
+
+          fbp->entityID = cdscontext.entityID;
+          fbp->itemID = cdscontext.itemID;
+          fbp->itemtype = OBJ_SEQFEAT;
+          fbp->featdeftype = cdscontext.featdeftype;
+          ifp = (IntFeatBlockPtr) fbp;
+          ifp->mapToNuc = FALSE;
+          ifp->mapToProt = FALSE;
+          ifp->mapToGen = TRUE;
+          ifp->mapToMrna = FALSE;
+          ifp->mapToPep = FALSE;
+          ifp->firstfeat = awp->firstfeat;
+          awp->firstfeat = FALSE;
+        }
+      }
+    }
+  }
+
+  if (fcontext->seqfeattype != SEQFEAT_CDREGION) return TRUE;
+
+  /* if feature table format, do not get features from protein product */
+
+  if (awp->format == FTABLE_FMT) return TRUE;
+
+  /* if CDS, collect more information from product protein bioseq - may be part */
+
+  sip = SeqLocIdForProduct (sfp->product);
+  bsp = BioseqFind (sip);
+  if (bsp == NULL || (! ISA_aa (bsp->mol))) return TRUE;
+
+  ifp->isCDS = TRUE;
+  icp = (IntCdsBlockPtr) ifp;
+
+  /* first explore pubs to pick up figure and maploc */
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pub, &dcontext);
+  while (sdp != NULL) {
+    pdp = (PubdescPtr) sdp->data.ptrvalue;
+    if (pdp != NULL) {
+      if (icp->fig == NULL) {
+        icp->fig = StringSaveNoNull (pdp->fig);
+      }
+      if (icp->maploc == NULL) {
+        icp->maploc = StringSaveNoNull (pdp->maploc);
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_pub, &dcontext);
+  }
+
+  /* product may be segmented part, and remaining features are indexed on parent */
+
+  parent = SeqMgrGetParentOfPart (bsp, NULL);
+  if (parent != NULL) {
+    bsp = parent;
+  }
+
+  /* then explore mat_peptides, sites, etc. */
+
+  GetFeatsOnCdsProduct (sfp, asp->bsp, bsp, ajp, awp);
+
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK GetFeatsOnSeg (
+  SeqLocPtr slp,
+  SeqMgrSegmentContextPtr context
+)
+
+{
+  IntAsn2gbJobPtr  ajp;
+  Asn2gbWorkPtr    awp;
+  BioseqPtr        bsp;
+  Uint2            entityID;
+  Int4             from;
+  Int4             left;
+  SeqLocPtr        loc;
+  Int4             right;
+  SeqIdPtr         sip;
+  Int4             to;
+
+  if (slp == NULL || context == NULL) return FALSE;
+  awp = (Asn2gbWorkPtr) context->userdata;
+  if (awp == NULL) return FALSE;
+  ajp = awp->ajp;
+  if (ajp == NULL) return FALSE;
+
+  /* do not fetch outside of desired component */
+
+  if (ajp->ajp.slp != NULL) {
+    left = GetOffsetInBioseq (ajp->ajp.slp, awp->parent, SEQLOC_LEFT_END);
+    right = GetOffsetInBioseq (ajp->ajp.slp, awp->parent, SEQLOC_RIGHT_END);
+
+    from = context->cumOffset;
+    to = from + context->to - context->from;
+
+    if (left > to) return TRUE;
+    if (right < from) return TRUE;
+  }
+ 
+  from = awp->from;
+  to = awp->to;
+
+  sip = SeqLocId (slp);
+  if (sip == NULL) {
+    loc = SeqLocFindNext (slp, NULL);
+    if (loc != NULL) {
+      sip = SeqLocId (loc);
+    }
+  }
+  if (sip == NULL) return TRUE;
+
+  /* may want to remote fetch genome component if not already in memory */
+
+  bsp = BioseqLockById (sip);
+
+  if (bsp == NULL) return TRUE;
+
+  entityID = ObjMgrGetEntityIDForPointer (bsp);
+
+  if (entityID != awp->entityID) {
+
+    /* if segment not packaged in record, may need to feature index it */
+
+    if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
+      SeqMgrIndexFeatures (entityID, NULL);
+    }
+
+    /* collect features indexed on the remote bioseq */
+
+    awp->from = 0;
+    awp->to = bsp->length - 1;
+  }
+
+  awp->lastsfp = NULL;
+  awp->lastsap = NULL;
+  awp->lastleft = 0;
+  awp->lastright = 0;
+
+  if (context->strand == Seq_strand_minus) {
+    SeqMgrExploreFeaturesRev (bsp, (Pointer) awp, GetFeatsOnBioseq, /* awp->slp */ slp, NULL, NULL);
+  } else {
+    SeqMgrExploreFeatures (bsp, (Pointer) awp, GetFeatsOnBioseq, /* awp->slp */ slp, NULL, NULL);
+  }
+
+  /* restore original from and to */
+
+  awp->from = from;
+  awp->to = to;
+
+  BioseqUnlock (bsp);
+
+  return TRUE;
+}
+
+NLM_EXTERN void AddFeatureBlock (
+  Asn2gbWorkPtr awp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  BioseqPtr          bsp;
+  SeqFeatPtr         cds;
+  SeqMgrDescContext  dcontext;
+  SeqMgrFeatContext  fcontext;
+  FeatBlockPtr       fbp;
+  SeqFeatPtr         gene;
+  IntFeatBlockPtr    ifp;
+  Boolean            is_other;
+  MolInfoPtr         mip;
+  SeqFeatPtr         mrna;
+  SeqFeatPtr         prot;
+  SeqDescrPtr        sdp;
+  SeqIdPtr           sip;
+  SeqLocPtr          slp;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->parent;
+  if (bsp == NULL) return;
+
+  awp->lastsfp = NULL;
+  awp->lastsap = NULL;
+  awp->lastleft = 0;
+  awp->lastright = 0;
+
+  /* optionally map gene from genomic onto cDNA */
+
+  if (awp->isGPS && ISA_na (bsp->mol) && awp->copyGpsGeneDown) {
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+    if (sdp != NULL && sdp->choice == Seq_descr_molinfo) {
+      mip = (MolInfoPtr) sdp->data.ptrvalue;
+      if (mip != NULL) {
+        if (mip->biomol == MOLECULE_TYPE_MRNA) {
+          mrna = SeqMgrGetRNAgivenProduct (bsp, NULL);
+          if (mrna != NULL) {
+            gene = SeqMgrGetOverlappingGene (mrna->location, &fcontext);
+            if (gene != NULL && gene->data.choice == SEQFEAT_GENE) {
+
+              fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
+              if (fbp != NULL) {
+
+                fbp->entityID = fcontext.entityID;
+                fbp->itemID = fcontext.itemID;
+                fbp->itemtype = OBJ_SEQFEAT;
+                fbp->featdeftype = fcontext.featdeftype;
+                ifp = (IntFeatBlockPtr) fbp;
+                ifp->mapToNuc = FALSE;
+                ifp->mapToProt = FALSE;
+                ifp->mapToGen = FALSE;
+                ifp->mapToMrna = TRUE;
+                ifp->mapToPep = FALSE;
+                ifp->isCDS = TRUE;
+                ifp->firstfeat = awp->firstfeat;
+                awp->firstfeat = FALSE;
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+
+  if (awp->farFeatsSuppress) {
+
+    if (bsp->repr == Seq_repr_seg || bsp->repr == Seq_repr_delta) {
+
+      /* if farFeatsSuppress first collect features on remote segments in MASTER_STYLE */
+
+      SeqMgrExploreSegments (bsp, (Pointer) awp, GetFeatsOnSeg);
+    }
+  }
+
+  if ((! awp->farFeatsSuppress) || (! awp->featseen)) {
+
+    /* reminder - features on near parts are indexed on segmented Bioseq */
+
+    slp = ajp->ajp.slp;
+    if (slp != NULL && SeqLocStrand (slp) == Seq_strand_minus) {
+      SeqMgrExploreFeaturesRev (bsp, (Pointer) awp, GetFeatsOnBioseq, awp->slp, NULL, NULL);
+    } else {
+      SeqMgrExploreFeatures (bsp, (Pointer) awp, GetFeatsOnBioseq, awp->slp, NULL, NULL);
+    }
+  }
+
+  if (awp->format == GENPEPT_FMT && ISA_aa (bsp->mol)) {
+    cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
+    if (cds != NULL && cds->data.choice == SEQFEAT_CDREGION) {
+
+      fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
+      if (fbp != NULL) {
+
+        fbp->entityID = fcontext.entityID;
+        fbp->itemID = fcontext.itemID;
+        fbp->itemtype = OBJ_SEQFEAT;
+        fbp->featdeftype = fcontext.featdeftype;
+        ifp = (IntFeatBlockPtr) fbp;
+        ifp->mapToNuc = FALSE;
+        ifp->mapToProt = TRUE;
+        ifp->mapToGen = FALSE;
+        ifp->mapToMrna = FALSE;
+        ifp->mapToPep = FALSE;
+        ifp->isCDS = TRUE;
+        ifp->firstfeat = awp->firstfeat;
+        awp->firstfeat = FALSE;
+      }
+    }
+    prot = SeqMgrGetPROTgivenProduct (bsp, &fcontext);
+    if (prot != NULL && prot->data.choice == SEQFEAT_PROT) {
+
+      is_other = FALSE;
+      for (sip = bsp->id; sip != NULL; sip = sip->next) {
+        if (sip->choice == SEQID_OTHER) {
+          is_other = TRUE;
+        }
+      }
+
+      /* for RefSeq records or GenBank not release_mode */
+      if (is_other || (! ajp->flags.forGbRelease)) {
+
+        fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock));
+        if (fbp != NULL) {
+
+          fbp->entityID = fcontext.entityID;
+          fbp->itemID = fcontext.itemID;
+          fbp->itemtype = OBJ_SEQFEAT;
+          fbp->featdeftype = fcontext.featdeftype;
+          ifp = (IntFeatBlockPtr) fbp;
+          ifp->mapToNuc = FALSE;
+          ifp->mapToProt = FALSE;
+          ifp->mapToGen = FALSE;
+          ifp->mapToMrna = FALSE;
+          ifp->mapToPep = TRUE;
+          ifp->firstfeat = awp->firstfeat;
+          awp->firstfeat = FALSE;
+        }
+      }
+    }
+  }
+
+  if (awp->onlyNearFeats) return;
+  if (awp->nearFeatsSuppress && awp->featseen) return;
+
+  if (! awp->farFeatsSuppress) {
+
+    if (bsp->repr == Seq_repr_seg || bsp->repr == Seq_repr_delta) {
+
+      /* if not farFeatsSuppress now collect features on remote segments in MASTER_STYLE */
+
+      SeqMgrExploreSegments (bsp, (Pointer) awp, GetFeatsOnSeg);
+    }
+  }
+}
+
diff --git a/api/asn2gnb4.c b/api/asn2gnb4.c
new file mode 100644
index 00000000..6b571a30
--- /dev/null
+++ b/api/asn2gnb4.c
@@ -0,0 +1,5056 @@
+/*   asn2gnb4.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  asn2gnb4.c
+*
+* Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans,
+*          Mati Shomrat
+*
+* Version Creation Date:   10/21/98
+*
+* $Revision: 1.3 $
+*
+* File Description:  New GenBank flatfile generator - work in progress
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <objall.h>
+#include <objsset.h>
+#include <objsub.h>
+#include <objfdef.h>
+#include <objpubme.h>
+#include <seqport.h>
+#include <sequtil.h>
+#include <sqnutils.h>
+#include <subutil.h>
+#include <tofasta.h>
+#include <explore.h>
+#include <gbfeat.h>
+#include <gbftdef.h>
+#include <edutil.h>
+#include <alignmgr2.h>
+#include <asn2gnbi.h>
+
+#ifdef WIN_MAC
+#if __profile__
+#include <Profiler.h>
+#endif
+#endif
+
+/* ordering arrays for qualifiers and note components */
+
+static FtQualType feat_qual_order [] = {
+  FTQUAL_partial,
+  FTQUAL_gene,
+
+  FTQUAL_locus_tag,
+  FTQUAL_gene_syn_refseq,
+
+  FTQUAL_gene_allele,
+
+  FTQUAL_operon,
+
+  FTQUAL_product,
+
+  FTQUAL_prot_EC_number,
+  FTQUAL_prot_activity,
+
+  FTQUAL_standard_name,
+  FTQUAL_coded_by,
+  FTQUAL_derived_from,
+
+  FTQUAL_prot_name,
+  FTQUAL_region_name,
+  FTQUAL_bond_type,
+  FTQUAL_site_type,
+  FTQUAL_sec_str_type,
+  FTQUAL_heterogen,
+
+  FTQUAL_note, 
+  FTQUAL_citation,
+
+  FTQUAL_number,
+
+  FTQUAL_pseudo,
+  FTQUAL_selenocysteine,
+
+  FTQUAL_codon_start,
+
+  FTQUAL_anticodon,
+  FTQUAL_bound_moiety,
+  FTQUAL_clone,
+  FTQUAL_cons_splice,
+  FTQUAL_direction,
+  FTQUAL_function,
+  FTQUAL_evidence,
+  FTQUAL_exception,
+  FTQUAL_frequency,
+  FTQUAL_EC_number,
+  FTQUAL_gene_map,
+  FTQUAL_allele,
+  FTQUAL_map,
+  FTQUAL_mod_base,
+  FTQUAL_PCR_conditions,
+  FTQUAL_phenotype,
+  FTQUAL_rpt_family,
+  FTQUAL_rpt_type,
+  FTQUAL_rpt_unit,
+  FTQUAL_insertion_seq,
+  FTQUAL_transposon,
+  FTQUAL_usedin,
+
+  FTQUAL_illegal_qual,
+
+  FTQUAL_replace,
+
+  FTQUAL_transl_except,
+  FTQUAL_transl_table,
+  FTQUAL_codon,
+  FTQUAL_organism,
+  FTQUAL_label,
+  FTQUAL_cds_product,
+  FTQUAL_protein_id,
+  FTQUAL_transcript_id,
+  FTQUAL_db_xref, 
+  FTQUAL_gene_xref,
+  FTQUAL_translation,
+  FTQUAL_transcription,
+  FTQUAL_peptide,
+  (FtQualType) 0
+};
+
+/*
+prot_names after seqfeat_note - gi|4210642|emb|AJ005084.1|HBVAJ5084
+prot_conflict after prot_desc - gi|61183|emb|V01135.1|PIVM02
+figure after prot_desc - gi|400553|gb|S64006.1|
+seqfeat_note after prot_desc - gi|431713|gb|L20354.1|STVPATPOLB
+  but prot_desc after seqfeat_note - AF252556.1
+prot_names after figure - gi|234022|gb|S56149.1|S56149
+seqfeat_note after prot_conflict after figure - gi|234046|gb|S51392.1|S51392
+prot_method after prot_comment (descriptor) after prot_note after prot_desc
+region after seqfeat_note - gi|6554164|gb|AF043644.3|AF043644
+prot_desc after prot_names - gi|6581069|gb|AF202541.1|AF202541 - cannot do !!!
+gene_syn after gene_desc - gi|3386543|gb|AF079528.1|AF079528
+pseudo after note - gi|6598562|gb|AC006419.3|AC006419
+*/
+
+static FtQualType feat_note_order [] = {
+  FTQUAL_transcript_id_note, /* !!! remove October 15, 2003 !!! */
+  FTQUAL_gene_desc,
+  FTQUAL_gene_syn,
+  FTQUAL_trna_codons,
+  FTQUAL_encodes,
+  FTQUAL_prot_desc,
+  FTQUAL_prot_note,
+  FTQUAL_prot_comment,
+  FTQUAL_prot_method,
+  FTQUAL_figure,
+  FTQUAL_maploc,
+  FTQUAL_prot_conflict,
+  FTQUAL_prot_missing,
+  FTQUAL_seqfeat_note,
+  FTQUAL_exception_note,
+  FTQUAL_region,
+  FTQUAL_selenocysteine_note,
+  FTQUAL_prot_names,
+  FTQUAL_bond,
+  FTQUAL_site,
+  FTQUAL_rrna_its,
+  FTQUAL_xtra_prod_quals,
+  FTQUAL_modelev,
+  /* GO terms appear as own qualifiers in RefSeq records, Sequin or Dump mode */
+  FTQUAL_go_component,
+  FTQUAL_go_function,
+  FTQUAL_go_process,
+  (FtQualType) 0
+};
+
+typedef struct featurqual {
+  CharPtr   name;
+  QualType  qualclass;
+} FeaturQual, PNTR FeaturQualPtr;
+
+static FeaturQual asn2gnbk_featur_quals [ASN2GNBK_TOTAL_FEATUR] = {
+  { "",               Qual_class_ignore        },
+  { "allele",         Qual_class_quote         },
+  { "anticodon",      Qual_class_anti_codon    },
+  { "bond",           Qual_class_bond          },
+  { "bond_type",      Qual_class_bond          },
+  { "bound_moiety",   Qual_class_quote         },
+  { "product",        Qual_class_string        },
+  { "citation",       Qual_class_pubset        },
+  { "clone",          Qual_class_quote         },
+  { "coded_by",       Qual_class_seq_loc       },
+  { "codon",          Qual_class_codon         },
+  { "codon_start",    Qual_class_int           },
+  { "cons_splice",    Qual_class_consplice     },
+  { "db_xref",        Qual_class_db_xref       },
+  { "derived_from",   Qual_class_seq_loc       },
+  { "direction",      Qual_class_L_R_B         },
+  { "EC_number",      Qual_class_EC_quote      },
+  { "encodes",        Qual_class_encodes       },
+  { "evidence",       Qual_class_evidence      },
+  { "exception",      Qual_class_string        },
+  { "exception_note", Qual_class_string        },
+  { "figure",         Qual_class_string        },
+  { "frequency",      Qual_class_quote         },
+  { "function",       Qual_class_quote         },
+  { "gene",           Qual_class_sgml          },
+  { "gene_desc",      Qual_class_string        },
+  { "allele",         Qual_class_string        },
+  { "map",            Qual_class_string        },
+  { "gene_syn",       Qual_class_gene_syn      },
+  { "synonym",        Qual_class_gene_syn      },
+  { "gene_note",      Qual_class_string        },
+  { "db_xref",        Qual_class_db_xref       },
+  { "go_component",   Qual_class_go            },
+  { "go_function",    Qual_class_go            },
+  { "go_process",     Qual_class_go            },
+  { "heterogen",      Qual_class_string        },
+  { "illegal",        Qual_class_illegal       },
+  { "insertion_seq",  Qual_class_quote         },
+  { "label",          Qual_class_label         },
+  { "locus_tag",      Qual_class_locus_tag     },
+  { "map",            Qual_class_quote         },
+  { "maploc",         Qual_class_string        },
+  { "mod_base",       Qual_class_noquote       },
+  { "model_evidence", Qual_class_model_ev      },
+  { "note",           Qual_class_note          },
+  { "number",         Qual_class_number        },
+  { "operon",         Qual_class_quote         },
+  { "organism",       Qual_class_quote         },
+  { "partial",        Qual_class_boolean       },
+  { "PCR_conditions", Qual_class_quote         },
+  { "peptide",        Qual_class_peptide       },
+  { "phenotype",      Qual_class_quote         },
+  { "product",        Qual_class_product       },
+  { "product",        Qual_class_quote         },
+  { "function",       Qual_class_valnode       },
+  { "prot_comment",   Qual_class_string        },
+  { "EC_number",      Qual_class_EC_valnode    },
+  { "prot_note",      Qual_class_string        },
+  { "prot_method",    Qual_class_method        },
+  { "prot_conflict",  Qual_class_string        },
+  { "prot_desc",      Qual_class_string        },
+  { "prot_missing",   Qual_class_string        },
+  { "name",           Qual_class_tilde         },
+  { "prot_names",     Qual_class_protnames     },
+  { "protein_id",     Qual_class_seq_id        },
+  { "pseudo",         Qual_class_boolean       },
+  { "region",         Qual_class_region        },
+  { "region_name",    Qual_class_string        },
+  { "replace",        Qual_class_replace       },
+  { "rpt_family",     Qual_class_quote         },
+  { "rpt_type",       Qual_class_rpt           },
+  { "rpt_unit",       Qual_class_rpt_unit      },
+  { "rrna_its",       Qual_class_its           },
+  { "sec_str_type",   Qual_class_sec_str       },
+  { "selenocysteine", Qual_class_boolean       },
+  { "selenocysteine", Qual_class_string        },
+  { "seqfeat_note",   Qual_class_string        },
+  { "site",           Qual_class_site          },
+  { "site_type",      Qual_class_site          },
+  { "standard_name",  Qual_class_quote         },
+  { "transcription",  Qual_class_transcription },
+  { "transcript_id",  Qual_class_seq_id        },
+  { "tscpt_id_note",  Qual_class_seq_id        }, /* !!! remove October 15, 2003 !!! */
+  { "transl_except",  Qual_class_code_break    },
+  { "transl_table",   Qual_class_int           },
+  { "translation",    Qual_class_translation   },
+  { "transposon",     Qual_class_quote         },
+  { "trna_aa",        Qual_class_ignore        },
+  { "trna_codons",    Qual_class_trna_codons   },
+  { "usedin",         Qual_class_paren         },
+  { "xtra_products",  Qual_class_xtraprds      }
+};
+
+
+typedef struct qualfeatur {
+  CharPtr     name;
+  FtQualType  featurclass;
+} QualFeatur, PNTR QualFeaturPtr;
+
+#define NUM_GB_QUALS 26
+
+static QualFeatur qualToFeature [NUM_GB_QUALS] = {
+  { "allele",         FTQUAL_allele         },
+  { "bound_moiety",   FTQUAL_bound_moiety   },
+  { "clone",          FTQUAL_clone          },
+  { "codon",          FTQUAL_codon          },
+  { "cons_splice",    FTQUAL_cons_splice    },
+  { "direction",      FTQUAL_direction      },
+  { "EC_number",      FTQUAL_EC_number      },
+  { "frequency",      FTQUAL_frequency      },
+  { "function",       FTQUAL_function       },
+  { "insertion_seq",  FTQUAL_insertion_seq  },
+  { "label",          FTQUAL_label          },
+  { "map",            FTQUAL_map            },
+  { "mod_base",       FTQUAL_mod_base       },
+  { "number",         FTQUAL_number         },
+  { "operon",         FTQUAL_operon         },
+  { "organism",       FTQUAL_organism       },
+  { "PCR_conditions", FTQUAL_PCR_conditions },
+  { "phenotype",      FTQUAL_phenotype      },
+  { "product",        FTQUAL_product_quals  },
+  { "replace",        FTQUAL_replace        },
+  { "rpt_family",     FTQUAL_rpt_family     },
+  { "rpt_type",       FTQUAL_rpt_type       },
+  { "rpt_unit",       FTQUAL_rpt_unit       },
+  { "standard_name",  FTQUAL_standard_name  },
+  { "transposon",     FTQUAL_transposon     },
+  { "usedin",         FTQUAL_usedin         }
+};
+
+static Int2 GbqualToFeaturIndex (
+  CharPtr qualname
+)
+
+{
+  Int2  L, R, mid;
+
+  if (qualname == NULL || *qualname == '\0') return 0;
+
+  L = 0;
+  R = NUM_GB_QUALS - 1;
+
+  while (L < R) {
+    mid = (L + R) / 2;
+    if (StringICmp (qualToFeature [mid].name, qualname) < 0) {
+      L = mid + 1;
+    } else {
+      R = mid;
+    }
+  }
+
+  if (StringICmp (qualToFeature [R].name, qualname) == 0) {
+    return qualToFeature [R].featurclass;
+  }
+
+  return 0;
+}
+
+#define NUM_ILLEGAL_QUALS 14
+
+static FeaturQual illegalGbqualList [NUM_ILLEGAL_QUALS] = {
+  { "anticodon",      Qual_class_noquote },
+  { "citation",       Qual_class_noquote },
+  { "codon_start",    Qual_class_noquote },
+  { "db_xref",        Qual_class_quote   },
+  { "evidence",       Qual_class_noquote },
+  { "exception",      Qual_class_quote   },
+  { "gene",           Qual_class_quote   },
+  { "note",           Qual_class_quote   },
+  { "protein_id",     Qual_class_quote   },
+  { "pseudo",         Qual_class_noquote },
+  { "transcript_id",  Qual_class_quote   },
+  { "transl_except",  Qual_class_noquote },
+  { "transl_table",   Qual_class_noquote },
+  { "translation",    Qual_class_quote   },
+};
+
+static Int2 IllegalGbqualToClass (
+  CharPtr qualname
+)
+
+{
+  Int2  L, R, mid;
+
+  if (qualname == NULL || *qualname == '\0') return 0;
+
+  L = 0;
+  R = NUM_ILLEGAL_QUALS - 1;
+
+  while (L < R) {
+    mid = (L + R) / 2;
+    if (StringICmp (illegalGbqualList [mid].name, qualname) < 0) {
+      L = mid + 1;
+    } else {
+      R = mid;
+    }
+  }
+
+  if (StringICmp (illegalGbqualList [R].name, qualname) == 0) {
+    return illegalGbqualList [R].qualclass;
+  }
+
+  return 0;
+}
+
+static CharPtr trnaList [] = {
+  "tRNA-Gap",
+  "tRNA-Ala",
+  "tRNA-Asx",
+  "tRNA-Cys",
+  "tRNA-Asp",
+  "tRNA-Glu",
+  "tRNA-Phe",
+  "tRNA-Gly",
+  "tRNA-His",
+  "tRNA-Ile",
+  "tRNA-Lys",
+  "tRNA-Leu",
+  "tRNA-Met",
+  "tRNA-Asn",
+  "tRNA-Pro",
+  "tRNA-Gln",
+  "tRNA-Arg",
+  "tRNA-Ser",
+  "tRNA-Thr",
+  "tRNA-Sec",
+  "tRNA-Val",
+  "tRNA-Trp",
+  "tRNA-OTHER",
+  "tRNA-Tyr",
+  "tRNA-Glx",
+  "tRNA-TERM",
+  NULL
+};
+
+static CharPtr evidenceText [] = {
+  NULL, "experimental", "not_experimental"
+};
+
+NLM_EXTERN CharPtr secStrText [] = {
+  NULL, "helix", "sheet", "turn"
+};
+
+static CharPtr  oops = "?";
+
+static CharPtr SeqCodeNameGet (
+  SeqCodeTablePtr table,
+  Uint1 residue
+)
+
+{
+  Uint1  index;
+
+  if (table != NULL) {
+    index = residue - table->start_at;
+    if ( /*index >= 0 && */ index < table->num) {
+      return (table->names) [index];
+    }
+  }
+
+  return oops;
+}
+
+NLM_EXTERN CharPtr Get3LetterSymbol (
+  IntAsn2gbJobPtr  ajp,
+  Uint1 seq_code,
+  SeqCodeTablePtr table,
+  Uint1 residue
+)
+
+{
+  Uint1            code = Seq_code_ncbieaa;
+  Int2             index;
+  Uint1            new_residue;
+  CharPtr          ptr;
+  CharPtr          retval = NULL;
+  SeqMapTablePtr   smtp;
+  SeqCodeTablePtr  table_3aa;
+
+  if (residue == 42) { /* stop codon in NCBIeaa */
+    retval = "TERM";
+    return retval;
+  }
+
+  if (ajp->flags.iupacaaOnly) {
+    code = Seq_code_iupacaa;
+  } else {
+    code = Seq_code_ncbieaa;
+  }
+
+  if (seq_code != code) {
+    /* if code and seq_code are identical, then smtp is NULL?? */
+    smtp = SeqMapTableFind (code, seq_code);
+    new_residue = SeqMapTableConvert (smtp, residue);
+  } else {
+    new_residue = residue;
+  }
+
+  /* The following looks for non-symbols (255) and "Undetermined" (88) */
+  if ((int) new_residue == 255 || (int) new_residue == 88) {
+    retval = "OTHER";
+    return retval;
+  } else {
+    ptr = SeqCodeNameGet (table, residue);
+    table_3aa=SeqCodeTableFind  (Seq_code_iupacaa3);
+    if (ptr != NULL && table_3aa != NULL) {
+      for (index=0; index < (int) table_3aa->num; index++) {
+        if (StringCmp(ptr, (table_3aa->names) [index]) == 0) {
+          retval = (table_3aa->symbols) [index];
+          return retval;
+        }
+      }
+    }
+  }
+
+  retval = "OTHER";
+  return retval;
+}
+
+static Boolean MatchCit (
+  ValNodePtr ppr,
+  RefBlockPtr rbp
+)
+
+{
+  Char        buf [121];
+  size_t      len;
+  Int4        uid;
+  ValNodePtr  vnp;
+
+  if (ppr == NULL || rbp == NULL) return FALSE;
+  switch (ppr->choice) {
+    case PUB_Muid :
+      uid = ppr->data.intvalue;
+      if (rbp->muid == uid) return TRUE;
+      break;
+    case PUB_PMid :
+      uid = ppr->data.intvalue;
+      if (rbp->pmid == uid) return TRUE;
+      break;
+    case PUB_Equiv :
+      for (vnp = (ValNodePtr) ppr->data.ptrvalue; vnp != NULL; vnp = vnp->next) {
+        if (MatchCit (vnp, rbp)) return TRUE;
+      }
+      break;
+    default :
+      PubLabelUnique (ppr, buf, sizeof (buf) - 1, OM_LABEL_CONTENT, TRUE);
+      len = StringLen (buf);
+      if (len > 0 && buf [len - 1] == '>') {
+        buf [len - 1] = '\0';
+        len--;
+      }
+      len = MIN (len, StringLen (rbp->uniquestr));
+      if (StringNICmp (rbp->uniquestr, buf, len) == 0) return TRUE;
+      break;
+  }
+  return FALSE;
+}
+
+NLM_EXTERN Int2 MatchRef (
+  ValNodePtr ppr,
+  RefBlockPtr PNTR rbpp,
+  Int2 numReferences
+)
+
+{
+  Int2         j;
+  RefBlockPtr  rbp;
+
+  if (ppr == NULL || rbpp == NULL) return 0;
+
+  for (j = 0; j < numReferences; j++) {
+    rbp = rbpp [j];
+    if (rbp == NULL) continue;
+    if (MatchCit (ppr, rbp)) return j + 1;
+  }
+  return 0;
+}
+
+/* taken from asn2ff4.c */
+
+static Boolean LookForFuzz (SeqLocPtr head)
+{
+  Boolean retval=FALSE;
+  IntFuzzPtr ifp;
+  PackSeqPntPtr pspp;
+  SeqIntPtr sip;
+  SeqLocPtr slp;
+  SeqPntPtr spp;
+
+  if (head == NULL)
+    return retval;
+
+  slp=NULL;
+  while ((slp = SeqLocFindNext(head, slp)) != NULL)
+  {
+    switch (slp->choice)
+    {
+      case SEQLOC_INT:
+        sip = (SeqIntPtr)(slp->data.ptrvalue);
+        ifp = sip->if_from;
+        if (ifp != NULL)
+        {
+          if (ifp->choice == 4)
+          {
+            if (ifp->a != 0)
+              retval=TRUE;
+          }
+          else
+            retval = TRUE;
+        }
+        ifp = sip->if_to;
+        if (ifp != NULL)
+        {
+          if (ifp->choice == 4)
+          {
+            if (ifp->a != 0)
+              retval=TRUE;
+          }
+          else
+            retval = TRUE;
+        }
+        break;
+      case SEQLOC_PNT:
+        spp = (SeqPntPtr)(slp->data.ptrvalue);
+        ifp = spp->fuzz;
+        if (ifp != NULL)
+        {
+          if (ifp->choice == 4)
+          {
+            if (ifp->a != 0)
+              retval=TRUE;
+          }
+          else
+            retval = TRUE;
+        }
+        break;
+      case SEQLOC_PACKED_PNT:
+        pspp = (PackSeqPntPtr)(slp->data.ptrvalue);
+        ifp = pspp->fuzz;
+        if (ifp != NULL)
+        {
+          if (ifp->choice == 4)
+          {
+            if (ifp->a != 0)
+              retval=TRUE;
+          }
+          else
+            retval = TRUE;
+        }
+        break;
+      default:
+        break;
+    }
+    if (retval == TRUE)
+      break;
+  }
+  return retval;
+}
+
+NLM_EXTERN CharPtr bondList [] = {
+  NULL,
+  "disulfide",
+  "thiolester",
+  "xlink",
+  "thioether",
+  "unclassified"
+};
+
+NLM_EXTERN CharPtr siteList [] = {
+  NULL,
+  "active",
+  "binding",
+  "cleavage",
+  "inhibit",
+  "modified",
+  "glycosylation",
+  "myristoylation",
+  "mutagenized",
+  "metal-binding",
+  "phosphorylation",
+  "acetylation",
+  "amidation",
+  "methylation",
+  "hydroxylation",
+  "sulfatation",
+  "oxidative-deamination",
+  "pyrrolidone-carboxylic-acid",
+  "gamma-carboxyglutamic-acid",
+  "blocked",
+  "lipid-binding",
+  "np-binding",
+  "DNA binding",
+  "signal-peptide",
+  "transit-peptide",
+  "transmembrane-region",
+  "unclassified"
+};
+
+static CharPtr conflict_msg =
+"Protein sequence is in conflict with the conceptual translation";
+
+static CharPtr no_protein_msg =
+"Coding region translates with internal stops";
+
+/**/
+/*  s_DisplayQVP () -- Displays the strings in a QVP structure.   */
+/*                     This is a debugging function only.         */
+/**/
+
+static void s_DisplayQVP(QualValPtr qvp, Uint1Ptr notetbl)
+{
+  Int2 j;
+  Int2 jdx;
+
+  fprintf(stderr,"\n");
+  for (j = 0, jdx = notetbl [j]; jdx != 0; j++, jdx = notetbl [j])
+    {
+      if (((int) qvp[jdx].str != 0x1000000) &&
+      ((int) qvp[jdx].str != 0x1) &&
+      ((int) qvp[jdx].str != 0xb) &&
+      (qvp[jdx].str != NULL))
+    fprintf(stderr, "%d\t%-25s %s\n", j, asn2gnbk_featur_quals[jdx].name,
+        qvp[jdx].str);
+      else
+    fprintf(stderr, "%d\t%-25s %s\n", j, asn2gnbk_featur_quals[jdx].name,
+        "NULL");
+    }
+}
+
+static Boolean NotInGeneSyn (
+  CharPtr str,
+  ValNodePtr gene_syn)
+
+{
+  CharPtr     syn;
+  ValNodePtr  vnp;
+
+  for (vnp = gene_syn; vnp != NULL; vnp = vnp->next) {
+    syn = (CharPtr) vnp->data.ptrvalue;
+    if (! StringHasNoText (syn)) {
+      if (StringICmp (str, syn) == 0) return FALSE;
+    }
+  }
+  return TRUE;
+}
+
+typedef struct valqualstruc {
+  Uint2       featdef;
+  FtQualType  ftqual;
+} ValQual, PNTR ValQualPtr;
+
+/*
+   WARNING - This list MUST be kept sorted in FEATDEF order as the primary
+   key, and within a FEATDEF group sorted by FTQUAL as the secondary key
+*/
+
+static ValQual legalGbqualList [] = {
+
+  { FEATDEF_GENE , FTQUAL_allele },
+  { FEATDEF_GENE , FTQUAL_function },
+  { FEATDEF_GENE , FTQUAL_label },
+  { FEATDEF_GENE , FTQUAL_map },
+  { FEATDEF_GENE , FTQUAL_operon },
+  { FEATDEF_GENE , FTQUAL_phenotype },
+  { FEATDEF_GENE , FTQUAL_product },
+  { FEATDEF_GENE , FTQUAL_standard_name },
+  { FEATDEF_GENE , FTQUAL_usedin },
+
+  { FEATDEF_CDS , FTQUAL_allele },
+  { FEATDEF_CDS , FTQUAL_codon },
+  { FEATDEF_CDS , FTQUAL_label },
+  { FEATDEF_CDS , FTQUAL_map },
+  { FEATDEF_CDS , FTQUAL_number },
+  { FEATDEF_CDS , FTQUAL_operon },
+  { FEATDEF_CDS , FTQUAL_standard_name },
+  { FEATDEF_CDS , FTQUAL_usedin },
+
+  { FEATDEF_PROT , FTQUAL_product },
+
+  { FEATDEF_preRNA , FTQUAL_allele },
+  { FEATDEF_preRNA , FTQUAL_function },
+  { FEATDEF_preRNA , FTQUAL_label },
+  { FEATDEF_preRNA , FTQUAL_map },
+  { FEATDEF_preRNA , FTQUAL_operon },
+  { FEATDEF_preRNA , FTQUAL_product },
+  { FEATDEF_preRNA , FTQUAL_standard_name },
+  { FEATDEF_preRNA , FTQUAL_usedin },
+
+  { FEATDEF_mRNA , FTQUAL_allele },
+  { FEATDEF_mRNA , FTQUAL_function },
+  { FEATDEF_mRNA , FTQUAL_label },
+  { FEATDEF_mRNA , FTQUAL_map },
+  { FEATDEF_mRNA , FTQUAL_operon },
+  { FEATDEF_mRNA , FTQUAL_product },
+  { FEATDEF_mRNA , FTQUAL_standard_name },
+  { FEATDEF_mRNA , FTQUAL_usedin },
+
+  { FEATDEF_tRNA , FTQUAL_allele },
+  { FEATDEF_tRNA , FTQUAL_function },
+  { FEATDEF_tRNA , FTQUAL_label },
+  { FEATDEF_tRNA , FTQUAL_map },
+  { FEATDEF_tRNA , FTQUAL_product },
+  { FEATDEF_tRNA , FTQUAL_standard_name },
+  { FEATDEF_tRNA , FTQUAL_usedin },
+
+  { FEATDEF_rRNA , FTQUAL_allele },
+  { FEATDEF_rRNA , FTQUAL_function },
+  { FEATDEF_rRNA , FTQUAL_label },
+  { FEATDEF_rRNA , FTQUAL_map },
+  { FEATDEF_rRNA , FTQUAL_product },
+  { FEATDEF_rRNA , FTQUAL_standard_name },
+  { FEATDEF_rRNA , FTQUAL_usedin },
+
+  { FEATDEF_snRNA , FTQUAL_allele },
+  { FEATDEF_snRNA , FTQUAL_function },
+  { FEATDEF_snRNA , FTQUAL_label },
+  { FEATDEF_snRNA , FTQUAL_map },
+  { FEATDEF_snRNA , FTQUAL_product },
+  { FEATDEF_snRNA , FTQUAL_standard_name },
+  { FEATDEF_snRNA , FTQUAL_usedin },
+
+  { FEATDEF_scRNA , FTQUAL_allele },
+  { FEATDEF_scRNA , FTQUAL_function },
+  { FEATDEF_scRNA , FTQUAL_label },
+  { FEATDEF_scRNA , FTQUAL_map },
+  { FEATDEF_scRNA , FTQUAL_product },
+  { FEATDEF_scRNA , FTQUAL_standard_name },
+  { FEATDEF_scRNA , FTQUAL_usedin },
+
+  { FEATDEF_otherRNA , FTQUAL_allele },
+  { FEATDEF_otherRNA , FTQUAL_function },
+  { FEATDEF_otherRNA , FTQUAL_label },
+  { FEATDEF_otherRNA , FTQUAL_map },
+  { FEATDEF_otherRNA , FTQUAL_operon },
+  { FEATDEF_otherRNA , FTQUAL_product },
+  { FEATDEF_otherRNA , FTQUAL_standard_name },
+  { FEATDEF_otherRNA , FTQUAL_usedin },
+
+  { FEATDEF_attenuator , FTQUAL_allele },
+  { FEATDEF_attenuator , FTQUAL_label },
+  { FEATDEF_attenuator , FTQUAL_map },
+  { FEATDEF_attenuator , FTQUAL_operon },
+  { FEATDEF_attenuator , FTQUAL_phenotype },
+  { FEATDEF_attenuator , FTQUAL_usedin },
+
+  { FEATDEF_C_region , FTQUAL_allele },
+  { FEATDEF_C_region , FTQUAL_label },
+  { FEATDEF_C_region , FTQUAL_map },
+  { FEATDEF_C_region , FTQUAL_product },
+  { FEATDEF_C_region , FTQUAL_standard_name },
+  { FEATDEF_C_region , FTQUAL_usedin },
+
+  { FEATDEF_CAAT_signal , FTQUAL_allele },
+  { FEATDEF_CAAT_signal , FTQUAL_label },
+  { FEATDEF_CAAT_signal , FTQUAL_map },
+  { FEATDEF_CAAT_signal , FTQUAL_usedin },
+
+  { FEATDEF_Imp_CDS , FTQUAL_codon },
+  { FEATDEF_Imp_CDS , FTQUAL_EC_number },
+  { FEATDEF_Imp_CDS , FTQUAL_function },
+  { FEATDEF_Imp_CDS , FTQUAL_label },
+  { FEATDEF_Imp_CDS , FTQUAL_map },
+  { FEATDEF_Imp_CDS , FTQUAL_number },
+  { FEATDEF_Imp_CDS , FTQUAL_operon },
+  { FEATDEF_Imp_CDS , FTQUAL_product },
+  { FEATDEF_Imp_CDS , FTQUAL_standard_name },
+  { FEATDEF_Imp_CDS , FTQUAL_usedin },
+
+  { FEATDEF_conflict , FTQUAL_allele },
+  { FEATDEF_conflict , FTQUAL_label },
+  { FEATDEF_conflict , FTQUAL_map },
+  { FEATDEF_conflict , FTQUAL_replace },
+  { FEATDEF_conflict , FTQUAL_usedin },
+
+  { FEATDEF_D_loop , FTQUAL_allele },
+  { FEATDEF_D_loop , FTQUAL_label },
+  { FEATDEF_D_loop , FTQUAL_map },
+  { FEATDEF_D_loop , FTQUAL_usedin },
+
+  { FEATDEF_D_segment , FTQUAL_allele },
+  { FEATDEF_D_segment , FTQUAL_label },
+  { FEATDEF_D_segment , FTQUAL_map },
+  { FEATDEF_D_segment , FTQUAL_product },
+  { FEATDEF_D_segment , FTQUAL_standard_name },
+  { FEATDEF_D_segment , FTQUAL_usedin },
+
+  { FEATDEF_enhancer , FTQUAL_allele },
+  { FEATDEF_enhancer , FTQUAL_label },
+  { FEATDEF_enhancer , FTQUAL_map },
+  { FEATDEF_enhancer , FTQUAL_standard_name },
+  { FEATDEF_enhancer , FTQUAL_usedin },
+
+  { FEATDEF_exon , FTQUAL_allele },
+  { FEATDEF_exon , FTQUAL_EC_number },
+  { FEATDEF_exon , FTQUAL_function },
+  { FEATDEF_exon , FTQUAL_label },
+  { FEATDEF_exon , FTQUAL_map },
+  { FEATDEF_exon , FTQUAL_number },
+  { FEATDEF_exon , FTQUAL_product },
+  { FEATDEF_exon , FTQUAL_standard_name },
+  { FEATDEF_exon , FTQUAL_usedin },
+
+  { FEATDEF_GC_signal , FTQUAL_allele },
+  { FEATDEF_GC_signal , FTQUAL_label },
+  { FEATDEF_GC_signal , FTQUAL_map },
+  { FEATDEF_GC_signal , FTQUAL_usedin },
+
+  { FEATDEF_iDNA , FTQUAL_allele },
+  { FEATDEF_iDNA , FTQUAL_function },
+  { FEATDEF_iDNA , FTQUAL_label },
+  { FEATDEF_iDNA , FTQUAL_map },
+  { FEATDEF_iDNA , FTQUAL_number },
+  { FEATDEF_iDNA , FTQUAL_standard_name },
+  { FEATDEF_iDNA , FTQUAL_usedin },
+
+  { FEATDEF_intron , FTQUAL_allele },
+  { FEATDEF_intron , FTQUAL_cons_splice },
+  { FEATDEF_intron , FTQUAL_function },
+  { FEATDEF_intron , FTQUAL_label },
+  { FEATDEF_intron , FTQUAL_map },
+  { FEATDEF_intron , FTQUAL_number },
+  { FEATDEF_intron , FTQUAL_standard_name },
+  { FEATDEF_intron , FTQUAL_usedin },
+
+  { FEATDEF_J_segment , FTQUAL_allele },
+  { FEATDEF_J_segment , FTQUAL_label },
+  { FEATDEF_J_segment , FTQUAL_map },
+  { FEATDEF_J_segment , FTQUAL_product },
+  { FEATDEF_J_segment , FTQUAL_standard_name },
+  { FEATDEF_J_segment , FTQUAL_usedin },
+
+  { FEATDEF_LTR , FTQUAL_allele },
+  { FEATDEF_LTR , FTQUAL_function },
+  { FEATDEF_LTR , FTQUAL_label },
+  { FEATDEF_LTR , FTQUAL_map },
+  { FEATDEF_LTR , FTQUAL_standard_name },
+  { FEATDEF_LTR , FTQUAL_usedin },
+
+  { FEATDEF_mat_peptide , FTQUAL_allele },
+  { FEATDEF_mat_peptide , FTQUAL_EC_number },
+  { FEATDEF_mat_peptide , FTQUAL_function },
+  { FEATDEF_mat_peptide , FTQUAL_label },
+  { FEATDEF_mat_peptide , FTQUAL_map },
+  { FEATDEF_mat_peptide , FTQUAL_product },
+  { FEATDEF_mat_peptide , FTQUAL_standard_name },
+  { FEATDEF_mat_peptide , FTQUAL_usedin },
+
+  { FEATDEF_misc_binding , FTQUAL_allele },
+  { FEATDEF_misc_binding , FTQUAL_bound_moiety },
+  { FEATDEF_misc_binding , FTQUAL_function },
+  { FEATDEF_misc_binding , FTQUAL_label },
+  { FEATDEF_misc_binding , FTQUAL_map },
+  { FEATDEF_misc_binding , FTQUAL_usedin },
+
+  { FEATDEF_misc_difference , FTQUAL_allele },
+  { FEATDEF_misc_difference , FTQUAL_clone },
+  { FEATDEF_misc_difference , FTQUAL_label },
+  { FEATDEF_misc_difference , FTQUAL_map },
+  { FEATDEF_misc_difference , FTQUAL_phenotype },
+  { FEATDEF_misc_difference , FTQUAL_replace },
+  { FEATDEF_misc_difference , FTQUAL_standard_name },
+  { FEATDEF_misc_difference , FTQUAL_usedin },
+
+  { FEATDEF_misc_feature , FTQUAL_allele },
+  { FEATDEF_misc_feature , FTQUAL_function },
+  { FEATDEF_misc_feature , FTQUAL_label },
+  { FEATDEF_misc_feature , FTQUAL_map },
+  { FEATDEF_misc_feature , FTQUAL_number },
+  { FEATDEF_misc_feature , FTQUAL_phenotype },
+  { FEATDEF_misc_feature , FTQUAL_product },
+  { FEATDEF_misc_feature , FTQUAL_standard_name },
+  { FEATDEF_misc_feature , FTQUAL_usedin },
+
+  { FEATDEF_misc_recomb , FTQUAL_allele },
+  { FEATDEF_misc_recomb , FTQUAL_label },
+  { FEATDEF_misc_recomb , FTQUAL_map },
+  { FEATDEF_misc_recomb , FTQUAL_organism },
+  { FEATDEF_misc_recomb , FTQUAL_standard_name },
+  { FEATDEF_misc_recomb , FTQUAL_usedin },
+
+  { FEATDEF_misc_signal , FTQUAL_allele },
+  { FEATDEF_misc_signal , FTQUAL_function },
+  { FEATDEF_misc_signal , FTQUAL_label },
+  { FEATDEF_misc_signal , FTQUAL_map },
+  { FEATDEF_misc_signal , FTQUAL_operon },
+  { FEATDEF_misc_signal , FTQUAL_phenotype },
+  { FEATDEF_misc_signal , FTQUAL_standard_name },
+  { FEATDEF_misc_signal , FTQUAL_usedin },
+
+  { FEATDEF_misc_structure , FTQUAL_allele },
+  { FEATDEF_misc_structure , FTQUAL_function },
+  { FEATDEF_misc_structure , FTQUAL_label },
+  { FEATDEF_misc_structure , FTQUAL_map },
+  { FEATDEF_misc_structure , FTQUAL_standard_name },
+  { FEATDEF_misc_structure , FTQUAL_usedin },
+
+  { FEATDEF_modified_base , FTQUAL_allele },
+  { FEATDEF_modified_base , FTQUAL_frequency },
+  { FEATDEF_modified_base , FTQUAL_label },
+  { FEATDEF_modified_base , FTQUAL_map },
+  { FEATDEF_modified_base , FTQUAL_mod_base },
+  { FEATDEF_modified_base , FTQUAL_usedin },
+
+  { FEATDEF_N_region , FTQUAL_allele },
+  { FEATDEF_N_region , FTQUAL_label },
+  { FEATDEF_N_region , FTQUAL_map },
+  { FEATDEF_N_region , FTQUAL_product },
+  { FEATDEF_N_region , FTQUAL_standard_name },
+  { FEATDEF_N_region , FTQUAL_usedin },
+
+  { FEATDEF_old_sequence , FTQUAL_allele },
+  { FEATDEF_old_sequence , FTQUAL_label },
+  { FEATDEF_old_sequence , FTQUAL_map },
+  { FEATDEF_old_sequence , FTQUAL_replace },
+  { FEATDEF_old_sequence , FTQUAL_usedin },
+
+  { FEATDEF_polyA_signal , FTQUAL_allele },
+  { FEATDEF_polyA_signal , FTQUAL_label },
+  { FEATDEF_polyA_signal , FTQUAL_map },
+  { FEATDEF_polyA_signal , FTQUAL_usedin },
+
+  { FEATDEF_polyA_site , FTQUAL_allele },
+  { FEATDEF_polyA_site , FTQUAL_label },
+  { FEATDEF_polyA_site , FTQUAL_map },
+  { FEATDEF_polyA_site , FTQUAL_usedin },
+
+  { FEATDEF_prim_transcript , FTQUAL_allele },
+  { FEATDEF_prim_transcript , FTQUAL_function },
+  { FEATDEF_prim_transcript , FTQUAL_label },
+  { FEATDEF_prim_transcript , FTQUAL_map },
+  { FEATDEF_prim_transcript , FTQUAL_operon },
+  { FEATDEF_prim_transcript , FTQUAL_standard_name },
+  { FEATDEF_prim_transcript , FTQUAL_usedin },
+
+  { FEATDEF_primer_bind , FTQUAL_allele },
+  { FEATDEF_primer_bind , FTQUAL_label },
+  { FEATDEF_primer_bind , FTQUAL_map },
+  { FEATDEF_primer_bind , FTQUAL_PCR_conditions },
+  { FEATDEF_primer_bind , FTQUAL_standard_name },
+  { FEATDEF_primer_bind , FTQUAL_usedin },
+
+  { FEATDEF_promoter , FTQUAL_allele },
+  { FEATDEF_promoter , FTQUAL_function },
+  { FEATDEF_promoter , FTQUAL_label },
+  { FEATDEF_promoter , FTQUAL_map },
+  { FEATDEF_promoter , FTQUAL_operon },
+  { FEATDEF_promoter , FTQUAL_phenotype },
+  { FEATDEF_promoter , FTQUAL_standard_name },
+  { FEATDEF_promoter , FTQUAL_usedin },
+
+  { FEATDEF_protein_bind , FTQUAL_allele },
+  { FEATDEF_protein_bind , FTQUAL_bound_moiety },
+  { FEATDEF_protein_bind , FTQUAL_function },
+  { FEATDEF_protein_bind , FTQUAL_label },
+  { FEATDEF_protein_bind , FTQUAL_map },
+  { FEATDEF_protein_bind , FTQUAL_standard_name },
+  { FEATDEF_protein_bind , FTQUAL_usedin },
+
+  { FEATDEF_RBS , FTQUAL_allele },
+  { FEATDEF_RBS , FTQUAL_label },
+  { FEATDEF_RBS , FTQUAL_map },
+  { FEATDEF_RBS , FTQUAL_standard_name },
+  { FEATDEF_RBS , FTQUAL_usedin },
+
+  { FEATDEF_repeat_region , FTQUAL_allele },
+  { FEATDEF_repeat_region , FTQUAL_function },
+  { FEATDEF_repeat_region , FTQUAL_insertion_seq },
+  { FEATDEF_repeat_region , FTQUAL_label },
+  { FEATDEF_repeat_region , FTQUAL_map },
+  { FEATDEF_repeat_region , FTQUAL_rpt_family },
+  { FEATDEF_repeat_region , FTQUAL_rpt_type },
+  { FEATDEF_repeat_region , FTQUAL_rpt_unit },
+  { FEATDEF_repeat_region , FTQUAL_standard_name },
+  { FEATDEF_repeat_region , FTQUAL_transposon },
+  { FEATDEF_repeat_region , FTQUAL_usedin },
+
+  { FEATDEF_repeat_unit , FTQUAL_allele },
+  { FEATDEF_repeat_unit , FTQUAL_function },
+  { FEATDEF_repeat_unit , FTQUAL_label },
+  { FEATDEF_repeat_unit , FTQUAL_map },
+  { FEATDEF_repeat_unit , FTQUAL_rpt_family },
+  { FEATDEF_repeat_unit , FTQUAL_rpt_type },
+  { FEATDEF_repeat_unit , FTQUAL_usedin },
+
+  { FEATDEF_rep_origin , FTQUAL_allele },
+  { FEATDEF_rep_origin , FTQUAL_direction },
+  { FEATDEF_rep_origin , FTQUAL_label },
+  { FEATDEF_rep_origin , FTQUAL_map },
+  { FEATDEF_rep_origin , FTQUAL_standard_name },
+  { FEATDEF_rep_origin , FTQUAL_usedin },
+
+  { FEATDEF_S_region , FTQUAL_allele },
+  { FEATDEF_S_region , FTQUAL_label },
+  { FEATDEF_S_region , FTQUAL_map },
+  { FEATDEF_S_region , FTQUAL_product },
+  { FEATDEF_S_region , FTQUAL_standard_name },
+  { FEATDEF_S_region , FTQUAL_usedin },
+
+  { FEATDEF_satellite , FTQUAL_allele },
+  { FEATDEF_satellite , FTQUAL_label },
+  { FEATDEF_satellite , FTQUAL_map },
+  { FEATDEF_satellite , FTQUAL_rpt_family },
+  { FEATDEF_satellite , FTQUAL_rpt_type },
+  { FEATDEF_satellite , FTQUAL_rpt_unit },
+  { FEATDEF_satellite , FTQUAL_standard_name },
+  { FEATDEF_satellite , FTQUAL_usedin },
+
+  { FEATDEF_sig_peptide , FTQUAL_allele },
+  { FEATDEF_sig_peptide , FTQUAL_function },
+  { FEATDEF_sig_peptide , FTQUAL_label },
+  { FEATDEF_sig_peptide , FTQUAL_map },
+  { FEATDEF_sig_peptide , FTQUAL_product },
+  { FEATDEF_sig_peptide , FTQUAL_standard_name },
+  { FEATDEF_sig_peptide , FTQUAL_usedin },
+
+  { FEATDEF_stem_loop , FTQUAL_allele },
+  { FEATDEF_stem_loop , FTQUAL_function },
+  { FEATDEF_stem_loop , FTQUAL_label },
+  { FEATDEF_stem_loop , FTQUAL_map },
+  { FEATDEF_stem_loop , FTQUAL_operon },
+  { FEATDEF_stem_loop , FTQUAL_standard_name },
+  { FEATDEF_stem_loop , FTQUAL_usedin },
+
+  { FEATDEF_STS , FTQUAL_allele },
+  { FEATDEF_STS , FTQUAL_label },
+  { FEATDEF_STS , FTQUAL_map },
+  { FEATDEF_STS , FTQUAL_standard_name },
+  { FEATDEF_STS , FTQUAL_usedin },
+
+  { FEATDEF_TATA_signal , FTQUAL_allele },
+  { FEATDEF_TATA_signal , FTQUAL_label },
+  { FEATDEF_TATA_signal , FTQUAL_map },
+  { FEATDEF_TATA_signal , FTQUAL_usedin },
+
+  { FEATDEF_terminator , FTQUAL_allele },
+  { FEATDEF_terminator , FTQUAL_label },
+  { FEATDEF_terminator , FTQUAL_map },
+  { FEATDEF_terminator , FTQUAL_operon },
+  { FEATDEF_terminator , FTQUAL_standard_name },
+  { FEATDEF_terminator , FTQUAL_usedin },
+
+  { FEATDEF_transit_peptide , FTQUAL_allele },
+  { FEATDEF_transit_peptide , FTQUAL_function },
+  { FEATDEF_transit_peptide , FTQUAL_label },
+  { FEATDEF_transit_peptide , FTQUAL_map },
+  { FEATDEF_transit_peptide , FTQUAL_product },
+  { FEATDEF_transit_peptide , FTQUAL_standard_name },
+  { FEATDEF_transit_peptide , FTQUAL_usedin },
+
+  { FEATDEF_unsure , FTQUAL_allele },
+  { FEATDEF_unsure , FTQUAL_label },
+  { FEATDEF_unsure , FTQUAL_map },
+  { FEATDEF_unsure , FTQUAL_replace },
+  { FEATDEF_unsure , FTQUAL_usedin },
+
+  { FEATDEF_V_region , FTQUAL_allele },
+  { FEATDEF_V_region , FTQUAL_label },
+  { FEATDEF_V_region , FTQUAL_map },
+  { FEATDEF_V_region , FTQUAL_product },
+  { FEATDEF_V_region , FTQUAL_standard_name },
+  { FEATDEF_V_region , FTQUAL_usedin },
+
+  { FEATDEF_V_segment , FTQUAL_allele },
+  { FEATDEF_V_segment , FTQUAL_label },
+  { FEATDEF_V_segment , FTQUAL_map },
+  { FEATDEF_V_segment , FTQUAL_product },
+  { FEATDEF_V_segment , FTQUAL_standard_name },
+  { FEATDEF_V_segment , FTQUAL_usedin },
+
+  { FEATDEF_variation , FTQUAL_allele },
+  { FEATDEF_variation , FTQUAL_frequency },
+  { FEATDEF_variation , FTQUAL_label },
+  { FEATDEF_variation , FTQUAL_map },
+  { FEATDEF_variation , FTQUAL_phenotype },
+  { FEATDEF_variation , FTQUAL_product },
+  { FEATDEF_variation , FTQUAL_replace },
+  { FEATDEF_variation , FTQUAL_standard_name },
+  { FEATDEF_variation , FTQUAL_usedin },
+
+  { FEATDEF_3clip , FTQUAL_allele },
+  { FEATDEF_3clip , FTQUAL_function },
+  { FEATDEF_3clip , FTQUAL_label },
+  { FEATDEF_3clip , FTQUAL_map },
+  { FEATDEF_3clip , FTQUAL_standard_name },
+  { FEATDEF_3clip , FTQUAL_usedin },
+
+  { FEATDEF_3UTR , FTQUAL_allele },
+  { FEATDEF_3UTR , FTQUAL_function },
+  { FEATDEF_3UTR , FTQUAL_label },
+  { FEATDEF_3UTR , FTQUAL_map },
+  { FEATDEF_3UTR , FTQUAL_standard_name },
+  { FEATDEF_3UTR , FTQUAL_usedin },
+
+  { FEATDEF_5clip , FTQUAL_allele },
+  { FEATDEF_5clip , FTQUAL_function },
+  { FEATDEF_5clip , FTQUAL_label },
+  { FEATDEF_5clip , FTQUAL_map },
+  { FEATDEF_5clip , FTQUAL_standard_name },
+  { FEATDEF_5clip , FTQUAL_usedin },
+
+  { FEATDEF_5UTR , FTQUAL_allele },
+  { FEATDEF_5UTR , FTQUAL_function },
+  { FEATDEF_5UTR , FTQUAL_label },
+  { FEATDEF_5UTR , FTQUAL_map },
+  { FEATDEF_5UTR , FTQUAL_standard_name },
+  { FEATDEF_5UTR , FTQUAL_usedin },
+
+  { FEATDEF_10_signal , FTQUAL_allele },
+  { FEATDEF_10_signal , FTQUAL_label },
+  { FEATDEF_10_signal , FTQUAL_map },
+  { FEATDEF_10_signal , FTQUAL_operon },
+  { FEATDEF_10_signal , FTQUAL_standard_name },
+  { FEATDEF_10_signal , FTQUAL_usedin },
+
+  { FEATDEF_35_signal , FTQUAL_allele },
+  { FEATDEF_35_signal , FTQUAL_label },
+  { FEATDEF_35_signal , FTQUAL_map },
+  { FEATDEF_35_signal , FTQUAL_operon },
+  { FEATDEF_35_signal , FTQUAL_standard_name },
+  { FEATDEF_35_signal , FTQUAL_usedin },
+
+  { FEATDEF_REGION , FTQUAL_function },
+  { FEATDEF_REGION , FTQUAL_label },
+  { FEATDEF_REGION , FTQUAL_map },
+  { FEATDEF_REGION , FTQUAL_number },
+  { FEATDEF_REGION , FTQUAL_phenotype },
+  { FEATDEF_REGION , FTQUAL_product },
+  { FEATDEF_REGION , FTQUAL_standard_name },
+  { FEATDEF_REGION , FTQUAL_usedin },
+
+  { FEATDEF_mat_peptide_aa , FTQUAL_allele },
+  { FEATDEF_mat_peptide_aa , FTQUAL_label },
+  { FEATDEF_mat_peptide_aa , FTQUAL_map },
+  { FEATDEF_mat_peptide_aa , FTQUAL_product },
+  { FEATDEF_mat_peptide_aa , FTQUAL_standard_name },
+  { FEATDEF_mat_peptide_aa , FTQUAL_usedin },
+
+  { FEATDEF_sig_peptide_aa , FTQUAL_allele },
+  { FEATDEF_sig_peptide_aa , FTQUAL_label },
+  { FEATDEF_sig_peptide_aa , FTQUAL_map },
+  { FEATDEF_sig_peptide_aa , FTQUAL_product },
+  { FEATDEF_sig_peptide_aa , FTQUAL_standard_name },
+  { FEATDEF_sig_peptide_aa , FTQUAL_usedin },
+
+  { FEATDEF_transit_peptide_aa , FTQUAL_allele },
+  { FEATDEF_transit_peptide_aa , FTQUAL_label },
+  { FEATDEF_transit_peptide_aa , FTQUAL_map },
+  { FEATDEF_transit_peptide_aa , FTQUAL_product },
+  { FEATDEF_transit_peptide_aa , FTQUAL_standard_name },
+  { FEATDEF_transit_peptide_aa , FTQUAL_usedin },
+
+  { FEATDEF_snoRNA , FTQUAL_allele },
+  { FEATDEF_snoRNA , FTQUAL_function },
+  { FEATDEF_snoRNA , FTQUAL_label },
+  { FEATDEF_snoRNA , FTQUAL_map },
+  { FEATDEF_snoRNA , FTQUAL_product },
+  { FEATDEF_snoRNA , FTQUAL_standard_name },
+  { FEATDEF_snoRNA , FTQUAL_usedin },
+
+  { FEATDEF_operon , FTQUAL_allele },
+  { FEATDEF_operon , FTQUAL_function },
+  { FEATDEF_operon , FTQUAL_label },
+  { FEATDEF_operon , FTQUAL_map },
+  { FEATDEF_operon , FTQUAL_operon },
+  { FEATDEF_operon , FTQUAL_phenotype },
+  { FEATDEF_operon , FTQUAL_standard_name },
+  { FEATDEF_operon , FTQUAL_usedin },
+
+  { FEATDEF_oriT , FTQUAL_allele },
+  { FEATDEF_oriT , FTQUAL_direction },
+  { FEATDEF_oriT , FTQUAL_label },
+  { FEATDEF_oriT , FTQUAL_map },
+  { FEATDEF_oriT , FTQUAL_rpt_type },
+  { FEATDEF_oriT , FTQUAL_rpt_type },
+  { FEATDEF_oriT , FTQUAL_rpt_unit },
+  { FEATDEF_oriT , FTQUAL_standard_name },
+  { FEATDEF_oriT , FTQUAL_usedin }
+};
+
+/* comparison of ValQual's -- first compare featdef then ftqual */
+
+/* macro did not work properly on linux machine, so using function instead */
+/* #define COMPARE_VALQUAL(av,aq,bv,bq) ( ((av)-(bv)) ? ((av)-(bv)) : ((aq)-(bq)) ) */
+
+static Int2 CompareValQual (Uint2 av, FtQualType aq, Uint2 bv, FtQualType bq)
+
+{
+  if (av == bv) return (aq - bq);
+  return (av - bv);
+}
+
+/* Returns TRUE if {featureKey, qualKey} exists in legalGbqualList */
+
+static Boolean AllowedValQual (Uint2 featureKey, FtQualType qualKey)
+
+{
+  Int2 L, R, mid;
+
+  L = 0;
+  R = sizeof (legalGbqualList) / sizeof (ValQual) - 1;
+  while (L < R) {
+    mid = (L + R) / 2;
+    if (CompareValQual (legalGbqualList [mid].featdef,
+       legalGbqualList [mid].ftqual,
+       featureKey, qualKey) < 0)
+      L = mid + 1;
+    else
+      R = mid;
+  }
+  if (CompareValQual (legalGbqualList [R].featdef,
+      legalGbqualList [R].ftqual,
+      featureKey, qualKey)) {
+    return 0;
+  }
+  return 1;
+}
+
+
+static CharPtr validRptString [] = {
+  "tandem", "inverted", "flanking", "terminal", "direct", "dispersed", "other", NULL
+};
+
+static CharPtr validLRBString [] = {
+  "LEFT", "RIGHT", "BOTH", NULL
+};
+
+static CharPtr validConsSpliceString [] = {
+  "(5'site:YES, 3'site:YES)",
+  "(5'site:YES, 3'site:NO)",
+  "(5'site:YES, 3'site:ABSENT)",
+  "(5'site:NO, 3'site:YES)",
+  "(5'site:NO, 3'site:NO)",
+  "(5'site:NO, 3'site:ABSENT)",
+  "(5'site:ABSENT, 3'site:YES)",
+  "(5'site:ABSENT, 3'site:NO)",
+  "(5'site:ABSENT, 3'site:ABSENT)",
+  NULL
+};
+
+static CharPtr validExceptionString [] = {
+  "RNA editing",
+  "reasons given in citation",
+  NULL
+};
+
+static CharPtr validRefSeqExceptionString [] = {
+  "RNA editing",
+  "reasons given in citation",
+  "ribosomal slippage",
+  "ribosome slippage",
+  "trans splicing",
+  "trans-splicing",
+  "alternative processing",
+  "alternate processing",
+  "artificial frameshift",
+  "non-consensus splice site",
+  "nonconsensus splice site",
+  "rearrangement required for product",
+  "modified codon recognition",
+  "unclassified transcription discrepancy",
+  "unclassified translation discrepancy",
+  NULL
+};
+
+static Boolean StringInStringList (CharPtr testString, CharPtr PNTR stringList) {
+  Int2 i;
+  i = 0;
+  while (stringList [i] != NULL) {
+    if (StringICmp (testString, stringList [i]) == 0)
+      return 1;
+    i++;
+  }
+  return 0;
+}
+
+/*
+Functions now public and prototyped in sequtil.h
+Return values are:
+ 0: no problem - Accession is in proper format
+-1: Accession did not start with a letter (or two letters)
+-2: Accession did not contain five numbers (or six numbers after 2 letters)
+-3: the original Accession number to be validated was NULL
+-4: the original Accession number is too long (>16)
+*/
+
+NLM_EXTERN Int2 ValidateAccn (
+  CharPtr accession
+)
+
+{
+  Char     ch;
+  Int2     numAlpha = 0;
+  Int2     numDigits = 0;
+  Int2     numUndersc = 0;
+  CharPtr  str;
+
+  if (accession == NULL || accession [0] == '\0') return -3;
+
+  if (StringLen (accession) >= 16) return -4;
+
+  if (accession [0] < 'A' || accession [0] > 'Z') return -1;
+
+  str = accession;
+  if (StringNCmp (str, "NZ_", 3) == 0) {
+    str += 3;
+  }
+  ch = *str;
+  while (IS_ALPHA (ch)) {
+    numAlpha++;
+    str++;
+    ch = *str;
+  }
+  while (ch == '_') {
+    numUndersc++;
+    str++;
+    ch = *str;
+  }
+  while (IS_DIGIT (ch)) {
+    numDigits++;
+    str++;
+    ch = *str;
+  }
+  if (ch != '\0' && ch != ' ' && ch != '.') return -2;
+
+  if (numUndersc > 1) return -2;
+
+  if (numUndersc == 0) {
+    if (numAlpha == 1 && numDigits == 5) return 0;
+    if (numAlpha == 2 && numDigits == 6) return 0;
+    if (numAlpha == 3 && numDigits == 5) return 0;
+    if (numAlpha == 4 && numDigits == 8) return 0;
+  } else if (numUndersc == 1) {
+    if (numAlpha != 2 || (numDigits != 6 && numDigits != 8)) return -2;
+    if (accession [0] == 'N' || accession [0] == 'X' || accession [0] == 'Z') {
+      if (accession [1] == 'M' ||
+          accession [1] == 'C' ||
+          accession [1] == 'T' ||
+          accession [1] == 'P' ||
+          accession [1] == 'G' ||
+          accession [1] == 'R' ||
+          accession [1] == 'S' ||
+          accession [1] == 'Z') {
+        return 0;
+      }
+    }
+  }
+
+  return -2;
+}
+
+NLM_EXTERN Int2 ValidateSeqID (
+  SeqIdPtr sip
+)
+
+{
+  Char  buf [41];
+
+  if (sip == NULL) return -3;
+  SeqIdWrite (sip, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
+  return ValidateAccn (buf);
+}
+
+static CharPtr mrnaevtext1 = "Derived by automated computational analysis";
+static CharPtr mrnaevtext2 = "using gene prediction method:";
+static CharPtr mrnaevtext3 = "Supporting evidence includes similarity to:";
+
+static void GetStrFormRNAEvidence (
+  UserObjectPtr uop,
+  Pointer userdata
+)
+
+{
+  size_t        len;
+  CharPtr       method = NULL;
+  Int2          nm = 0;
+  ObjectIdPtr   oip;
+  CharPtr       str = NULL;
+  CharPtr PNTR  strp;
+  Char          tmp [20];
+  UserFieldPtr  u, ufp, uu;
+
+  if (uop == NULL) return;
+  oip = uop->type;
+  if (oip == NULL) return;
+  if (StringCmp (oip->str, "ModelEvidence") != 0) return;
+  strp = (CharPtr PNTR) userdata;
+
+  for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+    oip = ufp->label;
+    if (oip == NULL || ufp->data.ptrvalue == NULL) continue;
+    if (StringCmp (oip->str, "Method") == 0) {
+      method = StringSaveNoNull ((CharPtr) ufp->data.ptrvalue);
+    }
+    if (StringCmp (oip->str, "mRNA") == 0) {
+      for (u = (UserFieldPtr) ufp->data.ptrvalue; u != NULL; u = u->next) {
+        if (u->data.ptrvalue == NULL) continue;
+        for (uu = (UserFieldPtr) u->data.ptrvalue; uu != NULL; uu = uu->next) {
+          oip = uu->label;
+          if (oip == NULL) continue;
+          if (StringCmp (oip->str, "accession") == 0) {
+            nm++;
+          }
+        }
+      }
+    }
+  }
+
+  len = StringLen (mrnaevtext1) + StringLen (mrnaevtext2) + StringLen (mrnaevtext3) + StringLen (method) + 30;
+  str = (CharPtr) MemNew (len);
+  if (str == NULL) return;
+
+  if (method != NULL) {
+    sprintf (str, "%s %s %s.", mrnaevtext1, mrnaevtext2, method);
+  } else {
+    sprintf (str, "%s.", mrnaevtext1);
+  }
+  if (nm > 0) {
+    StringCat (str, " ");
+    StringCat (str, mrnaevtext3);
+    if (nm > 1) {
+      sprintf (tmp, " %d mRNAs", (int) nm);
+    } else {
+      sprintf (tmp, " %d mRNA", (int) nm);
+    }
+    StringCat (str, tmp);
+  }
+
+  *strp = str;
+}
+
+static Boolean ValidateRptUnit (
+  CharPtr buf
+)
+
+{
+#if 0
+  CharPtr  str;
+  Char     tmp [255];
+
+  StringNCpy_0 (tmp, buf, sizeof (tmp));
+  TrimSpacesAroundString (tmp);
+
+  str = tmp;
+  /* first check for sequence letters with optional semicolons */
+  while (IS_ALPHA (*str) || *str == ';') str++;
+  if (*str == '\0') return TRUE;
+  /* next check for letters, digits, commas, parentheses, dashes, and underscores */
+  str = tmp;
+  while (IS_ALPHANUM (*str) || *str == '(' || *str == ')' || *str == ',' || *str == ';' || *str == '-' || *str == '_') str++;
+  if (*str == '\0') return TRUE;
+  /* now check for officially legal styles */
+  str = tmp;
+  while (IS_ALPHANUM (*str)) str++;
+  if (*str != '\0') { /* wasn't pure alphanumeric; now check for xxx..yyy */
+    str = buf;
+    while (IS_DIGIT (*str)) str++; /* xxx */
+    if (*str == '\0' /* must be something after the xxx */
+      || StringLen (str) < 3  /* need at least 2 '.'s and a digit*/
+      || str[0] != '.' || str[1] != '.') return FALSE;
+    str+=2;
+    while (IS_DIGIT (*str)) str++;
+    if (*str != '\0') return FALSE;  /* mustn't be anything after the yyy */
+  }
+#endif
+  return TRUE;
+}
+
+
+NLM_EXTERN CharPtr goFieldType [] = {
+  "", "text string", "go id", "pubmed id", "evidence", NULL
+};
+
+static CharPtr GetGOtext (
+  UserFieldPtr topufp
+)
+
+{
+  CharPtr       evidence = NULL;
+  Char          gid [32];
+  CharPtr       goid = NULL;
+  Int2          j;
+  ObjectIdPtr   oip;
+  Int4          pmid = 0;
+  CharPtr       str;
+  CharPtr       textstr = NULL;
+  Char          tmp [32];
+  UserFieldPtr  ufp;
+
+  for (ufp = topufp; ufp != NULL; ufp = ufp->next) {
+    oip = ufp->label;
+    if (oip == NULL) continue;
+    for (j = 0; goFieldType [j] != NULL; j++) {
+      if (StringICmp (oip->str, goFieldType [j]) == 0) break;
+    }
+    if (goFieldType [j] == NULL) continue;
+    switch (j) {
+      case 1 :
+        if (ufp->choice == 1) {
+          textstr = (CharPtr) ufp->data.ptrvalue;
+        }
+        break;
+      case 2 :
+        if (ufp->choice == 1) {
+          goid = (CharPtr) ufp->data.ptrvalue;
+        } else if (ufp->choice == 2) {
+          sprintf (gid, "%ld", (long) (Int4) ufp->data.intvalue);
+          goid = (CharPtr) gid;
+        }
+        break;
+      case 3 :
+        if (ufp->choice == 2) {
+          pmid = (Int4) ufp->data.intvalue;
+        }
+        break;
+      case 4 :
+        if (ufp->choice == 1) {
+          evidence = (CharPtr) ufp->data.ptrvalue;
+        }
+        break;
+      default :
+        break;
+    }
+  }
+  /* if (StringHasNoText (textstr)) return NULL; */
+
+  str = (CharPtr) MemNew (StringLen (textstr) + StringLen (goid) + StringLen (evidence) + 50);
+  if (str == NULL) return NULL;
+
+  StringCpy (str, textstr);
+  if (! StringHasNoText (goid)) {
+    StringCat (str, " [goid ");
+    StringCat (str, goid);
+    StringCat (str, "]");
+  }
+  if (! StringHasNoText (evidence)) {
+    StringCat (str, " [evidence ");
+    StringCat (str, evidence);
+    StringCat (str, "]");
+  }
+  if (pmid != 0) {
+    sprintf (tmp, " [pmid %ld", (long) pmid);
+    StringCat (str, tmp);
+    StringCat (str, "]");
+  }
+  TrimSpacesAroundString (str);
+
+  return str;
+}
+
+static Boolean DbxrefAlreadyInGeneXref (
+  DbtagPtr dbt,
+  ValNodePtr dbxref
+)
+
+{
+  DbtagPtr    gdbt;
+  ValNodePtr  vnp;
+
+  if (dbt == NULL) return FALSE;
+
+  for (vnp = dbxref; vnp != NULL; vnp = vnp->next) {
+    gdbt = (DbtagPtr) vnp->data.ptrvalue;
+    if (gdbt == NULL) continue;
+    if (DbtagMatch (dbt, gdbt)) return TRUE;
+  }
+
+  return FALSE;
+}
+
+static void FF_www_protein_id(
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr seqid
+)
+{
+
+  if ( GetWWW(ajp) ) {
+    FFAddOneString(ffstring, "<a href=", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, link_seq, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, "val=", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, seqid, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneChar(ffstring, '>', FALSE);  
+    FFAddOneString(ffstring, seqid, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+  } else {
+    FFAddOneString(ffstring, seqid, FALSE, FALSE, TILDE_IGNORE);
+  }
+}
+
+static void FF_www_gcode (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr gcode
+)
+{
+
+  if ( GetWWW(ajp) ) {
+    FFAddOneString(ffstring, "<a href=", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, link_code, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, "mode=c#SG", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, gcode, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneChar(ffstring, '>', FALSE);  
+    FFAddOneString(ffstring, gcode, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+  } else {
+    FFAddOneString(ffstring, gcode, FALSE, FALSE, TILDE_IGNORE);
+  }
+}
+
+static void FF_AddECnumber (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr str
+)
+{
+  if ( GetWWW(ajp) ) {
+    FFAddOneString(ffstring, "<a href=", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, ec_link, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneChar(ffstring, '>', FALSE);  
+    FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+  } else {
+    FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
+  }
+}
+
+
+/* FormatFeatureblockQuals should not be called directly,
+   except from FormatFeatureBlock.  It performs no input
+   validation.  (perhaps it should?) */
+
+static void FormatFeatureBlockQuals (
+  StringItemPtr    ffstring,
+  IntAsn2gbJobPtr  ajp,
+  Asn2gbSectPtr    asp,
+  BioseqPtr        bsp,
+  Uint1            featdeftype,
+  ValNodePtr       gene_syn,
+  CharPtr          lasttype,
+  SeqLocPtr        location,
+  BioseqPtr        prod,
+  CharPtr          protein_pid_g,
+  QualValPtr       qvp,
+  Int4             left,
+  Int4             right,
+  Uint1            strand,
+  SeqFeatPtr       sfp,
+  BioseqPtr        target,
+  Boolean          is_other,
+  Boolean          is_journalscan,
+  Boolean          is_gps
+)
+
+{
+  Boolean            add_period;
+  CharPtr            ascii;
+  Int2               ascii_len;
+  Boolean            at_end = FALSE;
+  ByteStorePtr       bs;
+  Char               buf[80];
+  Choice             cbaa;
+  CodeBreakPtr       cbp;
+  Char               ch;
+  Uint1              choice;
+  Uint1              code = Seq_code_ncbieaa;
+  Int4               gi;
+  Boolean            hadProtDesc = FALSE;
+  DbtagPtr           dbt;
+  UserFieldPtr       entry;
+  Int4               exp_ev;
+  GBQualPtr          gbq;
+  Int2               i;
+  FtQualType         idx;
+  Boolean            isTRNA;
+  Int2               j;
+  FtQualType         jdx;
+  Int4               len;
+  SeqLocPtr          newloc;
+  CharPtr            notestr;
+  Char               numbuf [32];
+  Int2               numcodons;
+  Int2               numsyns;
+  ObjectIdPtr        oip;
+  Boolean            okay;
+  Boolean            only_digits;
+  BioseqPtr          pbsp;
+  ValNodePtr         ppr;
+  CharPtr            prefix;
+  CharPtr            protein_seq = NULL;
+  size_t             prtlen;
+  CharPtr            ptr;
+  Uint1              residue;
+  SeqCodeTablePtr    sctp;
+  Int4               sec_str;
+  Uint1              seqcode;
+  Char               seqid [50];
+  SeqIntPtr          sintp;
+  SeqIdPtr           sip;
+  SeqLocPtr          slp;
+  Boolean            split;
+  SeqPortPtr         spp;
+  CharPtr            start;
+  CharPtr            str;
+  Boolean            suppress_period;
+  CharPtr            tmp;
+  tRNAPtr            trna;
+  UserFieldPtr       ufp;
+  UserObjectPtr      uop;
+  ValNodePtr         vnp;
+  StringItemPtr      unique;
+
+  unique = FFGetString(ajp);
+  if ( unique == NULL ) return;
+
+  for (i = 0, idx = feat_qual_order [i]; idx != (FtQualType) 0; i++, idx = feat_qual_order [i]) {
+
+    lasttype = NULL;
+    switch (asn2gnbk_featur_quals [idx].qualclass) {
+
+      case Qual_class_ignore :
+        break;
+
+      case Qual_class_string :
+        if (! StringHasNoText (qvp [idx].str)) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+            FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"",
+            FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_locus_tag :
+        if (! StringHasNoText (qvp [idx].str)) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+            FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"",
+            FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_tilde :
+        if (! StringHasNoText (qvp [idx].str)) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+            FALSE, TRUE, TILDE_EXPAND);
+          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"",
+            FALSE, TRUE, TILDE_EXPAND);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_product :
+        if (StringHasNoText (qvp [idx].str) ||
+            (ajp->flags.dropIllegalQuals &&
+             (! AllowedValQual (featdeftype, FTQUAL_product)))) break;
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+            FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"",
+            FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        break;
+
+      case Qual_class_sgml :
+        if (! StringHasNoText (qvp [idx].str)) {
+          if (is_journalscan) {
+            ascii_len = Sgml2AsciiLen (qvp [idx].str);
+            start = ascii = MemNew ((size_t) (10 + ascii_len));
+            if (start != NULL) {
+              ascii = Sgml2Ascii (qvp [idx].str, ascii, ascii_len + 1);
+
+              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+                FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddTextToString(ffstring, "\"", start, "\"",
+                FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddOneChar(ffstring, '\n', FALSE);
+
+              MemFree (start);
+            }
+          } else {
+              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+                FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddTextToString(ffstring, "\"", qvp[idx].str, "\"",
+                FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddOneChar(ffstring, '\n', FALSE);
+          }
+        }
+        break;
+
+      case Qual_class_boolean :
+        if (qvp [idx].ble) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "\n",
+                            FALSE, TRUE, TILDE_IGNORE);
+        }
+        break;
+
+      case Qual_class_int :
+        if (qvp [idx].num > 0) {
+          if (idx == FTQUAL_transl_table) {
+            sprintf (numbuf, "%ld", (long) qvp [idx].num);
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+              FALSE, TRUE, TILDE_IGNORE);
+            FF_www_gcode (ajp, ffstring, numbuf);
+          } else {
+            sprintf (numbuf, "%ld", (long) qvp [idx].num);
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+              FALSE, TRUE, TILDE_IGNORE);
+            FFAddTextToString(ffstring, NULL, numbuf, NULL,
+              FALSE, TRUE, TILDE_IGNORE);
+          }
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_evidence :
+        exp_ev = qvp [idx].num;
+        if (exp_ev > 0 && exp_ev <= 2) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+              FALSE, TRUE, TILDE_IGNORE);
+          FFAddOneString(ffstring, evidenceText [exp_ev], FALSE, TRUE, TILDE_IGNORE);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_valnode :
+        for (vnp = qvp[idx].vnp; vnp != NULL; vnp = vnp->next) {
+          str = (CharPtr) vnp->data.ptrvalue;
+          if (str != NULL) {
+              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+                  FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddTextToString(ffstring, "\"", str, "\"",
+                  FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddOneChar(ffstring, '\n', FALSE);
+          }
+        }
+        break;
+
+      case Qual_class_gene_syn :
+        /*
+        for (vnp = qvp[idx].vnp; vnp != NULL; vnp = vnp->next) {
+          str = (CharPtr) vnp->data.ptrvalue;
+          if (str != NULL) {
+              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+                  FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddTextToString(ffstring, "\"", str, "\"",
+                  FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddOneChar(ffstring, '\n', FALSE);
+          }
+        }
+        */
+        numsyns = 0;
+        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
+          str = (CharPtr) vnp->data.ptrvalue;
+          if (! StringHasNoText (str)) {
+            numsyns++;
+          }
+        }
+        if (numsyns > 0) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
+                FALSE, TRUE, TILDE_TO_SPACES);
+          prefix = NULL;
+          for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
+            str = (CharPtr) vnp->data.ptrvalue;
+            if (! StringHasNoText (str)) {
+              FFAddTextToString (ffstring, prefix, str, NULL, FALSE, FALSE, TILDE_IGNORE);
+              prefix = ", ";
+            }
+          }
+          FFAddOneChar(ffstring, '\"', FALSE);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_EC_valnode :
+        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
+          str = (CharPtr) vnp->data.ptrvalue;
+          okay = TRUE;
+
+          if (str == NULL) continue;
+
+          if (ajp->flags.dropIllegalQuals) {
+            tmp = str;
+            while (*tmp != '\0' && *tmp == '\"')
+              tmp++;
+            for (; *tmp != '\0' && *tmp != '\"'; tmp++) {
+              if (!IS_DIGIT(*tmp) && *tmp != '.' && *tmp != '-') {
+                okay = FALSE;
+              }
+            }
+          }
+          if (!okay) continue;
+
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+                FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddOneChar(ffstring, '\"', FALSE);
+          FF_AddECnumber(ajp, ffstring, str);
+          FFAddOneChar(ffstring, '\"', FALSE);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_EC_quote :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          okay = TRUE;
+          if (gbq->val == NULL) {
+            okay = FALSE;
+          }
+
+          if (ajp->flags.dropIllegalQuals && okay) {
+            tmp = gbq->val;
+            while (*tmp != '\0' && *tmp == '\"')
+              tmp++;
+            for (; *tmp != '\0' && *tmp != '\"'; tmp++) {
+              if (!IS_DIGIT(*tmp) && *tmp != '.' && *tmp != '-') {
+                okay = FALSE;
+              }
+            }
+          }
+
+          if (StringHasNoText (gbq->val)) {
+            okay = FALSE;
+          }
+
+          if (okay) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+                  FALSE, TRUE, TILDE_TO_SPACES);
+            FFAddOneChar(ffstring, '\"', FALSE);
+            if (!StringIsJustQuotes (gbq->val)) {
+              FF_AddECnumber (ajp, ffstring, gbq->val);
+            }
+            FFAddOneChar(ffstring, '\"', FALSE);
+            FFAddOneChar(ffstring, '\n', FALSE);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_quote :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
+                  FALSE, TRUE, TILDE_IGNORE);
+            if (!StringIsJustQuotes (gbq->val)) {
+              FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_IGNORE);
+            }
+            FFAddOneChar(ffstring, '\"', FALSE);
+            FFAddOneChar(ffstring, '\n', FALSE);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_noquote :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=",
+                  FALSE, TRUE, TILDE_IGNORE);
+            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
+            FFAddOneChar(ffstring, '\n', FALSE);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_label :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            if (ajp->flags.checkQualSyntax) { /* single token, not just numeric */
+              str = gbq->val;
+              ch = *str;
+              only_digits = TRUE;
+              while (ch != '\0') {
+                if (IS_WHITESP (ch)) break; /* only single token allowed */
+                if (! IS_DIGIT (ch)) {
+                  only_digits = FALSE;
+                }
+                str++;
+                ch = *str;
+              }
+              if (only_digits) break; /* must not be just numeric */
+            }
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                  FALSE, TRUE, TILDE_IGNORE);
+            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
+            FFAddOneChar(ffstring, '\n', FALSE);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_number :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+
+        if (ajp->flags.checkQualSyntax) {
+          str = gbq->val;
+
+          if ( StringHasNoText (str) )
+            break;
+          while (!IS_WHITESP (*str) && *str != '\0')
+            str++;
+          if (! StringHasNoText (str) )
+            break;
+        }
+
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                  FALSE, TRUE, TILDE_IGNORE);
+            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
+            FFAddOneChar(ffstring, '\n', FALSE);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_paren :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            tmp = StringSave (gbq->val);
+            str = tmp;
+            len = StringLen (str);
+            if (len > 1 && *str == '(' && str [len - 1] == ')' &&
+                StringChr (str, ',') != NULL) {
+              str++;
+              while (! StringHasNoText (str)) {
+                ptr = StringChr (str, ',');
+                if (ptr == NULL) {
+                  ptr = StringChr (str, ')');
+                }
+                if (ptr != NULL) {
+                  *ptr = '\0';
+                  ptr++;
+                }
+                FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                  FALSE, TRUE, TILDE_IGNORE);
+                FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
+                FFAddOneChar(ffstring, '\n', FALSE);
+                str = ptr;
+              }
+            } else {
+              FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                  FALSE, TRUE, TILDE_IGNORE);
+              FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddOneChar(ffstring, '\n', FALSE);
+            }
+            MemFree (tmp);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_rpt :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            tmp = StringSave (gbq->val);
+            str = tmp;
+            len = StringLen (str);
+            if (len > 1 && *str == '(' && str [len - 1] == ')' &&
+                StringChr (str, ',') != NULL) {
+              str++;
+              while (! StringHasNoText (str)) {
+                ptr = StringChr (str, ',');
+                if (ptr == NULL) {
+                  ptr = StringChr (str, ')');
+                }
+                if (ptr != NULL) {
+                  *ptr = '\0';
+                  ptr++;
+                }
+                if ((! ajp->flags.checkQualSyntax) || (StringInStringList (str, validRptString))) {
+                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                                    FALSE, TRUE, TILDE_IGNORE);
+                  FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
+                  FFAddOneChar(ffstring, '\n', FALSE);
+                }
+                str = ptr;
+              }
+            } else {
+              if ((! ajp->flags.checkQualSyntax) || (StringInStringList (str, validRptString))) {
+                FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                                  FALSE, TRUE, TILDE_IGNORE);
+                FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
+                FFAddOneChar(ffstring, '\n', FALSE);
+              }
+            }
+            MemFree (tmp);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_rpt_unit :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+
+        /* in release_mode, must be of the form 123..4567 or a single-token label,
+           or (technically illegal but common) letters and semicolons - NO LONGER CHECKED */
+
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            tmp = StringSave (gbq->val);
+            str = tmp;
+            len = StringLen (str);
+            if (len > 1 && *str == '(' && str [len - 1] == ')' /* && StringChr (str, ',') != NULL */) {
+              str++;
+              while (! StringHasNoText (str)) {
+                ptr = StringChr (str, ',');
+                if (ptr == NULL) {
+                  ptr = StringChr (str, ')');
+                }
+                if (ptr != NULL) {
+                  *ptr = '\0';
+                  ptr++;
+                }
+                if ((! ajp->flags.checkQualSyntax) || (ValidateRptUnit (str))) {
+                  TrimSpacesAroundString (str);
+                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=\"",
+                                    FALSE, TRUE, TILDE_IGNORE);
+                  FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
+                  FFAddOneChar(ffstring, '\"', FALSE);
+                  FFAddOneChar(ffstring, '\n', FALSE);
+                }
+                str = ptr;
+              }
+            } else {
+              if ((! ajp->flags.checkQualSyntax) || (ValidateRptUnit (str))) {
+                TrimSpacesAroundString (str);
+                FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=\"",
+                                  FALSE, TRUE, TILDE_IGNORE);
+                FFAddOneString(ffstring, str, FALSE, TRUE, TILDE_TO_SPACES);
+                FFAddOneChar(ffstring, '\"', FALSE);
+                FFAddOneChar(ffstring, '\n', FALSE);
+              }
+            }
+            MemFree (tmp);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_replace :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                            FALSE, TRUE, TILDE_IGNORE);
+          FFAddOneChar(ffstring, '\"', FALSE);
+          if (!StringHasNoText (gbq->val)) {
+            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
+          }
+          FFAddOneChar(ffstring, '\"', FALSE);
+          FFAddOneChar(ffstring, '\n', FALSE);
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_consplice :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+
+        if (ajp->flags.checkQualSyntax && (! StringInStringList (gbq->val, validConsSpliceString)) ) {
+          break;
+        }
+
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                              FALSE, TRUE, TILDE_IGNORE);
+            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
+            FFAddOneChar(ffstring, '\n', FALSE);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_site :
+        if (! StringHasNoText (qvp [idx].str)) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                            FALSE, TRUE, TILDE_IGNORE);
+          FFAddTextToString(ffstring, "\"", qvp[idx].str, "\"", FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_bond :
+        if (! StringHasNoText (qvp [idx].str)) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                            FALSE, TRUE, TILDE_IGNORE);
+          FFAddTextToString(ffstring, "\"", qvp[idx].str, "\"", FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_L_R_B :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+
+        if (ajp->flags.checkQualSyntax && (! StringInStringList (gbq->val, validLRBString)) ) {
+          break;
+        }
+
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                              FALSE, TRUE, TILDE_IGNORE);
+            FFAddOneString(ffstring, gbq->val, FALSE, TRUE, TILDE_TO_SPACES);
+            FFAddOneChar(ffstring, '\n', FALSE);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_sec_str :
+        sec_str = qvp [idx].num;
+        if (sec_str > 0 && sec_str <= 3) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                            FALSE, TRUE, TILDE_IGNORE);
+          FFAddTextToString(ffstring, "\"", secStrText[sec_str], "\"", 
+                            FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_seq_loc :
+        slp = qvp [idx].slp;
+        if (slp != NULL) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                            FALSE, TRUE, TILDE_IGNORE);
+          str = FFFlatLoc (ajp, target, slp, /* ajp->masterStyle */ FALSE);
+          FFAddTextToString(ffstring, "\"", str, "\"", 
+                            FALSE, TRUE, TILDE_TO_SPACES);
+          FFAddOneChar(ffstring, '\n', FALSE);
+          MemFree (str);
+        }
+        break;
+
+      case Qual_class_code_break :
+        cbp = qvp [idx].cbp;
+        seqcode = 0;
+        sctp = NULL;
+        while (cbp != NULL) {
+          cbaa = cbp->aa;
+          switch (cbaa.choice) {
+            case 1 :
+              seqcode = Seq_code_ncbieaa;
+              break;
+            case 2 :
+              seqcode = Seq_code_ncbi8aa;
+              break;
+            case 3 :
+              seqcode = Seq_code_ncbistdaa;
+              break;
+            default :
+              break;
+          }
+          if (seqcode != 0) {
+            sctp = SeqCodeTableFind (seqcode);
+            if (sctp != NULL) {
+              slp = NULL;
+              while ((slp = SeqLocFindNext (cbp->loc, slp)) != NULL) {
+                str = NULL;
+                if (ajp->ajp.slp != NULL) {
+                  sip = SeqIdParse ("lcl|dummy");
+                  split = FALSE;
+                  newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
+ 
+                  SeqIdFree (sip);
+                  if (newloc != NULL) {
+                    A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
+                    str = FFFlatLoc (ajp, target, newloc, ajp->masterStyle);
+                    SeqLocFree (newloc);
+                  }
+                } else {
+                  str = FFFlatLoc (ajp, target, slp, ajp->masterStyle);
+                }
+                if (str != NULL) {
+                  residue = cbaa.value.intvalue;
+                  ptr = Get3LetterSymbol (ajp, seqcode, sctp, residue);
+                  if (ptr == NULL) {
+                    ptr = "OTHER";
+                  }
+                  FFAddOneString(ffstring, "/transl_except=", FALSE, FALSE, TILDE_IGNORE);
+                  FFAddTextToString(ffstring, "(pos:", str, ",", FALSE, FALSE, TILDE_IGNORE);
+                  FFAddTextToString(ffstring, "aa:", ptr, ")", FALSE, FALSE, TILDE_IGNORE);
+                  FFAddOneChar(ffstring, '\n', FALSE);
+                }
+                MemFree (str);
+              }
+            }
+          }
+          cbp = cbp->next;
+        }
+        break;
+
+      case Qual_class_anti_codon :
+        slp = qvp [FTQUAL_anticodon].slp;
+        newloc = NULL;
+        if (slp != NULL && ajp->ajp.slp != NULL) {
+          sip = SeqIdParse ("lcl|dummy");
+          split = FALSE;
+          newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
+          /*
+          newloc = SeqLocCopyRegion (sip, slp, bsp, left, right, strand, &split);
+          */
+          SeqIdFree (sip);
+          slp = newloc;
+          if (newloc != NULL) {
+            A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
+          }
+        }
+        if (slp != NULL && slp->choice == SEQLOC_INT) {
+          sintp = (SeqIntPtr) slp->data.ptrvalue;
+          if (sintp != NULL) {
+            str = qvp [FTQUAL_trna_aa].str;
+            if (! StringHasNoText (str)) {
+              sprintf(numbuf, "%ld", (long) sintp->from + 1);
+              FFAddTextToString(ffstring, "/anticodon=(pos:", numbuf, "..",
+                                FALSE, FALSE, TILDE_IGNORE);
+              sprintf(numbuf, "%ld", (long) sintp->to + 1);
+              FFAddTextToString(ffstring, NULL, numbuf, ",",
+                                FALSE, FALSE, TILDE_IGNORE);
+              FFAddTextToString(ffstring, "aa:", str, ")",
+                                FALSE, FALSE, TILDE_IGNORE);
+              FFAddOneChar(ffstring, '\n', FALSE);
+            }
+          }
+        }
+        if (newloc != NULL) {
+          SeqLocFree (newloc);
+        }
+        break;
+
+      case Qual_class_codon :
+        gbq = qvp [idx].gbq;
+        if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break;
+        if (lasttype == NULL) {
+          lasttype = gbq->qual;
+        }
+        while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+          if (! StringHasNoText (gbq->val)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                              FALSE, FALSE, TILDE_IGNORE);
+            FFAddOneString(ffstring, gbq->val, FALSE, FALSE, TILDE_TO_SPACES);
+            FFAddOneChar(ffstring, '\n', FALSE);
+          }
+          gbq = gbq->next;
+        }
+        break;
+
+      case Qual_class_pubset :
+        vnp = qvp [idx].vnp;
+        if (vnp != NULL && asp != NULL && asp->referenceArray != NULL) {
+          for (ppr = vnp->data.ptrvalue; ppr != NULL; ppr = ppr->next) {
+            j = MatchRef (ppr, asp->referenceArray, asp->numReferences);
+            if (j > 0) {
+              sprintf (numbuf, "%d", (int) j);
+              FFAddTextToString(ffstring, "/citation=[", numbuf, "]",
+                                FALSE, TRUE, TILDE_TO_SPACES);
+              FFAddOneChar(ffstring, '\n', FALSE);
+            }
+          }
+        }
+        break;
+
+      case Qual_class_db_xref :
+        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
+          buf [0] = '\0';
+          dbt = (DbtagPtr) vnp->data.ptrvalue;
+          if (dbt != NULL && (! StringHasNoText (dbt->db))) {
+            oip = dbt->tag;
+            if (oip != NULL) {
+
+              okay = TRUE;
+              if (StringCmp (dbt->db, "PID") == 0 || StringCmp (dbt->db, "GI") == 0) {
+                okay = FALSE;
+              }
+              if (ajp->flags.dropBadDbxref) {
+                /* if RELEASE_MODE, drop unknown dbtag */
+                okay = FALSE;
+                for (j = 0; legalDbXrefs [j] != NULL; j++) {
+                  if (StringCmp (dbt->db, legalDbXrefs [j]) == 0) {
+                    okay = TRUE;
+                  }
+                }
+                if (! okay) {
+                  if (is_gps || is_other) {
+                    for (j = 0; legalRefSeqDbXrefs [j] != NULL; j++) {
+                      if (StringCmp (dbt->db, legalRefSeqDbXrefs [j]) == 0) {
+                        okay = TRUE;
+                      }
+                    }
+                  }
+                }
+              }
+              if (okay && idx == FTQUAL_db_xref && qvp [FTQUAL_gene_xref].vnp != NULL) {
+                if (DbxrefAlreadyInGeneXref (dbt, qvp [FTQUAL_gene_xref].vnp)) {
+                  okay = FALSE;
+                }
+              }
+
+              if (okay) {
+                if (! StringHasNoText (oip->str)) {
+                  if (StringLen (oip->str) < 80) {
+                    sprintf (buf, "%s", oip->str);
+                  }
+                } else {
+                  sprintf (buf, "%ld", (long) oip->id);
+                }
+              }
+            }
+          }
+          if (! StringHasNoText (buf)) {
+            if (StringICmp (buf, protein_pid_g) != 0) {
+              /* already sorted and uniqued by BasicSeqEntryCleanup, per feature */
+              if (StringICmp (dbt->db, "LocusID") == 0 || StringICmp (dbt->db, "InterimID") == 0) {
+                if (FFStringSearch (ffstring, dbt->db, 0) >= 0) {
+                  okay = FALSE;
+                }
+              }
+              if (okay) {
+                FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
+                FF_www_db_xref(ajp, ffstring, dbt->db, buf);
+                FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+              }
+            }
+          }
+        }
+        break;
+
+      
+      case Qual_class_seq_id :
+        sip = qvp [idx].sip;
+        if (sip != NULL) {
+          /* should always be found above for protein_id or transcript_id
+          prod = BioseqFind (sip);
+          */
+          if (prod != NULL) {
+            choice = 0;
+            for (sip = prod->id; sip != NULL; sip = sip->next) {
+              if (sip->choice == SEQID_GENBANK ||
+                  sip->choice == SEQID_EMBL ||
+                  sip->choice == SEQID_DDBJ ||
+                  sip->choice == SEQID_OTHER ||
+                  sip->choice == SEQID_TPG ||
+                  sip->choice == SEQID_TPE ||
+                  sip->choice == SEQID_TPD) {
+                choice = sip->choice;
+                if (SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
+                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
+                                    FALSE, FALSE, TILDE_IGNORE);
+                  FF_www_protein_id(ajp, ffstring, seqid);
+                  FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+                }
+              } else if (sip->choice == SEQID_GI) {
+                if (choice == 0) {
+                  sprintf (seqid, "%ld", (long) sip->data.intvalue);
+                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
+                                    FALSE, FALSE, TILDE_IGNORE);
+                  FF_www_protein_id(ajp, ffstring, seqid);
+                  FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+                }
+                sprintf (seqid, "%ld", (long) sip->data.intvalue);
+                FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
+                FF_www_db_xref(ajp, ffstring, "GI", seqid);
+                FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+              } else if (sip->choice == SEQID_GENERAL) {
+                dbt = (DbtagPtr) sip->data.ptrvalue;
+                if (dbt != NULL && StringCmp (dbt->db, "PID") == 0) {
+                  /*
+                  oip = dbt->tag;
+                  if (oip != NULL) {
+                    if (! StringHasNoText (oip->str)) {
+                      sprintf (seqid, "PID:%s", oip->str);
+                      NewContLine ();
+                      gb_AddString ("/db_xref=\"", seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES);
+                    }
+                  }
+                  */
+                } else if (dbt != NULL) {
+                  pbsp = BioseqFind (sip);
+                  if (pbsp != NULL && pbsp->id != NULL && pbsp->id->next == NULL) {
+                    if (SeqIdWrite (sip, seqid, PRINTID_REPORT, sizeof (seqid)) != NULL) {
+                      FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
+                                        FALSE, FALSE, TILDE_IGNORE);
+                      FF_www_protein_id(ajp, ffstring, seqid);
+                      FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+                    }
+                  }
+                }
+              }
+            }
+          } else {
+            if (sip->choice == SEQID_GI) {
+              gi = sip->data.intvalue;
+              if (GetAccnVerFromServer (gi, seqid)) {
+                if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
+                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
+                                    FALSE, FALSE, TILDE_IGNORE);
+                  FF_www_protein_id(ajp, ffstring, seqid);
+                  FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+                } else {
+                  ajp->relModeError = TRUE;
+                }
+              } else {
+                sip = GetSeqIdForGI(gi);
+                if (sip != NULL && SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
+                  if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
+                    FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
+                                    FALSE, FALSE, TILDE_IGNORE);
+                    FF_www_protein_id(ajp, ffstring, seqid);
+                    FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+                  } else {
+                    ajp->relModeError = TRUE;
+                  }
+                } else if (! ajp->flags.dropIllegalQuals) {
+                  sprintf (seqid, "%ld", (long) gi);
+                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
+                                    FALSE, FALSE, TILDE_IGNORE);
+                  FF_www_protein_id(ajp, ffstring, seqid);
+                  FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+                } else {
+                  ajp->relModeError = TRUE;
+                }
+              }
+
+              sprintf (seqid, "%ld", (long) gi);
+              FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
+              FF_www_db_xref(ajp, ffstring, "GI", seqid);
+              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) {
+                FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
+                                  FALSE, FALSE, TILDE_IGNORE);
+                FF_www_protein_id(ajp, ffstring, seqid);
+                FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+              } else {
+                ajp->relModeError = TRUE;
+              }
+
+              gi = GetGIForSeqId (sip);
+              if (gi > 0) {
+                sprintf (seqid, "%ld", (long) gi);
+                FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
+                FF_www_db_xref(ajp, ffstring, "GI", seqid);
+                FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+              }
+            }
+          }
+        }
+        break;
+
+      case Qual_class_translation :
+        if (qvp [idx].ble) {
+          if ((prod == NULL && ajp->transIfNoProd) || ajp->alwaysTranslCds) {
+            bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
+            if (bs != NULL) {
+              str = BSMerge (bs, NULL);
+              bs = BSFree (bs);
+              if (str != NULL) {
+                ptr = str;
+                ch = *ptr;
+                while (ch != '\0') {
+                  *ptr = TO_UPPER (ch);
+                  ptr++;
+                  ch = *ptr;
+                }
+                prtlen = StringLen (str);
+                if (prtlen > 1) {
+                   if (str [prtlen - 1] == '*') {
+                     str [prtlen - 1] = '\0';
+                   }
+                }
+                if (! StringHasNoText (str)) {
+                  FFAddTextToString(ffstring, "/translation=\"", str, "\"", 
+                                    FALSE, TRUE, TILDE_TO_SPACES);
+                  FFAddOneChar(ffstring, '\n', FALSE);
+                }
+                MemFree (str);
+              }
+            } else {
+              ajp->relModeError = TRUE;
+            }
+          } else if (prod != NULL) {
+            len = SeqLocLen (sfp->product);
+            if (len > 0) {
+              if (SeqLocStart (location) == 0 || (bsp != NULL && SeqLocStop (location) == bsp->length - 1)) {
+                at_end = TRUE;
+              }
+              str = (CharPtr) MemNew ((size_t) (len + 1) * sizeof (Char));
+              protein_seq = str;
+              if (ajp->flags.iupacaaOnly) {
+                code = Seq_code_iupacaa;
+              } else {
+                code = Seq_code_ncbieaa;
+              }
+              spp = SeqPortNewByLoc (sfp->product, code);
+              if (spp != NULL) {
+                SeqPortSet_do_virtual (spp, TRUE);
+                while ((residue = SeqPortGetResidue (spp)) != SEQPORT_EOF) {
+                  if (! (IS_residue (residue))) continue;
+                  if (residue == INVALID_RESIDUE) {
+                    residue = (Uint1) 'X';
+                  }
+                  *protein_seq = residue;
+                  protein_seq++;
+                }
+                /*
+                if (at_end && StringLen (str) < GENPEPT_MIN) {
+                  str = MemFree (str);
+                }
+                */
+                if (! StringHasNoText (str)) {
+                  FFAddTextToString(ffstring, "/translation=\"", str, "\"", 
+                                    FALSE, TRUE, TILDE_TO_SPACES);
+                  FFAddOneChar(ffstring, '\n', FALSE);
+                }
+                MemFree (str);
+              } else {
+                ajp->relModeError = TRUE;
+              }
+              SeqPortFree (spp);
+            } else {
+              ajp->relModeError = TRUE;
+            }
+          }
+        }
+        break;
+      
+      case Qual_class_transcription :
+        if (qvp [idx].ble) {
+          if (ajp->showTranscript) {
+            str = GetSequenceByFeature (sfp);
+            if (str != NULL) {
+              ptr = str;
+              ch = *ptr;
+              while (ch != '\0') {
+                *ptr = TO_UPPER (ch);
+                ptr++;
+                ch = *ptr;
+              }
+              if (! StringHasNoText (str)) {
+                FFAddTextToString(ffstring, "/transcription=\"", str, "\"", 
+                                  FALSE, TRUE, TILDE_TO_SPACES);
+                FFAddOneChar(ffstring, '\n', FALSE);
+              }
+              MemFree (str);
+            }
+          }
+        }
+        break;
+      
+      case Qual_class_peptide :
+        if (qvp [idx].ble) {
+          if (ajp->showPeptide) {
+            str = GetSequenceByFeature (sfp);
+            if (str != NULL) {
+              ptr = str;
+              ch = *ptr;
+              while (ch != '\0') {
+                *ptr = TO_UPPER (ch);
+                ptr++;
+                ch = *ptr;
+              }
+              if (! StringHasNoText (str)) {
+                FFAddTextToString(ffstring, "/peptide=\"", str, "\"", 
+                                  FALSE, TRUE, TILDE_TO_SPACES);
+                FFAddOneChar(ffstring, '\n', FALSE);
+              }
+              MemFree (str);
+            }
+          }
+        }
+        break;
+      
+      case Qual_class_illegal :
+        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
+          str = (CharPtr) vnp->data.ptrvalue;
+          if (str != NULL) {
+            FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_TO_SPACES);
+            FFAddNewLine(ffstring);
+          }
+        }
+        break;
+
+      case Qual_class_note :
+        if (! ajp->flags.goQualsToNote) {
+
+          /* in sequin_mode and dump_mode in RefSeq, GO terms show up as separate /qualifiers */
+
+          for (j = 0, jdx = feat_note_order [j]; jdx != 0; j++, jdx = feat_note_order [j]) {
+            switch (asn2gnbk_featur_quals [jdx].qualclass) {
+
+              case Qual_class_go :
+                if (qvp [jdx].ufp != NULL) {
+                  for (entry = qvp [jdx].ufp; entry != NULL; entry = entry->next) {
+                    if (entry == NULL || entry->choice != 11) break;
+                    ufp = (UserFieldPtr)  entry->data.ptrvalue;
+                    str = GetGOtext (ufp);
+                    if (! StringHasNoText (str)) {
+                      FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[jdx].name, "=",
+                                        FALSE, TRUE, TILDE_IGNORE);
+                      FFAddTextToString(ffstring, "\"", str, "\"", 
+                                        FALSE, FALSE, TILDE_IGNORE);
+                      FFAddOneChar(ffstring, '\n', FALSE);
+                    }
+                    MemFree (str);
+                  }
+                }
+                break;
+
+              default :
+                break;
+            }
+          }
+        }
+
+        /*head = NULL;*/
+        notestr = NULL;
+        prefix = NULL;
+        add_period = FALSE;
+        suppress_period = FALSE;
+        lasttype = NULL;
+        isTRNA = TRUE;
+        
+
+#ifdef DISPLAY_STRINGS
+        s_DisplayQVP (qvp, feat_note_order);
+#endif
+        for (j = 0, jdx = feat_note_order [j]; jdx != 0; j++, jdx = feat_note_order [j]) {
+          switch (asn2gnbk_featur_quals [jdx].qualclass) {
+
+            case Qual_class_string :
+              if (! StringHasNoText (qvp [jdx].str)) {
+                if (jdx == FTQUAL_figure) {
+                  if (!IsEllipsis (qvp [jdx].str))
+                    s_RemovePeriodFromEnd (qvp [jdx].str);
+                  sprintf (buf, "This sequence comes from %s", qvp [jdx].str);
+                  FFAddString_NoRedund (unique, prefix, buf, NULL);
+                  add_period = FALSE;
+                } else if (jdx == FTQUAL_maploc) {
+                  if (!IsEllipsis (qvp [jdx].str))
+                    s_RemovePeriodFromEnd (qvp [jdx].str);
+                  sprintf (buf, "Map location %s", qvp [jdx].str);
+                  FFAddString_NoRedund (unique, prefix, buf, NULL);
+                  add_period = FALSE;
+                } else if (jdx == FTQUAL_seqfeat_note) {
+                  str = StringSave (qvp [jdx].str);
+                  TrimSpacesAndJunkFromEnds (str, TRUE);
+                  if (! IsEllipsis (str))
+                    add_period = s_RemovePeriodFromEnd (str);
+                  /*  NOTE -- The following function call cleans up some strings
+                      (i.e., U34661 & U31565) but should be commented back
+                      in only if the problem can't be fixed upstream of here
+
+                  s_StringCleanup(str);
+
+                  */
+                  FFAddString_NoRedund (unique, prefix, str, NULL);
+                  MemFree (str);
+                  if (hadProtDesc) {
+                    suppress_period = TRUE;
+                  }
+                } else if (jdx == FTQUAL_prot_note) {
+                  str = StringSave (qvp [jdx].str);
+                  TrimSpacesAndJunkFromEnds (str, TRUE);
+                  if (! IsEllipsis (str))
+                    s_RemovePeriodFromEnd (str);
+                  FFAddString_NoRedund (unique, prefix, str, NULL);
+                  MemFree (str);
+                  add_period = FALSE;
+                } else if (jdx == FTQUAL_prot_desc) {
+                  str = StringSave (qvp [jdx].str);
+                  TrimSpacesAndJunkFromEnds (str, TRUE);
+                  if (! IsEllipsis (str))
+                    add_period = s_RemovePeriodFromEnd (str);
+                  FFAddString_NoRedund (unique, prefix, str, NULL);
+                  MemFree (str);
+                  hadProtDesc = TRUE; /* gi|347886|gb|M96268.1|ECOUBIA */
+                } else {
+                  if (! IsEllipsis (qvp [jdx].str)) {
+                    s_RemovePeriodFromEnd (qvp [jdx].str);
+                  }
+                  FFAddString_NoRedund (unique, prefix, qvp [jdx].str, NULL);
+                  add_period = FALSE;
+                }
+                prefix = "; ";
+              }
+              break;
+
+            case Qual_class_encodes :
+              if (! StringHasNoText (qvp [jdx].str)) {
+                if (! IsEllipsis (qvp [jdx].str)) {
+                  s_RemovePeriodFromEnd (qvp [jdx].str);
+                }
+                FFAddTextToString (unique, prefix, "encodes ", NULL, FALSE, FALSE, TILDE_IGNORE);
+                FFAddString_NoRedund (unique, NULL, qvp [jdx].str, NULL);
+                prefix = "; ";
+                add_period = FALSE;
+              }
+              break;
+
+            case Qual_class_locus_tag :
+              if (! StringHasNoText (qvp [jdx].str)) {
+                if (! IsEllipsis (qvp [jdx].str)) {
+                  s_RemovePeriodFromEnd (qvp [jdx].str);
+                }
+                FFAddTextToString (unique, prefix, "locus_tag: ", NULL, FALSE, FALSE, TILDE_IGNORE);
+                FFAddString_NoRedund (unique, NULL, qvp [jdx].str, NULL);
+                prefix = "; ";
+                add_period = FALSE;
+              }
+              break;
+
+            case Qual_class_go :
+              if (ajp->flags.goQualsToNote && qvp [jdx].ufp != NULL) {
+                for (entry = qvp [jdx].ufp; entry != NULL; entry = entry->next) {
+                  if (entry == NULL || entry->choice != 11) break;
+                  ufp = (UserFieldPtr)  entry->data.ptrvalue;
+                  str = GetGOtext (ufp);
+                  if (! StringHasNoText (str)) {
+                    if (StringCmp (prefix, "; ") == 0) {
+                      prefix = ";\n";
+                    }
+                    FFAddTextToString (unique, prefix, asn2gnbk_featur_quals[jdx].name, ": ", FALSE, FALSE, TILDE_IGNORE);
+                    FFAddTextToString(unique, NULL, str, NULL, FALSE, FALSE, TILDE_IGNORE);
+                  }
+                  MemFree (str);
+                  prefix = "; ";
+                  add_period = FALSE;
+                }
+              }
+              break;
+
+            case Qual_class_method :
+              if (! StringHasNoText (qvp [jdx].str)) {
+                if ( FFEmpty(unique) ) {
+                  prefix = "Method: ";
+                } else {
+                  prefix = "; Method: ";
+                }
+                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, NULL);
+                prefix = "; ";
+                add_period = FALSE;
+              }
+              break;
+
+            case Qual_class_valnode :
+              for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
+                str = (CharPtr) vnp->data.ptrvalue;
+                if (! StringHasNoText (str)) {
+                  FFAddString_NoRedund (unique, prefix, str, NULL);
+                  prefix = "; ";
+                  add_period = FALSE;
+                }
+              }
+              break;
+
+            case Qual_class_gene_syn :
+              numsyns = 0;
+              for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
+                str = (CharPtr) vnp->data.ptrvalue;
+                if (! StringHasNoText (str)) {
+                  numsyns++;
+                }
+              }
+              if (numsyns > 0) {
+                if (numsyns > 1) {
+                  FFAddTextToString (unique, prefix, "synonyms: ", NULL, FALSE, FALSE, TILDE_IGNORE);
+                } else {
+                  FFAddTextToString (unique, prefix, "synonym: ", NULL, FALSE, FALSE, TILDE_IGNORE);
+                }
+                prefix = NULL;
+                for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
+                  str = (CharPtr) vnp->data.ptrvalue;
+                  if (! StringHasNoText (str)) {
+                    FFAddTextToString (unique, prefix, str, NULL, FALSE, FALSE, TILDE_IGNORE);
+                    prefix = ", ";
+                  }
+                }
+                prefix = "; ";
+                add_period = FALSE;
+              }
+              break;
+
+            case Qual_class_region :
+              if (! StringHasNoText (qvp [jdx].str)) {
+                if ( FFEmpty(unique) ) {
+                  prefix = "Region: ";
+                } else {
+                  prefix = "; Region: ";
+                }
+#ifdef ASN2GNBK_STRIP_NOTE_PERIODS
+                FFAddTextToString(unique, prefix, qvp [jdx].str, NULL, FALSE, FALSE, TILDE_IGNORE);
+#else
+                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, NULL);
+#endif
+                prefix = "; ";
+                add_period = FALSE;
+              }
+              break;
+
+            case Qual_class_site :
+              if (! StringHasNoText (qvp [jdx].str)) {
+                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, " site");
+                add_period = FALSE;
+                prefix = "\n";
+              }
+              break;
+
+            case Qual_class_bond :
+              if (! StringHasNoText (qvp [jdx].str)) {
+                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, " bond");
+                add_period = FALSE;
+                prefix = "\n";
+              }
+              break;
+
+            case Qual_class_protnames :
+              /* process gene sgml for check against subsequent protein names */
+              start = NULL;
+              if (! StringHasNoText (qvp [FTQUAL_gene].str)) {
+                if (is_journalscan) {
+                  ascii_len = Sgml2AsciiLen (qvp [FTQUAL_gene].str);
+                  start = ascii = MemNew ((size_t) (10 + ascii_len));
+                  if (start != NULL) {
+                    ascii = Sgml2Ascii (qvp [FTQUAL_gene].str, ascii, ascii_len + 1);
+                  }
+                } else {
+                  start = StringSaveNoNull (qvp [FTQUAL_gene].str);
+                }
+              }
+              for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
+                str = (CharPtr) vnp->data.ptrvalue;
+                if (! StringHasNoText (str)) {
+                  /* case sensitive - gi|4973426|gb|AF148501.1|AF148501 */
+                  /* check with and without sgml conversion */
+                  if (StringCmp (start, str) != 0 &&
+                      StringCmp (qvp [FTQUAL_gene].str, str) != 0) {
+                    if (! StringStr (qvp [FTQUAL_prot_desc].str, str)) {
+                      /* if (NotInGeneSyn (str, gene_syn)) { */
+                        FFAddString_NoRedund (unique, prefix, str, NULL);
+                        prefix = "; ";
+                        add_period = FALSE;
+                      /* } */
+                    }
+                  }
+                }
+              }
+              MemFree (start);
+              break;
+
+            case Qual_class_xtraprds :
+              gbq = qvp [jdx].gbq;
+              if (lasttype == NULL && gbq != NULL) {
+                lasttype = gbq->qual;
+              }
+              while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+                if (! StringHasNoText (gbq->val)) {
+                  if (StringCmp(gbq->val,qvp[FTQUAL_gene].str) != 0 &&
+                      StringCmp(gbq->val,qvp[FTQUAL_product].str) != 0) {
+                    if (!isTRNA || !StringStr (gbq->val, "RNA")) {
+                      FFAddString_NoRedund (unique, prefix, gbq->val, NULL);
+                      prefix = "; ";
+                      add_period = FALSE;
+                    }
+                  }
+                }
+                gbq = gbq->next;
+              }
+              break;
+
+            case Qual_class_its :
+              str = qvp [jdx].str;
+              if (! StringHasNoText (str)) {
+                if (sfp->comment == NULL || StringStr (sfp->comment, str) == NULL) {
+                  FFAddString_NoRedund (unique, prefix, str, NULL);
+                  prefix = "; ";
+                  add_period = FALSE;
+                }
+              }
+              break;
+
+            case Qual_class_trna_codons :
+              trna = qvp [jdx].trp;
+              if (trna) {
+                numcodons = ComposeCodonsRecognizedString (trna, numbuf, sizeof (numbuf));
+                if (numcodons < 1 || StringHasNoText (numbuf)) {
+                } else if (numcodons == 1) {
+                  isTRNA = TRUE;
+                  sprintf (buf, "codon recognized: %s", numbuf);
+                  if (StringStr (qvp [FTQUAL_seqfeat_note].str, buf) == NULL) {
+                    FFAddString_NoRedund (unique, prefix, "codon recognized: ", numbuf);
+                    prefix = "; ";
+                  }
+                } else {
+                  isTRNA = TRUE;
+                  FFAddString_NoRedund (unique, prefix, "codons recognized: ", numbuf);
+                  prefix = "; ";
+                  add_period = FALSE;
+                }
+              }
+              break;
+
+            case Qual_class_model_ev :
+              uop = qvp [jdx].uop;
+              if (uop != NULL) {
+                str = NULL;
+                VisitUserObjectsInUop (sfp->ext, (Pointer) &str, GetStrFormRNAEvidence);
+                if (! StringHasNoText (str)) {
+                  FFAddString_NoRedund (unique, prefix, str, NULL);
+                  prefix = "; ";
+                  add_period = FALSE;
+                }
+              }
+              break;
+
+            case Qual_class_seq_id :
+              sip = qvp [jdx].sip;
+              if (sip != NULL) {
+                /* should always be found above for protein_id or transcript_id
+                prod = BioseqFind (sip);
+                */
+                if (prod != NULL) {
+                  choice = 0;
+                  for (sip = prod->id; sip != NULL; sip = sip->next) {
+                    if (sip->choice == SEQID_GENBANK ||
+                        sip->choice == SEQID_EMBL ||
+                        sip->choice == SEQID_DDBJ ||
+                        sip->choice == SEQID_OTHER ||
+                        sip->choice == SEQID_TPG ||
+                        sip->choice == SEQID_TPE ||
+                        sip->choice == SEQID_TPD) {
+                      choice = sip->choice;
+                      if (SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
+                        FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
+                                          FALSE, FALSE, TILDE_IGNORE);
+                      }
+                    } else if (sip->choice == SEQID_GI) {
+                      if (choice == 0) {
+                        sprintf (seqid, "%ld", (long) sip->data.intvalue);
+                        FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
+                                          FALSE, FALSE, TILDE_IGNORE);
+                      }
+                    }
+                  }
+                } else {
+                  if (sip->choice == SEQID_GI) {
+                    gi = sip->data.intvalue;
+                    if (GetAccnVerFromServer (gi, seqid)) {
+                      if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
+                        FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
+                                          FALSE, FALSE, TILDE_IGNORE);
+                      }
+                    } else {
+                      sip = GetSeqIdForGI(gi);
+                      if (sip != NULL && SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
+                        if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
+                          FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
+                                          FALSE, FALSE, TILDE_IGNORE);
+                        }
+                      } else if (! ajp->flags.dropIllegalQuals) {
+                        sprintf (seqid, "%ld", (long) gi);
+                          FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
+                                          FALSE, FALSE, TILDE_IGNORE);
+                      }
+                    }
+                  } else if (SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
+                    if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
+                          FFAddTextToString(unique, prefix, "transcript found in: ", seqid,
+                                          FALSE, FALSE, TILDE_IGNORE);
+                    }
+                  }
+                }
+                prefix = "; ";
+                add_period = FALSE;
+              }
+              break;
+
+            default :
+              break;
+          }
+        }
+
+        if ( !FFEmpty(unique) ) {
+          notestr = FFToCharPtr(unique);
+          TrimSpacesAroundString (notestr);
+          if (add_period) {
+            if (! suppress_period) {
+              s_AddPeriodToEnd (notestr);
+            }
+          }
+
+#ifdef ASN2GNBK_STRIP_NOTE_PERIODS
+          if (! IsEllipsis (notestr))
+            s_RemovePeriodFromEnd (notestr);
+#endif
+    
+          FFAddOneString(ffstring, "/note=\"", FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString(ffstring, notestr, FALSE, TRUE, TILDE_EXPAND);
+          FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+
+          MemFree (notestr);
+          /*ValNodeFreeData (head);*/
+        }
+        break;
+
+      default:
+        break;
+
+    }
+  }
+  FFRecycleString(ajp, unique);
+}
+
+
+
+static void FF_asn2gb_www_featkey (
+  StringItemPtr ffstring,
+  CharPtr key,
+  SeqLocPtr slp,
+  Int4 from,
+  Int4 to,
+  Uint1 strand,
+  Uint4 itemID
+)
+
+{
+  BioseqPtr  bsp;
+  Int4       gi = 0;
+  SeqIdPtr   sip;
+  Boolean    is_aa = FALSE;
+  Char gi_buf[16];
+  Char itemID_buf[16];
+
+  bsp = BioseqFindFromSeqLoc (slp);
+  if (bsp != NULL) {
+    is_aa = ISA_aa (bsp->mol);
+    for (sip = bsp->id; sip != NULL; sip = sip->next) {
+      if (sip->choice == SEQID_GI) {
+        gi = (Int4) sip->data.intvalue;
+      }
+    }
+  }
+
+  sprintf(gi_buf, "%ld", (long)gi);
+  sprintf(itemID_buf, "%ld", (long)itemID);
+
+
+  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) {
+    FFAddOneString(ffstring, "&itemID=", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, itemID_buf, FALSE, FALSE, TILDE_IGNORE);
+  }
+  
+
+  if ( is_aa ) {
+    FFAddOneString(ffstring, "&view=gpwithparts>", FALSE, FALSE, TILDE_IGNORE);
+  } else {
+    FFAddOneString(ffstring, "&view=gbwithparts>", FALSE, FALSE, TILDE_IGNORE);
+  }
+
+  FFAddOneString(ffstring, key, FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+}
+
+
+NLM_EXTERN SeqIdPtr SeqLocIdForProduct (
+  SeqLocPtr product
+)
+
+{
+  SeqIdPtr   sip;
+  SeqLocPtr  slp;
+
+  /* in case product is a SEQLOC_EQUIV */
+
+  if (product == NULL) return NULL;
+  sip = SeqLocId (product);
+  if (sip != NULL) return sip;
+  slp = SeqLocFindNext (product, NULL);
+  while (slp != NULL) {
+    sip = SeqLocId (slp);
+    if (sip != NULL) return sip;
+    slp = SeqLocFindNext (product, slp);
+  }
+  return NULL;
+}
+
+NLM_EXTERN CharPtr goQualType [] = {
+  "", "Process", "Component", "Function", NULL
+};
+
+static void RecordGoFieldsInQVP (
+  UserFieldPtr ufp,
+  Pointer userdata
+)
+
+{
+  UserFieldPtr  entry;
+  Int2          i;
+  ObjectIdPtr   oip;
+  QualValPtr    qvp;
+
+  qvp = (QualValPtr) userdata;
+
+  if (ufp == NULL || ufp->choice != 11) return;
+  oip = ufp->label;
+  if (oip == NULL) return;
+  for (i = 0; goQualType [i] != NULL; i++) {
+    if (StringICmp (oip->str, goQualType [i]) == 0) break;
+  }
+  if (goQualType [i] == NULL) return;
+
+  entry = ufp->data.ptrvalue;
+  if (entry == NULL || entry->choice != 11) return;
+
+  /* ufp = (UserFieldPtr)  entry->data.ptrvalue; */
+  switch (i) {
+    case 1 :
+      qvp [FTQUAL_go_process].ufp = entry;
+      break;
+    case 2 :
+      qvp [FTQUAL_go_component].ufp = entry;
+      break;
+    case 3 :
+      qvp [FTQUAL_go_function].ufp = entry;
+      break;
+    default :
+      break;
+  }
+}
+
+static void RecordUserObjectsInQVP (
+  UserObjectPtr uop,
+  Pointer userdata
+)
+
+{
+  ObjectIdPtr  oip;
+  QualValPtr   qvp;
+
+  if (uop == NULL || userdata == NULL) return;
+  qvp = (QualValPtr) userdata;
+  oip = uop->type;
+  if (oip == NULL) return;
+  if (StringCmp (oip->str, "ModelEvidence") == 0) {
+    qvp [FTQUAL_modelev].uop = uop;
+  } else if (StringCmp (oip->str, "GeneOntology") == 0) {
+    VisitUserFieldsInUop (uop, (Pointer) qvp, RecordGoFieldsInQVP);
+  }
+}
+
+static void AddIntervalsToGbfeat (
+  GBFeaturePtr gbfeat,
+  SeqLocPtr location,
+  BioseqPtr target
+)
+
+{
+  Char           accn [41];
+  SeqLocPtr      copy = NULL;
+  Int4           from;
+  GBIntervalPtr  gbint;
+  Int4           gi;
+  GBIntervalPtr  last = NULL;
+  Int4           point;
+  SeqIntPtr      sint;
+  SeqIdPtr       sip;
+  SeqLocPtr      slp;
+  SeqPntPtr      spp;
+  Int4           to;
+  Int4           swap;
+
+  if (gbfeat == NULL || location == NULL) return;
+  if (target != NULL) {
+    copy = SeqLocMerge (target, location, NULL, FALSE, TRUE, FALSE);
+    location = copy;
+  }
+
+  slp = SeqLocFindNext (location, NULL);
+  while (slp != NULL) {
+    from = 0;
+    to = 0;
+    point = 0;
+    sip = NULL;
+    switch (slp->choice) {
+      case SEQLOC_WHOLE :
+        sip = (SeqIdPtr) slp->data.ptrvalue;
+        if (sip != NULL) {
+          from = 1;
+          to = SeqLocLen (slp);
+          if (to < 0) {
+            sip = NULL;
+          }
+        }
+        break;
+      case SEQLOC_INT :
+        sint = (SeqIntPtr) slp->data.ptrvalue;
+        if (sint != NULL) {
+          from = sint->from + 1;
+          to = sint->to + 1;
+          sip = sint->id;
+          if (sint->strand == Seq_strand_minus && from < to) {
+            swap = from;
+            from = to;
+            to = swap;
+          }
+        }
+        break;
+      case SEQLOC_PNT :
+        spp = (SeqPntPtr) slp->data.ptrvalue;
+        if (spp != NULL) {
+          point = spp->point + 1;
+          sip = spp->id;
+        }
+        break;
+      default :
+        break;
+    }
+    if (sip != NULL) {
+      accn [0] = '\0';
+      if (sip->choice == SEQID_GI) {
+        gi = sip->data.intvalue;
+        if (! GetAccnVerFromServer (gi, accn)) {
+          accn [0] = '\0';
+        }
+        if (StringHasNoText (accn)) {
+          sip = GetSeqIdForGI (gi);
+          SeqIdWrite (sip, accn, PRINTID_TEXTID_ACC_VER, sizeof (accn));
+          SeqIdFree (sip);
+        }
+      } else {
+        SeqIdWrite (sip, accn, PRINTID_TEXTID_ACC_VER, sizeof (accn));
+      }
+      if (! StringHasNoText (accn)) {
+        gbint = GBIntervalNew ();
+        if (gbint != NULL) {
+          gbint->from = from;
+          gbint->to = to;
+          gbint->point = point;
+          gbint->accession = StringSave (accn);
+          if (gbfeat->intervals == NULL) {
+            gbfeat->intervals = gbint;
+          } else {
+            last->next = gbint;
+          }
+          last = gbint;
+        }
+      }
+    }
+    slp = SeqLocFindNext (location, slp);
+  }
+
+  SeqLocFree (copy);
+}
+
+static void ParseException (
+  CharPtr original,
+  CharPtr PNTR exception_string,
+  CharPtr PNTR exception_note,
+  Boolean dropIllegalQuals,
+  Boolean isRefSeq
+)
+
+{
+  ValNodePtr  excpt = NULL, note = NULL, vnp;
+  Boolean     first, found;
+  Int2        i;
+  size_t      len;
+  CharPtr     ptr, str, tmp;
+
+  if (StringHasNoText (original) || exception_string == NULL || exception_note == NULL) return;
+
+  if (! dropIllegalQuals) {
+    *exception_string = StringSave (original);
+    return;
+  }
+
+  str = StringSave (original);
+  if (str == NULL) return;
+
+  tmp = str;
+  while (! StringHasNoText (tmp)) {
+    ptr = StringChr (tmp, ',');
+    if (ptr != NULL) {
+      *ptr = '\0';
+      ptr++;
+    }
+    TrimSpacesAroundString (tmp);
+    found = FALSE;
+    for (i = 0; validExceptionString [i] != NULL; i++) {
+      if (StringICmp (tmp, validExceptionString [i]) == 0) {
+        found = TRUE;
+        break;
+      }
+    }
+    if (! found) {
+      if (isRefSeq) {
+        for (i = 0; validRefSeqExceptionString [i] != NULL; i++) {
+          if (StringICmp (tmp, validRefSeqExceptionString [i]) == 0) {
+            found = TRUE;
+            break;
+          }
+        }
+      }
+    }
+    if (found) {
+      ValNodeCopyStr (&excpt, 0, tmp);
+    } else {
+      ValNodeCopyStr (&note, 0, tmp);
+    }
+    tmp = ptr;
+  }
+
+  if (excpt != NULL) {
+    for (vnp = excpt, len = 0; vnp != NULL; vnp = vnp->next) {
+      tmp = (CharPtr) vnp->data.ptrvalue;
+      len += StringLen (tmp) + 3;
+    }
+    ptr = (CharPtr) MemNew (len + 2);
+    if (ptr != NULL) {
+      for (vnp = excpt, first = TRUE; vnp != NULL; vnp = vnp->next) {
+        if (! first) {
+          StringCat (ptr, ", ");
+        }
+        tmp = (CharPtr) vnp->data.ptrvalue;
+        StringCat (ptr, tmp);
+        first = FALSE;
+      }
+    }
+    *exception_string = ptr;
+  }
+
+  if (note != NULL) {
+    for (vnp = note, len = 0; vnp != NULL; vnp = vnp->next) {
+      tmp = (CharPtr) vnp->data.ptrvalue;
+      len += StringLen (tmp) + 3;
+    }
+    ptr = (CharPtr) MemNew (len + 2);
+    if (ptr != NULL) {
+      for (vnp = note, first = TRUE; vnp != NULL; vnp = vnp->next) {
+        if (! first) {
+          StringCat (ptr, ", ");
+        }
+        tmp = (CharPtr) vnp->data.ptrvalue;
+        StringCat (ptr, tmp);
+        first = FALSE;
+      }
+    }
+    *exception_note = ptr;
+  }
+
+  ValNodeFreeData (excpt);
+  ValNodeFreeData (note);
+  MemFree (str);
+}
+
+static CharPtr FormatFeatureBlockEx (
+  IntAsn2gbJobPtr ajp,
+  Asn2gbSectPtr asp,
+  BioseqPtr bsp,
+  BioseqPtr target,
+  SeqFeatPtr sfp,
+  SeqMgrFeatContextPtr fcontext,
+  QualValPtr qvp,
+  FmtType format,
+  IntFeatBlockPtr ifp,
+  Boolean isProt,
+  Boolean doKey
+)
+
+{
+  Uint1              aa;
+  Int2               bondidx;
+  BioseqSetPtr       bssp;
+  Choice             cbaa;
+  CodeBreakPtr       cbp;
+  BioseqPtr          cdna;
+  SeqFeatPtr         cds;
+  Char               ch;
+  Uint1              code = Seq_code_ncbieaa;
+  CdRegionPtr        crp;
+  SeqMgrDescContext  dcontext;
+  Boolean            encode_prefix = FALSE;
+  CharPtr            exception_note = NULL;
+  CharPtr            exception_string = NULL;
+  Uint1              featdeftype;
+  Uint1              from;
+  GBQualPtr          gbq;
+  GBFeaturePtr       gbfeat = NULL;
+  GBSeqPtr           gbseq;
+  SeqMgrFeatContext  gcontext;
+  ValNodePtr         gcp;
+  SeqFeatPtr         gene = NULL;
+  ValNodePtr         gene_syn = NULL;
+  GeneRefPtr         grp;
+  IntCdsBlockPtr     icp;
+  Uint2              idx;
+  ValNodePtr         illegal = NULL;
+  ImpFeatPtr         imp = NULL;
+  IndxPtr            index;
+  Boolean            is_gps = FALSE;
+  Boolean            is_journalscan = FALSE;
+  Boolean            is_other = FALSE;
+  Uint4              itemID;
+  CharPtr            key = NULL;
+  CharPtr            lasttype = NULL;
+  Int4               left = -1;
+  SeqLocPtr          loc = NULL;
+  SeqLocPtr          location = NULL;
+  SeqLocPtr          locforgene = NULL;
+  SeqMgrFeatContext  mcontext;
+  MolInfoPtr         mip;
+  SeqFeatPtr         mrna;
+  SeqLocPtr          newloc;
+  Boolean            noLeft;
+  Boolean            noRight;
+  SeqMgrFeatContext  ocontext;
+  SeqEntryPtr        oldscope;
+  SeqFeatPtr         operon = NULL;
+  Uint2              partial;
+  SeqMgrFeatContext  pcontext;
+  BioseqPtr          prd;
+  CharPtr            precursor_comment = NULL;
+  BioseqPtr          prod = NULL;
+  SeqFeatPtr         prot;
+  Boolean            protein = FALSE;
+  Char               protein_pid_g [32];
+  ProtRefPtr         prp;
+  ProtRefPtr         prpxref;
+  Boolean            pseudo = FALSE;
+  CharPtr            ptr;
+  Int2               qualclass;
+  Uint1              residue;
+  Int4               right = -1;
+  RnaRefPtr          rrp;
+  SeqCodeTablePtr    sctp;
+  SeqDescrPtr        sdp;
+  SeqEntryPtr        sep;
+  Uint1              seqcode;
+  Uint1              shift;
+  SeqIdPtr           sip;
+  Int2               siteidx;
+  SeqMapTablePtr     smtp;
+  Boolean            split;
+  CharPtr            str;
+  Uint1              strand = Seq_strand_unknown;
+  CharPtr            tmp;
+  tRNAPtr            trna;
+  BioseqPtr          unlockme = NULL;
+  ValNodePtr         vnp;
+  StringItemPtr      ffstring;
+
+
+  if (ajp == NULL || fcontext == NULL || qvp == NULL || ifp == NULL) return NULL;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return NULL;
+
+  if (ajp->index && asp != NULL) {
+    index = &asp->index;
+  } else {
+    index = NULL;
+  }
+
+  if (ajp->gbseq && asp != NULL) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+  
+  protein_pid_g [0] = '\0';
+
+  itemID = fcontext->itemID;
+
+  if (doKey) {
+	/* may need to map location between aa and dna */
+  
+	if (ifp->mapToNuc) {
+  
+	  /* map mat_peptide, etc., to nucleotide coordinates */
+  
+	  sip = SeqLocId (sfp->location);
+	  prd = BioseqFind (sip);
+	  cds = SeqMgrGetCDSgivenProduct (prd, NULL);
+	  CheckSeqLocForPartial (sfp->location, &noLeft, &noRight);
+	  location = aaFeatLoc_to_dnaFeatLoc (cds, sfp->location);
+	  SetSeqLocPartial (location, noLeft, noRight);
+	  locforgene = location;
+	  loc = location;
+  
+	} else if (ifp->mapToProt) {
+  
+	  /* map CDS to protein product coordinates */
+  
+	  sip = SeqLocIdForProduct (sfp->product);
+	  prd = BioseqFind (sip);
+	  cds = SeqMgrGetCDSgivenProduct (prd, NULL);
+	  location = dnaLoc_to_aaLoc (cds, sfp->location, TRUE, NULL, FALSE);
+	  SetSeqLocPartial (location, FALSE, FALSE);
+	  locforgene = sfp->location;
+	  loc = location;
+  
+	} else if (ifp->mapToGen) {
+  
+	  /* map CDS from cDNA to genomic Bioseq */
+  
+	  cdna = BioseqFindFromSeqLoc (sfp->location);
+	  mrna = SeqMgrGetRNAgivenProduct (cdna, &mcontext);
+	  CheckSeqLocForPartial (sfp->location, &noLeft, &noRight);
+	  location = productLoc_to_locationLoc (mrna, sfp->location);
+	  SetSeqLocPartial (location, noLeft, noRight);
+	  locforgene = location;
+	  loc = location;
+  
+	} else if (ifp->mapToMrna) {
+  
+	  /* map gene from genomic to cDNA Bioseq */
+  
+	  sep = SeqMgrGetSeqEntryForData (bsp);
+	  location = CreateWholeInterval (sep);
+	  SetSeqLocPartial (location, FALSE, FALSE);
+	  locforgene = location;
+	  loc = location;
+  
+	} else if (ifp->mapToPep) {
+  
+	  /* map protein processing from precursor to subpeptide Bioseq */
+  
+	  sep = SeqMgrGetSeqEntryForData (bsp);
+	  location = CreateWholeInterval (sep);
+	  SetSeqLocPartial (location, FALSE, FALSE);
+	  locforgene = location;
+	  loc = location;
+  
+	} else {
+  
+	  /* no aa-dna or dna-aa mapping, just use location */
+  
+	  location = sfp->location;
+	  locforgene = sfp->location;
+	}
+	if (location == NULL) return NULL;
+  
+	sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
+	if (sep == NULL && IS_Bioseq_set (sep)) {
+	  bssp = (BioseqSetPtr) sep->data.ptrvalue;
+	  if (bssp != NULL && bssp->_class == BioseqseqSet_class_gen_prod_set) {
+		is_gps = TRUE;
+	  }
+	}
+
+    if (bsp != NULL) {
+	  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+	    if (sip->choice == SEQID_OTHER) {
+          is_other = TRUE;
+	    } else if (sip->choice == SEQID_GIBBSQ ||
+	  			 sip->choice == SEQID_GIBBMT ||
+		  		 sip->choice == SEQID_GIIM) {
+		  is_journalscan = TRUE;
+	    }
+	  }
+    }
+  
+	featdeftype = fcontext->featdeftype;
+	if (featdeftype < FEATDEF_GENE || featdeftype >= FEATDEF_MAX) {
+	  featdeftype = FEATDEF_BAD;
+	}
+	key = FindKeyFromFeatDefType (featdeftype, TRUE);
+  
+	if (format == GENPEPT_FMT && isProt) {
+	  if (featdeftype == FEATDEF_REGION) {
+		key = "Region";
+	  } else if (featdeftype == FEATDEF_BOND) {
+		key = "Bond";
+	  } else if (featdeftype == FEATDEF_SITE) {
+		key = "Site";
+	  }
+	  if (ifp->mapToPep) {
+		if (featdeftype >= FEATDEF_preprotein && featdeftype <= FEATDEF_transit_peptide_aa) {
+		  key = "Precursor";
+		  itemID = 0;
+		}
+	  }
+	}
+	if (! isProt) {
+	  if (featdeftype == FEATDEF_preprotein) {
+	    if (! is_other) {
+	      key = "misc_feature";
+	      encode_prefix = TRUE;
+	    }
+	  }
+	}
+  
+	/* deal with unmappable impfeats */
+  
+	if (featdeftype == FEATDEF_BAD && fcontext->seqfeattype == SEQFEAT_IMP) {
+	  imp = (ImpFeatPtr) sfp->data.value.ptrvalue;
+	  if (imp != NULL) {
+		key = imp->key;
+	  }
+	}
+  
+	FFStartPrint(ffstring, format, 5, 21, NULL, 0, 5, 21, "FT", /* ifp->firstfeat */ FALSE);
+	if (ajp->ajp.slp != NULL) {
+	  FFAddOneString(ffstring, key, FALSE, FALSE, TILDE_IGNORE);
+	} else if ( GetWWW(ajp) /* && SeqMgrGetParentOfPart (bsp, NULL) == NULL */ ) {
+	  FF_asn2gb_www_featkey (ffstring, key, sfp->location, fcontext->left + 1, fcontext->right + 1, fcontext->strand, itemID);
+	} else {
+	  FFAddOneString(ffstring, key, FALSE, FALSE, TILDE_IGNORE);
+	}
+	FFAddNChar(ffstring, ' ', 21 - 5 - StringLen(key), FALSE);
+  
+	if (gbseq != NULL) {
+	  gbfeat = GBFeatureNew ();
+	  if (gbfeat != NULL) {
+		gbfeat->key = StringSave (key);
+	  }
+	}
+  
+	if (imp == NULL || StringHasNoText (imp->loc)) {
+  
+	  
+	  if (ajp->ajp.slp != NULL) {
+		sip = SeqIdParse ("lcl|dummy");
+		left = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_LEFT_END);
+		right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END);
+		strand = SeqLocStrand (ajp->ajp.slp);
+		split = FALSE;
+		newloc = SeqLocReMapEx (sip, ajp->ajp.slp, location, 0, FALSE, ajp->masterStyle);
+		/*
+		newloc = SeqLocCopyRegion (sip, location, bsp, left, right, strand, &split);
+		*/
+		SeqIdFree (sip);
+		if (newloc == NULL) return NULL;
+		A2GBSeqLocReplaceID (newloc, ajp->ajp.slp);
+		str = FFFlatLoc (ajp, target, newloc, ajp->masterStyle);
+		SeqLocFree (newloc);
+	  } else {
+		str = FFFlatLoc (ajp, target, location, ajp->masterStyle);
+	  }
+	} else {
+	  str = StringSave (imp->loc);
+	}
+	if ( GetWWW(ajp) ) {
+	  FF_www_featloc (ffstring, str);
+	} else {
+	  FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
+	}
+  
+	if (gbseq != NULL) {
+	  if (gbfeat != NULL) {
+		gbfeat->location = StringSave (str);
+		if (ajp->masterStyle) {
+		  AddIntervalsToGbfeat (gbfeat, location, target);
+		} else {
+		  AddIntervalsToGbfeat (gbfeat, location, NULL);
+		}
+	  }
+	}
+  
+	MemFree (str);
+
+  } else {
+
+    location = sfp->location;
+    locforgene = sfp->location;
+  }
+
+  /* populate qualifier table from feature fields */
+
+  /*
+  if (sfp->partial == TRUE)
+    sfp->partial = FlatAnnotPartial(sfp, use_product);
+  */
+
+  if (sfp->partial) {
+    partial = SeqLocPartialCheck (location);
+    if (partial == SLP_COMPLETE /* || partial > SLP_OTHER */ ) {
+      qvp [FTQUAL_partial].ble = TRUE;
+    }
+    if (LookForFuzz (location)) {
+      qvp [FTQUAL_partial].ble = FALSE;
+    }
+    if (imp != NULL) {
+      if (StringChr (imp->loc, '<') != NULL || StringChr (imp->loc, '>') != NULL) {
+        qvp [FTQUAL_partial].ble = FALSE;
+      }
+    }
+
+    /* hide unclassified /partial in RELEASE_MODE and ENTREZ_MODE */
+
+    if (ajp->mode == RELEASE_MODE || ajp->mode == ENTREZ_MODE) {
+      qvp [FTQUAL_partial].ble = FALSE;
+    }
+    /*
+    if (ajp->flags.checkQualSyntax) {
+      switch (featdeftype) {
+      case FEATDEF_conflict:
+      case FEATDEF_mutation:
+      case FEATDEF_N_region:
+      case FEATDEF_polyA_site:
+        qvp [FTQUAL_partial].ble = FALSE;
+        break;
+      default:
+        break;
+      }
+    }
+    */
+  }
+  if (ifp->mapToProt) {
+    qvp [FTQUAL_partial].ble = FALSE;
+  }
+
+  if (sfp->pseudo) {
+    pseudo = TRUE;
+  }
+
+  if (fcontext->seqfeattype == SEQFEAT_GENE) {
+    grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+    if (grp != NULL) {
+      if (! StringHasNoText (grp->locus)) {
+        qvp [FTQUAL_gene].str = grp->locus;
+        qvp [FTQUAL_locus_tag].str = grp->locus_tag;
+        qvp [FTQUAL_gene_desc].str = grp->desc;
+        qvp [FTQUAL_gene_syn].vnp = grp->syn;
+      } else if (grp->locus_tag != NULL) {
+        qvp [FTQUAL_locus_tag].str = grp->locus_tag;
+        qvp [FTQUAL_gene_desc].str = grp->desc;
+        qvp [FTQUAL_gene_syn].vnp = grp->syn;
+      } else if (! StringHasNoText (grp->desc)) {
+        qvp [FTQUAL_gene].str = grp->desc;
+        qvp [FTQUAL_gene_syn].vnp = grp->syn;
+      } else if (grp->syn != NULL) {
+        vnp = grp->syn;
+        qvp [FTQUAL_gene].str = (CharPtr) vnp->data.ptrvalue;
+        vnp = vnp->next;
+        qvp [FTQUAL_gene_syn].vnp = vnp;
+      }
+      qvp [FTQUAL_gene_map].str = grp->maploc;
+      qvp [FTQUAL_gene_allele].str = grp->allele;
+      qvp [FTQUAL_gene_xref].vnp = grp->db;
+      if (grp->pseudo) {
+        pseudo = TRUE;
+      }
+    }
+    if (! ajp->flags.geneSynsToNote) {
+      qvp [FTQUAL_gene_syn_refseq].vnp = qvp [FTQUAL_gene_syn].vnp;
+      qvp [FTQUAL_gene_syn].vnp = NULL;
+    }
+    operon = SeqMgrGetOverlappingOperon (locforgene, &ocontext);
+    if (operon != NULL) {
+      for (gbq = operon->qual; gbq != NULL; gbq = gbq->next) {
+        if (StringCmp (gbq->qual, "operon") == 0) {
+          qvp [FTQUAL_operon].gbq = gbq;
+        }
+      }
+    }
+
+  } else {
+
+    grp = SeqMgrGetGeneXref (sfp);
+    if (grp != NULL) {
+      qvp [FTQUAL_gene_xref].vnp = grp->db;
+    }
+    if (grp == NULL) {
+      sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
+      oldscope = SeqEntrySetScope (sep);
+      gene = SeqMgrGetOverlappingGene (locforgene, &gcontext);
+      SeqEntrySetScope (oldscope);
+      if (gene != NULL) {
+        qvp [FTQUAL_gene_note].str = gene->comment;
+        grp = (GeneRefPtr) gene->data.value.ptrvalue;
+        if (gene->pseudo) {
+          pseudo = TRUE;
+        }
+        if (grp != NULL && grp->db != NULL) {
+          qvp [FTQUAL_gene_xref].vnp = grp->db;
+        } else {
+          qvp [FTQUAL_gene_xref].vnp = gene->dbxref;
+        }
+      }
+    }
+    if (grp != NULL && grp->pseudo) {
+      pseudo = TRUE;
+    }
+    if (grp != NULL && (! SeqMgrGeneIsSuppressed (grp)) &&
+        (fcontext->featdeftype != FEATDEF_repeat_region || gene == NULL)) {
+      if (! StringHasNoText (grp->locus)) {
+        qvp [FTQUAL_gene].str = grp->locus;
+        qvp [FTQUAL_locus_tag].str = grp->locus_tag;
+        gene_syn = grp->syn;
+      } else if (! StringHasNoText (grp->locus_tag)) {
+        qvp [FTQUAL_locus_tag].str = grp->locus_tag;
+        gene_syn = grp->syn;
+      } else if (! StringHasNoText (grp->desc)) {
+        qvp [FTQUAL_gene].str = grp->desc;
+        gene_syn = grp->syn;
+      } else if (grp->syn != NULL) {
+        vnp = grp->syn;
+        qvp [FTQUAL_gene].str = (CharPtr) vnp->data.ptrvalue;
+        vnp = vnp->next;
+        gene_syn = vnp;
+      }
+    }
+    if (grp != NULL && fcontext->featdeftype != FEATDEF_variation) {
+      qvp [FTQUAL_gene_allele].str = grp->allele; /* now propagating /allele */
+    }
+    if (fcontext->seqfeattype != SEQFEAT_CDREGION &&
+        fcontext->seqfeattype != SEQFEAT_RNA) {
+      qvp [FTQUAL_gene_xref].vnp = NULL;
+    }
+    if (fcontext->featdeftype != FEATDEF_operon) {
+      grp = SeqMgrGetGeneXref (sfp);
+      if (grp == NULL || (! SeqMgrGeneIsSuppressed (grp))) {
+        operon = SeqMgrGetOverlappingOperon (locforgene, &ocontext);
+        if (operon != NULL) {
+          for (gbq = operon->qual; gbq != NULL; gbq = gbq->next) {
+            if (StringCmp (gbq->qual, "operon") == 0) {
+              qvp [FTQUAL_operon].gbq = gbq;
+            }
+          }
+        }
+      }
+    }
+
+    /* specific fields set here */
+
+    switch (fcontext->seqfeattype) {
+      case SEQFEAT_CDREGION :
+        if (! ifp->mapToProt) {
+          crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+          if (crp != NULL) {
+
+            qvp [FTQUAL_codon_start].num = crp->frame;
+            if (qvp [FTQUAL_codon_start].num == 0) {
+              qvp [FTQUAL_codon_start].num = 1;
+            }
+            qvp [FTQUAL_transl_except].cbp = crp->code_break;
+            for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
+              seqcode = 0;
+              sctp = NULL;
+              cbaa = cbp->aa;
+              switch (cbaa.choice) {
+                case 1 :
+                  seqcode = Seq_code_ncbieaa;
+                  break;
+                case 2 :
+                  seqcode = Seq_code_ncbi8aa;
+                  break;
+                case 3 :
+                  seqcode = Seq_code_ncbistdaa;
+                  break;
+                default :
+                  break;
+              }
+              if (seqcode != 0) {
+                sctp = SeqCodeTableFind (seqcode);
+                if (sctp != NULL) {
+                  residue = cbaa.value.intvalue;
+                  if (residue != 42) {
+                    if (seqcode != Seq_code_ncbieaa) {
+                      smtp = SeqMapTableFind (seqcode, Seq_code_ncbieaa);
+                      residue = SeqMapTableConvert (smtp, residue);
+                    }
+                    if (residue == 'U') {
+                      if (ajp->flags.selenocysteineToNote) {
+                        qvp [FTQUAL_selenocysteine_note].str = "selenocysteine";
+                      } else {
+                        qvp [FTQUAL_selenocysteine].ble = TRUE;
+                      }
+                    }
+                  }
+                }
+              }
+            }
+
+            gcp = crp->genetic_code;
+            if (gcp != NULL) {
+              for (vnp = gcp->data.ptrvalue; vnp != NULL; vnp = vnp->next) {
+                if (vnp->choice == 2 && vnp->data.intvalue != 0) {
+                  qvp [FTQUAL_transl_table].num = vnp->data.intvalue;
+                }
+              }
+
+              /* suppress table 1, but always show it in GBSeqXML */
+
+              if (qvp [FTQUAL_transl_table].num == 1 && ajp->gbseq == NULL) {
+                qvp [FTQUAL_transl_table].num = 0;
+              }
+            }
+
+            if (sfp->product != NULL && SeqLocLen (sfp->product) != 0) {
+              protein = TRUE;
+            }
+            if (crp->conflict && (protein || (! sfp->excpt))) {
+              if (protein) {
+                qvp [FTQUAL_prot_conflict].str = conflict_msg;
+              } else {
+                /*
+                qvp [FTQUAL_prot_missing].str = no_protein_msg;
+                */
+              }
+            }
+          }
+
+          sip = SeqLocIdForProduct (sfp->product);
+          qvp [FTQUAL_protein_id].sip = sip;
+
+          sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
+
+          if (! ajp->alwaysTranslCds) {
+
+            /* by default only show /translation if product bioseq is within entity */
+
+            oldscope = SeqEntrySetScope (sep);
+            prod = BioseqFind (sip);
+            SeqEntrySetScope (oldscope);
+
+            if (prod == NULL && ajp->showFarTransl) {
+
+              /* but flag can override and force far /translation */
+
+              prod = BioseqLockById (sip);
+              unlockme = prod;
+            }
+          }
+
+          prp = NULL;
+
+          if (prod != NULL) {
+            for (sip = prod->id; sip != NULL; sip = sip->next) {
+              if (sip->choice == SEQID_GI) {
+                sprintf (protein_pid_g, "PID:g%ld", (long) sip->data.intvalue);
+              }
+            }
+            sdp = SeqMgrGetNextDescriptor (prod, NULL, Seq_descr_comment, &dcontext);
+            if (sdp != NULL && dcontext.level == 0) {
+              if (! StringHasNoText ((CharPtr) sdp->data.ptrvalue)) {
+                qvp [FTQUAL_prot_comment].str = (CharPtr) sdp->data.ptrvalue;
+              }
+            }
+            sdp = SeqMgrGetNextDescriptor (prod, NULL, Seq_descr_molinfo, &dcontext);
+            if (sdp != NULL && dcontext.level == 0) {
+              mip = (MolInfoPtr) sdp->data.ptrvalue;
+              if (mip != NULL && mip->tech > 1 &&
+                  mip->tech != MI_TECH_concept_trans &&
+                  mip->tech != MI_TECH_concept_trans_a) {
+                str = StringForSeqTech (mip->tech);
+                if (! StringHasNoText (str)) {
+                  qvp [FTQUAL_prot_method].str = str;
+                }
+              }
+            }
+            prot = SeqMgrGetBestProteinFeature (prod, &pcontext);
+            if (prot != NULL) {
+              prp = (ProtRefPtr) prot->data.value.ptrvalue;
+              if (prp != NULL && prp->processed < 2) {
+                qvp [FTQUAL_prot_note].str = prot->comment;
+              }
+            }
+          }
+
+          /* protein xref overrides names, but should not prevent /protein_id, etc. */
+
+          prpxref = SeqMgrGetProtXref (sfp);
+          if (prpxref != NULL) {
+            prp = prpxref;
+          }
+          if (prp != NULL) {
+            vnp = prp->name;
+            if (vnp != NULL && (! StringHasNoText ((CharPtr) vnp->data.ptrvalue))) {
+              qvp [FTQUAL_cds_product].str = (CharPtr) vnp->data.ptrvalue;
+              vnp = vnp->next;
+              qvp [FTQUAL_prot_names].vnp = vnp;
+            }
+            qvp [FTQUAL_prot_desc].str = prp->desc;
+            qvp [FTQUAL_prot_activity].vnp = prp->activity;
+            qvp [FTQUAL_prot_EC_number].vnp = prp->ec;
+          }
+
+          if (! pseudo) {
+            if (prod != NULL || ajp->transIfNoProd || ajp->alwaysTranslCds) {
+              if (doKey) {
+                qvp [FTQUAL_translation].ble = TRUE;
+              }
+            }
+          }
+
+          if (ifp->isCDS) {
+            icp = (IntCdsBlockPtr) ifp;
+            qvp [FTQUAL_figure].str = icp->fig;
+            qvp [FTQUAL_maploc].str = icp->maploc;
+          }
+        } else {
+          qvp [FTQUAL_coded_by].slp = sfp->location;
+
+          crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+          if (crp != NULL) {
+            gcp = crp->genetic_code;
+            if (gcp != NULL) {
+              for (vnp = gcp->data.ptrvalue; vnp != NULL; vnp = vnp->next) {
+                if (vnp->choice == 2 && vnp->data.intvalue != 0) {
+                  qvp [FTQUAL_transl_table].num = vnp->data.intvalue;
+                }
+              }
+
+              /* suppress table 1 */
+
+              if (qvp [FTQUAL_transl_table].num == 1) {
+                qvp [FTQUAL_transl_table].num = 0;
+              }
+            }
+            for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
+              seqcode = 0;
+              sctp = NULL;
+              cbaa = cbp->aa;
+              switch (cbaa.choice) {
+                case 1 :
+                  seqcode = Seq_code_ncbieaa;
+                  break;
+                case 2 :
+                  seqcode = Seq_code_ncbi8aa;
+                  break;
+                case 3 :
+                  seqcode = Seq_code_ncbistdaa;
+                  break;
+                default :
+                  break;
+              }
+              if (seqcode != 0) {
+                sctp = SeqCodeTableFind (seqcode);
+                if (sctp != NULL) {
+                  residue = cbaa.value.intvalue;
+                  if (residue != 42) {
+                    if (seqcode != Seq_code_ncbieaa) {
+                      smtp = SeqMapTableFind (seqcode, Seq_code_ncbieaa);
+                      residue = SeqMapTableConvert (smtp, residue);
+                    }
+                    if (residue == 'U') {
+                      if (ajp->flags.selenocysteineToNote) {
+                        qvp [FTQUAL_selenocysteine_note].str = "selenocysteine";
+                      } else {
+                        qvp [FTQUAL_selenocysteine].ble = TRUE;
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+        break;
+      case SEQFEAT_PROT :
+        if (! ifp->mapToPep) {
+          prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+          if (prp != NULL) {
+            vnp = prp->name;
+            if (vnp != NULL && (! StringHasNoText ((CharPtr) vnp->data.ptrvalue))) {
+              qvp [FTQUAL_product].str = (CharPtr) vnp->data.ptrvalue;
+              vnp = vnp->next;
+              qvp [FTQUAL_prot_names].vnp = vnp;
+            }
+            if (format != GENPEPT_FMT) {
+              qvp [FTQUAL_prot_desc].str = prp->desc;
+            } else {
+              qvp [FTQUAL_prot_name].str = prp->desc;
+            }
+            if (format != GENPEPT_FMT || prp->processed != 2) {
+              qvp [FTQUAL_prot_activity].vnp = prp->activity;
+            }
+            qvp [FTQUAL_prot_EC_number].vnp = prp->ec;
+          }
+          sip = SeqLocIdForProduct (sfp->product);
+          if (sip != NULL) {
+            /* for RefSeq records or GenBank not release_mode */
+            if (is_other || (! ajp->flags.forGbRelease)) {
+              qvp [FTQUAL_protein_id].sip = sip;
+            }
+            prod = BioseqFind (sip);
+          }
+        } else {
+          qvp [FTQUAL_derived_from].slp = sfp->location;
+          sip = SeqLocIdForProduct (sfp->product);
+          if (sip != NULL) {
+            prod = BioseqFind (sip);
+            if (prod != NULL) {
+              prot = SeqMgrGetBestProteinFeature (prod, NULL);
+              if (prot != NULL) {
+                precursor_comment = prot->comment;
+              }
+            }
+          }
+        }
+        prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+        if (prp != NULL) {
+          if (! pseudo) {
+            if (ajp->showPeptide) {
+              if (prp->processed == 2 || prp->processed == 3 || prp->processed == 4) {
+                qvp [FTQUAL_peptide].ble = TRUE;
+              }
+            }
+          }
+          if (prp->processed == 3 || prp->processed == 4) {
+            if (! is_other) {
+              /* Only RefSeq allows product on signal or transit peptide */
+              qvp [FTQUAL_product].str = NULL;
+            }
+          }
+          if (prp->processed == 1 && encode_prefix && (! is_other)) {
+            qvp [FTQUAL_encodes].str = qvp [FTQUAL_product].str;
+            qvp [FTQUAL_product].str = NULL;
+          }
+        }
+        break;
+      case SEQFEAT_RNA :
+        rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+        if (rrp != NULL) {
+          if (rrp->pseudo) {
+            pseudo = TRUE;
+          }
+          if (rrp->type == 2) {
+            sip = SeqLocIdForProduct (sfp->product);
+            if (sip != NULL) {
+              /* for RefSeq records or GenBank not release_mode or entrez_mode */
+              if (is_other || (ajp->mode == SEQUIN_MODE || ajp->mode == DUMP_MODE)) {
+                qvp [FTQUAL_transcript_id].sip = sip;
+              } else {
+                /* otherwise now goes in note */
+                qvp [FTQUAL_transcript_id_note].sip = sip; /* !!! remove October 15, 2003 !!! */
+              }
+              prod = BioseqFind (sip);
+            }
+            if (! pseudo) {
+              if (ajp->showTranscript) {
+                qvp [FTQUAL_transcription].ble = TRUE;
+              }
+            }
+          }
+          if (rrp->type == 3) {
+            if (rrp->ext.choice == 1) {
+              /* amino acid could not be parsed into structured form */
+              if (! ajp->flags.dropIllegalQuals) {
+                str = (CharPtr) rrp->ext.value.ptrvalue;
+                qvp [FTQUAL_product].str = str;
+              } else {
+                qvp [FTQUAL_product].str = "tRNA-OTHER";
+              }
+            } else if (rrp->ext.choice == 2) {
+              trna = (tRNAPtr) rrp->ext.value.ptrvalue;
+              if (trna != NULL) {
+                aa = 0;
+                if (trna->aatype == 2) {
+                  aa = trna->aa;
+                } else {
+                  from = 0;
+                  switch (trna->aatype) {
+                    case 0 :
+                      from = 0;
+                      break;
+                    case 1 :
+                      from = Seq_code_iupacaa;
+                      break;
+                    case 2 :
+                      from = Seq_code_ncbieaa;
+                      break;
+                    case 3 :
+                      from = Seq_code_ncbi8aa;
+                      break;
+                    case 4 :
+                      from = Seq_code_ncbistdaa;
+                      break;
+                    default:
+                      break;
+                  }
+                  if (ajp->flags.iupacaaOnly) {
+                    code = Seq_code_iupacaa;
+                  } else {
+                    code = Seq_code_ncbieaa;
+                  }
+                  smtp = SeqMapTableFind (code, from);
+                  if (smtp != NULL) {
+                    aa = SeqMapTableConvert (smtp, trna->aa);
+                    if (aa == 255 && from == Seq_code_iupacaa && trna->aa == 'U') {
+                      aa = 'U';
+                    }
+                  }
+                }
+                if (ajp->flags.iupacaaOnly) {
+                  smtp = SeqMapTableFind (Seq_code_iupacaa, Seq_code_ncbieaa);
+                  if (smtp != NULL) {
+                    aa = SeqMapTableConvert (smtp, trna->aa);
+                  } else {
+                    aa = 'X';
+                  }
+                }
+                if (aa > 0 && aa != 255) {
+                  if (aa <= 74) {
+                    shift = 0;
+                  } else if (aa > 79) {
+                    shift = 2;
+                  } else {
+                    shift = 1;
+                  }
+                  if (aa != '*') {
+                    idx = aa - (64 + shift);
+                  } else {
+                    idx = 25;
+                  }
+                  if (idx > 0 && idx < 26) {
+                    str = trnaList [idx];
+                    qvp [FTQUAL_product].str = str;
+                    if (StringNICmp (str, "tRNA-", 5) == 0) {
+                      qvp [FTQUAL_trna_aa].str = str + 5;
+                    }
+                  }
+                }
+                qvp [FTQUAL_anticodon].slp = trna->anticodon;
+                qvp [FTQUAL_trna_codons].trp = trna;
+              }
+            }
+          } else {
+            if (rrp->ext.choice == 1) {
+              str = (CharPtr) rrp->ext.value.ptrvalue;
+              qvp [FTQUAL_product].str = str;
+
+              /*
+              if (rrp->type == 255 && (! StringHasNoText (str))) {
+                if        (StringICmp (str, "internal transcribed spacer 1") == 0 ||
+                           StringICmp (str, "internal transcribed spacer ITS1") == 0 ||
+                           StringICmp (str, "ITS1") == 0) {
+                  qvp [FTQUAL_rrna_its].str = "ITS1";
+                } else if (StringICmp (str, "internal transcribed spacer 2") == 0 ||
+                           StringICmp (str, "internal transcribed spacer ITS2") == 0 ||
+                           StringICmp (str, "ITS2") == 0) {
+                  qvp [FTQUAL_rrna_its].str = "ITS2";
+                } else if (StringICmp (str, "internal transcribed spacer 3") == 0 ||
+                           StringICmp (str, "internal transcribed spacer ITS3") == 0 ||
+                           StringICmp (str, "ITS3") == 0) {
+                  qvp [FTQUAL_rrna_its].str = "ITS3";
+                }
+              }
+              */
+            }
+          }
+        }
+        break;
+      case SEQFEAT_REGION :
+        if (format == GENPEPT_FMT && featdeftype == FEATDEF_REGION && isProt) {
+          qvp [FTQUAL_region_name].str = (CharPtr) sfp->data.value.ptrvalue;
+        } else {
+          qvp [FTQUAL_region].str = (CharPtr) sfp->data.value.ptrvalue;
+        }
+        break;
+      case SEQFEAT_COMMENT :
+        break;
+      case SEQFEAT_BOND :
+        bondidx = (Int2) sfp->data.value.intvalue;
+        if (bondidx == 255) {
+          bondidx = 5;
+        }
+        if (bondidx > 0 && bondidx < 6) {
+          if (format == GENPEPT_FMT && isProt) {
+            qvp [FTQUAL_bond_type].str = bondList [bondidx];
+          } else {
+            qvp [FTQUAL_bond].str = bondList [bondidx];
+          }
+        }
+        break;
+      case SEQFEAT_SITE :
+        siteidx = (Int2) sfp->data.value.intvalue;
+        if (siteidx == 255) {
+          siteidx = 26;
+        }
+        if (siteidx > 0 && siteidx < 27) {
+          if (format == GENPEPT_FMT && isProt) {
+            qvp [FTQUAL_site_type].str = siteList [siteidx];
+          } else {
+            qvp [FTQUAL_site].str = siteList [siteidx];
+          }
+        }
+        break;
+      case SEQFEAT_PSEC_STR :
+        qvp [FTQUAL_sec_str_type].num = sfp->data.value.intvalue;
+        break;
+      case SEQFEAT_HET :
+        qvp [FTQUAL_heterogen].str = (CharPtr) sfp->data.value.ptrvalue;
+        break;
+      default :
+        break;
+    }
+  }
+
+  /* common fields set here */
+
+  VisitUserObjectsInUop (sfp->ext, (Pointer) qvp, RecordUserObjectsInQVP);
+
+  if (fcontext->featdeftype == FEATDEF_repeat_region) {
+    pseudo = FALSE;
+  }
+
+  qvp [FTQUAL_pseudo].ble = pseudo;
+
+  qvp [FTQUAL_seqfeat_note].str = sfp->comment;
+
+  /* if RELEASE_MODE, check list of features that can have /pseudo */
+
+  if (ajp->flags.dropIllegalQuals && pseudo  &&
+      (fcontext->seqfeattype == SEQFEAT_RNA || fcontext->seqfeattype == SEQFEAT_IMP) ) {
+    switch (featdeftype) {
+
+    case  FEATDEF_allele:
+    case  FEATDEF_attenuator:
+    case  FEATDEF_CAAT_signal:
+    case  FEATDEF_conflict:
+    case  FEATDEF_D_loop:
+    case  FEATDEF_enhancer:
+    case  FEATDEF_GC_signal:
+    case  FEATDEF_iDNA:
+    case  FEATDEF_intron:
+    case  FEATDEF_LTR:
+    case  FEATDEF_misc_binding:
+    case  FEATDEF_misc_difference:
+    case  FEATDEF_misc_recomb:
+    case  FEATDEF_misc_RNA:
+    case  FEATDEF_misc_signal:
+    case  FEATDEF_misc_structure:
+    case  FEATDEF_modified_base:
+    case  FEATDEF_mutation:
+    case  FEATDEF_old_sequence:
+    case  FEATDEF_polyA_signal:
+    case  FEATDEF_polyA_site:
+    case  FEATDEF_precursor_RNA:
+    case  FEATDEF_prim_transcript:
+    case  FEATDEF_primer_bind:
+    case  FEATDEF_protein_bind:
+    case  FEATDEF_RBS:
+    case  FEATDEF_repeat_region:
+    case  FEATDEF_repeat_unit:
+    case  FEATDEF_rep_origin:
+    case  FEATDEF_satellite:
+    case  FEATDEF_stem_loop:
+    case  FEATDEF_STS:
+    case  FEATDEF_TATA_signal:
+    case  FEATDEF_terminator:
+    case  FEATDEF_unsure:
+    case  FEATDEF_variation:
+    case  FEATDEF_3clip:
+    case  FEATDEF_3UTR:
+    case  FEATDEF_5clip:
+    case  FEATDEF_5UTR:
+    case  FEATDEF_10_signal:
+    case  FEATDEF_35_signal:
+      qvp [FTQUAL_pseudo].ble = FALSE;
+        break;
+    default:
+        break;
+    }
+  }
+
+  if (format != GENPEPT_FMT) {
+    qvp [FTQUAL_evidence].num = sfp->exp_ev;
+  }
+
+  /* exception currently legal only on CDS */
+
+  if ((! ajp->flags.dropIllegalQuals) || fcontext->seqfeattype == SEQFEAT_CDREGION) {
+    qvp [FTQUAL_exception].str = sfp->except_text;
+
+    if (sfp->excpt && qvp [FTQUAL_exception].str == NULL) {
+      if (qvp [FTQUAL_seqfeat_note].str != NULL) {
+        if (ajp->flags.dropIllegalQuals &&
+            (! StringInStringList (qvp [FTQUAL_seqfeat_note].str, validExceptionString))) {
+        /* !!! if ajp->flags.dropIllegalQuals, check CDS list to avoid losing note !!! */
+          qvp [FTQUAL_exception].str = NULL;
+        } else {
+          /* if no /exception text, use text in comment, remove from /note */
+
+          qvp [FTQUAL_exception].str = qvp [FTQUAL_seqfeat_note].str;
+          qvp [FTQUAL_seqfeat_note].str = NULL;
+        }
+      } else {
+        qvp [FTQUAL_exception].str = "No explanation supplied";
+      }
+
+      /* !!! if ajp->flags.dropIllegalQuals, check CDS list here as well !!! */
+      if (ajp->flags.dropIllegalQuals &&
+          (! StringInStringList (qvp [FTQUAL_seqfeat_note].str, validExceptionString))) {
+        qvp [FTQUAL_exception].str = NULL;
+      }
+    }
+    if (ajp->flags.dropIllegalQuals) {
+      str = qvp [FTQUAL_exception].str;
+      ParseException (str, &exception_string, &exception_note, TRUE, is_other);
+      qvp [FTQUAL_exception].str = exception_string;
+      qvp [FTQUAL_exception_note].str = exception_note;
+      /*
+      if (is_other) {
+        if (! StringInStringList (qvp [FTQUAL_exception].str, validRefSeqExceptionString)) {
+          qvp [FTQUAL_exception_note].str = qvp [FTQUAL_exception].str;
+          qvp [FTQUAL_exception].str = NULL;
+        }
+      } else {
+        if (! StringInStringList (qvp [FTQUAL_exception].str, validExceptionString)) {
+          qvp [FTQUAL_exception_note].str = qvp [FTQUAL_exception].str;
+          qvp [FTQUAL_exception].str = NULL;
+        }
+      }
+      */
+    }
+  } else {
+    qvp [FTQUAL_exception_note].str = sfp->except_text;
+  }
+  if (StringHasNoText (qvp [FTQUAL_exception].str)) {
+    qvp [FTQUAL_exception].str = NULL;
+  }
+  if (StringHasNoText (qvp [FTQUAL_exception_note].str)) {
+    qvp [FTQUAL_exception_note].str = NULL;
+  }
+
+  qvp [FTQUAL_db_xref].vnp = sfp->dbxref;
+  qvp [FTQUAL_citation].vnp = sfp->cit;
+
+  /* /product same as sfp->comment will suppress /note */
+
+  if (! StringHasNoText (qvp [FTQUAL_product].str) &&
+      StringICmp (sfp->comment, qvp [FTQUAL_product].str) == 0) {
+    qvp [FTQUAL_seqfeat_note].str = NULL;
+  }
+  /* case sensitive AJ011317.1 */
+  if (! StringHasNoText (qvp [FTQUAL_cds_product].str) &&
+      StringCmp (sfp->comment, qvp [FTQUAL_cds_product].str) == 0) {
+    qvp [FTQUAL_seqfeat_note].str = NULL;
+  }
+
+  /* /gene same as sfp->comment will suppress /note */
+  /* case sensitive -gi|6572973|gb|AF195052.1|AF195052 */
+
+  if (! StringHasNoText (qvp [FTQUAL_gene].str) &&
+      StringCmp (sfp->comment, qvp [FTQUAL_gene].str) == 0) {
+    qvp [FTQUAL_seqfeat_note].str = NULL;
+  }
+
+  /* gene /note same as sfp->comment will suppress /note - U92435.1 says do not do this */
+
+  /*
+  if (! StringHasNoText (qvp [FTQUAL_gene_note].str) &&
+      StringICmp (sfp->comment, qvp [FTQUAL_gene_note].str) == 0) {
+    qvp [FTQUAL_seqfeat_note].str = NULL;
+  }
+  */
+
+  /* if site sfp->comment contains site name, suppress site in /note */
+
+  if (! StringHasNoText (qvp [FTQUAL_site].str) &&
+      StringStr (sfp->comment, qvp [FTQUAL_site].str) != NULL) {
+    qvp [FTQUAL_site].str = NULL;
+  }
+
+  /* /EC_number same as sfp->comment will suppress /note */
+
+  for (vnp = qvp [FTQUAL_prot_EC_number].vnp; vnp != NULL; vnp = vnp->next) {
+    str = (CharPtr) vnp->data.ptrvalue;
+    if ((! StringHasNoText (str)) &&
+        StringICmp (sfp->comment, str) == 0) {
+      qvp [FTQUAL_seqfeat_note].str = NULL;
+    }
+  }
+
+  /* mat_peptide precursor same as sfp->comment will suppress /note in GenPept */
+
+  if (precursor_comment != NULL && StringCmp (precursor_comment, sfp->comment) == 0) {
+    qvp [FTQUAL_seqfeat_note].str = NULL;
+  }
+
+
+  /* now go through gbqual list */
+
+  for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
+    idx = GbqualToFeaturIndex (gbq->qual);
+    if (idx > 0 && idx < ASN2GNBK_TOTAL_FEATUR) {
+      if (qvp [idx].gbq == NULL) {
+        if (idx == FTQUAL_product_quals) {
+          if (qvp [FTQUAL_product].str == NULL) {
+            qvp [FTQUAL_product].str = gbq->val;
+          } else if (qvp [FTQUAL_xtra_prod_quals].gbq == NULL) {
+            /* chain will include remaining product gbquals */
+            qvp [FTQUAL_xtra_prod_quals].gbq = gbq;
+          }
+        } else {
+          qvp [idx].gbq = gbq;
+        }
+      }
+
+    } else if (idx == 0) {
+
+      qualclass = IllegalGbqualToClass (gbq->qual);
+      if (qualclass == 0) {
+        qualclass = Qual_class_quote;
+      }
+      tmp = StringSave (gbq->val);
+      if (tmp != NULL) {
+        str = MemNew (sizeof (Char) * (StringLen (gbq->qual) + StringLen (tmp) + 10));
+        if (str != NULL) {
+          if (qualclass == Qual_class_quote) {
+            if (StringIsJustQuotes (tmp)) {
+              sprintf (str, "/%s", gbq->qual);
+            } else {
+              ptr = tmp;
+              ch = *ptr;
+              while (ch != '\0') {
+                if (ch == '"') {
+                  *ptr = '\'';
+                }
+                ptr++;
+                ch = *ptr;
+              }
+              sprintf (str, "/%s=\"%s\"", gbq->qual, tmp);
+            }
+            ValNodeCopyStr (&illegal, 0, str);
+          } else if (qualclass == Qual_class_noquote || qualclass == Qual_class_label) {
+            if (StringIsJustQuotes (tmp)) {
+              sprintf (str, "/%s", gbq->qual);
+            } else {
+              sprintf (str, "/%s=%s", gbq->qual, tmp);
+            }
+            ValNodeCopyStr (&illegal, 0, str);
+          }
+          MemFree (str);
+        }
+        MemFree (tmp);
+      }
+    }
+  }
+
+  /* illegal qualifiers are copied and formatted in valnode chain */
+
+  if (! ajp->flags.dropIllegalQuals) {
+    qvp [FTQUAL_illegal_qual].vnp = illegal;
+  }
+
+  /* remove protein description that equals the gene name, case sensitive */
+
+  if (StringCmp (qvp [FTQUAL_gene].str, qvp [FTQUAL_prot_desc].str) == 0) {
+    qvp [FTQUAL_prot_desc].str = NULL;
+  }
+
+  /* remove protein description that equals the cds product, case sensitive */
+
+  if (StringCmp (qvp [FTQUAL_cds_product].str, qvp [FTQUAL_prot_desc].str) == 0) {
+    qvp [FTQUAL_prot_desc].str = NULL;
+  }
+
+  /* remove comment contained in prot_desc - gi|4530123|gb|AF071539.1|AF071539 */
+
+  if (StringStr (qvp [FTQUAL_prot_desc].str, qvp [FTQUAL_seqfeat_note].str) != NULL) {
+    qvp [FTQUAL_seqfeat_note].str = NULL;
+  }
+
+  /* remove protein description that equals the standard name */
+
+  if (qvp [FTQUAL_standard_name].gbq != NULL && qvp [FTQUAL_prot_desc].str != NULL) {
+    gbq = qvp [FTQUAL_standard_name].gbq;
+    lasttype = gbq->qual;
+    while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
+      if (StringICmp (gbq->val, qvp [FTQUAL_prot_desc].str) == 0) {
+        qvp [FTQUAL_prot_desc].str = NULL;
+      }
+      gbq = gbq->next;
+    }
+  }
+
+  /* remove protein description that equals a gene synonym - case insensitive AF109216.1 */
+
+  for (vnp = gene_syn; vnp != NULL; vnp = vnp->next) {
+    str = (CharPtr) vnp->data.ptrvalue;
+    if ((! StringHasNoText (str)) &&
+        StringCmp (str, qvp [FTQUAL_prot_desc].str) == 0) {
+      /* NC_001823 leave in prot_desc if no cds_product */
+      if (qvp [FTQUAL_cds_product].str != NULL) {
+        qvp [FTQUAL_prot_desc].str = NULL;
+      }
+    }
+  }
+
+  /* remove comment that equals a gene synonym */
+
+  if (format != GENPEPT_FMT && (! ifp->mapToProt)) {
+    for (vnp = gene_syn; vnp != NULL; vnp = vnp->next) {
+      str = (CharPtr) vnp->data.ptrvalue;
+      if ((! StringHasNoText (str)) &&
+          StringICmp (str, qvp [FTQUAL_seqfeat_note].str) == 0) {
+        qvp [FTQUAL_seqfeat_note].str = NULL;
+      }
+    }
+  }
+
+  /* remove protein comment descriptor that equals the protein note */
+
+  if (StringCmp (qvp [FTQUAL_prot_note].str, qvp [FTQUAL_prot_comment].str) == 0) {
+    qvp [FTQUAL_prot_comment].str = NULL;
+  }
+
+  /* suppress cds comment if a subset of protein note - AF002218.1 */
+
+  if (StringStr (qvp [FTQUAL_prot_note].str, qvp [FTQUAL_seqfeat_note].str) != NULL) {
+    qvp [FTQUAL_seqfeat_note].str = NULL;
+  }
+
+  /* suppress selenocysteine note if already in comment */
+
+  if (StringStr (sfp->comment, "selenocysteine") != NULL) {
+    qvp [FTQUAL_selenocysteine_note].str = NULL;
+  }
+
+  /* if /allele inherited from gene, suppress allele gbqual on feature */
+
+  if (qvp [FTQUAL_gene_allele].str != NULL) {
+    qvp [FTQUAL_allele].gbq = NULL;
+  }
+
+  /* now print qualifiers from table */
+
+#ifdef DISPLAY_STRINGS
+  s_DisplayQVP(qvp, feat_note_order);
+#endif
+
+  /* Strip duplicate notes */
+
+  if ((StringCmp(qvp[FTQUAL_product].str,
+         qvp[FTQUAL_seqfeat_note].str) == 0)) {
+    qvp[FTQUAL_seqfeat_note].str = NULL;
+  }
+
+  if ((qvp[FTQUAL_standard_name].gbq != NULL) &&
+      (qvp[FTQUAL_standard_name].gbq->val != NULL)) {
+    if ((StringCmp(qvp[FTQUAL_seqfeat_note].str,
+           qvp[FTQUAL_standard_name].gbq->val) == 0)) {
+      qvp[FTQUAL_seqfeat_note].str = NULL;
+    }
+  }
+
+  /* Display strings for debugging purposes */
+
+#ifdef DISPLAY_STRINGS
+  s_DisplayQVP(qvp, feat_qual_order);
+#endif
+
+  /* optionally populate indexes for NCBI internal database */
+
+  if (index != NULL) {
+    if (! StringHasNoText (qvp [FTQUAL_gene].str)) {
+      ValNodeCopyStrToHead (&(index->genes), 0, qvp [FTQUAL_gene].str);
+    }
+  }
+
+  if (doKey) {
+    FFAddOneChar(ffstring, '\n', FALSE);
+  }
+
+  /* Build the flat file */
+  FormatFeatureBlockQuals (ffstring, ajp, asp, bsp, featdeftype, gene_syn,
+                           lasttype, location, prod,
+                           protein_pid_g, qvp,
+                           left, right, strand,
+                           sfp, target, is_other,
+                           is_journalscan, is_gps);
+
+  /* ??? and then deal with the various note types separately (not in order table) ??? */
+
+  /* free aa-dna or dna-aa mapped location */
+
+  SeqLocFree (loc);
+
+  ValNodeFreeData (illegal);
+  MemFree (exception_string);
+  MemFree (exception_note);
+
+  BioseqUnlock (unlockme);
+
+  str = FFEndPrint (ajp, ffstring, format, 21, 21, 21, 21, "FT");
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (gbseq != NULL) {
+    if (gbfeat != NULL) {
+      AddFeatureToGbseq (gbseq, gbfeat, str, sfp);
+    }
+  }
+
+  FFRecycleString(ajp, ffstring);
+  return str;
+}
+
+NLM_EXTERN CharPtr FormatFeatureBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  BioseqPtr          bsp;
+  SeqMgrFeatContext  fcontext;
+  FmtType            format;
+  QualValPtr         qvp;
+  SeqFeatPtr         sfp;
+  BioseqPtr          target;
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+  target = asp->target;
+  bsp = asp->bsp;
+  if (target == NULL || bsp == NULL) return NULL;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+  qvp = afp->qvp;
+  if (qvp == NULL) return NULL;
+  format = afp->format;
+
+  /* all features in this list are known to be valid for the designated mode */
+
+  sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
+  if (sfp == NULL) return NULL;
+
+  return FormatFeatureBlockEx (ajp, asp, bsp, target, sfp, &fcontext, qvp,
+                               format, (IntFeatBlockPtr) bbp, ISA_aa (bsp->mol), TRUE);
+}
+
+
+/* stand alone function to produce qualifiers in genbank style */
+
+static void StripLeadingSpaces (
+  CharPtr str
+)
+
+{
+  Uchar    ch;
+  CharPtr  dst;
+  CharPtr  ptr;
+
+
+  if (str == NULL || str [0] == '\0') return;
+
+  dst = str;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    while (ch == ' ') {
+      ptr++;
+      ch = *ptr;
+    }
+    while (ch != '\n' && ch != '\r') {
+      *dst = ch;
+      dst++;
+      ptr++;
+      ch = *ptr;
+    }
+    *dst = ch;
+    dst++;
+    ptr++;
+    ch = *ptr;
+  }
+  *dst = '\0';
+}
+
+NLM_EXTERN CharPtr FormatFeatureQuals (
+  SeqFeatPtr sfp
+)
+
+{
+  IntAsn2gbJob       ajb;
+  IntAsn2gbJobPtr    ajp;
+  BioseqPtr          bsp;
+  SeqMgrFeatContext  fcontext;
+  IntCdsBlock        ifb;
+  IntFeatBlockPtr    ifp;
+  size_t             max;
+  QualValPtr         qvp;
+  CharPtr            str;
+
+  if (sfp == NULL) return NULL;
+  bsp = BioseqFindFromSeqLoc (sfp->location);
+  if (bsp == NULL) return NULL;
+
+  if (SeqMgrGetDesiredFeature (0, bsp, 0, 0, sfp, &fcontext) != sfp) return NULL;
+
+  MemSet ((Pointer) &ajb, 0, sizeof (IntAsn2gbJob));
+  ajp = &ajb;
+  MemSet ((Pointer) &ifb, 0, sizeof (IntCdsBlock));
+  ifp = (IntFeatBlockPtr) &ifb;
+
+  max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR));
+  qvp = MemNew (sizeof (QualVal) * (max + 5));
+  if (qvp == NULL) return NULL;
+
+  str = FormatFeatureBlockEx (ajp, NULL, NULL, NULL, sfp, &fcontext, qvp,
+                              GENBANK_FMT, ifp, FALSE, FALSE);
+
+  MemFree (qvp);
+  StripLeadingSpaces (str);
+  return str;
+}
+
diff --git a/api/asn2gnb5.c b/api/asn2gnb5.c
new file mode 100644
index 00000000..e338a417
--- /dev/null
+++ b/api/asn2gnb5.c
@@ -0,0 +1,3618 @@
+/*   asn2gnb5.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  asn2gnb5.c
+*
+* Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans,
+*          Mati Shomrat
+*
+* Version Creation Date:   10/21/98
+*
+* $Revision: 1.3 $
+*
+* File Description:  New GenBank flatfile generator - work in progress
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <objall.h>
+#include <objsset.h>
+#include <objsub.h>
+#include <objfdef.h>
+#include <objpubme.h>
+#include <seqport.h>
+#include <sequtil.h>
+#include <sqnutils.h>
+#include <subutil.h>
+#include <tofasta.h>
+#include <explore.h>
+#include <gbfeat.h>
+#include <gbftdef.h>
+#include <edutil.h>
+#include <alignmgr2.h>
+#include <asn2gnbi.h>
+
+#ifdef WIN_MAC
+#if __profile__
+#include <Profiler.h>
+#endif
+#endif
+
+/* URLs */
+
+NLM_EXTERN Char link_feat [MAX_WWWBUF];
+#define DEF_LINK_FEAT  "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
+
+NLM_EXTERN Char link_seq [MAX_WWWBUF];
+#define DEF_LINK_SEQ  "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
+
+NLM_EXTERN Char link_wgs [MAX_WWWBUF];
+#define DEF_LINK_WGS  "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?"
+
+NLM_EXTERN Char link_omim [MAX_WWWBUF];
+#define DEF_LINK_OMIM "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id="
+
+NLM_EXTERN Char ref_link [MAX_WWWBUF];
+#define DEF_LINK_REF  "http://www.ncbi.nlm.nih.gov/RefSeq/"
+
+NLM_EXTERN Char nt_link [MAX_WWWBUF];
+#define DEF_LINK_NT  "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?view=graph&val="
+
+NLM_EXTERN Char doc_link [MAX_WWWBUF];
+#define DEF_LINK_DOC  "http://www.ncbi.nlm.nih.gov/genome/guide/build.html"
+
+NLM_EXTERN Char ev_link [MAX_WWWBUF];
+#define DEF_LINK_EV  "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?"
+
+NLM_EXTERN Char ec_link [MAX_WWWBUF];
+#define DEF_LINK_EC "http://www.expasy.ch/cgi-bin/nicezyme.pl?"
+
+NLM_EXTERN Char link_tax [MAX_WWWBUF];
+#define DEF_LINK_TAX "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?"
+
+static Char link_ff [MAX_WWWBUF];
+#define DEF_LINK_FF  "/cgi-bin/Entrez/getfeat?"
+
+NLM_EXTERN Char link_muid [MAX_WWWBUF];
+#define DEF_LINK_MUID  "/entrez/utils/qmap.cgi?"
+
+static Char link_ace [MAX_WWWBUF];
+#define DEF_LINK_ACE  "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=gene&q="
+
+NLM_EXTERN Char link_code [MAX_WWWBUF];
+#define DEF_LINK_CODE "http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?"
+
+static Char link_fly [MAX_WWWBUF];
+#define DEF_LINK_FLY "http://flybase.bio.indiana.edu/.bin/fbidq.html?"
+
+static Char link_fly_fban [MAX_WWWBUF];
+#define DEF_LINK_FBAN "http://www.fruitfly.org/cgi-bin/annot/fban?"
+
+static Char link_fly_fbgn [MAX_WWWBUF];
+#define DEF_LINK_FBGN "http://flybase.bio.indiana.edu/.bin/fbidq.html?"
+
+static Char link_cog [MAX_WWWBUF];
+#define DEF_LINK_COG "http://www.ncbi.nlm.nih.gov/cgi-bin/COG/palox?"
+
+static Char link_sgd [MAX_WWWBUF];
+#define DEF_LINK_SGD "/cgi-bin/Entrez/referer?http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus="
+
+static Char link_gdb [MAX_WWWBUF];
+#define DEF_LINK_GDB "http://www.gdb.org/gdb-bin/genera/genera/hgd/DBObject/GDB:"
+
+static Char link_ck [MAX_WWWBUF];
+#define DEF_LINK_CK "http://flybane.berkeley.edu/cgi-bin/cDNA/CK_clone.pl?db=CK&dbid="
+
+static Char link_rice [MAX_WWWBUF];
+#define DEF_LINK_RICE "http://ars-genome.cornell.edu/cgi-bin/WebAce/webace?db=ricegenes&class=Marker&object="
+
+static Char link_sp [MAX_WWWBUF];
+#define DEF_LINK_SP "/cgi-bin/Entrez/referer?http://expasy.hcuge.ch/cgi-bin/sprot-search-ac%3f"
+
+static Char link_pdb [MAX_WWWBUF];
+#define DEF_LINK_PDB "/cgi-bin/Entrez/referer?http://expasy.hcuge.ch/cgi-bin/get-pdb-entry%3f"
+
+static Char link_UniSTS [MAX_WWWBUF];
+#define DEF_LINK_UniSTS "http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid="
+
+static Char link_dbSTS [MAX_WWWBUF];
+#define DEF_LINK_dbSTS "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
+
+static Char link_dbEST [MAX_WWWBUF];
+#define DEF_LINK_dbEST "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
+
+static Char link_locus [MAX_WWWBUF];
+#define DEF_LINK_LOCUS "http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l="
+
+static Char link_snp [MAX_WWWBUF];
+#define DEF_LINK_SNP "http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs="
+
+static Char link_ratmap [MAX_WWWBUF];
+#define DEF_LINK_RATMAP "http://ratmap.gen.gu.se/action.lasso?-database=RATMAPfmPro&-layout=Detail&-response=/RM/Detail+Format.html&-search&-recid="
+
+static Char link_rgd [MAX_WWWBUF];
+#define DEF_LINK_RGD "http://rgd.mcw.edu/query/query.cgi?id="
+
+static Char link_mgd [MAX_WWWBUF];
+#define DEF_LINK_MGD "http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:"
+
+static Char link_cdd [MAX_WWWBUF];
+#define DEF_LINK_CDD "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid="
+
+static Char link_niaest [MAX_WWWBUF];
+#define DEF_LINK_NIAEST "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1="
+
+static Char link_worm_base [MAX_WWWBUF];
+#define DEF_LINK_WORM_BASE "http://www.wormbase.org/db/get?class=Sequence;name="
+
+static Char link_worfdb [MAX_WWWBUF];
+#define DEF_LINK_WORFDB "http://worfdb.dfci.harvard.edu/search.pl?form=1&search="
+
+static Char link_nextdb [MAX_WWWBUF];
+#define DEF_LINK_NEXTDB "http://nematode.lab.nig.ac.jp/cgi-bin/db/ShowGeneInfo.sh?celk="
+
+static Char link_imgt [MAX_WWWBUF];
+#define DEF_LINK_IMGT "http://imgt.cines.fr:8104/cgi-bin/IMGTlect.jv?query=202+"
+
+static Char link_ifo [MAX_WWWBUF];
+#define DEF_LINK_IFO "http://www.ifo.or.jp/index_e.html"
+
+static Char link_jcm [MAX_WWWBUF];
+#define DEF_LINK_JCM "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM="
+
+static Char link_isfinder [MAX_WWWBUF];
+#define DEF_LINK_ISFINDER "http://www-is.biotoul.fr/scripts/is/is_spec.idc?name="
+
+static Char link_gabi [MAX_WWWBUF];
+#define DEF_LINK_GABI "https://gabi.rzpd.de/cgi-bin-protected/GreenCards.pl.cgi?Mode=ShowBioObject&BioObjectName="
+
+static Char link_fantom [MAX_WWWBUF];
+#define DEF_LINK_FANTOM "http://fantom.gsc.riken.go.jp/db/view/main.cgi?masterid="
+
+static Char link_interpro [MAX_WWWBUF];
+#define DEF_LINK_INTERPRO "http://www.ebi.ac.uk/interpro/ISearch?mode=ipr&query="
+
+static Char link_genedb [MAX_WWWBUF];
+#define DEF_LINK_GENEDB "http://www.genedb.org/genedb/Dispatcher?formType=navBar&submit=Search+for&organism=All%3Apombe%3Acerevisiae%3Adicty%3Aasp%3Atryp%3Aleish%3Amalaria%3Astyphi%3Aglossina&desc=yes&ohmr=%2F&name="
+
+static Char link_geneid [MAX_WWWBUF];
+#define DEF_LINK_GENEID "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids="
+
+static Char link_zfin [MAX_WWWBUF];
+#define DEF_LINK_ZFIN "http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID="
+
+static Char link_rebase [MAX_WWWBUF];
+#define DEF_LINK_REBASE "http://rebase.neb.com/rebase/enz/"
+
+NLM_EXTERN Char link_encode [MAX_WWWBUF];
+#define DEF_LINK_ENCODE  "http://www.nhgri.nih.gov/10005107"
+
+/* www utility functions */
+
+NLM_EXTERN Boolean GetWWW (IntAsn2gbJobPtr ajp) {
+    return ajp->www;
+}
+
+NLM_EXTERN void FiniWWW (IntAsn2gbJobPtr ajp) {
+    ajp->www = FALSE;
+}
+
+NLM_EXTERN void InitWWW (IntAsn2gbJobPtr ajp)
+{
+  ajp->www = TRUE;
+
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FEAT", DEF_LINK_FEAT, link_feat, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_WGS", DEF_LINK_WGS, link_wgs, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_OMIM", DEF_LINK_OMIM, link_omim, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_REF", DEF_LINK_REF, ref_link, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_NT", DEF_LINK_NT, nt_link, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_DOC", DEF_LINK_DOC, doc_link, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_EV", DEF_LINK_EV, ev_link, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_EC", DEF_LINK_EC, ec_link, 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_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SEQ", DEF_LINK_SEQ, link_seq, 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_SEQ", DEF_LINK_SEQ, link_seq, 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);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FLY", DEF_LINK_FLY, link_fly, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_COG", DEF_LINK_COG, link_cog, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SGD", DEF_LINK_SGD, link_sgd, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SGD", DEF_LINK_GDB, link_gdb, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_CK", DEF_LINK_CK, link_ck, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_RICE", DEF_LINK_RICE, link_rice, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SP", DEF_LINK_SP, link_sp, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_PDB", DEF_LINK_PDB, link_pdb, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_OMIM", DEF_LINK_OMIM, link_omim, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_UniSTS", DEF_LINK_UniSTS, link_UniSTS, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_dbSTS", DEF_LINK_dbSTS, link_dbSTS, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_dbEST", DEF_LINK_dbEST, link_dbEST, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_LOCUS", DEF_LINK_LOCUS, link_locus, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_SNP", DEF_LINK_SNP, link_snp, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_RATMAP", DEF_LINK_RATMAP, link_ratmap, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_RGD", DEF_LINK_RGD, link_rgd, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_MGD", DEF_LINK_MGD, link_mgd, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FBGN", DEF_LINK_FBGN, link_fly_fbgn, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FBAN", DEF_LINK_FBAN, link_fly_fban, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_CDD", DEF_LINK_CDD, link_cdd, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_NIAEST", DEF_LINK_NIAEST, link_niaest, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_WORM_BASE", DEF_LINK_WORM_BASE, link_worm_base, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_WORFDB", DEF_LINK_WORFDB, link_worfdb, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_NEXTDB", DEF_LINK_NEXTDB, link_nextdb, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_IMGT", DEF_LINK_IMGT, link_imgt, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_IFO", DEF_LINK_IFO, link_ifo, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_JCM", DEF_LINK_JCM, link_jcm, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_ISFINDER", DEF_LINK_ISFINDER, link_isfinder, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_GABI", DEF_LINK_GABI, link_gabi, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FANTOM", DEF_LINK_FANTOM, link_fantom, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_INTERPRO", DEF_LINK_INTERPRO, link_interpro, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_GENEDB", DEF_LINK_GENEDB, link_genedb, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_GENEID", DEF_LINK_GENEID, link_geneid, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_ZFIN", DEF_LINK_ZFIN, link_zfin, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_REBASE", DEF_LINK_REBASE, link_rebase, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_ENCODE", DEF_LINK_ENCODE, link_encode, MAX_WWWBUF);
+}
+
+
+
+NLM_EXTERN void FF_www_featloc(StringItemPtr ffstring, CharPtr loc)
+{
+  CharPtr ptr;
+
+  if (loc == NULL) return;
+
+  for ( ptr = loc; *ptr != '\0'; ++ptr ) {
+    switch (*ptr) {
+    case '<' :
+      /*FFAddOneString(ffstring, "<", FALSE, FALSE, TILDE_IGNORE);*/
+      FFAddOneString(ffstring, "&lt;", FALSE, FALSE, TILDE_IGNORE);
+      break;
+    case '>' :
+      /*FFAddOneString(ffstring, ">", FALSE, FALSE, TILDE_IGNORE);*/
+      FFAddOneString(ffstring, "&gt;", FALSE, FALSE, TILDE_IGNORE);
+      break;
+    default:
+      FFAddOneChar(ffstring, *ptr, FALSE);
+      break;
+    }
+  }
+}
+
+
+static void FF_www_db_xref_std (
+  StringItemPtr ffstring,
+  CharPtr db,
+  CharPtr identifier,
+  CharPtr link
+)
+{
+  while (*identifier == ' ')
+    identifier++;
+
+  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, "<a href=", link, identifier, FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, ">", identifier, "</a>", FALSE, FALSE, TILDE_IGNORE);
+}
+
+static void FF_www_db_xref_fly (
+  StringItemPtr ffstring,
+  CharPtr db, 
+  CharPtr identifier
+)
+{
+  CharPtr link = link_fly;
+  
+  if ( StringStr(identifier, "FBa") != NULL ) {
+    link = link_fly_fban;
+  }
+  if ( StringStr(identifier, "FBg") != NULL ) {
+    link = link_fly_fbgn;
+  }
+
+  FF_www_db_xref_std(ffstring, db, identifier, link);
+}
+
+static void FF_www_db_xref_mgd (
+  StringItemPtr ffstring,
+  CharPtr db, 
+  CharPtr identifier
+)
+{
+  if (StringNICmp (identifier, "MGI:", 4) == 0) {
+    identifier += 4;
+  } else if (StringNICmp (identifier, "MGD:", 4) == 0) {
+    identifier += 4;
+  }
+
+  FF_www_db_xref_std(ffstring, "MGI", identifier, link_mgd);
+}
+
+static void FF_www_db_xref_pid(
+  StringItemPtr ffstring,
+  CharPtr db, 
+  CharPtr identifier
+)
+{
+  if ( *identifier != 'g' ) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_seq);
+    return;
+  }
+  ++identifier;
+
+  FFAddTextToString(ffstring, NULL, db, ":g", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, "<a href=", link_seq, "val=", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, identifier, ">", identifier, FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+}
+
+/*prefix = "<a href=%sval=gnl|dbest|%s>"; */
+static void FF_www_db_xref_dbEST(
+  StringItemPtr ffstring,
+  CharPtr db, 
+  CharPtr identifier
+)
+{
+  while (*identifier == ' ')
+    identifier++;
+
+  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, "<a href=", link_dbEST, "val=gnl|dbest|", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, identifier, ">", identifier, FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+}
+
+static void FF_www_db_xref_dbSTS(
+  StringItemPtr ffstring,
+  CharPtr db, 
+  CharPtr identifier
+)
+{
+  while (*identifier == ' ')
+    identifier++;
+
+  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, "<a href=", link_dbSTS, "val=gnl|dbsst|", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, identifier, ">", identifier, FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+}
+
+static void FF_www_db_xref_niaEST(
+  StringItemPtr ffstring,
+  CharPtr db, 
+  CharPtr identifier
+)
+{
+  while (*identifier == ' ')
+    identifier++;
+
+  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, "<a href=", link_niaest, identifier, FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString(ffstring, "&val=1>", FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString(ffstring, identifier, FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+}
+
+
+static void FF_www_db_xref_ifo(
+  StringItemPtr ffstring,
+  CharPtr db, 
+  CharPtr identifier
+)
+{
+  while (*identifier == ' ')
+    identifier++;
+
+  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, "<a href=", link_ifo, ">", FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString(ffstring, identifier, FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+}
+
+
+static void FF_www_db_xref_gdb(
+  StringItemPtr ffstring,
+  CharPtr db, 
+  CharPtr identifier
+)
+{
+  CharPtr start;
+  Char id[20], PNTR idp = id;
+
+  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
+
+  if ( (start = StringStr(identifier, "G00-")) != NULL ) {
+    /* G00-id-id */
+    start += StringLen("G00-");
+    while ( *start != '\0' ) {
+      if ( *start != '-' ) {
+        *idp++ = *start++;
+      } else {
+        *start++;
+      }
+    }
+    *idp = '\0';
+    FFAddTextToString(ffstring, "<a href=", link_gdb, id, FALSE, FALSE, TILDE_IGNORE);  
+    FFAddTextToString(ffstring, ">", identifier, "</a>", FALSE, FALSE, TILDE_IGNORE);
+  } else if ( IS_DIGIT(*identifier) ) {
+    /* id */
+    FFAddTextToString(ffstring, "<a href=", link_gdb, identifier, FALSE, FALSE, TILDE_IGNORE);  
+    FFAddTextToString(ffstring, ">", identifier, "</a>", FALSE, FALSE, TILDE_IGNORE);
+  } else {
+    FFAddOneString(ffstring, identifier, FALSE, FALSE, TILDE_IGNORE);
+  }
+}
+
+static void FF_www_db_xref_rebase (
+  StringItemPtr ffstring,
+  CharPtr db,
+  CharPtr identifier
+)
+{
+  while (*identifier == ' ')
+    identifier++;
+
+  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, "<a href=", link_rebase, identifier, FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString(ffstring, ".html>", identifier, "</a>", FALSE, FALSE, TILDE_IGNORE);
+}
+
+
+static void Do_www_db_xref(
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr db, CharPtr identifier
+)
+{
+  if ( ffstring == NULL || db == NULL || identifier == NULL ) return;
+
+  if ( StringCmp(db, "FLYBASE") == 0) {
+    FF_www_db_xref_fly(ffstring, db, identifier);
+  } else if ( StringCmp(db , "COG") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_cog);
+  } else if ( StringCmp(db , "UniSTS") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_UniSTS);
+  } else if ( StringCmp(db , "LocusID") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_locus);
+  } else if ( StringCmp(db , "InterimID") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_locus);
+  } else if ( StringCmp(db , "MIM") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_omim);
+  } else if ( StringCmp(db , "SGD") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_sgd);
+  } else if ( StringCmp(db , "IMGT/LIGM") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_imgt);
+  } else if ( StringCmp(db , "CK") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_ck);
+  } else if ( StringCmp(db , "RiceGenes") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_rice);
+  } else if ( StringCmp(db , "dbSNP") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_snp);
+  } else if ( StringCmp(db , "RATMAP") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_ratmap);
+  } else if ( StringCmp(db , "RGD") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_rgd);
+  } else if ( StringCmp(db , "MGI") == 0) {
+    FF_www_db_xref_mgd(ffstring, db, identifier);
+  } else if ( StringCmp(db , "MGD") == 0) {
+    FF_www_db_xref_mgd(ffstring, db, identifier);
+  } else if ( StringCmp(db , "CDD") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_cdd);
+  } else if ( StringCmp(db , "JCM") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_jcm);
+  } else if ( StringCmp(db , "ISFinder") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_isfinder);
+  } else if ( StringCmp(db , "GABI") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_gabi);
+  } else if ( StringCmp(db , "ZFIN") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_zfin);
+  } else if ( StringCmp(db , "FANTOM_DB") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_fantom);
+  } else if ( StringCmp(db , "Interpro") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_interpro);
+  } else if ( StringCmp(db , "GeneDB") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_genedb);
+  } else if ( StringCmp(db , "GeneID") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_geneid);
+  } else if ( StringCmp(db , "PID") == 0) {
+    FF_www_db_xref_pid(ffstring, db, identifier);
+  } else if ( StringCmp(db , "dbEST") == 0) {
+    FF_www_db_xref_dbEST(ffstring, db, identifier);
+  } else if ( StringCmp(db , "dbSTS") == 0) {
+    FF_www_db_xref_dbSTS(ffstring, db, identifier);
+  } else if ( StringCmp(db , "niaEST") == 0) {
+    FF_www_db_xref_niaEST(ffstring, db, identifier);
+  } else if ( StringCmp(db , "WormBase") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_worm_base);
+  } else if ( StringCmp(db , "AceView/WormGenes") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_ace);
+  } else if ( StringCmp(db , "WorfDB") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_worfdb);
+  } else if ( StringCmp(db , "NextDB") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_nextdb);
+  } else if ( StringCmp(db , "IFO") == 0) {
+    FF_www_db_xref_ifo(ffstring, db, identifier);
+  } else if ( StringCmp(db , "GDB") == 0) {
+    FF_www_db_xref_gdb(ffstring, db, identifier);
+  } else if ( StringCmp(db , "REBASE") == 0) {
+    FF_www_db_xref_rebase(ffstring, db, identifier);
+
+  } else {  
+    /* default: no link just the text */
+    FFAddTextToString(ffstring, db, ":", identifier, FALSE, FALSE, TILDE_IGNORE);
+  }             
+}
+
+NLM_EXTERN void FF_www_db_xref(
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr db, CharPtr identifier
+)
+{
+  if ( ffstring == NULL || db == NULL || identifier == NULL ) return;
+  
+  if ( GetWWW(ajp) ) {
+    Do_www_db_xref (ajp, ffstring, db, identifier);
+  } else { /* not in www mode */
+    if (StringCmp(db , "MGD") == 0 || StringCmp(db , "MGI") == 0) {
+      if (StringNICmp (identifier, "MGI:", 4) == 0) {
+        identifier += 4;
+      } else if (StringNICmp (identifier, "MGD:", 4) == 0) {
+        identifier += 4;
+      }
+      FFAddTextToString(ffstring, "MGI", ":", identifier, FALSE, FALSE, TILDE_IGNORE);
+    } else {
+      FFAddTextToString(ffstring, db, ":", identifier, FALSE, FALSE, TILDE_IGNORE);
+    }
+  }
+}
+
+/* public function to get URLs for collaboration-approved db_xrefs */
+
+static Boolean links_loaded = FALSE;
+
+NLM_EXTERN CharPtr asn2gnbk_dbxref (
+  DbtagPtr dbt
+)
+
+{
+  IntAsn2gbJobPtr  ajp;
+  Char             buf [80];
+  StringItemPtr    ffstring;
+  ObjectIdPtr      oip;
+  CharPtr          ptr;
+  CharPtr          str;
+  CharPtr          tmp;
+
+  if (dbt == NULL) return NULL;
+  if (StringHasNoText (dbt->db)) return NULL;
+  oip = dbt->tag;
+  if (oip == NULL) return NULL;
+
+  if (! StringHasNoText (oip->str)) {
+    if (StringLen (dbt->db) + StringLen (oip->str) < 80) {
+      sprintf (buf, "%s", oip->str);
+    }
+  } else {
+    sprintf (buf, "%ld", (long) oip->id);
+  }
+
+  ajp = (IntAsn2gbJobPtr) MemNew (sizeof (IntAsn2gbJob));
+  if (ajp == NULL) return NULL;
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return NULL;
+
+  if (! links_loaded) {
+    InitWWW (ajp);
+    links_loaded = TRUE;
+  }
+  ajp->www = TRUE;
+
+  Do_www_db_xref (ajp, ffstring, dbt->db, buf);
+
+  ajp->www = FALSE;
+
+  str = FFToCharPtr (ffstring);
+
+  FFRecycleString (ajp, ffstring);
+  MemFree (ajp);
+
+  tmp = StringChr (str, '<');
+  if (tmp != NULL) {
+    ptr = StringSave (tmp);
+    tmp = StringChr (ptr, '>');
+    if (tmp != NULL) {
+      tmp++;
+      *tmp = '\0';
+    }
+    MemFree (str);
+    str = ptr;
+  } else {
+    str = MemFree (str);
+  }
+
+  return str;
+}
+
+/* format references section */
+
+NLM_EXTERN AuthListPtr GetAuthListPtr (
+  PubdescPtr pdp,
+  CitSubPtr csp
+)
+
+{
+  AuthListPtr  alp = NULL;
+  CitArtPtr    cap;
+  CitBookPtr   cbp;
+  CitGenPtr    cgp;
+  CitPatPtr    cpp;
+  ValNodePtr   vnp;
+
+  if (csp != NULL) {
+    alp = csp->authors;
+    if (alp != NULL) return alp;
+  }
+  if (pdp == NULL) return NULL;
+
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    switch (vnp->choice) {
+      case PUB_Gen :
+        cgp = (CitGenPtr) vnp->data.ptrvalue;
+        if (cgp != NULL) {
+          alp = cgp->authors;
+        }
+        break;
+      case PUB_Sub :
+        csp = (CitSubPtr) vnp->data.ptrvalue;
+        if (csp != NULL) {
+          alp = csp->authors;
+        }
+        break;
+      case PUB_Article :
+        cap = (CitArtPtr) vnp->data.ptrvalue;
+        if (cap != NULL) {
+          alp = cap->authors;
+        }
+        break;
+      case PUB_Book :
+      case PUB_Proc :
+      case PUB_Man :
+        cbp = (CitBookPtr) vnp->data.ptrvalue;
+        if (cbp != NULL) {
+          alp = cbp->authors;
+        }
+        break;
+      case PUB_Patent :
+        cpp = (CitPatPtr) vnp->data.ptrvalue;
+        if (cpp != NULL) {
+          alp = cpp->authors;
+        }
+        break;
+      default :
+        break;
+    }
+
+    if (alp != NULL) return alp;
+  }
+
+  return NULL;
+}
+
+static CharPtr MakeSingleAuthorString (
+  FmtType format,
+  CharPtr prefix,
+  CharPtr name,
+  CharPtr initials,
+  CharPtr suffix,
+  IndxPtr index,
+  GBReferencePtr gbref
+)
+
+{
+  Char     ch;
+  Char     dummy [10];
+  size_t   len;
+  CharPtr  nametoindex;
+  CharPtr  ptr;
+  CharPtr  str;
+  CharPtr  tmp;
+
+  if (name == NULL) return NULL;
+
+  /* !!! clean up 'et al' as (presumably) last author !!! */
+
+  /* !!! temporary to suppress diff !!! */
+  {
+  if (StringLen (name) <= 6 &&
+      (StringNICmp (name, "et al", 5) == 0 || StringNICmp (name, "et,al", 5) == 0)) {
+    if (StringCmp (prefix, " and ") == 0) {
+      prefix = NULL;
+      dummy [0] = ' ';
+      StringNCpy_0 (dummy + 1, name, sizeof (dummy) - 1);
+      name = dummy;
+    }
+  }
+  }
+  /*
+  if (StringLen (name) <= 6 &&
+      (StringNICmp (name, "et al", 5) == 0 || StringNICmp (name, "et,al", 5) == 0)) {
+    name = "et al.";
+    if (StringCmp (prefix, " and ") == 0) {
+      prefix = ", ";
+    }
+  }
+  */
+
+  len = StringLen (name) + StringLen (initials) + StringLen (suffix) + StringLen (prefix);
+  str = MemNew (sizeof (Char) * (len + 4));
+  if (str == NULL) return NULL;
+
+  ptr = str;
+  if (! StringHasNoText (prefix)) {
+    ptr = StringMove (ptr, prefix);
+  }
+  nametoindex = ptr;
+
+  /* initials and suffix to support structured name fields */
+
+  tmp = StringMove (ptr, name);
+  if (! StringHasNoText (initials)) {
+    tmp = StringMove (tmp, ",");
+    tmp = StringMove (tmp, initials);
+  }
+  if (! StringHasNoText (suffix)) {
+    tmp = StringMove (tmp, " ");
+    tmp = StringMove (tmp, suffix);
+  }
+
+  /* optionally populate indexes for NCBI internal database */
+
+  if (index != NULL) {
+    ValNodeCopyStrToHead (&(index->authors), 0, nametoindex);
+  }
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (gbref != NULL) {
+    ValNodeCopyStr (&(gbref->authors), 0, nametoindex);
+  }
+
+  /* if embl, remove commas in individual names, starting after prefix */
+
+  if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
+    tmp = ptr;
+    ch = *tmp;
+    while (ch != '\0') {
+      if (ch == ',') {
+        *tmp = ' ';
+      }
+      tmp++;
+      ch = *tmp;
+    }
+  }
+
+  return str;
+}
+
+NLM_EXTERN CharPtr GetAuthorsString (
+  FmtType format,
+  AuthListPtr alp,
+  CharPtr PNTR consortP,
+  IndxPtr index,
+  GBReferencePtr gbref
+)
+
+{
+  AuthorPtr    ap;
+  ValNodePtr   conslist;
+  Int2         count;
+  ValNodePtr   head = NULL;
+  ValNodePtr   names;
+  ValNodePtr   next;
+  NameStdPtr   nsp;
+  PersonIdPtr  pid;
+  ValNodePtr   pidlist;
+  CharPtr      prefix = NULL;
+  CharPtr      str;
+  ValNodePtr   vnp;
+
+  if (alp == NULL) return NULL;
+
+  alp = AsnIoMemCopy ((Pointer) alp,
+                      (AsnReadFunc) AuthListAsnRead,
+                      (AsnWriteFunc) AuthListAsnWrite);
+  if (alp == NULL) return NULL;
+
+  count = 0;
+  if (alp->choice == 1) {
+
+    pidlist = NULL;
+    conslist = NULL;
+
+    for (names = alp->names; names != NULL; names = names->next) {
+      ap = (AuthorPtr) names->data.ptrvalue;
+      if (ap == NULL) continue;
+      pid = ap->name;
+      if (pid == NULL) continue;
+      if (pid->choice == 2 || pid->choice == 3 || pid->choice == 4) {
+        ValNodeAddPointer (&pidlist, 0, (Pointer) pid);
+      } else if (pid->choice == 5) {
+        ValNodeAddPointer (&conslist, 0, (Pointer) pid);
+      }
+    }
+
+    for (vnp = pidlist; vnp != NULL; vnp = vnp->next) {
+      next = vnp->next;
+      if (next == NULL) {
+        if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+          if (count == 0) {
+            prefix = NULL;
+          } else {
+            prefix = " and ";
+          }
+        }
+      }
+      str = NULL;
+      pid = (PersonIdPtr) vnp->data.ptrvalue;
+      if (pid->choice == 2) {
+        nsp = (NameStdPtr) pid->data;
+        if (nsp != NULL) {
+          if (! StringHasNoText (nsp->names [0])) {
+            str = MakeSingleAuthorString (format, prefix, nsp->names [0], nsp->names [4], nsp->names [5], index, gbref);
+          } else if (! StringHasNoText (nsp->names [3])) {
+            str = MakeSingleAuthorString (format, prefix, nsp->names [3], NULL, NULL, index, gbref);
+          }
+        }
+      } else if (pid->choice == 3 || pid->choice == 4) {
+        str = MakeSingleAuthorString (format, prefix, (CharPtr) pid->data, NULL, NULL, index, gbref);
+      }
+      if (str != NULL) {
+        ValNodeAddStr (&head, 0, str);
+        count++;
+      }
+      prefix = ", ";
+    }
+
+    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);
+        }
+
+        /* optionally populate gbseq for XML-ized GenBank format */
+
+        if (gbref != NULL) {
+          gbref->consortium = StringSave (str);
+        }
+
+        str = MemFree (str);
+      }
+    }
+
+    ValNodeFree (pidlist);
+    ValNodeFree (conslist);
+
+  } else if (alp->choice == 2 || alp->choice == 3) {
+    for (vnp = alp->names; vnp != NULL; vnp = vnp->next) {
+      next = vnp->next;
+      if (next == NULL) {
+        if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+          if (count == 0) {
+            prefix = NULL;
+          } else {
+            prefix = " and ";
+          }
+        }
+      }
+      str = MakeSingleAuthorString (format, prefix, (CharPtr) vnp->data.ptrvalue, NULL, NULL, index, gbref);
+      if (str != NULL) {
+        ValNodeAddStr (&head, 0, str);
+        count++;
+      }
+      prefix = ", ";
+    }
+  }
+
+  str = MergeFFValNodeStrs (head);
+
+  ValNodeFreeData (head);
+
+  AuthListFree (alp);
+
+  return str;
+}
+
+/*
+Strips all spaces in string in following manner. If the function
+meet several spaces (spaces and tabs) in succession it replaces them
+with one space. Strips all spaces after '(' and before ')'
+*/
+
+static void StrStripSpaces (
+  CharPtr str
+)
+
+{
+  CharPtr  new_str;
+
+  if (str == NULL) return;
+
+  new_str = str;
+  while (*str != '\0') {
+    *new_str++ = *str;
+    if (*str == ' ' || *str == '\t' || *str == '(') {
+      for (str++; *str == ' ' || *str == '\t'; str++) continue;
+      if (*str == ')' || *str == ',') {
+        new_str--;
+      }
+    } else {
+      str++;
+    }
+  }
+  *new_str = '\0';
+}
+
+static Boolean AllCaps (
+  CharPtr p
+)
+
+{
+  if (p == NULL) return FALSE;
+
+  for (p++; p != NULL && *p != '\0'; p++) {
+    if (IS_LOWER (*p)) return FALSE;
+  }
+  return TRUE;
+}
+
+static void CleanEquals (
+  CharPtr p
+)
+
+{
+  if (p == NULL) return;
+
+  for (; *p != '\0'; p++) {
+    if (*p == '\"') {
+      *p = '\'';
+    }
+  }
+}
+
+static CharPtr GetPubTitle (
+  FmtType format,
+  PubdescPtr pdp,
+  CitSubPtr csp
+)
+
+{
+  CitArtPtr        cap;
+  CitBookPtr       cbp;
+  CitGenPtr        cgp;
+  Char             ch;
+  CitPatPtr        cpp;
+  MedlineEntryPtr  mep;
+  CharPtr          ptr;
+  CharPtr          title = NULL;
+  ValNodePtr       ttl = NULL;
+  ValNodePtr       vnp;
+
+  if (csp != NULL) {
+    if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+      title = "Direct Submission";
+      return StringSave (title);
+    } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
+      return NULL;
+    }
+  }
+  if (pdp == NULL) return NULL;
+
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    switch (vnp->choice) {
+      case PUB_Gen :
+        cgp = (CitGenPtr) vnp->data.ptrvalue;
+        if (cgp != NULL) {
+          if (! StringHasNoText (cgp->title)) return StringSave (cgp->title);
+          if (! StringHasNoText (cgp->cit)) {
+            ptr = StringStr (cgp->cit, "Title=\"");
+            if (ptr != NULL) {
+              title = StringSave (ptr + 7);
+              for (ptr = title; *ptr != '\0'; ptr++) {
+                if (*ptr == '"') {
+                  *ptr = '\0';
+                  break;
+                }
+              }
+              return title;
+            }
+          }
+        }
+        break;
+      case PUB_Sub :
+        csp = (CitSubPtr) vnp->data.ptrvalue;
+        if (csp != NULL) {
+          if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+            title = "Direct Submission";
+            return StringSave (title);
+          } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
+            return NULL;
+          }
+        }
+        break;
+      case PUB_Medline :
+        mep = (MedlineEntryPtr) vnp->data.ptrvalue;
+        if (mep != NULL) {
+          cap = mep->cit;
+          if (cap != NULL) {
+            ttl = cap->title;
+          }
+        }
+        break;
+      case PUB_Article :
+        cap = (CitArtPtr) vnp->data.ptrvalue;
+        if (cap != NULL) {
+          ttl = cap->title;
+        }
+        break;
+      /* case PUB_Book : */
+      case PUB_Proc :
+      case PUB_Man :
+        cbp = (CitBookPtr) vnp->data.ptrvalue;
+        if (cbp != NULL) {
+          ttl = cbp->title;
+          if (ttl != NULL) {
+            title = (CharPtr) ttl->data.ptrvalue;
+            if (! StringHasNoText (title)) {
+              title = StringSave (title);
+              if (StringLen (title) > 3) {
+                ch = *title;
+                if (IS_LOWER (ch)) {
+                  *title = TO_UPPER (ch);
+                }
+                ptr = title;
+                if (AllCaps (ptr)) {
+                  for (ptr++; ptr != NULL && *ptr != '\0'; ptr++) {
+                    ch = *ptr;
+                    *ptr = TO_LOWER (ch);
+                  }
+                }
+              }
+              return title;
+            }
+          }
+        }
+        break;
+      case PUB_Patent :
+        cpp = (CitPatPtr) vnp->data.ptrvalue;
+        if (cpp != NULL) {
+          title = cpp->title;
+          if (! StringHasNoText (title)) {
+            return StringSave (title);
+          }
+        }
+        break;
+      default :
+        break;
+    }
+
+    if (ttl != NULL) {
+      title = (CharPtr) ttl->data.ptrvalue;
+      if (! StringHasNoText (title)) {
+        return StringSave (title);
+      }
+    }
+  }
+
+  return NULL;
+}
+
+static void CleanPubTitle (
+  CharPtr title
+)
+
+{
+  CharPtr  p;
+  Boolean  remove_it;
+
+  if (title == NULL) return;
+
+  CleanEquals (title);
+
+  for (p = title + StringLen (title) - 1; p > title + 2; p--) {
+    if (*p == ' ') {
+      *p = '\0';
+    } else if (*p == '.') {
+      remove_it = FALSE;
+      if (p > title + 5) {
+        if (*(p - 1) != '.' || *(p - 2) != '.') {
+          remove_it = TRUE;
+        }
+      }
+      if (remove_it) {
+        *p = '\0';
+      }
+      break;
+    } else {
+      break;
+    }
+  }
+}
+
+/*
+medline type page numbering is expanded (e.g., 125-35 -> 125-135,
+F124-34 -> F124-F134, 12a-c -> 12a-12c).
+If only one page is given, this is output without a dash.
+Expanded numbering is validated to ensure that the
+first number is smaller than or equal to the second and
+that the first letter is less than or identical to the second
+(i.e., a < c).  If the input is all letters (i.e., roman numerals)
+this is not validated.
+
+Return values:
+ 0 : valid page numbering.
+-1 : invalid page numbering.
+*/
+
+#define MAX_PAGE_DIGITS 12
+
+static Int2 FixPages (
+  CharPtr out_pages,
+  CharPtr in_pages
+)
+
+{
+  Boolean dash=TRUE, first_alpha;
+  Char firstbegin[MAX_PAGE_DIGITS];
+  Char secondbegin[MAX_PAGE_DIGITS];
+  Char firstend[MAX_PAGE_DIGITS];
+  Char secondend[MAX_PAGE_DIGITS];
+  Char temp[MAX_PAGE_DIGITS];
+  CharPtr alphabegin, numbegin, alphaend, numend, ptr, in=in_pages;
+  Int2 diff, index, retval=0;
+  Int2 length_nb, length_ab, length_ne, length_ae;
+  Int4 num1=0, num2=0;
+
+  if (in_pages == NULL) return retval;
+
+  while (*in != '\0')
+  {      /* Check for digits in input*/
+    if (IS_DIGIT(*in))
+      break;
+    in++;
+  }
+
+  if (*in == '\0' || (in != in_pages && *(in-1) == ' '))
+  {    /* if all letters (i.e. roman numerals), put out. */
+    out_pages = StringCpy(out_pages, in_pages);
+    return retval;
+  }
+
+  in = in_pages;
+  if (IS_DIGIT(*in))
+  {      /* Do digits come first? */
+    first_alpha = FALSE;
+    index=0;
+    while (IS_DIGIT(*in) || *in == ' ')
+    {
+      firstbegin[index] = *in;
+      if (*in != ' ')
+        index++;
+      in++;
+      if (*in == '-')
+        break;
+
+    }
+    firstbegin[index] = '\0';
+    index=0;
+    if (*in != '-')
+    {    /* After digits look for letters. */
+      while (IS_ALPHA(*in)  || *in == ' ')
+      {
+        secondbegin[index] = *in;
+        index++;
+        in++;
+        if (*in == '-')
+          break;
+      }
+    }
+    secondbegin[index] = '\0';
+    if (*in == '-')    /* if dash is not present, note */
+      in++;
+    else
+      dash=FALSE;
+    index=0;
+    while (IS_DIGIT(*in) || *in == ' ')
+    {      /* Look for digits.  */
+      firstend[index] = *in;
+      if (*in != ' ')
+        index++;
+      in++;
+    }
+    firstend[index] = '\0';
+    index=0;
+    if (*in != '\0')
+    {      /* Look for letters again. */
+      while (IS_ALPHA(*in)  || *in == ' ')
+      {
+        secondend[index] = *in;
+        index++;
+        in++;
+      }
+    }
+    secondend[index] = '\0';
+  }
+  else
+  {      /* Do letters come first? */
+    first_alpha = TRUE;
+    index=0;
+    while (IS_ALPHA(*in) || *in == ' ')
+    {
+      firstbegin[index] = *in;
+      index++;
+      in++;
+      if (*in == '-')
+        break;
+    }
+    firstbegin[index] = '\0';
+    index=0;
+    if (*in != '-')
+    {    /* After letters look for digits.   */
+      while (IS_DIGIT(*in)  || *in == ' ')
+      {
+        secondbegin[index] = *in;
+        if (*in != ' ')
+          index++;
+        in++;
+        if (*in == '-')
+          break;
+      }
+    }
+    secondbegin[index] = '\0';
+    if (*in == '-')    /* Note if dash is missing. */
+      in++;
+    else
+      dash=FALSE;
+    index=0;
+    while (IS_ALPHA(*in) || *in == ' ')
+    {    /* Look for letters again. */
+      firstend[index] = *in;
+      index++;
+      in++;
+    }
+    firstend[index] = '\0';
+    index=0;
+    if (*in != '\0')
+    {    /* Any digits here? */
+      while (IS_DIGIT(*in)  || *in == ' ')
+      {
+        secondend[index] = *in;
+        if (*in != ' ')
+          index++;
+        in++;
+      }
+    }
+    secondend[index] = '\0';
+  }
+
+  if (first_alpha)
+  {
+    alphabegin = firstbegin;
+    numbegin = secondbegin;
+    alphaend = firstend;
+    numend = secondend;
+  }
+  else
+  {
+    numbegin = firstbegin;
+    alphabegin = secondbegin;
+    numend = firstend;
+    alphaend = secondend;
+  }
+
+  length_nb = StringLen(numbegin);
+  length_ab = StringLen(alphabegin);
+  length_ne = StringLen(numend);
+  length_ae = StringLen(alphaend);
+
+  /* If no dash, but second letters or numbers present, reject. */
+  if (dash == FALSE)
+  {
+    if (length_ne != 0 || length_ae != 0)
+      retval = -1;
+  }
+  /* Check for situations like "AAA-123" or "222-ABC". */
+  if (dash == TRUE)
+  {
+    if (length_ne == 0 && length_ab == 0)
+      retval = -1;
+    else if (length_ae == 0 && length_nb == 0)
+      retval = -1;
+  }
+
+  /* The following expands "F502-512" into "F502-F512" and
+  checks, for entries like "12a-12c" that a > c.  "12aa-12ab",
+  "125G-137A", "125-G137" would be rejected. */
+  if (retval == 0)
+  {
+    if (length_ab > 0)
+    {
+      if (length_ae > 0)
+      {
+        if (StringCmp(alphabegin, alphaend) != 0)
+        {
+          if (length_ab != 1 || length_ae != 1)
+            retval = -1;
+          else if (*alphabegin > *alphaend)
+            retval = -1;
+        }
+      }
+      else
+      {
+        alphaend = alphabegin;
+        length_ae = length_ab;
+      }
+    }
+    else if (length_ae > 0)
+      retval = -1;
+  }
+
+/* The following expands "125-37" into "125-137".  */
+  if (retval == 0)
+  {
+    if (length_nb > 0)
+    {
+      if (length_ne > 0)
+      {
+        diff = length_nb - length_ne;
+        if (diff > 0)
+        {
+          index=0;
+          while (numend[index] != '\0')
+          {
+            temp[index+diff] = numend[index];
+            index++;
+          }
+          temp[index+diff] = numend[index];
+          for (index=0; index<diff; index++)
+            temp[index] = numbegin[index];
+          index=0;
+          while (temp[index] != '\0')
+          {
+            numend[index] = temp[index];
+            index++;
+          }
+          numend[index] = temp[index];
+        }
+      }
+      else
+      {
+        numend = numbegin;
+        length_ne = length_nb;
+      }
+
+    }
+    else if (length_ne > 0)
+      retval = -1;
+  /* Check that the first number is <= the second (expanded) number. */
+    if (retval == 0)
+    {
+  /*    sscanf(numbegin, "%ld", &num_type);
+      num1 = (Int4) num_type;
+      sscanf(  numend, "%ld", &num_type);
+      num2 = (Int4) num_type;
+  */
+      num1 = (Int4) atol(numbegin);
+      num2 = (Int4) atol(numend);
+      if (num2 < num1)
+        retval = -1;
+    }
+  }
+
+  if (retval == -1)
+  {
+    out_pages = StringCpy(out_pages, in_pages);
+  }
+  else
+  {
+    ptr = out_pages;
+  /* Place expanded and validated page numbers into "out_pages". */
+    if (first_alpha)
+    {
+      while (*alphabegin != '\0')
+      {
+        *ptr = *alphabegin;
+        alphabegin++;
+        ptr++;
+      }
+      while (*numbegin != '\0')
+      {
+        *ptr = *numbegin;
+        numbegin++;
+        ptr++;
+      }
+      if (dash == TRUE)
+      {
+        *ptr = '-';
+        ptr++;
+        while (*alphaend != '\0')
+        {
+          *ptr = *alphaend;
+          alphaend++;
+          ptr++;
+        }
+        while (*numend != '\0')
+        {
+          *ptr = *numend;
+          numend++;
+          ptr++;
+        }
+      }
+      *ptr = '\0';
+    }
+    else
+    {
+      while (*numbegin != '\0')
+      {
+        *ptr = *numbegin;
+        numbegin++;
+        ptr++;
+      }
+      while (*alphabegin != '\0')
+      {
+        *ptr = *alphabegin;
+        alphabegin++;
+        ptr++;
+      }
+      if (dash == TRUE)
+      {
+        *ptr = '-';
+        ptr++;
+        while (*numend != '\0')
+        {
+          *ptr = *numend;
+          numend++;
+          ptr++;
+        }
+        while (*alphaend != '\0')
+        {
+          *ptr = *alphaend;
+          alphaend++;
+          ptr++;
+        }
+      }
+      *ptr = '\0';
+    }
+  }
+  return retval;
+}
+
+/* !!! still need to add StripParanthesis equivalent !!! */
+
+static void DoSup (
+  ValNodePtr PNTR head,
+  CharPtr issue,
+  CharPtr part_sup,
+  CharPtr part_supi
+)
+
+{
+  size_t   len;
+  CharPtr  str;
+  CharPtr  temp;
+
+  len = StringLen (issue) + StringLen (part_sup) + StringLen (part_supi) + 25;
+  str = MemNew (sizeof (Char) * len);
+  if (str == NULL) return;
+  temp = str;
+
+  if (! StringHasNoText (part_sup)) {
+    *temp = ' ';
+    temp++;
+    temp = StringMove (temp, part_sup);
+  }
+  if (StringHasNoText (issue) && StringHasNoText (part_supi)) {
+    ValNodeCopyStr (head, 0, str);
+    MemFree (str);
+    return;
+  }
+  *temp = ' ';
+  temp++;
+  *temp = '(';
+  temp++;
+  if (! StringHasNoText (issue)) {
+    temp = StringMove (temp, issue);
+  }
+  if (! StringHasNoText (part_supi)) {
+    *temp = ' ';
+    temp++;
+    temp = StringMove (temp, part_supi);
+  }
+  *temp = ')';
+  temp++;
+  ValNodeCopyStr (head, 0, str);
+  MemFree (str);
+}
+
+static CharPtr FormatCitJour (
+  FmtType format,
+  Boolean citArtIsoJta,
+  CitJourPtr cjp
+)
+
+{
+  Char        buf [256];
+  DatePtr     dp;
+  Boolean     electronic_journal = FALSE;
+  ValNodePtr  head = NULL;
+  ImprintPtr  imp;
+  CharPtr     issue = NULL;
+  Char        pages [128];
+  CharPtr     part_sup = NULL;
+  CharPtr     part_supi = NULL;
+  CharPtr     rsult = NULL;
+  CharPtr     title;
+  ValNodePtr  ttl;
+  CharPtr     volume;
+  Char        year [8];
+
+  if (cjp == NULL) return NULL;
+
+  ttl = cjp->title;
+  if (ttl == NULL) return NULL;
+
+  /* always use iso_jta title if present */
+
+  while (ttl != NULL && ttl->choice != Cit_title_iso_jta) {
+    ttl = ttl->next;
+  }
+
+  /* release mode requires iso_jta title */
+
+  if (ttl == NULL) {
+    ttl = cjp->title;
+    if (ttl != NULL && ttl->choice == Cit_title_name) {
+      title = (CharPtr) ttl->data.ptrvalue;
+      if (title != NULL && StringNCmp (title, "(er)", 4) == 0) {
+        electronic_journal = TRUE;
+      }
+    }
+    if (citArtIsoJta && (! electronic_journal)) return NULL;
+  }
+
+  imp = cjp->imp;
+  if (imp == NULL) return NULL;
+
+  dp = imp->date;
+  year [0] = '\0';
+  if (dp != NULL) {
+    if (dp->data [0] == 1) {
+      if (dp->data [1] != 0) {
+        sprintf (year, " (%ld)", (long) (1900 + dp->data [1]));
+      }
+    } else {
+      StringCpy (year, " (");
+      StringNCat (year, dp->str, 4);
+      StringCat (year, ")");
+    }
+  }
+
+  if (imp->prepub == 1 || imp->prepub == 255) {
+    sprintf (buf, "Unpublished %s", year);
+    return StringSave (buf);
+  }
+
+  title = (CharPtr) ttl->data.ptrvalue;
+  if (StringLen (title) < 3) return StringSave (".");
+
+  ValNodeCopyStr (&head, 0, title);
+
+  volume = imp->volume;
+  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+    issue = imp->issue;
+    part_sup = imp->part_sup;
+    part_supi = imp->part_supi;
+  }
+  pages [0] = '\0';
+  if (electronic_journal) {
+    StringNCpy_0 (pages, imp->pages, sizeof (pages));
+  } else {
+    FixPages (pages, imp->pages);
+  }
+
+  if (! StringHasNoText (volume)) {
+    AddValNodeString (&head, " ", volume, NULL);
+  }
+
+  if ((! StringHasNoText (volume)) || (! StringHasNoText (pages))) {
+    DoSup (&head, issue, part_sup, part_supi);
+  }
+
+  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+    if (! StringHasNoText (pages)) {
+      AddValNodeString (&head, ", ", pages, NULL);
+    }
+  } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
+    if (! StringHasNoText (pages)) {
+      AddValNodeString (&head, ":", pages, NULL);
+    } else if (imp->prepub == 2 || (StringHasNoText (volume))) {
+      ValNodeCopyStr (&head, 0, " 0:0-0");
+    }
+  }
+
+  ValNodeCopyStr (&head, 0, year);
+
+  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+    if (imp->prepub == 2) {
+      ValNodeCopyStr (&head, 0, " In press");
+    }
+  }
+
+  rsult = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  return rsult;
+}
+
+static CharPtr MakeAffilStr (
+  AffilPtr afp
+)
+
+{
+  ValNodePtr  head = NULL;
+  CharPtr     prefix = "";
+  CharPtr     rsult = NULL;
+
+  if (afp == NULL) return NULL;
+
+  if (! StringHasNoText (afp->affil)) {
+    ValNodeCopyStr (&head, 0, afp->affil);
+    prefix = ", ";
+  }
+
+  if (afp->choice == 2) {
+    if (! StringHasNoText (afp->div)) {
+      AddValNodeString (&head, prefix, afp->div, NULL);
+      prefix = ", ";
+    }
+    if (! StringHasNoText (afp->street)) {
+      AddValNodeString (&head, prefix, afp->street, NULL);
+      prefix = ", ";
+    }
+    if (! StringHasNoText (afp->city)) {
+      AddValNodeString (&head, prefix, afp->city, NULL);
+      prefix = ", ";
+    }
+    if (! StringHasNoText (afp->sub)) {
+      AddValNodeString (&head, prefix, afp->sub, NULL);
+      prefix = ", ";
+    }
+    if (! StringHasNoText (afp->country)) {
+      AddValNodeString (&head, prefix, afp->country, NULL);
+      prefix = ", ";
+    }
+  }
+
+  rsult = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  return rsult;
+}
+
+static CharPtr GetAffil (
+  AffilPtr afp
+)
+
+{
+  Boolean need_comma=FALSE;
+  CharPtr string=NULL, temp, ptr;
+  Char ch;
+  Int2 aflen=15;
+
+  if (afp == NULL) return NULL;
+  if (afp) {
+    if (afp -> choice == 1){
+      if (afp -> affil){
+        aflen += StringLen(afp -> affil);
+      }
+    }else if (afp -> choice == 2){
+      aflen += StringLen (afp -> affil) +
+      StringLen (afp -> div) +
+      StringLen (afp -> city) +
+      StringLen (afp -> sub) +
+      StringLen (afp -> street) +
+      StringLen (afp -> country) + StringLen(afp->postal_code);
+    }
+
+    temp = string = MemNew(aflen);
+
+    if ( afp -> choice == 1){
+       if (afp -> affil){
+        ptr = afp->affil;
+        while ((*temp = *ptr) != '\0')
+        {
+          temp++; ptr++;
+        }
+       }
+    }else if (afp -> choice == 2){
+
+      if( afp -> div) {
+        if (need_comma)
+        {
+          *temp = ','; temp++;
+          *temp = ' '; temp++;
+        }
+        ptr = afp->div;
+        while ((*temp = *ptr) != '\0')
+        {
+          temp++; ptr++;
+        }
+        need_comma = TRUE;
+      }
+
+      if(afp -> affil) {
+        if (need_comma)
+        {
+          *temp = ','; temp++;
+          *temp = ' '; temp++;
+        }
+        ptr = afp->affil;
+        while ((*temp = *ptr) != '\0')
+        {
+          temp++; ptr++;
+        }
+        need_comma = TRUE;
+      }
+
+      if(afp -> street) {
+        if (need_comma)
+        {
+          *temp = ','; temp++;
+          *temp = ' '; temp++;
+        }
+        ptr = afp->street;
+        while ((*temp = *ptr) != '\0')
+        {
+          temp++; ptr++;
+        }
+        need_comma = TRUE;
+      }
+
+      if( afp -> city) {
+        if (need_comma)
+        {
+          *temp = ','; temp++;
+          *temp = ' '; temp++;
+        }
+        ptr = afp->city;
+        while ((*temp = *ptr) != '\0')
+        {
+          temp++; ptr++;
+        }
+        need_comma = TRUE;
+      }
+
+      if( afp -> sub) {
+        if (need_comma)
+        {
+          *temp = ','; temp++;
+          *temp = ' '; temp++;
+        }
+        ptr = afp->sub;
+        while ((*temp = *ptr) != '\0')
+        {
+          temp++; ptr++;
+        }
+        need_comma = TRUE;
+      }
+
+      if( afp -> postal_code){
+        *temp = ' ';
+        temp++;
+        ptr = afp->postal_code;
+        while ((*temp = *ptr) != '\0')
+        {
+          temp++; ptr++;
+        }
+      }
+
+      if( afp -> country){
+        if (need_comma)
+        {
+          *temp = ','; temp++;
+          *temp = ' '; temp++;
+        }
+        ptr = afp->country;
+        while ((*temp = *ptr) != '\0')
+        {
+          temp++; ptr++;
+        }
+        need_comma = TRUE;
+      }
+    }
+    temp++;
+    *temp = '\0';
+  }
+
+    /* convert double quotes to single quotes */
+
+    ptr = string;
+    ch = *ptr;
+    while (ch != '\0') {
+      if (ch == '\"') {
+        *ptr = '\'';
+      }
+      ptr++;
+      ch = *ptr;
+    }
+
+  return string;
+}
+
+static CharPtr FormatCitBookArt (
+  FmtType format,
+  CitBookPtr cbp
+)
+
+{
+  AffilPtr     afp;
+  AuthListPtr  alp;
+  CharPtr      book_title = NULL;
+  Char         buf [256];
+  Char         ch;
+  DatePtr      dp;
+  ValNodePtr   head = NULL;
+  ImprintPtr   imp;
+  CharPtr      issue = NULL;
+  ValNodePtr   names = NULL;
+  Char         pages [128];
+  CharPtr      part_sup = NULL;
+  CharPtr      part_supi = NULL;
+  CharPtr      rsult = NULL;
+  CharPtr      str;
+  CharPtr      title;
+  ValNodePtr   ttl;
+  ValNodePtr   vnp;
+  CharPtr      volume;
+  Char         year [8];
+
+  if (cbp == NULL) return NULL;
+
+  ttl = cbp->title;
+  if (ttl == NULL) return NULL;
+
+  imp = cbp->imp;
+  if (imp == NULL) return NULL;
+
+  dp = imp->date;
+  year [0] = '\0';
+  if (dp != NULL) {
+    if (dp->data [0] == 1) {
+      if (dp->data [1] != 0) {
+        sprintf (year, "(%ld)", (long) (1900 + dp->data [1]));
+      }
+    } else {
+      StringCpy (year, "(");
+      StringNCat (year, dp->str, 4);
+      StringCpy (year, ")");
+    }
+  }
+
+  if (imp->prepub == 1 || imp->prepub == 255) {
+    sprintf (buf, "Unpublished %s", year);
+    return StringSave (buf);
+  }
+
+  title = (CharPtr) ttl->data.ptrvalue;
+  if (StringLen (title) < 3) return StringSave (".");
+
+  ValNodeCopyStr (&head, 0, "(in) ");
+
+  alp = cbp->authors;
+  if (alp != NULL) {
+    str = GetAuthorsString (format, alp, NULL, NULL, NULL);
+    if (str != NULL) {
+      ValNodeCopyStr (&head, 0, str);
+      names = alp->names;
+      if (names != NULL) {
+        if (names->next != NULL) {
+          ValNodeCopyStr (&head, 0, " (Eds.);");
+        } else {
+          ValNodeCopyStr (&head, 0, " (Ed.);");
+        }
+      }
+      ValNodeCopyStr (&head, 0, "\n");
+    }
+    MemFree (str);
+  }
+
+  book_title = StringSaveNoNull (title);
+  vnp = ValNodeAddStr (&head, 0, book_title);
+  if (book_title != NULL) {
+
+    /* make book title all caps */
+
+    title = book_title;
+    ch = *title;
+    while (ch != '\0') {
+      *title = TO_UPPER (ch);
+      title++;
+      ch = *title;
+    }
+  }
+
+  volume = imp->volume;
+  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+    issue = imp->issue;
+    part_sup = imp->part_sup;
+    part_supi = imp->part_supi;
+  }
+  pages [0] = '\0';
+  FixPages (pages, imp->pages);
+
+  if ((! StringHasNoText (volume)) && (StringCmp (volume, "0") != 0)) {
+    AddValNodeString (&head, ", Vol. ", volume, NULL);
+    DoSup (&head, issue, part_sup, part_supi);
+  }
+
+  if (! StringHasNoText (pages)) {
+    AddValNodeString (&head, ": ", pages, NULL);
+  }
+
+  if (book_title != NULL) {
+    ValNodeCopyStr (&head, 0, ";\n");
+  }
+
+  afp = imp->pub;
+  if (afp != NULL) {
+    str = MakeAffilStr (afp);
+    if (str != NULL) {
+      ValNodeCopyStr (&head, 0, str);
+      ValNodeCopyStr (&head, 0, " ");
+      MemFree (str);
+    }
+  }
+
+  AddValNodeString (&head, NULL, year, NULL);
+
+  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+    if (imp->prepub == 2) {
+      ValNodeCopyStr (&head, 0, " In press");
+    }
+  }
+
+  rsult = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  return rsult;
+}
+
+static CharPtr FormatCitBook (
+  FmtType format,
+  CitBookPtr cbp
+)
+
+{
+  AffilPtr   afp;
+  char       year[5];
+  CharPtr    bookTitle=NULL;
+  CharPtr    retval = NULL;
+  CharPtr    temp;
+  DatePtr    dp;
+  ImprintPtr ip;
+  int        aflen = 0;
+  CharPtr    p;
+  CharPtr    affilStr = NULL;
+
+  /* Check parameters */
+
+  if (cbp == NULL)
+    return NULL;
+
+  if ( cbp -> othertype != 0)
+    return NULL;
+
+  ip = cbp -> imp;
+
+  /* Format the year */
+
+  dp = ip -> date;
+  year[0] = '\0';
+
+  if ( dp -> data[0] == 1)
+    sprintf(year,"%ld",(long) ( 1900+dp -> data[1]));
+  else
+    {
+      StringNCpy( (CharPtr) year, (CharPtr) dp -> str, (size_t) 4);
+      year[4] = '\0';
+    }
+
+  /* Get the book title */
+
+  if (cbp->title)
+    bookTitle = StringSave(cbp -> title -> data.ptrvalue);
+
+  /* Get the affiliation length */
+
+  if ( ip -> pub){
+    afp = ip -> pub;
+    aflen = StringLen(afp -> affil)+ 5;
+    if ( afp -> choice == 2){
+      aflen += 3 + StringLen(afp -> div);
+      aflen += 3 + StringLen(afp -> street);
+      aflen += 3 + StringLen(afp -> city);
+      aflen += 3 + StringLen(afp -> sub);
+      aflen += 3 + StringLen(afp -> country);
+    }
+  } else{
+    aflen = 22;
+  }
+  if (ip->prepub == 2)
+    aflen += 10;
+
+  /* Create a Char String big enough to hold */
+  /* the title, year, and affiliation.       */
+
+  temp = retval = MemNew( (size_t) (30+StringLen( bookTitle)+StringLen( year) + aflen) );
+
+  /* Convert the title to upper case and */
+  /* add it to the string.               */
+
+  for ( p = bookTitle; *p; p++)
+    *p = TO_UPPER(*p);
+
+  /* temp = StringMove(temp, "Book: "); */
+  temp = StringMove(temp, "(in) ");
+  temp = StringMove(temp, bookTitle);
+  temp = StringMove(temp, ".");
+
+  /* Add the affiliation to the string */
+
+  if ( ip -> pub)
+    {
+      afp = ip -> pub;
+      *temp = ' ';
+      temp++;
+      affilStr = MakeAffilStr(afp);
+      temp = StringMove(temp,affilStr);
+    }
+
+  /* Add the year to the string */
+
+  if (year[0] != '\0')
+    {
+      if (affilStr != NULL)
+        temp = StringMove(temp," (");
+      else
+        temp = StringMove(temp, "(");
+      temp = StringMove(temp, year);
+      temp = StringMove(temp, ")");
+    }
+
+  /* If in press, add note */
+
+  if (ip->prepub == 2)
+    temp = StringMove(temp, ", In press");
+
+  /* Clean up and return */
+
+  if (bookTitle)
+    MemFree(bookTitle);
+
+  return retval;
+
+}
+
+static CharPtr FormatThesis (
+  FmtType format,
+  CitBookPtr cbp
+)
+
+{
+  AffilPtr     afp;
+  Char         ch;
+  DatePtr      dp;
+  ValNodePtr   head = NULL;
+  ImprintPtr   imp;
+  CharPtr      ptr;
+  CharPtr      rsult = NULL;
+  CharPtr      str;
+  CharPtr      suffix = NULL;
+  Char         year [8];
+
+  if (cbp == NULL) return NULL;
+  if (cbp->othertype != 2 || cbp->let_type != 3) return NULL;
+
+  imp = cbp->imp;
+  if (imp == NULL) return NULL;
+
+  dp = imp->date;
+  year [0] = '\0';
+  if (dp != NULL) {
+    if (dp->data [0] == 1) {
+      if (dp->data [1] != 0) {
+        sprintf (year, "%ld", (long) (1900 + dp->data [1]));
+      }
+    } else {
+      StringNCpy (year, dp->str, (size_t) 4);
+      year [4] = '\0';
+    }
+  }
+
+  AddValNodeString (&head, "Thesis (", year, ")");
+
+  if (imp->prepub == 2) {
+    suffix = ", In press";
+  }
+
+  str = NULL;
+  afp = imp->pub;
+  if (afp != NULL) {
+    if (afp->choice == 1) {
+      if (StringLen (afp->affil) > 7) {
+        str = StringSave (afp->affil);
+      }
+    } else if (afp->choice == 2) {
+      str = MakeAffilStr (afp);
+    }
+  }
+
+  if (str != NULL) {
+
+    /* convert double quotes to single quotes */
+
+    ptr = str;
+    ch = *ptr;
+    while (ch != '\0') {
+      if (ch == '\"') {
+        *ptr = '\'';
+      }
+      ptr++;
+      ch = *ptr;
+    }
+    AddValNodeString (&head, " ", str, suffix);
+    MemFree (str);
+  }
+
+  rsult = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  return rsult;
+}
+
+static CharPtr FormatCitArt (
+  FmtType format,
+  Boolean citArtIsoJta,
+  CitArtPtr cap
+)
+
+{
+  CitBookPtr  cbp;
+  CitJourPtr  cjp;
+  CharPtr     rsult = NULL;
+
+  if (cap == NULL) return NULL;
+
+  switch (cap->from) {
+    case 1 :
+      cjp = (CitJourPtr) cap->fromptr;
+      if (cjp != NULL) {
+        rsult = FormatCitJour (format, citArtIsoJta, cjp);
+      }
+      break;
+    case 2 :
+      cbp = (CitBookPtr) cap->fromptr;
+      if (cbp != NULL) {
+        rsult = FormatCitBookArt (format, cbp);
+      }
+      break;
+    case 3 :
+      cbp = (CitBookPtr) cap->fromptr;
+      if (cbp != NULL) {
+        rsult = FormatCitBookArt (format, cbp);
+      }
+      break;
+    default :
+      break;
+  }
+
+  return rsult;
+}
+
+static CharPtr FormatCitPat (
+  FmtType   format,
+  CitPatPtr cpp,
+  SeqIdPtr  seqidp
+)
+
+{
+  AffilPtr       afp;
+  AuthListPtr    alp;
+  Char           date [40];
+  ValNodePtr     head = NULL;
+  CharPtr        prefix = NULL;
+  CharPtr        rsult = NULL;
+  SeqIdPtr       sip;
+  CharPtr        suffix = NULL;
+  PatentSeqIdPtr psip;
+  Int4           pat_seqid = 0;
+  Char           buf[10];
+
+  if (cpp == NULL) return NULL;
+
+  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+    ValNodeCopyStr (&head, 0, "Patent: ");
+    suffix = " ";
+  } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
+    ValNodeCopyStr (&head, 0, "Patent number ");
+  }
+
+  if (! StringHasNoText (cpp->country)) {
+    AddValNodeString (&head, NULL, cpp->country, suffix);
+  }
+
+  if (! StringHasNoText (cpp->number)) {
+    ValNodeCopyStr (&head, 0, cpp->number);
+  } else if (! StringHasNoText (cpp->app_number)) {
+    AddValNodeString (&head, "(", cpp->app_number, ")");
+  }
+
+  if (! StringHasNoText (cpp->doc_type)) {
+    AddValNodeString (&head, "-", cpp->doc_type, NULL);
+  }
+
+  /* pat_seqid test */
+
+  for (sip = seqidp; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_PATENT) {
+      psip = (PatentSeqIdPtr) sip -> data.ptrvalue;
+      if (psip != NULL) {
+        pat_seqid = psip->seqid;
+      }
+    }
+  }
+  if (pat_seqid > 0) {
+    if (format == EMBL_FMT) {
+      sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", ");
+      ValNodeCopyStr (&head, 0, buf);
+    } else {
+      sprintf(buf,"%s%ld ", " ", (long) pat_seqid);
+      ValNodeCopyStr (&head, 0, buf);
+    }
+  } else {
+    ValNodeCopyStr (&head, 0, " ");
+  }
+
+  /* Date */
+
+  date [0] = '\0';
+  if (cpp->date_issue != NULL) {
+    DateToFF (date, cpp->date_issue, FALSE);
+  } else if (cpp->app_date != NULL) {
+    DateToFF (date, cpp->app_date, FALSE);
+  }
+  if (! StringHasNoText (date)) {
+    ValNodeCopyStr (&head, 0, date);
+  }
+
+  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+    ValNodeCopyStr (&head, 0, ";");
+  } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
+    ValNodeCopyStr (&head, 0, ".");
+  }
+
+  alp = cpp->authors;
+  if (alp != NULL) {
+    afp = alp->affil;
+    if (afp != NULL) {
+      suffix = NULL;
+      if (afp->choice == 2) {
+        suffix = ";";
+      }
+
+      /* If and of the affiliation fields are */
+      /* non-blank, put them on a new line.   */
+
+      if ((! StringHasNoText (afp->affil)) ||
+          (! StringHasNoText (afp->street)) ||
+          (! StringHasNoText (afp->div)) ||
+          (! StringHasNoText (afp->city)) ||
+          (! StringHasNoText (afp->sub)) ||
+          (! StringHasNoText (afp->country)))
+        ValNodeCopyStr (&head, 0, "\n");
+
+      /* Write out the affiliation fields */
+
+      if (! StringHasNoText (afp->affil)) {
+        AddValNodeString (&head, NULL, afp->affil, suffix);
+        prefix = " ";
+      }
+      if (! StringHasNoText (afp->street)) {
+        AddValNodeString (&head, prefix, afp->street, ";");
+        prefix = " ";
+      }
+      if (! StringHasNoText (afp->div)) {
+        AddValNodeString (&head, prefix, afp->div, ";");
+        prefix = " ";
+      }
+      if (! StringHasNoText (afp->city)) {
+        AddValNodeString (&head, prefix, afp->city, NULL);
+        prefix = ", ";
+      }
+      if (! StringHasNoText (afp->sub)) {
+        AddValNodeString (&head, prefix, afp->sub, NULL);
+      }
+      if (! StringHasNoText (afp->country)) {
+        AddValNodeString (&head, ";\n", afp->country, ";");
+      }
+    }
+  }
+
+  rsult = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  /*
+  s_StringCleanup(rsult);
+  */
+
+  return rsult;
+}
+
+static CharPtr FormatCitGen (
+  FmtType format,
+  Boolean dropBadCitGens,
+  Boolean noAffilOnUnpub,
+  CitGenPtr cgp
+)
+
+{
+  CharPtr      affil = NULL;
+  AuthListPtr  alp = NULL;
+  Char         ch;
+  DatePtr      dp;
+  ValNodePtr   head = NULL;
+  CharPtr      inpress = NULL;
+  CharPtr      journal = NULL;
+  Char         pages [128];
+  CharPtr      prefix = NULL;
+  CharPtr      ptr;
+  CharPtr      rsult = NULL;
+  Char         year [8];
+
+  if (cgp == NULL) return NULL;
+
+  if (cgp->journal == NULL && StringNICmp (cgp->cit, "unpublished", 11) == 0) {
+    if (noAffilOnUnpub) {
+
+      /* !!! temporarily put date in unpublished citation for QA !!! */
+
+      if (dropBadCitGens) {
+        year [0] = '\0';
+        dp = cgp->date;
+        if (dp != NULL) {
+          if (dp->data [0] == 1) {
+            if (dp->data [1] != 0) {
+              sprintf (year, " (%ld)", (long) (1900 + dp->data [1]));
+            }
+          } else {
+            StringCpy (year, " (");
+            StringNCat (year, dp->str, 4);
+            StringCat (year, ")");
+          }
+        }
+        AddValNodeString (&head, NULL, "Unpublished", NULL);
+        AddValNodeString (&head, NULL, year, NULL);
+        rsult = MergeFFValNodeStrs (head);
+        ValNodeFreeData (head);
+        return rsult;
+      }
+
+      /* !!! remove above section once QA against asn2ff is done !!! */
+
+      return StringSave ("Unpublished");
+    }
+
+    alp = cgp->authors;
+    if (alp != NULL) {
+      affil = GetAffil (alp->affil);
+      if (! StringHasNoText (affil)) {
+        rsult = MemNew ((size_t) StringLen (affil) + (size_t) StringLen (cgp->cit) + 15);
+        StringCpy (rsult, "Unpublished ");
+        StringCat (rsult, affil);
+        TrimSpacesAroundString (rsult);
+        return rsult;
+      }
+    }
+
+    rsult = StringSave (cgp->cit);
+    TrimSpacesAroundString (rsult);
+    return rsult;
+  }
+
+  year [0] = '\0';
+  dp = cgp->date;
+  if (dp != NULL) {
+    if (dp->data [0] == 1) {
+      if (dp->data [1] != 0) {
+        sprintf (year, " (%ld)", (long) (1900 + dp->data [1]));
+      }
+    } else {
+      StringCpy (year, " (");
+      StringNCat (year, dp->str, 4);
+      StringCat (year, ")");
+    }
+  }
+
+  pages [0] = '\0';
+  if (cgp->pages != NULL) {
+    FixPages (pages, cgp->pages);
+  }
+
+  if (cgp->journal != NULL) {
+    journal = (CharPtr) cgp->journal->data.ptrvalue;
+  }
+  if (cgp->cit != NULL) {
+    ptr = StringStr (cgp->cit, "Journal=\"");
+    if (ptr != NULL) {
+      journal = ptr + 9;
+    } else if (StringNICmp (cgp->cit, "submitted", 8) == 0 ||
+               StringNICmp (cgp->cit, "unpublished", 11) == 0) {
+
+      if ((! dropBadCitGens) || journal != NULL) {
+        inpress = cgp->cit;
+      } else {
+        inpress = "Unpublished";
+      }
+    } else if (StringNICmp (cgp->cit, "Online Publication", 18) == 0 ||
+               StringNICmp (cgp->cit, "Published Only in DataBase", 26) == 0) {
+
+      inpress = cgp->cit;
+    } else if ((! dropBadCitGens) && journal == NULL) {
+      journal = cgp->cit;
+    }
+  }
+  if (journal != NULL) {
+    journal = StringSave (journal);
+    for (ptr = journal, ch = *ptr; ch != '\0'; ptr++, ch = *ptr) {
+      if (ch == '=' || ch == '\"') {
+        *ptr = '\0';
+      }
+    }
+    ValNodeAddStr (&head, 0, journal);
+    prefix = " ";
+  }
+
+  if (! StringHasNoText (inpress)) {
+    AddValNodeString (&head, prefix, inpress, NULL);
+    prefix = " ";
+  }
+
+  if (! StringHasNoText (cgp->volume)) {
+    AddValNodeString (&head, prefix, cgp->volume, NULL);
+  }
+
+  if (! StringHasNoText (pages)) {
+    if (format == GENBANK_FMT) {
+      AddValNodeString (&head, ", ", pages, NULL);
+    } else if (format == EMBL_FMT) {
+      AddValNodeString (&head, ":", pages, NULL);
+    }
+  }
+
+  if (! StringHasNoText (year)) {
+    AddValNodeString (&head, NULL, year, NULL);
+  }
+
+  rsult = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  return rsult;
+}
+
+static CharPtr FormatCitSub (
+  FmtType format,
+  CitSubPtr csp
+)
+
+{
+  CharPtr      affil;
+  AffilPtr     afp;
+  AuthListPtr  alp;
+  Char         buf [256];
+  Char         date [40];
+  ValNodePtr   head = NULL;
+  CharPtr      rsult = NULL;
+
+  if (csp == NULL) return NULL;
+
+  date [0] = '\0';
+  if (csp->date != NULL) {
+    DateToFF (date, csp->date, TRUE);
+  }
+  if (StringHasNoText (date)) {
+    StringCpy (date, "??-???-????");
+  }
+
+  sprintf (buf, "Submitted (%s)", date);
+  ValNodeCopyStr (&head, 0, buf);
+
+  alp = csp->authors;
+  if (alp != NULL) {
+    afp = alp->affil;
+    if (afp != NULL) {
+      affil = GetAffil (afp);
+      if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
+        if (StringNCmp(affil, " to the EMBL/GenBank/DDBJ databases.", 36) != 0) {
+          ValNodeCopyStr (&head, 0, " to the EMBL/GenBank/DDBJ databases.\n");
+        } else {
+          ValNodeCopyStr (&head, 0, " ");
+        }
+      } else {
+        ValNodeCopyStr (&head, 0, " ");
+      }
+      ValNodeCopyStr (&head, 0, affil);
+      MemFree (affil);
+    } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
+      ValNodeCopyStr (&head, 0, " to the EMBL/GenBank/DDBJ databases.\n");
+    }
+  }
+
+  rsult = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  return rsult;
+}
+
+static CharPtr GetPubJournal (
+  FmtType format,
+  Boolean dropBadCitGens,
+  Boolean noAffilOnUnpub,
+  Boolean citArtIsoJta,
+  PubdescPtr pdp,
+  CitSubPtr csp,
+  SeqIdPtr  seqidp,
+  IndxPtr index
+)
+
+{
+  CitArtPtr        cap;
+  CitBookPtr       cbp;
+  CitGenPtr        cgp;
+  CitPatPtr        cpp;
+  CharPtr          journal = NULL;
+  MedlineEntryPtr  mep;
+  ValNodePtr       vnp;
+
+  if (csp != NULL) {
+    return FormatCitSub (format, csp);
+  }
+  if (pdp == NULL) return NULL;
+
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    switch (vnp->choice) {
+      case PUB_Gen :
+        cgp = (CitGenPtr) vnp->data.ptrvalue;
+        if (cgp != NULL) {
+          if (StringNICmp ("BackBone id_pub", cgp->cit, 15) != 0) {
+            if (cgp->cit == NULL && cgp->journal == NULL && cgp->date == NULL && cgp->serial_number) {
+              break; /* skip just serial number */
+            }
+          }
+          journal = FormatCitGen (format, dropBadCitGens, noAffilOnUnpub, cgp);
+        }
+        break;
+      case PUB_Sub :
+        csp = (CitSubPtr) vnp->data.ptrvalue;
+        if (csp != NULL) {
+          journal = FormatCitSub (format, csp);
+        }
+        break;
+      case PUB_Medline :
+        mep = (MedlineEntryPtr) vnp->data.ptrvalue;
+        if (mep != NULL) {
+          cap = mep->cit;
+          if (cap != NULL) {
+            journal = FormatCitArt (format, citArtIsoJta, cap);
+          }
+        }
+        break;
+      case PUB_Article :
+        cap = (CitArtPtr) vnp->data.ptrvalue;
+        if (cap != NULL) {
+          journal = FormatCitArt (format, citArtIsoJta, cap);
+        }
+        break;
+      case PUB_Book :
+      case PUB_Proc :
+        cbp = (CitBookPtr) vnp->data.ptrvalue;
+        if (cbp != NULL) {
+          journal = FormatCitBook (format, cbp);
+        }
+        break;
+      case PUB_Man :
+        cbp = (CitBookPtr) vnp->data.ptrvalue;
+        if (cbp != NULL) {
+          journal = FormatThesis (format, cbp);
+        }
+        break;
+      case PUB_Patent :
+        cpp = (CitPatPtr) vnp->data.ptrvalue;
+        if (cpp != NULL) {
+          journal = FormatCitPat (format, cpp, seqidp);
+        }
+        break;
+      default :
+        break;
+    }
+
+    /* optionally populate indexes for NCBI internal database */
+
+    if (index != NULL && journal != NULL) {
+
+      /* skip non-informative cit-gens */
+
+      if (StringNICmp (journal, "submitted", 8) == 0 ||
+          StringNICmp (journal, "unpublished", 11) == 0 ||
+          StringNICmp (journal, "Online Publication", 18) == 0 ||
+          StringNICmp (journal, "Published Only in DataBase", 26) == 0) {
+      } else {
+        ValNodeCopyStrToHead (&(index->journals), 0, journal);
+      }
+    }
+
+    if (journal != NULL) return journal;
+  }
+
+  return NULL;
+}
+
+static Int4 GetMuid (
+  PubdescPtr pdp
+)
+
+{
+  MedlineEntryPtr  mep;
+  ValNodePtr       vnp;
+
+  if (pdp == NULL) return 0;
+
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    switch (vnp->choice) {
+      case PUB_Medline :
+        mep = (MedlineEntryPtr) vnp->data.ptrvalue;
+        if (mep != NULL) {
+          return mep->uid;
+        }
+        break;
+      case PUB_Muid :
+        return vnp->data.intvalue;
+      default :
+        break;
+    }
+  }
+
+  return 0;
+}
+
+static Int4 GetPmid (
+  PubdescPtr pdp
+)
+
+{
+  MedlineEntryPtr  mep;
+  ValNodePtr       vnp;
+
+  if (pdp == NULL) return 0;
+
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    switch (vnp->choice) {
+      case PUB_Medline :
+        mep = (MedlineEntryPtr) vnp->data.ptrvalue;
+        if (mep != NULL) {
+          return mep->pmid;
+        }
+        break;
+      case PUB_PMid :
+        return vnp->data.intvalue;
+      default :
+        break;
+    }
+  }
+
+  return 0;
+}
+
+NLM_EXTERN CharPtr CleanQualValue (
+  CharPtr str
+)
+
+{
+  Char     ch;
+  CharPtr  dst;
+  CharPtr  ptr;
+
+  if (str == NULL || str [0] == '\0') return NULL;
+
+  dst = str;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    if (ch == '\n' || ch == '\r' || ch == '\t' || ch == '"') {
+      *dst = ' ';
+      dst++;
+    } else {
+      *dst = ch;
+      dst++;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+  *dst = '\0';
+
+  return str;
+}
+
+NLM_EXTERN CharPtr Asn2gnbkCompressSpaces (CharPtr str)
+
+{
+  Char     ch;
+  CharPtr  dst;
+  Char     last;
+  CharPtr  ptr;
+
+  if (str != NULL && str [0] != '\0') {
+    dst = str;
+    ptr = str;
+    ch = *ptr;
+    while (ch != '\0' && ch <= ' ') {
+      ptr++;
+      ch = *ptr;
+    }
+    while (ch != '\0') {
+      *dst = ch;
+      dst++;
+      ptr++;
+      last = ch;
+      ch = *ptr;
+      if (ch != '\0' && ch < ' ') {
+        *ptr = ' ';
+        ch = *ptr;
+      }
+      while (ch != '\0' && last <= ' ' && ch <= ' ') {
+        ptr++;
+        ch = *ptr;
+      }
+    }
+    *dst = '\0';
+    dst = NULL;
+    ptr = str;
+    ch = *ptr;
+    while (ch != '\0') {
+      if (ch != ' ') {
+        dst = NULL;
+      } else if (dst == NULL) {
+        dst = ptr;
+      }
+      ptr++;
+      ch = *ptr;
+    }
+    if (dst != NULL) {
+      *dst = '\0';
+    }
+  }
+  return str;
+}
+
+NLM_EXTERN CharPtr StripAllSpaces (
+  CharPtr str
+)
+
+{
+  Char     ch;
+  CharPtr  dst;
+  CharPtr  ptr;
+
+  if (str == NULL || str [0] == '\0') return NULL;
+
+  dst = str;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    if (ch == ' ' || ch == '\t') {
+    } else {
+      *dst = ch;
+      dst++;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+  *dst = '\0';
+
+  return str;
+}
+
+static CharPtr remarksText [] = {
+  "full automatic", "full staff_review", "full staff_entry",
+  "simple staff_review", "simple staff_entry", "simple automatic",
+  "unannotated automatic", "unannotated staff_review", "unannotated staff_entry",
+  NULL
+};
+
+static void AddReferenceToGbseq (
+  GBSeqPtr gbseq,
+  GBReferencePtr gbref,
+  CharPtr str
+)
+
+{
+  CharPtr  copy;
+  CharPtr  ptr;
+  CharPtr  ref;
+
+  if (gbseq == NULL || gbref == NULL || StringHasNoText (str)) return;
+
+  copy = StringSave (str);
+
+  /* link in reverse order, to be reversed in slash block */
+
+  gbref->next = gbseq->references;
+  gbseq->references = gbref;
+
+  /* now parse or make ASN required default values for remaining fields */
+
+  if (StringNCmp (copy, "REFERENCE   ", 12) == 0) {
+    ref = copy + 12;
+    ptr = StringStr (ref, "\n  AUTHORS");
+    if (ptr == NULL) {
+      ptr = StringStr (ref, ")\n");
+    }
+    if (ptr != NULL) {
+      *ptr = '\0';
+      gbref->reference = StringSave (ref);
+    }
+  }
+
+  if (gbref->reference == NULL) {
+    gbref->reference = StringSave ("?");
+  }
+
+  CleanQualValue (gbref->reference);
+  Asn2gnbkCompressSpaces (gbref->reference);
+
+  if (gbref->journal == NULL) {
+    gbref->journal = StringSave ("?");
+  }
+
+  CleanQualValue (gbref->journal);
+  Asn2gnbkCompressSpaces (gbref->journal);
+
+  MemFree (copy);
+}
+
+static Boolean IsCitSub (
+  PubdescPtr pdp,
+  CitSubPtr csp
+)
+
+{
+  ValNodePtr  vnp;
+
+  if (csp != NULL) return TRUE;
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == PUB_Sub) return TRUE;
+  }
+  return FALSE;
+}
+
+static void  FF_www_muid(
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  Int4 muid
+)
+{
+  Char numbuf[40];
+  
+  if ( GetWWW(ajp) ) {
+    FFAddTextToString(ffstring, "<a href=", link_muid, NULL, FALSE, FALSE, TILDE_IGNORE);
+    sprintf(numbuf, "%ld", (long)muid);
+    FFAddTextToString(ffstring, "uid=", numbuf, "&form=6&db=m&Dopt=r>", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, numbuf, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+  } else {
+    sprintf(numbuf, "%ld", (long)muid);
+    FFAddOneString(ffstring, numbuf, FALSE, FALSE, TILDE_IGNORE);
+  }
+}
+
+NLM_EXTERN CharPtr FormatReferenceBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  AuthListPtr        alp;
+  Asn2gbSectPtr      asp;
+  BioseqPtr          bsp;
+  Char               buf [150];
+  CitArtPtr          cap;
+  Char               ch;
+  CitJourPtr         cjp;
+  Boolean            citArtIsoJta;
+  CharPtr            consortium;
+  CitRetractPtr      crp;
+  CitSubPtr          csp = NULL;
+  SeqMgrDescContext  dcontext;
+  SeqMgrFeatContext  fcontext;
+  Int4               gibbsq;
+  GBReferencePtr     gbref = NULL;
+  GBSeqPtr           gbseq;
+  Int2               i;
+  ImprintPtr         imp;
+  IndxPtr            index;
+  IntRefBlockPtr     irp;
+  size_t             len;
+  SeqLocPtr          loc = NULL;
+  MedlineEntryPtr    mep;
+  Int4               muid = 0;
+  Boolean            needsPeriod = FALSE;
+  SeqLocPtr          nextslp;
+  Boolean            notFound;
+  ObjMgrDataPtr      omdp;
+  PubdescPtr         pdp = NULL;
+  PubdescPtr         pdpcopy = NULL;
+  PubmedEntryPtr     pep = NULL;
+  Int4               pmid = 0;
+  CharPtr            prefix = NULL;
+  RefBlockPtr        rbp;
+  SubmitBlockPtr     sbp;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp = NULL;
+  SeqIdPtr           sip;
+  SeqLocPtr          slp;
+  SeqSubmitPtr       ssp;
+  Int4               start;
+  Int4               stop;
+  CharPtr            str;
+  Boolean            strict_isojta;
+  CharPtr            suffix = NULL;
+  CharPtr            tmp;
+  Boolean            trailingPeriod = TRUE;
+  ValNodePtr         vnp;
+  StringItemPtr      ffstring, temp;
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  rbp = (RefBlockPtr) bbp;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+  bsp = asp->bsp;
+  if (bsp == NULL) return NULL;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return NULL;
+
+  if (ajp->index) {
+    index = &asp->index;
+  } else {
+    index = NULL;
+  }
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (! StringHasNoText (rbp->string)) return StringSave (rbp->string);
+
+  /* could be descriptor, feature, or submit block citation */
+
+  if (rbp->itemtype == OBJ_SEQDESC) {
+
+    sdp = SeqMgrGetDesiredDescriptor (rbp->entityID, NULL, rbp->itemID, 0, NULL, &dcontext);
+    if (sdp != NULL && dcontext.seqdesctype == Seq_descr_pub) {
+      pdp = (PubdescPtr) sdp->data.ptrvalue;
+    }
+
+  } else if (rbp->itemtype == OBJ_SEQFEAT) {
+
+    sfp = SeqMgrGetDesiredFeature (rbp->entityID, NULL, rbp->itemID, 0, NULL, &fcontext);
+    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_PUB) {
+      pdp = (PubdescPtr) sfp->data.value.ptrvalue;
+    }
+
+  } else if (rbp->itemtype == OBJ_SEQSUB_CIT) {
+
+    omdp = ObjMgrGetData (rbp->entityID);
+    if (omdp != NULL && omdp->datatype == OBJ_SEQSUB) {
+      ssp = (SeqSubmitPtr) omdp->dataptr;
+      if (ssp != NULL && ssp->datatype == 1) {
+        sbp = ssp->sub;
+        if (sbp != NULL) {
+          csp = sbp->cit;
+        }
+      }
+    }
+  }
+
+  if (pdp == NULL && csp == NULL) return NULL;
+
+  temp = FFGetString(ajp);
+  if ( temp == NULL ) {
+    FFRecycleString(ajp, ffstring);
+    return NULL;
+  }
+
+  /* any justuids left at this point is RefSeq protein, and should be fetched */
+
+  irp = (IntRefBlockPtr) rbp;
+  if (irp->justuids) {
+    if (rbp->pmid != 0) {
+      pep = GetPubMedForUid (rbp->pmid);
+    } else if (rbp->muid != 0) {
+      pep = GetPubMedForUid (rbp->muid);
+    }
+    if (pep != NULL) {
+      mep = (MedlineEntryPtr) pep->medent;
+      if (mep != NULL && mep->cit != NULL) {
+        pdpcopy = AsnIoMemCopy ((Pointer) pdp,
+                                 (AsnReadFunc) PubdescAsnRead,
+                                 (AsnWriteFunc) PubdescAsnWrite);
+        cap = AsnIoMemCopy ((Pointer) mep->cit,
+                            (AsnReadFunc) CitArtAsnRead,
+                            (AsnWriteFunc) CitArtAsnWrite);
+        vnp = ValNodeAddPointer (&(pdpcopy->pub), PUB_Article, (Pointer) cap);
+        pdp = pdpcopy;
+      }
+    }
+  }
+
+  /* print serial number */
+  FFStartPrint(temp, afp->format, 0, 12, "REFERENCE", 12, 5, 5, "RN", TRUE);
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+    if (rbp->serial > 99) {
+      sprintf (buf, "%d ", (int) rbp->serial);
+    } else {
+      sprintf (buf, "%d", (int) rbp->serial);
+    }
+  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+    sprintf (buf, "[%d]", (int) rbp->serial);
+  }
+
+  FFAddOneString(temp, buf, FALSE, FALSE, TILDE_TO_SPACES);
+
+  /* print base range */
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+
+    if (rbp->sites != 3) {
+      FFAddNChar(temp, ' ', 15 - temp->pos, FALSE);
+    }
+  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+
+    if (rbp->sites == 0) {
+      FFLineWrap(ffstring, temp, 0, 5, ASN2FF_EMBL_MAX, "RN");   
+      FFRecycleString(ajp, temp);
+      temp = FFGetString(ajp);
+      FFStartPrint(temp, afp->format, 0, 0, NULL, 0, 5, 5, "RP", FALSE);
+    }
+  }
+
+  if (rbp->sites == 1 || rbp->sites == 2) {
+
+    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+      FFAddOneString(temp, "(sites)", FALSE, FALSE, TILDE_TO_SPACES);
+      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+    } else {
+      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RP");
+    }
+  } else if (rbp->sites == 3) {
+    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+    } else {
+      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RP");
+    }
+  } else {
+    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+      FFAddNChar(temp, ' ', 15 - temp->pos, FALSE);
+      if (afp->format == GENBANK_FMT) {
+        FFAddOneString(temp, "(bases ", FALSE, FALSE, TILDE_TO_SPACES);
+      } else {
+        FFAddOneString(temp, "(residues ", FALSE, FALSE, TILDE_TO_SPACES);
+      }
+    }
+
+    irp = (IntRefBlockPtr) rbp;
+    loc = irp->loc;
+
+    if (loc != NULL) {
+      if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+        suffix = "; ";
+      } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+        suffix = ", ";
+      }
+
+      slp = SeqLocFindNext (loc, NULL);
+      while (slp != NULL) {
+        nextslp = SeqLocFindNext (loc, slp);
+        start = SeqLocStart (slp) + 1;
+        stop = SeqLocStop (slp) + 1;
+        if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+          sprintf (buf, "%ld to %ld", (long) start, (long) stop);
+        } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+          sprintf (buf, "%ld-%ld", (long) start, (long) stop);
+        }
+        if (nextslp == NULL) {
+          suffix = NULL;
+        }
+        FFAddTextToString(temp, NULL, buf, suffix, FALSE, FALSE, TILDE_TO_SPACES);
+        slp = nextslp;
+      }
+
+    } else {
+
+      /* code still used for ssp->cit */
+
+      start = 1;
+      stop = bsp->length;
+      if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+        sprintf (buf, "%ld to %ld", (long) start, (long) stop);
+      } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+        sprintf (buf, "%ld-%ld", (long) start, (long) stop);
+      }
+      FFAddOneString(temp, buf, FALSE, FALSE, TILDE_TO_SPACES);
+    }
+
+    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+      FFAddOneString(temp, ")", FALSE, FALSE, TILDE_TO_SPACES);
+    }
+    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+    } else {
+      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RP");
+    }
+  }
+
+  if (gbseq != NULL) {
+    gbref = GBReferenceNew ();
+  }
+
+  /* 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;
+
+  alp = GetAuthListPtr (pdp, csp);
+  if (alp != NULL) {
+    str = GetAuthorsString (afp->format, alp, &consortium, index, gbref);
+    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 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);
+    } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+      FFAddOneChar(temp, ';', FALSE);
+    }    
+  }
+
+  MemFree (str);
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+  } else {
+      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RA");
+  }
+
+  /* print consortium */
+
+  FFRecycleString(ajp, temp);
+  temp = FFGetString(ajp);
+  if (! StringHasNoText (consortium)) {
+    FFStartPrint (temp, afp->format, 2, 12, "CONSRTM", 12, 5, 5, "CM", FALSE);
+    FFAddTextToString (temp, NULL, consortium, suffix, FALSE, FALSE, TILDE_TO_SPACES);
+    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+    } else {
+      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "CM");
+    }
+  }
+  MemFree (consortium);
+
+  /* print title */
+  FFRecycleString(ajp, temp);
+  temp = FFGetString(ajp);
+
+  str = GetPubTitle (afp->format, pdp, csp);
+  CleanPubTitle (str);
+  StrStripSpaces (str);
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+    prefix = NULL;
+    suffix = NULL;
+  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+    if (str != NULL) {
+      prefix = "\"";
+      suffix = "\";";
+    } else {
+      prefix = NULL;
+      suffix = ";";
+    }
+  }
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+    if (! StringHasNoText (str)) {
+      FFStartPrint (temp, afp->format, 2, 12, "TITLE", 12, 5, 5, "RT", FALSE);
+
+      FFAddTextToString (temp, prefix, str, suffix, FALSE, FALSE, TILDE_TO_SPACES);
+      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+    }
+  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+    FFStartPrint (temp, afp->format, 2, 12, "TITLE", 12, 5, 5, "RT", FALSE);
+    if (! StringHasNoText (str)) {
+
+      FFAddTextToString (temp, prefix, str, suffix, FALSE, FALSE, TILDE_TO_SPACES);
+
+    } else {
+      FFAddOneChar (temp, ';', FALSE);
+    }
+    FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RT");
+  }
+
+  if (gbseq != NULL) {
+    if (gbref != NULL) {
+      gbref->title = StringSaveNoNull (str);
+    }
+  }
+
+  MemFree (str);
+
+  /* print journal */
+  FFRecycleString(ajp, temp);
+  temp = FFGetString(ajp);
+
+  FFStartPrint (temp, afp->format, 2, 12, "JOURNAL", 12, 5, 5, "RL", FALSE);
+
+  /* Only GenBank/EMBL/DDBJ require ISO JTA in ENTREZ/RELEASE modes (RefSeq should later) */
+
+  citArtIsoJta = ajp->flags.citArtIsoJta;
+  strict_isojta = FALSE;
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_GENBANK ||
+        sip->choice == SEQID_EMBL ||
+        sip->choice == SEQID_DDBJ ||
+        /* sip->choice == SEQID_OTHER || */
+        sip->choice == SEQID_TPG ||
+        sip->choice == SEQID_TPE ||
+        sip->choice == SEQID_TPD) {
+      strict_isojta = TRUE;
+    }
+  }
+  if (! strict_isojta) {
+    citArtIsoJta = FALSE;
+  }
+
+  str = GetPubJournal (afp->format, ajp->flags.dropBadCitGens,
+                       ajp->flags.noAffilOnUnpub, citArtIsoJta,
+                       pdp, csp, bsp->id, index);
+  if (str == NULL) {
+    str = StringSave ("Unpublished");
+  }
+  StrStripSpaces (str);
+  TrimSpacesAroundString (str);
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+    needsPeriod = FALSE;
+  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+    if (! IsCitSub (pdp, csp)) {
+      needsPeriod = TRUE;
+    }
+  }
+
+  FFAddOneString (temp, str, FALSE, FALSE, TILDE_IGNORE);
+  if (needsPeriod) {
+    FFAddOneChar(temp, '.', FALSE);
+  }
+
+  if (gbseq != NULL) {
+    if (gbref != NULL) {
+      gbref->journal = StringSaveNoNull (str);
+      tmp = gbref->journal;
+      if (tmp != NULL) {
+        ch = *tmp;
+        while (ch != '\0') {
+          if (ch == '\n' || ch == '\r' || ch == '\t') {
+            *tmp = ' ';
+          }
+          tmp++;
+          ch = *tmp;
+        }
+        TrimSpacesAroundString (gbref->journal);
+      }
+    }
+  }
+
+  MemFree (str);
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+    FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+  } else {
+    FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RL");
+  }
+
+  /* print muid */
+  FFRecycleString(ajp, temp);
+  temp = FFGetString(ajp);
+  
+  muid = GetMuid (pdp);
+  if (muid > 0) {
+    FFStartPrint (temp, afp->format, 2, 12, "MEDLINE", 12, 5, 5, "RX", FALSE);
+
+    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+      FF_www_muid (ajp, temp, muid);
+      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+    } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+      sprintf (buf, "MEDLINE; %ld.", (long) muid);
+      FFAddOneString (temp, buf, FALSE, FALSE, TILDE_TO_SPACES);
+      FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RX");
+    }
+  }
+
+  FFRecycleString(ajp, temp);
+  temp = FFGetString(ajp);
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+    pmid = GetPmid (pdp);
+    if (pmid > 0) {
+      FFStartPrint (temp, afp->format, 3, 12, "PUBMED", 12, 5, 5, "RX", FALSE);
+
+      FF_www_muid (ajp, temp, pmid);
+      FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+    }
+  }
+
+  if (gbseq != NULL) {
+    if (gbref != NULL) {
+      gbref->medline = muid;
+      gbref->pubmed = pmid;
+    }
+  }
+
+  if (pdp == NULL) {
+    str = FFToCharPtr(ffstring);
+
+    if (gbseq != NULL) {
+      if (gbref != NULL) {
+        AddReferenceToGbseq (gbseq, gbref, str);
+      }
+    }
+
+    FFRecycleString(ajp, ffstring);
+    FFRecycleString(ajp, temp);
+    if (pep != NULL) {
+      PubmedEntryFree (pep);
+    }
+    if (pdpcopy != NULL) {
+      PubdescFree (pdpcopy);
+    }
+
+    return str;
+  }
+
+
+  /* !!! remainder of fields are only for GenBank !!! */
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+
+    prefix = "REMARK";
+
+    if (pdp->comment != NULL) {
+      for (i = 0, notFound = TRUE; notFound && remarksText [i] != NULL; i++) {
+        if (StringCmp (pdp->comment, remarksText [i]) == 0) {
+          notFound = FALSE;
+        }
+      }
+      if (notFound) {
+        FFRecycleString(ajp, temp);
+        temp = FFGetString(ajp);
+
+        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); */
+        FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+        prefix = NULL;
+
+        if (gbseq != NULL) {
+          if (gbref != NULL) {
+            gbref->remark = StringSave (pdp->comment);
+          }
+        }
+
+      }
+    }
+
+    gibbsq = 0;
+    for (sip = bsp->id; sip != NULL; sip = sip->next) {
+      if (sip->choice == SEQID_GIBBSQ) {
+        gibbsq = sip->data.intvalue;
+      }
+    }
+    csp = NULL;
+    for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+      if (vnp->choice == PUB_Sub) {
+        csp = (CitSubPtr) vnp->data.ptrvalue;
+      }
+    }
+    if (gibbsq > 0 /* && csp == NULL */) {
+      FFRecycleString(ajp, temp);
+      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);
+      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);
+      prefix = NULL;
+
+      /* gibbsq comment section (fields may be copied from degenerate pubdesc) */
+
+      str = pdp->fig;
+      if (StringHasNoText (str)) {
+        str = irp->fig;
+      }
+      if (! StringHasNoText (str)) {
+        FFRecycleString(ajp, temp);
+        temp = FFGetString(ajp);
+
+        sprintf (buf, "This sequence comes from %s", str);
+        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);
+        prefix = NULL;
+      }
+
+      if (pdp->poly_a || irp->poly_a) {
+        FFRecycleString(ajp, temp);
+        temp = FFGetString(ajp);
+
+        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;
+      }
+
+      str = pdp->maploc;
+      if (StringHasNoText (str)) {
+        str = irp->maploc;
+      }
+      if (! StringHasNoText (str)) {
+        FFRecycleString(ajp, temp);
+        temp = FFGetString(ajp);
+
+        sprintf (buf, "Map location: %s", str);
+        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);
+        prefix = NULL;
+      }
+
+    }
+
+    for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+      if (vnp->choice == PUB_Article) {
+        cap = (CitArtPtr) vnp->data.ptrvalue;
+        if (cap != NULL && cap->from == 1) {
+          cjp = (CitJourPtr) cap->fromptr;
+          if (cjp != NULL) {
+            imp = cjp->imp;
+            if (imp != NULL) {
+              crp = imp->retract;
+              if (crp != NULL && crp->type == 3) {
+                FFRecycleString(ajp, temp);
+                temp = FFGetString(ajp);
+
+                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);
+                FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+                prefix = NULL;
+              }
+            }
+          }
+        }
+      } else if (vnp->choice == PUB_Sub) {
+        csp = (CitSubPtr) vnp->data.ptrvalue;
+        if (csp != NULL) {
+          if (! StringHasNoText (csp->descr)) {
+            FFRecycleString(ajp, temp);
+            temp = FFGetString(ajp);
+
+            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);
+            FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+            prefix = NULL;
+          }
+        }
+      }
+    }
+
+  }
+
+  str = FFToCharPtr(ffstring);
+
+  if (gbseq != NULL) {
+    if (gbref != NULL) {
+      AddReferenceToGbseq (gbseq, gbref, str);
+    }
+  }
+
+  FFRecycleString(ajp, ffstring);
+  FFRecycleString(ajp, temp);
+  if (pep != NULL) {
+    PubmedEntryFree (pep);
+  }
+  if (pdpcopy != NULL) {
+    PubdescFree (pdpcopy);
+  }
+
+  return str;
+}
+
+
diff --git a/api/asn2gnb6.c b/api/asn2gnb6.c
new file mode 100644
index 00000000..70e3366c
--- /dev/null
+++ b/api/asn2gnb6.c
@@ -0,0 +1,3851 @@
+/*   asn2gnb6.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  asn2gnb6.c
+*
+* Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans,
+*          Mati Shomrat
+*
+* Version Creation Date:   10/21/98
+*
+* $Revision: 1.2 $
+*
+* File Description:  New GenBank flatfile generator - work in progress
+*
+* Modifications:
+* --------------------------------------------------------------------------
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <objall.h>
+#include <objsset.h>
+#include <objsub.h>
+#include <objfdef.h>
+#include <objpubme.h>
+#include <seqport.h>
+#include <sequtil.h>
+#include <sqnutils.h>
+#include <subutil.h>
+#include <tofasta.h>
+#include <explore.h>
+#include <gbfeat.h>
+#include <gbftdef.h>
+#include <edutil.h>
+#include <alignmgr2.h>
+#include <asn2gnbi.h>
+
+#ifdef WIN_MAC
+#if __profile__
+#include <Profiler.h>
+#endif
+#endif
+
+/* ordering arrays for qualifiers and note components */
+
+static SourceType source_qual_order [] = {
+  SCQUAL_organism,
+
+  SCQUAL_organelle,
+
+  SCQUAL_mol_type,
+
+  SCQUAL_strain,
+  SCQUAL_sub_strain,
+  SCQUAL_variety,
+  SCQUAL_serotype,
+  SCQUAL_serovar,
+  SCQUAL_cultivar,
+  SCQUAL_isolate,
+  SCQUAL_isolation_source,
+  SCQUAL_spec_or_nat_host,
+  SCQUAL_sub_species,
+  SCQUAL_specimen_voucher,
+
+  SCQUAL_db_xref,
+  SCQUAL_org_xref,
+
+  SCQUAL_chromosome,
+
+  SCQUAL_segment,
+
+  SCQUAL_map,
+  SCQUAL_clone,
+  SCQUAL_sub_clone,
+  SCQUAL_haplotype,
+  SCQUAL_sex,
+  SCQUAL_cell_line,
+  SCQUAL_cell_type,
+  SCQUAL_tissue_type,
+  SCQUAL_clone_lib,
+  SCQUAL_dev_stage,
+  SCQUAL_ecotype,
+  SCQUAL_frequency,
+
+  SCQUAL_germline,
+  SCQUAL_rearranged,
+  SCQUAL_transgenic,
+  SCQUAL_environmental_sample,
+
+  SCQUAL_lab_host,
+  SCQUAL_pop_variant,
+  SCQUAL_tissue_lib,
+
+  SCQUAL_plasmid_name,
+  SCQUAL_transposon_name,
+  SCQUAL_ins_seq_name,
+
+  SCQUAL_country,
+
+  SCQUAL_focus,
+
+  SCQUAL_note,
+
+  SCQUAL_sequenced_mol,
+  SCQUAL_label,
+  SCQUAL_usedin,
+  SCQUAL_citation,
+  (SourceType) 0
+};
+
+static SourceType source_desc_note_order [] = {
+  SCQUAL_seqfeat_note,
+  SCQUAL_orgmod_note,
+  SCQUAL_subsource_note,
+
+  SCQUAL_type,
+  SCQUAL_sub_type,
+  SCQUAL_serogroup,
+  SCQUAL_pathovar,
+  SCQUAL_chemovar,
+  SCQUAL_biovar,
+  SCQUAL_biotype,
+  SCQUAL_group,
+  SCQUAL_sub_group,
+  SCQUAL_common,
+  SCQUAL_acronym,
+  SCQUAL_dosage,
+
+  SCQUAL_authority,
+  SCQUAL_forma,
+  SCQUAL_forma_specialis,
+  SCQUAL_synonym,
+  SCQUAL_anamorph,
+  SCQUAL_teleomorph,
+  SCQUAL_breed,
+
+  SCQUAL_genotype,
+  SCQUAL_plastid_name,
+
+  SCQUAL_endogenous_virus_name,
+
+  SCQUAL_common_name,
+
+  SCQUAL_zero_orgmod,
+  SCQUAL_one_orgmod,
+  SCQUAL_zero_subsrc,
+
+  /* SCQUAL_old_lineage, */
+
+  /* SCQUAL_old_name, */
+  (SourceType) 0
+};
+
+static SourceType source_feat_note_order [] = {
+  SCQUAL_unstructured,
+
+  SCQUAL_type,
+  SCQUAL_sub_type,
+  SCQUAL_serogroup,
+  SCQUAL_pathovar,
+  SCQUAL_chemovar,
+  SCQUAL_biovar,
+  SCQUAL_biotype,
+  SCQUAL_group,
+  SCQUAL_sub_group,
+  SCQUAL_common,
+  SCQUAL_acronym,
+  SCQUAL_dosage,
+
+  SCQUAL_authority,
+  SCQUAL_forma,
+  SCQUAL_forma_specialis,
+  SCQUAL_synonym,
+  SCQUAL_anamorph,
+  SCQUAL_teleomorph,
+  SCQUAL_breed,
+
+  SCQUAL_genotype,
+  SCQUAL_plastid_name,
+
+  SCQUAL_endogenous_virus_name,
+
+  SCQUAL_seqfeat_note,
+  SCQUAL_orgmod_note,
+  SCQUAL_subsource_note,
+
+  SCQUAL_common_name,
+
+  SCQUAL_zero_orgmod,
+  SCQUAL_one_orgmod,
+  SCQUAL_zero_subsrc,
+
+  /* SCQUAL_old_lineage, */
+
+  /* SCQUAL_old_name, */
+  (SourceType) 0
+};
+
+NLM_EXTERN SourceQual asn2gnbk_source_quals [ASN2GNBK_TOTAL_SOURCE] = {
+  { "",                     Qual_class_ignore    },
+  { "acronym",              Qual_class_orgmod    },
+  { "anamorph",             Qual_class_orgmod    },
+  { "authority",            Qual_class_orgmod    },
+  { "biotype",              Qual_class_orgmod    },
+  { "biovar",               Qual_class_orgmod    },
+  { "breed",                Qual_class_orgmod    },
+  { "cell_line",            Qual_class_subsource },
+  { "cell_type",            Qual_class_subsource },
+  { "chemovar",             Qual_class_orgmod    },
+  { "chromosome",           Qual_class_subsource },
+  { "citation",             Qual_class_pubset    },
+  { "clone",                Qual_class_subsource },
+  { "clone_lib",            Qual_class_subsource },
+  { "common",               Qual_class_orgmod    },
+  { "common",               Qual_class_string    },
+  { "country",              Qual_class_subsource },
+  { "cultivar",             Qual_class_orgmod    },
+  { "db_xref",              Qual_class_db_xref   },
+  { "db_xref",              Qual_class_db_xref   },
+  { "dev_stage",            Qual_class_subsource },
+  { "dosage",               Qual_class_orgmod    },
+  { "ecotype",              Qual_class_orgmod    },
+  { "endogenous_virus",     Qual_class_subsource },
+  { "environmental_sample", Qual_class_subsource },
+  { "extrachromosomal",     Qual_class_boolean   },
+  { "focus",                Qual_class_boolean   },
+  { "forma",                Qual_class_orgmod    },
+  { "forma_specialis",      Qual_class_orgmod    },
+  { "frequency",            Qual_class_subsource },
+  { "gb_acronym",           Qual_class_orgmod    },
+  { "gb_anamorph",          Qual_class_orgmod    },
+  { "gb_synonym",           Qual_class_orgmod    },
+  { "genotype",             Qual_class_subsource },
+  { "germline",             Qual_class_subsource },
+  { "group",                Qual_class_orgmod    },
+  { "haplotype",            Qual_class_subsource },
+  { "insertion_seq",        Qual_class_subsource },
+  { "isolate",              Qual_class_orgmod    },
+  { "isolation_source",     Qual_class_subsource },
+  { "lab_host",             Qual_class_subsource },
+  { "label",                Qual_class_label     },
+  { "macronuclear",         Qual_class_boolean   },
+  { "map",                  Qual_class_subsource },
+  { "mol_type",             Qual_class_string    },
+  { "note",                 Qual_class_note      },
+  { "old_lineage",          Qual_class_orgmod    },
+  { "old_name",             Qual_class_orgmod    },
+  { "organism",             Qual_class_string    },
+  { "organelle",            Qual_class_organelle },
+  { "orgmod_note",          Qual_class_orgmod    },
+  { "pathovar",             Qual_class_orgmod    },
+  { "plasmid",              Qual_class_subsource },
+  { "plastid",              Qual_class_subsource },
+  { "pop_variant",          Qual_class_subsource },
+  { "rearranged",           Qual_class_subsource },
+  { "segment",              Qual_class_subsource },
+  { "seqfeat_note",         Qual_class_string    },
+  { "sequenced_mol",        Qual_class_quote     },
+  { "serogroup",            Qual_class_orgmod    },
+  { "serotype",             Qual_class_orgmod    },
+  { "serovar",              Qual_class_orgmod    },
+  { "sex",                  Qual_class_subsource },
+  { "specific_host",        Qual_class_orgmod    },
+  { "specimen_voucher",     Qual_class_orgmod    },
+  { "strain",               Qual_class_orgmod    },
+  { "sub_clone",            Qual_class_subsource },
+  { "subgroup",             Qual_class_orgmod    },
+  { "sub_species",          Qual_class_orgmod    },
+  { "sub_strain",           Qual_class_orgmod    },
+  { "subtype",              Qual_class_orgmod    },
+  { "subsource_note",       Qual_class_subsource },
+  { "synonym",              Qual_class_orgmod    },
+  { "teleomorph",           Qual_class_orgmod    },
+  { "tissue_lib",           Qual_class_subsource },
+  { "tissue_type",          Qual_class_subsource },
+  { "transgenic",           Qual_class_subsource },
+  { "transposon",           Qual_class_subsource },
+  { "type",                 Qual_class_orgmod    },
+  { "unstructured",         Qual_class_valnode   },
+  { "usedin",               Qual_class_quote     },
+  { "variety",              Qual_class_orgmod    },
+  { "?",                    Qual_class_orgmod    },
+  { "?",                    Qual_class_orgmod    },
+  { "?",                    Qual_class_subsource },
+};
+
+NLM_EXTERN SourceType subSourceToSourceIdx [30] = {
+  SCQUAL_zero_subsrc,
+  SCQUAL_chromosome,
+  SCQUAL_map,
+  SCQUAL_clone,
+  SCQUAL_sub_clone,
+  SCQUAL_haplotype,
+  SCQUAL_genotype,
+  SCQUAL_sex,
+  SCQUAL_cell_line,
+  SCQUAL_cell_type,
+  SCQUAL_tissue_type,
+  SCQUAL_clone_lib,
+  SCQUAL_dev_stage,
+  SCQUAL_frequency,
+  SCQUAL_germline,
+  SCQUAL_rearranged,
+  SCQUAL_lab_host,
+  SCQUAL_pop_variant,
+  SCQUAL_tissue_lib,
+  SCQUAL_plasmid_name,
+  SCQUAL_transposon_name,
+  SCQUAL_ins_seq_name,
+  SCQUAL_plastid_name,
+  SCQUAL_country,
+  SCQUAL_segment,
+  SCQUAL_endogenous_virus_name,
+  SCQUAL_transgenic,
+  SCQUAL_environmental_sample,
+  SCQUAL_isolation_source,
+  SCQUAL_subsource_note
+};
+
+/* ********************************************************************** */
+
+/* ********************************************************************** */
+
+/* format functions allocate printable string for given paragraph */
+
+/* superset of http://www.ncbi.nlm.nih.gov/collab/db_xref.html and RefSeq db_xrefs */
+
+NLM_EXTERN CharPtr legalDbXrefs [] = {
+  "PIDe", "PIDd", "PIDg", "PID",
+  "AceView/WormGenes",
+  "ATCC",
+  "ATCC(in host)",
+  "ATCC(dna)",
+  "BDGP_EST",
+  "BDGP_INS",
+  "CDD",
+  "CK",
+  "COG",
+  "dbEST",
+  "dbSNP",
+  "dbSTS",
+  "ENSEMBL",
+  "ESTLIB",
+  "FANTOM_DB",
+  "FLYBASE",
+  "GABI",
+  "GDB",
+  "GeneDB",
+  "GeneID",
+  "GI",
+  "GO",
+  "GOA",
+  "IFO",
+  "IMGT/LIGM",
+  "IMGT/HLA",
+  "InterimID",
+  "Interpro",
+  "ISFinder",
+  "JCM",
+  "LocusID",
+  "MaizeDB",
+  "MGD",
+  "MGI",
+  "MIM",
+  "NextDB",
+  "niaEST",
+  "PIR",
+  "PSEUDO",
+  "RATMAP",
+  "RiceGenes",
+  "REMTREMBL",
+  "RGD",
+  "RZPD",
+  "SGD",
+  "SoyBase",
+  "SPTREMBL",
+  "SWISS-PROT",
+  "taxon",
+  "UniGene",
+  "UniSTS",
+  "WorfDB",
+  "WormBase",
+  "ZFIN",
+  NULL
+};
+
+NLM_EXTERN CharPtr legalRefSeqDbXrefs [] = {
+  "REBASE",
+  NULL
+};
+
+static CharPtr organellePrefix [] = {
+  NULL,
+  NULL,
+  "Chloroplast ",
+  "Chromoplast ",
+  "Kinetoplast ",
+  "Mitochondrion ",
+  "Plastid ",
+  NULL,
+  NULL,
+  NULL,
+  NULL,
+  NULL,
+  "Cyanelle ",
+  NULL,
+  NULL,
+  "Nucleomorph ",
+  "Apicoplast ",
+  "Leucoplast ",
+  "Proplastid ",
+  NULL
+};
+
+static CharPtr newOrganellePrefix [] = {
+  NULL,
+  NULL,
+  "chloroplast ",
+  "chromoplast ",
+  "kinetoplast ",
+  "mitochondrion ",
+  "plastid ",
+  NULL,
+  NULL,
+  NULL,
+  NULL,
+  NULL,
+  "cyanelle ",
+  NULL,
+  NULL,
+  "nucleomorph ",
+  "apicoplast ",
+  "leucoplast ",
+  "proplastid ",
+  NULL
+};
+
+NLM_EXTERN CharPtr FormatSourceBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  CharPtr            acr = NULL;
+  Boolean            addPeriod = TRUE;
+  IntAsn2gbJobPtr    ajp;
+  CharPtr            ana = NULL;
+  Asn2gbSectPtr      asp;
+  BioSourcePtr       biop = NULL;
+  CharPtr            com = NULL;
+  CharPtr            common = NULL;
+  SeqMgrDescContext  dcontext;
+  SeqMgrFeatContext  fcontext;
+  CharPtr            gbacr = NULL;
+  CharPtr            gbana = NULL;
+  GBBlockPtr         gbp = NULL;
+  GBSeqPtr           gbseq;
+  CharPtr            gbsyn = NULL;
+  Uint1              genome;
+  ValNodePtr         mod = NULL;
+  OrgModPtr          omp = NULL;
+  OrgNamePtr         onp;
+  CharPtr            organelle = NULL;
+  OrgRefPtr          orp;
+  CharPtr            prefix = " (";
+  SeqDescrPtr        sdp;
+  CharPtr            second = NULL;
+  SeqFeatPtr         sfp;
+  CharPtr            str;
+  CharPtr            syn = NULL;
+  CharPtr            taxname = NULL;
+  Boolean            using_anamorph = FALSE;
+  StringItemPtr      ffstring, temp;
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+
+  if (! StringHasNoText (bbp->string)) return StringSave (bbp->string);
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return NULL;
+
+  if (bbp->itemtype == OBJ_SEQDESC) {
+    sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext);
+    if (sdp != NULL) {
+      if (dcontext.seqdesctype == Seq_descr_source) {
+        biop = (BioSourcePtr) sdp->data.ptrvalue;
+      } else if (dcontext.seqdesctype == Seq_descr_genbank) {
+        gbp = (GBBlockPtr) sdp->data.ptrvalue;
+      }
+    }
+  } else if (bbp->itemtype == OBJ_SEQFEAT) {
+    sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
+    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_BIOSRC) {
+      biop = (BioSourcePtr) sfp->data.value.ptrvalue;
+    }
+  }
+  if (gbp != NULL) {
+    common = gbp->source;
+  }
+
+  if (biop != NULL) {
+    genome = biop->genome;
+    if (genome <= 19) {
+      if (ajp->newSourceOrg && (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT)) {
+        organelle = newOrganellePrefix [genome];
+      } else {
+        organelle = organellePrefix [genome];
+      }
+    }
+    orp = biop->org;
+    if (orp != NULL) {
+      taxname = orp->taxname;
+      common = orp->common;
+      mod = orp->mod;
+      onp = orp->orgname;
+      if (onp != NULL) {
+
+        if (ajp->newSourceOrg) {
+          for (omp = onp->mod; omp != NULL; omp = omp->next) {
+            switch (omp->subtype) {
+              case ORGMOD_common :
+                com = omp->subname;
+                break;
+              case ORGMOD_acronym :
+                acr = omp->subname;
+                break;
+              case ORGMOD_synonym :
+                syn = omp->subname;
+                break;
+              case ORGMOD_anamorph :
+                ana = omp->subname;
+                break;
+              case ORGMOD_gb_acronym :
+                gbacr = omp->subname;
+                break;
+              case ORGMOD_gb_anamorph :
+                gbana = omp->subname;
+                break;
+              case ORGMOD_gb_synonym :
+                gbsyn = omp->subname;
+                break;
+              default :
+                break;
+            }
+          }
+
+          if (StringHasNoText (second)) {
+            second = syn;
+            using_anamorph = FALSE;
+          }
+           if (StringHasNoText (second)) {
+             second = acr;
+             using_anamorph = FALSE;
+          }
+          if (StringHasNoText (second)) {
+            second = ana;
+            using_anamorph = TRUE;
+          }
+          if (StringHasNoText (second)) {
+            second = com;
+            using_anamorph = FALSE;
+          }
+
+          if (StringHasNoText (second)) {
+            second = gbsyn;
+            using_anamorph = FALSE;
+          }
+          if (StringHasNoText (second)) {
+            second = gbacr;
+            using_anamorph = FALSE;
+          }
+          if (StringHasNoText (second)) {
+            second = gbana;
+            using_anamorph = TRUE;
+          }
+
+          if (StringHasNoText (second)) {
+            second = common;
+            using_anamorph = FALSE;
+          }
+          if (using_anamorph) {
+            prefix = " (anamorph: ";
+          }
+        }
+      }
+    }
+  }
+
+  /* If the organelle prefix is already on the */
+  /* name, don't add it.                       */
+
+  if (StringNCmp (organelle, taxname, StringLen (organelle)) == 0)
+    organelle = "";
+
+  if (StringHasNoText (common)) {
+    common = taxname;
+  }
+  if (StringHasNoText (common)) {
+    common = "Unknown.";
+  }
+  if (StringHasNoText (taxname)) {
+    taxname = "Unknown.";
+  }
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+    
+    temp = FFGetString(ajp);
+
+    if (ajp->newSourceOrg) {
+
+      if (! StringHasNoText (organelle)) {
+        FFAddTextToString(temp, NULL, organelle, NULL, FALSE, FALSE, TILDE_IGNORE);
+      }
+      FFAddTextToString(temp, NULL, taxname, NULL, FALSE, FALSE, TILDE_IGNORE);
+      if (! StringHasNoText (second)) {
+        FFAddTextToString(temp, prefix, second, ")", FALSE, FALSE, TILDE_IGNORE);
+      }
+      addPeriod = FALSE;
+
+    } else {
+      FFAddTextToString(temp, NULL, common, NULL, FALSE, FALSE, TILDE_IGNORE);
+      while (mod != NULL) {
+        str = (CharPtr) mod->data.ptrvalue;
+        if (! StringHasNoText (str)) {
+          FFAddTextToString(temp, " ", str, NULL, FALSE, FALSE, TILDE_IGNORE);
+        }
+        mod = mod->next;
+      }
+    }
+
+    str = FFToCharPtr(temp);
+    if (StringCmp (str, ".") == 0) {
+      str = MemFree (str);
+    }
+    FFRecycleString(ajp, temp);
+    /* optionally populate gbseq for XML-ized GenBank format */
+
+    if (ajp->gbseq) {
+      gbseq = &asp->gbseq;
+    } else {
+      gbseq = NULL;
+    }
+
+    if (gbseq != NULL) {
+      gbseq->source = StringSave (str);
+    }
+
+    
+    FFStartPrint(ffstring, afp->format, 0, 12, "SOURCE", 12, 5, 5, "OS", TRUE);
+    if (str != NULL) {
+      FFAddTextToString(ffstring, NULL, str, NULL, addPeriod, FALSE, TILDE_TO_SPACES);
+    } else {
+      FFAddOneChar(ffstring, '.', FALSE);
+    }
+    
+    MemFree (str);
+
+  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+
+    FFStartPrint(ffstring, afp->format, 0, 12, "SOURCE", 12, 5, 5, "OS", TRUE);
+    FFAddTextToString(ffstring, NULL, taxname, NULL, FALSE, FALSE, TILDE_TO_SPACES);
+    if ( StringICmp(taxname, common) != 0 ) {
+        FFAddTextToString(ffstring, " (", common, ")", FALSE, FALSE, TILDE_TO_SPACES);
+    }
+  }
+  
+  str = FFEndPrint(ajp, ffstring, afp->format, 12, 12, 0, 5, "OS");
+  FFRecycleString(ajp, ffstring);
+  return str;
+}
+
+NLM_EXTERN CharPtr FormatOrganismBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  BioSourcePtr       biop = NULL;
+  Char               ch;
+  CharPtr            common = NULL;
+  DbtagPtr           dbt;
+  SeqMgrDescContext  dcontext;
+  SeqMgrFeatContext  fcontext;
+  GBSeqPtr           gbseq;
+  Uint1              genome;
+  CharPtr            lineage = NULL;
+  ObjectIdPtr        oip;
+  OrgNamePtr         onp;
+  CharPtr            organelle = NULL;
+  OrgRefPtr          orp;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  CharPtr            str;
+  Int4               taxid = -1;
+  CharPtr            taxname = NULL;
+  CharPtr            tmp;
+  CharPtr            ptr;
+  ValNodePtr         vnp;
+  StringItemPtr      ffstring, temp;
+  Char               buf [16];
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+
+
+  if (! StringHasNoText (bbp->string)) return StringSave (bbp->string);
+
+  if (bbp->itemtype == OBJ_SEQDESC) {
+    sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext);
+    if (sdp != NULL && dcontext.seqdesctype == Seq_descr_source) {
+      biop = (BioSourcePtr) sdp->data.ptrvalue;
+    }
+  } else if (bbp->itemtype == OBJ_SEQFEAT) {
+    sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
+    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_BIOSRC) {
+      biop = (BioSourcePtr) sfp->data.value.ptrvalue;
+    }
+  }
+  if (biop != NULL) {
+    genome = biop->genome;
+    if (genome <= 19) {
+      organelle = organellePrefix [genome];
+    }
+    orp = biop->org;
+    if (orp != NULL) {
+      taxname = orp->taxname;
+      common = orp->common;
+      onp = orp->orgname;
+      if (onp != NULL) {
+        lineage = onp->lineage;
+      }
+      for (vnp = orp->db; vnp != NULL; vnp = vnp->next) {
+        dbt = (DbtagPtr) vnp->data.ptrvalue;
+        if (dbt == NULL) continue;
+        if (StringCmp (dbt->db, "taxon") == 0) {
+          oip = dbt->tag;
+          if (oip != NULL) {
+            taxid = oip->id;
+          }
+        }
+      }
+    }
+  }
+
+  /* If the organelle prefix is already on the */
+  /* name, don't add it.                       */
+
+  if (StringNCmp (organelle, taxname, StringLen (organelle)) == 0)
+    organelle = "";
+
+  if (StringHasNoText (common)) {
+    common = taxname;
+  }
+  if (StringHasNoText (common)) {
+    common = "Unknown.";
+  }
+  if (StringHasNoText (taxname)) {
+    taxname = "Unknown.";
+  }
+  if (StringHasNoText (lineage)) {
+    lineage = "Unclassified.";
+  }
+
+  ffstring = FFGetString(ajp);
+  temp = FFGetString(ajp);
+  if ( ffstring == NULL || temp == NULL ) return NULL;
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+    
+    FFStartPrint(temp, afp->format, 2, 12, "ORGANISM", 12, 5, 5, "OC", FALSE);
+    if (! ajp->newSourceOrg) {
+      FFAddOneString(temp, organelle, FALSE, FALSE, TILDE_IGNORE);
+    }
+    if (StringNICmp (taxname, "Unknown", 7) != 0) {
+      if ( GetWWW(ajp) ) { 
+        if (taxid != -1) {
+          FFAddOneString(temp, "<a href=", FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString(temp, link_tax, FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString(temp, "id=", FALSE, FALSE, TILDE_IGNORE);
+          sprintf (buf, "%ld", (long) taxid);
+          FFAddOneString(temp, buf, FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString(temp, ">", FALSE, FALSE, TILDE_IGNORE);
+        } else {
+          FFAddOneString(temp, "<a href=", FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString(temp, link_tax, FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString(temp, "name=", FALSE, FALSE, TILDE_IGNORE);
+          tmp = StringSave (taxname);
+          if (tmp != NULL) {
+            ptr = tmp;
+            ch = *ptr;
+            while (ch != '\0') {
+              if (IS_WHITESP (ch)) {
+                *ptr = '+';
+              }
+              ptr++;
+              ch = *ptr;
+            }
+            FFAddOneString(temp, tmp, FALSE, FALSE, TILDE_IGNORE);
+            MemFree (tmp);
+          }
+          FFAddOneString(temp, ">", FALSE, FALSE, TILDE_IGNORE);
+        }
+        FFAddOneString(temp, taxname, FALSE, FALSE, TILDE_IGNORE);
+        FFAddOneString(temp, "</a>", FALSE, FALSE, TILDE_IGNORE);
+      } else {
+        FFAddOneString(temp, taxname, FALSE, FALSE, TILDE_IGNORE);
+      }
+    } else {
+      FFAddOneString(temp, taxname, FALSE, FALSE, TILDE_IGNORE);
+    }
+    FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+    FFRecycleString(ajp, temp);
+
+    temp = FFGetString(ajp);
+    FFStartPrint(temp, afp->format, 12, 12, NULL, 0, 5, 5, "OC", FALSE);
+    FFAddTextToString(temp, NULL, lineage, NULL, TRUE, FALSE, TILDE_TO_SPACES);
+    FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+    FFRecycleString(ajp, temp);
+    /* optionally populate gbseq for XML-ized GenBank format */
+
+    if (ajp->gbseq) {
+      gbseq = &asp->gbseq;
+    } else {
+      gbseq = NULL;
+    }
+
+    if (gbseq != NULL) {
+      temp = FFGetString(ajp);
+      if (! ajp->newSourceOrg) {
+        FFAddOneString(temp, organelle, FALSE, FALSE, TILDE_IGNORE);
+      }
+      FFAddOneString(temp, taxname, FALSE, FALSE, TILDE_IGNORE);
+      gbseq->organism = FFToCharPtr(temp);
+      gbseq->taxonomy = StringSave (lineage);
+      FFRecycleString(ajp, temp);
+    }
+
+  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+    FFStartPrint(temp, afp->format, 12, 12, NULL, 0, 5, 5, "OC", FALSE);
+    FFAddTextToString(temp, NULL, lineage, NULL, TRUE, FALSE, TILDE_TO_SPACES);
+    FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "OC");
+    FFRecycleString(ajp, temp);
+    if ( !StringHasNoText(organelle) ) {
+      temp = FFGetString(ajp);
+      if ( temp != NULL ) {
+        FFStartPrint(temp, afp->format, 12, 12, NULL, 0, 5, 5, "OG", FALSE);
+        FFAddTextToString(temp, NULL, organelle, NULL, TRUE, FALSE, TILDE_TO_SPACES);
+        FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "OG");
+        FFRecycleString(ajp, temp);
+      }
+    }
+  }
+  
+  str = FFToCharPtr(ffstring);
+  FFRecycleString(ajp, ffstring);
+  return str;
+}
+
+/* A tilde is not an EOL if it is found in a sring of the form:    */
+/* /~alpahnumdot/ where alphanumdot is either alpha numeric or '.' */
+/*                                                                 */
+/* str points to the tilde in question.                            */
+static Boolean IsTildeEOL(CharPtr str) {
+  CharPtr ptr;
+
+  if ( *(str - 1) != '/' ) return TRUE;
+
+  ++str;
+
+  
+  for ( ptr = str; 
+    IS_ALPHANUM(*ptr) || *ptr == '_' || *ptr == '-' || *ptr == '.';
+    ++ptr) continue;
+
+  return *ptr == '/' ? FALSE : TRUE;
+}
+
+/* returns a pointer to the first character past the url */
+static CharPtr FindUrlEnding(CharPtr str) {
+  CharPtr ptr;
+
+  for ( ptr = str;
+        !IS_WHITESP(*ptr) && *ptr != '\0' && *ptr != '(' && *ptr != '\"';
+        ++ptr  ) {
+    if ( *ptr == '~' ) {
+      if ( IsTildeEOL(ptr) ) break;
+    }
+  }
+
+  --ptr;
+
+  /* back up over any trailing periods, commas, or parentheses */
+  while ( (*ptr == '.') || (*ptr == ',') || (*ptr == ')') ) {
+    --ptr;
+  }
+
+  ++ptr;
+
+  return ptr;
+}
+
+NLM_EXTERN void AddCommentWithURLlinks (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr prefix,
+  CharPtr str,
+  CharPtr suffix
+)
+
+{
+  Char     ch;
+  CharPtr  ptr;
+
+  while (! StringHasNoText (str)) {
+    ptr = StringStr (str, "http://");
+    if (ptr == NULL) {
+      if (prefix != NULL) {
+        FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+      }
+      AddCommentStringWithTildes (ffstring, str);
+      if (suffix != NULL) {
+        FFAddOneString(ffstring, suffix, FALSE, FALSE, TILDE_IGNORE);
+      }
+      return;
+    }
+
+    *ptr = '\0';
+    AddCommentStringWithTildes (ffstring, str); 
+    *ptr = 'h';
+
+    str = ptr;
+    ptr = FindUrlEnding(str);
+
+
+    ch = *ptr;
+    *ptr = '\0';
+    if ( GetWWW(ajp) ) {
+      FFAddTextToString(ffstring, "<a href=", str, ">", FALSE, FALSE, TILDE_IGNORE);
+      FFAddTextToString(ffstring, NULL, str, "</a>", FALSE, FALSE, TILDE_IGNORE);
+    } else {
+      FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
+    }
+
+    *ptr = ch;
+    str = ptr;
+  }
+}
+
+static void CatenateCommentInGbseq (
+  GBSeqPtr gbseq,
+  CharPtr str
+)
+
+{
+  Char     ch;
+  CharPtr  tmp;
+
+  if (gbseq == NULL || StringHasNoText (str)) return;
+
+  if (StringNCmp (str, "COMMENT     ", 12) == 0) {
+    str += 12;
+  }
+  if (gbseq->comment == NULL) {
+    gbseq->comment = StringSave (str);
+  } else {
+    tmp = (CharPtr) MemNew (StringLen (gbseq->comment) + StringLen (str) + 4);
+    StringCpy (tmp, gbseq->comment);
+    StringCat (tmp, "; ");
+    StringCat (tmp, str);
+    gbseq->comment = MemFree (gbseq->comment);
+    gbseq->comment = tmp;
+  }
+
+  tmp = gbseq->comment;
+  if (tmp == NULL) return;
+  ch = *tmp;
+  while (ch != '\0') {
+    if (ch == '\n' || ch == '\r' || ch == '\t') {
+      *tmp = ' ';
+    }
+    tmp++;
+    ch = *tmp;
+  }
+  TrimSpacesAroundString (gbseq->comment);
+  Asn2gnbkCompressSpaces (gbseq->comment);
+}
+
+
+NLM_EXTERN CharPtr FormatCommentBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  Boolean            add_period;
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  CommentBlockPtr    cbp;
+  CharPtr            db;
+  DbtagPtr           dbt;
+  SeqMgrDescContext  dcontext;
+  SeqMgrFeatContext  fcontext;
+  GBSeqPtr           gbseq;
+  size_t             len;
+  ObjectIdPtr        oip;
+  CharPtr            prefix;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  Char               sfx [32];
+  CharPtr            str;
+  CharPtr            suffix;
+  CharPtr            title;
+  StringItemPtr      ffstring;
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+
+  cbp = (CommentBlockPtr) bbp;
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  /* some comments are allocated (along with possible first COMMENT label) */
+
+  if (! StringHasNoText (bbp->string)) {
+    str = StringSave (bbp->string);
+    CatenateCommentInGbseq (gbseq, str);
+    return str;
+  }
+
+  title = NULL;
+  prefix = NULL;
+  suffix = NULL;
+  add_period = FALSE;
+  sfx [0] = '\0';
+
+  if (bbp->itemtype == OBJ_SEQDESC) {
+
+    /* usually should reference comment, maploc, or region descriptor IDs */
+
+    sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext);
+    if (sdp != NULL) {
+
+      if (dcontext.seqdesctype == Seq_descr_comment) {
+
+        title = (CharPtr) sdp->data.ptrvalue;
+
+      } else if (dcontext.seqdesctype == Seq_descr_maploc) {
+
+        dbt = (DbtagPtr) sdp->data.ptrvalue;
+        if (dbt != NULL) {
+          db = dbt->db;
+          oip = dbt->tag;
+          if (oip != NULL) {
+            if (oip->str != NULL) {
+
+              title = oip->str;
+              prefix = ("Map location: ");
+
+            } else if (db != NULL && oip->id != 0) {
+
+              title = db;
+              prefix = ("Map location: (Database ");
+              sprintf (sfx, "; id # %ld).", (long) oip->id);
+              suffix = sfx;
+
+            }
+          }
+        }
+
+      } else if (dcontext.seqdesctype == Seq_descr_region) {
+
+        title = (CharPtr) sdp->data.ptrvalue;
+        prefix = "Region: ";
+
+      }
+    }
+
+  } else if (bbp->itemtype == OBJ_SEQFEAT) {
+
+    /* also have to deal with comment feature across entire sequence */
+
+    sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
+    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_COMMENT) {
+
+      title = sfp->comment;
+    }
+  }
+
+  if (title == NULL) return NULL;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return NULL;
+
+  if (cbp->first) {
+    FFStartPrint (ffstring, afp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+  } else {
+    FFStartPrint (ffstring, afp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+  }
+
+  str = StringSave (title);
+  TrimSpacesAndJunkFromEnds (str, TRUE);
+  if (! IsEllipsis (str)) {
+    s_RemovePeriodFromEnd (str);
+    len = StringLen (str);
+    if (len > 0 && str [len - 1] != '.') {
+      add_period = TRUE;
+    }
+  }
+  AddCommentWithURLlinks(ajp, ffstring, prefix, str, suffix);
+  /*
+  if ( GetWWW(ajp) && prefix == NULL && suffix == NULL) {
+    
+    AddCommentWithURLlinks (ffstring, str);
+  } else {
+    FFAddTextToString (ffstring, prefix, str, suffix, FALSE, TRUE, TILDE_OLD_EXPAND);
+  }
+  */
+  if (add_period) {
+    FFAddOneChar (ffstring, '.',FALSE);
+  }
+  MemFree (str);
+
+  str = FFEndPrint(ajp, ffstring, afp->format, 12, 12, 5, 5, "CC");
+
+  CatenateCommentInGbseq (gbseq, str);
+
+  FFRecycleString(ajp, ffstring);
+  return str;
+}
+
+/* format features section */
+
+static Boolean is_real_id (
+  SeqIdPtr sip,
+  SeqIdPtr this_sip
+)
+
+{
+  BioseqPtr  bsp;
+
+  if (sip == NULL || this_sip == NULL) return FALSE;
+
+  if (! SeqIdIn (sip, this_sip)) {
+    bsp = BioseqFind (sip);
+    if (bsp == NULL) return TRUE;  /* ??? */
+    if (bsp->repr == Seq_repr_virtual) return FALSE;
+  }
+
+  return TRUE;
+}
+
+static Boolean FlatVirtLoc (
+  BioseqPtr bsp,
+  SeqLocPtr location
+)
+
+{
+  SeqIntPtr  sintp;
+  SeqIdPtr   sip;
+  SeqPntPtr  spp;
+
+  if (bsp == NULL || location == NULL) return FALSE;
+
+  switch (location->choice) {
+    case SEQLOC_WHOLE :
+      sip = (SeqIdPtr) location->data.ptrvalue;
+      if (sip == NULL) return TRUE;
+      if (! is_real_id (sip, bsp->id)) return TRUE;
+      break;
+    case SEQLOC_INT :
+      sintp = (SeqIntPtr) location->data.ptrvalue;
+      if (sintp == NULL) return TRUE;
+      sip = sintp->id;
+      if (sip == NULL) return TRUE;
+      if (! is_real_id (sip, bsp->id)) return TRUE;
+      break;
+    case SEQLOC_PNT :
+      spp = (SeqPntPtr) location->data.ptrvalue;
+      if (spp == NULL) return TRUE;
+      sip = spp->id;
+      if (sip == NULL) return TRUE;
+      if (! is_real_id (sip, bsp->id)) return TRUE;
+      break;
+    default :
+      break;
+  }
+
+  return FALSE;
+}
+
+static Uint1    order [NUM_SEQID];
+static Boolean  order_initialized = FALSE;
+
+static CharPtr lim_str [5] = { "", ">","<", ">", "<" };
+
+NLM_EXTERN Boolean GetAccnVerFromServer (Int4 gi, CharPtr buf)
+
+{
+  AccnVerLookupFunc  func;
+  SeqMgrPtr          smp;
+  CharPtr            str;
+
+  if (buf == NULL) return FALSE;
+  *buf = '\0';
+  smp = SeqMgrWriteLock ();
+  if (smp == NULL) return FALSE;
+  func = smp->accn_ver_lookup_func;
+  SeqMgrUnlock ();
+  if (func == NULL) return FALSE;
+  str = (*func) (gi);
+  if (str == NULL) return FALSE;
+  if (StringLen (str) < 40) {
+    StringCpy (buf, str);
+  }
+  MemFree (str);
+  return TRUE;
+}
+
+
+/******************************************************************************/
+/*                              FFFlatLoc functions  .                          */
+/******************************************************************************/
+
+static Boolean FF_FlatNullAhead (
+  BioseqPtr bsp,
+  ValNodePtr location
+)
+
+{
+  SeqLocPtr  next;
+
+  if (bsp == NULL || location == NULL) return FALSE;
+
+  next = location->next;
+  if (next == NULL) return TRUE;
+  if (next->choice == SEQLOC_NULL) return TRUE;
+  if (FlatVirtLoc (bsp, next)) return TRUE;
+
+  return FALSE;
+}
+
+
+
+static void FlatLocSeqId (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  SeqIdPtr sip
+)
+
+{
+  BioseqPtr    bsp;
+  Char         buf [40];
+  ObjectIdPtr  oip;
+  SeqIdPtr     use_id = NULL;
+  Boolean      was_lock = FALSE;
+
+  if (ffstring == NULL || sip == NULL) return;
+
+  buf [0] = '\0';
+  bsp = BioseqFind (sip);
+  if (bsp != NULL) {
+    use_id = SeqIdSelect (bsp->id, order, NUM_SEQID);
+  } else if (sip->choice == SEQID_GI) {
+    if (GetAccnVerFromServer (sip->data.intvalue, buf)) {
+      FFAddTextToString(ffstring, NULL, buf, ":", FALSE, FALSE, TILDE_IGNORE);
+      /*AddValNodeString (head, NULL, buf, ":");*/
+      return;
+    }
+    use_id = GetSeqIdForGI (sip->data.intvalue);
+  }
+  if (use_id == NULL && bsp == NULL) {
+    bsp = BioseqLockById (sip);
+    was_lock = TRUE;
+    if (bsp != NULL) {
+      use_id = SeqIdSelect (bsp->id, order, NUM_SEQID);
+    }
+  }
+  if (use_id != NULL) {
+    SeqIdWrite (use_id, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
+    if (use_id->choice == SEQID_GI) {
+      ajp->relModeError = TRUE;
+    }
+  } else if (sip->choice == SEQID_GI) {
+    SeqIdWrite (sip, buf, PRINTID_FASTA_LONG, sizeof (buf) - 1);
+    ajp->relModeError = TRUE;
+  } else {
+    SeqIdWrite (sip, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
+    if (sip->choice == SEQID_GI) {
+      ajp->relModeError = TRUE;
+    }
+  }
+  if (was_lock) {
+    BioseqUnlock (bsp);
+  }
+  if (StringHasNoText (buf)) {
+    StringCpy (buf, "?00000");
+    ajp->relModeError = TRUE;
+    if (use_id != NULL && use_id->choice == SEQID_LOCAL) {
+      oip = (ObjectIdPtr) use_id->data.ptrvalue;
+      if (oip != NULL && (! StringHasNoText (oip->str))) {
+        StringNCpy_0 (buf, oip->str, 13);
+      }
+    }
+  }
+  FFAddTextToString(ffstring, NULL, buf, ":", FALSE, FALSE, TILDE_IGNORE);
+}
+
+
+
+static void FlatLocCaret (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  SeqIdPtr sip,
+  SeqIdPtr this_sip,
+  Int4 point,
+  IntFuzzPtr fuzz
+)
+
+{
+  Char   buf [128];
+  Uint1  index;
+
+  if (ffstring == NULL) return;
+
+  if (sip != NULL && (! SeqIdIn (sip, this_sip))) {
+    FlatLocSeqId (ajp, ffstring, sip);
+  }
+
+  buf [0] = '\0';
+  point++; /* orginal FlatLocHalfCaret was called with point + 1 */
+
+  if (fuzz != NULL) {
+    switch (fuzz->choice) {
+      case 1 :
+        sprintf (buf, "(%ld.%ld)..(%ld.%ld)",
+                 (long) (point - fuzz->a),
+                 (long) point,
+                 (long) point,
+                 (long) (point + fuzz->a));
+        break;
+      case 2 :
+        sprintf (buf, "%ld^%ld",
+                 (long) (1 + fuzz->b),
+                 (long) (1 + fuzz->a));
+        break;
+      case 3 :
+        sprintf (buf, "%ld^%ld",
+                 (long) (point - point * ((double) fuzz->a / 1000.0)),
+                 (long) (point + point * ((double) fuzz->a / 1000.0)));
+        break;
+      case 4 :
+        if (fuzz->a == 3) { /* space to right */
+          sprintf (buf, "%ld^%ld", (long) (point), (long) (point + 1));
+        } else if (fuzz->a == 4 && point > 1) { /* space to left */
+          sprintf (buf, "%ld^%ld", (long) (point - 1), (long) point);
+        } else {
+          index = (Uint1) fuzz->a;
+          if (index > 4) {
+            index = 0;
+          }
+          sprintf (buf, "%s%ld", lim_str [index], (long) point);
+        }
+        break;
+      default :
+        sprintf (buf, "%ld", (long) point);
+        break;
+    }
+  } else {
+    sprintf (buf, "%ld", (long) point);
+  }
+
+  FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+}
+
+
+static void FlatLocPoint (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  SeqIdPtr sip,
+  SeqIdPtr this_sip,
+  Int4 point,
+  IntFuzzPtr fuzz
+)
+
+{
+  Char   buf [128];
+  Uint1  index;
+
+  if (ffstring == NULL) return;
+
+  if (sip != NULL && (! SeqIdIn (sip, this_sip))) {
+    FlatLocSeqId (ajp, ffstring, sip);
+  }
+
+  buf [0] = '\0';
+  point++;
+
+  if (fuzz != NULL) {
+    switch (fuzz->choice) {
+      case 1 :
+        sprintf (buf, "(%ld.%ld)",
+                 (long) (point - fuzz->a),
+                 (long) (point + fuzz->a));
+        break;
+      case 2 :
+        sprintf (buf, "(%ld.%ld)",
+                 (long) (1 + fuzz->b),
+                 (long) (1 + fuzz->a));
+        break;
+      case 3 :
+        sprintf (buf, "(%ld.%ld)",
+                 (long) (point - point * ((double) fuzz->a / 1000.0)),
+                 (long) (point + point * ((double) fuzz->a / 1000.0)));
+        break;
+      case 4 :
+        index = (Uint1) fuzz->a;
+        if (index > 4) {
+          index = 0;
+        }
+        sprintf (buf, "%s%ld", lim_str [index], (long) point);
+        break;
+      default :
+        sprintf (buf, "%ld", (long) point);
+        break;
+    }
+  } else {
+    sprintf (buf, "%ld", (long) point);
+  }
+
+  FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+}
+
+
+static void FlatLocElement (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  BioseqPtr bsp,
+  SeqLocPtr location
+)
+
+{
+  Boolean     minus_strand = FALSE;
+  SeqBondPtr  sbp;
+  SeqIntPtr   sintp;
+  SeqIdPtr    sip;
+  SeqPntPtr   spp;
+  BioseqPtr   wholebsp;
+
+  if (ffstring == NULL || bsp == NULL || location == NULL) return;
+
+  switch (location->choice) {
+    case SEQLOC_WHOLE :
+      sip = (SeqIdPtr) location->data.ptrvalue;
+      if (sip == NULL) return;
+      wholebsp = BioseqFind (sip);
+      if (wholebsp == NULL) return;
+      if (is_real_id (sip, bsp->id)) {
+        FlatLocPoint (ajp, ffstring, sip, bsp->id, 0, NULL);
+        if (bsp->length > 0) {
+          FFAddOneString(ffstring, "..", FALSE, FALSE, TILDE_IGNORE);
+          FlatLocPoint (ajp, ffstring, NULL, bsp->id, bsp->length - 1, NULL);
+        }
+      }
+      break;
+    case SEQLOC_INT :
+      sintp = (SeqIntPtr) location->data.ptrvalue;
+      if (sintp == NULL) return;
+      sip = sintp->id;
+      if (sip == NULL) return;
+      if (is_real_id (sip, bsp->id)) {
+        minus_strand = (Boolean) (sintp->strand == Seq_strand_minus);
+        if (minus_strand) {
+          FFAddOneString(ffstring, "complement(", FALSE, FALSE, TILDE_IGNORE);
+        }
+        FlatLocPoint (ajp, ffstring, sip, bsp->id, sintp->from, sintp->if_from);
+        if (sintp->to > 0 &&
+            (sintp->to != sintp->from ||
+             sintp->if_from != NULL ||
+             sintp->if_to != NULL)) {
+          FFAddOneString(ffstring, "..", FALSE, FALSE, TILDE_IGNORE);
+          FlatLocPoint (ajp, ffstring, NULL, bsp->id, sintp->to, sintp->if_to);
+        }
+        if (minus_strand) {
+          FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
+        }
+      }
+      break;
+    case SEQLOC_PNT :
+      spp = (SeqPntPtr) location->data.ptrvalue;
+      if (spp == NULL) return;
+      sip = spp->id;
+      if (sip == NULL) return;
+      if (is_real_id (sip, bsp->id)) {
+        minus_strand = (Boolean) (spp->strand == Seq_strand_minus);
+        if (minus_strand) {
+          FFAddOneString(ffstring, "complement(", FALSE, FALSE, TILDE_IGNORE);
+        }
+        if (spp->fuzz != NULL) {
+          FlatLocCaret (ajp, ffstring, sip, bsp->id, spp->point, spp->fuzz);
+        } else {
+          FlatLocPoint (ajp, ffstring, sip, bsp->id, spp->point, NULL);
+        }
+        if (minus_strand) {
+          FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
+        }
+      }
+      break;
+    case SEQLOC_BOND :
+      sbp = (SeqBondPtr) location->data.ptrvalue;
+      if (sbp == NULL) return;
+      spp = sbp->a;
+      if (spp == NULL) return;
+      sip = spp->id;
+      if (sip == NULL) return;
+      FFAddOneString(ffstring, "bond(", FALSE, FALSE, TILDE_IGNORE);
+      FlatLocPoint (ajp, ffstring, sip, bsp->id, spp->point, spp->fuzz);
+      spp = sbp->b;
+      if (spp != NULL) {
+        FFAddOneString(ffstring, ",", FALSE, FALSE, TILDE_IGNORE);
+        FlatLocPoint (ajp, ffstring, NULL, bsp->id, spp->point, spp->fuzz);
+      }
+      FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
+      break;
+    default :
+      /* unexpected internal complex type or unimplemented SEQLOC_FEAT */
+      return;
+  }
+}
+
+
+
+static void FF_FlatPackedPoint (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  PackSeqPntPtr pspp,
+  BioseqPtr bsp
+)
+
+{
+  Uint1  dex;
+
+  if (ffstring == NULL || pspp == NULL || bsp == NULL) return;
+
+  for (dex = 0; dex < pspp->used; dex++) {
+    FlatLocPoint (ajp, ffstring, pspp->id, bsp->id, pspp->pnts [dex], pspp->fuzz);
+  }
+}
+
+
+static void FF_DoFlatLoc (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  BioseqPtr bsp,
+  SeqLocPtr location,
+  Boolean ok_to_complement
+);
+
+static void FF_GroupFlatLoc (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  BioseqPtr bsp,
+  SeqLocPtr location,
+  CharPtr prefix,
+  Boolean is_flat_order
+)
+
+{
+  Boolean        found_non_virt = FALSE;
+  SeqIdPtr       hold_next;
+  Int2           parens = 1;
+  PackSeqPntPtr  pspp;
+  SeqLocPtr      slp;
+  Boolean        special_mode = FALSE; /* join in order */
+
+  if (ffstring == NULL || bsp == NULL || location == NULL) return;
+
+  /* prefix will have the first parenthesis */
+
+  FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+
+  for (slp = (SeqLocPtr) location->data.ptrvalue; slp != NULL; slp = slp->next) {
+
+    if (slp->choice == SEQLOC_NULL || FlatVirtLoc (bsp, slp)) {
+      if (slp != location && slp->next != NULL) {
+        if (special_mode) {
+          special_mode = FALSE;
+          FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
+          parens--;
+        }
+      }
+      continue;
+    }
+
+    if (found_non_virt && slp->choice != SEQLOC_EMPTY && slp->choice != SEQLOC_NULL) {
+      FFAddOneString(ffstring, ",", FALSE, FALSE, TILDE_IGNORE);
+    }
+
+    switch (slp->choice) {
+      case SEQLOC_WHOLE :
+      case SEQLOC_PNT :
+      case SEQLOC_BOND :
+      case SEQLOC_FEAT :
+        found_non_virt = TRUE;
+        if (FlatVirtLoc (bsp, slp)) {
+          if (slp != location && slp->next != NULL) {
+            if (special_mode) {
+              special_mode = FALSE;
+              FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
+              parens--;
+            }
+          }
+        } else {
+          FlatLocElement (ajp, ffstring, bsp, slp);
+        }
+        break;
+      case SEQLOC_INT :
+        found_non_virt = TRUE;
+        if (is_flat_order && (! FF_FlatNullAhead (bsp, slp))) {
+          special_mode = TRUE;
+          FFAddOneString(ffstring, "join(", FALSE, FALSE, TILDE_IGNORE);
+          parens++;
+        }
+        FlatLocElement (ajp, ffstring, bsp, slp);
+        break;
+      case SEQLOC_PACKED_PNT :
+        found_non_virt = TRUE;
+        pspp = (PackSeqPntPtr) slp->data.ptrvalue;
+        if (pspp != NULL) {
+          FF_FlatPackedPoint (ajp, ffstring, pspp, bsp);
+        }
+        break;
+      case SEQLOC_PACKED_INT :
+      case SEQLOC_MIX :
+      case SEQLOC_EQUIV :
+        found_non_virt = TRUE;
+        hold_next = slp->next;
+        slp->next = NULL;
+        FF_DoFlatLoc (ajp, ffstring, bsp, slp, FALSE);
+        slp->next = hold_next;
+        break;
+      default :
+        break;
+    }
+
+  }
+
+  while (parens > 0) {
+    FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
+    parens--;
+  }
+}
+
+
+
+
+static void FF_DoFlatLoc (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  BioseqPtr bsp,
+  SeqLocPtr location,
+  Boolean ok_to_complement
+)
+
+{
+  Boolean        found_null;
+  SeqLocPtr      next_loc;
+  PackSeqPntPtr  pspp;
+  SeqLocPtr      slp;
+
+  if (ffstring == NULL || bsp == NULL || location == NULL) return;
+
+  /* deal with complement of entire location */
+
+  if (ok_to_complement && SeqLocStrand (location) == Seq_strand_minus) {
+    slp = AsnIoMemCopy ((Pointer) location,
+                        (AsnReadFunc) SeqLocAsnRead,
+                        (AsnWriteFunc) SeqLocAsnWrite);
+    if (slp != NULL) {
+      SeqLocRevCmp (slp);
+      FFAddOneString(ffstring, "complement(", FALSE, FALSE, TILDE_IGNORE);
+      FF_DoFlatLoc (ajp, ffstring, bsp, slp, FALSE);
+      FFAddOneString(ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
+    }
+    SeqLocFree (slp);
+    return;
+  }
+
+  /* handle each location component */
+
+  for (slp = location; slp != NULL; slp = slp->next) {
+
+    if (slp->choice == SEQLOC_NULL || FlatVirtLoc (bsp, slp)) continue;
+
+    /* print comma between components */
+
+    if (slp != location) {
+      FFAddOneString(ffstring, ",", FALSE, FALSE, TILDE_IGNORE);
+    }
+
+    switch (slp->choice) {
+      case SEQLOC_MIX :
+      case SEQLOC_PACKED_INT :
+        found_null = FALSE;
+        for (next_loc = (SeqLocPtr) slp->data.ptrvalue;
+         next_loc != NULL;
+         next_loc = next_loc->next) {
+          if (next_loc->choice == SEQLOC_NULL ||
+              FlatVirtLoc (bsp, next_loc) /* ||
+              LocationHasNullsBetween (slp) */ )
+            found_null = TRUE;
+        }
+        if (found_null) {
+          FF_GroupFlatLoc (ajp, ffstring, bsp, slp, "order(", TRUE);
+        } else {
+          FF_GroupFlatLoc (ajp, ffstring, bsp, slp, "join(", FALSE);
+        }
+        break;
+      case SEQLOC_EQUIV :
+        FF_GroupFlatLoc (ajp, ffstring, bsp, slp, "one-of(", FALSE);
+        break;
+      case SEQLOC_PACKED_PNT :
+        pspp = (PackSeqPntPtr) slp->data.ptrvalue;
+        if (pspp != NULL) {
+          FF_FlatPackedPoint (ajp, ffstring, pspp, bsp);
+        }
+        break;
+      default :
+        FlatLocElement (ajp, ffstring, bsp, slp);
+        break;
+    }
+
+  }
+}
+
+
+
+
+NLM_EXTERN CharPtr FFFlatLoc (
+  IntAsn2gbJobPtr ajp,
+  BioseqPtr bsp,
+  SeqLocPtr location,
+  Boolean masterStyle
+)
+
+{
+  Boolean     hasNulls;
+  IntFuzzPtr  fuzz = NULL;
+  SeqLocPtr   loc;
+  Boolean     noLeft;
+  Boolean     noRight;
+  Uint1       num = 1;
+  SeqPntPtr   spp;
+  CharPtr     str;
+  SeqLocPtr   tmp;
+  StringItemPtr ffstring = NULL;
+
+  if (bsp == NULL || location == NULL) return NULL;
+
+  ffstring = FFGetString(ajp);
+
+  if (! order_initialized) {
+    order [SEQID_GENBANK] = num++;
+    order [SEQID_EMBL] = num++;
+    order [SEQID_DDBJ] = num++;
+    order [SEQID_OTHER] = num++;
+    order [SEQID_TPG] = num++;
+    order [SEQID_TPE] = num++;
+    order [SEQID_TPD] = num++;
+    order [SEQID_GIBBSQ] = num++;
+    order [SEQID_GIBBMT] = num++;
+    order [SEQID_PRF] = num++;
+    order [SEQID_PDB] = num++;
+    order [SEQID_PIR] = num++;
+    order [SEQID_SWISSPROT] = num++;
+    order [SEQID_PATENT] = num++;
+    order [SEQID_GI] = num++;;
+    order [SEQID_GENERAL] = num++;
+    order [SEQID_LOCAL] = num++;
+    order [SEQID_GIIM] = num++;
+    order_initialized = TRUE;
+  }
+
+  if (masterStyle) {
+
+    /* map location from parts to segmented bioseq */
+
+    if (location->choice == SEQLOC_PNT) {
+      spp = (SeqPntPtr) location->data.ptrvalue;
+      if (spp != NULL) {
+        fuzz = spp->fuzz;
+      }
+    }
+
+    CheckSeqLocForPartial (location, &noLeft, &noRight);
+    hasNulls = LocationHasNullsBetween (location);
+    loc = SeqLocMerge (bsp, location, NULL, FALSE, TRUE, hasNulls);
+    if (loc == NULL) {
+      tmp = TrimLocInSegment (bsp, location, &noLeft, &noRight);
+      loc = SeqLocMerge (bsp, tmp, NULL, FALSE, TRUE, hasNulls);
+      SeqLocFree (tmp);
+    }
+    if (loc == NULL) {
+      return StringSave ("?");
+    }
+    FreeAllFuzz (loc);
+    SetSeqLocPartial (loc, noLeft, noRight);
+
+    if (loc->choice == SEQLOC_PNT && fuzz != NULL) {
+      spp = (SeqPntPtr) loc->data.ptrvalue;
+      if (spp != NULL && spp->fuzz == NULL) {
+        spp->fuzz = AsnIoMemCopy ((Pointer) fuzz,
+                                  (AsnReadFunc) IntFuzzAsnRead,
+                                  (AsnWriteFunc) IntFuzzAsnWrite);
+      }
+    }
+
+    FF_DoFlatLoc (ajp, ffstring, bsp, loc, TRUE);
+
+    SeqLocFree (loc);
+
+  } else {
+    FF_DoFlatLoc (ajp, ffstring, bsp, location, TRUE);
+  }
+
+  str = FFToCharPtr(ffstring);
+  FFRecycleString(ajp, ffstring);
+  return str;
+}
+
+
+
+
+static void PromoteSeqId (SeqIdPtr sip, Pointer userdata)
+
+{
+  SeqIdPtr  bestid, newid, oldid;
+
+  bestid = (SeqIdPtr) userdata;
+
+  newid = SeqIdDup (bestid);
+  if (newid == NULL) return;
+
+  oldid = ValNodeNew (NULL);
+  if (oldid == NULL) return;
+
+  MemCopy (oldid, sip, sizeof (ValNode));
+  oldid->next = NULL;
+
+  sip->choice = newid->choice;
+  sip->data.ptrvalue = newid->data.ptrvalue;
+
+  SeqIdFree (oldid);
+  ValNodeFree (newid);
+
+  SeqIdStripLocus (sip);
+}
+
+NLM_EXTERN SeqLocPtr SeqLocReMapEx (
+  SeqIdPtr newid,
+  SeqLocPtr seq_loc,
+  SeqLocPtr location,
+  Int4 offset,
+  Boolean rev,
+  Boolean masterStyle
+)
+
+{
+  BioseqPtr    bsp;
+  Boolean      hasNulls;
+  IntFuzzPtr   fuzz = NULL;
+  SeqLocPtr    loc;
+  Boolean      noLeft;
+  Boolean      noRight;
+  SeqEntryPtr  scope;
+  SeqIdPtr     sip;
+  SeqLocPtr    slp = NULL;
+  SeqPntPtr    spp;
+  SeqLocPtr    tmp;
+
+  if (newid == NULL || seq_loc == NULL || location == NULL) return NULL;
+
+  if (masterStyle) {
+
+    sip = SeqLocId (seq_loc);
+    if (sip == NULL) return NULL;
+    bsp = BioseqFind (sip);
+    if (bsp == NULL) {
+      scope = SeqEntrySetScope (NULL);
+      bsp = BioseqFind (sip);
+      SeqEntrySetScope (scope);
+    }
+    if (bsp == NULL) return NULL;
+    sip = SeqIdFindBest (bsp->id, 0);
+
+    /* map location from parts to segmented bioseq */
+
+    if (location->choice == SEQLOC_PNT) {
+      spp = (SeqPntPtr) location->data.ptrvalue;
+      if (spp != NULL) {
+        fuzz = spp->fuzz;
+      }
+    }
+
+    CheckSeqLocForPartial (location, &noLeft, &noRight);
+    hasNulls = LocationHasNullsBetween (location);
+    loc = SeqLocMerge (bsp, location, NULL, FALSE, TRUE, hasNulls);
+    if (loc == NULL) {
+      tmp = TrimLocInSegment (bsp, location, &noLeft, &noRight);
+      loc = SeqLocMerge (bsp, tmp, NULL, FALSE, TRUE, hasNulls);
+      SeqLocFree (tmp);
+    }
+    if (loc == NULL) {
+      return NULL;
+    }
+    FreeAllFuzz (loc);
+    SetSeqLocPartial (loc, noLeft, noRight);
+
+    if (loc->choice == SEQLOC_PNT && fuzz != NULL) {
+      spp = (SeqPntPtr) loc->data.ptrvalue;
+      if (spp != NULL && spp->fuzz == NULL) {
+        spp->fuzz = AsnIoMemCopy ((Pointer) fuzz,
+                                  (AsnReadFunc) IntFuzzAsnRead,
+                                  (AsnWriteFunc) IntFuzzAsnWrite);
+      }
+    }
+
+    scope = SeqEntrySetScope (NULL);
+    slp = SeqLocReMap (newid, seq_loc, loc, offset, rev);
+    SeqEntrySetScope (scope);
+
+    SeqLocFree (loc);
+
+    VisitSeqIdsInSeqLoc (slp, (Pointer) sip, PromoteSeqId);
+  } else {
+
+    scope = SeqEntrySetScope (NULL);
+    slp = SeqLocReMap (newid, seq_loc, location, offset, rev);
+    SeqEntrySetScope (scope);
+  }
+
+  return slp;
+}
+
+
+/******************************************************************************/
+/*                            End FFFlatLoc functions.                          */
+/******************************************************************************/
+
+
+
+static void SubSourceToQualArray (
+  SubSourcePtr ssp,
+  QualValPtr qvp
+)
+
+{
+  SourceType  idx;
+  Uint1       subtype;
+
+  if (ssp == NULL || qvp == NULL) return;
+
+  while (ssp != NULL) {
+    subtype = ssp->subtype;
+    if (subtype == 255) {
+      subtype = 29;
+    }
+    if (subtype < 30) {
+      idx = subSourceToSourceIdx [subtype];
+      if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) {
+        if (qvp [idx].ssp == NULL) {
+          qvp [idx].ssp = ssp;
+        }
+      }
+    }
+    ssp = ssp->next;
+  }
+}
+
+NLM_EXTERN SourceType orgModToSourceIdx [38] = {
+  SCQUAL_zero_orgmod,
+  SCQUAL_one_orgmod,
+  SCQUAL_strain,
+  SCQUAL_sub_strain,
+  SCQUAL_type,
+  SCQUAL_sub_type,
+  SCQUAL_variety,
+  SCQUAL_serotype,
+  SCQUAL_serogroup,
+  SCQUAL_serovar,
+  SCQUAL_cultivar,
+  SCQUAL_pathovar,
+  SCQUAL_chemovar,
+  SCQUAL_biovar,
+  SCQUAL_biotype,
+  SCQUAL_group,
+  SCQUAL_sub_group,
+  SCQUAL_isolate,
+  SCQUAL_common,
+  SCQUAL_acronym,
+  SCQUAL_dosage,
+  SCQUAL_spec_or_nat_host,
+  SCQUAL_sub_species,
+  SCQUAL_specimen_voucher,
+  SCQUAL_authority,
+  SCQUAL_forma,
+  SCQUAL_forma_specialis,
+  SCQUAL_ecotype,
+  SCQUAL_synonym,
+  SCQUAL_anamorph,
+  SCQUAL_teleomorph,
+  SCQUAL_breed,
+  SCQUAL_gb_acronym,
+  SCQUAL_gb_anamorph,
+  SCQUAL_gb_synonym,
+  SCQUAL_old_lineage,
+  SCQUAL_old_name,
+  SCQUAL_orgmod_note
+};
+
+static void OrgModToQualArray (
+  OrgModPtr omp,
+  QualValPtr qvp
+)
+
+{
+  SourceType  idx;
+  Uint1       subtype;
+
+  if (omp == NULL || qvp == NULL) return;
+
+  while (omp != NULL) {
+    subtype = omp->subtype;
+    if (subtype == 253) {
+      subtype = 35;
+    } else if (subtype == 254) {
+      subtype = 36;
+    } else if (subtype == 255) {
+      subtype = 37;
+    }
+    if (subtype < 38) {
+      idx = orgModToSourceIdx [subtype];
+      if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) {
+        if (qvp [idx].omp == NULL) {
+          qvp [idx].omp = omp;
+        }
+      }
+    }
+    omp = omp->next;
+  }
+}
+
+static CharPtr organelleQual [] = {
+  NULL,
+  NULL,
+  "/organelle=\"plastid:chloroplast\"",
+  "/organelle=\"plastid:chromoplast\"",
+  "/organelle=\"mitochondrion:kinetoplast\"",
+  "/organelle=\"mitochondrion\"",
+  "/organelle=\"plastid\"",
+  "/macronuclear",
+  NULL,
+  "/plasmid=\"\"",
+  "/transposon=\"\"",
+  "/insertion_seq=\"\"",
+  "/organelle=\"plastid:cyanelle\"",
+  "/proviral",
+  "/virion",
+  "/organelle=\"nucleomorph\"",
+  "/organelle=\"plastid:apicoplast\"",
+  "/organelle=\"plastid:leucoplast\"",
+  "/organelle=\"plastid:proplastid\"",
+  NULL
+};
+
+NLM_EXTERN Boolean StringIsJustQuotes (
+  CharPtr str
+)
+
+{
+  Nlm_Uchar  ch;    /* to use 8bit characters in multibyte languages */
+
+  if (str != NULL) {
+    ch = *str;
+    while (ch != '\0') {
+      if (ch > ' ' && ch != '"' && ch != '\'') {
+        return FALSE;
+      }
+      str++;
+      ch = *str;
+    }
+  }
+  return TRUE;
+}
+
+static CharPtr RemoveAllSpaces (
+  CharPtr str
+)
+
+{
+  Char     ch;
+  CharPtr  dst;
+  CharPtr  ptr;
+
+  if (str == NULL || str [0] == '\0') return NULL;
+
+  dst = str;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    if (ch != ' ') {
+      *dst = ch;
+      dst++;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+  *dst = '\0';
+
+  return str;
+}
+
+NLM_EXTERN void AddFeatureToGbseq (
+  GBSeqPtr gbseq,
+  GBFeaturePtr gbfeat,
+  CharPtr str,
+  SeqFeatPtr sfp
+)
+
+{
+  Char            ch;
+  CharPtr         copy;
+  GBQualifierPtr  gbqual;
+  GBQualifierPtr  last = NULL;
+  CharPtr         ptr;
+  CharPtr         qual;
+  CharPtr         val;
+
+  if (gbseq == NULL || gbfeat == NULL || StringHasNoText (str)) return;
+
+  copy = StringSave (str);
+
+  /* link in reverse order, to be reversed in slash block */
+
+  gbfeat->next = gbseq->feature_table;
+  gbseq->feature_table = gbfeat;
+
+  /* now parse qualifiers */
+
+  ptr = StringStr (copy, "                     /");
+  while (ptr != NULL) {
+    qual = ptr + 22;
+    val = qual;
+    ch = *val;
+    while (ch != '=' && ch != '\n' && ch != '\0') {
+      val++;
+      ch = *val;
+    }
+    /*
+    val = StringChr (qual, '=');
+    if (val == NULL) {
+      val = StringChr (qual, '\n');
+    }
+    */
+    if (ch != '\0' /* val != NULL */) {
+      *val = '\0';
+      val++;
+      if (ch == '=') {
+        if (*val == '"') {
+          val++;
+        }
+        ptr = StringStr (val, "\n                     /");
+        if (ptr != NULL) {
+          *ptr = '\0';
+          ptr++;
+        }
+      } else {
+        ptr = StringStr (val, "                     /");
+        val = NULL;
+      }
+      gbqual = GBQualifierNew ();
+      if (gbqual != NULL) {
+        gbqual->name = StringSave (qual);
+        if (! StringHasNoText (val)) {
+          gbqual->value = StringSave (val);
+          CleanQualValue (gbqual->value);
+          Asn2gnbkCompressSpaces (gbqual->value);
+          if (sfp != NULL) {
+            if (sfp->data.choice == SEQFEAT_CDREGION &&
+                StringICmp (qual, "translation") == 0) {
+              RemoveAllSpaces (gbqual->value);
+            } else if (sfp->data.choice == SEQFEAT_RNA &&
+                       StringICmp (qual, "transcription") == 0) {
+              RemoveAllSpaces (gbqual->value);
+            } else if (sfp->data.choice == SEQFEAT_PROT &&
+                       StringICmp (qual, "peptide") == 0) {
+              RemoveAllSpaces (gbqual->value);
+            }
+          }
+        }
+      }
+    } else {
+      gbqual = GBQualifierNew ();
+      if (gbqual != NULL) {
+        gbqual->name = StringSave (qual);
+      }
+    }
+    if (gbfeat->quals == NULL) {
+      gbfeat->quals = gbqual;
+    } else if (last != NULL) {
+      last->next = gbqual;
+    }
+    last = gbqual;
+  }
+
+  MemFree (copy);
+}
+
+NLM_EXTERN CharPtr GetMolTypeQual (
+  BioseqPtr bsp
+)
+
+{
+  SeqMgrDescContext  dcontext;
+  MolInfoPtr         mip;
+  SeqDescrPtr        sdp;
+
+  if (bsp == NULL) return NULL;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp == NULL) return NULL;
+  mip = (MolInfoPtr) sdp->data.ptrvalue;
+  if (mip == NULL) return NULL;
+
+  switch (mip->biomol) {
+    case 0 :
+      switch (bsp->mol) {
+        case Seq_mol_dna :
+          return "unassigned DNA";
+        case Seq_mol_rna :
+          return "unassigned RNA";
+        case Seq_mol_na :
+          break;
+        default :
+          break;
+      }
+      break;
+    case MOLECULE_TYPE_GENOMIC :
+      switch (bsp->mol) {
+        case Seq_mol_dna :
+          return "genomic DNA";
+        case Seq_mol_rna :
+          return "genomic RNA";
+        case Seq_mol_na :
+          break;
+        default :
+          break;
+      }
+      break;
+    case MOLECULE_TYPE_PRE_MRNA :
+      return "pre-RNA";
+    case MOLECULE_TYPE_MRNA :
+      return "mRNA";
+    case MOLECULE_TYPE_RRNA :
+      return "rRNA";
+    case MOLECULE_TYPE_TRNA :
+      return "tRNA";
+    case MOLECULE_TYPE_SNRNA :
+      return "snRNA";
+    case MOLECULE_TYPE_SCRNA :
+      return "scRNA";
+    case MOLECULE_TYPE_PEPTIDE :
+      break;
+    case MOLECULE_TYPE_OTHER_GENETIC_MATERIAL :
+      switch (bsp->mol) {
+        case Seq_mol_dna :
+          return "other DNA";
+        case Seq_mol_rna :
+          return "other RNA";
+        case Seq_mol_na :
+          break;
+        default :
+          break;
+      }
+      break;
+    case MOLECULE_TYPE_GENOMIC_MRNA_MIX :
+      break;
+    case MOLECULE_TYPE_CRNA :
+      return "other RNA";
+      break;
+    case MOLECULE_TYPE_SNORNA :
+      return "snoRNA";
+      break;
+    case MOLECULE_TYPE_TRANSCRIBED_RNA :
+      return "other RNA";
+      break;
+    case 255 :
+      switch (bsp->mol) {
+        case Seq_mol_dna :
+          return "other DNA";
+        case Seq_mol_rna :
+          return "other RNA";
+        case Seq_mol_na :
+          break;
+        default :
+          break;
+      }
+      break;
+    default :
+      break;
+  }
+
+  return NULL;
+}
+
+NLM_EXTERN CharPtr FormatSourceFeatBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  Boolean            add_period;
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  BioSourcePtr       biop = NULL;
+  BioseqPtr          bsp;
+  Char               buf [80];
+  CharPtr            common = NULL;
+  DbtagPtr           dbt;
+  SeqMgrDescContext  dcontext;
+  SeqMgrFeatContext  fcontext;
+  GBFeaturePtr       gbfeat = NULL;
+  GBSeqPtr           gbseq;
+  Int2               i;
+  Uint1              idx;
+  IntSrcBlockPtr     isp;
+  Boolean            is_desc = TRUE;
+  Int2               j;
+  Uint1              jdx;
+  Uint1              lastomptype;
+  Uint1              lastssptype;
+  SeqLocPtr          location = NULL;
+  CharPtr            notestr;
+  SourceType PNTR    notetbl = NULL;
+  Boolean            okay;
+  ObjectIdPtr        oip;
+  OrgModPtr          omp;
+  OrgNamePtr         onp = NULL;
+  OrgRefPtr          orp = NULL;
+  CharPtr            prefix;
+  SourceType PNTR    qualtbl = NULL;
+  QualValPtr         qvp;
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp = NULL;
+  SubSourcePtr       ssp;
+  CharPtr            str;
+  CharPtr            taxname = NULL;
+  ValNodePtr         vnp;
+  StringItemPtr      ffstring, unique;
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+  bsp = asp->bsp;
+  if (bsp == NULL) return NULL;
+  qvp = afp->qvp;
+  if (qvp == NULL) return NULL;
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (! StringHasNoText (bbp->string)) return StringSave (bbp->string);
+
+  isp = (IntSrcBlockPtr) bbp;
+
+  /* could be descriptor or feature */
+
+  if (bbp->itemtype == OBJ_SEQDESC) {
+    sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext);
+    if (sdp != NULL && dcontext.seqdesctype == Seq_descr_source) {
+      biop = (BioSourcePtr) sdp->data.ptrvalue;
+    }
+  } else if (bbp->itemtype == OBJ_SEQFEAT) {
+    sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
+    if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_BIOSRC) {
+      biop = (BioSourcePtr) sfp->data.value.ptrvalue;
+    }
+    is_desc = FALSE;
+  }
+
+  if (biop == NULL) return NULL;
+
+  unique = FFGetString(ajp);
+  if ( unique == NULL ) return NULL;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return NULL;
+
+  FFStartPrint (ffstring, afp->format, 5, 21, NULL, 0, 5, 21, "FT", FALSE);
+  FFAddOneString (ffstring, "source", FALSE, FALSE, TILDE_IGNORE);
+  FFAddNChar(ffstring, ' ', 21 - 5 - StringLen("source"), FALSE);
+
+  if (gbseq != NULL) {
+    gbfeat = GBFeatureNew ();
+    if (gbfeat != NULL) {
+      gbfeat->key = StringSave ("source");
+    }
+  }
+
+  location = isp->loc;
+
+  str = FFFlatLoc (ajp, bsp, location, ajp->masterStyle);
+  if ( GetWWW(ajp) ) {
+    FF_www_featloc (ffstring, str);
+  } else {
+    FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_IGNORE);
+  }
+  FFAddOneChar(ffstring, '\n', FALSE);
+
+  if (gbseq != NULL) {
+    if (gbfeat != NULL) {
+      if (! StringHasNoText (str)) {
+        gbfeat->location = StringSave (str);
+      } else {
+        gbfeat->location = StringSave ("");
+      }
+    }
+  }
+
+  MemFree (str);
+
+  orp = biop->org;
+  if (orp != NULL) {
+    taxname = orp->taxname;
+    /* common = orp->common; */
+  }
+  if (StringHasNoText (taxname)) {
+    if (ajp->flags.needOrganismQual) {
+      taxname = "unknown";
+      common = orp->common;
+#ifdef ASN2GNBK_PRINT_UNKNOWN_ORG
+    } else {
+      taxname = "unknown";
+      common = orp->common;
+#endif
+    }
+  }
+
+  /* populate qualifier table from biosource fields */
+
+  qvp [SCQUAL_organism].str = taxname;
+  qvp [SCQUAL_common_name].str = common;
+
+  if (biop->is_focus) {
+    qvp [SCQUAL_focus].ble = TRUE;
+  }
+
+  str = GetMolTypeQual (bsp);
+  if (str == NULL) {
+    switch (bsp->mol) {
+      case Seq_mol_dna :
+        str = "unassigned DNA";
+        break;
+      case Seq_mol_rna :
+        str = "unassigned RNA";
+        break;
+      case Seq_mol_aa :
+        break;
+      default :
+        str = "unassigned DNA";
+        break;
+    }
+  }
+  qvp [SCQUAL_mol_type].str = str;
+
+  SubSourceToQualArray (biop->subtype, qvp);
+
+  if (orp != NULL) {
+    onp = orp->orgname;
+    if (onp != NULL) {
+      OrgModToQualArray (onp->mod, qvp);
+    }
+
+    if (! is_desc) {
+      qvp [SCQUAL_unstructured].vnp = orp->mod;
+    }
+    qvp [SCQUAL_db_xref].vnp = orp->db;
+  }
+
+  if (sfp != NULL) {
+    qvp [SCQUAL_org_xref].vnp = sfp->dbxref;
+  }
+
+  /* organelle currently prints /mitochondrion, /virion, etc. */
+
+  qvp [SCQUAL_organelle].num = biop->genome;
+
+  /* some qualifiers are flags in genome and names in subsource, print once with name */
+
+  if (qvp [SCQUAL_ins_seq_name].ssp != NULL &&
+      qvp [SCQUAL_organelle].num == GENOME_insertion_seq) {
+    qvp [SCQUAL_organelle].num = 0;
+  }
+  if (qvp [SCQUAL_plasmid_name].ssp != NULL &&
+      qvp [SCQUAL_organelle].num == GENOME_plasmid) {
+    qvp [SCQUAL_organelle].num = 0;
+  }
+  /* AF095904.1
+  if (qvp [SCQUAL_plastid_name].ssp != NULL &&
+      qvp [SCQUAL_organelle].num == GENOME_plastid) {
+    qvp [SCQUAL_organelle].num = 0;
+  }
+  */
+  if (qvp [SCQUAL_transposon_name].ssp != NULL &&
+      qvp [SCQUAL_organelle].num == GENOME_transposon) {
+    qvp [SCQUAL_organelle].num = 0;
+  }
+
+  if (sfp != NULL) {
+    qvp [SCQUAL_seqfeat_note].str = sfp->comment;
+  }
+
+  /* now print qualifiers from table */
+
+  qualtbl = source_qual_order;
+  if (is_desc) {
+    notetbl = source_desc_note_order;
+  } else {
+    notetbl = source_feat_note_order;
+  }
+
+  for (i = 0, idx = qualtbl [i]; idx != 0; i++, idx = qualtbl [i]) {
+
+    lastomptype = 0;
+    lastssptype = 0;
+    switch (asn2gnbk_source_quals [idx].qualclass) {
+
+      case Qual_class_ignore :
+        break;
+
+      case Qual_class_string :
+        if (! StringHasNoText (qvp [idx].str)) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=", 
+                            FALSE, FALSE, TILDE_IGNORE);
+          FFAddTextToString(ffstring, "\"", qvp [idx].str, "\"", 
+                            FALSE, FALSE, TILDE_TO_SPACES);
+          FFAddOneChar(ffstring, '\n', FALSE);
+        }
+        break;
+
+      case Qual_class_boolean :
+        if (qvp [idx].ble) {
+          FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "\n",
+                            FALSE, TRUE, TILDE_IGNORE);
+        }
+        break;
+
+      case Qual_class_organelle :
+        j = (Int2) qvp [idx].num;
+        if (organelleQual [j] != NULL) {
+          FFAddTextToString(ffstring, NULL, organelleQual[j], "\n",
+                            FALSE, FALSE, TILDE_IGNORE);
+        }
+        break;
+
+      case Qual_class_orgmod :
+        omp = qvp [idx].omp;
+        if (lastomptype == 0 && omp != NULL) {
+          lastomptype = omp->subtype;
+        }
+        while (omp != NULL && omp->subtype == lastomptype) {
+          if (StringIsJustQuotes (omp->subname)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=\"\"\n",
+                              FALSE, TRUE, TILDE_IGNORE);
+          } else if (! StringHasNoText (omp->subname)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=",
+                              FALSE, TRUE, TILDE_IGNORE);
+            FFAddTextToString(ffstring, "\"", omp->subname, "\"\n",
+                              FALSE, TRUE, TILDE_TO_SPACES);
+          }
+          omp = omp->next;
+        }
+        break;
+
+      case Qual_class_subsource :
+        ssp = qvp [idx].ssp;
+        if (lastssptype == 0 && ssp != NULL) {
+          lastssptype = ssp->subtype;
+        }
+        while (ssp != NULL && ssp->subtype == lastssptype) {
+          if (ssp->subtype == SUBSRC_germline ||
+              ssp->subtype == SUBSRC_rearranged ||
+              ssp->subtype == SUBSRC_transgenic ||
+              ssp->subtype == SUBSRC_environmental_sample) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "\n",
+                              FALSE, TRUE, TILDE_TO_SPACES);
+          } else if (StringIsJustQuotes (ssp->name)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=\"\"\n",
+                              FALSE, TRUE, TILDE_IGNORE);
+          } else if (! StringHasNoText (ssp->name)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=",
+                              FALSE, TRUE, TILDE_IGNORE);
+            FFAddTextToString(ffstring, "\"", ssp->name, "\"\n",
+                              FALSE, TRUE, TILDE_TO_SPACES);
+          }
+          ssp = ssp->next;
+        }
+        break;
+
+      case Qual_class_pubset :
+        break;
+
+      case Qual_class_quote :
+        break;
+
+      case Qual_class_noquote :
+        break;
+
+      case Qual_class_label :
+        break;
+
+      case Qual_class_db_xref :
+        for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) {
+          buf [0] = '\0';
+          dbt = (DbtagPtr) vnp->data.ptrvalue;
+          if (dbt != NULL && (! StringHasNoText (dbt->db))) {
+            oip = dbt->tag;
+            if (oip != NULL) {
+
+              okay = TRUE;
+              if (ajp->flags.dropBadDbxref) {
+                /* if RELEASE_MODE, drop unknown dbtag */
+                okay = FALSE;
+                for (j = 0; legalDbXrefs [j] != NULL; j++) {
+                  if (StringCmp (dbt->db, legalDbXrefs [j]) == 0) {
+                    okay = TRUE;
+                  }
+                }
+              }
+
+              if (okay) {
+                if (! StringHasNoText (oip->str)) {
+                  if (StringLen (dbt->db) + StringLen (oip->str) < 80) {
+                    sprintf (buf, "%s", oip->str);
+                  }
+                } else {
+                  sprintf (buf, "%ld", (long) oip->id);
+                }
+              }
+            }
+          }
+          if (! StringHasNoText (buf)) {
+            FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
+            FF_www_db_xref(ajp, ffstring, dbt->db, buf);
+            FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+          }
+        }
+        break;
+
+      case Qual_class_illegal :
+        break;
+
+      case Qual_class_note :
+        if (! ajp->flags.srcQualsToNote) {
+
+          /* in sequin_mode and dump_mode, all orgmods and subsources show up as separate /qualifiers */
+
+          for (j = 0, jdx = notetbl [j]; jdx != 0; j++, jdx = notetbl [j]) {
+
+            lastomptype = 0;
+            lastssptype = 0;
+            switch (asn2gnbk_source_quals [jdx].qualclass) {
+
+              case Qual_class_orgmod :
+                if (jdx == SCQUAL_orgmod_note) break;
+                omp = qvp [jdx].omp;
+                if (lastomptype == 0 && omp != NULL) {
+                  lastomptype = omp->subtype;
+                }
+                while (omp != NULL && omp->subtype == lastomptype) {
+                  if (StringIsJustQuotes (omp->subname)) {
+                    FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [jdx].name, "=\"\"\n",
+                              FALSE, TRUE, TILDE_IGNORE);
+                  } else if (! StringHasNoText (omp->subname)) {
+                    FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [jdx].name, "=",
+                                      FALSE, TRUE, TILDE_IGNORE);
+                    FFAddTextToString(ffstring, "\"", omp->subname, "\"\n",
+                                      FALSE, TRUE, TILDE_TO_SPACES);
+                  }
+                  omp = omp->next;
+                }
+                break;
+
+              case Qual_class_subsource :
+                if (jdx == SCQUAL_subsource_note) break;
+                ssp = qvp [jdx].ssp;
+                if (lastssptype == 0 && ssp != NULL) {
+                  lastssptype = ssp->subtype;
+                }
+                while (ssp != NULL && ssp->subtype == lastssptype) {
+                  if (StringIsJustQuotes (ssp->name)) {
+                    FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [jdx].name, "=\"\"\n",
+                                      FALSE, TRUE, TILDE_IGNORE);
+
+                  } else if (! StringHasNoText (ssp->name)) {
+                    FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [jdx].name, "=",
+                                      FALSE, TRUE, TILDE_IGNORE);
+                    FFAddTextToString(ffstring, "\"", ssp->name, "\"\n",
+                                      FALSE, TRUE, TILDE_TO_SPACES);
+                  }
+                  ssp = ssp->next;
+                }
+                break;
+
+              default :
+                break;
+            }
+          }
+        }
+
+        notestr = NULL;
+        prefix = "";
+        add_period = FALSE;
+
+        if (biop->genome == 8) {
+          FFAddTextToString(unique, "", "extrachromosomal", NULL, FALSE, FALSE, TILDE_IGNORE); 
+          prefix = "\n";
+        }
+
+        for (j = 0, jdx = notetbl [j]; jdx != 0; j++, jdx = notetbl [j]) {
+
+          lastomptype = 0;
+          lastssptype = 0;
+          switch (asn2gnbk_source_quals [jdx].qualclass) {
+
+            case Qual_class_string :
+              if (! StringHasNoText (qvp [jdx].str)) {
+                FFAddString_NoRedund (unique, prefix, qvp [jdx].str, NULL);
+                add_period = FALSE;
+                prefix = "\n";
+              }
+              break;
+
+            case Qual_class_orgmod :
+              if ((! ajp->flags.srcQualsToNote) && jdx != SCQUAL_orgmod_note) break;
+              omp = qvp [jdx].omp;
+              if (lastomptype == 0 && omp != NULL) {
+                lastomptype = omp->subtype;
+              }
+              while (omp != NULL && omp->subtype == lastomptype) {
+                if (! StringHasNoText (omp->subname)) {
+                  if (jdx == SCQUAL_orgmod_note) {
+                    sprintf (buf, "%s", prefix);
+                  } else {
+                    sprintf (buf, "%s%s: ", prefix, asn2gnbk_source_quals [jdx].name);
+                  }
+
+                  str = StringSave (omp->subname);
+                  add_period = s_RemovePeriodFromEnd (str);
+                  if (jdx == SCQUAL_orgmod_note) {
+                    FFAddString_NoRedund (unique, buf, str, NULL);
+                  } else {
+                    FFAddTextToString(unique, buf, str, NULL, FALSE, FALSE, TILDE_IGNORE);
+                  }
+                  MemFree (str);
+
+                  if (jdx == SCQUAL_orgmod_note) {
+                    if (add_period) {
+                      prefix = ".\n";
+                    } else {
+                      prefix = "\n";
+                    }
+                  } else {
+                    prefix = "; ";
+                  }
+                }
+                omp = omp->next;
+              }
+              break;
+
+            case Qual_class_subsource :
+              if ((! ajp->flags.srcQualsToNote) && jdx != SCQUAL_subsource_note) break;
+              ssp = qvp [jdx].ssp;
+              if (lastssptype == 0 && ssp != NULL) {
+                lastssptype = ssp->subtype;
+              }
+              while (ssp != NULL && ssp->subtype == lastssptype) {
+                if (! StringHasNoText (ssp->name)) {
+                  if (jdx == SCQUAL_subsource_note) {
+                    sprintf (buf, "%s", prefix);
+                  } else {
+                    sprintf (buf, "%s%s: ", prefix, asn2gnbk_source_quals [jdx].name);
+                  }
+
+                  str = StringSave (ssp->name);
+                  add_period = s_RemovePeriodFromEnd (str);
+                  if (jdx == SCQUAL_subsource_note) {
+                    FFAddString_NoRedund (unique, buf, str, NULL);
+                  } else {
+                    FFAddTextToString(unique, buf, str, NULL, FALSE, FALSE, TILDE_IGNORE);
+                  }
+                  MemFree (str);
+
+                  if (jdx == SCQUAL_subsource_note) {
+                    if (add_period) {
+                      prefix = ".\n";
+                    } else {
+                      prefix = "\n";
+                    }
+                  } else {
+                    prefix = "; ";
+                 }
+                }
+                ssp = ssp->next;
+              }
+              break;
+
+            case Qual_class_valnode :
+              for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) {
+                str = (CharPtr) vnp->data.ptrvalue;
+                if (! StringHasNoText (str)) {
+                  FFAddString_NoRedund (unique, prefix, str, NULL);
+                  add_period = FALSE;
+                  prefix = "; ";
+                }
+              }
+              break;
+
+            default :
+              break;
+          }
+        }
+        if ( !FFEmpty(unique) ) {
+          notestr = FFToCharPtr(unique);
+        
+          if (add_period) {
+            s_AddPeriodToEnd (notestr);
+          }
+
+#ifdef ASN2GNBK_STRIP_NOTE_PERIODS
+          if (! IsEllipsis (notestr))
+            s_RemovePeriodFromEnd (notestr);
+#endif
+
+          FFAddOneString (ffstring, "/note=\"", FALSE, FALSE, TILDE_IGNORE);
+          if (is_desc) {
+            /* AB055064.1 says TILDE_IGNORE on descriptors */
+            FFAddOneString (ffstring, notestr, FALSE, TRUE, TILDE_IGNORE);
+          } else {
+            /* ASZ93724.1 says TILDE_EXPAND on features */
+            FFAddOneString (ffstring, notestr, FALSE, TRUE, TILDE_EXPAND);
+          }
+          FFAddOneString (ffstring, "\"", FALSE, FALSE, TILDE_IGNORE);
+
+          MemFree (notestr);
+        }
+        break;
+      default :
+        break;
+    }
+  }
+
+  /* and then deal with the various note types separately (not in order table) */
+
+  str = FFEndPrint(ajp, ffstring, afp->format, 21, 21, 5, 21, "FT"); 
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (gbseq != NULL) {
+    if (gbfeat != NULL) {
+      AddFeatureToGbseq (gbseq, gbfeat, str, NULL);
+    }
+  }
+
+  FFRecycleString(ajp, unique);
+  FFRecycleString(ajp, ffstring);
+  return str;
+}
+
+
+static Boolean CountBasesByRead (
+  IntAsn2gbJobPtr ajp,
+  BioseqPtr bsp,
+  Int4Ptr base_count
+)
+
+{
+  Byte        bases [400];
+  Uint1       code = Seq_code_iupacna;
+  Int2        ctr;
+  Int2        i;
+  Int4        len;
+  Uint1       residue;
+  SeqPortPtr  spp = NULL;
+  Int4        total = 0;
+
+  if (ISA_aa (bsp->mol)) {
+    code = Seq_code_ncbieaa;
+  }
+
+  if (ajp->ajp.slp != NULL) {
+    spp = SeqPortNewByLoc (ajp->ajp.slp, code);
+    len = SeqLocLen (ajp->ajp.slp);
+  } else {
+    spp = SeqPortNew (bsp, 0, -1, 0, code);
+    len = bsp->length;
+  }
+  if (spp == NULL) return FALSE;
+  if (bsp->repr == Seq_repr_delta || bsp->repr == Seq_repr_virtual) {
+    SeqPortSet_do_virtual (spp, TRUE);
+  }
+
+  /* use SeqPortRead rather than SeqPortGetResidue for faster performance */
+
+  ctr = SeqPortRead (spp, bases, sizeof (bases));
+  i = 0;
+  residue = (Uint1) bases [i];
+  while (residue != SEQPORT_EOF) {
+    if (IS_residue (residue)) {
+      total++;
+      switch (residue) {
+        case 'A' :
+          (base_count [0])++;
+          break;
+        case 'C' :
+          (base_count [1])++;
+          break;
+        case 'G' :
+          (base_count [2])++;
+          break;
+        case 'T' :
+          (base_count [3])++;
+          break;
+        default :
+          (base_count [4])++;
+          break;
+      }
+    }
+    i++;
+    if (i >= ctr) {
+      i = 0;
+      ctr = SeqPortRead (spp, bases, sizeof (bases));
+      if (ctr < 0) {
+        bases [0] = -ctr;
+      } else if (ctr < 1) {
+        bases [0] = SEQPORT_EOF;
+      }
+    }
+    residue = (Uint1) bases [i];
+  }
+
+  SeqPortFree (spp);
+
+  return TRUE;
+}
+
+static void LIBCALLBACK CountBasesByStream (
+  CharPtr sequence,
+  Pointer userdata
+)
+
+{
+  Int4Ptr  base_count;
+  Char     ch;
+  CharPtr  ptr;
+
+  base_count = (Int4Ptr) userdata;
+
+  ptr = sequence;
+  ch = *ptr;
+  while (ch != '\0') {
+    ch = TO_UPPER (ch);
+    switch (ch) {
+      case 'A' :
+        (base_count [0])++;
+        break;
+      case 'C' :
+        (base_count [1])++;
+        break;
+      case 'G' :
+        (base_count [2])++;
+        break;
+      case 'T' :
+        (base_count [3])++;
+        break;
+      default :
+        (base_count [4])++;
+        break;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+}
+
+NLM_EXTERN CharPtr FormatBasecountBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  IntAsn2gbJobPtr  ajp;
+  Asn2gbSectPtr    asp;
+  Int4             base_count [5];
+  BioseqPtr        bsp;
+  Char             buf [80];
+  Int2             i;
+  Int4             len;
+  StringItemPtr    ffstring;
+  CharPtr          str;
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+  bsp = (asp->bsp);
+  if (bsp == NULL) return NULL;
+
+  /* after first formatting, result is cached into bbp->string */
+
+  if (! StringHasNoText (bbp->string)) return StringSave (bbp->string);
+
+  for (i = 0; i < 5; i++) {
+    base_count [i] = 0;
+  }
+
+  if (ajp->ajp.slp != NULL) {
+    len = SeqLocLen (ajp->ajp.slp);
+    if (! CountBasesByRead (ajp, bsp, base_count)) return NULL;
+  } else {
+    len = bsp->length;
+    SeqPortStream (bsp, TRUE, (Pointer) base_count, CountBasesByStream);
+  }
+
+  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+
+    if (base_count [4] == 0) {
+      sprintf (buf, "%7ld a%7ld c%7ld g%7ld t",
+               (long) base_count [0], (long) base_count [1],
+               (long) base_count [2], (long) base_count [3]);
+    } else {
+      sprintf (buf, "%7ld a%7ld c%7ld g%7ld t%7ld others",
+               (long) base_count [0], (long) base_count [1],
+               (long) base_count [2], (long) base_count [3],
+               (long) base_count [4]);
+    }
+
+  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+
+    sprintf (buf, "Sequence %ld BP; %ld A; %ld C; %ld G; %ld T; %ld other;",
+             (long) len,
+             (long) base_count [0], (long) base_count [1],
+             (long) base_count [2], (long) base_count [3],
+             (long) base_count [4]);
+  }
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return NULL;
+
+  if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+    FFAddOneString(ffstring, "XX\n", FALSE, FALSE, TILDE_IGNORE);
+  }
+  FFStartPrint (ffstring, afp->format, 0, 0, "BASE COUNT", 12, 5, 5, "SQ", FALSE);
+  FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+  str = FFEndPrint(ajp, ffstring, afp->format, 12, 0, 5, 5, "SQ");
+  FFRecycleString(ajp, ffstring);
+
+  return str;
+}
+
+static void PrintSeqLine (
+  StringItemPtr ffstring,
+  FmtType format,
+  CharPtr buf,
+  Int4 start,
+  Int4 stop
+)
+
+{
+  size_t  len;
+  Char    pos [16];
+  Int4    pad;
+
+  len = StringLen (buf);
+  if (len > 0 && buf [len - 1] == ' ') {
+    buf [len - 1] = '\0';
+  }
+
+  if (format == GENBANK_FMT || format == GENPEPT_FMT) {
+
+    sprintf (pos, "%9ld", (long) (start + 1));
+    FFAddOneString(ffstring, pos, FALSE, FALSE, TILDE_TO_SPACES);
+    FFAddOneChar(ffstring, ' ', FALSE);
+    FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+    FFAddOneChar(ffstring, '\n', FALSE);
+  } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
+
+    sprintf (pos, "%8ld", (long) (stop));
+    FFAddNChar(ffstring, ' ', 5, FALSE);
+    FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
+    pad = 72 - 5 - StringLen(buf);
+    FFAddNChar(ffstring, ' ', pad, FALSE);
+    FFAddOneString(ffstring, pos, FALSE, FALSE, TILDE_TO_SPACES);
+    FFAddOneChar(ffstring, '\n', FALSE);
+  }
+}
+
+static CharPtr CompressNonBases (CharPtr str)
+
+{
+  Char     ch;
+  CharPtr  dst;
+  CharPtr  ptr;
+
+  if (str == NULL || str [0] == '\0') return NULL;
+
+  dst = str;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    if (IS_ALPHA (ch)) {
+      *dst = ch;
+      dst++;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+  *dst = '\0';
+
+  return str;
+}
+
+/*
+static void CatenateSequenceInGbseq (
+  GBSeqPtr gbseq,
+  CharPtr str
+)
+
+{
+  Char     ch;
+  CharPtr  tmp;
+
+  if (gbseq == NULL || StringHasNoText (str)) return;
+
+  if (gbseq->sequence == NULL) {
+    gbseq->sequence = StringSave (str);
+  } else {
+    tmp = (CharPtr) MemNew (StringLen (gbseq->sequence) + StringLen (str) + 2);
+    StringCpy (tmp, gbseq->sequence);
+    StringCat (tmp, str);
+    gbseq->sequence = MemFree (gbseq->sequence);
+    gbseq->sequence = tmp;
+  }
+
+  tmp = gbseq->sequence;
+  if (tmp == NULL) return;
+  ch = *tmp;
+  while (ch != '\0') {
+    if (ch == '\n' || ch == '\r' || ch == '\t') {
+      *tmp = ' ';
+    }
+    tmp++;
+    ch = *tmp;
+  }
+  TrimSpacesAroundString (gbseq->sequence);
+  CompressNonBases (gbseq->sequence);
+}
+*/
+
+  static Uint1 fasta_order [NUM_SEQID] = {
+    33, /* 0 = not set */
+    20, /* 1 = local Object-id */
+    15, /* 2 = gibbsq */
+    16, /* 3 = gibbmt */
+    30, /* 4 = giim Giimport-id */
+    10, /* 5 = genbank */
+    10, /* 6 = embl */
+    10, /* 7 = pir */
+    10, /* 8 = swissprot */
+    15, /* 9 = patent */
+    20, /* 10 = other TextSeqId */
+    20, /* 11 = general Dbtag */
+    255, /* 12 = gi */
+    10, /* 13 = ddbj */
+    10, /* 14 = prf */
+    12, /* 15 = pdb */
+    10, /* 16 = tpg */
+    10, /* 17 = tpe */
+    10  /* 18 = tpd */
+  };
+
+static void PrintGenome (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  SeqLocPtr slp_head, 
+  CharPtr prefix, 
+  Boolean segWithParts
+)
+{
+  Char         buf[40], val[166];
+  Boolean      first = TRUE;
+  SeqLocPtr    slp;
+  Int4         from, to, start, stop;
+  SeqIdPtr     sid, newid;
+  BioseqPtr    bsp = NULL;
+  Int2         p1=0, p2=0;
+
+  for (slp = slp_head; slp; slp = slp->next) {
+    from = to = 0;
+    sid = SeqLocId(slp);
+    if (slp->choice == SEQLOC_INT || slp->choice == SEQLOC_WHOLE) {
+      start = from = SeqLocStart(slp);
+      stop = to = SeqLocStop(slp);
+    } else if (slp->choice == SEQLOC_NULL){
+      sprintf(val, ",%s", "gap()");
+      FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
+      continue;
+    } else {
+      continue;
+    }
+    if (sid == NULL) {
+      continue;
+    }
+    newid = NULL;
+    buf [0] = '\0';
+    if (sid->choice == SEQID_GI) {
+      if (GetAccnVerFromServer (sid->data.intvalue, buf)) {
+        /* no need to call GetSeqIdForGI */
+      } else {
+        newid = GetSeqIdForGI (sid->data.intvalue);
+        if (newid != NULL && segWithParts) {
+          if (newid->choice == SEQID_GIBBSQ ||
+              newid->choice == SEQID_GIBBMT ||
+              newid->choice == SEQID_GIIM) {
+            bsp = BioseqFind (newid);
+            if (bsp != NULL && bsp->repr == Seq_repr_virtual) {
+              if (bsp->length > 0) {
+                sprintf (val, ",gap(%ld)", (long) bsp->length);
+              } else {
+                sprintf(val, ",%s", "gap()");
+              }
+              FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
+              continue;
+            }
+          }
+        }
+      }
+    } else if (sid->choice == SEQID_GENERAL) {
+      newid = sid;
+    } else {
+      newid = sid;
+    }
+    if (prefix != NULL) {
+      FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
+    }
+    if (first) {
+      first = FALSE;
+    } else {
+      FFAddOneChar(ffstring, ',', FALSE);
+      /*ff_AddChar(',');*/
+    }
+    if (! StringHasNoText (buf)) {
+      /* filled in by GetAccnVerFromServer */
+    } else if (newid != NULL) {
+      SeqIdWrite (SeqIdSelect (newid, fasta_order, NUM_SEQID),
+                 buf, PRINTID_TEXTID_ACC_VER, sizeof(buf) -1 );
+    } else if (sid->choice == SEQID_GI) {
+      SeqIdWrite (sid, buf, PRINTID_FASTA_LONG, sizeof (buf) - 1);
+    }
+
+    if (SeqLocStrand (slp) == Seq_strand_minus) {
+      FFAddOneString(ffstring, "complement(", FALSE, FALSE, TILDE_IGNORE);
+    }
+    if ( GetWWW(ajp) ) {
+      if (newid == NULL) {
+        newid = sid;
+      }
+      if (newid->choice != SEQID_GENERAL) {
+        FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
+        FFAddTextToString(ffstring, "val=", buf, ">", FALSE, FALSE, TILDE_IGNORE);
+        FFAddTextToString(ffstring, NULL, buf, "</a>", FALSE, FALSE, TILDE_IGNORE);
+      }
+    } else {
+      FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+    }
+
+    if (SeqLocStrand(slp) == Seq_strand_minus) {
+      sprintf (val,":%ld..%ld)", (long) start+1, (long) stop+1);
+    } else {
+      sprintf (val,":%ld..%ld", (long) start+1, (long) stop+1);
+    }
+    FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
+    p1 += StringLen (val);
+    p2 += StringLen (val);
+  }
+}
+
+static Boolean SegHasParts (
+  BioseqPtr bsp
+)
+
+{
+  BioseqSetPtr  bssp;
+  SeqEntryPtr   sep;
+
+  if (bsp == NULL || bsp->repr != Seq_repr_seg) return FALSE;
+  sep = bsp->seqentry;
+  if (sep == NULL) return FALSE;
+  sep = sep->next;
+  if (sep == NULL || (! IS_Bioseq_set (sep))) return FALSE;
+  bssp = (BioseqSetPtr) sep->data.ptrvalue;
+  if (bssp != NULL && bssp->_class == BioseqseqSet_class_parts) return TRUE;
+  return FALSE;
+}
+
+static Boolean DeltaLitOnly (
+  BioseqPtr bsp
+)
+
+{
+  ValNodePtr  vnp;
+
+  if (bsp == NULL || bsp->repr != Seq_repr_delta) return FALSE;
+  for (vnp = (ValNodePtr)(bsp->seq_ext); vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == 1) return FALSE;
+  }
+  return TRUE;
+}
+
+NLM_EXTERN CharPtr FormatContigBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  IntAsn2gbJobPtr  ajp;
+  Asn2gbSectPtr    asp;
+  BioseqPtr        bsp;
+  DeltaSeqPtr      dsp;
+  GBSeqPtr         gbseq;
+  SeqLitPtr        litp;
+  CharPtr          prefix = NULL;
+  Boolean          segWithParts = FALSE;
+  SeqLocPtr        slp_head = NULL;
+  CharPtr          str;
+  Char             val [20];
+  StringItemPtr    ffstring;
+/*  CharPtr          label;*/
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+  bsp = (asp->bsp);
+  if (bsp == NULL) return NULL;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return NULL;
+
+  FFStartPrint (ffstring, afp->format, 0, 0, "CONTIG", 12, 5, 5, "CO", FALSE);
+  /*
+  if ( GetWWW(ajp) ) {
+    label = "CONTIG   ";
+  } else {
+    label = "CONTIG";
+  }
+  
+  FFAddOneString(ffstring, label,  FALSE, FALSE, TILDE_IGNORE);  
+  FFAddNChar(ffstring, ' ', 12 - StringLen(label), FALSE);
+  */
+
+  FFAddOneString(ffstring, "join(", FALSE, FALSE, TILDE_IGNORE);
+
+  if (bsp->seq_ext_type == 1) {
+
+    if (bsp->repr == Seq_repr_seg && SegHasParts (bsp)) {
+      segWithParts = TRUE;
+    }
+
+    slp_head = (SeqLocPtr) bsp->seq_ext;
+    PrintGenome (ajp, ffstring, slp_head, prefix, segWithParts);
+
+  } else if (bsp->seq_ext_type == 4) {
+
+    for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp=dsp->next) {
+      if (dsp->choice == 1) {
+
+        slp_head = (SeqLocPtr) dsp->data.ptrvalue;
+        PrintGenome (ajp, ffstring, slp_head, prefix, FALSE);
+
+      } else {
+
+        litp = (SeqLitPtr) dsp->data.ptrvalue;
+        if (litp != NULL) {
+          if (litp->seq_data != NULL) {
+            if (litp->length == 0) {
+              sprintf (val, "gap(%ld)", (long) litp->length);
+              FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
+            } else {
+              /* don't know what to do here */
+            }
+          } else {
+            if (prefix != NULL) {
+              sprintf (val, "%sgap(%ld)", prefix, (long) litp->length);
+            } else {
+              sprintf (val, "gap(%ld)", (long) litp->length);
+            }
+            FFAddOneString(ffstring, val, FALSE, FALSE, TILDE_IGNORE);
+          }
+        }
+      }
+
+      prefix = ",";
+    }
+  }
+
+  FFAddOneChar(ffstring, ')', FALSE);
+
+  str = FFEndPrint(ajp, ffstring, afp->format, 12, 12, 5, 5, "CO");
+  FFRecycleString(ajp, ffstring);
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (gbseq != NULL) {
+    if (StringLen (str) > 12) {
+      gbseq->contig = StringSave (str + 12);
+    } else {
+      gbseq->contig = StringSave (str);
+    }
+
+    CleanQualValue (gbseq->contig);
+    Asn2gnbkCompressSpaces (gbseq->contig);
+    StripAllSpaces (gbseq->contig);
+  }
+
+  return str;
+}
+
+static void LIBCALLBACK SaveGBSeqSequence (
+  CharPtr sequence,
+  Pointer userdata
+)
+
+{
+  CharPtr       tmp;
+  CharPtr PNTR  tmpp;
+
+  tmpp = (CharPtr PNTR) userdata;
+  tmp = *tmpp;
+
+  tmp = StringMove (tmp, sequence);
+
+  *tmpp = tmp;
+}
+
+NLM_EXTERN CharPtr FormatSequenceBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  IntAsn2gbJobPtr   ajp;
+  Asn2gbSectPtr     asp;
+  Byte              bases [400];
+  Int2              blk;
+  BioseqPtr         bsp;
+  Char              buf [80];
+  Char              ch;
+  Int2              cnt;
+  Uint1             code = Seq_code_iupacna;
+  Int2              count;
+  Int2              ctr;
+  GBSeqPtr          gbseq;
+  Int2              i;
+  IntAsn2gbSectPtr  iasp;
+  Boolean           is_na;
+  Int2              lin;
+  Int4              pos;
+  CharPtr           ptr;
+  Uint1             residue;
+  SeqBlockPtr       sbp;
+  SeqPortPtr        spp;
+  Int4              start;
+  Int4              stop;
+  CharPtr           str;
+  CharPtr           tmp;
+  StringItemPtr     ffstring;
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  sbp = (SeqBlockPtr) bbp;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+  iasp = (IntAsn2gbSectPtr) asp;
+  bsp = (asp->bsp);
+  if (bsp == NULL) return NULL;
+
+  /* if GBSeq XML, use SeqPortStream on single block */
+
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+
+    str = MemNew (sizeof (Char) * (bsp->length + 10));
+    if (str == NULL) return NULL;
+
+    tmp = str;
+    SeqPortStream (bsp, TRUE, (Pointer) &tmp, SaveGBSeqSequence);
+    gbseq->sequence = StringSave (str);
+
+    tmp = gbseq->sequence;
+    if (tmp == NULL) return NULL;
+    ch = *tmp;
+    while (ch != '\0') {
+      if (ch == '\n' || ch == '\r' || ch == '\t') {
+        *tmp = ' ';
+      }
+      tmp++;
+      ch = *tmp;
+    }
+    TrimSpacesAroundString (gbseq->sequence);
+    CompressNonBases (gbseq->sequence);
+
+    return str;
+  }
+
+  /* if subsequence cached with SeqPortStream, use it */
+
+  if (sbp->bases != NULL) {
+    ffstring = FFGetString (ajp);
+
+    start = sbp->start;
+    stop = sbp->stop;
+
+    count = 0;
+    blk = 0;
+    lin = 0;
+
+    ptr = sbp->bases;
+    ch = *ptr;
+
+    while (ch != '\0') {
+      buf [count] = (Char) (TO_LOWER (ch));
+      count++;
+      ptr++;
+      ch = *ptr;
+
+      blk++;
+      lin++;
+      if (lin >= 60) {
+
+        buf [count] = '\0';
+        PrintSeqLine (ffstring, afp->format, buf, start, start + cnt);
+        count = 0;
+        cnt = 0;
+        blk = 0;
+        lin = 0;
+        start += 60;
+
+      } else if (blk >= 10) {
+
+        buf [count] = ' ';
+        count++;
+        blk = 0;
+
+      }
+    }
+
+    buf [count] = '\0';
+    if (count > 0) {
+      PrintSeqLine (ffstring, afp->format, buf, start, start + cnt);
+    }
+
+    str = FFToCharPtr(ffstring);
+
+    FFRecycleString (ajp, ffstring);
+    return str;
+  }
+
+  /* otherwise split into smaller blocks */
+
+  spp = iasp->spp;
+  if (spp == NULL) {
+
+    /* if first time, create SeqPort for this section */
+
+    if (ISA_aa (bsp->mol)) {
+      if (ajp->flags.iupacaaOnly) {
+        code = Seq_code_iupacaa;
+      } else {
+        code = Seq_code_ncbieaa;
+      }
+    }
+
+    if (ajp->ajp.slp != NULL) {
+      spp = SeqPortNewByLoc (ajp->ajp.slp, code);
+    } else {
+      spp = SeqPortNew (bsp, 0, -1, 0, code);
+    }
+    if (spp == NULL) return NULL;
+    if (bsp->repr == Seq_repr_delta || bsp->repr == Seq_repr_virtual) {
+      SeqPortSet_do_virtual (spp, TRUE);
+    }
+
+    iasp->spp = spp;
+  }
+
+  start = sbp->start;
+  stop = sbp->stop;
+
+  if (start != spp->curpos) {
+    SeqPortSeek (spp, start, SEEK_SET);
+  }
+
+  pos = start;
+
+  count = 0;
+  cnt = 0;
+  blk = 0;
+  lin = 0;
+
+  is_na = ISA_na (bsp->mol);
+
+  ctr = (Int2) MIN ((Int4) (stop - pos), (Int4) sizeof (bases));
+  ctr = SeqPortRead (spp, bases, ctr);
+
+  i = 0;
+
+  if (ctr < 0) {
+    residue = -ctr;
+  } else if (ctr < 1) {
+    residue = SEQPORT_EOF;
+  } else {
+    residue = (Uint1) bases [i];
+  }
+
+
+  ffstring = FFGetString(ajp);
+  while (pos < stop && residue != SEQPORT_EOF) {
+
+    if (residue == INVALID_RESIDUE) {
+      if (is_na) {
+        residue = 'N';
+      } else {
+        residue = 'X';
+      }
+    }
+
+    if (IS_residue (residue)) {
+
+      buf [count] = (Char) (TO_LOWER (residue));
+      count++;
+      cnt++;
+      pos++;
+
+      blk++;
+      lin++;
+      if (lin >= 60) {
+
+        buf [count] = '\0';
+        PrintSeqLine (ffstring, afp->format, buf, start, start + cnt);
+        count = 0;
+        cnt = 0;
+        blk = 0;
+        lin = 0;
+        start += 60;
+
+      } else if (blk >= 10) {
+
+        buf [count] = ' ';
+        count++;
+        blk = 0;
+
+      }
+    }
+
+    i++;
+    if (i >= ctr) {
+      i = 0;
+      ctr = (Int2) MIN ((Int4) (stop - pos), (Int4) sizeof (bases));
+      ctr = SeqPortRead (spp, bases, ctr);
+      if (ctr < 0) {
+        bases [0] = -ctr;
+      } else if (ctr < 1) {
+        bases [0] = SEQPORT_EOF;
+      }
+    }
+    residue = (Uint1) bases [i];
+  }
+
+  buf [count] = '\0';
+  if (count > 0) {
+    PrintSeqLine (ffstring, afp->format, buf, start, start + cnt);
+  }
+
+  if (ajp->transientSeqPort) {
+    iasp->spp = SeqPortFree (iasp->spp);
+  }
+
+  str = FFToCharPtr(ffstring);
+
+  /* optionally populate gbseq for XML-ized GenBank format */
+
+  /*
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
+  if (gbseq != NULL) {
+    CatenateSequenceInGbseq (gbseq, str);
+  }
+  */
+
+  FFRecycleString(ajp, ffstring);
+  return str;
+}
+
+NLM_EXTERN CharPtr FormatSlashBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+)
+
+{
+  IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
+  GBFeaturePtr       currf, headf, nextf;
+  GBReferencePtr     currr, headr, nextr;
+  GBSeqPtr           gbseq;
+  IndxPtr            index;
+
+  if (afp == NULL || bbp == NULL) return NULL;
+  ajp = afp->ajp;
+  if (ajp == NULL) return NULL;
+  asp = afp->asp;
+  if (asp == NULL) return NULL;
+
+  /* sort and unique indexes */
+
+  index = ajp->index;
+
+  if (index != NULL) {
+
+    MemCopy (index, &asp->index, sizeof (IndxBlock));
+    MemSet (&asp->index, 0, sizeof (IndxBlock));
+
+    index->authors = ValNodeSort (index->authors, SortVnpByString);
+    index->authors = UniqueValNode (index->authors);
+
+    index->genes = ValNodeSort (index->genes, SortVnpByString);
+    index->genes = UniqueValNode (index->genes);
+
+    index->journals = ValNodeSort (index->journals, SortVnpByString);
+    index->journals = UniqueValNode (index->journals);
+
+    index->keywords = ValNodeSort (index->keywords, SortVnpByString);
+    index->keywords = UniqueValNode (index->keywords);
+
+    index->secondaries = ValNodeSort (index->secondaries, SortVnpByString);
+    index->secondaries = UniqueValNode (index->secondaries);
+  }
+
+  /* adjust XML-ized GenBank format */
+
+  gbseq = ajp->gbseq;
+
+  if (gbseq != NULL) {
+
+    MemCopy (gbseq, &asp->gbseq, sizeof (GBSeq));
+    MemSet (&asp->gbseq, 0, sizeof (GBSeq));
+
+    /* reverse order of references */
+
+    headr = NULL;
+    for (currr = gbseq->references; currr != NULL; currr = nextr) {
+      nextr = currr->next;
+      currr->next = headr;
+      headr = currr;
+    }
+    gbseq->references = headr;
+
+    /* reverse order of features */
+
+    headf = NULL;
+    for (currf = gbseq->feature_table; currf != NULL; currf = nextf) {
+      nextf = currf->next;
+      currf->next = headf;
+      headf = currf;
+    }
+    gbseq->feature_table = headf;
+  }
+
+  /* slash always has string pre-allocated by add slash block function */
+
+  return StringSaveNoNull (bbp->string);
+}
+
+
diff --git a/api/asn2gnbi.h b/api/asn2gnbi.h
new file mode 100644
index 00000000..e9232dd7
--- /dev/null
+++ b/api/asn2gnbi.h
@@ -0,0 +1,1008 @@
+/*   asn2gnbi.h
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  asn2gnbi.h
+*
+* Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans
+*
+* Version Creation Date:   12/30/03
+*
+* $Revision: 1.3 $
+*
+* File Description:  New GenBank flatfile generator, internal header
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* ==========================================================================
+*/
+
+#ifndef _ASN2NGNBI_
+#define _ASN2NGNBI_
+
+#include <asn2gnbp.h>
+
+#undef NLM_EXTERN
+#ifdef NLM_IMPORT
+#define NLM_EXTERN NLM_IMPORT
+#else
+#define NLM_EXTERN extern
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+
+#define ASN2FF_EMBL_MAX 78
+#define ASN2FF_GB_MAX   79
+#define SEQID_MAX_LEN   41
+
+#define TILDE_IGNORE     0
+#define TILDE_TO_SPACES  1
+#define TILDE_EXPAND     2
+#define TILDE_OLD_EXPAND 3
+
+
+/* flags set by mode to customize behavior */
+
+typedef struct asn2gbflags {
+  Boolean             suppressLocalID;
+  Boolean             validateFeats;
+  Boolean             ignorePatPubs;
+  Boolean             dropShortAA;
+  Boolean             avoidLocusColl;
+  Boolean             iupacaaOnly;
+  Boolean             dropBadCitGens;
+  Boolean             noAffilOnUnpub;
+  Boolean             dropIllegalQuals;
+  Boolean             checkQualSyntax;
+  Boolean             needRequiredQuals;
+  Boolean             needOrganismQual;
+  Boolean             needAtLeastOneRef;
+  Boolean             citArtIsoJta;
+  Boolean             dropBadDbxref;
+  Boolean             useEmblMolType;
+  Boolean             hideBankItComment;
+  Boolean             checkCDSproductID;
+  Boolean             suppressSegLoc;
+  Boolean             srcQualsToNote;
+  Boolean             hideEmptySource;
+  Boolean             goQualsToNote;
+  Boolean             geneSynsToNote;
+  Boolean             selenocysteineToNote;
+  Boolean             forGbRelease;
+} Asn2gbFlags, PNTR Asn2gbFlagsPtr;
+
+/* internal Asn2gbSect structure has fields on top of Asn2gbSect fields */
+
+typedef struct int_Asn2gbSect {
+  Asn2gbSect  asp;
+  SeqPortPtr  spp;
+} IntAsn2gbSect, PNTR IntAsn2gbSectPtr;
+
+/* string structure */
+
+#define STRING_BUF_LEN  1024
+
+typedef struct stringitem {
+  struct stringitem  *curr;
+  struct stringitem  *next;
+  Pointer            iajp;
+  Char               buf [STRING_BUF_LEN];
+  Int4               pos;
+} StringItem, PNTR StringItemPtr;
+
+/* internal asn2gbjob structure has fields on top of Asn2gbJob fields */
+
+typedef struct int_asn2gb_job {
+  Asn2gbJob      ajp;
+  FmtType        format;
+  ModType        mode;
+  Asn2gbFlags    flags;
+  Boolean        showFarTransl;
+  Boolean        transIfNoProd;
+  Boolean        alwaysTranslCds;
+  Boolean        showTranscript;
+  Boolean        showPeptide;
+  Boolean        transientSeqPort;
+  Boolean        masterStyle;
+  Boolean        newSourceOrg;
+  ValNodePtr     lockedBspList;
+  Boolean        relModeError;
+  Boolean        skipProts;
+  Boolean        skipMrnas;
+  IndxPtr        index;
+  GBSeqPtr       gbseq;
+  StringItemPtr  pool;
+  Boolean        www;
+} IntAsn2gbJob, PNTR IntAsn2gbJobPtr;
+
+/* structure for storing working parameters while building asn2gb_job structure */
+
+typedef struct asn2gbwork {
+  IntAsn2gbJobPtr  ajp;
+  Uint2            entityID;
+
+  FmtType          format;
+  ModType          mode;
+  StlType          style;
+
+  ValNodePtr       pubhead;    /* for collecting publications */
+  ValNodePtr       srchead;    /* for collecting biosources */
+
+  /* linked lists of paragraphs, sections, blocks */
+
+  ValNodePtr       sectionList;
+  ValNodePtr       blockList;    /* reset for each new section */
+
+  /* most recent node of linked lists, for quickly adding next node */
+
+  ValNodePtr       lastsection;
+  ValNodePtr       lastblock;    /* reset for each new section */
+
+  Int4             currsection;
+
+  /* section fields needed for populating blocks */
+
+  Asn2gbSectPtr    asp;
+
+  BioseqPtr        target;
+  BioseqPtr        parent;
+  BioseqPtr        bsp;
+  BioseqPtr        refs;
+  SeqLocPtr        slp;
+  Uint2            seg;
+  Int4             numsegs;
+  Int4             partcount;
+  Int4             from;
+  Int4             to;
+  Boolean          showAllFeats;
+
+  Boolean          contig;
+  Boolean          showconfeats;
+  Boolean          showconsource;
+
+  Boolean          onlyNearFeats;
+  Boolean          farFeatsSuppress;
+  Boolean          nearFeatsSuppress;
+
+  Boolean          citSubsFirst;
+  Boolean          hideGeneFeats;
+  Boolean          newLocusLine;
+  Boolean          showBaseCount;
+
+  Boolean          hideImpFeats;
+  Boolean          hideRemImpFeats;
+  Boolean          hideSnpFeats;
+  Boolean          hideExonFeats;
+  Boolean          hideIntronFeats;
+  Boolean          hideMiscFeats;
+  Boolean          hideCddFeats;
+  Boolean          hideCdsProdFeats;
+
+  Boolean          hideGeneRIFs;
+  Boolean          onlyGeneRIFs;
+  Boolean          latestGeneRIFs;
+
+  Boolean          showRefs;
+
+  Boolean          isGPS;
+  Boolean          copyGpsCdsUp;
+  Boolean          copyGpsGeneDown;
+
+  Boolean          showContigAndSeq;
+
+  Char             basename [SEQID_MAX_LEN];
+
+  SeqFeatPtr       lastsfp;
+  SeqAnnotPtr      lastsap;
+  Int4             lastleft;
+  Int4             lastright;
+
+  Boolean          firstfeat;
+  Boolean          featseen;
+
+  SeqSubmitPtr     ssp;
+  Boolean          hup;
+
+  Boolean          stream;
+
+  Boolean          failed;
+} Asn2gbWork, PNTR Asn2gbWorkPtr;
+
+/* array for assigning biosource and feature data fields to qualifiers */
+/* should be allocated to MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR) */
+
+typedef union qualval {
+  CharPtr        str;
+  Boolean        ble;
+  Int4           num;
+  ValNodePtr     vnp;
+  GBQualPtr      gbq;
+  OrgModPtr      omp;
+  SubSourcePtr   ssp;
+  CodeBreakPtr   cbp;
+  SeqLocPtr      slp;
+  SeqIdPtr       sip;
+  tRNAPtr        trp;
+  UserObjectPtr  uop;
+  UserFieldPtr   ufp;
+} QualVal, PNTR QualValPtr;
+
+/* structure passed to individual paragraph format functions */
+
+typedef struct asn2gbformat {
+  IntAsn2gbJobPtr ajp;
+  Asn2gbSectPtr   asp;
+  QualValPtr      qvp;
+
+  FmtType         format;
+} Asn2gbFormat, PNTR Asn2gbFormatPtr;
+
+
+/* Seq-hist replacedBy is preformatted into string field, */
+/* then comment descriptors, Map location:, and Region:, */
+/* then comment features, finally HTGS */
+
+typedef struct comment_block {
+  ASN2GB_BASE_BLOCK
+  Boolean           first;
+} CommentBlock, PNTR CommentBlockPtr;
+
+/* internal reference block has fields on top of RefBlock fields */
+
+typedef struct int_ref_block {
+  RefBlock   rb;
+  DatePtr    date;     /* internal sorting use only */
+  SeqLocPtr  loc;      /* final location on target bioseq */
+  CharPtr    authstr;  /* author string */
+  Uint2      index;    /* index if feature on target bioseq */
+  Boolean    justuids; /* gibb pub with uids and Figure, etc. */
+  CharPtr    fig;      /* figure string from equivalent gibb pub */
+  CharPtr    maploc;   /* maploc string from equivalent gibb pub */
+  Boolean    poly_a;   /* poly_a field from equivalent gibb pub */
+} IntRefBlock, PNTR IntRefBlockPtr;
+
+/* internal source block has fields on top of BaseBlock fields */
+
+typedef struct int_src_block {
+  BaseBlock         bb;
+  Boolean           is_descriptor;
+  Boolean           is_focus;
+  Boolean           is_synthetic;
+  BioSourcePtr      biop;
+  Uint4             orghash;
+  Uint4             modhash;
+  Uint4             subhash;
+  Uint4             xrfhash;
+  SeqLocPtr         loc;     /* final location on target bioseq */
+  CharPtr           taxname;
+  CharPtr           comment;
+  OrgModPtr         omp;
+  SubSourcePtr      ssp;
+  ValNodePtr        vnp;
+  Int4              left;
+  Int4              right;
+} IntSrcBlock, PNTR IntSrcBlockPtr;
+
+/* internal feature block has fields on top of FeatBlock fields */
+
+typedef struct int_feat_block {
+  FeatBlock  fb;
+  Boolean     mapToNuc;
+  Boolean     mapToProt;
+  Boolean     mapToGen;
+  Boolean     mapToMrna;
+  Boolean     mapToPep;
+  Boolean     isCDS;     /* set if using IntCdsBlock */
+  Boolean     firstfeat;
+} IntFeatBlock, PNTR IntFeatBlockPtr;
+
+/* internal cds block has fields on top of IntFeatBlock fields */
+
+typedef struct int_cds_block {
+  IntFeatBlock  ifb;
+  CharPtr       fig;    /* figure string from pub */
+  CharPtr       maploc; /* maploc string from pub */
+} IntCdsBlock, PNTR IntCdsBlockPtr;
+
+
+/* enumerated qualifier category definitions */
+
+typedef enum {
+  Qual_class_ignore = 0,
+  Qual_class_string,
+  Qual_class_tilde,
+  Qual_class_sgml,
+  Qual_class_boolean,
+  Qual_class_int,
+  Qual_class_evidence,
+  Qual_class_valnode,
+  Qual_class_EC_valnode,
+  Qual_class_xtraprds,
+  Qual_class_quote,
+  Qual_class_EC_quote,
+  Qual_class_noquote,
+  Qual_class_label,
+  Qual_class_number,
+  Qual_class_paren,
+  Qual_class_region,
+  Qual_class_replace,
+  Qual_class_consplice,
+  Qual_class_bond,
+  Qual_class_site,
+  Qual_class_L_R_B,
+  Qual_class_rpt,
+  Qual_class_organelle,
+  Qual_class_orgmod,
+  Qual_class_subsource,
+  Qual_class_code_break,
+  Qual_class_anti_codon,
+  Qual_class_codon,
+  Qual_class_method,
+  Qual_class_pubset,
+  Qual_class_db_xref,
+  Qual_class_seq_id,
+  Qual_class_seq_loc,
+  Qual_class_its,
+  Qual_class_sec_str,
+  Qual_class_trna_codons,
+  Qual_class_translation,
+  Qual_class_transcription,
+  Qual_class_peptide,
+  Qual_class_protnames,
+  Qual_class_encodes,
+  Qual_class_illegal,
+  Qual_class_note,
+  Qual_class_rpt_unit,
+  Qual_class_product,
+  Qual_class_model_ev,
+  Qual_class_gene_syn,
+  Qual_class_locus_tag,
+  Qual_class_go
+}  QualType;
+
+/* source 'feature' */
+
+/* some qualifiers will require additional content verification not
+   explicitly indicated by the class type */
+
+typedef enum {
+  SCQUAL_acronym = 1,
+  SCQUAL_anamorph,
+  SCQUAL_authority,
+  SCQUAL_biotype,
+  SCQUAL_biovar,
+  SCQUAL_breed,
+  SCQUAL_cell_line,
+  SCQUAL_cell_type,
+  SCQUAL_chemovar,
+  SCQUAL_chromosome,
+  SCQUAL_citation,
+  SCQUAL_clone,
+  SCQUAL_clone_lib,
+  SCQUAL_common,
+  SCQUAL_common_name,
+  SCQUAL_country,
+  SCQUAL_cultivar,
+  SCQUAL_db_xref,
+  SCQUAL_org_xref,
+  SCQUAL_dev_stage,
+  SCQUAL_dosage,
+  SCQUAL_ecotype,
+  SCQUAL_endogenous_virus_name,
+  SCQUAL_environmental_sample,
+  SCQUAL_extrachrom,
+  SCQUAL_focus,
+  SCQUAL_forma,
+  SCQUAL_forma_specialis,
+  SCQUAL_frequency,
+  SCQUAL_gb_acronym,
+  SCQUAL_gb_anamorph,
+  SCQUAL_gb_synonym,
+  SCQUAL_genotype,
+  SCQUAL_germline,
+  SCQUAL_group,
+  SCQUAL_haplotype,
+  SCQUAL_ins_seq_name,
+  SCQUAL_isolate,
+  SCQUAL_isolation_source,
+  SCQUAL_lab_host,
+  SCQUAL_label,
+  SCQUAL_macronuclear,
+  SCQUAL_map,
+  SCQUAL_mol_type,
+  SCQUAL_note,
+  SCQUAL_old_lineage,
+  SCQUAL_old_name,
+  SCQUAL_organism,
+  SCQUAL_organelle,
+  SCQUAL_orgmod_note,
+  SCQUAL_pathovar,
+  SCQUAL_plasmid_name,
+  SCQUAL_plastid_name,
+  SCQUAL_pop_variant,
+  SCQUAL_rearranged,
+  SCQUAL_segment,
+  SCQUAL_seqfeat_note,
+  SCQUAL_sequenced_mol,
+  SCQUAL_serogroup,
+  SCQUAL_serotype,
+  SCQUAL_serovar,
+  SCQUAL_sex,
+  SCQUAL_spec_or_nat_host,
+  SCQUAL_specimen_voucher,
+  SCQUAL_strain,
+  SCQUAL_sub_clone,
+  SCQUAL_sub_group,
+  SCQUAL_sub_species,
+  SCQUAL_sub_strain,
+  SCQUAL_sub_type,
+  SCQUAL_subsource_note,
+  SCQUAL_synonym,
+  SCQUAL_teleomorph,
+  SCQUAL_tissue_lib,
+  SCQUAL_tissue_type,
+  SCQUAL_transgenic,
+  SCQUAL_transposon_name,
+  SCQUAL_type,
+  SCQUAL_unstructured,
+  SCQUAL_usedin,
+  SCQUAL_variety,
+  SCQUAL_zero_orgmod,
+  SCQUAL_one_orgmod,
+  SCQUAL_zero_subsrc,
+  ASN2GNBK_TOTAL_SOURCE
+}  SourceType;
+
+NLM_EXTERN SourceType orgModToSourceIdx [38];
+
+typedef enum {
+  FTQUAL_allele = 1,
+  FTQUAL_anticodon,
+  FTQUAL_bond,
+  FTQUAL_bond_type,
+  FTQUAL_bound_moiety,
+  FTQUAL_cds_product,
+  FTQUAL_citation,
+  FTQUAL_clone,
+  FTQUAL_coded_by,
+  FTQUAL_codon,
+  FTQUAL_codon_start,
+  FTQUAL_cons_splice,
+  FTQUAL_db_xref,
+  FTQUAL_derived_from,
+  FTQUAL_direction,
+  FTQUAL_EC_number,
+  FTQUAL_encodes,
+  FTQUAL_evidence,
+  FTQUAL_exception,
+  FTQUAL_exception_note,
+  FTQUAL_figure,
+  FTQUAL_frequency,
+  FTQUAL_function,
+  FTQUAL_gene,
+  FTQUAL_gene_desc,
+  FTQUAL_gene_allele,
+  FTQUAL_gene_map,
+  FTQUAL_gene_syn,
+  FTQUAL_gene_syn_refseq,
+  FTQUAL_gene_note,
+  FTQUAL_gene_xref,
+  FTQUAL_go_component,
+  FTQUAL_go_function,
+  FTQUAL_go_process,
+  FTQUAL_heterogen,
+  FTQUAL_illegal_qual,
+  FTQUAL_insertion_seq,
+  FTQUAL_label,
+  FTQUAL_locus_tag,
+  FTQUAL_map,
+  FTQUAL_maploc,
+  FTQUAL_mod_base,
+  FTQUAL_modelev,
+  FTQUAL_note,
+  FTQUAL_number,
+  FTQUAL_operon,
+  FTQUAL_organism,
+  FTQUAL_partial,
+  FTQUAL_PCR_conditions,
+  FTQUAL_peptide,
+  FTQUAL_phenotype,
+  FTQUAL_product,
+  FTQUAL_product_quals,
+  FTQUAL_prot_activity,
+  FTQUAL_prot_comment,
+  FTQUAL_prot_EC_number,
+  FTQUAL_prot_note,
+  FTQUAL_prot_method,
+  FTQUAL_prot_conflict,
+  FTQUAL_prot_desc,
+  FTQUAL_prot_missing,
+  FTQUAL_prot_name,
+  FTQUAL_prot_names,
+  FTQUAL_protein_id,
+  FTQUAL_pseudo,
+  FTQUAL_region,
+  FTQUAL_region_name,
+  FTQUAL_replace,
+  FTQUAL_rpt_family,
+  FTQUAL_rpt_type,
+  FTQUAL_rpt_unit,
+  FTQUAL_rrna_its,
+  FTQUAL_sec_str_type,
+  FTQUAL_selenocysteine,
+  FTQUAL_selenocysteine_note,
+  FTQUAL_seqfeat_note,
+  FTQUAL_site,
+  FTQUAL_site_type,
+  FTQUAL_standard_name,
+  FTQUAL_transcription,
+  FTQUAL_transcript_id,
+  FTQUAL_transcript_id_note, /* !!! remove October 15, 2003 !!! */
+  FTQUAL_transl_except,
+  FTQUAL_transl_table,
+  FTQUAL_translation,
+  FTQUAL_transposon,
+  FTQUAL_trna_aa,
+  FTQUAL_trna_codons,
+  FTQUAL_usedin,
+  FTQUAL_xtra_prod_quals,
+  ASN2GNBK_TOTAL_FEATUR
+}  FtQualType;
+
+#define MAX_WWWBUF 328
+
+NLM_EXTERN Char link_feat [MAX_WWWBUF];
+NLM_EXTERN Char link_seq [MAX_WWWBUF];
+NLM_EXTERN Char link_wgs [MAX_WWWBUF];
+NLM_EXTERN Char link_omim [MAX_WWWBUF];
+NLM_EXTERN Char ref_link [MAX_WWWBUF];
+NLM_EXTERN Char nt_link [MAX_WWWBUF];
+NLM_EXTERN Char doc_link [MAX_WWWBUF];
+NLM_EXTERN Char ev_link [MAX_WWWBUF];
+NLM_EXTERN Char ec_link [MAX_WWWBUF];
+NLM_EXTERN Char link_tax [MAX_WWWBUF];
+NLM_EXTERN Char link_muid [MAX_WWWBUF];
+NLM_EXTERN Char link_code [MAX_WWWBUF];
+NLM_EXTERN Char link_encode [MAX_WWWBUF];
+
+NLM_EXTERN void FF_www_db_xref(
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr db, CharPtr identifier
+);
+
+NLM_EXTERN Boolean StringIsJustQuotes (
+  CharPtr str
+);
+
+
+typedef struct sourcequal {
+  CharPtr   name;
+  QualType  qualclass;
+} SourceQual, PNTR SourceQualPtr;
+
+NLM_EXTERN SourceQual asn2gnbk_source_quals [ASN2GNBK_TOTAL_SOURCE];
+
+NLM_EXTERN SourceType subSourceToSourceIdx [30];
+
+NLM_EXTERN void DoOneSection (
+  BioseqPtr target,
+  BioseqPtr parent,
+  BioseqPtr bsp,
+  BioseqPtr refs,
+  SeqLocPtr slp,
+  Uint2 seg,
+  Int4 from,
+  Int4 to,
+  Boolean contig,
+  Boolean onePartOfSeg,
+  Asn2gbWorkPtr awp
+);
+
+NLM_EXTERN void DoOneBioseq (
+  BioseqPtr bsp,
+  Pointer userdata
+);
+
+NLM_EXTERN BaseBlockPtr Asn2gbAddBlock (
+  Asn2gbWorkPtr awp,
+  BlockType blocktype,
+  size_t size
+);
+
+NLM_EXTERN void InitWWW (IntAsn2gbJobPtr ajp);
+NLM_EXTERN void FiniWWW (IntAsn2gbJobPtr ajp);
+NLM_EXTERN Boolean GetWWW (IntAsn2gbJobPtr ajp);
+
+NLM_EXTERN StringItemPtr FFGetString (IntAsn2gbJobPtr ajp);
+NLM_EXTERN void FFRecycleString (IntAsn2gbJobPtr ajp, StringItemPtr ffstring);
+NLM_EXTERN void FFAddOneChar (
+  StringItemPtr sip, 
+  Char ch,
+  Boolean convertQuotes
+);
+NLM_EXTERN void FFAddNewLine(StringItemPtr ffstring);
+NLM_EXTERN void FFAddNChar (
+  StringItemPtr sip, 
+  Char ch,
+  Int4 n,
+  Boolean convertQuotes
+);
+NLM_EXTERN void FFExpandTildes (StringItemPtr sip, CharPtr PNTR cpp);
+NLM_EXTERN void FFReplaceTildesWithSpaces (StringItemPtr ffstring, CharPtr PNTR cpp);
+NLM_EXTERN void FFOldExpand (StringItemPtr sip, CharPtr PNTR cpp);
+NLM_EXTERN void AddCommentStringWithTildes (StringItemPtr ffstring, CharPtr string);
+NLM_EXTERN void AddCommentWithURLlinks (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr prefix,
+  CharPtr str,
+  CharPtr suffix
+);
+NLM_EXTERN void AddStringWithTildes (StringItemPtr ffstring, CharPtr string);
+NLM_EXTERN void FFProcessTildes (StringItemPtr sip, CharPtr PNTR cpp, Int2 tildeAction);
+NLM_EXTERN void FFAddPeriod (StringItemPtr sip);
+NLM_EXTERN void FFAddOneString (
+  StringItemPtr sip, 
+  CharPtr string,
+  Boolean addPeriod, 
+  Boolean convertQuotes,
+  Int2 tildeAction
+);
+NLM_EXTERN void FFCatenateSubString (
+  StringItemPtr dest,
+  StringItemPtr start_sip, Int4 start_pos,
+  StringItemPtr end_sip, Int4 end_pos
+);
+NLM_EXTERN CharPtr FFToCharPtr (StringItemPtr sip);
+NLM_EXTERN void FFSkipLink (StringItemPtr PNTR iterp, Int4Ptr ip);
+NLM_EXTERN Boolean FFIsStartOfLink (StringItemPtr iter, Int4 pos);
+NLM_EXTERN void FFSavePosition(StringItemPtr ffstring, StringItemPtr PNTR bufptr, Int4 PNTR posptr);
+NLM_EXTERN void FFTrim (
+    StringItemPtr ffstring,
+    StringItemPtr line_start,
+    Int4 line_pos,
+    Int4 line_prefix_len
+);NLM_EXTERN void FFCalculateLineBreak (
+  StringItemPtr PNTR break_sip, Int4 PNTR break_pos,
+  Int4 init_indent, Int4 visible
+);
+NLM_EXTERN void FFLineWrap (
+  StringItemPtr dest, 
+  StringItemPtr src, 
+  Int4 init_indent,
+  Int4 cont_indent, 
+  Int4 line_max,
+  CharPtr eb_line_prefix
+);
+NLM_EXTERN void FFStartPrint (
+  StringItemPtr sip,
+  FmtType format,
+  Int4 gb_init_indent,
+  Int4 gb_cont_indent,
+  CharPtr gb_label,
+  Int4 gb_tab_to,
+  Int4 eb_init_indent,
+  Int4 eb_cont_indent,
+  CharPtr eb_line_prefix,
+  Boolean eb_print_xx 
+);
+NLM_EXTERN void FFAddTextToString (
+  StringItemPtr ffstring, 
+  CharPtr prefix,
+  CharPtr string,
+  CharPtr suffix,
+  Boolean addPeriod,
+  Boolean convertQuotes,
+  Int2 tildeAction
+);
+NLM_EXTERN CharPtr FFEndPrint (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  FmtType format,
+  Int2 gb_init_indent,
+  Int2 gb_cont_indent,
+  Int2 eb_init_indent,
+  Int2 eb_cont_indent,
+  CharPtr eb_line_prefix
+);
+NLM_EXTERN Uint4 FFLength(StringItemPtr ffstring);
+NLM_EXTERN Char FFCharAt(StringItemPtr ffstring, Uint4 pos);
+NLM_EXTERN Char FFFindChar (
+  StringItemPtr ffstring,
+  StringItemPtr start_buf,
+  Uint4 start_pos,
+  Uint4 old_pos,
+  Uint4 new_pos
+);
+NLM_EXTERN Boolean FFEmpty(StringItemPtr ffstring);
+NLM_EXTERN Int4 FFStringSearch (
+  StringItemPtr text,
+  const CharPtr pattern,
+  Uint4 position
+);
+NLM_EXTERN Boolean IsWholeWordSubstr (
+  StringItemPtr searchStr,
+  Uint4 foundPos,
+  CharPtr subStr
+);
+
+NLM_EXTERN ValNodePtr ValNodeCopyStrToHead (ValNodePtr PNTR head, Int2 choice, CharPtr str);
+NLM_EXTERN CharPtr MergeFFValNodeStrs (
+  ValNodePtr list
+);
+NLM_EXTERN void AddValNodeString (
+  ValNodePtr PNTR head,
+  CharPtr prefix,
+  CharPtr string,
+  CharPtr suffix
+);
+NLM_EXTERN void FFAddString_NoRedund (
+  StringItemPtr unique,
+  CharPtr prefix,
+  CharPtr string,
+  CharPtr suffix
+);
+NLM_EXTERN void s_AddPeriodToEnd (CharPtr someString);
+NLM_EXTERN Boolean s_RemovePeriodFromEnd (CharPtr someString);
+NLM_EXTERN Boolean IsEllipsis (
+  CharPtr str
+);
+NLM_EXTERN void A2GBSeqLocReplaceID (
+  SeqLocPtr newloc,
+  SeqLocPtr ajpslp
+);
+NLM_EXTERN CharPtr asn2gb_PrintDate (
+  DatePtr dp
+);
+NLM_EXTERN CharPtr DateToFF (
+  CharPtr buf,
+  DatePtr dp,
+  Boolean citSub
+);
+
+NLM_EXTERN CharPtr FFFlatLoc (
+  IntAsn2gbJobPtr ajp,
+  BioseqPtr bsp,
+  SeqLocPtr location,
+  Boolean masterStyle
+);
+
+NLM_EXTERN void FF_www_featloc(StringItemPtr ffstring, CharPtr loc);
+
+NLM_EXTERN CharPtr GetMolTypeQual (
+  BioseqPtr bsp
+);
+
+NLM_EXTERN void AddFeatureToGbseq (
+  GBSeqPtr gbseq,
+  GBFeaturePtr gbfeat,
+  CharPtr str,
+  SeqFeatPtr sfp
+);
+
+NLM_EXTERN SeqIdPtr SeqLocIdForProduct (
+  SeqLocPtr product
+);
+
+NLM_EXTERN CharPtr GetAuthorsString (
+  FmtType format,
+  AuthListPtr alp,
+  CharPtr PNTR consortP,
+  IndxPtr index,
+  GBReferencePtr gbref
+);
+
+NLM_EXTERN AuthListPtr GetAuthListPtr (
+  PubdescPtr pdp,
+  CitSubPtr csp
+);
+
+NLM_EXTERN Int2 MatchRef (
+  ValNodePtr ppr,
+  RefBlockPtr PNTR rbpp,
+  Int2 numReferences
+);
+
+NLM_EXTERN SeqLocPtr SeqLocReMapEx (
+  SeqIdPtr newid,
+  SeqLocPtr seq_loc,
+  SeqLocPtr location,
+  Int4 offset,
+  Boolean rev,
+  Boolean masterStyle
+);
+
+NLM_EXTERN CharPtr Get3LetterSymbol (
+  IntAsn2gbJobPtr  ajp,
+  Uint1 seq_code,
+  SeqCodeTablePtr table,
+  Uint1 residue
+);
+
+NLM_EXTERN CharPtr CleanQualValue (
+  CharPtr str
+);
+NLM_EXTERN CharPtr Asn2gnbkCompressSpaces (CharPtr str);
+NLM_EXTERN CharPtr StripAllSpaces (
+  CharPtr str
+);
+
+NLM_EXTERN Boolean GetAccnVerFromServer (Int4 gi, CharPtr buf);
+
+NLM_EXTERN CharPtr bondList [];
+NLM_EXTERN CharPtr siteList [];
+NLM_EXTERN CharPtr secStrText [];
+
+NLM_EXTERN CharPtr goQualType [];
+NLM_EXTERN CharPtr goFieldType [];
+
+NLM_EXTERN CharPtr legalDbXrefs [];
+NLM_EXTERN CharPtr legalRefSeqDbXrefs [];
+
+
+NLM_EXTERN void AddFeatureBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN Boolean AddReferenceBlock (
+  Asn2gbWorkPtr awp,
+  Boolean isRefSeq
+);
+NLM_EXTERN void AddSourceFeatBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddFeatureBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddLocusBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddAccessionBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddVersionBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddDbsourceBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddDateBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddDeflineBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddKeywordsBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddSegmentBlock (
+  Asn2gbWorkPtr awp,
+  Boolean onePartOfSeg
+);
+NLM_EXTERN void AddSourceBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddOrganismBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddCommentBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddPrimaryBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddFeatHeaderBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddSourceFeatBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddWGSBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddGenomeBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddContigBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddBasecountBlock (
+  Asn2gbWorkPtr awp,
+  CharPtr bases
+);
+NLM_EXTERN void AddOriginBlock (
+  Asn2gbWorkPtr awp
+);
+NLM_EXTERN void AddSequenceBlock (
+  Asn2gbWorkPtr awp,
+  CharPtr bases
+);
+NLM_EXTERN void AddSlashBlock (
+  Asn2gbWorkPtr awp
+);
+
+NLM_EXTERN CharPtr DefaultFormatBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatSourceBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatOrganismBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatReferenceBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatCommentBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatSourceFeatBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatFeatureBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatBasecountBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatSequenceBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatContigBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+NLM_EXTERN CharPtr FormatSlashBlock (
+  Asn2gbFormatPtr afp,
+  BaseBlockPtr bbp
+);
+
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
+#endif /* ndef _ASN2NGNBI_ */
+
diff --git a/api/asn2gnbp.h b/api/asn2gnbp.h
index 2c550826..9ef75af3 100644
--- a/api/asn2gnbp.h
+++ b/api/asn2gnbp.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 6.27 $
+* $Revision: 6.28 $
 *
 * File Description:  New GenBank flatfile generator, private header
 *
@@ -274,6 +274,12 @@ NLM_EXTERN CharPtr asn2gnbk_dbxref (
   DbtagPtr dbt
 );
 
+/* public function to get string of genbank-style feature qualifiers */
+
+NLM_EXTERN CharPtr FormatFeatureQuals (
+  SeqFeatPtr sfp
+);
+
 
 #ifdef __cplusplus
 }
diff --git a/api/edutil.c b/api/edutil.c
index b6ea951e..6949eef2 100644
--- a/api/edutil.c
+++ b/api/edutil.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 2/4/94
 *
-* $Revision: 6.20 $
+* $Revision: 6.21 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -39,6 +39,9 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: edutil.c,v $
+* Revision 6.21  2003/11/03 19:37:42  bollin
+* SegLocToPartsEx now handles SEQLOC_PNT as well as SEQLOC_INT
+*
 * Revision 6.20  2003/06/03 20:25:34  kans
 * SeqLocReplaceID works on bonds if both ends bonded to the same Seq-id
 *
@@ -441,24 +444,36 @@ NLM_EXTERN SeqLocPtr LIBCALL SegLocToPartsEx (BioseqPtr seg, SeqLocPtr slp, Bool
 					&split);
 				while (tmp2 != NULL)
 				{
-					next = tmp2->next;
-					tmp2->next = NULL;
-					if (tmp2->choice == SEQLOC_INT)
-					{
-						if (nullsBetween  && notFirst) {
-							tmp3 = ValNodeNew (NULL);
-							if (tmp3 != NULL) {
-								tmp3->choice = SEQLOC_NULL;
-								SeqLocAdd (&newloc, tmp3, TRUE, FALSE);
-							}
-						}
-						notFirst = TRUE;
-						sintp = (SeqIntPtr)(tmp2->data.ptrvalue);
-						sintp->from += tstart;
-						sintp->to += tstart;
-						SeqLocAdd(&newloc, tmp2, TRUE, FALSE);
-					}
-					tmp2 = next;
+				  next = tmp2->next;
+				  tmp2->next = NULL;
+				  if (tmp2->choice == SEQLOC_INT)
+				  {
+				    if (nullsBetween  && notFirst) {
+				      tmp3 = ValNodeNew (NULL);
+				      if (tmp3 != NULL) {
+				        tmp3->choice = SEQLOC_NULL;
+				        SeqLocAdd (&newloc, tmp3, TRUE, FALSE);
+				      }
+				    }
+				    notFirst = TRUE;
+				    sintp = (SeqIntPtr)(tmp2->data.ptrvalue);
+				    sintp->from += tstart;
+				    sintp->to += tstart;
+				    SeqLocAdd(&newloc, tmp2, TRUE, FALSE);
+				  }
+                                  else if (tmp2->choice == SEQLOC_PNT)
+                                  {
+				    if (nullsBetween  && notFirst) {
+				      tmp3 = ValNodeNew (NULL);
+				      if (tmp3 != NULL) {
+				        tmp3->choice = SEQLOC_NULL;
+				        SeqLocAdd (&newloc, tmp3, TRUE, FALSE);
+				      }
+				    }
+				    notFirst = TRUE;
+                                    SeqLocAdd (&newloc, tmp2, TRUE, FALSE);
+                                  }
+				  tmp2 = next;
 				}
 				left_end = right_end + 1;
 			}
diff --git a/api/findrepl.c b/api/findrepl.c
index 37e91158..862d87cc 100644
--- a/api/findrepl.c
+++ b/api/findrepl.c
@@ -44,6 +44,9 @@
 * RCS Modification History:
 * -------------------------
 * $Log: findrepl.c,v $
+* Revision 6.11  2003/11/21 17:58:46  bollin
+* remove tax ref and common name when changing taxonomy name via ASN Find/Replace
+*
 * Revision 6.10  2003/07/31 20:54:54  kans
 * FindReplaceString does not need do_replace argument
 *
@@ -906,6 +909,30 @@ static void FindReplPubdesc (
   }
 }
 
+static void RemoveTaxRef (OrgRefPtr orp)
+{
+  ValNodePtr      vnp, next;
+  ValNodePtr PNTR prev;
+  DbtagPtr        dbt;
+
+  vnp = orp->db;
+  if (vnp == NULL) return;
+  prev = (ValNodePtr PNTR) &(orp->db);
+  while (vnp != NULL) {
+    next = vnp->next;
+    dbt = (DbtagPtr) vnp->data.ptrvalue;
+    if (dbt != NULL && StringICmp ((CharPtr) dbt->db, "taxon") == 0) {
+      *prev = vnp->next;
+      vnp->next = NULL;
+      DbtagFree (dbt);
+      ValNodeFree (vnp);
+    } else {
+      prev = (ValNodePtr PNTR) &(vnp->next);
+    }
+    vnp = next;
+  }
+}
+
 static void FindReplBioSource (
   BioSourcePtr biop,
   OrgRefPtr orp,
@@ -916,6 +943,7 @@ static void FindReplBioSource (
   OrgModPtr      omp;
   OrgNamePtr     onp;
   SubSourcePtr   ssp;
+  CharPtr        old_taxname;
 
   if (biop != NULL) {
     orp = biop->org;
@@ -930,7 +958,14 @@ static void FindReplBioSource (
     }
   }
   if (orp != NULL) {
+    old_taxname = StringSave (orp->taxname);
     FindReplString (&(orp->taxname), fsp);
+    if (StringCmp (old_taxname, orp->taxname) != 0)
+    {
+      RemoveTaxRef (orp);
+      orp->common = MemFree (orp->common);
+    }
+    MemFree (old_taxname);
     FindReplString (&(orp->common), fsp);
     FindReplStringList (orp->mod, fsp);
     FindReplStringList (orp->syn, fsp);
diff --git a/api/gbparint.c b/api/gbparint.c
index 0f0bf761..fe07f1ee 100644
--- a/api/gbparint.c
+++ b/api/gbparint.c
@@ -28,6 +28,10 @@
 * Author:  Karl Sirotkin
 *
 * $Log: gbparint.c,v $
+* Revision 6.6  2003/12/05 16:42:11  bazhin
+* Nlm_gbparselex() and Nlm_gbparselex_ver() functions now can handle
+* RefSeq and WGS accessions.
+*
 * Revision 6.5  2001/06/07 17:00:54  tatiana
 * added gi option in Nlm_gbparselex()
 *
@@ -1830,6 +1834,35 @@ NLM_EXTERN SeqLocPtr Nlm_gbreplace_ver(Boolean PNTR keep_rawPt, int PNTR parenPt
 	return retval;
 }
 
+/**********************************************************/
+static int Nlm_gbparse_accprefix(CharPtr acc)
+{
+    CharPtr p;
+    int     ret;
+
+    if(acc == NULL || *acc == '\0')
+        return(0);
+
+    for(p = acc; IS_ALPHA(*p) != 0;)
+        p++;
+    ret = p - acc;
+    if(*p == '_')
+    {
+        if(ret == 2)
+        {
+            for(p++; IS_ALPHA(*p) != 0;)
+                p++;
+            ret = p - acc;
+            if(ret != 3 && ret != 7)
+                ret = 1;
+        }
+        else
+            ret = 1;
+    }
+    else if(ret != 1 && ret != 2 && ret != 4)
+        ret = 1;
+    return(ret);
+}
 
 
 char Saved_ch;
@@ -1919,7 +1952,7 @@ Nlm_gbparselex(CharPtr linein, ValNodePtr PNTR lexed)
 			case '5': case '6': case '7': case '8': case '9':
 				skip_new_token = FALSE;
 				current_token -> choice = GBPARSE_INT_NUMBER;
-				for (dex=0, spare = current_col; isdigit(*spare); spare ++){
+				for (dex=0, spare = current_col; isdigit((int) *spare); spare ++){
 					dex ++ ;
 				}
 				current_token -> data.ptrvalue = MemNew(dex+1);
@@ -2176,19 +2209,14 @@ Nlm_gbparselex(CharPtr linein, ValNodePtr PNTR lexed)
 /* new accessions have .version !!  2/15/1999 */
 				skip_new_token = FALSE;
 				current_token -> choice = GBPARSE_INT_ACCESION;
-				if (IS_ALPHA(*(current_col + 1))) {
-					spare = current_col + 2;
-					dex = 2;
-				} else {
-					spare = current_col + 1;
-					dex = 1;
-				}
-				for (; isdigit(*spare); spare ++){
+				dex = Nlm_gbparse_accprefix(current_col);
+				spare = current_col + dex;
+				for (; isdigit((int) *spare); spare ++){
 					dex ++ ;
 				}
 				if (*spare == '.') {
 					dex ++ ;
-					for (spare++; isdigit(*spare); spare ++){
+					for (spare++; isdigit((int) *spare); spare ++){
 						dex ++ ;
 					}
 				}
@@ -2302,7 +2330,7 @@ Nlm_gbparselex_ver(CharPtr linein, ValNodePtr PNTR lexed, Boolean accver)
 			case '5': case '6': case '7': case '8': case '9':
 				skip_new_token = FALSE;
 				current_token -> choice = GBPARSE_INT_NUMBER;
-				for (dex=0, spare = current_col; isdigit(*spare); spare ++){
+				for (dex=0, spare = current_col; isdigit((int) *spare); spare ++){
 					dex ++ ;
 				}
 				current_token -> data.ptrvalue = MemNew(dex+1);
@@ -2559,19 +2587,14 @@ Nlm_gbparselex_ver(CharPtr linein, ValNodePtr PNTR lexed, Boolean accver)
 /* new accessions have .version !!  2/15/1999 */
 				skip_new_token = FALSE;
 				current_token -> choice = GBPARSE_INT_ACCESION;
-				if (IS_ALPHA(*(current_col + 1))) {
-					spare = current_col + 2;
-					dex = 2;
-				} else {
-					spare = current_col + 1;
-					dex = 1;
-				}
-				for (; isdigit(*spare); spare ++){
+				dex = Nlm_gbparse_accprefix(current_col);
+				spare = current_col + dex;
+				for (; isdigit((int) *spare); spare ++){
 					dex ++ ;
 				}
 				if (accver != FALSE && *spare == '.') {
 					dex ++ ;
-					for (spare++; isdigit(*spare); spare ++){
+					for (spare++; isdigit((int) *spare); spare ++){
 						dex ++ ;
 					}
 				}
@@ -2616,7 +2639,7 @@ Nlm_gbparselex_ver(CharPtr linein, ValNodePtr PNTR lexed, Boolean accver)
 NLM_EXTERN CharPtr
 Nlm_non_white(CharPtr ch)
 {
-   while (isspace(*++ch))if (! *ch) break;
+   while (isspace((int) *++ch))if (! *ch) break;
       ;
    return ch;
 }
diff --git a/api/lsqfetch.c b/api/lsqfetch.c
index 68378ca3..d56f3026 100644
--- a/api/lsqfetch.c
+++ b/api/lsqfetch.c
@@ -37,6 +37,15 @@
 * Date     Name        Description of modification
 *
 * $Log: lsqfetch.c,v $
+* Revision 6.19  2003/11/13 17:18:02  kans
+* added SearchAltIndex, finished Alt fetch for chimp revision
+*
+* Revision 6.18  2003/11/12 23:49:11  kans
+* SortIfpByID needed LIBCALLBACK for PC
+*
+* Revision 6.17  2003/11/12 23:38:48  kans
+* changing AltIndexedFastaLibFetchEnable prototype, implementation not yet finished
+*
 * Revision 6.16  2003/08/27 21:24:05  kans
 * enable alt indexed fasta looks up previously registered function, changes settings for new path
 *
@@ -87,6 +96,15 @@
 * Revision changed to 6.0
 *
 * $Log: lsqfetch.c,v $
+* Revision 6.19  2003/11/13 17:18:02  kans
+* added SearchAltIndex, finished Alt fetch for chimp revision
+*
+* Revision 6.18  2003/11/12 23:49:11  kans
+* SortIfpByID needed LIBCALLBACK for PC
+*
+* Revision 6.17  2003/11/12 23:38:48  kans
+* changing AltIndexedFastaLibFetchEnable prototype, implementation not yet finished
+*
 * Revision 6.16  2003/08/27 21:24:05  kans
 * enable alt indexed fasta looks up previously registered function, changes settings for new path
 *
@@ -1374,6 +1392,18 @@ NLM_EXTERN void IndexedFastaLibFetchDisable (void)
 
 static CharPtr altfastalibfetchproc = "AltIndexedFastaLibBioseqFetch";
 
+typedef struct idfip {
+  CharPtr        seqid;
+  FastaIndexPtr  fip;
+} IdFip, PNTR IdFipPtr;
+
+typedef struct alibftch {
+  CharPtr     path;
+  ValNodePtr  fiplist;
+  IdFipPtr    index;
+  Int4        numids;
+} AltLibFetchData, PNTR AltLibFetchPtr;
+
 static void ChangeLocalToGenbank (BioseqPtr bsp, Pointer userdata)
 
 {
@@ -1390,38 +1420,79 @@ static void ChangeLocalToGenbank (BioseqPtr bsp, Pointer userdata)
   SeqMgrReplaceInBioseqIndex (bsp);
 }
 
+static FastaIndexPtr SearchAltIndex (
+  AltLibFetchPtr alfp,
+  CharPtr seqid
+)
+
+{
+  int       compare;
+  IdFipPtr  ifp;
+  Int4      L, R, mid;
+
+  if (alfp == NULL || alfp->index == NULL) return NULL;
+  ifp = alfp->index;
+  if (StringHasNoText (seqid)) return NULL;
+
+  L = 0;
+  R = alfp->numids - 1;
+  while (L < R) {
+    mid = (L + R) / 2;
+    compare = StringICmp (ifp [mid].seqid, seqid);
+    if (compare < 0) {
+      L = mid + 1;
+    } else {
+      R = mid;
+    }
+  }
+
+  if (StringICmp (ifp [R].seqid, seqid) == 0) {
+    return ifp [R].fip;
+  }
+
+  return NULL;
+}
+
 static Int2 LIBCALLBACK AltIndexedFastaLibBioseqFetchFunc (Pointer data)
 
 {
+  AltLibFetchPtr    alfp;
   BioseqPtr         bsp;
   Pointer           dataptr = NULL;
   Uint2             datatype, entityID = 0;
   Char              file [FILENAME_MAX], path [PATH_MAX], id [41];
-  FastaLibFetchPtr  flfp;
+  FastaIndexPtr     fip;
   FILE              *fp;
   Int4              offset;
   OMProcControlPtr  ompcp;
   ObjMgrProcPtr     ompp;
   SeqEntryPtr       sep = NULL;
   SeqIdPtr          sip;
+  CharPtr           tmp;
 
   ompcp = (OMProcControlPtr) data;
   if (ompcp == NULL) return OM_MSG_RET_ERROR;
   ompp = ompcp->proc;
   if (ompp == NULL) return OM_MSG_RET_ERROR;
-  flfp = (FastaLibFetchPtr) ompp->procdata;
-  if (flfp == NULL) return OM_MSG_RET_ERROR;
+  alfp = (AltLibFetchPtr) ompp->procdata;
+  if (alfp == NULL) return OM_MSG_RET_ERROR;
   sip = (SeqIdPtr) ompcp->input_data;
   if (sip == NULL) return OM_MSG_RET_ERROR;
 
   if (sip->choice == SEQID_GENBANK) {
 
     SeqIdWrite (sip, id, PRINTID_REPORT, sizeof (id));
-    if (flfp->currentfip != NULL) {
-      offset = SearchFastaIndex (flfp->currentfip, id);
+    fip = SearchAltIndex (alfp, id);
+    if (fip != NULL) {
+      offset = SearchFastaIndex (fip, id);
       if (offset < 0) return OM_MSG_RET_ERROR;
-      sprintf (file, "%s.fsa", flfp->fastaname);
-      StringNCpy_0 (path, flfp->path, sizeof (path));
+      StringCpy (file, fip->file);
+      tmp = StringStr (file, ".idx");
+      if (tmp != NULL) {
+        *tmp = '\0';
+      }
+      StringCat (file, ".fa");
+      StringNCpy_0 (path, fip->path, sizeof (path));
       FileBuildPath (path, NULL, file);
       fp = FileOpen (path, "r");
       if (fp == NULL) return OM_MSG_RET_ERROR;
@@ -1443,41 +1514,94 @@ static Int2 LIBCALLBACK AltIndexedFastaLibBioseqFetchFunc (Pointer data)
   return OM_MSG_RET_DONE;
 }
 
-NLM_EXTERN Boolean AltIndexedFastaLibFetchEnable (CharPtr path, CharPtr fastaname)
+static int LIBCALLBACK SortIfpByID (VoidPtr vp1, VoidPtr vp2)
 
 {
-  Char              file [FILENAME_MAX];
-  FastaLibFetchPtr  flfp = NULL;
-  Boolean           is_new = FALSE;
-  ObjMgrPtr         omp;
-  ObjMgrProcPtr     ompp;
-  Char              str [PATH_MAX];
+  IdFipPtr ifp1, ifp2;
+
+  if (vp1 == NULL || vp2 == NULL) return 0;
+  ifp1 = (IdFipPtr) vp1;
+  ifp2 = (IdFipPtr) vp2;
+  if (ifp1 == NULL || ifp2 == NULL) return 0;
+  return StringICmp (ifp1->seqid, ifp2->seqid);
+}
+
+NLM_EXTERN Boolean AltIndexedFastaLibFetchEnable (CharPtr path)
+
+{
+  AltLibFetchPtr  alfp = NULL;
+  Char            file [FILENAME_MAX];
+  FastaIndexPtr   fip;
+  ValNodePtr      head;
+  Int4            i;
+  IdFipPtr        ifp;
+  Boolean         is_new = FALSE;
+  Int4            j;
+  Int4            numids = 0;
+  ObjMgrPtr       omp;
+  ObjMgrProcPtr   ompp;
+  Char            str [PATH_MAX];
+  CharPtr         tmp;
+  ValNodePtr      vnp;
 
   StringNCpy_0 (str, path, sizeof (str));
   TrimSpacesAroundString (str);
   omp = ObjMgrGet ();
   ompp = ObjMgrProcFind (omp, 0, altfastalibfetchproc, OMPROC_FETCH);
   if (ompp != NULL) {
-    flfp = (FastaLibFetchPtr) ompp->procdata;
-    if (flfp != NULL) {
-      flfp->path = MemFree (flfp->path);
-      flfp->fastaname = MemFree (flfp->fastaname);
-      flfp->currentfip = FreeFastaIndex (flfp->currentfip);
+    alfp = (AltLibFetchPtr) ompp->procdata;
+    if (alfp != NULL) {
+      alfp->path = MemFree (alfp->path);
+      for (vnp = alfp->fiplist; vnp != NULL; vnp = vnp->next) {
+        fip = (FastaIndexPtr) vnp->data.ptrvalue;
+        FreeFastaIndex (fip);
+      }
+      alfp->fiplist = ValNodeFree (alfp->fiplist);
+      alfp->index = MemFree (alfp->index);
     }
   } else {
-    flfp = (FastaLibFetchPtr) MemNew (sizeof (FastaLibFetchData));
+    alfp = (AltLibFetchPtr) MemNew (sizeof (AltLibFetchData));
     is_new = TRUE;
   }
-  if (flfp != NULL) {
-    flfp->path = StringSave (str);
-    flfp->fastaname = StringSave (fastaname);
-    sprintf (file, "%s.idx", fastaname);
-    FileBuildPath (str, NULL, file);
-    flfp->currentfip = ReadFastaIndex (str);
+  if (alfp != NULL) {
+    alfp->path = StringSave (str);
+    head = DirCatalog (str);
+    for (vnp = head; vnp != NULL; vnp = vnp->next) {
+      if (vnp->choice == 0) {
+        tmp = (CharPtr) vnp->data.ptrvalue;
+        if (StringStr (tmp, ".idx") != NULL) {
+          StringCpy (str, alfp->path);
+          sprintf (file, "%s", tmp);
+          FileBuildPath (str, NULL, file);
+          fip = ReadFastaIndex (str);
+          if (fip != NULL) {
+            ValNodeAddPointer (&(alfp->fiplist), 0, (Pointer) fip);
+            numids += fip->numlines;
+          }
+        }
+      }
+    }
+    ValNodeFreeData (head);
+    ifp = (IdFipPtr) MemNew (sizeof (IdFip) * (numids + 2));
+    alfp->index = ifp;
+    alfp->numids = numids;
+    if (ifp != NULL) {
+      i = 0;
+      for (vnp = alfp->fiplist; vnp != NULL; vnp = vnp->next) {
+        fip = (FastaIndexPtr) vnp->data.ptrvalue;
+        if (fip != NULL) {
+          for (j = 0; j < fip->numlines; j++, i++) {
+            ifp [i].seqid = fip->seqids [j];
+            ifp [i].fip = fip;
+          }
+        }
+      }
+      HeapSort (ifp, (size_t) numids, sizeof (IdFip), SortIfpByID);
+    }
   }
   if (is_new) {
     ObjMgrProcLoad (OMPROC_FETCH, altfastalibfetchproc, altfastalibfetchproc,
-                    OBJ_SEQID, 0, OBJ_BIOSEQ, 0, (Pointer) flfp,
+                    OBJ_SEQID, 0, OBJ_BIOSEQ, 0, (Pointer) alfp,
                     AltIndexedFastaLibBioseqFetchFunc, PROC_PRIORITY_DEFAULT);
   }
   return TRUE;
@@ -1486,20 +1610,26 @@ NLM_EXTERN Boolean AltIndexedFastaLibFetchEnable (CharPtr path, CharPtr fastanam
 NLM_EXTERN void AltIndexedFastaLibFetchDisable (void)
 
 {
-  FastaLibFetchPtr  flfp;
-  ObjMgrPtr         omp;
-  ObjMgrProcPtr     ompp;
+  AltLibFetchPtr  alfp;
+  FastaIndexPtr   fip;
+  ObjMgrPtr       omp;
+  ObjMgrProcPtr   ompp;
+  ValNodePtr      vnp;
 
   omp = ObjMgrGet ();
   ompp = ObjMgrProcFind (omp, 0, altfastalibfetchproc, OMPROC_FETCH);
   if (ompp == NULL) return;
   ObjMgrFreeUserData (0, ompp->procid, OMPROC_FETCH, 0);
-  flfp = (FastaLibFetchPtr) ompp->procdata;
-  if (flfp == NULL) return;
-  MemFree (flfp->path);
-  MemFree (flfp->fastaname);
-  FreeFastaIndex (flfp->currentfip);
-  MemFree (flfp);
+  alfp = (AltLibFetchPtr) ompp->procdata;
+  if (alfp == NULL) return;
+  alfp->path = MemFree (alfp->path);
+  for (vnp = alfp->fiplist; vnp != NULL; vnp = vnp->next) {
+    fip = (FastaIndexPtr) vnp->data.ptrvalue;
+    FreeFastaIndex (fip);
+  }
+  alfp->fiplist = ValNodeFree (alfp->fiplist);
+  alfp->index = MemFree (alfp->index);
+  MemFree (alfp);
 }
 
 /* common function for creating indexes of fasta library files */
diff --git a/api/lsqfetch.h b/api/lsqfetch.h
index 52a59363..55ad3377 100644
--- a/api/lsqfetch.h
+++ b/api/lsqfetch.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 5/25/95
 *
-* $Revision: 6.3 $
+* $Revision: 6.4 $
 *
 * File Description:  Utilities for fetching local sequences
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: lsqfetch.h,v $
+* Revision 6.4  2003/11/12 23:38:49  kans
+* changing AltIndexedFastaLibFetchEnable prototype, implementation not yet finished
+*
 * Revision 6.3  2003/08/27 19:27:43  kans
 * added AltIndexedFastaLibFetch functions for chimpanzee genome project
 *
@@ -254,9 +257,9 @@ NLM_EXTERN Boolean CheckDnaResidue PROTO((CharPtr seq_ptr, Int4 ck_len, Int4Ptr
 NLM_EXTERN Boolean IndexedFastaLibFetchEnable (CharPtr path);
 NLM_EXTERN void IndexedFastaLibFetchDisable (void);
 
-/* alternative indexed FASTA lib functions - currently uses chimpanzee genome contig naming convention */
+/* alternative indexed FASTA lib functions - currently uses new chimpanzee genome contig naming convention */
 
-NLM_EXTERN Boolean AltIndexedFastaLibFetchEnable (CharPtr path, CharPtr fastaname);
+NLM_EXTERN Boolean AltIndexedFastaLibFetchEnable (CharPtr path);
 NLM_EXTERN void AltIndexedFastaLibFetchDisable (void);
 
 /* common function for creating indexes of fasta library files */
diff --git a/api/objmgr.c b/api/objmgr.c
index 0bcdbf29..a9ad80df 100644
--- a/api/objmgr.c
+++ b/api/objmgr.c
@@ -29,13 +29,16 @@
 *   
 * Version Creation Date: 9/94
 *
-* $Revision: 6.49 $
+* $Revision: 6.50 $
 *
 * File Description:  Manager for Bioseqs and BioseqSets
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: objmgr.c,v $
+* Revision 6.50  2003/12/22 15:29:28  kans
+* ObjMgrSendMsg calls SeqMgrClearFeatureIndexes on OM_MSG_DEL as well as OM_MSG_UPDATE
+*
 * Revision 6.49  2002/07/30 14:41:45  kans
 * removed omdp->rearranged
 *
@@ -4416,7 +4419,8 @@ NLM_EXTERN Boolean LIBCALL ObjMgrSendMsg(Uint2 msg, Uint2 entityID, Uint2 itemID
 
 	if (msg == OM_MSG_UPDATE) {
 		SeqMgrClearFeatureIndexes (entityID, NULL);
-	}
+	} else if (msg == OM_MSG_DEL)
+		SeqMgrClearFeatureIndexes (entityID, NULL);
 	omp = ObjMgrReadLock();
 	omdp = ObjMgrFindByEntityID(omp, entityID, NULL);
 	if (omdp != NULL)
diff --git a/api/salpedit.c b/api/salpedit.c
index ae017372..5fd26dfd 100644
--- a/api/salpedit.c
+++ b/api/salpedit.c
@@ -1,3 +1,4 @@
+/* $Id: salpedit.c,v 6.31 2003/11/07 21:22:06 kans Exp $ */
 #include <ncbi.h>
 #include <ncbimisc.h> /* ValNodeLen */
 #include <sequtil.h> /* for GetScoreAndEvalue, SeqIdDupList */
@@ -2199,7 +2200,7 @@ static void sort_list_order(ValNodePtr PNTR ph_list, Uint1 strand)
             }
 
         }
-        /* 
+#if 0
         {
             FILE *tmp_fp;
             tmp_fp = FileOpen("Ins.test", "w");
@@ -2222,7 +2223,7 @@ static void sort_list_order(ValNodePtr PNTR ph_list, Uint1 strand)
                     Message(MSG_ERROR, "Fail in get_lns");
                     exit(1);
                 }
-                // inconsistent orientation from LNS //
+                /* inconsistent orientation from LNS */
             if((strand == Seq_strand_minus && val == 0) || 
                (strand != Seq_strand_minus && val== 1)) 
                 {
@@ -2245,7 +2246,7 @@ static void sort_list_order(ValNodePtr PNTR ph_list, Uint1 strand)
                 }
             FileClose(tmp_fp);
         }
-*/
+#endif
 	delete_bad_node(&h_list, 1);
 
 	if(h_list == NULL)
diff --git a/api/seqmgr.c b/api/seqmgr.c
index 9994a256..d90546fc 100644
--- a/api/seqmgr.c
+++ b/api/seqmgr.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 9/94
 *
-* $Revision: 6.210 $
+* $Revision: 6.212 $
 *
 * File Description:  Manager for Bioseqs and BioseqSets
 *
@@ -39,6 +39,12 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: seqmgr.c,v $
+* Revision 6.212  2003/12/12 20:59:48  kans
+* added StrandsMatch to consolate code after TestForOverlap, allow both on candidate to be treated as plus
+*
+* Revision 6.211  2003/11/13 21:59:24  kans
+* GetSeqIdForGI separates SEQID_OTHER from other types, so RefSeq takes higher priority over General
+*
 * Revision 6.210  2003/10/24 19:49:11  kans
 * operon feature of equal range sorted before gene, mRNA, CDS
 *
@@ -2095,7 +2101,7 @@ NLM_EXTERN SeqIdPtr LIBCALL GetSeqIdForGI (Int4 gi)
 	ObjMgrProcPtr ompp;
 	OMProcControl ompc;
 	Int2 ret;
-	SeqIdPtr sip, sip2=NULL, other=NULL, gb=NULL;
+	SeqIdPtr sip, sip2=NULL, otherh=NULL, otherl = NULL, gb=NULL;
 	ValNode vn;
 
 
@@ -2118,7 +2124,7 @@ NLM_EXTERN SeqIdPtr LIBCALL GetSeqIdForGI (Int4 gi)
 		        case SEQID_GIBBMT:
       		  case SEQID_PATENT:
 		        case SEQID_GENERAL:
-						other = sip;
+						otherl = sip;
 						break;
 					case SEQID_GI:
 					   break;
@@ -2135,8 +2141,8 @@ NLM_EXTERN SeqIdPtr LIBCALL GetSeqIdForGI (Int4 gi)
 						gb = sip;
 						break;
 					default:
-						if (other == NULL)
-							other = sip;
+						if (otherh == NULL)
+							otherh = sip;
 						break;
 		    }
 		}
@@ -2145,8 +2151,10 @@ NLM_EXTERN SeqIdPtr LIBCALL GetSeqIdForGI (Int4 gi)
 
 	if (gb != NULL)
 		sip2 = gb;
-	else if (other != NULL)
-		sip2 = other;
+	else if (otherh != NULL)
+		sip2 = otherh;
+	else if (otherl != NULL)
+		sip2 = otherl;
 
 	if (sip2 != NULL)
 		return SeqIdDup(sip2);
@@ -7670,6 +7678,17 @@ static Boolean CheckInternalExonBoundaries (Int2 numivalsA, Int4Ptr ivalsA, Int2
   return TRUE;
 }
 
+static Boolean StrandsMatch (Uint1 featstrand, Uint1 locstrand)
+
+{
+  if (featstrand == locstrand) return TRUE;
+  if (locstrand == Seq_strand_unknown && featstrand != Seq_strand_minus) return TRUE;
+  if (featstrand == Seq_strand_unknown && locstrand != Seq_strand_minus) return TRUE;
+  if (featstrand == Seq_strand_both && locstrand != Seq_strand_minus) return TRUE;
+  if (locstrand == Seq_strand_both) return TRUE;
+  return FALSE;
+}
+
 static Int4 TestForOverlap (SMFeatItemPtr feat, SeqLocPtr slp,
                             Int4 left, Int4 right, Int2 overlapType,
                             Int2 numivals, Int4Ptr ivals)
@@ -7972,10 +7991,7 @@ static SeqFeatPtr SeqMgrGetBestOverlappingFeat (SeqLocPtr slp, Uint2 subtype,
     diff = TestForOverlap (feat, slp, left, right, overlapType, numivals, ivals);
     if (diff >= 0) {
 
-      if (feat->strand == strand ||
-          (strand == Seq_strand_unknown && feat->strand != Seq_strand_minus) ||
-          (feat->strand == Seq_strand_unknown && strand != Seq_strand_minus) ||
-          strand == Seq_strand_both) {
+      if (StrandsMatch (feat->strand, strand)) {
 
         if (userfunc != NULL && context != NULL && goOn) {
           SeqMgrBestOverlapSetContext (feat, omdp, userdata, context);
@@ -8009,9 +8025,7 @@ static SeqFeatPtr SeqMgrGetBestOverlappingFeat (SeqLocPtr slp, Uint2 subtype,
       diff = TestForOverlap (feat, slp, left, right, overlapType, numivals, ivals);
       if (diff >= 0) {
 
-        if (feat->strand == strand ||
-            (strand == Seq_strand_unknown && feat->strand != Seq_strand_minus) ||
-            (feat->strand == Seq_strand_unknown && strand != Seq_strand_minus)) {
+        if (StrandsMatch (feat->strand, strand)) {
 
           if (userfunc != NULL && context != NULL && goOn) {
             SeqMgrBestOverlapSetContext (feat, omdp, userdata, context);
@@ -8069,10 +8083,7 @@ NLM_EXTERN Int4 TestFeatOverlap (SeqFeatPtr sfpA, SeqFeatPtr sfpB, Int2 overlapT
                          overlapType, sfipA->numivals, sfipA->ivals);
   if (diff < 0) return -1;
 
-  if (sfipB->strand == sfipA->strand ||
-      (sfipA->strand == Seq_strand_unknown && sfipB->strand != Seq_strand_minus) ||
-      (sfipB->strand == Seq_strand_unknown && sfipA->strand != Seq_strand_minus) ||
-      sfipA->strand == Seq_strand_both) {
+  if (StrandsMatch (sfipB->strand, sfipA->strand)) {
     return diff;
   }
 
diff --git a/api/seqport.c b/api/seqport.c
index a42d70d3..50190746 100644
--- a/api/seqport.c
+++ b/api/seqport.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/13/91
 *
-* $Revision: 6.82 $
+* $Revision: 6.86 $
 *
 * File Description:  Ports onto Bioseqs
 *
@@ -39,6 +39,18 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: seqport.c,v $
+* Revision 6.86  2003/11/18 17:08:46  kans
+* added MapNa4ByteTo4BitString, use in seqport read and get char
+*
+* Revision 6.85  2003/11/18 16:23:05  kans
+* fixed InitNa2to4Bit, use MapNa2ByteTo4BitString in SeqPortQuickGetResidue
+*
+* Revision 6.84  2003/11/17 22:44:31  kans
+* added MapNa2ByteTo4BitString in preparation for faster SeqPortRead from 2na to 4na
+*
+* Revision 6.83  2003/11/05 21:17:22  bollin
+* added new option for Retranslate Coding Regions to handle stop codons at end of complete CDS during retranslate while ignoring stop codons
+*
 * Revision 6.82  2003/08/18 21:07:35  kans
 * RevCompStr was stepping on str variable
 *
@@ -420,6 +432,8 @@ NLM_EXTERN Boolean LIBCALL SeqPortAdjustLength (SeqPortPtr spp);
 static Uint1Ptr Na2toIUPAC = NULL;
 static Uint1Ptr Na4toIUPAC = NULL;
 static Uint1Ptr Na2toNa4 = NULL;
+static Uint1Ptr Na2to4Bit = NULL;
+static Uint1Ptr Na4to4Bit = NULL;
 static TNlmMutex seqport_mutex = NULL;
 
 
@@ -661,6 +675,160 @@ NLM_EXTERN Uint2Ptr LIBCALL MapNa2ByteToNa4String (Uint1Ptr bytep, Uint2Ptr buf,
   return ptr;
 }
 
+static void InitNa2to4Bit (void)
+
+{
+  Int2  base [4], index, j;
+  Uint1  convert [4] = {1, 2, 4, 8};
+  Int4  ret;
+  Uint1Ptr Na2to4Bit_local = NULL;
+
+  ret = NlmMutexLockEx (&seqport_mutex);  /* protect this section */
+  if (ret) {
+    ErrPostEx (SEV_FATAL, 0, 0, "MapNa2ByteTo4BitString mutex failed [%ld]", (long) ret);
+    return;
+  }
+
+  if (Na2to4Bit == NULL) {
+    Na2to4Bit_local = MemNew (sizeof (Uint1) * 1024);
+
+    if (Na2to4Bit_local != NULL) {
+      for (base [0] = 0; base [0] < 4; (base [0])++) {
+        for (base [1] = 0; base [1] < 4; (base [1])++) {
+          for (base [2] = 0; base [2] < 4; (base [2])++) {
+            for (base [3] = 0; base [3] < 4; (base [3])++) {
+              index = 4 * (base [0] * 64 + base [1] * 16 + base [2] * 4 + base [3]);
+              for (j = 0; j < 4; j++) {
+                Na2to4Bit_local [index + j] = convert [(base [j])];
+              }
+            }
+          }
+        }
+      }
+    }
+    Na2to4Bit = Na2to4Bit_local;
+  }
+
+  NlmMutexUnlock (seqport_mutex);
+}
+
+NLM_EXTERN Uint4Ptr LIBCALL MapNa2ByteTo4BitString (Uint1Ptr bytep, Uint4Ptr buf, Int4 total)
+
+{
+  Uint4Ptr  bp;
+  Uint1     byte;
+  Int2      index;
+  Int4      k;
+  Uint4Ptr  ptr;
+
+  if (bytep == NULL || buf == NULL) return buf;
+  ptr = buf;
+
+  /* initialize array if not yet set (first time function is called) */
+
+  if (Na2to4Bit == NULL) {
+    InitNa2to4Bit ();
+  }
+
+  if (Na2to4Bit == NULL) return buf;
+
+  /* now return 4 byte string for each compressed byte */
+
+  for (k = 0; k < total; k++) {
+    byte = *bytep;
+    bytep++;
+    index = 4 * byte;
+    bp = (Uint4Ptr) (Na2to4Bit + index);
+    /* copy 4 bytes at a time */
+    /*
+    for (j = 0; j < 4; j++) {
+      *ptr = *bp;
+      ptr++;
+      bp++;
+    }
+    */
+    *ptr = *bp;
+    ptr++;
+  }
+
+  return ptr;
+}
+
+static void InitNa4to4Bit (void)
+
+{
+  Int2  base [2], index, j;
+  Char  convert [16] = {15, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15};
+  Int4  ret;
+  Uint1Ptr Na4to4Bit_local = NULL;
+
+  ret = NlmMutexLockEx (&seqport_mutex);  /* protect this section */
+  if (ret) {
+    ErrPostEx (SEV_FATAL, 0, 0, "MapNa4ByteToIUPACString mutex failed [%ld]", (long) ret);
+    return;
+  }
+
+  if (Na4to4Bit == NULL) {
+    Na4to4Bit_local = MemNew (sizeof (Uint1) * 512);
+
+    if (Na4to4Bit_local != NULL) {
+      for (base [0] = 0; base [0] < 16; (base [0])++) {
+        for (base [1] = 0; base [1] < 16; (base [1])++) {
+          index = 2 * (base [0] * 16 + base [1]);
+          for (j = 0; j < 2; j++) {
+            Na4to4Bit_local [index + j] = convert [(base [j])];
+          }
+        }
+      }
+    }
+    Na4to4Bit = Na4to4Bit_local;
+  }
+
+  NlmMutexUnlock (seqport_mutex);
+}
+
+NLM_EXTERN Uint2Ptr LIBCALL MapNa4ByteTo4BitString (Uint1Ptr bytep, Uint2Ptr buf, Int4 total)
+
+{
+  Uint2Ptr  bp;
+  Uint1     byte;
+  Int2      index;
+  Int4      k;
+  Uint2Ptr  ptr;
+
+  if (bytep == NULL || buf == NULL) return buf;
+  ptr = buf;
+
+  /* initialize array if not yet set (first time function is called) */
+
+  if (Na4to4Bit == NULL) {
+    InitNa4to4Bit ();
+  }
+
+  if (Na4to4Bit == NULL) return buf;
+
+  /* now return 2 character string for each compressed byte */
+
+  for (k = 0; k < total; k++) {
+    byte = *bytep;
+    bytep++;
+    index = 2 * byte;
+    bp = (Uint2Ptr)  (Na4to4Bit + index);
+    /* copy 2 bytes at a time */
+    /*
+    for (j = 0; j < 2; j++) {
+      *ptr = *bp;
+      ptr++;
+      bp++;
+    }
+    */
+    *ptr = *bp;
+    ptr++;
+  }
+
+  return ptr;
+}
+
 /*****************************************************************************
 *
 *   SeqPort Routines
@@ -1210,11 +1378,10 @@ SeqLocFindNext((SeqLocPtr)(currchunk->data.ptrvalue), currseg);
 		SeqPortSetUpAlphabet(spp, curr_code, newcode);
 		spp->bp = bsp->seq_data;
 
-	 /* allocate fast lookup caches for 2na or 4na to iupacna conversion */
+	 /* allocate fast lookup caches for 2na or 4na to iupacna or 4na conversion */
 
-		if (newcode == Seq_code_iupacna &&
-		    (curr_code == Seq_code_ncbi2na ||
-		     curr_code == Seq_code_ncbi4na)) {
+		if ((newcode == Seq_code_iupacna || newcode == Seq_code_ncbi4na) &&
+		    (curr_code == Seq_code_ncbi2na || curr_code == Seq_code_ncbi4na)) {
 		    spp->cacheq = (SPCacheQPtr) MemNew (sizeof (SPCacheQ));
 		}
 
@@ -1656,10 +1823,18 @@ static Uint1 LIBCALL SeqPortQuickGetResidue (SeqPortPtr spp, SPCacheQPtr spcpq,
 
       ptr = spcpq->buf;
 
-      if (spp->oldcode == Seq_code_ncbi2na) {
-        ptr = (CharPtr) MapNa2ByteToIUPACString (bytes, (Uint4Ptr) ptr, total);
-      } else if (spp->oldcode == Seq_code_ncbi4na) {
-        ptr = (CharPtr) MapNa4ByteToIUPACString (bytes, (Uint2Ptr) ptr, total);
+      if (spp->newcode == Seq_code_iupacna) {
+        if (spp->oldcode == Seq_code_ncbi2na) {
+          ptr = (CharPtr) MapNa2ByteToIUPACString (bytes, (Uint4Ptr) ptr, total);
+        } else if (spp->oldcode == Seq_code_ncbi4na) {
+          ptr = (CharPtr) MapNa4ByteToIUPACString (bytes, (Uint2Ptr) ptr, total);
+        }
+      } else if (spp->newcode == Seq_code_ncbi4na) {
+        if (spp->oldcode == Seq_code_ncbi2na) {
+          ptr = (CharPtr) MapNa2ByteTo4BitString (bytes, (Uint4Ptr) ptr, total);
+        } else if (spp->oldcode == Seq_code_ncbi4na) {
+          ptr = (CharPtr) MapNa4ByteTo4BitString (bytes, (Uint2Ptr) ptr, total);
+        }
       }
 
       spcpq->total = ptr - spcpq->buf;
@@ -2441,7 +2616,70 @@ NLM_EXTERN ByteStorePtr ProteinFromCdRegionEx (SeqFeatPtr sfp, Boolean include_s
   tbl = (TransTablePtr) GetAppProperty (str);
   tableExists = (Boolean) (tbl != NULL);
 
-  bs = TransTableTranslateCdRegion (&tbl, sfp, include_stop, remove_trailingX);
+  bs = TransTableTranslateCdRegion (&tbl, sfp, include_stop, remove_trailingX,
+                                    FALSE);
+
+  /* save FSA in genetic code-specific app property name */
+
+  if (! tableExists) {
+    SetAppProperty (str, (Pointer) tbl);
+  }
+
+  return bs;
+}
+
+NLM_EXTERN ByteStorePtr ProteinFromCdRegionExWithTrailingCodonHandling
+(
+  SeqFeatPtr sfp,
+  Boolean include_stop,
+  Boolean remove_trailingX,
+  Boolean no_stop_at_end_of_complete_cds
+)
+
+{
+  ByteStorePtr   bs;
+  CdRegionPtr    crp;
+  Int2           genCode = 0;
+  Char           str [32];
+  Boolean        tableExists = FALSE;
+  TransTablePtr  tbl = NULL;
+  ValNodePtr     vnp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return NULL;
+  crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+  if (crp == NULL) return NULL;
+
+  /* find genetic code */
+
+  if (crp->genetic_code != NULL) {
+    vnp = (ValNodePtr) crp->genetic_code->data.ptrvalue;
+    while (vnp != NULL) {
+      if (vnp->choice == 2) {
+        genCode = (Int2) vnp->data.intvalue;
+      }
+      vnp = vnp->next;
+    }
+  }
+
+  if (genCode == 7) {
+    genCode = 4;
+  } else if (genCode == 8) {
+    genCode = 1;
+  } else if (genCode == 0) {
+    genCode = 1;
+  }
+
+  /* set app property name for storing desired FSA */
+
+  sprintf (str, "TransTableFSAforGenCode%d", (int) genCode);
+
+  /* get FSA for desired genetic code if it already exists */
+
+  tbl = (TransTablePtr) GetAppProperty (str);
+  tableExists = (Boolean) (tbl != NULL);
+
+  bs = TransTableTranslateCdRegion (&tbl, sfp, include_stop, remove_trailingX,
+                                    no_stop_at_end_of_complete_cds);
 
   /* save FSA in genetic code-specific app property name */
 
@@ -4944,7 +5182,8 @@ static ByteStorePtr TransTableTranslateCommon (
   Uint1 frame,
   CodeBreakPtr code_break,
   Boolean include_stop,
-  Boolean remove_trailingX
+  Boolean remove_trailingX,
+  Boolean no_stop_at_end_of_complete_cds
 )
 
 {
@@ -5084,7 +5323,10 @@ static ByteStorePtr TransTableTranslateCommon (
     }
     is_first = FALSE;
 
-    if ((! include_stop) && aa == '*') {
+    if (aa == '*'
+      && (! include_stop
+        || (no_stop_at_end_of_complete_cds && ! partial && *(txt + 1) == 0)))
+    {
       got_stop = TRUE;
       residue = '\0'; /* signal end of loop */
 
@@ -5152,14 +5394,16 @@ NLM_EXTERN ByteStorePtr TransTableTranslateSeqLoc (
 
 {
   return TransTableTranslateCommon (tblptr, location, NULL, FALSE, genCode,
-                                    frame, NULL, include_stop, remove_trailingX);
+                                    frame, NULL, include_stop,
+                                    remove_trailingX, FALSE);
 }
 
 NLM_EXTERN ByteStorePtr TransTableTranslateCdRegion (
   TransTablePtr  PNTR tblptr,
   SeqFeatPtr cds,
   Boolean include_stop,
-  Boolean remove_trailingX
+  Boolean remove_trailingX,
+  Boolean no_stop_at_end_of_complete_cds
 )
 
 {
@@ -5185,7 +5429,8 @@ NLM_EXTERN ByteStorePtr TransTableTranslateCdRegion (
 
   return TransTableTranslateCommon (tblptr, cds->location, cds->product, cds->partial,
                                     genCode, crp->frame, crp->code_break,
-                                    include_stop, remove_trailingX);
+                                    include_stop, remove_trailingX,
+                                    no_stop_at_end_of_complete_cds);
 }
 
 /* allow reuse of translation tables by saving as AppProperty */
diff --git a/api/seqport.h b/api/seqport.h
index 37709155..5be68a8f 100644
--- a/api/seqport.h
+++ b/api/seqport.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/13/91
 *
-* $Revision: 6.33 $
+* $Revision: 6.36 $
 *
 * File Description:  Ports onto Bioseqs
 *
@@ -40,6 +40,15 @@
 *
 *
 * $Log: seqport.h,v $
+* Revision 6.36  2003/11/18 17:08:46  kans
+* added MapNa4ByteTo4BitString, use in seqport read and get char
+*
+* Revision 6.35  2003/11/17 22:44:31  kans
+* added MapNa2ByteTo4BitString in preparation for faster SeqPortRead from 2na to 4na
+*
+* Revision 6.34  2003/11/05 21:17:22  bollin
+* added new option for Retranslate Coding Regions to handle stop codons at end of complete CDS during retranslate while ignoring stop codons
+*
 * Revision 6.33  2002/11/11 18:02:40  kans
 * added SeqPortStream to efficiently stream through a sequence
 *
@@ -344,6 +353,9 @@ Uint2 or Uint4 for fast integer copying.
 NLM_EXTERN Uint4Ptr LIBCALL MapNa2ByteToIUPACString PROTO((Uint1Ptr bytep, Uint4Ptr buf, Int4 total));
 NLM_EXTERN Uint2Ptr LIBCALL MapNa4ByteToIUPACString PROTO((Uint1Ptr bytep, Uint2Ptr buf, Int4 total));
 NLM_EXTERN Uint2Ptr LIBCALL MapNa2ByteToNa4String PROTO((Uint1Ptr bytep, Uint2Ptr buf, Int4 total));
+NLM_EXTERN Uint4Ptr LIBCALL MapNa2ByteTo4BitString PROTO((Uint1Ptr bytep, Uint4Ptr buf, Int4 total));
+NLM_EXTERN Uint2Ptr LIBCALL MapNa4ByteTo4BitString PROTO((Uint1Ptr bytep, Uint2Ptr buf, Int4 total));
+
 
 /*****************************************************************************
 *
@@ -420,6 +432,7 @@ NLM_EXTERN Uint4 BioseqHash PROTO((BioseqPtr bsp));
 *****************************************************************************/
 NLM_EXTERN ByteStorePtr ProteinFromCdRegion PROTO(( SeqFeatPtr sfp, Boolean include_stop));
 NLM_EXTERN ByteStorePtr ProteinFromCdRegionEx PROTO((SeqFeatPtr sfp, Boolean include_stop, Boolean remove_trailingX));
+NLM_EXTERN ByteStorePtr ProteinFromCdRegionExWithTrailingCodonHandling PROTO((SeqFeatPtr sfp, Boolean include_stop, Boolean remove_trailingX, Boolean no_stop_at_end_of_complete_cds));
 
 /*****************************************************************************
 *
@@ -662,7 +675,8 @@ NLM_EXTERN ByteStorePtr TransTableTranslateCdRegion (
   TransTablePtr  PNTR tblptr,
   SeqFeatPtr cds,
   Boolean include_stop,
-  Boolean remove_trailingX
+  Boolean remove_trailingX,
+  Boolean no_stop_at_end_of_complete_cds
 );
 
 NLM_EXTERN ByteStorePtr TransTableTranslateSeqLoc (
diff --git a/api/sequtil.c b/api/sequtil.c
index 6b014789..cac63358 100644
--- a/api/sequtil.c
+++ b/api/sequtil.c
@@ -29,13 +29,28 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.139 $
+* $Revision: 6.144 $
 *
 * File Description:  Sequence Utilities for objseq and objsset
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: sequtil.c,v $
+* Revision 6.144  2004/01/16 16:37:01  kans
+* added CM as scaffold/CON record
+*
+* Revision 6.143  2003/12/18 19:35:53  kans
+* added CQ and CR prefixes
+*
+* Revision 6.142  2003/12/16 16:03:04  kans
+* added CL as ncbi gss
+*
+* Revision 6.141  2003/11/10 16:12:33  kans
+* added CK as genbank est
+*
+* Revision 6.140  2003/10/31 20:51:24  kans
+* added CI and CJ as DDBJ ESTs to WHICH_db_accession
+*
 * Revision 6.139  2003/10/24 14:36:12  kans
 * added CH as GenBank CONN to WHICH_db_accession
 *
@@ -8765,7 +8780,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
 	      (StringICmp(temp,"CA") == 0) || 
 	      (StringICmp(temp,"CB") == 0) || 
 	      (StringICmp(temp,"CD") == 0) || 
-	      (StringICmp(temp,"CF") == 0) ) {                /* NCBI EST */
+	      (StringICmp(temp,"CF") == 0) || 
+	      (StringICmp(temp,"CK") == 0) ) {                /* NCBI EST */
               retcode = ACCN_NCBI_EST;
           } else if ((StringICmp(temp,"BV") == 0)) {      /* NCBI STS */
               retcode = ACCN_NCBI_STS;
@@ -8777,7 +8793,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
           } else if ((StringICmp(temp,"AE") == 0)) {      /* NCBI genome project data */
               retcode = ACCN_NCBI_GENOME;
           } else if ((StringICmp(temp,"AH") == 0) ||
-                     (StringICmp(temp,"CH") == 0)) {      /* NCBI segmented set header Bioseq */
+                     (StringICmp(temp,"CH") == 0) ||      /* NCBI segmented set header Bioseq */
+                     (StringICmp(temp,"CM") == 0)) {
               retcode = ACCN_NCBI_SEGSET | ACCN_AMBIGOUS_MOL; /* A few segmented
                                                                  proteins are AH */
           } else if ((StringICmp(temp,"AS") == 0)) {      /* NCBI "other" */
@@ -8790,7 +8807,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
                      (StringICmp(temp,"BZ") == 0) ||
                      (StringICmp(temp,"CC") == 0) ||
                      (StringICmp(temp,"CE") == 0) ||
-                     (StringICmp(temp,"CG") == 0) )  {     /* NCBI GSS */
+                     (StringICmp(temp,"CG") == 0) ||
+                     (StringICmp(temp,"CL") == 0) )  {     /* NCBI GSS */
               retcode = ACCN_NCBI_GSS;
           } else if ((StringICmp(temp,"AR") == 0)) {      /* NCBI patent */
               retcode = ACCN_NCBI_PATENT;
@@ -8809,11 +8827,13 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
                      (StringICmp(temp,"AM") == 0)) {     /* EMBL direct submission */
               retcode = ACCN_EMBL_DIRSUB;
           } else if ((StringICmp(temp,"AL") == 0) ||
-                     (StringICmp(temp,"BX") == 0)) {      /* EMBL genome project data */
+                     (StringICmp(temp,"BX") == 0)||
+                     (StringICmp(temp,"CR") == 0)) {      /* EMBL genome project data */
               retcode = ACCN_EMBL_GENOME;
           } else if ((StringICmp(temp,"AN") == 0)) {      /* EMBL CON division */
               retcode = ACCN_EMBL_CON;
-          } else if ((StringICmp(temp,"AX") == 0)) {      /* EMBL patent division */
+          } else if ((StringICmp(temp,"AX") == 0) ||
+                     (StringICmp(temp,"CQ") == 0)) {      /* EMBL patent division */
               retcode = ACCN_EMBL_PATENT;
           } else if ((StringICmp(temp,"AT") == 0) || 
                      (StringICmp(temp,"AU") == 0) ||
@@ -8822,7 +8842,9 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
                      (StringICmp(temp,"BJ") == 0) ||
                      (StringICmp(temp,"BP") == 0) ||
                      (StringICmp(temp,"BW") == 0) ||
-                     (StringICmp(temp,"BY") == 0)) {      /* DDBJ EST's */
+                     (StringICmp(temp,"BY") == 0) ||
+                     (StringICmp(temp,"CI") == 0) ||
+                     (StringICmp(temp,"CJ") == 0)) {      /* DDBJ EST's */
               retcode = ACCN_DDBJ_EST;
           } else if ((StringICmp(temp,"AB") == 0)) {      /* DDBJ direct submission */
               retcode = ACCN_DDBJ_DIRSUB;
diff --git a/api/sqnutil1.c b/api/sqnutil1.c
index 41e84d32..05f820ed 100644
--- a/api/sqnutil1.c
+++ b/api/sqnutil1.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.283 $
+* $Revision: 6.288 $
 *
 * File Description: 
 *
@@ -1671,6 +1671,7 @@ NLM_EXTERN void PromoteXrefsEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID, B
   CharPtr              ptr;
   CharPtr              rnaseq;
   SeqEntryPtr          sep;
+  SeqHistPtr           shp;
   SeqIdPtr             sip;
   SeqEntryPtr          target = NULL;
   Uint4                version = 0;
@@ -1964,6 +1965,14 @@ NLM_EXTERN void PromoteXrefsEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID, B
                       gbq->next = NULL;
                       StringNCpy_0 (id, gbq->val, sizeof (id));
                       GBQualFree (gbq);
+                    } else if (StringICmp (gbq->qual, "secondary_accession") == 0) {
+                      *(prevqual) = gbq->next;
+                      gbq->next = NULL;
+                      shp = ParseStringIntoSeqHist (NULL, gbq->val);
+                      if (shp != NULL) {
+                        pbsp->hist = shp;
+                      }
+                      GBQualFree (gbq);
                     } else {
                       prevqual = (GBQualPtr PNTR) &(gbq->next);
                     }
@@ -2285,6 +2294,41 @@ static void CleanDoubleQuote (CharPtr str)
   }
 }
 
+static CharPtr RemoveSpacesBetweenTildes (CharPtr str)
+
+{
+  Char     ch;
+  CharPtr  dst;
+ CharPtr  ptr;
+  CharPtr  tmp;
+
+  if (str == NULL || str [0] == '\0') return str;
+
+  dst = str;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    *dst = ch;
+    dst++;
+    ptr++;
+    if (ch == '~') {
+      tmp = ptr;
+      ch = *tmp;
+      while (ch != 0 && ch <= ' ') {
+        tmp++;
+        ch = *tmp;
+      }
+      if (ch == '~') {
+        ptr = tmp;
+      }
+    }
+    ch = *ptr;
+  }
+  *dst = '\0';
+
+  return str;
+}
+
 static Boolean AlreadyInVnpList (ValNodePtr head, ValNodePtr curr)
 
 {
@@ -2493,43 +2537,53 @@ extern Boolean ParseCodeBreak (SeqFeatPtr sfp, CharPtr val)
   /* parse location */
   pos = SimpleValuePos (val);
   cbp->loc = Nlm_gbparseint (pos, &locmap, &sitesmap, &num_errs, sip);
-  MemFree (pos);
   if (cbp->loc == NULL) {
     CodeBreakFree (cbp);
     ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing,
                "transl_except parsing failed, %s, drop the transl_except", pos);
+    MemFree (pos);
     return FALSE;
   }
-  sintp = cbp->loc->data.ptrvalue;
-  if (sintp == NULL) return FALSE;
-  if (sintp->from > sintp->to) {
-    temp = sintp->from;
-    sintp->from = sintp->to;
-    sintp->to = temp;
-  }
-  sintp->strand = SeqLocStrand (sfp->location);
-  strand = sintp->strand;
-  diff = SeqLocStop(cbp->loc) - SeqLocStart(cbp->loc); /* SeqLocStop/Start does not do what you think */
-  /*
-  if ((diff != 2 && (strand != Seq_strand_minus)) ||
-      (diff != -2 && (strand == Seq_strand_minus))) {
-    pos_range = TRUE;
-  }
-  */
-  if (diff != 2) {
-    pos_range = TRUE;
-  }
-  if (num_errs > 0 || pos_range) {
-    CodeBreakFree (cbp);
-    ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing,
-               "transl_except range is wrong, %s, drop the transl_except", pos);
-    return FALSE;
+  if (cbp->loc->choice == SEQLOC_PNT) {
+    /* allow a single point */
   }
-  if (SeqLocCompare (sfp->location, cbp->loc) != SLC_B_IN_A) {
-    CodeBreakFree (cbp);
-    ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing,
-               "/transl_except not in CDS: %s", val);
-    return FALSE;
+  if (cbp->loc->choice == SEQLOC_INT) {
+    sintp = cbp->loc->data.ptrvalue;
+    if (sintp == NULL) {
+      MemFree (pos);
+      return FALSE;
+    }
+    if (sintp->from > sintp->to) {
+      temp = sintp->from;
+      sintp->from = sintp->to;
+      sintp->to = temp;
+    }
+    sintp->strand = SeqLocStrand (sfp->location);
+    strand = sintp->strand;
+    diff = SeqLocStop(cbp->loc) - SeqLocStart(cbp->loc); /* SeqLocStop/Start does not do what you think */
+    /*
+    if ((diff != 2 && (strand != Seq_strand_minus)) ||
+        (diff != -2 && (strand == Seq_strand_minus))) {
+      pos_range = TRUE;
+    }
+    */
+    if (diff != 2) {
+      pos_range = TRUE;
+    }
+    if (num_errs > 0 || pos_range) {
+      CodeBreakFree (cbp);
+      ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing,
+                 "transl_except range is wrong, %s, drop the transl_except", pos);
+      MemFree (pos);
+      return FALSE;
+    }
+    if (SeqLocCompare (sfp->location, cbp->loc) != SLC_B_IN_A) {
+      CodeBreakFree (cbp);
+      ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing,
+                 "/transl_except not in CDS: %s", val);
+      MemFree (pos);
+      return FALSE;
+    }
   }
 
   /* add to code break list */
@@ -2542,6 +2596,7 @@ extern Boolean ParseCodeBreak (SeqFeatPtr sfp, CharPtr val)
     }
     lastcbp->next = cbp;
   }
+  MemFree (pos);
   return TRUE;
 }
 
@@ -5825,7 +5880,7 @@ static void CleanupFeatureStrings (SeqFeatPtr sfp, Boolean stripSerial, ValNodeP
           }
         }
       }
-      if (prp->processed == 2 && prp->name == NULL) {
+      if ((prp->processed == 1 || prp->processed == 2) && prp->name == NULL) {
         ValNodeCopyStr (&(prp->name), 0, "unnamed");
       }
       break;
@@ -6250,6 +6305,7 @@ static void CleanupDescriptorStrings (ValNodePtr sdp, Boolean stripSerial, ValNo
       break;
     case Seq_descr_comment :
       CleanVisStringJunk ((CharPtr PNTR) &sdp->data.ptrvalue);
+      RemoveSpacesBetweenTildes ((CharPtr) sdp->data.ptrvalue);
       break;
     case Seq_descr_num :
       break;
@@ -7588,7 +7644,8 @@ static Boolean CheckAsnloadPath (CharPtr dirname, CharPtr subdir)
 static Boolean CheckDataPath (CharPtr dirname, CharPtr subdir)
 
 {
-  return (Boolean) (FileExists (dirname, subdir, "seqcode.val"));
+  if (FileExists (dirname, subdir, "seqcode.val")) return TRUE;
+  return (Boolean) (FileExists (dirname, subdir, "objprt.prt"));
 }
 
 static Boolean CheckErrMsgPath (CharPtr dirname, CharPtr subdir)
@@ -7616,7 +7673,7 @@ NLM_EXTERN Boolean UseLocalAsnloadDataAndErrMsg (void)
   Char     appPath[PATH_MAX];
   CharPtr  ptr;
 
-  ProgramPath (appPath, sizeof (path));
+  ProgramPath (appPath, sizeof (appPath));
   StrCpy(path, appPath);
   /* data a sibling of our application? */
   ptr = StringRChr (path, DIRDELIMCHR);
diff --git a/api/sqnutil2.c b/api/sqnutil2.c
index a5817f57..42d07c72 100644
--- a/api/sqnutil2.c
+++ b/api/sqnutil2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.152 $
+* $Revision: 6.160 $
 *
 * File Description: 
 *
@@ -1308,6 +1308,7 @@ NLM_EXTERN CharPtr SqnTagFind (SqnTagPtr stp, CharPtr tag)
   if (stp == NULL || StringHasNoText (tag)) return NULL;
   for (i = 0; i < stp->num_tags; i++) {
     if (stp->tag [i] != NULL && StringICmp (stp->tag [i], tag) == 0) {
+      stp->used [i] = TRUE;
       return stp->val [i];
     }
   }
@@ -1734,6 +1735,52 @@ static void AddStringToSeqHist (
   tsip->accession = StringSave (str);
 }
 
+NLM_EXTERN SeqHistPtr ParseStringIntoSeqHist (
+  SeqHistPtr shp,
+  CharPtr str
+)
+
+{
+  Char     ch;
+  CharPtr  last;
+  CharPtr  ptr;
+  CharPtr  tmp;
+
+  if (shp == NULL) {
+    shp = SeqHistNew ();
+    if (shp == NULL) return shp;
+  }
+
+  if (str != NULL) {
+    tmp = StringSave (str);
+    last = tmp;
+    ptr = last;
+    ch = *ptr;
+    while (ch != '\0') {
+      if (ch == ',') {
+        *ptr = '\0';
+        if (! StringHasNoText (last)) {
+          TrimSpacesAroundString (last);
+          AddStringToSeqHist (shp, last);
+        }
+        ptr++;
+        last = ptr;
+        ch = *ptr;
+      } else {
+        ptr++;
+        ch = *ptr;
+      }
+    }
+    if (! StringHasNoText (last)) {
+      TrimSpacesAroundString (last);
+      AddStringToSeqHist (shp, last);
+    }
+    MemFree (tmp);
+  }
+
+  return shp;
+}
+
 NLM_EXTERN SeqHistPtr ParseTitleIntoSeqHist (
   SqnTagPtr stp,
   SeqHistPtr shp
@@ -3150,11 +3197,11 @@ static Boolean ParseFeatTableLine (CharPtr line, Int4Ptr startP, Int4Ptr stopP,
   *partial3P = partial3;
   *ispointP = ispoint;
   *isminusP = isminus;
-  *featP = featType;
-  *qualP = qualType;
-  *valP = qualVal;
+  *featP = StringSaveNoNull (featType);
+  *qualP = StringSaveNoNull (qualType);
+  *valP = StringSaveNoNull (qualVal);
 
-  ValNodeFree (parsed);
+  ValNodeFreeData (parsed);
   return TRUE;
 }
 
@@ -4146,6 +4193,8 @@ NLM_EXTERN void AddQualifierToFeature (SeqFeatPtr sfp, CharPtr qual, CharPtr val
         prp->desc = MemFree (prp->desc);
         prp->desc = StringSaveNoNull (val);
       }
+    } else if (sfp->data.choice == SEQFEAT_CDREGION && StringCmp (qual, "secondary_accession") == 0) {
+      bail = FALSE;
     } 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)) {
     } else if (ifp != NULL && StringICmp (ifp->key, "misc_feature") == 0 && ParseQualIntoCloneUserObject (sfp, qual, val)) {
@@ -4661,6 +4710,10 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
         ParseWhitespaceIntoTabs (line);
       }
 
+      feat = NULL;
+      qual = NULL;
+      val = NULL;
+
       if (ParseFeatTableLine (line, &start, &stop, &partial5, &partial3, &ispoint, &isminus, &feat, &qual, &val, offset)) {
         if (feat != NULL && start >= 0 && stop >= 0) {
 
@@ -4865,6 +4918,10 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
           }
           ErrPostEx (SEV_ERROR, ERR_SEQ_FEAT_WrongQualOnImpFeat, "Qualifier '%s' has no value on %s feature at %s", qual, label, loc);
           MemFree (loc);
+
+        } else if (feat != NULL) {
+
+          ErrPostEx (SEV_ERROR, ERR_SEQ_FEAT_ImpFeatBadLoc, "Bad location on feature %s (start %ld, stop %ld)", feat, (long) start, (long) stop);
         }
 
       } else if (*line == '[') {
@@ -4881,13 +4938,11 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
         SqnTagFree (stp);
       }
 
-/* Uncomment next lines if Purify reports memory leaks here. */
+      /* ParseFeatTableLine copies these three strings, so free here */
 
-      /*
-      MemFree (feat);
-      MemFree (qual);
-      MemFree (val);
-      */
+      feat = MemFree (feat);
+      qual = MemFree (qual);
+      val = MemFree (val);
 
     }
 
@@ -5786,6 +5841,7 @@ NLM_EXTERN Pointer ReadAsnFastaOrFlatFile (FILE *fp, Uint2Ptr datatypeptr, Uint2
           tmp = StringChr (line + 1, '[');
           if (tmp != NULL) {
             if (StringStr (tmp, "[") != NULL && StringStr (tmp, "=") != NULL) {
+              TrimSpacesAroundString (tmp);
               title = StringSave (tmp);
             }
           } else if (fastaAsSimpleSeq) {
@@ -5815,6 +5871,7 @@ NLM_EXTERN Pointer ReadAsnFastaOrFlatFile (FILE *fp, Uint2Ptr datatypeptr, Uint2
                 tmp += StringLen (seqid);
                 if (! StringHasNoText (tmp)) {
                   TrimSpacesAroundString (tmp);
+                  title = MemFree (title);
                   title = StringSaveNoNull (tmp);
                 }
               }
@@ -6360,6 +6417,9 @@ NLM_EXTERN TextFsaPtr TextFsaFree (TextFsaPtr tbl)
   }
 
   MemFree (statePtr);
+
+  ValNodeFreeData (tbl->siteList);
+
   return MemFree (tbl);
 }
 
diff --git a/api/sqnutils.h b/api/sqnutils.h
index e3a061e3..0e5bb878 100644
--- a/api/sqnutils.h
+++ b/api/sqnutils.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.92 $
+* $Revision: 6.94 $
 *
 * File Description: 
 *
@@ -216,6 +216,7 @@ typedef struct sqntag {
   Int2     num_tags;
   CharPtr  tag [MAX_SQN_TAGS];
   CharPtr  val [MAX_SQN_TAGS];
+  Boolean  used [MAX_SQN_TAGS];
 } SqnTag, PNTR SqnTagPtr;
 
 NLM_EXTERN SqnTagPtr SqnTagParse (CharPtr ttl);
@@ -261,6 +262,11 @@ NLM_EXTERN SeqHistPtr ParseTitleIntoSeqHist (
   SeqHistPtr shp
 );
 
+NLM_EXTERN SeqHistPtr ParseStringIntoSeqHist (
+  SeqHistPtr shp,
+  CharPtr str
+);
+
 NLM_EXTERN UserObjectPtr ParseTitleIntoTpaAssembly (
   SqnTagPtr stp,
   UserObjectPtr uop
diff --git a/api/tofasta.c b/api/tofasta.c
index c605b2a0..f0970b93 100644
--- a/api/tofasta.c
+++ b/api/tofasta.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/12/91
 *
-* $Revision: 6.121 $
+* $Revision: 6.125 $
 *
 * File Description:  various sequence objects to fasta output
 *
@@ -39,6 +39,18 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: tofasta.c,v $
+* Revision 6.125  2004/01/21 19:22:14  kans
+* UseOrgMods capitalizes first letter of created defline
+*
+* Revision 6.124  2003/12/23 20:58:51  kans
+* ProtDefLine takes prp->activity if prp->name and prp->desc are not set
+*
+* Revision 6.123  2003/11/18 19:04:29  kans
+* added BioseqFastaStream, rapid generator based on SeqPortStream
+*
+* Revision 6.122  2003/11/05 19:24:55  kans
+* BioseqToFastaX checks for virtual with do_virtual not set, prints a single dash as the sequence
+*
 * Revision 6.121  2003/08/04 19:51:02  kans
 * for complete chromosome title, if > 3 clones (by counting semicolons) then just display count, not full text of clones
 *
@@ -1366,6 +1378,15 @@ NLM_EXTERN Boolean BioseqToFastaX (BioseqPtr bsp, MyFsaPtr mfp, Boolean is_na)
 		code = mfp->code;
 	    }
 
+	    if (repr == Seq_repr_virtual && (! mfp->do_virtual)) {
+	        StringCpy (mfp->buf, "-");
+                (*(mfp->myfunc))(bsp, FASTA_SEQLINE, mfp->buf, StringLen(mfp->buf),
+                                 mfp->mydata);
+            (*(mfp->myfunc))(bsp, FASTA_EOS, mfp->buf, StringLen(mfp->buf),
+                             mfp->mydata);
+            return TRUE;
+	    }
+
             spp = FastaSeqPortEx (bsp, is_na, mfp->do_virtual, code, mfp->seqloc);
             if (spp == NULL) return FALSE;
             
@@ -1384,6 +1405,85 @@ NLM_EXTERN Boolean BioseqToFastaX (BioseqPtr bsp, MyFsaPtr mfp, Boolean is_na)
 
 /*****************************************************************************
 *
+*   BioseqFastaStream(bsp, fp, expandGaps, maxlen)
+*
+*   	Rapid FASTA generator using SeqPortStream
+*
+*****************************************************************************/
+
+typedef struct streamfsa {
+  FILE     *fp;
+  Char     buf [130];
+  Int2     idx;
+  Int2     linelen;
+} StreamFsa, PNTR StreamFsaPtr;
+
+static void LIBCALLBACK FsaStreamProc (
+  CharPtr sequence,
+  Pointer userdata
+)
+
+{
+  Char          ch;
+  StreamFsaPtr  sfp;
+
+  if (StringHasNoText (sequence) || userdata == NULL) return;
+  sfp = (StreamFsaPtr) userdata;
+
+  ch = *sequence;
+  while (ch != '\0') {
+    sfp->buf [sfp->idx] = ch;
+    (sfp->idx)++;
+
+    if (sfp->idx >= sfp->linelen) {
+      sfp->buf [sfp->idx] = '\0';
+      fprintf (sfp->fp, "%s\n", sfp->buf);
+      sfp->idx = 0;
+    }
+
+    sequence++;
+    ch = *sequence;
+  }
+}
+
+NLM_EXTERN void BioseqFastaStream (BioseqPtr bsp, FILE *fp, Boolean expandGaps, Int2 linelen)
+
+{
+  Char         buf [4096];
+  Char         id [42];
+  StreamFsa    sf;
+
+  if (bsp == NULL || fp == NULL) return;
+  if (linelen > 128) {
+    linelen = 128;
+  }
+  if (linelen < 1) {
+    linelen = 60;
+  }
+
+  id [0] = '\0';
+  SeqIdWrite (bsp->id, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
+
+  buf [0] = '\0';
+  CreateDefLine (NULL, bsp, buf, sizeof (buf) - 1, 0, NULL, NULL);
+
+  fprintf (fp, ">%s %s\n", id, buf);
+
+  MemSet ((Pointer) &sf, 0, sizeof (StreamFsa));
+  sf.fp = fp;
+  sf.idx = 0;
+  sf.linelen = linelen;
+  SeqPortStream (bsp, expandGaps, (Pointer) &sf, FsaStreamProc);
+
+  if (sf.idx > 0) {
+    sf.buf [sf.idx] = '\0';
+    fprintf (fp, "%s\n", sf.buf);
+  }
+}
+
+
+/*****************************************************************************
+*
 *   Here are functions that convert FASTA format from file or from memory
 *
 *****************************************************************************/
@@ -3037,8 +3137,12 @@ static CharPtr FindProtDefLine(BioseqPtr bsp)
 					}
 				}
 			}
-		} else if (prp->desc) {
+		} else if (prp && prp->desc) {
 			title = StringSave(prp->desc);
+		} else if (prp && prp->activity) {
+		    if (prp->activity->data.ptrvalue) {
+		        title = StringSave (prp->activity->data.ptrvalue);
+		    }
 		}
 	} 
 	if (title == NULL) {
@@ -3271,6 +3375,7 @@ static CharPtr UseOrgMods(BioseqPtr bsp, CharPtr suffix)
 	OrgNamePtr         	onp;
 	OrgRefPtr          	orp;
 	SubSourcePtr       	ssp;
+	Char                ch;
 	CharPtr				name = NULL, chr = NULL, str = NULL,
 						cln = NULL, map = NULL, def=NULL;
 	Int2 				deflen = 0;
@@ -3333,6 +3438,7 @@ static CharPtr UseOrgMods(BioseqPtr bsp, CharPtr suffix)
 	}
 	deflen += StringLen (suffix) + 2;
 	def = (CharPtr) MemNew(deflen+1);
+	if (def == NULL) return NULL;
 	if (name) {
 		def = StringCat(def, name);
 		MemFree(name);
@@ -3357,6 +3463,9 @@ static CharPtr UseOrgMods(BioseqPtr bsp, CharPtr suffix)
 		def = StringCat(def, " ");
 		def = StringCat(def, suffix);
 	}
+	TrimSpacesAroundString (def);
+	ch = def [0];
+	def [0] = TO_UPPER (ch);
 	return def;
 }
 
diff --git a/api/tofasta.h b/api/tofasta.h
index 23a30263..6dbedb14 100644
--- a/api/tofasta.h
+++ b/api/tofasta.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/12/91
 *
-* $Revision: 6.20 $
+* $Revision: 6.21 $
 *
 * File Description:  various sequence objects to fasta output
 *
@@ -39,6 +39,9 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: tofasta.h,v $
+* Revision 6.21  2003/11/18 19:04:29  kans
+* added BioseqFastaStream, rapid generator based on SeqPortStream
+*
 * Revision 6.20  2002/07/18 19:28:35  kans
 *  working implementation of BioseqRawToFastaExtraEx, always zero out all of MyFsa struct, no need for fake seqloc
 *
@@ -239,6 +242,16 @@ NLM_EXTERN Boolean BioseqToFastaX PROTO((BioseqPtr bsp, MyFsaPtr mfp, Boolean is
 
 /*****************************************************************************
 *
+*   BioseqFastaStream(bsp, fp, expandGaps, maxlen)
+*
+*   	Rapid FASTA generator using SeqPortStream
+*
+*****************************************************************************/
+NLM_EXTERN void BioseqFastaStream PROTO((BioseqPtr bsp, FILE *fp, Boolean expandGaps, Int2 linelen));
+
+
+/*****************************************************************************
+*
 *   FastaFileFunc(key, buf, data)
 *   	standard "write to file" callback
 *
diff --git a/api/txalign.c b/api/txalign.c
index 127cc1a5..21bfec8b 100644
--- a/api/txalign.c
+++ b/api/txalign.c
@@ -1,4 +1,4 @@
-/* $Id: txalign.c,v 6.79 2003/09/26 20:54:10 dondosha Exp $
+/* $Id: txalign.c,v 6.81 2003/11/25 16:24:03 dondosha Exp $
 ***************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -27,13 +27,19 @@
 *
 * File Name:  txalign.c
 *
-* $Revision: 6.79 $
+* $Revision: 6.81 $
 * 
 * File Description:  Formating of text alignment for the BLAST output
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: txalign.c,v $
+* Revision 6.81  2003/11/25 16:24:03  dondosha
+* Use query number for synchronizeCheck; do not show structure link if RID not available
+*
+* Revision 6.80  2003/11/20 22:09:26  dondosha
+* Added a PrindDefLinesFromSeqAlignWithPath function with an argument to provide root path for image links
+*
 * Revision 6.79  2003/09/26 20:54:10  dondosha
 * Revert change in revision 6.77, as it turned trace.cgi links should have stayed as they were
 *
@@ -688,15 +694,17 @@ static void addLinkoutForDefline(BioseqPtr bsp, SeqIdPtr sip, FILE* fp){
 	  bdlpTemp=bdlpTemp->next;
 	}
 	bdlpTemp=bdlp;
-	while(bdlpTemp){
-	  if(checkLinkoutType(bdlpTemp, linkout_structure)){
-	    hasLinkout=TRUE;
-	    gi=GetGIForSeqId(bdlpTemp->seqid);
-	    fprintf(fp, URL_Structure, RID_glb, firstGi, gi, CDD_RID_glb, "onegroup", StringCmp(Entrez_Query_Term, "") ? Entrez_Query_Term:"none");
-	    break;
-	  }
-	  bdlpTemp=bdlpTemp->next;
-	}
+        if (RID_glb) {
+           while(bdlpTemp){
+              if(checkLinkoutType(bdlpTemp, linkout_structure)){
+                 hasLinkout=TRUE;
+                 gi=GetGIForSeqId(bdlpTemp->seqid);
+                 fprintf(fp, URL_Structure, RID_glb, firstGi, gi, CDD_RID_glb, "onegroup", StringCmp(Entrez_Query_Term, "") ? Entrez_Query_Term:"none");
+                 break;
+              }
+              bdlpTemp=bdlpTemp->next;
+           }
+        }
 	bdlpTemp=bdlp;
 	while(bdlpTemp){
 	  if(checkLinkoutType(bdlpTemp, linkout_geo)){
@@ -749,7 +757,7 @@ static void addLinkoutForBioseq(BioseqPtr bsp, SeqIdPtr sip, SeqIdPtr firstSip,
 	  hasLinkout=TRUE;	
 	  fprintf(fp, URL_Unigene,  gi);
 	}
-	if(checkLinkoutType(actualBdlp, linkout_structure)){
+	if(RID_glb && checkLinkoutType(actualBdlp, linkout_structure)){
 	  hasLinkout=TRUE;
 	  fprintf(fp, URL_Structure, RID_glb, firstGi, gi, CDD_RID_glb, "onepair", StringCmp(Entrez_Query_Term, "") ? Entrez_Query_Term:"none");
 	}
@@ -1712,7 +1720,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
 					/*check box for getting sequence*/
 					if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
 					  Char checkboxBuf[200];
-					  sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment', 'getSeqGi', this.checked)\">", sip->data.intvalue);
+					  sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb);
 					  sprintf(docbuf+pos,checkboxBuf);
 					  
 					  pos += StringLen(checkboxBuf);
@@ -1761,7 +1769,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
 		if(!load){
 		  if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
 		    Char checkboxBuf[200];
-		    sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment', 'getSeqMaster')\">");
+		    sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld', 'getSeqMaster')\">", query_number_glb);
 		    sprintf(docbuf+pos,checkboxBuf);
 		  
 		    pos += StringLen(checkboxBuf);
@@ -4580,9 +4588,9 @@ Tx_PrintDefLine(BlastDefLinePtr bdsp, CharPtr buffer, Int4 length)
 }
 
 NLM_EXTERN Boolean LIBCALL
-PrintDefLinesFromSeqAlignEx2(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp, Uint4 options,
+PrintDefLinesFromSeqAlignWithPath(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp, Uint4 options,
 		Int4 mode, Int2Ptr marks, Int4 number_of_descriptions,
-		CharPtr db_name, CharPtr blast_type)
+		CharPtr db_name, CharPtr blast_type, CharPtr www_root_path)
 {
     BioseqPtr bsp;
     Boolean found_next_one, found_gnl_id, same_id, found_score=FALSE, make_link=FALSE;
@@ -4602,7 +4610,6 @@ PrintDefLinesFromSeqAlignEx2(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp
     Char tool_url[128];
     DbtagPtr db_tag;
     ObjectIdPtr oip;
-    CharPtr www_root_path = NULL;
     Int2 ColumnDistance=2, extraSpace=0, extraSpace2=0, strLen=0, maxEvalWidth=5, maxNWidth=2;
     Char tempBuf[64], tempBuf2[64];
       
@@ -4617,7 +4624,8 @@ PrintDefLinesFromSeqAlignEx2(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp
     }
 
 #ifdef OS_UNIX
-    www_root_path = getenv("WWW_ROOT_PATH");
+    if (!www_root_path)
+       www_root_path = getenv("WWW_ROOT_PATH");
 #endif
     
     if(!StringICmp(blast_type, "fruitfly")) {
@@ -4651,7 +4659,7 @@ PrintDefLinesFromSeqAlignEx2(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp
     /*AAS*/
     if (!(options & TXALIGN_DO_NOT_PRINT_TITLE)) {
         if ((mode == FIRST_PASS) || (mode == NOT_FIRST_PASS_REPEATS)) {
-	  if(options&TXALIGN_SHOW_LINKOUT&&options&TXALIGN_HTML){
+	  if(RID_glb && options&TXALIGN_SHOW_LINKOUT&&options&TXALIGN_HTML){
 	    if(PairwiseSeqAlignHasLinkout(seqalign, linkout_structure)){
 	    
 	      fprintf(outfp, URL_Structure_Overview,  RID_glb, 0, 0, CDD_RID_glb, "overview", StringCmp(Entrez_Query_Term, "") ? Entrez_Query_Term:"none");
@@ -4883,14 +4891,14 @@ PrintDefLinesFromSeqAlignEx2(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp
                             firstnew = FALSE;
                             fprintf(outfp, "<a name = Evalue></a>");
                         }
-                        fprintf(outfp, "<br><IMG SRC=\"%s/images/new.gif\" WIDTH=25 HEIGHT=15 ALT=\"New sequence mark\">", www_root_path == NULL? "/blast" : www_root_path);
+                        fprintf(outfp, "<br><IMG SRC=\"%s/blast/images/new.gif\" WIDTH=25 HEIGHT=15 ALT=\"New sequence mark\">", www_root_path == NULL? "" : www_root_path);
                     } else {
-                        fprintf(outfp, "<br><IMG SRC=\"%s/images/bg.gif\" WIDTH=25 HEIGHT=15 ALT=\" \">",  www_root_path == NULL? "/blast" : www_root_path);
+                        fprintf(outfp, "<br><IMG SRC=\"%s/blast/images/bg.gif\" WIDTH=25 HEIGHT=15 ALT=\" \">",  www_root_path == NULL? "" : www_root_path);
                     }
                     if (txsp->waschecked) {
-                        fprintf(outfp, "<IMG SRC=\"%s/images/checked.gif\" WIDTH=15 HEIGHT=15 ALT=\"Checked mark\">",  www_root_path == NULL? "/blast" : www_root_path);
+                        fprintf(outfp, "<IMG SRC=\"%s/blast/images/checked.gif\" WIDTH=15 HEIGHT=15 ALT=\"Checked mark\">",  www_root_path == NULL? "" : www_root_path);
                     } else {
-                        fprintf(outfp, "<IMG SRC=\"%s/images/bg.gif\" WIDTH=15 HEIGHT=15 ALT=\" \">",  www_root_path == NULL? "/blast" : www_root_path);
+                        fprintf(outfp, "<IMG SRC=\"%s/blast/images/bg.gif\" WIDTH=15 HEIGHT=15 ALT=\" \">",  www_root_path == NULL? "" : www_root_path);
                     }
                 }
                 fprintf(outfp, "%s", HTML_buffer);
@@ -5183,6 +5191,16 @@ PrintDefLinesFromSeqAlignEx2(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp
 }
 
 NLM_EXTERN Boolean LIBCALL
+PrintDefLinesFromSeqAlignEx2(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp, Uint4 options,
+		Int4 mode, Int2Ptr marks, Int4 number_of_descriptions,
+		CharPtr db_name, CharPtr blast_type)
+{
+   return PrintDefLinesFromSeqAlignWithPath(seqalign, line_length, outfp,
+             options, mode, marks, number_of_descriptions, db_name, 
+             blast_type, NULL);
+}
+
+NLM_EXTERN Boolean LIBCALL
 PrintDefLinesFromSeqAlign(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp, Uint4 options, Int4 mode, Int2Ptr marks)
 {
     Boolean	retval;
@@ -5576,7 +5594,7 @@ static Boolean TX_PrintDeflinesWithAsn(BlastDefLinePtr PNTR bdsp,
 	  bestid = SeqIdFindBest(tbdsp->seqid, SEQID_GI);
 	  firstSip=bestid;
 	  if(bestid->choice == SEQID_GI&&asop->html_hot_link&&(asop->txalign_options&TXALIGN_GET_SEQUENCE)){
-	    fprintf(asop->fp,  "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment', 'getSeqGi', this.checked)\">", bestid->data.intvalue);
+	    fprintf(asop->fp,  "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", bestid->data.intvalue, query_number_glb);
 	  }
 		    
 	  fprintf(asop->fp, ">");
@@ -5696,7 +5714,7 @@ NLM_EXTERN int LIBCALLBACK FormatScoreFunc(AlignStatOptionPtr asop)
 		      bestid = SeqIdFindBest(bsp->id, SEQID_GI);
 		      firstSip=bestid;
 		      if(bestid->choice == SEQID_GI&&asop->html_hot_link&&(asop->txalign_options&TXALIGN_GET_SEQUENCE)){
-			fprintf(asop->fp,  "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment', 'getSeqGi', this.checked)\">", bestid->data.intvalue);
+			fprintf(asop->fp,  "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", bestid->data.intvalue, query_number_glb);
 		      }
 		      fprintf(asop->fp, ">");
 		      first = FALSE;
diff --git a/api/txalign.h b/api/txalign.h
index 0c7099c0..949ba262 100644
--- a/api/txalign.h
+++ b/api/txalign.h
@@ -1,4 +1,4 @@
-/* $Id: txalign.h,v 6.15 2002/12/11 16:24:51 jianye Exp $
+/* $Id: txalign.h,v 6.16 2003/11/20 22:09:26 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
 *
 * Initial Version Creation Date: 03/13/94
 *
-* $Revision: 6.15 $
+* $Revision: 6.16 $
 *
 * File Description:
 *         External include file for various alignments
@@ -38,6 +38,9 @@
 *
 *
 * $Log: txalign.h,v $
+* Revision 6.16  2003/11/20 22:09:26  dondosha
+* Added a PrindDefLinesFromSeqAlignWithPath function with an argument to provide root path for image links
+*
 * Revision 6.15  2002/12/11 16:24:51  jianye
 * added structure linkout
 *
@@ -475,8 +478,6 @@ NLM_EXTERN Boolean ShowTextAlignFromAnnot3 PROTO((
                     CharPtr blast_type,
                     Int4Ptr PNTR posMatrix
                     ));
-
-
 /* Simple printing function:
    Can be used while debugging.. options kept to a minimum 
    fp==NULL ==> stdout 
@@ -571,6 +572,19 @@ NLM_EXTERN Boolean LIBCALL PrintDefLinesFromSeqAlignEx2 PROTO((
 		    CharPtr blast_type
 		    ));
 
+NLM_EXTERN Boolean LIBCALL PrintDefLinesFromSeqAlignWithPath PROTO((
+		    SeqAlignPtr seqalign, 
+		    Int4 line_length, 
+		    FILE *outfp, 
+		    Uint4 options, 
+		    Int4 mode, 
+		    Int2Ptr marks, 
+		    Int4 number_of_descriptions,
+		    CharPtr db_name,
+		    CharPtr blast_type,
+                    CharPtr www_root_path
+		    ));
+
 /*
 	Fills in the slots with score, bit_score, etc. from the SeqAlign.
 */
diff --git a/api/valid.c b/api/valid.c
index 667a2876..f386b72b 100644
--- a/api/valid.c
+++ b/api/valid.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 1/1/94
 *
-* $Revision: 6.403 $
+* $Revision: 6.427 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -39,6 +39,78 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: valid.c,v $
+* Revision 6.427  2004/01/20 22:25:49  kans
+* when run from tbl2asn, suppress MissingLineage, GenCodeMismatch, and NoTaxonID messages
+*
+* Revision 6.426  2004/01/20 22:09:36  kans
+* tbl2asn sets vsp->seqSubmitParent flag, use this to drop MissingLineage from error to warning
+*
+* Revision 6.425  2004/01/16 17:10:50  kans
+* implemented ERR_SEQ_FEAT_LocusTagProblem
+*
+* Revision 6.424  2004/01/13 18:33:26  kans
+* ValidateCitSub checks ap->affil, set vsp->gcp fields for sbp->sub call to it
+*
+* Revision 6.423  2004/01/12 18:08:36  kans
+* ValidateCitSub called from ValidatePubdesc, gives error if no affiliation fields set
+*
+* Revision 6.422  2004/01/07 20:47:21  kans
+* validate dbxref with legalDbXrefs in asn2gnbi.h instead of old flatfile generator symbols
+*
+* Revision 6.421  2004/01/02 15:06:23  kans
+* modified codon recognition exception text suppresses TrnaCodonWrong error
+*
+* Revision 6.420  2003/12/15 16:47:17  kans
+* artificial, mutagenized, or synthetic suppress other-genetic message
+*
+* Revision 6.419  2003/12/11 20:49:09  kans
+* allow multiple adjacent 3prime UTRs, used in segmented sequences
+*
+* Revision 6.418  2003/12/11 19:22:24  kans
+* electronic journal suppresses no volume, no iso jta errors
+*
+* Revision 6.417  2003/12/10 18:24:10  kans
+* Implemented ERR_SEQ_FEAT_BadConflictFlag and ERR_SEQ_FEAT_ConflictFlagSet
+*
+* Revision 6.416  2003/12/09 22:25:46  kans
+* implemented ERR_SEQ_INST_SeqLocLength test
+*
+* Revision 6.415  2003/12/08 21:10:03  kans
+* added ERR_SEQ_PKG_GraphPackagingProblem, now can only collect graphs on bioseq to validate
+*
+* Revision 6.414  2003/12/08 19:10:23  kans
+* ValidateGraphsOnBioseq uses BSRead instead of BSGetByte for great speedup
+*
+* Revision 6.413  2003/12/05 18:52:12  kans
+* ValidateSeqEntry does not set do_many if BioseqseqSet_class_genbank.  GatherSeqEntry visits everything, and should not be called in a loop.
+*
+* Revision 6.412  2003/12/04 22:30:43  kans
+* ValidateGraphOnBioseq uses visit instead of nested gather
+*
+* Revision 6.411  2003/12/03 19:52:11  kans
+* TerminalNs is warning if NC_ record, never error
+*
+* Revision 6.410  2003/12/02 19:54:49  kans
+* ValidateSeqEntry does not need to AssignIDsInEntity every time through the loop, just at beginning
+*
+* Revision 6.409  2003/12/02 15:37:37  kans
+* added vsp->seqSubmitParent for use by tbl2asn, which usually has a Seq-submit wrapper that is added on-the-fly and not indexed
+*
+* Revision 6.408  2003/11/19 18:54:42  kans
+* segmented sequence does not need TPA user object, 5prime UTR only needs to abut first CDS, if mRNA is segmented
+*
+* Revision 6.407  2003/11/18 22:51:20  kans
+* ValidStructClear saves/restores new alignFindRemoteBsp and doSeqHistAssembly fields
+*
+* Revision 6.406  2003/11/14 18:07:16  kans
+* alignment parameters to find remote bsp, do seqhist assembly
+*
+* Revision 6.405  2003/11/13 21:51:42  kans
+* added ERR_SEQ_INST_TpaAssmeblyProblem check
+*
+* Revision 6.404  2003/11/12 20:13:36  kans
+* added East Timor to the legal country codes
+*
 * Revision 6.403  2003/10/24 21:31:00  kans
 * added test for ERR_SEQ_FEAT_UTRdoesNotAbutCDS on mRNA
 *
@@ -1415,7 +1487,7 @@ static char    *this_file = __FILE__;
 #include <gbftdef.h>
 #include <gbfeat.h>
 #include <objsub.h>
-#include <asn2ffp.h>
+#include <asn2gnbi.h>
 #include <explore.h>
 #include <subutil.h>
 #include <tofasta.h>
@@ -1453,6 +1525,7 @@ NLM_EXTERN CharPtr FindIDForEntry (SeqEntryPtr sep, CharPtr buf);
 NLM_EXTERN void SpellCheckSeqFeat (GatherContextPtr gcp);
 NLM_EXTERN void SpellCheckString (ValidStructPtr vsp, CharPtr str);
 NLM_EXTERN void SpliceCheck (ValidStructPtr vsp, SeqFeatPtr sfp);
+static void     CdConflictCheck (ValidStructPtr vsp, SeqFeatPtr sfp);
 static void     SpliceCheckEx (ValidStructPtr vsp, SeqFeatPtr sfp, Boolean checkAll);
 static void     CdsProductIdCheck (ValidStructPtr vsp, SeqFeatPtr sfp);
 static void     ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSourcePtr biop);
@@ -1460,7 +1533,7 @@ static void     ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, Pubde
 static void     ValidateSfpCit (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPtr sfp);
 
 /* alignment validator */
-NLM_EXTERN Boolean ValidateSeqAlignWithinValidator (ValidStructPtr vsp, SeqEntryPtr sep);
+NLM_EXTERN Boolean ValidateSeqAlignWithinValidator (ValidStructPtr vsp, SeqEntryPtr sep, Boolean find_remote_bsp, Boolean do_hist_assembly);
 
 /*****************************************************************************
 *
@@ -1481,9 +1554,12 @@ NLM_EXTERN void ValidStructClear (ValidStructPtr vsp)
   Boolean         suppressContext;
   Boolean         validateAlignments;
   Boolean         farIDsInAlignments;
+  Boolean         alignFindRemoteBsp;
+  Boolean         doSeqHistAssembly;
   Boolean         alwaysRequireIsoJTA;
   Boolean         farFetchCDSproducts;
   Boolean         validateIDSet;
+  Boolean         seqSubmitParent;
   TextFsaPtr      sourceQualTags;
 
   if (vsp == NULL)
@@ -1500,9 +1576,12 @@ NLM_EXTERN void ValidStructClear (ValidStructPtr vsp)
   suppressContext = vsp->suppressContext;
   validateAlignments = vsp->validateAlignments;
   farIDsInAlignments = vsp->farIDsInAlignments;
+  alignFindRemoteBsp = vsp->alignFindRemoteBsp;
+  doSeqHistAssembly = vsp->doSeqHistAssembly;
   alwaysRequireIsoJTA = vsp->alwaysRequireIsoJTA;
   farFetchCDSproducts = vsp->farFetchCDSproducts;
   validateIDSet = vsp->validateIDSet;
+  seqSubmitParent = vsp->seqSubmitParent;
   sourceQualTags = vsp->sourceQualTags;
   MemSet ((VoidPtr) vsp, 0, sizeof (ValidStruct));
   vsp->errbuf = errbuf;
@@ -1516,9 +1595,12 @@ NLM_EXTERN void ValidStructClear (ValidStructPtr vsp)
   vsp->suppressContext = suppressContext;
   vsp->validateAlignments = validateAlignments;
   vsp->farIDsInAlignments = farIDsInAlignments;
+  vsp->alignFindRemoteBsp = alignFindRemoteBsp;
+  vsp->doSeqHistAssembly = doSeqHistAssembly;
   vsp->alwaysRequireIsoJTA = alwaysRequireIsoJTA;
   vsp->farFetchCDSproducts = farFetchCDSproducts;
   vsp->validateIDSet = validateIDSet;
+  vsp->seqSubmitParent = seqSubmitParent;
   vsp->sourceQualTags = sourceQualTags;
   return;
 }
@@ -2051,8 +2133,11 @@ typedef struct ftprob {
   Uint4  num_misplaced_features;
   Uint4  num_archaic_locations;
   Uint4  num_archaic_products;
+  Uint4  num_misplaced_graphs;
   Uint4  num_gene_feats;
   Uint4  num_gene_xrefs;
+  Uint4  num_tpa_with_hist;
+  Uint4  num_tpa_without_hist;
 } FeatProb, PNTR FeatProbPtr;
 
 static void CheckFeatPacking (BioseqPtr bsp, SeqFeatPtr sfp, Uint4Ptr num_misplaced_features)
@@ -2152,6 +2237,32 @@ static void CheckFeatLocAndProd (SeqFeatPtr sfp, FeatProbPtr fpp)
   }
 }
 
+static void CheckGraphPacking (SeqGraphPtr sgp, Pointer userdata)
+
+{
+  BioseqPtr    bsp;
+  FeatProbPtr  fpp;
+  SeqAnnotPtr  sap;
+  BioseqPtr    par;
+
+  if (sgp == NULL || userdata == NULL) return;
+  fpp = (FeatProbPtr) userdata;
+  bsp = BioseqFindFromSeqLoc (sgp->loc);
+  if (sgp->idx.parenttype == OBJ_SEQANNOT) {
+    sap = (SeqAnnotPtr) sgp->idx.parentptr;
+    if (sap == NULL) return;
+    if (sap->idx.parenttype == OBJ_BIOSEQ) {
+      /* if graph packaged on bioseq, must be target bioseq */
+      par = (BioseqPtr) sap->idx.parentptr;
+      if (par != bsp && SeqMgrGetParentOfPart (par, NULL) != bsp) {
+        (fpp->num_misplaced_graphs)++;
+      }
+      return;
+    }
+    (fpp->num_misplaced_graphs)++;
+  }
+}
+
 static Boolean LIBCALLBACK CountMisplacedFeatures (BioseqPtr bsp, SeqMgrBioseqContextPtr bcontext)
 {
   FeatProbPtr     fpp;
@@ -2188,6 +2299,44 @@ static void CountGeneXrefs (SeqFeatPtr sfp, Pointer userdata)
   (fpp->num_gene_xrefs)++;
 }
 
+static Boolean HasTpaUserObject (BioseqPtr bsp)
+
+{
+  SeqMgrDescContext  context;
+  UserObjectPtr      uop;
+  ObjectIdPtr        oip;
+  ValNodePtr         vnp;
+
+  if (bsp == NULL) return FALSE;
+  vnp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &context);
+  while (vnp != NULL) {
+    uop = (UserObjectPtr) vnp->data.ptrvalue;
+    if (uop != NULL) {
+      oip = uop->type;
+      if (oip != NULL && StringICmp (oip->str, "TpaAssembly") == 0) return TRUE;
+    }
+    vnp = SeqMgrGetNextDescriptor (bsp, vnp, Seq_descr_user, &context);
+  }
+  return FALSE;
+}
+
+static void CheckTpaHist (BioseqPtr bsp, Pointer userdata)
+
+{
+  FeatProbPtr  fpp;
+  SeqHistPtr   shp;
+
+  if (bsp == NULL || userdata == NULL) return;
+  fpp = (FeatProbPtr) userdata;
+  if (! HasTpaUserObject (bsp)) return;
+  shp = bsp->hist;
+  if (shp != NULL && shp->assembly != NULL) {
+    (fpp->num_tpa_with_hist)++;
+  } else {
+    (fpp->num_tpa_without_hist)++;
+  }
+}
+
 static Boolean IsNoncuratedRefSeq (BioseqPtr bsp, ErrSev *sev)
 
 {
@@ -2258,7 +2407,9 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
     SeqMgrExploreBioseqs (entityID, NULL, (Pointer) &featprob, CountMisplacedFeatures, TRUE, TRUE, TRUE);
 
     topsep = GetTopSeqEntryForEntityID (entityID);
+    VisitGraphsInSep (topsep, (Pointer) &featprob, CheckGraphPacking);
     VisitFeaturesInSep (topsep, (Pointer) &featprob, CountGeneXrefs);
+    VisitBioseqsInSep (topsep, (Pointer) &featprob, CheckTpaHist);
   } else {
 
     /* if not using indexing, still need feature->idx.subtype now */
@@ -2283,7 +2434,7 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
   if (IS_Bioseq_set (sep)) {
     bssp = (BioseqSetPtr) (sep->data.ptrvalue);
     switch (bssp->_class) {
-    case BioseqseqSet_class_genbank:
+    /* case BioseqseqSet_class_genbank: */
     case BioseqseqSet_class_pir:
     case BioseqseqSet_class_gibb:
     case BioseqseqSet_class_gi:
@@ -2364,7 +2515,7 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
     }
 
     if (first) {
-      if (suppress_no_pubs) {
+      if (suppress_no_pubs && (! vsp->seqSubmitParent)) {
         omdp = ObjMgrGetData (gc.entityID);
         if (omdp == NULL || omdp->datatype != OBJ_SEQSUB) {
           sev = SEV_ERROR;
@@ -2385,6 +2536,12 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
         ValidErr (vsp, SEV_REJECT, ERR_SEQ_PKG_FeaturePackagingProblem, "There is %d mispackaged feature in this record.", (int) featprob.num_misplaced_features);
       }
 
+      if (featprob.num_misplaced_graphs > 1) {
+        ValidErr (vsp, SEV_REJECT, ERR_SEQ_PKG_GraphPackagingProblem, "There are %d mispackaged graphs in this record.", (int) featprob.num_misplaced_graphs);
+      } else if (featprob.num_misplaced_graphs == 1) {
+        ValidErr (vsp, SEV_REJECT, ERR_SEQ_PKG_GraphPackagingProblem, "There is %d mispackaged graph in this record.", (int) featprob.num_misplaced_graphs);
+      }
+
       /*
       if (featprob.num_archaic_locations > 1) {
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_PKG_ArchaicFeatureLocation, "There are %d archaic feature locations in this record.", (int) featprob.num_archaic_locations);
@@ -2403,6 +2560,11 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_OnlyGeneXrefs, "There are %ld gene xrefs and no gene features in this record.", (long) featprob.num_gene_xrefs);
       }
 
+      if (featprob.num_tpa_with_hist > 0 && featprob.num_tpa_without_hist > 0) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_TpaAssmeblyProblem, "There are %ld TPAs with history and %ld without history in this record.",
+                  (long) featprob.num_tpa_with_hist, (long) featprob.num_tpa_without_hist);
+      }
+
       first = FALSE;
     }
 
@@ -2411,13 +2573,13 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
     topsep = GetTopSeqEntryForEntityID (gc.entityID);
     oldsep = SeqEntrySetScope (topsep);
 
-    AssignIDsInEntity (gc.entityID, 0, NULL);
+    /* AssignIDsInEntity (gc.entityID, 0, NULL); */
 
     GatherSeqEntry (sep, (Pointer) vsp, Valid1GatherProc, &gs);
 
     if (vsp->validateAlignments) {
       vsp->gcp = NULL;
-      ValidateSeqAlignWithinValidator (vsp, sep);
+      ValidateSeqAlignWithinValidator (vsp, sep, vsp->alignFindRemoteBsp, vsp->doSeqHistAssembly);
       vsp->gcp = NULL;
     }
 
@@ -3392,6 +3554,7 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
   Boolean         isGenBankEMBLorDDBJ;
   Boolean         isPatent = FALSE;
   Boolean         isPDB = FALSE;
+  Boolean         isNC = FALSE;
   Boolean         isNTorNC = FALSE;
   Boolean         isNZ;
   Boolean         is_gps = FALSE;
@@ -3451,6 +3614,7 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
           isNTorNC = TRUE;
         } else if (StringNICmp (tsip->accession, "NC_", 3) == 0) {
           isNTorNC = TRUE;
+          isNC = TRUE;
         }
       }
     } else if (sip1->choice == SEQID_GI) {
@@ -3473,7 +3637,7 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
     case SEQID_TPD:
       hist = bsp->hist;
       if (hist == NULL || hist->assembly == NULL) {
-        if (ISA_na (bsp->mol)) {
+        if (ISA_na (bsp->mol) && bsp->repr != Seq_repr_seg) {
           SeqIdWrite (bsp->id, buf1, PRINTID_FASTA_SHORT, 40);
           ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_HistAssemblyMissing, "TPA record %s should have Seq-hist.assembly for PRIMARY block", buf1);
         }
@@ -4107,6 +4271,14 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
             ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_SeqDataLenWrong, "-1 length on seq-loc of delta seq_ext");
           else
             len += len2;
+          if (len2 <= 10) {
+            str = SeqLocPrint ((SeqLocPtr) (vnp->data.ptrvalue));
+            if (str == NULL) {
+              str = StringSave ("?");
+            }
+            ValidErr (vsp, SEV_WARNING, ERR_SEQ_INST_SeqLocLength, "Short length (%ld) on seq-loc (%s) of delta seq_ext", (long) len2, str);
+            MemFree (str);
+          }
           break;
         case 2:                /* SeqLitPtr */
           slitp = (SeqLitPtr) (vnp->data.ptrvalue);
@@ -4380,7 +4552,9 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
     str = GetSequenceByFeature (sfp);
     if (str != NULL) {
       if (str [0] == 'n' || str [0] == 'N') {
-        if (StringICmp (str, "NNNNNNNNNN") == 0) {
+        if (isNC) {
+          sev = SEV_WARNING;
+        } else if (StringICmp (str, "NNNNNNNNNN") == 0) {
           sev = SEV_ERROR;
         } else {
           sev = SEV_WARNING;
@@ -4396,7 +4570,9 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
     len = StringLen (str);
     if (str != NULL && len > 0) {
       if (str [len - 1] == 'n' || str [len - 1] == 'N') {
-        if (StringICmp (str, "NNNNNNNNNN") == 0) {
+        if (isNC) {
+          sev = SEV_WARNING;
+        } else if (StringICmp (str, "NNNNNNNNNN") == 0) {
           sev = SEV_ERROR;
         } else {
           sev = SEV_WARNING;
@@ -4499,13 +4675,59 @@ static Boolean IS_NC_IN_SEP (SeqEntryPtr sep)
   return is_nc;
 }
 
+static void ValidateCitSub (ValidStructPtr vsp, CitSubPtr csp)
+{
+  AffilPtr        ap;
+  AuthListPtr     alp;
+  ValNodePtr      name;
+  Boolean         hasAffil = FALSE;
+  Boolean         hasName = FALSE;
+
+  if (vsp == NULL || csp == NULL)
+    return;
+  alp = csp->authors;
+  if (alp != NULL) {
+    if (alp->choice == 1) {
+      for (name = alp->names; name != NULL; name = name->next) {
+        if (!HasNoName (name)) {
+          hasName = TRUE;
+        }
+      }
+    } else if (alp->choice == 2 || alp->choice == 3) {
+      for (name = alp->names; name != NULL; name = name->next) {
+        if (!HasNoText ((CharPtr) name->data.ptrvalue)) {
+          hasName = TRUE;
+        }
+      }
+    }
+    ap = alp->affil;
+    if (ap != NULL) {
+      if (ap->affil == NULL && ap->div == NULL && ap->street == NULL && ap->city == NULL &&
+           ap->sub == NULL && ap->postal_code == NULL && ap->country == NULL &&
+           ap->phone == NULL && ap->fax == NULL && ap->email == NULL) {
+        /* no affiliation */
+      } else {
+        hasAffil = TRUE;
+      }
+    }
+  }
+  if (!hasName) {
+    ValidErr (vsp, SEV_ERROR, ERR_GENERIC_MissingPubInfo, "Submission citation has no author names");
+  }
+  if (!hasAffil) {
+    ValidErr (vsp, SEV_ERROR, ERR_GENERIC_MissingPubInfo, "Submission citation has no affiliation");
+  }
+}
+
 static void ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, PubdescPtr pdp)
 {
   AuthListPtr     alp;
   CitArtPtr       cap = NULL;
   CitGenPtr       cgp;
   CitJourPtr      cjp = NULL;
-  Boolean         hasName, hasTitle, hasIsoJTA = FALSE, inPress = FALSE;
+  CitSubPtr       csp;
+  Boolean         hasName, hasTitle, hasIsoJTA = FALSE,
+                  inPress = FALSE, electronic_journal = FALSE;
   ImprintPtr      imp;
   Boolean         noVol, noPages;
   ValNodePtr      name;
@@ -4543,6 +4765,12 @@ static void ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, PubdescPt
         uid = vnp->data.intvalue;
       }
       break;
+    case PUB_Sub :
+      csp = (CitSubPtr) vnp->data.ptrvalue;
+      if (csp != NULL) {
+        ValidateCitSub (vsp, csp);
+      }
+      break;
     case PUB_Article:
       cap = (CitArtPtr) vnp->data.ptrvalue;
       hasName = FALSE;
@@ -4588,6 +4816,11 @@ static void ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, PubdescPt
             }
             if (!HasNoText ((CharPtr) title->data.ptrvalue)) {
               hasTitle = TRUE;
+              if (title->choice == Cit_title_name) {
+                if (StringNCmp ((CharPtr) title->data.ptrvalue, "(er)", 4) == 0) {
+                  electronic_journal = TRUE;
+                }
+              }
             }
           }
           if (!hasTitle) {
@@ -4608,7 +4841,9 @@ static void ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, PubdescPt
               if (noVol && noPages) {
                 ValidErr (vsp, sev, ERR_GENERIC_MissingPubInfo, "Journal volume and pages missing");
               } else if (noVol) {
-                ValidErr (vsp, sev, ERR_GENERIC_MissingPubInfo, "Journal volume missing");
+                if (! electronic_journal) {
+                  ValidErr (vsp, sev, ERR_GENERIC_MissingPubInfo, "Journal volume missing");
+                }
               } else if (noPages) {
                 ValidErr (vsp, sev, ERR_GENERIC_MissingPubInfo, "Journal pages missing");
               }
@@ -4657,7 +4892,9 @@ static void ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, PubdescPt
   }
   if (cap != NULL && cjp != NULL && (uid > 0 || inPress || vsp->alwaysRequireIsoJTA)) {
     if (! hasIsoJTA) {
-      ValidErr (vsp, SEV_WARNING, ERR_GENERIC_MissingPubInfo, "ISO journal title abbreviation missing");
+      if (! electronic_journal) {
+        ValidErr (vsp, SEV_WARNING, ERR_GENERIC_MissingPubInfo, "ISO journal title abbreviation missing");
+      }
     }
   }
 }
@@ -5059,6 +5296,7 @@ static CharPtr  countrycodes[] = {
   "Djibouti",
   "Dominica",
   "Dominican Republic",
+  "East Timor",
   "Ecuador",
   "Egypt",
   "El Salvador",
@@ -5488,7 +5726,9 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
     return;
   onp = orp->orgname;
   if (onp == NULL || StringHasNoText (onp->lineage)) {
-    ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_MissingLineage, "No lineage for this BioSource.");
+    if (! vsp->seqSubmitParent) { /* suppress when validator run from tbl2asn */
+      ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_MissingLineage, "No lineage for this BioSource.");
+    }
   } else {
     if (biop->genome == GENOME_kinetoplast) {
       if (StringStr (onp->lineage, "Kinetoplastida") == 0) {
@@ -5520,8 +5760,8 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
     id = -1;
     dbt = (DbtagPtr) db->data.ptrvalue;
     if (dbt != NULL && dbt->db != NULL) {
-      for (i = 0; i < DBNUM; i++) {
-        if (StringCmp (dbt->db, dbtag [i]) == 0) {
+      for (i = 0; legalDbXrefs [i] != NULL; i++) {
+        if (StringCmp (dbt->db, legalDbXrefs [i]) == 0) {
           id = i;
           break;
         }
@@ -5541,7 +5781,9 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
         return;
     }
   }
-  ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_NoTaxonID, "BioSource is missing taxon ID");
+  if (! vsp->seqSubmitParent) { /* suppress when validator run from tbl2asn */
+    ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_NoTaxonID, "BioSource is missing taxon ID");
+  }
 }
 
 static Boolean IsXr (ValNodePtr sdp)
@@ -6007,35 +6249,6 @@ static void ValidateSeqDescrContext (GatherContextPtr gcp)
 *      Gather callback for validating context on a Bioseq
 *
 *****************************************************************************/
-static void ValidateCitSub (ValidStructPtr vsp, CitSubPtr csp)
-{
-  AuthListPtr     alp;
-  ValNodePtr      name;
-  Boolean         hasName = FALSE;
-
-  if (vsp == NULL || csp == NULL)
-    return;
-  alp = csp->authors;
-  if (alp != NULL) {
-    if (alp->choice == 1) {
-      for (name = alp->names; name != NULL; name = name->next) {
-        if (!HasNoName (name)) {
-          hasName = TRUE;
-        }
-      }
-    } else if (alp->choice == 2 || alp->choice == 3) {
-      for (name = alp->names; name != NULL; name = name->next) {
-        if (!HasNoText ((CharPtr) name->data.ptrvalue)) {
-          hasName = TRUE;
-        }
-      }
-    }
-  }
-  if (!hasName) {
-    ValidErr (vsp, SEV_ERROR, ERR_GENERIC_MissingPubInfo, "Submission citation has no author names");
-  }
-}
-
 static Boolean DifferentDbxrefs (ValNodePtr dbxref1, ValNodePtr dbxref2)
 {
   DbtagPtr        dbt1, dbt2;
@@ -6224,6 +6437,7 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
   SeqFeatPtr      sfp;
   SeqMgrFeatContext fcontext;
   Uint2           featdeftype = 0;
+  Boolean         firstCDS;
   SeqFeatPtr      last = NULL;
   Boolean         leave;
   CharPtr         label = NULL;
@@ -6250,6 +6464,7 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
   OrgRefPtr       orp = NULL;
   Int4            fiveUTRright;
   Int4            cdsRight;
+  Int4            threeUTRright;
 
   gcp = bvsp->gcp;
   vsp = bvsp->vsp;
@@ -6437,13 +6652,15 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
   if (bvsp->is_mrna) {
     fiveUTRright = 0;
     cdsRight = 0;
+    threeUTRright = 0;
+    firstCDS = TRUE;
     sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
     while (sfp != NULL) {
       if (sfp->idx.subtype == FEATDEF_5UTR) {
         fiveUTRright = fcontext.right;
       } else if (sfp->idx.subtype == FEATDEF_CDS) {
         cdsRight = fcontext.right;
-        if (fiveUTRright > 0) {
+        if (fiveUTRright > 0 && firstCDS) {
           if (fiveUTRright + 1 != fcontext.left) {
             if (gcp != NULL) {
               gcp->itemID = fcontext.itemID;
@@ -6459,8 +6676,23 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
             }
           }
         }
+        firstCDS = FALSE;
       } else if (sfp->idx.subtype == FEATDEF_3UTR) {
-        if (cdsRight > 0) {
+        if (threeUTRright > 0) {
+          if (threeUTRright + 1 != fcontext.left) {
+            if (gcp != NULL) {
+              gcp->itemID = fcontext.itemID;
+              gcp->thistype = OBJ_SEQFEAT;
+            }
+            vsp->descr = NULL;
+            vsp->sfp = sfp;
+            ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_UTRdoesNotAbutCDS, "Previous 3'UTR does not abut next 3'UTR");
+            if (gcp != NULL) {
+              gcp->itemID = olditemid;
+              gcp->thistype = olditemtype;
+            }
+          }
+        } else if (cdsRight > 0) {
           if (cdsRight + 1 != fcontext.left) {
             if (gcp != NULL) {
               gcp->itemID = fcontext.itemID;
@@ -6475,6 +6707,7 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
             }
           }
         }
+        threeUTRright = fcontext.right;
       }
       sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
     }
@@ -6491,7 +6724,18 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
         bvsp->got_a_pub = TRUE;
         csp = sbp->cit;
         /* csp = (CitSubPtr) gcp->thisitem; */
+        if (gcp != NULL) {
+          gcp->itemID = 1;
+          gcp->thistype = OBJ_SEQSUB_CIT;
+        }
+        vsp->descr = NULL;
+        vsp->sfp = NULL;
+        vsp->bssp = NULL;
         ValidateCitSub (vsp, csp);
+        if (gcp != NULL) {
+          gcp->itemID = olditemid;
+          gcp->thistype = olditemtype;
+        }
       }
     }
   }
@@ -6607,7 +6851,7 @@ static void ValidateBioseqContext (GatherContextPtr gcp)
     if (vnp != NULL) {
       biop = (BioSourcePtr) vnp->data.ptrvalue;
       if (biop != NULL) {
-        if (biop->origin == ORG_ARTIFICIAL) {
+        if (biop->origin == ORG_ARTIFICIAL || biop->origin == ORG_MUT || biop->origin == ORG_SYNTHETIC) {
           bvs.is_artificial = TRUE;
         }
       }
@@ -6680,7 +6924,7 @@ static void ValidateBioseqContext (GatherContextPtr gcp)
   vsp->descr = NULL;
   vsp->sfp = NULL;
 
-  if ((!bvs.got_a_pub) && (!vsp->suppress_no_pubs)) {
+  if ((!bvs.got_a_pub) && (!vsp->suppress_no_pubs) && (! vsp->seqSubmitParent)) {
     omdp = NULL;
     if (gcp != NULL) {
       omdp = ObjMgrGetData (gcp->entityID);
@@ -7273,7 +7517,9 @@ static void CheckTrnaCodons (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPt
           if (aa == 'U') {
             sev = SEV_WARNING;
           }
-          ValidErr (vsp, sev, ERR_SEQ_FEAT_TrnaCodonWrong, "tRNA codon does not match genetic code");
+          if (StringISearch (sfp->except_text, "modified codon recognition") == NULL) {
+            ValidErr (vsp, sev, ERR_SEQ_FEAT_TrnaCodonWrong, "tRNA codon does not match genetic code");
+          }
         }
       }
     } else if (trp->codon [j] < 255) {
@@ -7712,8 +7958,8 @@ static void CheckForIllegalDbxref (ValidStructPtr vsp, GatherContextPtr gcp, Seq
     id = -1;
     db = vnp->data.ptrvalue;
     if (db != NULL && db->db != NULL) {
-      for (i = 0; i < DBNUM; i++) {
-        if (StringCmp (db->db, dbtag[i]) == 0) {
+      for (i = 0; legalDbXrefs [i] != NULL; i++) {
+        if (StringCmp (db->db, legalDbXrefs [i]) == 0) {
           id = i;
           break;
         }
@@ -7766,6 +8012,7 @@ static CharPtr legal_exception_strings [] = {
   "non-consensus splice site",
   "nonconsensus splice site",
   "rearrangement required for product",
+  "modified codon recognition",
   NULL
 };
 
@@ -7815,7 +8062,7 @@ static void ValidateExceptText (ValidStructPtr vsp, GatherContextPtr gcp, SeqFea
         if (IsNCorNT (vsp->sep, sfp->location)) {
           sev = SEV_WARNING;
         }
-        ValidErr (vsp, sev, ERR_SEQ_FEAT_InvalidQualifierValue, "%s is not legal exception explanation", tmp);
+        ValidErr (vsp, sev, ERR_SEQ_FEAT_InvalidQualifierValue, "%s is not a legal exception explanation", tmp);
       }
     }
     tmp = ptr;
@@ -8003,6 +8250,9 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
   TextSeqIdPtr    tsip;
   BioseqPtr       protBsp;
   ErrSev          sev;
+  Boolean         multitoken;
+  Char            ch;
+  CharPtr         ptr;
 
   vsp = (ValidStructPtr) (gcp->userdata);
   sfp = (SeqFeatPtr) (gcp->thisitem);
@@ -8151,6 +8401,17 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
           grp->db == NULL && grp->syn == NULL) {
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_GeneRefHasNoData, "There is a gene feature where all fields are empty");
       }
+      if (! StringHasNoText (grp->locus_tag)) {
+        multitoken = FALSE;
+        for (ptr = grp->locus_tag, ch = *ptr; ch != '\0'; ptr++, ch = *ptr) {
+          if (IS_WHITESP (ch)) {
+            multitoken = TRUE;
+          }
+        }
+        if (multitoken) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_LocusTagProblem, "Gene locus_tag '%s' should be a single word without any spaces", grp->locus_tag);
+        }
+      }
       CheckForIllegalDbxref (vsp, gcp, sfp, grp->db);
       /*
       for (vnp = grp->db; vnp != NULL; vnp = vnp->next) {
@@ -8215,6 +8476,8 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
     if ((!pseudo) && (!conflict)) {
       CdTransCheck (vsp, sfp);
       SpliceCheck (vsp, sfp);
+    } else if (conflict) {
+      CdConflictCheck (vsp, sfp);
     }
     CdsProductIdCheck (vsp, sfp);
     crp = (CdRegionPtr) (sfp->data.value.ptrvalue);
@@ -8276,12 +8539,14 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
               }
             }
             if (biopgencode != cdsgencode) {
-              if (plastid) {
-                ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_GenCodeMismatch,
-                          "Genetic code conflict between CDS (code %d) and BioSource.genome biological context (%s) (uses code 11)", (int) cdsgencode, plastidtxt [biop->genome]);
-              } else {
-                ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_GenCodeMismatch,
-                          "Genetic code conflict between CDS (code %d) and BioSource (code %d)", (int) cdsgencode, (int) biopgencode);
+              if (! vsp->seqSubmitParent) { /* suppress when validator run from tbl2asn */
+                if (plastid) {
+                  ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_GenCodeMismatch,
+                            "Genetic code conflict between CDS (code %d) and BioSource.genome biological context (%s) (uses code 11)", (int) cdsgencode, plastidtxt [biop->genome]);
+                } else {
+                  ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_GenCodeMismatch,
+                            "Genetic code conflict between CDS (code %d) and BioSource (code %d)", (int) cdsgencode, (int) biopgencode);
+                }
               }
             }
           }
@@ -8808,6 +9073,31 @@ static Boolean Loc_is_RefSeq (SeqLocPtr location)
   return FALSE;
 }
 
+static void CdConflictCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
+
+{
+  ByteStorePtr  bs;
+  BioseqPtr     bsp;
+  CharPtr       str1, str2;
+
+  if (sfp == NULL || vsp == NULL) return;
+
+  bsp = BioseqFindFromSeqLoc (sfp->product);
+  str1 = GetSequenceByBsp (bsp);
+  bs = TransTableTranslateCdRegion (NULL, sfp, FALSE, FALSE, TRUE);
+  str2 = (CharPtr) BSMerge (bs, NULL);
+  BSFree (bs);
+
+  if (str1 != NULL && str2 != NULL && StringCmp (str1, str2) == 0) {
+    ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_BadConflictFlag, "Coding region conflict flag should not be set");
+  } else {
+    ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_ConflictFlagSet, "Coding region conflict flag is set");
+  }
+
+  MemFree (str1);
+  MemFree (str2);
+}
+
 static CharPtr bypass_cds_trans_check [] = {
   "RNA editing",
   "reasons given in citation",
@@ -9765,26 +10055,20 @@ typedef struct grphitem
 }
 GrphItem       , PNTR GrphItemPtr;
 
-static Boolean GetGraphsProc (GatherObjectPtr gop)
+static void GetGraphsProc (SeqGraphPtr sgp, Pointer userdata)
 {
   GphGetPtr       ggp;
   GrphItemPtr     gip;
-  SeqGraphPtr     sgp;
 
-  if (gop == NULL || gop->itemtype != OBJ_SEQGRAPH)
-    return TRUE;
-  ggp = (GphGetPtr) gop->userdata;
-  sgp = (SeqGraphPtr) gop->dataptr;
-  if (ggp == NULL || sgp == NULL)
-    return TRUE;
+  ggp = (GphGetPtr) userdata;
+  if (ggp == NULL || sgp == NULL) return;
   /* only phrap or gap4 currently allowed */
   if (StringICmp (sgp->title, "Phrap Quality") == 0 || StringICmp (sgp->title, "Phred Quality") == 0 || StringICmp (sgp->title, "Gap4") == 0) {
     /* data type must be bytes */
     if (sgp->flags[2] == 3) {
       if (SeqIdIn (SeqLocId (sgp->loc), ggp->bsp->id)) {
         gip = (GrphItemPtr) MemNew (sizeof (GrphItem));
-        if (gip == NULL)
-          return TRUE;
+        if (gip == NULL) return;
         gip->sgp = sgp;
         gip->left = GetOffsetInBioseq (sgp->loc, ggp->bsp, SEQLOC_LEFT_END);
         gip->right = GetOffsetInBioseq (sgp->loc, ggp->bsp, SEQLOC_RIGHT_END);
@@ -9792,7 +10076,7 @@ static Boolean GetGraphsProc (GatherObjectPtr gop)
       }
     }
   }
-  return TRUE;
+  return;
 }
 
 static int LIBCALLBACK SortSeqGraphProc (VoidPtr ptr1, VoidPtr ptr2)
@@ -9826,17 +10110,14 @@ static int LIBCALLBACK SortSeqGraphProc (VoidPtr ptr1, VoidPtr ptr2)
 
 static ValNodePtr GetSeqGraphsOnBioseq (Uint2 entityID, BioseqPtr bsp)
 {
-  GphGetData      ggd;
-  GrphItemPtr     gip;
-  Int2            index;
-  Boolean         objMgrFilter[OBJ_MAX];
-  ValNodePtr      vnp;
+  GphGetData   ggd;
+  GrphItemPtr  gip;
+  Int2         index;
+  ValNodePtr   vnp;
 
   ggd.vnp = NULL;
   ggd.bsp = bsp;
-  MemSet ((Pointer) &objMgrFilter, 0, sizeof (objMgrFilter));
-  objMgrFilter[OBJ_SEQGRAPH] = TRUE;
-  GatherObjectsInEntity (entityID, 0, NULL, GetGraphsProc, (Pointer) &ggd, objMgrFilter);
+  VisitGraphsOnBsp (bsp, (Pointer) &ggd, GetGraphsProc);
   for (vnp = ggd.vnp, index = 1; vnp != NULL; vnp = vnp->next, index++) {
     gip = (GrphItemPtr) vnp->data.ptrvalue;
     if (gip != NULL) {
@@ -9863,10 +10144,10 @@ static Boolean NextLitLength (DeltaSeqPtr next, Int4Ptr lenp)
 
 static void ValidateGraphsOnBioseq (GatherContextPtr gcp)
 {
-  Byte            bases[400];
+  Byte            bases[400], scores [400];
   ByteStorePtr    bs;
   BioseqPtr       bsp;
-  Int2            ctr, i, val, index;
+  Int2            ctr, i, k, val, index, scount;
   Int4            curroffset = 0, gphlen = 0, seqlen = 0, slplen,
                   bslen, min = INT4_MAX, max = INT4_MIN, j, lastloc = -1,
                   NsWithScore, GapsWithScore, ACGTsWithoutScore, valsBelowMin,
@@ -10122,6 +10403,9 @@ static void ValidateGraphsOnBioseq (GatherContextPtr gcp)
     i = 0;
     residue = (Uint1) bases[i];
 
+    scount = (Int2) BSRead (bs, scores, sizeof (scores));
+    k = 0;
+
     NsWithScore = 0;
     GapsWithScore = 0;
     ACGTsWithoutScore = 0;
@@ -10133,7 +10417,19 @@ static void ValidateGraphsOnBioseq (GatherContextPtr gcp)
 
     while (residue != SEQPORT_EOF && j < sgp->numval) {
       if (IS_residue (residue)) {
-        val = (Int2) BSGetByte (bs);
+        /* val = (Int2) BSGetByte (bs); */
+        if (k >= scount) {
+          if (scount > 0) {
+            scount = (Int2) BSRead (bs, scores, sizeof (scores));
+          }
+          k = 0;
+        }
+        if (scount > 0) {
+          val = (Int2) scores [k];
+          k++;
+        } else {
+          val = 0;
+        }
         if (val < sgp->min.intvalue || val < 0) {
           valsBelowMin++;
         }
diff --git a/api/valid.h b/api/valid.h
index 8c210331..b15a5828 100644
--- a/api/valid.h
+++ b/api/valid.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 1/1/94
 *
-* $Revision: 6.10 $
+* $Revision: 6.12 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -39,6 +39,12 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: valid.h,v $
+* Revision 6.12  2003/12/02 15:37:37  kans
+* added vsp->seqSubmitParent for use by tbl2asn, which usually has a Seq-submit wrapper that is added on-the-fly and not indexed
+*
+* Revision 6.11  2003/11/14 18:07:17  kans
+* alignment parameters to find remote bsp, do seqhist assembly
+*
 * Revision 6.10  2003/03/05 18:47:45  ford
 * Added prototype for IsNuclAcc().
 *
@@ -151,8 +157,8 @@ typedef struct validstruct {
 	CharPtr errbuf;
 	Boolean patch_seq;             /* repair invalid sequence residues? */
 	Boolean non_ascii_chars;       /* non ascii chars found in read? */
-	Boolean suppress_no_pubs;
-	Boolean suppress_no_biosrc;
+	Boolean suppress_no_pubs;      /* internal use for no pub anywhere message */
+	Boolean suppress_no_biosrc;    /* internal use for no biosource anywhere message */
 	SpellCheckFunc spellfunc;
 	SpellCallBackFunc spellcallback;
 	GatherContextPtr gcp;          /* used for reporting the errors */
@@ -164,9 +170,12 @@ typedef struct validstruct {
 	Boolean suppressContext;       /* suppress context part of message */
 	Boolean validateAlignments;    /* call alignval test suite */
 	Boolean farIDsInAlignments;    /* fetch to get far IDs in alignments */
+	Boolean alignFindRemoteBsp;    /* do remote fetching in alignment validation */
+	Boolean doSeqHistAssembly;     /* do alignment validation in Seq-hist.assembly */
 	Boolean alwaysRequireIsoJTA;   /* force check for iso_jta */
 	Boolean farFetchCDSproducts;   /* lock CDS->products for CdTransCheck, if necessary */
 	Boolean validateIDSet;         /* look for gain or loss of general IDs on sequence update */
+	Boolean seqSubmitParent;       /* flag from tbl2asn to suppress no pub message */
 	TextFsaPtr sourceQualTags;     /* for detecting structured qual tags in notes */
 } ValidStruct, PNTR ValidStructPtr;
 
diff --git a/api/valid.msg b/api/valid.msg
index a7923795..bc138e16 100644
--- a/api/valid.msg
+++ b/api/valid.msg
@@ -159,6 +159,13 @@ $^   SeqLitGapLength0, 43
 A SeqLit component of a delta Bioseq can specify a gap, but it should not be a gap
 of 0 length.
 
+$^   TpaAssmeblyProblem, 44
+Third party annotation records should have a TpaAssembly user object and a
+Seq-hist.assembly alignment for the PRIMARY block.
+
+$^   SeqLocLength, 45
+A SeqLoc component of a delta Bioseq is suspiciously small.
+
 $$ SEQ_DESCR, 2
 
 $^   BioSourceMissing, 1
@@ -334,6 +341,9 @@ A feature location should refer to the accession or gi number, not a local or ge
 $^   ArchaicFeatureProduct, 14
 A feature product should refer to the accession or gi number, not a local or general ID.
 
+$^   GraphPackagingProblem, 15
+A graph should be packaged on its bioseq, or on a set containing the Bioseq.
+
 $$ SEQ_FEAT, 5
 
 $^   InvalidForType, 1
@@ -608,6 +618,17 @@ the inheritance by overlap.
 $^   UTRdoesNotAbutCDS, 66
 The 5'UTR and 3'UTR features should exactly abut the CDS feature.
 
+$^   BadConflictFlag, 67
+The coding region conflict flag is set, but the translated product is the
+same as the instantiated product Bioseq.
+
+$^   ConflictFlagSet, 68
+The coding region conflict flag is appropriately set, but this record should
+be brought to the attention of the source database for possible correction.
+
+$^   LocusTagProblem, 69
+A gene locus_tag should be a single token, with no spaces.
+
 $$ SEQ_ALIGN, 6
 
 $^   SeqIdProblem, 1
diff --git a/api/validerr.h b/api/validerr.h
index b4ced162..a6806594 100644
--- a/api/validerr.h
+++ b/api/validerr.h
@@ -45,6 +45,8 @@
 #define ERR_SEQ_INST_UnexpectedIdentifierChange  1,41
 #define ERR_SEQ_INST_InternalNsInSeqLit  1,42
 #define ERR_SEQ_INST_SeqLitGapLength0  1,43
+#define ERR_SEQ_INST_TpaAssmeblyProblem  1,44
+#define ERR_SEQ_INST_SeqLocLength  1,45
 #define ERR_SEQ_DESCR  2,0
 #define ERR_SEQ_DESCR_BioSourceMissing  2,1
 #define ERR_SEQ_DESCR_InvalidForType  2,2
@@ -93,6 +95,7 @@
 #define ERR_SEQ_PKG_InconsistentMolInfoBiomols  4,12
 #define ERR_SEQ_PKG_ArchaicFeatureLocation  4,13
 #define ERR_SEQ_PKG_ArchaicFeatureProduct  4,14
+#define ERR_SEQ_PKG_GraphPackagingProblem  4,15
 #define ERR_SEQ_FEAT  5,0
 #define ERR_SEQ_FEAT_InvalidForType  5,1
 #define ERR_SEQ_FEAT_PartialProblem  5,2
@@ -160,6 +163,9 @@
 #define ERR_SEQ_FEAT_BadTrnaAA  5,64
 #define ERR_SEQ_FEAT_OnlyGeneXrefs  5,65
 #define ERR_SEQ_FEAT_UTRdoesNotAbutCDS  5,66
+#define ERR_SEQ_FEAT_BadConflictFlag  5,67
+#define ERR_SEQ_FEAT_ConflictFlagSet  5,68
+#define ERR_SEQ_FEAT_LocusTagProblem  5,69
 #define ERR_SEQ_ALIGN  6,0
 #define ERR_SEQ_ALIGN_SeqIdProblem  6,1
 #define ERR_SEQ_ALIGN_StrandRev  6,2
diff --git a/asnlib/asn.h b/asnlib/asn.h
index aecb424e..1f3179a1 100644
--- a/asnlib/asn.h
+++ b/asnlib/asn.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 1/1/91
 *
-* $Revision: 6.10 $
+* $Revision: 6.11 $
 *
 * File Description:
 *   This header the interface to all the routines in the ASN.1 libraries
@@ -48,6 +48,9 @@
 * 02-24-94 Schuler     AsnTypeStringToHex moved here (from asntypes.h)
 *
 * $Log: asn.h,v $
+* Revision 6.11  2003/12/03 19:31:09  gouriano
+* Corrected DTD generation (a different approach)
+*
 * Revision 6.10  2003/09/15 16:16:32  kans
 * added AsnWriteEx, AsnTxtWriteEx, and AsnPrintStream
 *
@@ -390,6 +393,7 @@ NLM_EXTERN AsnTypePtr LIBCALL AsnTypeFind PROTO((AsnModulePtr amp, CharPtr str))
 #define AsnFind(x) AsnTypeFind(NULL,x)    /* find type (all) */
 NLM_EXTERN CharPtr LIBCALL AsnFindPrimName PROTO((AsnTypePtr atp));
 NLM_EXTERN AsnTypePtr LIBCALL AsnFindBaseType PROTO((AsnTypePtr atp));
+NLM_EXTERN AsnTypePtr LIBCALL AsnFindBaseTypeDTD PROTO((AsnTypePtr atp));
 NLM_EXTERN CharPtr LIBCALL AsnFindBaseName PROTO((AsnTypePtr atp));
 NLM_EXTERN Int2 LIBCALL AsnFindBaseIsa PROTO((AsnTypePtr atp));
 NLM_EXTERN AsnTypePtr LIBCALL AsnLinkType PROTO((AsnTypePtr type, AsnTypePtr localtype));
diff --git a/asnlib/asndebin.c b/asnlib/asndebin.c
index 124b32e4..86e1c4f6 100644
--- a/asnlib/asndebin.c
+++ b/asnlib/asndebin.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 3/4/91
 *
-* $Revision: 6.5 $
+* $Revision: 6.6 $
 *
 * File Description:
 *   Special binary form (BER) decoder for ASN.1
@@ -45,6 +45,9 @@
 * 08-01-93 Gish        AsnDeBinReadString calls MemGet instead of MemNew
 *
 * $Log: asndebin.c,v $
+* Revision 6.6  2003/12/10 15:41:19  sirotkin
+* As per toolkit RT request 15030485 and Jim Ostell, afety checks after ato2=AsnFindBaseIsa(atp) were added.
+*
 * Revision 6.5  2002/10/09 19:16:31  ivanov
 * Fixed buffer overrun in the AsnDeBinReadReal()
 *
@@ -118,9 +121,15 @@ NLM_EXTERN AsnTypePtr LIBCALL  AsnBinReadId (AsnIoPtr aip, AsnTypePtr atp)
 
 		if (used == ASNDEBIN_EOF)      /* end of file */
 			return NULL;
+                /* see RT toolbox ticket 15030485 for the below fix */
 
 		atp2 = AsnFindBaseType(atp);   /* find the base type */
-		if (atp2 == NULL) return NULL;
+		if (atp2 == NULL)
+			return atp2;
+		if (atp2->type == NULL)
+			return atp2->type;
+		isa = atp2->type->isa;
+
 
 		if (atp2->type->isa != CHOICE_TYPE)
 		{
diff --git a/asnlib/asnenbin.c b/asnlib/asnenbin.c
index 1c34be40..afcf1432 100644
--- a/asnlib/asnenbin.c
+++ b/asnlib/asnenbin.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 3/4/91
 *
-* $Revision: 6.5 $
+* $Revision: 6.6 $
 *
 * File Description:
 *   Special binary (BER) encoder for ASN.1
@@ -42,6 +42,9 @@
 * 04-20-93 Schuler     LIBCALL calling convention
 *
 * $Log: asnenbin.c,v $
+* Revision 6.6  2003/11/07 20:57:02  beloslyu
+* fix the c++ style comments to a C ones
+*
 * Revision 6.5  2003/08/01 16:55:24  gouriano
 * workaround MSVC++.NET optimization bug
 *
@@ -360,7 +363,7 @@ NLM_EXTERN void AsnEnBinInteger (Int4 theInt, AsnIoPtr aip, AsnTypePtr atp)
 	{
 		for (i = 0; i < 3; i++)
 			octets[i] = octets[i+1];
-// dirty workaround of an optimization bug of MSVC++.NET compiler
+/* dirty workaround of an optimization bug of MSVC++.NET compiler */
 #if defined(_MSC_VER) 
 #  if _MSC_VER < 1300
 		octets[3] = 0;
@@ -424,7 +427,7 @@ NLM_EXTERN void AsnEnBinBigInt (Int8 theInt, AsnIoPtr aip, AsnTypePtr atp)
 	{
 		for (i = 0; i < 7; i++)
 			octets[i] = octets[i+1];
-// dirty workaround of an optimization bug of MSVC++.NET compiler
+/* dirty workaround of an optimization bug of MSVC++.NET compiler */
 #if defined(_MSC_VER) 
 #  if _MSC_VER < 1300
 		octets[7] = 0;
diff --git a/asnlib/asnprint.c b/asnlib/asnprint.c
index 5328c5c4..5d142c66 100644
--- a/asnlib/asnprint.c
+++ b/asnlib/asnprint.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 3/4/91
 *
-* $Revision: 6.18 $
+* $Revision: 6.20 $
 *
 * File Description:
 *   Routines for printing ASN.1 value notation (text) messages and
@@ -42,6 +42,12 @@
 * 3/4/91   Kans        Stricter typecasting for GNU C and C++
 *
 * $Log: asnprint.c,v $
+* Revision 6.20  2003/12/03 19:31:09  gouriano
+* Corrected DTD generation (a different approach)
+*
+* Revision 6.19  2003/12/02 19:52:48  gouriano
+* Corrected DTD generation
+*
 * Revision 6.18  2003/09/15 16:16:32  kans
 * added AsnWriteEx, AsnTxtWriteEx, and AsnPrintStream
 *
@@ -1901,7 +1907,7 @@ static void AsnXMLElementStart(AsnTypePtr atp, AsnIoPtr aip)
 
 	AsnPrintString(GetXMLname(atp), aip);
 
-	atp2 = AsnFindBaseType(atp);
+	atp2 = AsnFindBaseTypeDTD(atp);
 	if (atp2 == atp)
 	{
 		if ((isa == ENUM_TYPE) || (isa == BOOLEAN_TYPE) ||
@@ -2351,7 +2357,8 @@ static Boolean AsnPrintTypeXML (AsnTypePtr atp, AsnIoPtr aip)
 				if ((atp->optional) || (atp->hasdefault))
 					repeat = "*";
 				else
-					repeat = "+";
+					repeat = "*";
+//					repeat = "+";
 				AsnXMLElementAdd(NULL, atp->branch, repeat, aip, FALSE);
 				break;
 			case INTEGER_TYPE:
@@ -2483,7 +2490,7 @@ static Boolean AsnPrintTypeXML (AsnTypePtr atp, AsnIoPtr aip)
 	}
 	else  /* primitive.. all text */
 	{
-		atp2 = AsnFindBaseType(atp);
+		atp2 = AsnFindBaseTypeDTD(atp);
 		if (atp2 != NULL)
 		{
 			isa = AsnFindBaseIsa(atp);
diff --git a/asnlib/asntypes.c b/asnlib/asntypes.c
index 11015913..cfce072c 100644
--- a/asnlib/asntypes.c
+++ b/asnlib/asntypes.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 3/4/91
 *
-* $Revision: 6.6 $
+* $Revision: 6.9 $
 *
 * File Description:
 *   Routines to deal with internal operations on AsnType objects.
@@ -43,6 +43,15 @@
 * 02-24-94 Schuler     Make AsnTypeStringToHex LIBCALL too
 *
 * $Log: asntypes.c,v $
+* Revision 6.9  2003/12/03 19:31:09  gouriano
+* Corrected DTD generation (a different approach)
+*
+* Revision 6.8  2003/12/02 21:40:17  gouriano
+* Revert back to rev 6.6
+*
+* Revision 6.7  2003/12/02 19:52:49  gouriano
+* Corrected DTD generation
+*
 * Revision 6.6  2000/07/25 20:30:58  ostell
 * added support for printing multiple ASN.1 modules as multiple XML DTD and .mod files
 *
@@ -233,6 +242,21 @@ NLM_EXTERN AsnTypePtr LIBCALL AsnFindBaseType (AsnTypePtr atp)
 	return atp;
 }
 
+NLM_EXTERN AsnTypePtr LIBCALL AsnFindBaseTypeDTD (AsnTypePtr atp)
+{
+	if (atp == NULL) return NULL;
+
+	if (atp->type == NULL) return NULL;
+
+	if (! ISA_BASETYPE(atp->type->isa))
+	{
+		atp = atp->type;
+		if (atp->type == NULL)   /* not found */
+			return atp;
+	}
+	return atp;
+}
+
 /*****************************************************************************
 *
 *   Int2 AsnFindBaseIsa(atp)
@@ -906,7 +930,7 @@ static void AddXMLname(AsnTypePtr atp, AsnTypePtr PNTR typestack, Int2 stackptr)
 			isa = AsnFindBaseIsa(atp2);
 			if ((doitem) && ((isa == SEQOF_TYPE) || (isa == SETOF_TYPE)))
 			{
-				atp2 = AsnFindBaseType(atp);
+				atp2 = AsnFindBaseTypeDTD(atp);
 				if (atp2 != NULL)
 				{
 				if (atp2->name == NULL)
@@ -957,12 +981,12 @@ static void AddXMLname(AsnTypePtr atp, AsnTypePtr PNTR typestack, Int2 stackptr)
 
 				for (i = (stackptr - 1); (i >= 0) && (! found); i--)
 				{
-					atp2 = AsnFindBaseType(typestack[i]);
+					atp2 = AsnFindBaseTypeDTD(typestack[i]);
 					if ((atp2 != NULL) && (atp2->name != NULL) && (IS_UPPER(*(atp2->name))))
 					{
 						while (i < stackptr)
 						{
-							atp2 = AsnFindBaseType(typestack[i]);
+							atp2 = AsnFindBaseTypeDTD(typestack[i]);
 							if (atp2->name == NULL)
 								tmp = StringMove(tmp, "E");
 							else
@@ -991,7 +1015,7 @@ static void AddXMLname(AsnTypePtr atp, AsnTypePtr PNTR typestack, Int2 stackptr)
 		}
 	}
 
-	atp2 = AsnFindBaseType(atp);
+	atp2 = AsnFindBaseTypeDTD(atp);
 	if ((! atp->imported) && (atp2 != NULL) && (atp2->type != NULL))
 	{
 		isa = atp2->type->isa;
diff --git a/biostruc/cdd/cdd.asn b/biostruc/cdd/cdd.asn
index 83b43ed0..b426377b 100644
--- a/biostruc/cdd/cdd.asn
+++ b/biostruc/cdd/cdd.asn
@@ -1,4 +1,4 @@
---$Revision: 1.18 $
+--$Revision: 1.20 $
 --**********************************************************************
 --
 --  Definitions for CDD's 
@@ -22,7 +22,7 @@ NCBI-Cdd DEFINITIONS ::=
 
 BEGIN
 
-EXPORTS  Cdd-id, Cdd-id-set, Cdd, Cdd-set, Cdd-tree, Cdd-tree-set;
+EXPORTS  Cdd-id, Cdd-id-set, Cdd, Cdd-set, Cdd-tree, Cdd-tree-set, Cdd-pref-nodes;
 
 IMPORTS  Date                    FROM NCBI-General
          Pub                     FROM NCBI-Pub
@@ -39,6 +39,28 @@ IMPORTS  Date                    FROM NCBI-General
          Cn3d-style-dictionary,
          Cn3d-user-annotations   FROM NCBI-Cn3d
          Score-matrix-parameters FROM NCBI-ScoreMat;
+         
+-- dealing with lists of preferred tax-nodes 
+
+Cdd-org-ref ::= SEQUENCE {
+  reference   Org-ref,
+  active      BOOLEAN DEFAULT TRUE 
+}
+Cdd-org-ref-set ::= SET OF Cdd-org-ref
+
+Cdd-pref-node-descr ::= CHOICE {
+  create-date      Date,
+  description      VisibleString
+}
+
+Cdd-pref-node-descr-set ::= SET OF Cdd-pref-node-descr
+
+Cdd-pref-nodes ::= SEQUENCE {
+   preferred-nodes Cdd-org-ref-set,
+   model-organisms Cdd-org-ref-set OPTIONAL,
+   optional-nodes  Cdd-org-ref-set OPTIONAL,
+   description     Cdd-pref-node-descr-set OPTIONAL
+}        
 
 -- Cdd's should not exist without a unique accession, but alternative id's may
 -- be present as well. It is conceivable that a CD which is created as a merged
@@ -272,19 +294,18 @@ Align-annot-set ::= SEQUENCE OF Align-annot
 -- deletions after duplication and do not need a special case for fissions.
 
 Domain-parent ::= SEQUENCE {
+
+  parent-type    INTEGER { classical           (0), -- the classification of parent child relations
+                           fusion              (1),
+                           deletion            (2),
+                           permutation         (3),
+                           other               (255) },
   parentid       Cdd-id,                -- identify the section parent by accession
   seqannot       Seq-annot OPTIONAL     -- contains the sequence alignment linking
                                         -- CD alignment models, should align the 
                                         -- masters/representatives of each CD
 }
 
-Lineage-info ::= CHOICE {
-  simpleparent                 Domain-parent,
-  complexparents SEQUENCE {
-    fusionparents  SEQUENCE OF Domain-parent OPTIONAL,
-    deletionparent SEQUENCE OF Domain-parent OPTIONAL
-  }
-}
 
 -- record sequence trees generated by a suitable algorithm.
 
@@ -385,7 +406,7 @@ Cdd ::= SEQUENCE {
   alignannot    Align-annot-set OPTIONAL,           -- alignment annotation
   style-dictionary Cn3d-style-dictionary OPTIONAL,  -- record rendering styles
   user-annotations Cn3d-user-annotations OPTIONAL,  -- user annotations in Cn3D
-  ancestors     Lineage-info             OPTIONAL,
+  ancestors     SEQUENCE OF Domain-parent OPTIONAL, -- list of parents
   scoreparams   Score-matrix-parameters  OPTIONAL,
   seqtree       Sequence-tree            OPTIONAL
 }
diff --git a/biostruc/cdd/cdd.h b/biostruc/cdd/cdd.h
index 315a0384..35b23ab0 100644
--- a/biostruc/cdd/cdd.h
+++ b/biostruc/cdd/cdd.h
@@ -9,8 +9,8 @@
 #include <asn.h>
 #endif
 
-static char * asnfilename = "cdd.h17";
-static AsnValxNode avnx[64] = {
+static char * asnfilename = "cdd.h19";
+static AsnValxNode avnx[70] = {
     {20,"unassigned" ,0,0.0,&avnx[1] } ,
     {20,"finished-ok" ,1,0.0,&avnx[2] } ,
     {20,"pending-release" ,2,0.0,&avnx[3] } ,
@@ -51,37 +51,43 @@ static AsnValxNode avnx[64] = {
     {20,"demoted" ,51,0.0,&avnx[38] } ,
     {20,"demoted-3d" ,52,0.0,&avnx[39] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unassigned" ,0,0.0,&avnx[41] } ,
-    {20,"percent-id" ,1,0.0,&avnx[42] } ,
-    {20,"kimura-corrected" ,2,0.0,&avnx[43] } ,
-    {20,"aligned-score" ,3,0.0,&avnx[44] } ,
-    {20,"aligned-score-ext" ,4,0.0,&avnx[45] } ,
-    {20,"aligned-score-filled" ,5,0.0,&avnx[46] } ,
-    {20,"blast-footprint" ,6,0.0,&avnx[47] } ,
-    {20,"blast-full" ,7,0.0,&avnx[48] } ,
+    {20,"classical" ,0,0.0,&avnx[41] } ,
+    {20,"fusion" ,1,0.0,&avnx[42] } ,
+    {20,"deletion" ,2,0.0,&avnx[43] } ,
+    {20,"permutation" ,3,0.0,&avnx[44] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unassigned" ,0,0.0,&avnx[50] } ,
-    {20,"single-linkage" ,1,0.0,&avnx[51] } ,
-    {20,"neighbor-joining" ,2,0.0,&avnx[52] } ,
-    {20,"fast-minimum-evolution" ,3,0.0,&avnx[53] } ,
+    {20,"unassigned" ,0,0.0,&avnx[46] } ,
+    {20,"percent-id" ,1,0.0,&avnx[47] } ,
+    {20,"kimura-corrected" ,2,0.0,&avnx[48] } ,
+    {20,"aligned-score" ,3,0.0,&avnx[49] } ,
+    {20,"aligned-score-ext" ,4,0.0,&avnx[50] } ,
+    {20,"aligned-score-filled" ,5,0.0,&avnx[51] } ,
+    {20,"blast-footprint" ,6,0.0,&avnx[52] } ,
+    {20,"blast-full" ,7,0.0,&avnx[53] } ,
     {20,"other" ,255,0.0,NULL } ,
     {20,"unassigned" ,0,0.0,&avnx[55] } ,
-    {20,"blosum45" ,1,0.0,&avnx[56] } ,
-    {20,"blosum62" ,2,0.0,&avnx[57] } ,
-    {20,"blosum80" ,3,0.0,&avnx[58] } ,
-    {20,"pam30" ,4,0.0,&avnx[59] } ,
-    {20,"pam70" ,5,0.0,&avnx[60] } ,
-    {20,"pam250" ,6,0.0,&avnx[61] } ,
+    {20,"single-linkage" ,1,0.0,&avnx[56] } ,
+    {20,"neighbor-joining" ,2,0.0,&avnx[57] } ,
+    {20,"fast-minimum-evolution" ,3,0.0,&avnx[58] } ,
     {20,"other" ,255,0.0,NULL } ,
+    {20,"unassigned" ,0,0.0,&avnx[60] } ,
+    {20,"blosum45" ,1,0.0,&avnx[61] } ,
+    {20,"blosum62" ,2,0.0,&avnx[62] } ,
+    {20,"blosum80" ,3,0.0,&avnx[63] } ,
+    {20,"pam30" ,4,0.0,&avnx[64] } ,
+    {20,"pam70" ,5,0.0,&avnx[65] } ,
+    {20,"pam250" ,6,0.0,&avnx[66] } ,
+    {20,"other" ,255,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
-    {2,NULL,0,0.0,NULL } };
+    {2,NULL,1,0.0,NULL } };
 
-static AsnType atx[184] = {
+static AsnType atx[194] = {
   {401, "Cdd-id" ,1,0,0,0,0,1,0,0,NULL,&atx[11],&atx[1],0,&atx[12]} ,
   {0, "uid" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[3]} ,
   {302, "INTEGER" ,0,2,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "gid" ,128,1,0,0,0,0,0,0,NULL,&atx[4],NULL,0,NULL} ,
-  {422, "Global-id" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[5],0,&atx[38]} ,
+  {427, "Global-id" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[5],0,&atx[38]} ,
   {0, "accession" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[7]} ,
   {323, "VisibleString" ,0,26,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "release" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[8]} ,
@@ -92,22 +98,22 @@ static AsnType atx[184] = {
   {402, "Cdd-id-set" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[13],0,&atx[15]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,NULL} ,
   {312, "SEQUENCE OF" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {403, "Cdd" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[16],0,&atx[172]} ,
+  {403, "Cdd" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[16],0,&atx[167]} ,
   {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[17]} ,
   {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[18]} ,
   {0, "description" ,128,2,0,1,0,0,0,0,NULL,&atx[19],NULL,0,&atx[54]} ,
-  {426, "Cdd-descr-set" ,1,0,0,0,0,0,0,0,NULL,&atx[53],&atx[20],0,&atx[66]} ,
+  {431, "Cdd-descr-set" ,1,0,0,0,0,0,0,0,NULL,&atx[53],&atx[20],0,&atx[66]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[21],NULL,0,NULL} ,
-  {425, "Cdd-descr" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[22],0,&atx[19]} ,
+  {430, "Cdd-descr" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[22],0,&atx[19]} ,
   {0, "othername" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[23]} ,
   {0, "category" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[24]} ,
   {0, "comment" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[25]} ,
   {0, "reference" ,128,3,0,0,0,0,0,0,NULL,&atx[26],NULL,0,&atx[27]} ,
-  {408, "Pub" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[58]} ,
+  {409, "Pub" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[58]} ,
   {0, "create-date" ,128,4,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[29]} ,
-  {407, "Date" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[26]} ,
+  {408, "Date" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[26]} ,
   {0, "tax-source" ,128,5,0,0,0,0,0,0,NULL,&atx[30],NULL,0,&atx[31]} ,
-  {413, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[106]} ,
+  {414, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[106]} ,
   {0, "source" ,128,6,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[32]} ,
   {0, "status" ,128,7,0,0,0,0,0,0,NULL,&atx[2],&avnx[0],0,&atx[33]} ,
   {0, "update-date" ,128,8,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[34]} ,
@@ -115,16 +121,16 @@ static AsnType atx[184] = {
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
   {0, "source-id" ,128,10,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[37]} ,
   {0, "repeats" ,128,11,0,0,0,0,0,0,NULL,&atx[38],NULL,0,&atx[43]} ,
-  {423, "Cdd-repeat" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[39],0,&atx[47]} ,
+  {428, "Cdd-repeat" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[39],0,&atx[47]} ,
   {0, "count" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[40]} ,
   {0, "location" ,128,1,0,1,0,0,0,0,NULL,&atx[41],NULL,0,&atx[42]} ,
-  {416, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[122]} ,
+  {417, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[122]} ,
   {0, "avglen" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {0, "old-root" ,128,12,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[44]} ,
   {0, "curation-status" ,128,13,0,0,0,0,0,0,NULL,&atx[2],&avnx[10],0,&atx[45]} ,
   {0, "readonly-status" ,128,14,0,0,0,0,0,0,NULL,&atx[2],&avnx[20],0,&atx[46]} ,
   {0, "book-ref" ,128,15,0,0,0,0,0,0,NULL,&atx[47],NULL,0,NULL} ,
-  {424, "Cdd-book-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[48],0,&atx[21]} ,
+  {429, "Cdd-book-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[48],0,&atx[21]} ,
   {0, "bookname" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[49]} ,
   {0, "textelement" ,128,1,0,0,0,0,0,0,NULL,&atx[50],&avnx[24],0,&atx[51]} ,
   {310, "ENUMERATED" ,0,10,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
@@ -133,17 +139,17 @@ static AsnType atx[184] = {
   {314, "SET OF" ,0,17,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "seqannot" ,128,3,0,1,0,0,0,0,NULL,&atx[14],&atx[55],0,&atx[57]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[56],NULL,0,NULL} ,
-  {411, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[60]} ,
+  {412, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[60]} ,
   {0, "features" ,128,4,0,1,0,0,0,0,NULL,&atx[58],NULL,0,&atx[59]} ,
-  {409, "Biostruc-annot-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[64]} ,
+  {410, "Biostruc-annot-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[64]} ,
   {0, "sequences" ,128,5,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[61]} ,
-  {412, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[30]} ,
+  {413, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[30]} ,
   {0, "profile-range" ,128,6,0,1,0,0,0,0,NULL,&atx[62],NULL,0,&atx[63]} ,
-  {415, "Seq-interval" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[41]} ,
+  {416, "Seq-interval" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[41]} ,
   {0, "trunc-master" ,128,7,0,1,0,0,0,0,NULL,&atx[64],NULL,0,&atx[65]} ,
-  {410, "Bioseq" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[56]} ,
+  {411, "Bioseq" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[56]} ,
   {0, "posfreq" ,128,8,0,1,0,0,0,0,NULL,&atx[66],NULL,0,&atx[74]} ,
-  {427, "Matrix" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[67],0,&atx[76]} ,
+  {432, "Matrix" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[67],0,&atx[76]} ,
   {0, "ncolumns" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[68]} ,
   {0, "nrows" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[69]} ,
   {0, "row-labels" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[70],0,&atx[71]} ,
@@ -153,10 +159,10 @@ static AsnType atx[184] = {
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {0, "scoremat" ,128,9,0,1,0,0,0,0,NULL,&atx[66],NULL,0,&atx[75]} ,
   {0, "distance" ,128,10,0,1,0,0,0,0,NULL,&atx[76],NULL,0,&atx[82]} ,
-  {428, "Triangle" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[77],0,&atx[91]} ,
+  {433, "Triangle" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[77],0,&atx[91]} ,
   {0, "nelements" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[78]} ,
   {0, "scores" ,128,1,0,1,0,0,0,0,NULL,&atx[79],NULL,0,&atx[80]} ,
-  {418, "Score-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[125]} ,
+  {419, "Score-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[125]} ,
   {0, "div-ranks" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[81],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {0, "parent" ,128,11,0,1,0,0,0,0,NULL,&atx[0],NULL,0,&atx[83]} ,
@@ -165,10 +171,10 @@ static AsnType atx[184] = {
   {0, "neighbors" ,128,14,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[86]} ,
   {0, "pending" ,128,15,0,1,0,0,0,0,NULL,&atx[14],&atx[87],0,&atx[99]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[88],NULL,0,NULL} ,
-  {430, "Update-align" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[89],0,&atx[101]} ,
+  {435, "Update-align" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[89],0,&atx[101]} ,
   {0, "description" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[90],0,&atx[97]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[91],NULL,0,NULL} ,
-  {429, "Update-comment" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[92],0,&atx[88]} ,
+  {434, "Update-comment" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[92],0,&atx[88]} ,
   {0, "comment" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[93]} ,
   {0, "addthis" ,128,1,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[94]} ,
   {0, "replaces" ,128,2,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[95]} ,
@@ -178,92 +184,102 @@ static AsnType atx[184] = {
   {0, "type" ,128,2,0,0,0,0,0,0,NULL,&atx[2],&avnx[34],0,NULL} ,
   {0, "rejects" ,128,16,0,1,0,0,0,0,NULL,&atx[14],&atx[100],0,&atx[107]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[101],NULL,0,NULL} ,
-  {431, "Reject-id" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[102],0,&atx[117]} ,
+  {436, "Reject-id" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[102],0,&atx[117]} ,
   {0, "description" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[103],0,&atx[104]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[91],NULL,0,NULL} ,
   {0, "ids" ,128,1,0,0,0,0,0,0,NULL,&atx[53],&atx[105],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[106],NULL,0,NULL} ,
-  {414, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[62]} ,
+  {415, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[62]} ,
   {0, "master3d" ,128,17,0,1,0,0,0,0,NULL,&atx[53],&atx[108],0,&atx[109]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[106],NULL,0,NULL} ,
   {0, "alignannot" ,128,18,0,1,0,0,0,0,NULL,&atx[110],NULL,0,&atx[124]} ,
-  {434, "Align-annot-set" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[111],0,&atx[131]} ,
+  {439, "Align-annot-set" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[111],0,&atx[130]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[112],NULL,0,NULL} ,
-  {433, "Align-annot" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[113],0,&atx[110]} ,
+  {438, "Align-annot" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[113],0,&atx[110]} ,
   {0, "location" ,128,0,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[114]} ,
   {0, "description" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[115]} ,
   {0, "evidence" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[116],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[117],NULL,0,NULL} ,
-  {432, "Feature-evidence" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[118],0,&atx[112]} ,
+  {437, "Feature-evidence" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[118],0,&atx[112]} ,
   {0, "comment" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[119]} ,
   {0, "reference" ,128,1,0,0,0,0,0,0,NULL,&atx[26],NULL,0,&atx[120]} ,
   {0, "bsannot" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[121]} ,
   {0, "seqfeat" ,128,3,0,0,0,0,0,0,NULL,&atx[122],NULL,0,&atx[123]} ,
-  {417, "Seq-feat" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[79]} ,
+  {418, "Seq-feat" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[79]} ,
   {0, "book-ref" ,128,4,0,0,0,0,0,0,NULL,&atx[47],NULL,0,NULL} ,
   {0, "style-dictionary" ,128,19,0,1,0,0,0,0,NULL,&atx[125],NULL,0,&atx[126]} ,
-  {419, "Cn3d-style-dictionary" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[127]} ,
+  {420, "Cn3d-style-dictionary" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[127]} ,
   {0, "user-annotations" ,128,20,0,1,0,0,0,0,NULL,&atx[127],NULL,0,&atx[128]} ,
-  {420, "Cn3d-user-annotations" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[140]} ,
-  {0, "ancestors" ,128,21,0,1,0,0,0,0,NULL,&atx[129],NULL,0,&atx[139]} ,
-  {436, "Lineage-info" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[130],0,&atx[142]} ,
-  {0, "simpleparent" ,128,0,0,0,0,0,0,0,NULL,&atx[131],NULL,0,&atx[134]} ,
-  {435, "Domain-parent" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[132],0,&atx[129]} ,
-  {0, "parentid" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[133]} ,
-  {0, "seqannot" ,128,1,0,1,0,0,0,0,NULL,&atx[56],NULL,0,NULL} ,
-  {0, "complexparents" ,128,1,0,0,0,0,0,0,NULL,&atx[10],&atx[135],0,NULL} ,
-  {0, "fusionparents" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[136],0,&atx[137]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[131],NULL,0,NULL} ,
-  {0, "deletionparent" ,128,1,0,1,0,0,0,0,NULL,&atx[14],&atx[138],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[131],NULL,0,NULL} ,
-  {0, "scoreparams" ,128,22,0,1,0,0,0,0,NULL,&atx[140],NULL,0,&atx[141]} ,
-  {421, "Score-matrix-parameters" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[4]} ,
-  {0, "seqtree" ,128,23,0,1,0,0,0,0,NULL,&atx[142],NULL,0,NULL} ,
-  {437, "Sequence-tree" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[143],0,&atx[145]} ,
-  {0, "cdAccession" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[144]} ,
-  {0, "algorithm" ,128,1,0,0,0,0,0,0,NULL,&atx[145],NULL,0,&atx[154]} ,
-  {438, "Algorithm-type" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[146],0,&atx[157]} ,
-  {0, "scoring-Scheme" ,128,0,0,0,0,0,0,0,NULL,&atx[2],&avnx[40],0,&atx[147]} ,
-  {0, "clustering-Method" ,128,1,0,0,0,0,0,0,NULL,&atx[2],&avnx[49],0,&atx[148]} ,
-  {0, "score-Matrix" ,128,2,0,1,0,0,0,0,NULL,&atx[2],&avnx[54],0,&atx[149]} ,
-  {0, "gapOpen" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[150]} ,
-  {0, "gapExtend" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[151]} ,
-  {0, "gapScaleFactor" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[152]} ,
-  {0, "nTerminalExt" ,128,6,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[153]} ,
+  {421, "Cn3d-user-annotations" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[135]} ,
+  {0, "ancestors" ,128,21,0,1,0,0,0,0,NULL,&atx[14],&atx[129],0,&atx[134]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[130],NULL,0,NULL} ,
+  {440, "Domain-parent" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[131],0,&atx[137]} ,
+  {0, "parent-type" ,128,0,0,0,0,0,0,0,NULL,&atx[2],&avnx[40],0,&atx[132]} ,
+  {0, "parentid" ,128,1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[133]} ,
+  {0, "seqannot" ,128,2,0,1,0,0,0,0,NULL,&atx[56],NULL,0,NULL} ,
+  {0, "scoreparams" ,128,22,0,1,0,0,0,0,NULL,&atx[135],NULL,0,&atx[136]} ,
+  {422, "Score-matrix-parameters" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[183]} ,
+  {0, "seqtree" ,128,23,0,1,0,0,0,0,NULL,&atx[137],NULL,0,NULL} ,
+  {441, "Sequence-tree" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[138],0,&atx[140]} ,
+  {0, "cdAccession" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[139]} ,
+  {0, "algorithm" ,128,1,0,0,0,0,0,0,NULL,&atx[140],NULL,0,&atx[149]} ,
+  {442, "Algorithm-type" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[141],0,&atx[152]} ,
+  {0, "scoring-Scheme" ,128,0,0,0,0,0,0,0,NULL,&atx[2],&avnx[45],0,&atx[142]} ,
+  {0, "clustering-Method" ,128,1,0,0,0,0,0,0,NULL,&atx[2],&avnx[54],0,&atx[143]} ,
+  {0, "score-Matrix" ,128,2,0,1,0,0,0,0,NULL,&atx[2],&avnx[59],0,&atx[144]} ,
+  {0, "gapOpen" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[145]} ,
+  {0, "gapExtend" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[146]} ,
+  {0, "gapScaleFactor" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[147]} ,
+  {0, "nTerminalExt" ,128,6,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[148]} ,
   {0, "cTerminalExt" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "isAnnotated" ,128,2,0,0,1,0,0,0,&avnx[62],&atx[155],NULL,0,&atx[156]} ,
+  {0, "isAnnotated" ,128,2,0,0,1,0,0,0,&avnx[67],&atx[150],NULL,0,&atx[151]} ,
   {301, "BOOLEAN" ,0,1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {0, "root" ,128,3,0,0,0,0,0,0,NULL,&atx[157],NULL,0,NULL} ,
-  {439, "SeqTree-node" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[158],0,&atx[169]} ,
-  {0, "isAnnotated" ,128,0,0,0,1,0,0,0,&avnx[63],&atx[155],NULL,0,&atx[159]} ,
-  {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[160]} ,
-  {0, "distance" ,128,2,0,1,0,0,0,0,NULL,&atx[161],NULL,0,&atx[162]} ,
+  {0, "root" ,128,3,0,0,0,0,0,0,NULL,&atx[152],NULL,0,NULL} ,
+  {443, "SeqTree-node" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[153],0,&atx[164]} ,
+  {0, "isAnnotated" ,128,0,0,0,1,0,0,0,&avnx[68],&atx[150],NULL,0,&atx[154]} ,
+  {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[155]} ,
+  {0, "distance" ,128,2,0,1,0,0,0,0,NULL,&atx[156],NULL,0,&atx[157]} ,
   {309, "REAL" ,0,9,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {0, "children" ,128,3,0,0,0,0,0,0,NULL,&atx[11],&atx[163],0,&atx[168]} ,
-  {0, "children" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[164],0,&atx[165]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[157],NULL,0,NULL} ,
-  {0, "footprint" ,128,1,0,0,0,0,0,0,NULL,&atx[10],&atx[166],0,NULL} ,
-  {0, "seqRange" ,128,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[167]} ,
+  {0, "children" ,128,3,0,0,0,0,0,0,NULL,&atx[11],&atx[158],0,&atx[163]} ,
+  {0, "children" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[159],0,&atx[160]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[152],NULL,0,NULL} ,
+  {0, "footprint" ,128,1,0,0,0,0,0,0,NULL,&atx[10],&atx[161],0,NULL} ,
+  {0, "seqRange" ,128,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[162]} ,
   {0, "rowId" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "annotation" ,128,4,0,1,0,0,0,0,NULL,&atx[169],NULL,0,NULL} ,
-  {440, "Node-annotation" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[170],0,NULL} ,
-  {0, "presentInChildCD" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[171]} ,
+  {0, "annotation" ,128,4,0,1,0,0,0,0,NULL,&atx[164],NULL,0,NULL} ,
+  {444, "Node-annotation" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[165],0,NULL} ,
+  {0, "presentInChildCD" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[166]} ,
   {0, "note" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {404, "Cdd-set" ,1,0,0,0,0,1,0,0,NULL,&atx[53],&atx[173],0,&atx[174]} ,
+  {404, "Cdd-set" ,1,0,0,0,0,1,0,0,NULL,&atx[53],&atx[168],0,&atx[169]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[15],NULL,0,NULL} ,
-  {405, "Cdd-tree" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[175],0,&atx[182]} ,
-  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[176]} ,
-  {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[177]} ,
-  {0, "description" ,128,2,0,1,0,0,0,0,NULL,&atx[19],NULL,0,&atx[178]} ,
-  {0, "parent" ,128,3,0,1,0,0,0,0,NULL,&atx[0],NULL,0,&atx[179]} ,
-  {0, "children" ,128,4,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[180]} ,
-  {0, "siblings" ,128,5,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[181]} ,
+  {405, "Cdd-tree" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[170],0,&atx[177]} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[171]} ,
+  {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[172]} ,
+  {0, "description" ,128,2,0,1,0,0,0,0,NULL,&atx[19],NULL,0,&atx[173]} ,
+  {0, "parent" ,128,3,0,1,0,0,0,0,NULL,&atx[0],NULL,0,&atx[174]} ,
+  {0, "children" ,128,4,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[175]} ,
+  {0, "siblings" ,128,5,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[176]} ,
   {0, "neighbors" ,128,6,0,1,0,0,0,0,NULL,&atx[12],NULL,0,NULL} ,
-  {406, "Cdd-tree-set" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[183],0,&atx[28]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[174],NULL,0,NULL} };
+  {406, "Cdd-tree-set" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[178],0,&atx[179]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[169],NULL,0,NULL} ,
+  {407, "Cdd-pref-nodes" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[180],0,&atx[28]} ,
+  {0, "preferred-nodes" ,128,0,0,0,0,0,0,0,NULL,&atx[181],NULL,0,&atx[186]} ,
+  {424, "Cdd-org-ref-set" ,1,0,0,0,0,0,0,0,NULL,&atx[53],&atx[182],0,&atx[191]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[183],NULL,0,NULL} ,
+  {423, "Cdd-org-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[184],0,&atx[181]} ,
+  {0, "reference" ,128,0,0,0,0,0,0,0,NULL,&atx[30],NULL,0,&atx[185]} ,
+  {0, "active" ,128,1,0,0,1,0,0,0,&avnx[69],&atx[150],NULL,0,NULL} ,
+  {0, "model-organisms" ,128,1,0,1,0,0,0,0,NULL,&atx[181],NULL,0,&atx[187]} ,
+  {0, "optional-nodes" ,128,2,0,1,0,0,0,0,NULL,&atx[181],NULL,0,&atx[188]} ,
+  {0, "description" ,128,3,0,1,0,0,0,0,NULL,&atx[189],NULL,0,NULL} ,
+  {426, "Cdd-pref-node-descr-set" ,1,0,0,0,0,0,0,0,NULL,&atx[53],&atx[190],0,&atx[4]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[191],NULL,0,NULL} ,
+  {425, "Cdd-pref-node-descr" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[192],0,&atx[189]} ,
+  {0, "create-date" ,128,0,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[193]} ,
+  {0, "description" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} };
 
 static AsnModule ampx[1] = {
-  { "NCBI-Cdd" , "cdd.h17",&atx[0],NULL,NULL,0,0} };
+  { "NCBI-Cdd" , "cdd.h19",&atx[0],NULL,NULL,0,0} };
 
 static AsnValxNodePtr avn = avnx;
 static AsnTypePtr at = atx;
@@ -311,23 +327,44 @@ static AsnModulePtr amp = ampx;
 #define CDD_style_dictionary &at[124]
 #define CDD_user_annotations &at[126]
 #define CDD_ancestors &at[128]
-#define CDD_scoreparams &at[139]
-#define CDD_seqtree &at[141]
+#define CDD_ancestors_E &at[129]
+#define CDD_scoreparams &at[134]
+#define CDD_seqtree &at[136]
+
+#define CDD_SET &at[167]
+#define CDD_SET_E &at[168]
+
+#define CDD_TREE &at[169]
+#define CDD_TREE_name &at[170]
+#define CDD_TREE_id &at[171]
+#define CDD_TREE_description &at[172]
+#define CDD_TREE_parent &at[173]
+#define CDD_TREE_children &at[174]
+#define CDD_TREE_siblings &at[175]
+#define CDD_TREE_neighbors &at[176]
+
+#define CDD_TREE_SET &at[177]
+#define CDD_TREE_SET_E &at[178]
+
+#define CDD_PREF_NODES &at[179]
+#define CDD_PREF_NODES_preferred_nodes &at[180]
+#define CDD_PREF_NODES_model_organisms &at[186]
+#define CDD_PREF_NODES_optional_nodes &at[187]
+#define CDD_PREF_NODES_description &at[188]
+
+#define CDD_ORG_REF &at[183]
+#define CDD_ORG_REF_reference &at[184]
+#define CDD_ORG_REF_active &at[185]
 
-#define CDD_SET &at[172]
-#define CDD_SET_E &at[173]
+#define CDD_ORG_REF_SET &at[181]
+#define CDD_ORG_REF_SET_E &at[182]
 
-#define CDD_TREE &at[174]
-#define CDD_TREE_name &at[175]
-#define CDD_TREE_id &at[176]
-#define CDD_TREE_description &at[177]
-#define CDD_TREE_parent &at[178]
-#define CDD_TREE_children &at[179]
-#define CDD_TREE_siblings &at[180]
-#define CDD_TREE_neighbors &at[181]
+#define CDD_PREF_NODE_DESCR &at[191]
+#define CDD_PREF_NODE_DESCR_create_date &at[192]
+#define CDD_PREF_NODE_DESCR_description &at[193]
 
-#define CDD_TREE_SET &at[182]
-#define CDD_TREE_SET_E &at[183]
+#define CDD_PREF_NODE_DESCR_SET &at[189]
+#define CDD_PREF_NODE_DESCR_SET_E &at[190]
 
 #define GLOBAL_ID &at[4]
 #define GLOBAL_ID_accession &at[5]
@@ -418,46 +455,39 @@ static AsnModulePtr amp = ampx;
 #define ALIGN_ANNOT_SET &at[110]
 #define ALIGN_ANNOT_SET_E &at[111]
 
-#define DOMAIN_PARENT &at[131]
+#define DOMAIN_PARENT &at[130]
+#define DOMAIN_PARENT_parent_type &at[131]
 #define DOMAIN_PARENT_parentid &at[132]
 #define DOMAIN_PARENT_seqannot &at[133]
 
-#define LINEAGE_INFO &at[129]
-#define LINEAGE_INFO_simpleparent &at[130]
-#define LINEAGE_INFO_complexparents &at[134]
-#define LINEAGE_INFO_complexparents_fusionparents &at[135]
-#define LINEAGE_INFO_complexparents_fusionparents_E &at[136]
-#define LINEAGE_INFO_complexparents_deletionparent &at[137]
-#define LINEAGE_INFO_complexparents_deletionparent_E &at[138]
-
-#define SEQUENCE_TREE &at[142]
-#define SEQUENCE_TREE_cdAccession &at[143]
-#define SEQUENCE_TREE_algorithm &at[144]
-#define SEQUENCE_TREE_isAnnotated &at[154]
-#define SEQUENCE_TREE_root &at[156]
-
-#define ALGORITHM_TYPE &at[145]
-#define ALGORITHM_TYPE_scoring_Scheme &at[146]
-#define ALGORITHM_TYPE_clustering_Method &at[147]
-#define ALGORITHM_TYPE_score_Matrix &at[148]
-#define ALGORITHM_TYPE_gapOpen &at[149]
-#define ALGORITHM_TYPE_gapExtend &at[150]
-#define ALGORITHM_TYPE_gapScaleFactor &at[151]
-#define ALGORITHM_TYPE_nTerminalExt &at[152]
-#define ALGORITHM_TYPE_cTerminalExt &at[153]
-
-#define SEQTREE_NODE &at[157]
-#define SEQTREE_NODE_isAnnotated &at[158]
-#define SEQTREE_NODE_name &at[159]
-#define SEQTREE_NODE_distance &at[160]
-#define SEQTREE_NODE_children &at[162]
-#define SEQTREE_NODE_children_children &at[163]
-#define SEQTREE_NODE_children_children_E &at[164]
-#define SEQTREE_NODE_children_footprint &at[165]
-#define SEQTREE_NODE_children_footprint_seqRange &at[166]
-#define SEQTREE_NODE_children_footprint_rowId &at[167]
-#define SEQTREE_NODE_annotation &at[168]
-
-#define NODE_ANNOTATION &at[169]
-#define NODE_ANNOTATION_presentInChildCD &at[170]
-#define NODE_ANNOTATION_note &at[171]
+#define SEQUENCE_TREE &at[137]
+#define SEQUENCE_TREE_cdAccession &at[138]
+#define SEQUENCE_TREE_algorithm &at[139]
+#define SEQUENCE_TREE_isAnnotated &at[149]
+#define SEQUENCE_TREE_root &at[151]
+
+#define ALGORITHM_TYPE &at[140]
+#define ALGORITHM_TYPE_scoring_Scheme &at[141]
+#define ALGORITHM_TYPE_clustering_Method &at[142]
+#define ALGORITHM_TYPE_score_Matrix &at[143]
+#define ALGORITHM_TYPE_gapOpen &at[144]
+#define ALGORITHM_TYPE_gapExtend &at[145]
+#define ALGORITHM_TYPE_gapScaleFactor &at[146]
+#define ALGORITHM_TYPE_nTerminalExt &at[147]
+#define ALGORITHM_TYPE_cTerminalExt &at[148]
+
+#define SEQTREE_NODE &at[152]
+#define SEQTREE_NODE_isAnnotated &at[153]
+#define SEQTREE_NODE_name &at[154]
+#define SEQTREE_NODE_distance &at[155]
+#define SEQTREE_NODE_children &at[157]
+#define SEQTREE_NODE_children_children &at[158]
+#define SEQTREE_NODE_children_children_E &at[159]
+#define SEQTREE_NODE_children_footprint &at[160]
+#define SEQTREE_NODE_children_footprint_seqRange &at[161]
+#define SEQTREE_NODE_children_footprint_rowId &at[162]
+#define SEQTREE_NODE_annotation &at[163]
+
+#define NODE_ANNOTATION &at[164]
+#define NODE_ANNOTATION_presentInChildCD &at[165]
+#define NODE_ANNOTATION_note &at[166]
diff --git a/biostruc/cdd/cddposutil.c b/biostruc/cdd/cddposutil.c
index e9c513cc..9ca4dbee 100644
--- a/biostruc/cdd/cddposutil.c
+++ b/biostruc/cdd/cddposutil.c
@@ -1,4 +1,4 @@
-/* $Id: cddposutil.c,v 1.16 2003/05/29 13:17:56 thiessen Exp $
+/* $Id: cddposutil.c,v 1.17 2004/01/22 15:43:57 bauer Exp $
 *===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
 *
 * Initial Version Creation Date: 12/21/1999
 *
-* $Revision: 1.16 $
+* $Revision: 1.17 $
 *
 * File Description: CDD utilities involving position-specific scoring 
 *                   matrices (PSSMs)
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: cddposutil.c,v $
+* Revision 1.17  2004/01/22 15:43:57  bauer
+* call BlastCalculateEffectiveLengths in CddSetUpSearchInternalByLoc
+*
 * Revision 1.16  2003/05/29 13:17:56  thiessen
 * fix memory leak in CddposFreeMemory()
 *
@@ -1708,32 +1711,19 @@ static Int2 LIBCALL CddSetUpSearchInternalByLoc
 	if (retval)
 		return retval;
 
+/* replaced code to calculate effecitve lengths with function call, AMB 1/22/04 */
 
-	if (search->pbp->gapped_calculation &&
-		StringCmp(search->prog_name, "blastn") != 0)
-		min_query_length = 1/(search->sbp->kbp_gap_std[search->first_context]->K);
-	else
-		min_query_length = 1/(search->sbp->kbp[search->first_context]->K);
-
-	last_length_adjustment = 0;
-	for (index=0; index<5; index++)
-	{
-		length_adjustment = ((search->sbp->kbp[search->first_context]->logK)+log((Nlm_FloatHi)(length-last_length_adjustment)*(Nlm_FloatHi)(MAX(1, (search->dblen)-(search->dbseq_num*last_length_adjustment)))))/(search->sbp->kbp[search->first_context]->H);
-		if (length_adjustment >= length-min_query_length)
-		{
-			length_adjustment = length-min_query_length;
-			break;
-		}
-	
-		if (ABS(last_length_adjustment-length_adjustment) <= 1)
-			break;
-		last_length_adjustment = length_adjustment;
+        if (!BlastCalculateEffectiveLengths(options, search->dbseq_num, search->dblen, 
+			length, search->sbp->kbp_gap_std[search->first_context],
+			&effective_query_length, &length_adjustment)) {
+	  ErrPostEx(SEV_WARNING, 0, 0, "BlastCalculateEffectiveLengths failed!");
 	}
-	search->length_adjustment = MAX(length_adjustment, 0);
 
+/* old code below to set values in 'search' */
+
+	search->length_adjustment = MAX(length_adjustment, 0);
 	search->dblen_eff = MAX(1, search->dblen - search->dbseq_num*search->length_adjustment);
-	effective_query_length = MAX(length - search->length_adjustment, min_query_length);
-	
+
 	for (index=search->first_context; index<=search->last_context; index++)
 	{
 		search->context[index].query->effective_length = effective_query_length;
diff --git a/biostruc/cdd/cddserver.c b/biostruc/cdd/cddserver.c
index 1e015e6c..a8a2522e 100644
--- a/biostruc/cdd/cddserver.c
+++ b/biostruc/cdd/cddserver.c
@@ -1,4 +1,4 @@
-/* $Id: cddserver.c,v 1.41 2003/10/07 21:21:09 bauer Exp $
+/* $Id: cddserver.c,v 1.42 2003/11/19 14:37:52 bauer Exp $
 *===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
 *
 * Initial Version Creation Date: 2/10/2000
 *
-* $Revision: 1.41 $
+* $Revision: 1.42 $
 *
 * File Description:
 *         CD WWW-Server, Cd summary pages and alignments directly from the
@@ -38,6 +38,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: cddserver.c,v $
+* Revision 1.42  2003/11/19 14:37:52  bauer
+* more consistent use of PSSM-IDs
+*
 * Revision 1.41  2003/10/07 21:21:09  bauer
 * initial changes to support drawing of hierarchies
 *
@@ -193,8 +196,8 @@
 
 #undef DEBUG
 #undef NOCN3D4
-#undef USE_CDTRK
-#undef DRAW_TREES
+#define USE_CDTRK
+#define DRAW_TREES
   
 typedef struct _private_tree_node_ {
   CdTreeNodePtr      pcdtree;
@@ -1752,7 +1755,10 @@ static void CDDSrvInfoBlk(CddPtr pcdd, FILE *table, CharPtr dbversion,
     }
   }    
   fprintf(table,"<FORM METHOD=\"POST\" ACTION=\"%scddsrv.cgi\" name=\"listform\" enctype=\"application/x-www-form-urlencoded\">\n",URLBase);
-  fprintf(table,"            <INPUT TYPE=\"HIDDEN\" NAME=\"uid\" VALUE=\"%s\">\n",cCDDid);
+  if (iPssmId > 0) {
+    fprintf(table,"            <INPUT TYPE=\"HIDDEN\" NAME=\"uid\" VALUE=\"%d\">\n",iPssmId);
+  } else
+    fprintf(table,"            <INPUT TYPE=\"HIDDEN\" NAME=\"uid\" VALUE=\"%s\">\n",cCDDid);
   fprintf(table,"            <INPUT TYPE=\"HIDDEN\" NAME=\"version\" VALUE=\"%s\">\n",dbversion);
   fprintf(table,"            <INPUT TYPE=\"HIDDEN\" NAME=\"ascbin\" VALUE=\"5\">\n");
   fprintf(table,"</FORM>\n");
@@ -1773,7 +1779,10 @@ static void CDDSrvInfoBlk(CddPtr pcdd, FILE *table, CharPtr dbversion,
 /* Begin Viewing Form                                                        */
 /*---------------------------------------------------------------------------*/
   fprintf(table,"          <FORM METHOD=\"POST\" ACTION=\"%scddsrv.cgi\" name=\"mainform\">\n",URLBase);
-  fprintf(table,"            <INPUT TYPE=\"HIDDEN\" NAME=\"uid\" VALUE=\"%s\">\n",cCDDid);
+  if (iPssmId > 0) {
+    fprintf(table,"            <INPUT TYPE=\"HIDDEN\" NAME=\"uid\" VALUE=\"%d\">\n",iPssmId); 
+  } else
+    fprintf(table,"            <INPUT TYPE=\"HIDDEN\" NAME=\"uid\" VALUE=\"%s\">\n",cCDDid);
   fprintf(table,"            <INPUT TYPE=\"HIDDEN\" NAME=\"version\" VALUE=\"%s\">\n",dbversion);
   if (txids) {
     vnp = txids; while (vnp) {
@@ -2613,6 +2622,56 @@ static void CddSrvRemoveNotes(CddPtr pcdd)
 
 /*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
+/* return the consensus sequence as a Seq-Entry                              */
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+static void CddSrvReturnConsensus(CddPtr pcdd, Int4 iPssmId)
+{
+
+  AsnIoPtr              aip;
+  SeqEntryPtr           sep, sepThis;
+  BioseqSetPtr          bssp;
+  BioseqPtr             bsp;
+  SeqIdPtr              sip, sipNew;
+  DbtagPtr              dbtp;
+  ObjectIdPtr           oidp;
+  
+  bssp = (BioseqSetPtr) pcdd->sequences->data.ptrvalue;
+  sepThis = (SeqEntryPtr) bssp->seq_set;
+  while (sepThis) {
+    bsp = sepThis->data.ptrvalue;
+    sip = bsp->id;
+    if (SipIsConsensus(sip)) {
+      sep = sepThis;
+      sep->next = NULL;
+      if (iPssmId > 0) {   /* add a SeqId to consensus, which records PSSMid */
+        sipNew = (SeqIdPtr) ValNodeNew(NULL);
+	sipNew->choice = SEQID_GENERAL;
+	dbtp = (DbtagPtr) DbtagNew();
+	dbtp->db = StringSave("CDD");
+	oidp = ObjectIdNew();
+	oidp->id = iPssmId;
+	dbtp->tag = oidp;
+	sipNew->data.ptrvalue = dbtp;
+	sipNew->next = sip;
+	bsp->id = sipNew;
+      }
+      break;
+    }
+    sepThis = sepThis->next;
+  }
+  strcpy(OutputName,GetTempName("cddsrv"));
+  aip = AsnIoOpen(OutputName, "w");
+  SeqEntryAsnWrite((SeqEntryPtr) sep, aip, NULL);
+  AsnIoClose(aip);
+  printf("Content-type: text/html\n\n");
+  PrintFile(OutputName);
+  RemoveTempFiles();   
+  return;
+}
+
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
 /* MAIN Function for cddserver                                               */
 /*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
@@ -2688,6 +2747,7 @@ Int2 Main()
   Boolean                  bHasConsensus      = FALSE;
   Boolean                  bShowTax           = FALSE;
   Boolean                  bEvidenceViewer    = FALSE;
+  Boolean                  bConsensusOnly     = FALSE;
   Char                     CDDalign[PATH_MAX], CDDidx[PATH_MAX];
   Char                     CDDfile[PATH_MAX], ErrMsg[PATH_MAX];
   Char                     chain[2], cChain;
@@ -2775,6 +2835,13 @@ Int2 Main()
   }
 
 /*---------------------------------------------------------------------------*/
+/* CD-Server as server for consensus sequences (formatted as SeqEntry)       */
+/*---------------------------------------------------------------------------*/
+  if ((indx = WWWFindName(www_info, "GETCSEQ")) >= 0) {
+    bConsensusOnly = TRUE;
+  }
+
+/*---------------------------------------------------------------------------*/
 /* retrieve the Cdd unique identifier                                        */
 /*---------------------------------------------------------------------------*/
   if ((indx = WWWFindName(www_info, "uid")) < 0) 
@@ -2887,6 +2954,18 @@ Int2 Main()
   }
   CddSrvRemoveNotes(pcdd);
   bHasConsensus = CddHasConsensus(pcdd);
+/*---------------------------------------------------------------------------*/
+/* return consensus sequence if required                                     */
+/*---------------------------------------------------------------------------*/
+  if (bConsensusOnly) {
+    if (bHasConsensus) {
+      CddSrvReturnConsensus(pcdd,iPssmId);
+    } else {
+      CddHtmlError("This CD does not have a consensus sequence!");
+    }
+    exit(0);
+  }
+
   alen = CddGetAlignmentLength(pcdd);
 
 /*---------------------------------------------------------------------------*/
diff --git a/biostruc/cdd/cddsrv.h b/biostruc/cdd/cddsrv.h
index 26ce4e8d..8dc64c0e 100644
--- a/biostruc/cdd/cddsrv.h
+++ b/biostruc/cdd/cddsrv.h
@@ -1,4 +1,4 @@
-/* $Id: cddsrv.h,v 1.16 2003/10/07 21:21:09 bauer Exp $
+/* $Id: cddsrv.h,v 1.17 2003/11/19 14:37:52 bauer Exp $
 *===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
 *
 * Initial Version Creation Date: 9/20/1999
 *
-* $Revision: 1.16 $
+* $Revision: 1.17 $
 *
 * File Description:
 *         header file for the CD-server CGI-bin
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: cddsrv.h,v $
+* Revision 1.17  2003/11/19 14:37:52  bauer
+* more consistent use of PSSM-IDs
+*
 * Revision 1.16  2003/10/07 21:21:09  bauer
 * initial changes to support drawing of hierarchies
 *
@@ -160,9 +163,11 @@ typedef struct cddsum {
 } CddSum, PNTR CddSumPtr;
 
 typedef struct cdddesc {
+  Int4                iPssmId;
   Char                cCddId[PATH_MAX];
   Char                cDescr[CDD_MAX_DESCR];
   Char                cSourc[PATH_MAX];
+  Int4                iPssmLength;
   struct cdddesc PNTR next;
 } CddDesc, PNTR CddDescPtr;
 
diff --git a/biostruc/cdd/cddutil.c b/biostruc/cdd/cddutil.c
index 9f0e00f1..6970757d 100644
--- a/biostruc/cdd/cddutil.c
+++ b/biostruc/cdd/cddutil.c
@@ -1,4 +1,4 @@
-/* $Id: cddutil.c,v 1.89 2003/10/07 21:19:39 bauer Exp $
+/* $Id: cddutil.c,v 1.91 2003/12/09 22:21:35 bauer Exp $
 *===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,13 +29,19 @@
 *
 * Initial Version Creation Date: 10/18/1999
 *
-* $Revision: 1.89 $
+* $Revision: 1.91 $
 *
 * File Description: CDD utility routines
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: cddutil.c,v $
+* Revision 1.91  2003/12/09 22:21:35  bauer
+* added CddCountResTypes
+*
+* Revision 1.90  2003/12/09 18:48:05  bauer
+* commented out deprecated fields in BlastKarlinBlkCopy
+*
 * Revision 1.89  2003/10/07 21:19:39  bauer
 * made CddMasterIs3D more general
 *
@@ -2016,6 +2022,73 @@ Nlm_FloatHiPtr LIBCALL SeqAlignInform(SeqAlignPtr salp, BioseqPtr bsp_master,
 /* Calculate per column information content for a CDD from the seqalign      */
 /*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
+Int4 ** LIBCALL CddCountResTypes(CddPtr pcdd, Int4 *ncols)
+{
+  BioseqSetPtr       bssp;
+  Boolean            bHasConsensus = CddHasConsensus(pcdd);
+  Int4               offset, qlength, i, j, c;
+  Int4             **ResFreqTable;
+  SeqAlignPtr        salp;
+  DenseDiagPtr       ddp;
+  SeqIdPtr           sip;
+  BioseqPtr          bsp;
+  Uint1             *buffer;
+  SeqPortPtr         spp;
+
+  if (!pcdd) return(NULL);
+  if (!pcdd->trunc_master) return(NULL);
+  bssp = pcdd->sequences->data.ptrvalue;
+  offset = pcdd->profile_range->from;
+  qlength = pcdd->trunc_master->length;
+  *ncols = qlength;  
+  ResFreqTable = MemNew(qlength*sizeof(Int4 *));
+  for (i=0;i<qlength;i++) {
+    ResFreqTable[i] = MemNew(26*sizeof(Int4));
+    for (j=0;j<26;j++) ResFreqTable[i][j] = 0;
+  }
+  salp = pcdd->seqannot->data;
+  if (!bHasConsensus) {   /* count residues in the master/representative too */
+    ddp = salp->segs;
+    sip = ddp->id;
+    bsp = CddRetrieveBioseqById(sip,bssp->seq_set);
+    buffer = MemNew((bsp->length)*sizeof(Uint1));
+    spp = SeqPortNew(bsp, 0, bsp->length-1, Seq_strand_unknown, Seq_code_ncbistdaa);
+    for (i=0; i<bsp->length;i++) buffer[i] = SeqPortGetResidue(spp);
+    spp = SeqPortFree(spp);
+    while (ddp) {
+      for (c=ddp->starts[0];c<ddp->starts[0]+ddp->len;c++) {
+        ResFreqTable[c-offset][buffer[c]]++;
+      }
+      ddp = ddp->next;
+    }
+    MemFree(buffer);
+  }  
+  while (salp) {
+    ddp = salp->segs;
+    sip = ddp->id->next;
+    bsp = CddRetrieveBioseqById(sip,bssp->seq_set);
+    buffer = MemNew((bsp->length)*sizeof(Uint1));
+    spp = SeqPortNew(bsp, 0, bsp->length-1, Seq_strand_unknown, Seq_code_ncbistdaa);
+    for (i=0; i<bsp->length;i++) buffer[i] = SeqPortGetResidue(spp);
+    spp = SeqPortFree(spp);
+    while (ddp) {
+      for (c=ddp->starts[1];c<ddp->starts[1]+ddp->len;c++) {
+        i = ddp->starts[0]-offset+c-ddp->starts[1];
+        ResFreqTable[i][buffer[c]]++;
+      }
+      ddp = ddp->next;
+    }
+    MemFree(buffer);
+    salp = salp->next;
+  }
+  return(ResFreqTable);
+}
+
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+/* Calculate per column information content for a CDD from the seqalign      */
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
 Nlm_FloatHiPtr LIBCALL CddAlignInform(CddPtr pcdd, Nlm_FloatHi * Niobs)
 {
   Int4               offset;
@@ -4603,12 +4676,12 @@ static void BlastKarlinBlkCopy(BLAST_KarlinBlkPtr kbp_in,BLAST_KarlinBlkPtr kbp_
   kbp_out->K = kbp_in->K;
   kbp_out->logK = kbp_in->logK;
   kbp_out->H = kbp_in->H;
-  kbp_out->Lambda_real = kbp_in->Lambda_real;
+/*  kbp_out->Lambda_real = kbp_in->Lambda_real;
   kbp_out->K_real = kbp_in->K_real;
   kbp_out->logK_real = kbp_in->logK_real;
   kbp_out->H_real = kbp_in->H_real;
   kbp_out->q_frame = kbp_in->q_frame;
-  kbp_out->s_frame = kbp_in->s_frame;
+  kbp_out->s_frame = kbp_in->s_frame; */
   kbp_out->paramC = kbp_in->paramC;
 }
 
@@ -4671,13 +4744,13 @@ Seq_Mtf * LIBCALL CddDenDiagCposComp2KBP(BioseqPtr bspFake, Int4 iPseudo,
   if (iPseudo <= 0) {                             /* need to determine first */
     AInf = SeqAlignInform(salp, bspFake, bHasConsensus, 0); 
     for (i=0;i<bspFake->length;i++) SumAInf += AInf[i];
-    if (SumAInf > 84) iPseudo = 10;                    /* purely empirical   */
-    else if (SumAInf > 55) iPseudo = 7;
-    else if (SumAInf > 43) iPseudo = 5;
-    else if (SumAInf > 41.5) iPseudo = 4;
-    else if (SumAInf > 40) iPseudo = 3;
-    else if (SumAInf > 39) iPseudo = 2;
-    else iPseudo = 1;
+    if      (SumAInf > 84  ) iPseudo = 10;             /* purely empirical   */
+    else if (SumAInf > 55  ) iPseudo =  7;
+    else if (SumAInf > 43  ) iPseudo =  5;
+    else if (SumAInf > 41.5) iPseudo =  4;
+    else if (SumAInf > 40  ) iPseudo =  3;
+    else if (SumAInf > 39  ) iPseudo =  2;
+    else                     iPseudo =  1;
     MemFree(AInf);
     if (pcdd && bWriteOut) printf("%s AInf:%6.1f PseudoCt: %d\n",cAccession,SumAInf, iPseudo);
   }
diff --git a/biostruc/cdd/cddutil.h b/biostruc/cdd/cddutil.h
index 6200793c..df5ffe64 100644
--- a/biostruc/cdd/cddutil.h
+++ b/biostruc/cdd/cddutil.h
@@ -1,4 +1,4 @@
-/* $Id: cddutil.h,v 1.51 2003/08/25 19:09:47 bauer Exp $
+/* $Id: cddutil.h,v 1.52 2003/12/09 22:21:35 bauer Exp $
 *===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,13 +29,16 @@
 *
 * Initial Version Creation Date: 12/15/1999
 *
-* $Revision: 1.51 $
+* $Revision: 1.52 $
 *
 * File Description: Header file for cdd api utility functions  
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: cddutil.h,v $
+* Revision 1.52  2003/12/09 22:21:35  bauer
+* added CddCountResTypes
+*
 * Revision 1.51  2003/08/25 19:09:47  bauer
 * added SeqAlignReadFromFile
 *
@@ -493,6 +496,7 @@ Int2        LIBCALL CddTrimSeqAligns(CddPtr pcdd);
 /*---------------------------------------------------------------------------*/
 Nlm_FloatHi    LIBCALL SeqAlignConservation(SeqAlignPtr salp, Nlm_FloatHi fract,BioseqPtr bsp_master, Boolean bHasConsensus, Int4 offset);
 Nlm_FloatHiPtr LIBCALL SeqAlignInform(SeqAlignPtr salp, BioseqPtr bsp_master,Boolean bHasConsensus,Int4 offset);
+Int4 **        LIBCALL CddCountResTypes(CddPtr pcdd, Int4 *ncols);
 Nlm_FloatHiPtr LIBCALL CddAlignInform(CddPtr pcdd, Nlm_FloatHi * Niobs);
 Nlm_FloatHiPtr LIBCALL CddPssmInform(CddPtr pcdd);
 Nlm_FloatHiPtr LIBCALL CddPosFreqInform(Nlm_FloatHi **posFreq, Int4 ncol, Int4 nrow);
diff --git a/biostruc/cdd/objcdd.c b/biostruc/cdd/objcdd.c
index bf488ee7..22af4d76 100644
--- a/biostruc/cdd/objcdd.c
+++ b/biostruc/cdd/objcdd.c
@@ -36,7 +36,7 @@ objcddAsnLoad(void)
 
 /**************************************************
 *    Generated object loaders for Module NCBI-Cdd
-*    Generated using ASNCODE Revision: 6.14 at Aug 14, 2003 10:05 AM
+*    Generated using ASNCODE Revision: 6.14 at Jan 15, 2004  1:40 PM
 *
 **************************************************/
 
@@ -361,7 +361,7 @@ CddFree(CddPtr ptr)
    MemFree(ptr -> name);
    CddIdSetFree(ptr -> id);
    CddDescrSetFree(ptr -> description);
-   { SeqAnnotPtr sap, next; sap = ptr -> seqannot; while(sap) { next = sap->next; sap->next = NULL; sap = SeqAnnotFree(sap); sap = next; } }
+   AsnGenericUserSeqOfFree(ptr -> seqannot, (AsnOptFreeFunc) SeqAnnotFree);
    BiostrucAnnotSetFree(ptr -> features);
    SeqEntryFree(ptr -> sequences);
    SeqIntFree(ptr -> profile_range);
@@ -379,7 +379,7 @@ CddFree(CddPtr ptr)
    AlignAnnotSetFree(ptr -> alignannot);
    Cn3dStyleDictionaryFree(ptr -> style_dictionary);
    Cn3dUserAnnotationsFree(ptr -> user_annotations);
-   LineageInfoFree(ptr -> ancestors);
+   AsnGenericUserSeqOfFree(ptr -> ancestors, (AsnOptFreeFunc) DomainParentFree);
    ScoreMatrixParametersFree(ptr -> scoreparams);
    SequenceTreeFree(ptr -> seqtree);
    return MemFree(ptr);
@@ -581,14 +581,14 @@ CddAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == CDD_ancestors) {
-      ptr -> ancestors = LineageInfoAsnRead(aip, atp);
-      if (aip -> io_failure) {
+      ptr -> ancestors = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) DomainParentAsnRead, (AsnOptFreeFunc) DomainParentFree);
+      if (isError && ptr -> ancestors == NULL) {
          goto erret;
       }
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == CDD_scoreparams) {
-      ptr -> scoreparams = (ScoreMatrixParameters *)ScoreMatrixParametersAsnRead(aip, atp);
+      ptr -> scoreparams = ScoreMatrixParametersAsnRead(aip, atp);
       if (aip -> io_failure) {
          goto erret;
       }
@@ -666,7 +666,7 @@ CddAsnWrite(CddPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
          goto erret;
       }
    }
-   if (ptr->seqannot != NULL) if (SeqAnnotSetAsnWrite(ptr->seqannot,aip,CDD_seqannot,CDD_seqannot_E)==FALSE) goto erret;
+   AsnGenericUserSeqOfAsnWrite(ptr -> seqannot, (AsnWriteFunc) SeqAnnotAsnWrite, aip, CDD_seqannot, CDD_seqannot_E);
    if (ptr -> features != NULL) {
       if ( ! BiostrucAnnotSetAsnWrite(ptr -> features, aip, CDD_features)) {
          goto erret;
@@ -740,11 +740,7 @@ CddAsnWrite(CddPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
          goto erret;
       }
    }
-   if (ptr -> ancestors != NULL) {
-      if ( ! LineageInfoAsnWrite(ptr -> ancestors, aip, CDD_ancestors)) {
-         goto erret;
-      }
-   }
+   AsnGenericUserSeqOfAsnWrite(ptr -> ancestors, (AsnWriteFunc) DomainParentAsnWrite, aip, CDD_ancestors, CDD_ancestors_E);
    if (ptr -> scoreparams != NULL) {
       if ( ! ScoreMatrixParametersAsnWrite(ptr -> scoreparams, aip, CDD_scoreparams)) {
          goto erret;
@@ -1230,6 +1226,772 @@ erret:
 
 /**************************************************
 *
+*    CddPrefNodesNew()
+*
+**************************************************/
+NLM_EXTERN 
+CddPrefNodesPtr LIBCALL
+CddPrefNodesNew(void)
+{
+   CddPrefNodesPtr ptr = MemNew((size_t) sizeof(CddPrefNodes));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    CddPrefNodesFree()
+*
+**************************************************/
+NLM_EXTERN 
+CddPrefNodesPtr LIBCALL
+CddPrefNodesFree(CddPrefNodesPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   CddOrgRefSetFree(ptr -> preferred_nodes);
+   CddOrgRefSetFree(ptr -> model_organisms);
+   CddOrgRefSetFree(ptr -> optional_nodes);
+   CddPrefNodeDescrSetFree(ptr -> description);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    CddPrefNodesAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CddPrefNodesPtr LIBCALL
+CddPrefNodesAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CddPrefNodesPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CddPrefNodes ::= (self contained) */
+      atp = AsnReadId(aip, amp, CDD_PREF_NODES);
+   } else {
+      atp = AsnLinkType(orig, CDD_PREF_NODES);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = CddPrefNodesNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == CDD_PREF_NODES_preferred_nodes) {
+      ptr -> preferred_nodes = CddOrgRefSetAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == CDD_PREF_NODES_model_organisms) {
+      ptr -> model_organisms = CddOrgRefSetAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == CDD_PREF_NODES_optional_nodes) {
+      ptr -> optional_nodes = CddOrgRefSetAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == CDD_PREF_NODES_description) {
+      ptr -> description = CddPrefNodeDescrSetAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CddPrefNodesFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CddPrefNodesAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CddPrefNodesAsnWrite(CddPrefNodesPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, CDD_PREF_NODES);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> preferred_nodes != NULL) {
+      if ( ! CddOrgRefSetAsnWrite(ptr -> preferred_nodes, aip, CDD_PREF_NODES_preferred_nodes)) {
+         goto erret;
+      }
+   }
+   if (ptr -> model_organisms != NULL) {
+      if ( ! CddOrgRefSetAsnWrite(ptr -> model_organisms, aip, CDD_PREF_NODES_model_organisms)) {
+         goto erret;
+      }
+   }
+   if (ptr -> optional_nodes != NULL) {
+      if ( ! CddOrgRefSetAsnWrite(ptr -> optional_nodes, aip, CDD_PREF_NODES_optional_nodes)) {
+         goto erret;
+      }
+   }
+   if (ptr -> description != NULL) {
+      if ( ! CddPrefNodeDescrSetAsnWrite(ptr -> description, aip, CDD_PREF_NODES_description)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    CddOrgRefNew()
+*
+**************************************************/
+NLM_EXTERN 
+CddOrgRefPtr LIBCALL
+CddOrgRefNew(void)
+{
+   CddOrgRefPtr ptr = MemNew((size_t) sizeof(CddOrgRef));
+
+   ptr -> active = 1;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    CddOrgRefFree()
+*
+**************************************************/
+NLM_EXTERN 
+CddOrgRefPtr LIBCALL
+CddOrgRefFree(CddOrgRefPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   OrgRefFree((OrgRefPtr)ptr -> reference);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    CddOrgRefAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CddOrgRefPtr LIBCALL
+CddOrgRefAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CddOrgRefPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CddOrgRef ::= (self contained) */
+      atp = AsnReadId(aip, amp, CDD_ORG_REF);
+   } else {
+      atp = AsnLinkType(orig, CDD_ORG_REF);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = CddOrgRefNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == CDD_ORG_REF_reference) {
+      ptr -> reference = OrgRefAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == CDD_ORG_REF_active) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> active = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CddOrgRefFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CddOrgRefAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CddOrgRefAsnWrite(CddOrgRefPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, CDD_ORG_REF);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> reference != NULL) {
+      if ( ! OrgRefAsnWrite((OrgRefPtr)ptr -> reference, aip, CDD_ORG_REF_reference)) {
+         goto erret;
+      }
+   }
+   av.boolvalue = ptr -> active;
+   retval = AsnWrite(aip, CDD_ORG_REF_active,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    CddOrgRefSetFree()
+*
+**************************************************/
+NLM_EXTERN 
+CddOrgRefSetPtr LIBCALL
+CddOrgRefSetFree(CddOrgRefSetPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr,  (AsnOptFreeFunc) CddOrgRefFree);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    CddOrgRefSetAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CddOrgRefSetPtr LIBCALL
+CddOrgRefSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CddOrgRefSetPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CddOrgRefSet ::= (self contained) */
+      atp = AsnReadId(aip, amp, CDD_ORG_REF_SET);
+   } else {
+      atp = AsnLinkType(orig, CDD_ORG_REF_SET);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) CddOrgRefAsnRead, (AsnOptFreeFunc) CddOrgRefFree);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CddOrgRefSetFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CddOrgRefSetAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CddOrgRefSetAsnWrite(CddOrgRefSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, CDD_ORG_REF_SET);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericUserSeqOfAsnWrite(ptr , (AsnWriteFunc) CddOrgRefAsnWrite, aip, atp, CDD_ORG_REF_SET_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    CddPrefNodeDescrFree()
+*
+**************************************************/
+NLM_EXTERN 
+CddPrefNodeDescrPtr LIBCALL
+CddPrefNodeDescrFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case CddPrefNodeDescr_create_date:
+      DateFree(anp -> data.ptrvalue);
+      break;
+   case CddPrefNodeDescr_description:
+      MemFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    CddPrefNodeDescrAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CddPrefNodeDescrPtr LIBCALL
+CddPrefNodeDescrAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CddPrefNodeDescr ::= (self contained) */
+      atp = AsnReadId(aip, amp, CDD_PREF_NODE_DESCR);
+   } else {
+      atp = AsnLinkType(orig, CDD_PREF_NODE_DESCR);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == CDD_PREF_NODE_DESCR_create_date) {
+      choice = CddPrefNodeDescr_create_date;
+      func = (AsnReadFunc) DateAsnRead;
+   }
+   else if (atp == CDD_PREF_NODE_DESCR_description) {
+      choice = CddPrefNodeDescr_description;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.ptrvalue = av.ptrvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    CddPrefNodeDescrAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CddPrefNodeDescrAsnWrite(CddPrefNodeDescrPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, CDD_PREF_NODE_DESCR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case CddPrefNodeDescr_create_date:
+      writetype = CDD_PREF_NODE_DESCR_create_date;
+      func = (AsnWriteFunc) DateAsnWrite;
+      break;
+   case CddPrefNodeDescr_description:
+      av.ptrvalue = anp->data.ptrvalue;
+      retval = AsnWrite(aip, CDD_PREF_NODE_DESCR_description, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    CddPrefNodeDescrSetFree()
+*
+**************************************************/
+NLM_EXTERN 
+CddPrefNodeDescrSetPtr LIBCALL
+CddPrefNodeDescrSetFree(CddPrefNodeDescrSetPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericChoiceSeqOfFree(ptr, (AsnOptFreeFunc) CddPrefNodeDescrFree);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    CddPrefNodeDescrSetAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CddPrefNodeDescrSetPtr LIBCALL
+CddPrefNodeDescrSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CddPrefNodeDescrSetPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CddPrefNodeDescrSet ::= (self contained) */
+      atp = AsnReadId(aip, amp, CDD_PREF_NODE_DESCR_SET);
+   } else {
+      atp = AsnLinkType(orig, CDD_PREF_NODE_DESCR_SET);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) CddPrefNodeDescrAsnRead, (AsnOptFreeFunc) CddPrefNodeDescrFree);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CddPrefNodeDescrSetFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CddPrefNodeDescrSetAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CddPrefNodeDescrSetAsnWrite(CddPrefNodeDescrSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objcddAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, CDD_PREF_NODE_DESCR_SET);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericChoiceSeqOfAsnWrite(ptr , (AsnWriteFunc) CddPrefNodeDescrAsnWrite, aip, atp, CDD_PREF_NODE_DESCR_SET_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
 *    GlobalIdNew()
 *
 **************************************************/
@@ -3718,6 +4480,13 @@ DomainParentAsnRead(AsnIoPtr aip, AsnTypePtr orig)
    atp = AsnReadId(aip,amp, atp);
    func = NULL;
 
+   if (atp == DOMAIN_PARENT_parent_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> parent_type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
    if (atp == DOMAIN_PARENT_parentid) {
       ptr -> parentid = CddIdAsnRead(aip, atp);
       if (aip -> io_failure) {
@@ -3783,6 +4552,8 @@ DomainParentAsnWrite(DomainParentPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
       goto erret;
    }
 
+   av.intvalue = ptr -> parent_type;
+   retval = AsnWrite(aip, DOMAIN_PARENT_parent_type,  &av);
    if (ptr -> parentid != NULL) {
       if ( ! CddIdAsnWrite(ptr -> parentid, aip, DOMAIN_PARENT_parentid)) {
          goto erret;
@@ -3807,341 +4578,6 @@ erret:
 
 /**************************************************
 *
-*    LineageInfo_complexparentsNew()
-*
-**************************************************/
-static 
-LineageInfo_complexparentsPtr LIBCALL
-LineageInfo_complexparentsNew(void)
-{
-   LineageInfo_complexparentsPtr ptr = MemNew((size_t) sizeof(LineageInfo_complexparents));
-
-   return ptr;
-
-}
-
-
-/**************************************************
-*
-*    LineageInfoFree()
-*
-**************************************************/
-NLM_EXTERN 
-LineageInfoPtr LIBCALL
-LineageInfoFree(ValNodePtr anp)
-{
-   Pointer pnt;
-
-   if (anp == NULL) {
-      return NULL;
-   }
-
-   pnt = anp->data.ptrvalue;
-   switch (anp->choice)
-   {
-   default:
-      break;
-   case LineageInfo_simpleparent:
-      DomainParentFree(anp -> data.ptrvalue);
-      break;
-   case LineageInfo_LineageInfo_Complexparents:
-      LineageInfo_complexparentsFree(anp -> data.ptrvalue);
-      break;
-   }
-   return MemFree(anp);
-}
-
-
-/**************************************************
-*
-*    LineageInfo_complexparentsFree()
-*
-**************************************************/
-static 
-LineageInfo_complexparentsPtr LIBCALL
-LineageInfo_complexparentsFree(LineageInfo_complexparentsPtr ptr)
-{
-
-   if(ptr == NULL) {
-      return NULL;
-   }
-   AsnGenericUserSeqOfFree(ptr -> fusionparents, (AsnOptFreeFunc) DomainParentFree);
-   AsnGenericUserSeqOfFree(ptr -> deletionparent, (AsnOptFreeFunc) DomainParentFree);
-   return MemFree(ptr);
-}
-
-
-/**************************************************
-*
-*    LineageInfoAsnRead()
-*
-**************************************************/
-NLM_EXTERN 
-LineageInfoPtr LIBCALL
-LineageInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
-{
-   DataVal av;
-   AsnTypePtr atp;
-   ValNodePtr anp;
-   Uint1 choice;
-   Boolean isError = FALSE;
-   Boolean nullIsError = FALSE;
-   AsnReadFunc func;
-
-   if (! loaded)
-   {
-      if (! objcddAsnLoad()) {
-         return NULL;
-      }
-   }
-
-   if (aip == NULL) {
-      return NULL;
-   }
-
-   if (orig == NULL) {         /* LineageInfo ::= (self contained) */
-      atp = AsnReadId(aip, amp, LINEAGE_INFO);
-   } else {
-      atp = AsnLinkType(orig, LINEAGE_INFO);    /* link in local tree */
-   }
-   if (atp == NULL) {
-      return NULL;
-   }
-
-   anp = ValNodeNew(NULL);
-   if (anp == NULL) {
-      goto erret;
-   }
-   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
-      goto erret;
-   }
-
-   func = NULL;
-
-   atp = AsnReadId(aip, amp, atp);  /* find the choice */
-   if (atp == NULL) {
-      goto erret;
-   }
-   if (atp == LINEAGE_INFO_simpleparent) {
-      choice = LineageInfo_simpleparent;
-      func = (AsnReadFunc) DomainParentAsnRead;
-   }
-   else if (atp == LINEAGE_INFO_complexparents) {
-      choice = LineageInfo_LineageInfo_Complexparents;
-      func = (AsnReadFunc) LineageInfo_complexparentsAsnRead;
-   }
-   anp->choice = choice;
-   if (func != NULL)
-   {
-      anp->data.ptrvalue = (* func)(aip, atp);
-      if (aip -> io_failure) goto erret;
-
-      if (nullIsError && anp->data.ptrvalue == NULL) {
-         goto erret;
-      }
-   }
-
-ret:
-   AsnUnlinkType(orig);       /* unlink local tree */
-   return anp;
-
-erret:
-   anp = MemFree(anp);
-   aip -> io_failure = TRUE;
-   goto ret;
-}
-
-
-/**************************************************
-*
-*    LineageInfo_complexparentsAsnRead()
-*
-**************************************************/
-static 
-LineageInfo_complexparentsPtr LIBCALL
-LineageInfo_complexparentsAsnRead(AsnIoPtr aip, AsnTypePtr orig)
-{
-   DataVal av;
-   AsnTypePtr atp;
-   Boolean isError = FALSE;
-   AsnReadFunc func;
-   LineageInfo_complexparentsPtr ptr;
-
-   if (! loaded)
-   {
-      if (! objcddAsnLoad()) {
-         return NULL;
-      }
-   }
-
-   if (aip == NULL) {
-      return NULL;
-   }
-
-   if (orig == NULL) {         /* LineageInfo_complexparents ::= (self contained) */
-      atp = AsnReadId(aip, amp, LINEAGE_INFO_complexparents);
-   } else {
-      atp = AsnLinkType(orig, LINEAGE_INFO_complexparents);
-   }
-   /* link in local tree */
-   if (atp == NULL) {
-      return NULL;
-   }
-
-   ptr = LineageInfo_complexparentsNew();
-   if (ptr == NULL) {
-      goto erret;
-   }
-   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
-      goto erret;
-   }
-
-   atp = AsnReadId(aip,amp, atp);
-   func = NULL;
-
-   if (atp == LINEAGE_INFO_complexparents_fusionparents) {
-      ptr -> fusionparents = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) DomainParentAsnRead, (AsnOptFreeFunc) DomainParentFree);
-      if (isError && ptr -> fusionparents == NULL) {
-         goto erret;
-      }
-      atp = AsnReadId(aip,amp, atp);
-   }
-   if (atp == LINEAGE_INFO_complexparents_deletionparent) {
-      ptr -> deletionparent = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) DomainParentAsnRead, (AsnOptFreeFunc) DomainParentFree);
-      if (isError && ptr -> deletionparent == NULL) {
-         goto erret;
-      }
-      atp = AsnReadId(aip,amp, atp);
-   }
-
-   if (AsnReadVal(aip, atp, &av) <= 0) {
-      goto erret;
-   }
-   /* end struct */
-
-ret:
-   AsnUnlinkType(orig);       /* unlink local tree */
-   return ptr;
-
-erret:
-   aip -> io_failure = TRUE;
-   ptr = LineageInfo_complexparentsFree(ptr);
-   goto ret;
-}
-
-
-
-/**************************************************
-*
-*    LineageInfoAsnWrite()
-*
-**************************************************/
-NLM_EXTERN Boolean LIBCALL 
-LineageInfoAsnWrite(LineageInfoPtr anp, AsnIoPtr aip, AsnTypePtr orig)
-
-{
-   DataVal av;
-   AsnTypePtr atp, writetype = NULL;
-   Pointer pnt;
-   AsnWriteFunc func = NULL;
-   Boolean retval = FALSE;
-
-   if (! loaded)
-   {
-      if (! objcddAsnLoad())
-      return FALSE;
-   }
-
-   if (aip == NULL)
-   return FALSE;
-
-   atp = AsnLinkType(orig, LINEAGE_INFO);   /* link local tree */
-   if (atp == NULL) {
-      return FALSE;
-   }
-
-   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
-
-   av.ptrvalue = (Pointer)anp;
-   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
-      goto erret;
-   }
-
-   pnt = anp->data.ptrvalue;
-   switch (anp->choice)
-   {
-   case LineageInfo_simpleparent:
-      writetype = LINEAGE_INFO_simpleparent;
-      func = (AsnWriteFunc) DomainParentAsnWrite;
-      break;
-   case LineageInfo_LineageInfo_Complexparents:
-      writetype = LINEAGE_INFO_complexparents;
-      func = (AsnWriteFunc) LineageInfo_complexparentsAsnWrite;
-      break;
-   }
-   if (writetype != NULL) {
-      retval = (* func)(pnt, aip, writetype);   /* write it out */
-   }
-   if (!retval) {
-      goto erret;
-   }
-   retval = TRUE;
-
-erret:
-   AsnUnlinkType(orig);       /* unlink local tree */
-   return retval;
-}
-
-
-/**************************************************
-*
-*    LineageInfo_complexparentsAsnWrite()
-*
-**************************************************/
-static Boolean LIBCALL 
-LineageInfo_complexparentsAsnWrite(LineageInfo_complexparentsPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
-{
-   DataVal av;
-   AsnTypePtr atp;
-   Boolean retval = FALSE;
-
-   if (! loaded)
-   {
-      if (! objcddAsnLoad()) {
-         return FALSE;
-      }
-   }
-
-   if (aip == NULL) {
-      return FALSE;
-   }
-
-   atp = AsnLinkType(orig, LINEAGE_INFO_complexparents);   /* link local tree */
-   if (atp == NULL) {
-      return FALSE;
-   }
-
-   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
-   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
-      goto erret;
-   }
-
-   AsnGenericUserSeqOfAsnWrite(ptr -> fusionparents, (AsnWriteFunc) DomainParentAsnWrite, aip, LINEAGE_INFO_complexparents_fusionparents, LINEAGE_INFO_complexparents_fusionparents_E);
-   AsnGenericUserSeqOfAsnWrite(ptr -> deletionparent, (AsnWriteFunc) DomainParentAsnWrite, aip, LINEAGE_INFO_complexparents_deletionparent, LINEAGE_INFO_complexparents_deletionparent_E);
-   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
-      goto erret;
-   }
-   retval = TRUE;
-
-erret:
-   AsnUnlinkType(orig);       /* unlink local tree */
-   return retval;
-}
-
-
-
-/**************************************************
-*
 *    SequenceTreeNew()
 *
 **************************************************/
diff --git a/biostruc/cdd/objcdd.h b/biostruc/cdd/objcdd.h
index 57347fc0..5be0a2b9 100644
--- a/biostruc/cdd/objcdd.h
+++ b/biostruc/cdd/objcdd.h
@@ -20,7 +20,7 @@ extern "C" { /* } */
 /**************************************************
 *
 *    Generated objects for Module NCBI-Cdd
-*    Generated using ASNCODE Revision: 6.14 at Aug 14, 2003 10:05 AM
+*    Generated using ASNCODE Revision: 6.14 at Jan 15, 2004  1:40 PM
 *
 **************************************************/
 
@@ -86,7 +86,7 @@ typedef struct struct_Cdd {
    struct struct_Align_annot PNTR   alignannot;
    struct struct_Cn3d_style_dictionary PNTR   style_dictionary;
    struct struct_Cn3d_user_annotations PNTR   user_annotations;
-   ValNodePtr   ancestors;
+   struct struct_Domain_parent PNTR   ancestors;
    struct struct_Score_matrix_parameters PNTR   scoreparams;
    struct struct_Sequence_tree PNTR   seqtree;
 } Cdd, PNTR CddPtr;
@@ -165,6 +165,95 @@ NLM_EXTERN Boolean LIBCALL CddTreeSetAsnWrite PROTO (( CddTreeSetPtr , AsnIoPtr,
 
 /**************************************************
 *
+*    CddPrefNodes
+*
+**************************************************/
+typedef struct struct_Cdd_pref_nodes {
+   struct struct_Cdd_org_ref PNTR   preferred_nodes;
+   struct struct_Cdd_org_ref PNTR   model_organisms;
+   struct struct_Cdd_org_ref PNTR   optional_nodes;
+   ValNodePtr   description;
+} CddPrefNodes, PNTR CddPrefNodesPtr;
+
+
+NLM_EXTERN CddPrefNodesPtr LIBCALL CddPrefNodesFree PROTO ((CddPrefNodesPtr ));
+NLM_EXTERN CddPrefNodesPtr LIBCALL CddPrefNodesNew PROTO (( void ));
+NLM_EXTERN CddPrefNodesPtr LIBCALL CddPrefNodesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CddPrefNodesAsnWrite PROTO (( CddPrefNodesPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    CddOrgRef
+*
+**************************************************/
+typedef struct struct_Cdd_org_ref {
+   struct struct_Cdd_org_ref PNTR next;
+   OrgRefPtr   reference;
+   Uint1   active;
+} CddOrgRef, PNTR CddOrgRefPtr;
+
+
+NLM_EXTERN CddOrgRefPtr LIBCALL CddOrgRefFree PROTO ((CddOrgRefPtr ));
+NLM_EXTERN CddOrgRefPtr LIBCALL CddOrgRefNew PROTO (( void ));
+NLM_EXTERN CddOrgRefPtr LIBCALL CddOrgRefAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CddOrgRefAsnWrite PROTO (( CddOrgRefPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    CddOrgRefSet
+*
+**************************************************/
+typedef struct struct_Cdd_org_ref CddOrgRefSet;
+typedef struct struct_Cdd_org_ref PNTR CddOrgRefSetPtr;
+#define CddOrgRefSetNew() Cdd_org_refNew() 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN CddOrgRefSetPtr LIBCALL CddOrgRefSetFree PROTO ((CddOrgRefSetPtr ));
+NLM_EXTERN CddOrgRefSetPtr LIBCALL CddOrgRefSetNew PROTO (( void ));
+NLM_EXTERN CddOrgRefSetPtr LIBCALL CddOrgRefSetAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CddOrgRefSetAsnWrite PROTO (( CddOrgRefSetPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+typedef ValNodePtr CddPrefNodeDescrPtr;
+typedef ValNode CddPrefNodeDescr;
+#define CddPrefNodeDescr_create_date 1
+#define CddPrefNodeDescr_description 2
+
+
+NLM_EXTERN CddPrefNodeDescrPtr LIBCALL CddPrefNodeDescrFree PROTO ((CddPrefNodeDescrPtr ));
+NLM_EXTERN CddPrefNodeDescrPtr LIBCALL CddPrefNodeDescrAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CddPrefNodeDescrAsnWrite PROTO (( CddPrefNodeDescrPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    CddPrefNodeDescrSet
+*
+**************************************************/
+typedef ValNode CddPrefNodeDescrSet;
+typedef ValNodePtr CddPrefNodeDescrSetPtr;
+#define CddPrefNodeDescrSetNew() ValNodeNew(NULL) 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN CddPrefNodeDescrSetPtr LIBCALL CddPrefNodeDescrSetFree PROTO ((CddPrefNodeDescrSetPtr ));
+NLM_EXTERN CddPrefNodeDescrSetPtr LIBCALL CddPrefNodeDescrSetNew PROTO (( void ));
+NLM_EXTERN CddPrefNodeDescrSetPtr LIBCALL CddPrefNodeDescrSetAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CddPrefNodeDescrSetAsnWrite PROTO (( CddPrefNodeDescrSetPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
 *    GlobalId
 *
 **************************************************/
@@ -430,6 +519,7 @@ NLM_EXTERN Boolean LIBCALL AlignAnnotSetAsnWrite PROTO (( AlignAnnotSetPtr , Asn
 **************************************************/
 typedef struct struct_Domain_parent {
    struct struct_Domain_parent PNTR next;
+   Int4   parent_type;
    ValNodePtr   parentid;
    struct seqannot PNTR   seqannot;
 } DomainParent, PNTR DomainParentPtr;
@@ -440,41 +530,6 @@ NLM_EXTERN DomainParentPtr LIBCALL DomainParentNew PROTO (( void ));
 NLM_EXTERN DomainParentPtr LIBCALL DomainParentAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
 NLM_EXTERN Boolean LIBCALL DomainParentAsnWrite PROTO (( DomainParentPtr , AsnIoPtr, AsnTypePtr));
 
-typedef ValNodePtr LineageInfoPtr;
-typedef ValNode LineageInfo;
-#define LineageInfo_simpleparent 1
-#define LineageInfo_LineageInfo_Complexparents 2
-
-
-NLM_EXTERN LineageInfoPtr LIBCALL LineageInfoFree PROTO ((LineageInfoPtr ));
-NLM_EXTERN LineageInfoPtr LIBCALL LineageInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
-NLM_EXTERN Boolean LIBCALL LineageInfoAsnWrite PROTO (( LineageInfoPtr , AsnIoPtr, AsnTypePtr));
-
-
-
-/**************************************************
-*
-*    LineageInfo_complexparents
-*
-**************************************************/
-
-#ifdef NLM_GENERATED_CODE_PROTO
-
-typedef struct struct_LineageInfo_Complexparents {
-   struct struct_Domain_parent PNTR   fusionparents;
-   struct struct_Domain_parent PNTR   deletionparent;
-} LineageInfo_complexparents, PNTR LineageInfo_complexparentsPtr;
-#endif /* NLM_GENERATED_CODE_PROTO */
-
-#ifdef NLM_GENERATED_CODE_PROTO
-
-static LineageInfo_complexparentsPtr LIBCALL LineageInfo_complexparentsFree PROTO ((LineageInfo_complexparentsPtr ));
-static LineageInfo_complexparentsPtr LIBCALL LineageInfo_complexparentsNew PROTO (( void ));
-static LineageInfo_complexparentsPtr LIBCALL LineageInfo_complexparentsAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
-static Boolean LIBCALL LineageInfo_complexparentsAsnWrite PROTO (( LineageInfo_complexparentsPtr , AsnIoPtr, AsnTypePtr));
-
-#endif /* NLM_GENERATED_CODE_PROTO */
-
 
 
 /**************************************************
diff --git a/biostruc/cdd/wrpsb.h b/biostruc/cdd/wrpsb.h
index df17492c..4d0ec534 100644
--- a/biostruc/cdd/wrpsb.h
+++ b/biostruc/cdd/wrpsb.h
@@ -1,4 +1,4 @@
-/* $Id: wrpsb.h,v 1.15 2003/10/07 21:15:15 bauer Exp $
+/* $Id: wrpsb.h,v 1.16 2003/11/19 14:34:31 bauer Exp $
 *===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
 *
 * Initial Version Creation Date: 1/19/2000
 *
-* $Revision: 1.15 $
+* $Revision: 1.16 $
 *
 * File Description:
 *         Header file for WWW-RPS BLAST client
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: wrpsb.h,v $
+* Revision 1.16  2003/11/19 14:34:31  bauer
+* changes to support SeqAnnot export
+*
 * Revision 1.15  2003/10/07 21:15:15  bauer
 * support generation of Sequence Annotation from CD-Search results
 *
@@ -92,10 +95,10 @@
 #define DEFAULT_DATALIB    "cdd"
 #define DEFAULT_EVALUE     "0.01"
 #define DEFAULT_NHITS      "25"
-#define NUMARGS            (sizeof(myargs)/sizeof(myargs[0]))
+/* #define NUMARGS            (sizeof(myargs)/sizeof(myargs[0])) */
 #define RPS_MAGIC_NUMBER   7702
 #define WRPSB_GRAPH_WIDTH  600
-#define WRPSB_GRAPH_MAXROW 25
+#define WRPSB_GRAPH_MAXROW 12
 #define WRPSB_GRAPH_HEIGHT 16
 #define WRPSB_GRAPH_SPACER  4
 #define BUFFER_LENGTH      3072
@@ -111,6 +114,9 @@
 #define RETRIEVEPRECALC    4
 #define DRAWQUEUED         5
 #define DRAWONLY           6
+#define DARTSIZELIMIT      1500
+#define DARTFAMILYNUM      15000
+
 
 
 typedef struct _txdfline_struct {
@@ -197,7 +203,7 @@ static Char    CDDpath[PATH_MAX];
 static Char    ENTREZurl[PATH_MAX];
 static Char    DOCSUMurl[PATH_MAX];
 static Char    MAILto[PATH_MAX];
-static FILE    *OutputFile = NULL;
+static FILE    *OutputFile;
 static Char    OutputName[200];
 static Char    gunzip[PATH_MAX];
 static Char    MMDBpath[PATH_MAX];
@@ -207,7 +213,7 @@ static Char    CDDextens[PATH_MAX];
 static Char    RAWextens[PATH_MAX];
 static Char    TREextens[PATH_MAX];
 static Char    SEQextens[PATH_MAX];
-static Int2    SortOn = 0;
+static Int2    SortOn;
 static Int4    cnt_MMDBid;
 static Char    cCDDid[PATH_MAX];
 static Char    CDDdescr[PATH_MAX];
@@ -241,6 +247,9 @@ static Char    ODBCINI[PATH_MAX];
 static Char    DARTUSER[PATH_MAX];
 static Char    DARTPASS[PATH_MAX];
 
+static unsigned iDartFam[DARTFAMILYNUM];
+static Int4   iDartFamNum;
+
 /*---------------------------------------------------------------------------*/
 /* DART color scheme                                                         */
 /*---------------------------------------------------------------------------*/
diff --git a/biostruc/cdd/wrpsbcl3.c b/biostruc/cdd/wrpsbcl3.c
index 7ad03ded..6824506f 100644
--- a/biostruc/cdd/wrpsbcl3.c
+++ b/biostruc/cdd/wrpsbcl3.c
@@ -1,4 +1,4 @@
-/* $Id: wrpsbcl3.c,v 1.35 2003/10/07 21:15:15 bauer Exp $
+/* $Id: wrpsbcl3.c,v 1.36 2003/11/19 14:34:31 bauer Exp $
 *===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
 *
 * Initial Version Creation Date: 4/19/2000
 *
-* $Revision: 1.35 $
+* $Revision: 1.36 $
 *
 * File Description:
 *         WWW-RPS BLAST client
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: wrpsbcl3.c,v $
+* Revision 1.36  2003/11/19 14:34:31  bauer
+* changes to support SeqAnnot export
+*
 * Revision 1.35  2003/10/07 21:15:15  bauer
 * support generation of Sequence Annotation from CD-Search results
 *
@@ -148,9 +151,6 @@
 #undef   CDSEARCH_TEST  /* use iblast1 instead of public service rpsblast */
 #define  WIN_GIF
 
-#define DARTSIZELIMIT 1500
-#define DARTFAMILYNUM 5000
-
 #include <ncbi.h>
 #include <ncbimain.h>
 #include <sequtil.h>
@@ -176,9 +176,6 @@
 #include <pmfapi.h>
 #include <entrez2.h>
 
-unsigned      iDartFam[DARTFAMILYNUM];
-Int4          iDartFamNum = 0;
-
 ReadDBFILEPtr rdfp        = NULL;
 
 /*---------------------------------------------------------------------------*/
@@ -633,9 +630,9 @@ static Boolean WRPSBDrawSearchPage()
     databases[4] = CDDSearch5;
     databases[5] = CDDSearch6;
     databases[6] = CDDSearch7;
+    datab_nam[6] = CDDSname7;
     datab_nam[4] = CDDSname5; 
     datab_nam[5] = CDDSname6; 
-    datab_nam[6] = CDDSname7;
   }
 
 
@@ -727,7 +724,7 @@ static Boolean WRPSBDrawSearchPage()
   printf("</FORM>\n");
   printf("<hr>\n");
 
-  printf("<b><a href=\"http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9254694&form=6&db=m&Dopt=r\">Reference</a>:</b>\n");
+  printf("<b><a href=\"http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9254694&dopt=Abstract\">Reference</a>:</b>\n");
   printf("Altschul, Stephen F., Thomas L. Madden, Alejandro A. Sch&auml;ffer, \n");
   printf("Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), \n");
   printf("\"Gapped BLAST and PSI-BLAST: a new generation of protein database search\n");
@@ -817,6 +814,7 @@ static void WRPSBCl3PrintGraphics(AlignmentAbstractPtr aap, FILE *table, Int4 ma
   Char                 aln[CDD_MAX_DESCR], cTmp2[24];
   CharPtr              buf;
 
+  biasstring[0] = '\0';
 
   if (query_bsp && querygi <= 0) {
     buf = MemNew((query_bsp->length+1)*sizeof(Char));
@@ -914,8 +912,7 @@ static void WRPSBCl3PrintGraphics(AlignmentAbstractPtr aap, FILE *table, Int4 ma
   }
   aapThis = aap;
   while (aapThis) {
-    if (aapThis->row <= WRPSB_GRAPH_MAXROW &&
-      (iGraphMode == 2 || aapThis->bDrawThisOne)) {
+    if (aapThis->row <= WRPSB_GRAPH_MAXROW && (iGraphMode == 2 || aapThis->bDrawThisOne)) {
       nblocks++;
       ulx = aapThis->gstart + 5;
       lrx = aapThis->gstop  + 5;
@@ -1063,7 +1060,7 @@ static void WRPSBCl3PrintGraphics(AlignmentAbstractPtr aap, FILE *table, Int4 ma
     fprintf(table,"<img src=\"%swrpsb.cgi?PIC=%d,%d,%d",
             URLcgi,GraphWidth,query_bsp->length,nblocks);
     aapThis = aap; while (aapThis) {
-      if (aapThis->bDrawThisOne) {
+      if (aapThis->row <= WRPSB_GRAPH_MAXROW && (iGraphMode == 2 || aapThis->bDrawThisOne)) {
         fprintf(table,",%d,%d,%d,%s,%d,%d,%d,%d",aapThis->gstart,aapThis->gstop - aapThis->gstart,
                 aapThis->row,aapThis->cGraphId,aapThis->colcyc,
 	        (Int4)(aapThis->nmissg * 100.0),(Int4)(aapThis->cmissg * 100.0),
@@ -1103,6 +1100,7 @@ static Dart_Connect *WRPSBConnectDart()
   } else {
     Connection = Dart_Init2("CDart", DARTUSER, DARTPASS); 
   } 
+  iDartFamNum = 0;
   Dart_CdFamily(Connection, iDartFam, DARTFAMILYNUM, &iDartFamNum);
   return (Connection);
 }
@@ -1114,524 +1112,6 @@ static void WRPSBDisConnectDart(Dart_Connect *Connection)
 
 /*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
-/* check whether a hit is unique, or to a CD hit somewhere else in the list  */
-/*---------------------------------------------------------------------------*/
-/*---------------------------------------------------------------------------*/
-static Boolean WRPSBHitIsNew(AlignmentAbstractPtr aapThis,
-                             AlignmentAbstractPtr aapHead,
-			     Dart_Connect *Connection)
-{
-  AlignmentAbstractPtr aap;
-  int                  Size, i;
-  unsigned             Gilist[DARTSIZELIMIT];
-  char                 Accession[DARTSIZELIMIT][30];
-  
-  if (!aapThis) return FALSE;
-  for (i=0;i<iDartFamNum;i++) {
-    if (iDartFam[i] == aapThis->pssmid) {
-     aapThis->bIsArch = TRUE;
-     return(TRUE);    
-    }
-  }
-  if (Connection) {
-    if (aapThis->pssmid > 0) {
-      if (Dart_SameSim(Connection,aapThis->pssmid,Gilist,DARTSIZELIMIT,&Size)) {
-        for (i=0;i<Size;i++) {
-          if (!Dart_CDGi2Acc(Connection,Gilist[i],Accession[i],30)) {
-	    Accession[i][0] = '\0';
-          }
-	}
-      }
-    } else {
-      if (Dart_Related(Connection,aapThis->cCDDid,Gilist,DARTSIZELIMIT,&Size,NULL)) {
-        for (i=0;i<Size;i++) {
-          if (!Dart_CDGi2Acc(Connection,Gilist[i],Accession[i],30)) {
-	    Accession[i][0] = '\0';
-          }
-	}
-      }
-    }
-  } else {
-    Size = 0;
-  }
-  
-  aap = aapHead; while (aap) {
-    if (aapThis->pssmid > -1 && aap->pssmid > -1) {
-      if (aapThis->pssmid == aap->pssmid) {
-        aapThis->colcyc = aap->colcyc;
-        return FALSE;
-      }
-    }
-    for (i=0;i<Size;i++) {
-      if (Nlm_StrCmp(Accession[i],aap->cCDDid) == 0) {
-        aapThis->colcyc = aap->colcyc;
-        return FALSE;
-      }
-    }
-    if (Nlm_StrCmp(CDDlocat,"inhouse")==0) {   /* map names just for inhouse */
-      if (aapThis->cCDDid && aap->cCDDid) {
-        if (Nlm_StrCmp(aapThis->cCDDid,aap->cCDDid) == 0) {
-          aapThis->colcyc = aap->colcyc;
-          return FALSE;
-        }
-      }
-      if (Nlm_StrICmp(aapThis->cGraphId,aap->cGraphId) == 0) {
-        aapThis->colcyc = aap->colcyc;
-        return FALSE;
-      }
-    }
-    aap = aap->next;
-  }
-  return TRUE;			     
-}
-
-/*---------------------------------------------------------------------------*/
-/*---------------------------------------------------------------------------*/
-/* define the indents on a block containing repeats according to the alignmt */
-/*---------------------------------------------------------------------------*/
-/*---------------------------------------------------------------------------*/
-static void WRPSBIndentsViaSeqAlign(CddRepeatPtr pcdr,
-                                    AlignmentAbstractPtr aap,
-				    Int4 iGraphWidth,
-				    Int4 length)
-{
-  SeqLocPtr      slp;
-  SeqIntPtr      sintp;
-  Int4Ptr        istarts;
-  Int4           i = 0, j, s1, s2;
-  CddExpAlignPtr pCDea;
-  DenseSegPtr    dsp;
-  
-  istarts = MemNew(pcdr->count * sizeof (Int4));
-  slp = (SeqLocPtr) pcdr->location->data.ptrvalue;
-  while (slp) {
-    sintp = (SeqIntPtr) slp->data.ptrvalue;
-    istarts[i] = sintp->from; i++;
-    slp = slp->next;
-  }
-  
-  pCDea = CddExpAlignNew();
-  CddExpAlignAlloc(pCDea,length);
-  dsp = aap->salp->segs;
-  for (i=0;i<dsp->numseg;i++) {
-    s1 = dsp->starts[i*2];
-    s2 = dsp->starts[i*2+1]; 
-    if (s1 >=0 && s2>= 0) {
-      for (j=0;j<dsp->lens[i];j++) {
-        pCDea->adata[s1+j]=s2+j;
-      }
-    }
-  }
-  aap->indents = MemNew(pcdr->count * sizeof (Int4));
-  aap->nindents = 0;
-  for (i=0;i<pcdr->count;i++) {
-    for (j=0;j<length;j++) {
-      if (pCDea->adata[j] >= istarts[i]) {
-        s1 = (j * iGraphWidth) / (length - 1);
-	if (s1 > aap->gstart && s1 < aap->gstop) {
-	  aap->indents[aap->nindents] = s1;
-	  aap->nindents++;
-	}
-	break;
-      }
-    }
-  }
-  MemFree(istarts);
-}
-
-
-/*---------------------------------------------------------------------------*/
-/*---------------------------------------------------------------------------*/
-/* fill in the Alignment Abstract Data Structure                             */
-/*---------------------------------------------------------------------------*/
-/*---------------------------------------------------------------------------*/
-static AlignmentAbstractPtr WRPSBCl3AbstractAlignment(BlastPruneSapStructPtr prune,
-                                                      BioseqPtr query_bsp,
-                                                      Int4 iGraphWidth,
-                                                      Int4 *mxr,
-                                                      Int4 iGraphMode,
-                                                      CharPtr dbversion,
-                                                      Boolean *bAnyPdb,
-						      Dart_Connect *Connection)
-{
-  Boolean              *bConflict;
-  Boolean              bDbIsOasis = TRUE, found_score = FALSE;
-  Int4                 maxrow = 1, i, pssmid;
-  Int4                 lastcol = -1;
-  Int4                 iCount = 0, replen;
-  Int4                 iColValue, number, score, fullCDstart, fullCDstop, nindent;
-  Int4                 *iOvrlap, *iMutual;
-  AlignmentAbstractPtr aap, aapThis, aapTmp, aapHead = NULL;
-  BioseqPtr            bsp;
-  CddTreePtr           pcddt;
-  CddDescrPtr          description;
-  CddRepeatPtr         pcdr;
-  CharPtr              cTemp;
-  CharPtr              cCurrDesc;
-  DbtagPtr             dbtp;
-  DenseSegPtr          dsp;
-  ObjectIdPtr          oidp;
-  ScorePtr             thisScorePtr;
-  SeqAlignPtr          sap;
-  SeqIdPtr             sip, gi_list;
-  TxDfLineStructPtr    txsp;
-  Nlm_FloatHi          evalue, bit_score;
-  Char                 path[PATH_MAX], hpath[PATH_MAX];
-  Char                 buffer[BUFFER_LENGTH+1];
-  Char                 cDatabase[16];
-  Char                 cCDDid[16];
-  Char                 CDDidx[PATH_MAX];
-
-  Nlm_StrCpy(CDDidx,DATApath);
-  Nlm_StrCat(CDDidx,"/cdd.idx");
-
-/*  if (Nlm_StrCmp(myargs[1].strvalue,"cdd_prop")==0) bDbIsOasis = FALSE; */
-  
-  sap = prune->sap;
-  *bAnyPdb = FALSE;
-  while (sap) {
-    iCount++;
-    aapThis = (AlignmentAbstractPtr)MemNew(sizeof(AlignmentAbstract));
-    aapThis->salp = sap; aapThis->pssmid = -1;
-    dsp = sap->segs;
-    for (i=0;i<dsp->numseg;i++) {
-      if (dsp->starts[2*i] > -1) {
-        aapThis->mstart = dsp->starts[2*i];
-	aapThis->nmissg = (Nlm_FloatHi) dsp->starts[2*i+1];
-	fullCDstart = aapThis->mstart - aapThis->nmissg;
-        break;
-      }
-    }
-    for (i=0;i<dsp->numseg;i++) {
-      if (dsp->starts[2*i] > -1) {
-        aapThis->mstop = dsp->starts[2*i]+dsp->lens[i]-1;
-	aapThis->cmissg = (Nlm_FloatHi) (dsp->starts[2*i+1]+dsp->lens[i]-1);
-      }
-    }
-    aapThis->gstart = (aapThis->mstart * iGraphWidth) / (query_bsp->length-1);
-    aapThis->gstop =  (aapThis->mstop  * iGraphWidth) / (query_bsp->length-1);
-    aapThis->score = sap->score;
-    sip = dsp->ids->next;
-    thisScorePtr = sap->score;
-    found_score = GetScoreAndEvalue(sap, &score, &bit_score, &evalue, &number);
-    if      (evalue >  100.0   ) iColValue = 204;
-    else if (evalue >    1.0   ) iColValue = 153;
-    else if (evalue >    0.01  ) iColValue = 102;
-    else if (evalue >    0.0001) iColValue =  51;
-    else                         iColValue =   0;
-    bsp = BioseqLockById(sip);
-    if (!bsp) {
-      if (sip->choice == SEQID_GENERAL) {
-        dbtp = sip->data.ptrvalue;
-	if (Nlm_StrCmp(dbtp->db,"Cdd") == 0) {
-	  oidp = dbtp->tag;
-	  CddPssmIdFromAcc(&pssmid, oidp->str, CDDidx);
-          oidp = ObjectIdNew();
-	  oidp->id = pssmid;
-	  dbtp = DbtagNew();
-	  dbtp->db = StringSave("CDD");
-	  dbtp->tag = oidp;
-	  sip->data.ptrvalue = dbtp;
-          bsp = BioseqLockById(sip);
-	}
-      }
-    }
-    if (bsp) aapThis->nmissg = aapThis->nmissg/(Nlm_FloatHi)bsp->length;
-    else aapThis->nmissg = 0;
-    if (bsp) {
-      fullCDstop = aapThis->mstop + bsp->length - 1 - aapThis->cmissg;
-      aapThis->cmissg = ((Nlm_FloatHi)bsp->length-1.0-aapThis->cmissg)/(Nlm_FloatHi) bsp->length;
-    } else aapThis->cmissg = 0;
-    txsp = (TxDfLineStructPtr) MemNew(sizeof(TxDfLineStruct));
-    txsp->segs_str = NULL;
-    txsp->segs_buflen = 0;
-    if(bsp != NULL) {
-      gi_list = GetUseThisGi(sap);
-      if (gi_list) {
-        FilterTheDefline(bsp, gi_list, buffer, BUFFER_LENGTH, &(txsp->title));
-        gi_list = SeqIdSetFree(gi_list);
-        sip = SeqIdFree(sip);
-        txsp->id = SeqIdParse(buffer);
-      } else {
-        SeqIdWrite(bsp->id, buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
-        txsp->title = StringSave(BioseqGetTitle(bsp));
-        txsp->id = sip;
-      }
-      txsp->is_na = (bsp->mol != Seq_mol_aa);
-    } else {
-      SeqIdWrite(sip, buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
-      txsp->title = StringSave("Unknown");
-      txsp->is_na = FALSE;
-      txsp->id = sip;
-    }
-    txsp->seqalign = sap;
-    txsp->buffer_id = StringSave(buffer);
-    txsp->score = score;
-    txsp->bit_score = bit_score;
-    txsp->evalue = evalue;
-    txsp->number = number;
-    txsp->found_score = found_score;
-    SeqAlignSegsStr(sap, 1, &txsp->segs_str, &txsp->segs_buflen, &txsp->segs_used);
-    txsp->isnew = FALSE;
-    txsp->waschecked = FALSE;
-    if(bsp != NULL) BioseqUnlock(bsp);
-    aapThis->defline = txsp;
-    aapThis->long_defline = MemNew(sizeof(Char)*(2+strlen(aapThis->defline->title)+strlen(aapThis->defline->buffer_id)));
-    StrCpy(aapThis->long_defline, aapThis->defline->buffer_id);
-    StrCat(aapThis->long_defline," ");
-    StrCat(aapThis->long_defline,aapThis->defline->title);
-    cTemp = StringSave(txsp->buffer_id);
-    if (strncmp(cTemp,"gnl|",4)==0) {
-      strtok(cTemp,"|");
-      aapThis->cDatabase = StringSave(strtok(NULL,"|"));
-      Nlm_StrCpy(path,strtok(NULL,"|"));
-      aapThis->cCDDid = StringSave(strtok(path," "));
-      MemFree(cTemp);
-    } else WRPSBHtmlError("Could not interpret subject defline!");
-    aapThis->bIsProfile = FALSE;
-    if (StringICmp(aapThis->cDatabase,"Smart")==0) {
-      aapThis->red = 255;
-      aapThis->green = aapThis->blue = iColValue;
-      if (StrNCmp(aapThis->cCDDid,"smart0",6) == 0) {
-        cTemp = StringSave(txsp->title);
-        aapThis->cGraphId = StringSave(strtok(cTemp,","));
-	MemFree(cTemp);
-      } else {
-        aapThis->cGraphId = aapThis->cCDDid;
-      }
-    } else if (StringICmp(aapThis->cDatabase,"Pfam") ==0) {
-      aapThis->blue = 255;
-      aapThis->red = aapThis->green = iColValue;
-      cTemp = StringSave(txsp->title);
-      aapThis->cGraphId = StringSave(strtok(cTemp,","));
-      MemFree(cTemp);
-    } else if (StringICmp(aapThis->cDatabase,"scop1.39") ==0) {
-      aapThis->green = 255;
-      aapThis->red = aapThis->blue = iColValue;
-      aapThis->bIsProfile = TRUE;    
-      aapThis->cGraphId = aapThis->cCDDid;
-    } else if (StringICmp(aapThis->cDatabase,"Load") ==0) {
-      aapThis->green = iColValue;
-      aapThis->red = aapThis->blue = 255;    
-      cTemp = StringSave(aapThis->cCDDid);
-      if (strstr(cTemp,":")) {
-        strtok(cTemp,":");
-        aapThis->cGraphId = StringSave(strtok(NULL,":"));
-      } else {
-        strtok(cTemp,"_");
-        aapThis->cGraphId = StringSave(strtok(NULL,"_"));
-      }
-      MemFree(cTemp);
-    } else if (StringCmp(aapThis->cDatabase,"CDD") == 0) {
-      aapThis->pssmid = atoi(aapThis->cCDDid);
-      cTemp = StringSave(txsp->title);
-      aapThis->cCDDid = StringSave(strtok(cTemp,","));
-      aapThis->cGraphId = StringSave(strtok(NULL,","));
-      if (!aapThis->cGraphId) aapThis->cGraphId = StringSave("obsolete");
-      if (Nlm_StrNCmp(aapThis->cGraphId," ",1) == 0) aapThis->cGraphId = aapThis->cGraphId+1;
-      CddTruncStringAtFirstPunct(aapThis->cGraphId);
-      CddFillBlanksInString(aapThis->cGraphId);
-    } else if (StringCmp(aapThis->cDatabase,"Cdd") == 0) {
-      cTemp = StringSave(txsp->title);
-      if (Nlm_StrStr(cTemp,",") != NULL) {
-        if (Nlm_StrStr(cTemp,";") == NULL ||
-	    Nlm_StrStr(cTemp,",") < Nlm_StrStr(cTemp,";")) {
-	  aapThis->cGraphId = StringSave(strtok(cTemp,","));
-	} else aapThis->cGraphId = StringSave(strtok(cTemp,";"));
-      } else aapThis->cGraphId = StringSave(strtok(cTemp,";"));
-    } else if (StringCmp(aapThis->cDatabase,"Cog") == 0) {
-      cTemp = StringSave(txsp->title);
-      if (Nlm_StrStr(cTemp,",") != NULL) {
-        if (Nlm_StrStr(cTemp,";") == NULL ||
-	    Nlm_StrStr(cTemp,",") < Nlm_StrStr(cTemp,";")) {
-	  aapThis->cGraphId = StringSave(strtok(cTemp,","));
-	} else aapThis->cGraphId = StringSave(strtok(cTemp,";"));
-      } else aapThis->cGraphId = StringSave(strtok(cTemp,";"));
-    } else {
-      aapThis->green = iColValue;
-      aapThis->red = aapThis->blue = 255;    
-      aapThis->cGraphId = aapThis->cCDDid;
-    }
-    aapThis->bIsArch = FALSE;
-    aapThis->bIsArchComplete = FALSE;
-    if (WRPSBHitIsNew(aapThis,aapHead,Connection)) {
-      if (!aapThis->bIsArch) {
-        aapThis->colcyc = lastcol + 1;
-        if (aapThis->colcyc >= iNcolors) {
-          aapThis->colcyc -= iNcolors;
-        }
-        lastcol = aapThis->colcyc;
-      } else {
-        aapThis->bIsArchComplete = (aapThis->nmissg + aapThis->cmissg < 0.1);
-      }
-    }
-
-/*
-    if (evalue > 0.01) {
-      aapThis->red   = iDartCol[aapThis->colcyc+iNcolors][0];
-      aapThis->green = iDartCol[aapThis->colcyc+iNcolors][1];
-      aapThis->blue  = iDartCol[aapThis->colcyc+iNcolors][2];
-    
-    } else {
-      aapThis->red   = iDartCol[aapThis->colcyc][0];
-      aapThis->green = iDartCol[aapThis->colcyc][1];
-      aapThis->blue  = iDartCol[aapThis->colcyc][2];
-    }
-*/
-    if (aapThis->bIsArch) {
-      aapThis->colcyc = 255;
-      aapThis->red    = 200;
-      aapThis->green  = 200;
-      aapThis->blue   = 200;
-    } else {
-      aapThis->red   = iDartCol[aapThis->colcyc][0];
-      aapThis->green = iDartCol[aapThis->colcyc][1];
-      aapThis->blue  = iDartCol[aapThis->colcyc][2];
-    }
-    sprintf(aapThis->name,"ali%d",(Int4)random());
-    aapThis->bIsOasis = bDbIsOasis;
-    if (bDbIsOasis) {
-      Nlm_StrCpy(path,CDDPrefix);
-      if (Nlm_StrNCmp(aapThis->cCDDid,"COG",3) == 0 || Nlm_StrNCmp(aapThis->cCDDid,"KOG",3) == 0) {
-        strcat(path,CDDefault);
-      } else strcat(path,dbversion);
-      strcat(path,CDDPost_O);
-      Nlm_StrCpy(hpath,OASIScgi);
-    } else {
-      Nlm_StrCpy(path,CDDPrefix);
-      strcat(path,dbversion);
-      strcat(path,CDDPost_C);
-      Nlm_StrCpy(hpath,CDDcgi);
-    }
-    strcat(path,"/"); strcat(path,aapThis->cCDDid); strcat(path,TREextens);
-    strcat(hpath,aapThis->cCDDid);
-    strcat(hpath,"&version=");
-    if (Nlm_StrNCmp(aapThis->cCDDid,"COG",3) == 0 || Nlm_StrNCmp(aapThis->cCDDid,"KOG",3) == 0) {
-      strcat(hpath,CDDefault);
-    } else strcat(hpath,dbversion);
-    aapThis->cHtmlLink = StringSave(hpath);
-/*---------------------------------------------------------------------------*/
-/* Open Cdd tree file and add description to aapThis data structure          */
-/* changed to binary read to get prepared for the v1.00 rollout. Aron 6/12/00*/
-/*---------------------------------------------------------------------------*/
-    pcddt = (CddTreePtr) CddTreeReadFromFile(path,TRUE);
-    aapThis->bHasStructure = FALSE;
-    if (pcddt) {
-      aapThis->description = pcddt->description;
-      description = aapThis->description;
-      while (description) {
-        if (description->choice == CddDescr_comment) {
-          cCurrDesc = description->data.ptrvalue;
-          if (Nlm_StrCmp(cCurrDesc,"linked to 3D-structure")==0) {
-            aapThis->bHasStructure = TRUE;
-            *bAnyPdb = TRUE;
-          }
-        }
-	if (description->choice == CddDescr_repeats) {
-	  pcdr = (CddRepeatPtr) description->data.ptrvalue;
-	  nindent = pcdr->count - 1;
-	  if (NULL == pcdr->location) {
-	    replen = (fullCDstop - fullCDstart + 1) / (nindent+1);
-	    aapThis->nindents = 0;
-	    aapThis->indents = MemNew(nindent * sizeof(Int4));
-	    for (i=0;i<nindent;i++) {
-	      fullCDstop = ((fullCDstart + (i+1)*replen) * iGraphWidth) / (query_bsp->length - 1);
-              if (fullCDstop > aapThis->gstart && fullCDstop < aapThis->gstop) {
-                aapThis->indents[aapThis->nindents] = fullCDstop;
-	        aapThis->nindents++;
-	      }
-	    }
-	  } else {
-	    WRPSBIndentsViaSeqAlign(pcdr,aapThis,iGraphWidth,query_bsp->length);
-	  }
-	}
-        description = description->next;
-      }
-    }
-/*---------------------------------------------------------------------------*/
-/* get the file name for the FASTA-sequence file which stores the subject..  */
-/*---------------------------------------------------------------------------*/
-    aapThis->cSeqFile = MemNew(PATH_MAX*sizeof(Char));
-    if (bDbIsOasis) {
-      Nlm_StrCpy(aapThis->cSeqFile,CDDPrefix);
-      if (Nlm_StrNCmp(aapThis->cCDDid,"COG",3) == 0 || Nlm_StrNCmp(aapThis->cCDDid,"KOG",3) == 0) {
-        strcat(aapThis->cSeqFile,CDDefault);
-      } else {
-        strcat(aapThis->cSeqFile,dbversion);
-      }
-      strcat(aapThis->cSeqFile,CDDPost_O);
-    } else {
-      Nlm_StrCpy(aapThis->cSeqFile,CDDPrefix); strcat(aapThis->cSeqFile,dbversion);
-      strcat(aapThis->cSeqFile,CDDPost_C);
-    }
-    strcat(aapThis->cSeqFile,"/"); strcat(aapThis->cSeqFile,aapThis->cCDDid);
-    strcat(aapThis->cSeqFile,SEQextens);
-       
-/*---------------------------------------------------------------------------*/
-/* Check for overlaps and determine row number                               */
-/* Check for mutal overlap if condensed graphics is selected                 */
-/*---------------------------------------------------------------------------*/
-    iOvrlap = MemNew(maxrow*sizeof(Int4));
-    iMutual = MemNew(maxrow*sizeof(Int4));
-    for (i=0;i<maxrow;i++) iOvrlap[i]=0;
-    aapThis->row = 1; aapThis->bDrawThisOne = TRUE;
-    if (aapHead) {    
-      aapTmp = aapHead;
-      while (aapTmp) {
-        if (aapTmp->bDrawThisOne) {
-          if (OverlapInterval(aapTmp->mstart,aapTmp->mstop, aapThis->mstart,aapThis->mstop))
-            iOvrlap[aapTmp->row-1] = 1;
-          if (iGraphMode == 1 || iGraphMode == 3) {
-            if (OverlapMutual(aapTmp->mstart,aapTmp->mstop,aapThis->mstart,aapThis->mstop)) {
-              iMutual[aapTmp->row-1] = 1;
-	      if (aapThis->bIsArch) {
-	        if (aapThis->bIsArchComplete) {
-		  if (!aapTmp->bIsArch || !aapTmp->bIsArchComplete) iMutual[aapTmp->row-1] = 0; 
-		}
-	      } else {
-	        if (aapTmp->bIsArch) iMutual[aapTmp->row-1] = 0;
-	      }
-            }
-          }
-        }
-        aapTmp = aapTmp->next;
-      }
-      aapThis->row = 0;
-      for (i=0;i<maxrow;i++) {
-        if (iOvrlap[i]==0) {
-          aapThis->row = i+1;
-          break;
-        }
-      }
-      if (iGraphMode == 1 || iGraphMode == 3) for (i=0;i<maxrow;i++) {
-        if (iMutual[i]==1) {
-          aapThis->bDrawThisOne = FALSE;
-          break;
-        }
-      }
-      if (aapThis->row == 0) aapThis->row = maxrow+1;
-    }
-    MemFree(iMutual);
-    MemFree(iOvrlap);
-    if (aapThis->row > maxrow) maxrow = aapThis->row;
-
-    aapThis->next = NULL;
-
-    if (aapHead==NULL) {
-       aapHead = aapThis;
-       aap = aapHead;
-    } else {
-       aap->next = aapThis;
-       aap = aapThis;
-    }
-    sap = sap->next;
-  }
-  *mxr = maxrow;
-  return(aapHead);
-}
-
-/*---------------------------------------------------------------------------*/
-/*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
 static Boolean WRPSBPrintDbInformationBasic (CharPtr database, Boolean is_aa, Int4 line_length, CharPtr definition, Int4 number_seqs, Int8 total_length, FILE *outfp, Boolean html)
@@ -1661,169 +1141,6 @@ static Boolean WRPSBPrintDbInformationBasic (CharPtr database, Boolean is_aa, In
 
 /*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
-/*---------------------------------------------------------------------------*/
-/*---------------------------------------------------------------------------*/
-static void WRPSBCl3SeqAnnot(AlignmentAbstractPtr aapIn, FILE *table,
-                             Boolean bSeqAlign)
-{
-  AsnIoPtr              aip;
-  AlignmentAbstractPtr  aap;
-  SeqAnnotPtr           sap;
-  SeqLocPtr             slp;
-  SeqFeatPtr            sfp, sfpHead = NULL, sfpTail = NULL;
-  DenseSegPtr           dsp;
-  SeqIdPtr              sipQuery;
-  SeqIntPtr             sintp;
-  DbtagPtr              dbtp;
-  ObjectIdPtr           oidp;
-  Char                  dupstr[PATH_MAX];
-  CharPtr               part1, rest, thispart;
-  UserObjectPtr         uop;
-  UserFieldPtr          ufp, ufpTail;
-  Nlm_FloatHi           evalue, bit_score;
-  Int4                  score, number, i, icnt;
-  Boolean               found_score;
-  AnnotDescPtr          adp, adp2;
-  DatePtr               dp;
-  SeqAlignPtr           salpTail = NULL, salpHead = NULL;
-
-  sap = SeqAnnotNew();
-  if (bSeqAlign) {
-    sap->type = 2; /* Sequence Alignment */
-  } else sap->type = 1; /* feature table */
-  adp = (AnnotDescPtr) ValNodeNew(NULL);
-  adp->choice = Annot_descr_name;
-  adp->data.ptrvalue = StringSave("CDDSearch");
-  sap->desc = adp;
-  adp2 = (AnnotDescPtr) ValNodeNew(NULL);
-  dp = DateCurr();
-  adp2->choice = Annot_descr_create_date;
-  adp2->data.ptrvalue = dp;
-  adp->next = adp2;
-  aap = aapIn;
-  while (aap) {
-    if (aap->bDrawThisOne) {
-      sfp = SeqFeatNew();
-      if (bSeqAlign) {
-        if (!salpHead) {
-	  salpHead = aap->salp;
-	} else salpTail->next = aap->salp;
-	  salpTail = aap->salp;
-	  salpTail->next = NULL;
-      } else {
-        sfp->data.choice = 9;
-        strncpy(dupstr,aap->long_defline,PATH_MAX);
-        part1 = strtok(dupstr," ");
-        if (part1) {
-          rest = dupstr + strlen(part1) + 1;
-        } else {
-          rest = StringSave(aap->long_defline);
-        }
-        icnt = 0;
-        for (i=0;i<Nlm_StrLen(rest);i++) {
-          if (rest[i] == ',') icnt++;
-	  if (icnt > 1) break;
-        }
-        if (icnt > 1) {
-          i = i+2;
-        } else i = 0;
-        thispart = &rest[i];
-        for (i=0;i<Nlm_StrLen(thispart);i++) {
-          if (thispart[i] == '.' || thispart[i] == ';') {
-	    thispart[i] = '\0';
-	    break;
-	  }
-        }
-        sfp->data.value.ptrvalue = StringSave(thispart);
-        sfp->comment = StringSave(aap->cGraphId);   /* comment is short name */
-        if (aap->nmissg >= 0.2 || aap->cmissg >= 0.2) sfp->partial = TRUE;
-        dsp = aap->salp->segs;
-        sipQuery = dsp->ids;
-        slp = (SeqLocPtr) ValNodeNew(NULL); slp->choice = SEQLOC_INT;
-        sintp=SeqIntNew(); sintp->from = aap->mstart; sintp->to = aap->mstop;
-        sintp->id = SeqIdDup(sipQuery); slp->data.ptrvalue = sintp;
-        sfp->location = slp;
-        if (sfp->partial) {
-          SetSeqLocPartial(sfp->location, aap->nmissg >= 0.2, aap->cmissg >= 0.2);
-        }
-        uop = UserObjectNew();
-        oidp = ObjectIdNew();
-        oidp->str = StringSave("cddScoreData");
-        uop->type = oidp;
-        ufp = UserFieldNew();
-        oidp = ObjectIdNew();
-        oidp->str = StringSave("definition");
-        ufp->label = oidp;
-        ufp->choice = 1;
-        ufp->data.ptrvalue =  StringSave(aap->cCDDid);
-        uop->data = ufp;
-        ufpTail = ufp;
-        ufp = UserFieldNew();
-        oidp = ObjectIdNew();
-        oidp->str = StringSave("short_name");
-        ufp->label = oidp;
-        ufp->choice = 1;
-        ufp->data.ptrvalue = StringSave(aap->cGraphId);     
-        ufpTail->next = ufp;
-        ufpTail = ufp;
-        found_score = GetScoreAndEvalue(aap->salp, &score, &bit_score, &evalue, &number);
-        if (found_score) {
-          ufp = UserFieldNew();
-          oidp = ObjectIdNew();
-          oidp->str = StringSave("score");
-          ufp->label = oidp;
-          ufp->choice = 2;
-          ufp->data.intvalue = score;     
-          ufpTail->next = ufp;
-          ufpTail = ufp;
-          ufp = UserFieldNew();
-          oidp = ObjectIdNew();
-          oidp->str = StringSave("evalue");
-          ufp->label = oidp;
-          ufp->choice = 3;
-          ufp->data.realvalue = score;     
-          ufpTail->next = ufp;
-          ufpTail = ufp;
-          ufp = UserFieldNew();
-          oidp = ObjectIdNew();
-          oidp->str = StringSave("bit_score");
-          ufp->label = oidp;
-          ufp->choice = 3;
-          ufp->data.realvalue = bit_score;     
-          ufpTail->next = ufp;
-          ufpTail = ufp;
-        }
-        sfp->ext = uop;
-        dbtp = DbtagNew();
-        dbtp->db = StringSave(aap->cDatabase);
-        oidp = ObjectIdNew();
-        oidp->id = aap->pssmid;
-        dbtp->tag = oidp;
-        sfp->dbxref = ValNodeNew(NULL);
-        sfp->dbxref->data.ptrvalue = dbtp;
-        if (!sfpHead) {
-          sfpHead = sfp;
-        } else {
-          sfpTail->next = sfp;
-        }
-        sfpTail = sfp;
-      }
-    }
-    aap = aap->next;
-  }
-  if (bSeqAlign) {
-    sap->data = salpHead;
-  } else sap->data = sfpHead;
-  strcpy(OutputName,GetTempName("wrpsbcl3"));
-  aip = AsnIoOpen(OutputName, "w");
-  SeqAnnotAsnWrite((SeqAnnotPtr) sap, aip, NULL);
-  AsnIoClose(aip);
-  PrintFile(OutputName);
-  RemoveTempFiles();   
-}
-
-/*---------------------------------------------------------------------------*/
-/*---------------------------------------------------------------------------*/
 /* this is the main wrapper routine for formatting html-rps-blast-output     */
 /*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
@@ -1874,7 +1191,7 @@ static void WRPSBCl3ViewSeqAlign(SeqAlignPtr seqalign, BioseqPtr query_bsp,
 #ifdef RESULTS_FILE
   Nlm_StrCpy(tableName,(CharPtr) GetTempName("wrpsb")); 
   if  (!(table = FileOpen(tableName,"w"))) {
-    WRPSBHtmlError("Temp File Open Failed on Server");
+    WRPSBHtmlError("Temp File Open Failed on Server",bAnnotOnly);
   }
 #endif
 #ifndef RESULTS_FILE
@@ -1935,12 +1252,16 @@ static void WRPSBCl3ViewSeqAlign(SeqAlignPtr seqalign, BioseqPtr query_bsp,
   if (prune->number == 0) {
     if (iGraphMode && !bAnnotOnly) {
       WRPSBCl3PrintGraphics(NULL,table,0,query_bsp,mask, iGraphMode, GraphWidth, bDirect, bIsPrecalc, querygi);
-    }
-    fprintf(table, "<br><strong>...No hits found!</strong>\n");
+    } 
+    if (bAnnotOnly) {
+      WRPSBCl3SeqAnnot(NULL, table, bSeqAlign, FALSE);
+    } else fprintf(table, "<br><strong>...No hits found!</strong>\n");
   } else {
-    aap = WRPSBCl3AbstractAlignment(prune,query_bsp,GraphWidth-10,&maxrow,iGraphMode,dbversion, &bAnyPdb, Connection);
+    aap = WRPSBCl3AbstractAlignment(prune,query_bsp,GraphWidth-10,&maxrow,iGraphMode,dbversion, &bAnyPdb, Connection, TRUE,
+                                    CDDefault,DATApath,CDDPrefix,CDDPost_C,CDDPost_O,
+				    TREextens,SEQextens,OASIScgi,CDDcgi,NULL,iDartFam,iDartFamNum, bAnnotOnly);
     if (bAnnotOnly) {
-      WRPSBCl3SeqAnnot(aap, table, bSeqAlign);
+      WRPSBCl3SeqAnnot(aap, table, bSeqAlign, FALSE);
       WRPSBSearchFoot(bAnnotOnly, bNoWrap);
     }
     if (iGraphMode && !bAnnotOnly) {
@@ -2092,7 +1413,7 @@ static AlignmentAbstractPtr WRPSBWWWargs(WWWInfoPtr www_info, Boolean *bIsQueued
     if (GetArgc() <2) *bMode = FALSE; else *bMode = TRUE; 
   } else if (WWWGetMethod(www_info) == WWW_GET) {
     if (WWWGetNumEntries(www_info)<1) {
-      if (!WRPSBDrawSearchPage()) WRPSBHtmlError("Could not draw initial page...");
+      if (!WRPSBDrawSearchPage()) WRPSBHtmlError("Could not draw initial page...", FALSE);
     } else *bMode = TRUE;
   } else if (WWWGetMethod(www_info) == WWW_POST) {
     *bMode = TRUE;
@@ -2128,26 +1449,26 @@ static AlignmentAbstractPtr WRPSBWWWargs(WWWInfoPtr www_info, Boolean *bIsQueued
     *bIsPic = TRUE;
     www_arg = WWWGetValueByIndex(www_info, indx);
     *GraphWidth = (Int4) atoi(strtok(www_arg,","));
-    if (*GraphWidth <= 0 || *GraphWidth > 10000) WRPSBHtmlError("Error in image formatting - invalid Graphics Width!");  
+    if (*GraphWidth <= 0 || *GraphWidth > 10000) WRPSBHtmlError("Error in image formatting - invalid Graphics Width!", FALSE);  
     *qlength = (Int4) atoi(strtok(NULL,","));
-    if (*qlength <= 0) WRPSBHtmlError("Error in image formatting - invalid query length!");  
+    if (*qlength <= 0) WRPSBHtmlError("Error in image formatting - invalid query length!", FALSE);  
     nhits = (Int4) atoi(strtok(NULL,","));
-    if (nhits < 0) WRPSBHtmlError("Error in image formatting - invalid number of hits");
+    if (nhits < 0) WRPSBHtmlError("Error in image formatting - invalid number of hits", FALSE);
     for (i=0;i<nhits;i++) {
       aapThis = MemNew(sizeof(AlignmentAbstract));
       from = (Int4) atoi(strtok(NULL,","));
-      if (from < 0) WRPSBHtmlError("Error in image formatting - invalid interval");
+      if (from < 0) WRPSBHtmlError("Error in image formatting - invalid interval", FALSE);
       aapThis->gstart = from;
       to = (Int4) atoi(strtok(NULL,",")) + from;
-      if (to < 0 || to < from) WRPSBHtmlError("Error in image formatting - invalid interval");
+      if (to < 0 || to < from) WRPSBHtmlError("Error in image formatting - invalid interval", FALSE);
       aapThis->gstop = to;
       row = (Int4) atoi(strtok(NULL,","));
       aapThis->row = row;
-      if (row < 0) WRPSBHtmlError("Error in image formatting - invalid row");
+      if (row < 0) WRPSBHtmlError("Error in image formatting - invalid row", FALSE);
       name = StringSave(strtok(NULL,","));
       aapThis->cGraphId = name;
       colcyc = (Int4) atoi(strtok(NULL,","));
-      if (colcyc < 0) WRPSBHtmlError("Error in image formatting - invalid color");
+      if (colcyc < 0) WRPSBHtmlError("Error in image formatting - invalid color", FALSE);
       aapThis->colcyc = colcyc;
       if (colcyc == 255) {
         aapThis->bIsArch = TRUE;
@@ -2161,13 +1482,13 @@ static AlignmentAbstractPtr WRPSBWWWargs(WWWInfoPtr www_info, Boolean *bIsQueued
         aapThis->bIsArch = FALSE;
       }
       nmiss = (Int4) atoi(strtok(NULL,","));
-      if (nmiss < 0 || nmiss >= 100) WRPSBHtmlError("Error in image formatting - invalid truncation");
+      if (nmiss < 0 || nmiss >= 100) WRPSBHtmlError("Error in image formatting - invalid truncation", FALSE);
       aapThis->nmissg = (Nlm_FloatHi) nmiss / 100.0;
       cmiss = (Int4) atoi(strtok(NULL,","));
-      if (cmiss < 0 || cmiss >= 100) WRPSBHtmlError("Error in image formatting - invalid truncation");
+      if (cmiss < 0 || cmiss >= 100) WRPSBHtmlError("Error in image formatting - invalid truncation", FALSE);
       aapThis->cmissg = (Nlm_FloatHi) cmiss / 100.0;
       nindent = (Int4) atoi(strtok(NULL,","));
-      if (nindent < 0) WRPSBHtmlError("Error in image formatting - invalid indentation");
+      if (nindent < 0) WRPSBHtmlError("Error in image formatting - invalid indentation", FALSE);
       aapThis->nindents = nindent;
       indents = (Int4Ptr) MemNew(nindent * sizeof(Int4));
       for (j=0;j<nindent;j++) {
@@ -2185,7 +1506,7 @@ static AlignmentAbstractPtr WRPSBWWWargs(WWWInfoPtr www_info, Boolean *bIsQueued
     }
 
     nhits = (Int4) atoi(strtok(NULL,","));
-    if (nhits < 0) WRPSBHtmlError("Error in image formatting - invalid number of biased regions");
+    if (nhits < 0) WRPSBHtmlError("Error in image formatting - invalid number of biased regions", FALSE);
     for (i=0;i<nhits;i++) {
       sintp = SeqIntNew();
       sintp->from = (Int4) atoi(strtok(NULL,","));
@@ -2281,7 +1602,7 @@ static AlignmentAbstractPtr WRPSBWWWargs(WWWInfoPtr www_info, Boolean *bIsQueued
       if (Nlm_StrCmp(www_arg,"precalc") == 0) *bIsPrecalc = TRUE;
     } else {
       *bQueryIsFasta = TRUE;
-      myargs[21].intvalue = 0;
+      if (!*bAnnotOnly) myargs[21].intvalue = 0;
     }
     if (*bIsPrecalc) {
       if ((indx = WWWFindName(www_info,"FULL")) >= 0) {
@@ -2296,7 +1617,7 @@ static AlignmentAbstractPtr WRPSBWWWargs(WWWInfoPtr www_info, Boolean *bIsQueued
   if ((indx = WWWFindName(www_info,"SEQUENCE")) >= 0) {
     *sequence = WWWGetValueByIndex(www_info,indx);
     if ((*sequence == NULL || *sequence[0]==NULLB) && *rid == NULL) {
-      WRPSBHtmlError("Query SEQUENCE missing from input!");
+      WRPSBHtmlError("Query SEQUENCE missing from input!", *bAnnotOnly);
     }
   }
   return(aapHead);
@@ -2345,13 +1666,15 @@ static Int4 WRPSBGiForAcc(CharPtr accession)
 /* return a bioseq using the SEQUENCE field supplied to the cgi-bin.         */
 /*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
-static BioseqPtr WRPSBGetSequence(CharPtr pcsq, Int4 *gi)
+static BioseqPtr WRPSBGetSequence(CharPtr pcsq, Int4 *gi, Boolean bBelieveQuery,
+                                  Boolean bAnnotOnly)
 {
   BioseqPtr    bsp;
   SeqEntryPtr  sep;
   SeqIdPtr     sip      = NULL;
   CharPtr      chptr, outptr;
   CharPtr      sequence, accession, tempstr;
+  CharPtr      errmsg;
   Int4Ptr      giptr;
   Int4         numgi    = 0;
   Boolean      bIsFasta = FALSE;
@@ -2391,8 +1714,9 @@ static BioseqPtr WRPSBGetSequence(CharPtr pcsq, Int4 *gi)
 }                                                                            */
 /*---------------------------------------------------------------------------*/
 
-  if (!pcsq) WRPSBHtmlError("No query sequence - nothing to report!");
-  sequence = StringSave(Nlm_StrUpper(pcsq));
+  if (!pcsq) WRPSBHtmlError("No query sequence - nothing to report!", bAnnotOnly);
+  sequence = StringSave(pcsq);
+  sequence = Nlm_StrUpper(sequence);
   chptr = sequence;
   while (IS_WHITESP(*chptr) && *chptr != NULLB) chptr++;
   if (chptr[0] == '>') {
@@ -2431,12 +1755,32 @@ static BioseqPtr WRPSBGetSequence(CharPtr pcsq, Int4 *gi)
     }
   }
   if (bIsFasta) {
-    if((sep=FastaToSeqBuffEx(pcsq, &outptr,FALSE,NULL,FALSE))==NULL)
-      WRPSBHtmlError("Can not convert FASTA formatted sequence!");
-    if(sep->choice != 1) WRPSBHtmlError("Conversion from FASTA failed!");
+    errmsg = MemNew(1024*sizeof(Char));
+    if((sep=FastaToSeqBuffEx(pcsq, &outptr,FALSE,&errmsg,bBelieveQuery))==NULL)
+      WRPSBHtmlError("Can not convert FASTA formatted sequence!", bAnnotOnly);
+    if(sep->choice != 1) WRPSBHtmlError("Conversion from FASTA failed!", bAnnotOnly);
     bsp = (BioseqPtr) sep->data.ptrvalue;
+    sip = bsp->id;
+    while (sip) {
+      if (sip->choice == SEQID_GI) {
+        *gi = sip->data.intvalue;
+	bsp->id = sip;
+	break;
+      }
+      sip = sip->next;
+    }
+/*
+    if (bBelieveQuery) {
+      if (*gi > 0) {
+        WRPSBHtmlError("Sequence conversion successful");
+      } else {
+        if (errmsg) WRPSBHtmlError(errmsg);
+	else WRPSBHtmlError(pcsq);
+      }
+    }
+ */   
   }
-  if (!bsp) WRPSBHtmlError("Could not find sequence!");
+  if (!bsp) WRPSBHtmlError("Could not find sequence!", bAnnotOnly);
   return(bsp);
 
 /*---------------------------------------------------------------------------*/
@@ -2631,26 +1975,26 @@ Int2 Main (void)
 /*---------------------------------------------------------------------------*/
 /* Get Default Arguments (but DON'T read from command line)                  */
 /*---------------------------------------------------------------------------*/
-  if (!WRPSBGetArgs ("blastcl3", NUMARGS, myargs)) WRPSBHtmlError("Can't read Arguments!");
+  if (!WRPSBGetArgs ("blastcl3", NUMARGS, myargs)) WRPSBHtmlError("Can't read Arguments!", FALSE);
 
 /*---------------------------------------------------------------------------*/
 /* retrieve names for directories etc.                                       */
 /*---------------------------------------------------------------------------*/
-  if (!CddGetParams()) WRPSBHtmlError("Couldn't read from config file...");
+  if (!CddGetParams()) WRPSBHtmlError("Couldn't read from config file...", FALSE);
   blast_program = StringSave(myargs[0].strvalue);
 
 /*---------------------------------------------------------------------------*/
 /* Begin processing www information block                                    */
 /*---------------------------------------------------------------------------*/
   if (WWWGetArgs(&www_info) != WWWErrOk) {
-    WRPSBHtmlError("Failed to process posting - check your get/post syntax.");
+    WRPSBHtmlError("Failed to process posting - check your get/post syntax.", FALSE);
   }
 
 /*---------------------------------------------------------------------------*/
 /* set the BLASTDB environment variable                                      */
 /*---------------------------------------------------------------------------*/
   if (putenv("BLASTDB=/blast/db/blast")) {
-    WRPSBHtmlError("Error setting environment variable BLASTDB");
+    WRPSBHtmlError("Error setting environment variable BLASTDB", FALSE);
   }
 
 /*---------------------------------------------------------------------------*/
@@ -2682,7 +2026,7 @@ Int2 Main (void)
 /*---------------------------------------------------------------------------*/
 /* if called without arguments, draw the initial WRPSB page                  */
 /*---------------------------------------------------------------------------*/
-  if (!bMode) if (!WRPSBDrawSearchPage()) WRPSBHtmlError("Could not draw initial page...");
+  if (!bMode) if (!WRPSBDrawSearchPage()) WRPSBHtmlError("Could not draw initial page...", bAnnotOnly);
 
 /*---------------------------------------------------------------------------*/
 /* start initializing stuff required for database access                     */
@@ -2697,9 +2041,9 @@ Int2 Main (void)
 /*---------------------------------------------------------------------------*/
   if (!rid) {
     EntrezSetService ("Entrez2");
-    if (!PubSeqFetchEnable()) WRPSBHtmlError("Cannot initialize PubSeqFetch!");
+    if (!PubSeqFetchEnable()) WRPSBHtmlError("Cannot initialize PubSeqFetch!", bAnnotOnly);
     if(!(rdfp = readdb_new_ex("nr", READDB_DB_IS_PROT, FALSE)))
-     WRPSBHtmlError("Readdb init failed");
+     WRPSBHtmlError("Readdb init failed", bAnnotOnly);
   }
     
 /*---------------------------------------------------------------------------*/
@@ -2714,7 +2058,7 @@ Int2 Main (void)
     }
 #else */
     if (putenv("NI_SERVICE_NAME_NETBLAST=rpsblast")) {
-      WRPSBHtmlError("Error setting environment");
+      WRPSBHtmlError("Error setting environment", bAnnotOnly);
     }
 /* #endif */
   }
@@ -2735,7 +2079,7 @@ Int2 Main (void)
   if (myargs[26].intvalue) html = TRUE;
   align_view = (Int1) myargs[4].intvalue;
   align_type = BlastGetTypes(blast_program, &query_is_na, &db_is_na);
-  if(align_type == blast_type_undefined) WRPSBHtmlError("Blast Type not defined!");
+  if(align_type == blast_type_undefined) WRPSBHtmlError("Blast Type not defined!", bAnnotOnly);
   if (StringICmp("blastx", blast_program) == 0) {
     if (align_view != 0) {
       ErrPostEx(SEV_FATAL, 0, 0, "This option is not available with blastx");
@@ -2749,7 +2093,7 @@ Int2 Main (void)
   }
     
   options = BLASTOptionNew(blast_program, (Boolean) myargs [16].intvalue);
-  if (options == NULL) WRPSBHtmlError("Could not initialize Blast Options!");
+  if (options == NULL) WRPSBHtmlError("Could not initialize Blast Options!", bAnnotOnly);
 /*---------------------------------------------------------------------------*/
 /* If option RPS Blast set - option "program" is ignored by the engine       */
 /*---------------------------------------------------------------------------*/
@@ -2758,17 +2102,18 @@ Int2 Main (void)
 /*---------------------------------------------------------------------------*/
 /* deal with sequence information - unless the query is retrieved from queue */
 /*---------------------------------------------------------------------------*/
+  believe_query = FALSE;
+  if (myargs[21].intvalue != 0 || bAnnotOnly) believe_query = TRUE;
   if (!rid) {
     gi = 0;
-    bsp = WRPSBGetSequence(sequence, &gi);
-    if (gi) {
+    bsp = WRPSBGetSequence(sequence, &gi, believe_query, bAnnotOnly);
+    if (gi || bAnnotOnly) {
       myargs[21].intvalue = 1;
     } else {
       myargs[21].intvalue = 0;
     }
     query_bsp = bsp;
   }
-  believe_query = FALSE; if (myargs[21].intvalue != 0) believe_query = TRUE;
 
 /*---------------------------------------------------------------------------*/
 /* Section to get data needed for displaying pre-calculated RPS-Blast alignmt*/
@@ -2777,7 +2122,7 @@ Int2 Main (void)
     Connection = WRPSBConnectDart();
     Dart_Gi2Seq(Connection,(unsigned)gi,NULL,NULL,NULL,0,NULL,0,NULL,0,
                 NULL,0,NULL,&sap,NULL);
-    if (!sap) WRPSBHtmlError("Could not read precalculated alignment!");
+    if (!sap) WRPSBHtmlError("Could not read precalculated alignment!", bAnnotOnly);
     myargs[13].intvalue = myargs[14].intvalue = 250;       /* number of hits */
   }
 
@@ -2841,10 +2186,10 @@ Int2 Main (void)
     else query_is_na = FALSE;
   }
 
-  if (!bsp) WRPSBHtmlError("Query SEQUENCE missing from input!");
+  if (!bsp) WRPSBHtmlError("Query SEQUENCE missing from input!", bAnnotOnly);
   if (ISA_na(bsp->mol)) query_is_na = TRUE;
   if (query_is_na) {
-    WRPSBHtmlError("Can not process nucleotide sequences!");
+    WRPSBHtmlError("Can not process nucleotide sequences!", bAnnotOnly);
   }
   qlength = query_bsp->length;
   
@@ -2923,7 +2268,7 @@ Int2 Main (void)
   if (!rid && !bIsQueued /* && !bIsPrecalc */) {
     if (! BlastInit("blastcl3", &bl3hp, &response)) {
       ErrPostEx(SEV_FATAL, 0, 0, "Unable to initialize BLAST service");
-      WRPSBHtmlError("Unable to initialize BLAST service!");
+      WRPSBHtmlError("Unable to initialize BLAST service!", bAnnotOnly);
       return (1);
     }
     
@@ -2934,11 +2279,11 @@ Int2 Main (void)
     } else {
 #ifdef CDSEARCH_TEST
       if (putenv("NI_SERVICE_NAME_NETBLAST=dart_test")) {
-        WRPSBHtmlError("Error setting environment");
+        WRPSBHtmlError("Error setting environment", bAnnotOnly);
       }
       if (! BlastInit("blastcl3", &bl3hp, &response)) {
         ErrPostEx(SEV_FATAL, 0, 0, "Unable to initialize BLAST service");
-        WRPSBHtmlError("Unable to initialize BLAST service!");
+        WRPSBHtmlError("Unable to initialize BLAST service!", bAnnotOnly);
         return (1);
       }
       if (response && response->choice == BlastResponse_init) {
@@ -2947,17 +2292,17 @@ Int2 Main (void)
         date = blast_version->date;
       } else {
         ErrPostEx(SEV_FATAL, 0, 0, "Unable to connect to service");
-        WRPSBHtmlError("Unable to connect to service!");
+        WRPSBHtmlError("Unable to connect to service!", bAnnotOnly);
         return (1);
       }
 #else
       ErrPostEx(SEV_FATAL, 0, 0, "Unable to connect to service");
-      WRPSBHtmlError("Unable to connect to service!");
+      WRPSBHtmlError("Unable to connect to service!", bAnnotOnly);
       return (1);
 #endif
     }
     if (!BlastNetBioseqFetchEnable(bl3hp, blast_database, db_is_na, TRUE)) 
-      WRPSBHtmlError("Unable to connect to Blast Database!");
+      WRPSBHtmlError("Unable to connect to Blast Database!", bAnnotOnly);
   }
 
   retval=0;
@@ -2997,7 +2342,7 @@ Int2 Main (void)
     blast_database = NULL; other_returns = NULL; error_returns = NULL;
     Qstatus = (Int2) QBlastGetResults(rid,&sap,&query_bsp,&blast_program,&blast_database,&other_returns, &error_returns);
     if (Qstatus < 0) {
-      WRPSBHtmlError("Error retrieving CD-Search request from BLAST Queue!");
+      WRPSBHtmlError("Error retrieving CD-Search request from BLAST Queue!", bAnnotOnly);
       return(1);
     }
     if (Qstatus > 0) {
@@ -3009,14 +2354,14 @@ Int2 Main (void)
     }
     ReadDBBioseqFetchEnable ("wrpsb", blast_database, db_is_na, TRUE);
     if (!sap) sap = (SeqAnnotPtr) BLASTGetSeqAnnotByRID(rid);
-    if (!sap)  WRPSBHtmlError("BLAST queue did not return alignment");
+    if (!sap)  WRPSBHtmlError("BLAST queue did not return alignment", bAnnotOnly);
     if (!query_bsp) {
       salp = sap->data;
       dsp = salp->segs;
       sip = dsp->ids;
       query_bsp = BioseqLockById(sip);
     }
-    if (!query_bsp)  WRPSBHtmlError("BLAST queue did not return query sequence");
+    if (!query_bsp)  WRPSBHtmlError("BLAST queue did not return query sequence", bAnnotOnly);
     else {
       sip = query_bsp->id;
       if (sip->choice != SEQID_LOCAL) believe_query = TRUE;
@@ -3027,7 +2372,7 @@ Int2 Main (void)
     version = BlastGetVersionNumber();
     if (!salp) {
       if (error_returns) {
-        WRPSBHtmlError("No sequence alignment retrieved from BLAST queue!");
+        WRPSBHtmlError("No sequence alignment retrieved from BLAST queue!", bAnnotOnly);
       }
     } 
   }
@@ -3039,7 +2384,7 @@ Int2 Main (void)
           ErrPostEx(SEV_ERROR, 0, 0, pBEM->msg);
         error_returns = error_returns->next;
       }
-      WRPSBHtmlError(pBEM->msg);
+      WRPSBHtmlError(pBEM->msg, bAnnotOnly);
     }
   } 
 
@@ -3098,14 +2443,14 @@ Int2 Main (void)
       } else {
         if (dbname[0] == '\0') {   /* worst case - don't know a thing about db */
           Nlm_StrCpy(dbname,"cdd");
-          Nlm_StrCpy(dbversion,"v1.62");
+          Nlm_StrCpy(dbversion,"v1.63");
         }
       }
     }
     if (Nlm_StrCmp(dbname,"unknown")) {
       if (! BlastInit("blastcl3", &bl3hp, &response)) {
         ErrPostEx(SEV_FATAL, 0, 0, "Unable to initialize BLAST service");
-        WRPSBHtmlError("Unable to initialize BLAST service!");
+        WRPSBHtmlError("Unable to initialize BLAST service!", bAnnotOnly);
         return (1);
       }
       BlastNetBioseqFetchEnable(bl3hp, dbname, db_is_na, TRUE);
@@ -3116,7 +2461,7 @@ Int2 Main (void)
 
   if (bIsQueued) {
     rid = QBlastSubmitJob(query_bsp,blast_program,blast_database,options);
-    if (!rid) WRPSBHtmlError("Error submitting CD-Search job to BLAST queue!");
+    if (!rid) WRPSBHtmlError("Error submitting CD-Search job to BLAST queue!", bAnnotOnly);
     QRPSBWait(rid,iGraphMode,iPairMode,iHowLong,options->expect_value,options->hitlist_size);
   }
   
diff --git a/biostruc/cdd/wrpsbtool.c b/biostruc/cdd/wrpsbtool.c
index fbb1f4ee..d2eeaf12 100644
--- a/biostruc/cdd/wrpsbtool.c
+++ b/biostruc/cdd/wrpsbtool.c
@@ -1,4 +1,4 @@
-/* $Id: wrpsbtool.c,v 1.20 2003/10/07 21:16:06 bauer Exp $
+/* $Id: wrpsbtool.c,v 1.21 2003/11/19 14:34:31 bauer Exp $
 *===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
 *
 * Initial Version Creation Date: 4/19/2000
 *
-* $Revision: 1.20 $
+* $Revision: 1.21 $
 *
 * File Description:
 *         tools for WWW-RPS BLAST 
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: wrpsbtool.c,v $
+* Revision 1.21  2003/11/19 14:34:31  bauer
+* changes to support SeqAnnot export
+*
 * Revision 1.20  2003/10/07 21:16:06  bauer
 * support generation of Sequence Annotation from CD-Search results
 *
@@ -87,7 +90,7 @@
 *
 * Revision 1.4  2000/08/01 21:23:03  bauer
 * added Entrez-Hotlink for Query
-*
+*
 * Revision 1.3  2000/07/24 15:43:37  bauer
 * fixed problem with pairwise alignment displays involvinb profile-only CDs
 *
@@ -104,6 +107,7 @@
 #include <blastdef.h>
 #include <ddvcreate.h>
 #include <wrpsb.h>
+#include "cddutil.h"
 #include <wrpsbtool.h>
 
 /*---------------------------------------------------------------------------*/
@@ -276,8 +280,29 @@ void WRPSBSearchFoot(Boolean bAnnotOnly, Boolean bNoWrap)
 /* output simple error message as HTML                                       */
 /*---------------------------------------------------------------------------*/
 /*---------------------------------------------------------------------------*/
-void WRPSBHtmlError(CharPtr cErrTxt) 
+void WRPSBHtmlError(CharPtr cErrTxt, Boolean bAnnotOnly) 
 {
+  AsnIoPtr      aip;
+  SeqAnnotPtr   sap;
+  AnnotDescPtr  adp;
+
+  if (bAnnotOnly) {
+    WRPSBSearchHead(NULL,NULL,TRUE,TRUE);
+    sap = SeqAnnotNew();
+    sap->type = 1;
+    sap->data = NULL;
+    adp = (AnnotDescPtr) ValNodeNew(NULL);
+    adp->choice = Annot_descr_name;
+    adp->data.ptrvalue = StringSave(cErrTxt);
+    sap->desc = adp;
+    strcpy(OutputName,GetTempName("wrpsbcl3"));
+    aip = AsnIoOpen(OutputName, "w");
+    SeqAnnotAsnWrite((SeqAnnotPtr) sap, aip, NULL);
+    AsnIoClose(aip);
+    PrintFile(OutputName);
+    RemoveTempFiles();   
+    exit(1);  
+  }
   WRPSBSearchHead("CD-Search Error","CD-Search Error Message",FALSE,FALSE);
   printf("<BR><h3>%s</h3>\n",cErrTxt);
   WRPSBSearchFoot(FALSE, FALSE);
@@ -1435,16 +1460,16 @@ Boolean WRPSBCl3DisplayBlastPairList(AlignmentAbstractPtr aap,
 /* need to explicitly get the subject sequence from a FASTA file (versions..)*/
 /*---------------------------------------------------------------------------*/
     sfp = FileOpen(aap->cSeqFile,"r");
-    if (!sfp) WRPSBHtmlError("Could not find subject sequence!");
+    if (!sfp) WRPSBHtmlError("Could not find subject sequence!", FALSE);
     sep = FastaToSeqEntry(sfp,FALSE);
     FileClose(sfp);
-    if (!sep) WRPSBHtmlError("Could not read subject sequence!");
+    if (!sep) WRPSBHtmlError("Could not read subject sequence!", FALSE);
     bsp = (BioseqPtr) sep->data.ptrvalue;
 
     /* bsp = BioseqLockById(new_id); */
     subject_length = bsp->length;
     if (maxsubjaln >= subject_length) {
-      WRPSBHtmlError("Error in RPS-Blast alignment!");
+      WRPSBHtmlError("Error in RPS-Blast alignment!", FALSE);
     }
     aligned_fraction = 1.0 - aap->nmissg - aap->cmissg;
     if (aap->nmissg >= 0.2 || aap->cmissg >= 0.2) {
@@ -1524,5 +1549,778 @@ static void borkPutchar( gdIOCtx* ctx, int a )
     borkPutbuf(ctx, onechar, 1);
 }
 
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+/* check whether a hit is unique, or to a CD hit somewhere else in the list  */
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+static Boolean WRPSBHitIsNew(AlignmentAbstractPtr aapThis,
+                             AlignmentAbstractPtr aapHead,
+			     Dart_Connect *Connection,
+			     Int4 *cDartFam, Int4 cDartFamNum)
+{
+  AlignmentAbstractPtr aap;
+  int                  Size, i;
+  unsigned             Gilist[DARTSIZELIMIT];
+  char                 Accession[DARTSIZELIMIT][30];
+  
+  if (!aapThis) return FALSE;
+  for (i=0;i<cDartFamNum;i++) {
+    if (cDartFam[i] == aapThis->pssmid) {
+     aapThis->bIsArch = TRUE;
+     return(TRUE);    
+    }
+  }
+  if (Connection) {
+    if (aapThis->pssmid > 0) {
+      if (Dart_SameSim(Connection,aapThis->pssmid,Gilist,DARTSIZELIMIT,&Size)) {
+        for (i=0;i<Size;i++) {
+          if (!Dart_CDGi2Acc(Connection,Gilist[i],Accession[i],30)) {
+	    Accession[i][0] = '\0';
+          }
+	}
+      }
+    } else {
+      if (Dart_Related(Connection,aapThis->cCDDid,Gilist,DARTSIZELIMIT,&Size,NULL)) {
+        for (i=0;i<Size;i++) {
+          if (!Dart_CDGi2Acc(Connection,Gilist[i],Accession[i],30)) {
+	    Accession[i][0] = '\0';
+          }
+	}
+      }
+    }
+  } else {
+    Size = 0;
+  }
+  
+  aap = aapHead; while (aap) {
+    if (aapThis->pssmid > -1 && aap->pssmid > -1) {
+      if (aapThis->pssmid == aap->pssmid) {
+        aapThis->colcyc = aap->colcyc;
+        return FALSE;
+      }
+    }
+    for (i=0;i<Size;i++) {
+      if (Nlm_StrCmp(Accession[i],aap->cCDDid) == 0) {
+        aapThis->colcyc = aap->colcyc;
+        return FALSE;
+      }
+    }
+    if (Nlm_StrCmp(CDDlocat,"inhouse")==0) {   /* map names just for inhouse */
+      if (aapThis->cCDDid && aap->cCDDid) {
+        if (Nlm_StrCmp(aapThis->cCDDid,aap->cCDDid) == 0) {
+          aapThis->colcyc = aap->colcyc;
+          return FALSE;
+        }
+      }
+      if (Nlm_StrICmp(aapThis->cGraphId,aap->cGraphId) == 0) {
+        aapThis->colcyc = aap->colcyc;
+        return FALSE;
+      }
+    }
+    aap = aap->next;
+  }
+  return TRUE;			     
+}
 
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+/* define the indents on a block containing repeats according to the alignmt */
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+static void WRPSBIndentsViaSeqAlign(CddRepeatPtr pcdr,
+                                    AlignmentAbstractPtr aap,
+				    Int4 iGraphWidth,
+				    Int4 length)
+{
+  SeqLocPtr      slp;
+  SeqIntPtr      sintp;
+  Int4Ptr        istarts;
+  Int4           i = 0, j, s1, s2;
+  CddExpAlignPtr pCDea;
+  DenseSegPtr    dsp;
+  
+  istarts = MemNew(pcdr->count * sizeof (Int4));
+  slp = (SeqLocPtr) pcdr->location->data.ptrvalue;
+  while (slp) {
+    sintp = (SeqIntPtr) slp->data.ptrvalue;
+    istarts[i] = sintp->from; i++;
+    slp = slp->next;
+  }
+  
+  pCDea = CddExpAlignNew();
+  CddExpAlignAlloc(pCDea,length);
+  dsp = aap->salp->segs;
+  for (i=0;i<dsp->numseg;i++) {
+    s1 = dsp->starts[i*2];
+    s2 = dsp->starts[i*2+1]; 
+    if (s1 >=0 && s2>= 0) {
+      for (j=0;j<dsp->lens[i];j++) {
+        pCDea->adata[s1+j]=s2+j;
+      }
+    }
+  }
+  aap->indents = MemNew(pcdr->count * sizeof (Int4));
+  aap->nindents = 0;
+  for (i=0;i<pcdr->count;i++) {
+    for (j=0;j<length;j++) {
+      if (pCDea->adata[j] >= istarts[i]) {
+        s1 = (j * iGraphWidth) / (length - 1);
+	if (s1 > aap->gstart && s1 < aap->gstop) {
+	  aap->indents[aap->nindents] = s1;
+	  aap->nindents++;
+	}
+	break;
+      }
+    }
+  }
+  MemFree(istarts);
+}
+
+static CddDescPtr FindDescByPSSMid(CddDescPtr pcdd, Int4 pssmid)
+{
+  CddDescPtr pcddThis;
+  pcddThis = pcdd;
+  while(pcddThis) {
+    if (pcddThis->iPssmId == pssmid) return (pcddThis);
+    pcddThis = pcddThis->next;
+  }
+  return(NULL);
+}
 
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+/* fill in the Alignment Abstract Data Structure                             */
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+AlignmentAbstractPtr WRPSBCl3AbstractAlignment(BlastPruneSapStructPtr prune,
+                                               BioseqPtr query_bsp,
+                                               Int4 iGraphWidth,
+                                               Int4 *mxr,
+                                               Int4 iGraphMode,
+                                               CharPtr dbversion,
+                                               Boolean *bAnyPdb,
+					       Dart_Connect *Connection,
+					       Boolean bFull,
+					       CharPtr cCDDefault,
+					       CharPtr cDATApath,
+					       CharPtr cCDDPrefix,
+					       CharPtr cCDDPost_C,
+					       CharPtr cCDDPost_O,
+					       CharPtr cTREextens,
+					       CharPtr cSEQextens,
+					       CharPtr cOASIScgi,
+					       CharPtr cCDDcgi,
+					       CddDescPtr pcdd,
+					       Int4    *cDartFam,
+					       Int4    cDartFamNum,
+					       Boolean bAnnotOnly)
+{
+  Boolean              *bConflict;
+  Boolean              bDbIsOasis = TRUE, found_score = FALSE;
+  Int4                 maxrow = 1, i, pssmid;
+  Int4                 lastcol = -1;
+  Int4                 iCount = 0, replen;
+  Int4                 iColValue, number, score, fullCDstart, fullCDstop, nindent;
+  Int4                 *iOvrlap, *iMutual, isize;
+  AlignmentAbstractPtr aap, aapThis, aapTmp, aapHead = NULL;
+  CddDescPtr           pcddThis;
+  BioseqPtr            bsp;
+  CddTreePtr           pcddt;
+  CddDescrPtr          description;
+  CddRepeatPtr         pcdr;
+  CharPtr              cTemp;
+  CharPtr              cCurrDesc;
+  DbtagPtr             dbtp;
+  DenseSegPtr          dsp;
+  ObjectIdPtr          oidp;
+  ScorePtr             thisScorePtr;
+  SeqAlignPtr          sap;
+  SeqIdPtr             sip, gi_list;
+  TxDfLineStructPtr    txsp;
+  Nlm_FloatHi          evalue, bit_score;
+  Char                 path[PATH_MAX], hpath[PATH_MAX];
+  Char                 buffer[BUFFER_LENGTH+1];
+  Char                 cDatabase[16];
+  Char                 cCDDid[16];
+  Char                 CDDidx[PATH_MAX];
+
+  if (bFull) {
+    Nlm_StrCpy(CDDidx,cDATApath);
+    Nlm_StrCat(CDDidx,"/cdd.idx");
+    *bAnyPdb = FALSE;
+  }
+/*  if (Nlm_StrCmp(myargs[1].strvalue,"cdd_prop")==0) bDbIsOasis = FALSE; */
+  
+  sap = prune->sap;
+  while (sap) {
+    iCount++;
+    aapThis = (AlignmentAbstractPtr)MemNew(sizeof(AlignmentAbstract));
+    aapThis->salp = sap; aapThis->pssmid = -1;
+    dsp = sap->segs;
+    for (i=0;i<dsp->numseg;i++) {
+      if (dsp->starts[2*i] > -1) {
+        aapThis->mstart = dsp->starts[2*i];
+	aapThis->nmissg = (Nlm_FloatHi) dsp->starts[2*i+1];
+	fullCDstart = aapThis->mstart - aapThis->nmissg;
+        break;
+      }
+    }
+    for (i=0;i<dsp->numseg;i++) {
+      if (dsp->starts[2*i] > -1) {
+        aapThis->mstop = dsp->starts[2*i]+dsp->lens[i]-1;
+	aapThis->cmissg = (Nlm_FloatHi) (dsp->starts[2*i+1]+dsp->lens[i]-1);
+      }
+    }
+    aapThis->score = sap->score;
+    sip = dsp->ids->next;
+    if (bFull) {
+      aapThis->gstart = (aapThis->mstart * iGraphWidth) / (query_bsp->length-1);
+      aapThis->gstop =  (aapThis->mstop  * iGraphWidth) / (query_bsp->length-1);
+    }
+    thisScorePtr = sap->score;
+    found_score = GetScoreAndEvalue(sap, &score, &bit_score, &evalue, &number);
+    if      (evalue >  100.0   ) iColValue = 204;
+    else if (evalue >    1.0   ) iColValue = 153;
+    else if (evalue >    0.01  ) iColValue = 102;
+    else if (evalue >    0.0001) iColValue =  51;
+    else                         iColValue =   0;
+    if (bFull) {
+      bsp = BioseqLockById(sip);
+      if (!bsp) {
+        if (sip->choice == SEQID_GENERAL) {
+          dbtp = sip->data.ptrvalue;
+	  if (Nlm_StrCmp(dbtp->db,"Cdd") == 0) {
+	    oidp = dbtp->tag;
+	    CddPssmIdFromAcc(&pssmid, oidp->str, CDDidx);
+            oidp = ObjectIdNew();
+	    oidp->id = pssmid;
+	    dbtp = DbtagNew();
+	    dbtp->db = StringSave("CDD");
+	    dbtp->tag = oidp;
+	    sip->data.ptrvalue = dbtp;
+            bsp = BioseqLockById(sip);
+          }
+	}
+      }
+    } else bsp = NULL;
+    if (bsp) aapThis->nmissg = aapThis->nmissg/(Nlm_FloatHi)bsp->length;
+    if (bsp) {
+      fullCDstop = aapThis->mstop + bsp->length - 1 - aapThis->cmissg;
+      aapThis->cmissg = ((Nlm_FloatHi)bsp->length-1.0-aapThis->cmissg)/(Nlm_FloatHi) bsp->length;
+    }
+    txsp = (TxDfLineStructPtr) MemNew(sizeof(TxDfLineStruct));
+    txsp->segs_str = NULL;
+    txsp->segs_buflen = 0;
+    if(bsp != NULL) {
+      gi_list = GetUseThisGi(sap);
+      if (gi_list) {
+        FilterTheDefline(bsp, gi_list, buffer, BUFFER_LENGTH, &(txsp->title));
+        gi_list = SeqIdSetFree(gi_list);
+        sip = SeqIdFree(sip);
+        txsp->id = SeqIdParse(buffer);
+      } else {
+        SeqIdWrite(bsp->id, buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
+        txsp->title = StringSave(BioseqGetTitle(bsp));
+        txsp->id = sip;
+      }
+      txsp->is_na = (bsp->mol != Seq_mol_aa);
+    } else {
+      SeqIdWrite(sip, buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
+      txsp->title = StringSave("Unknown");
+      txsp->is_na = FALSE;
+      txsp->id = sip;
+    }
+    txsp->seqalign = sap;
+    txsp->buffer_id = StringSave(buffer);
+    txsp->score = score;
+    txsp->bit_score = bit_score;
+    txsp->evalue = evalue;
+    txsp->number = number;
+    txsp->found_score = found_score;
+    SeqAlignSegsStr(sap, 1, &txsp->segs_str, &txsp->segs_buflen, &txsp->segs_used);
+    txsp->isnew = FALSE;
+    txsp->waschecked = FALSE;
+    if(NULL != bsp) BioseqUnlock(bsp);
+    aapThis->defline = txsp;
+    isize = 2+strlen(aapThis->defline->title)+strlen(aapThis->defline->buffer_id);
+    if (isize < CDD_MAX_DESCR) isize = CDD_MAX_DESCR;
+    aapThis->long_defline = MemNew(sizeof(Char)*isize);
+    StrCpy(aapThis->long_defline, aapThis->defline->buffer_id);
+    StrCat(aapThis->long_defline," ");
+     cTemp = StringSave(txsp->buffer_id);
+    if (strncmp(cTemp,"gnl|",4)==0) {
+      strtok(cTemp,"|");
+      aapThis->cDatabase = StringSave(strtok(NULL,"|"));
+      Nlm_StrCpy(path,strtok(NULL,"|"));
+      aapThis->cCDDid = StringSave(strtok(path," "));
+      MemFree(cTemp);
+    } else WRPSBHtmlError("Could not interpret subject defline!", bAnnotOnly);
+   if (bFull) {
+      StrCat(aapThis->long_defline,aapThis->defline->title);
+    } else {
+      pcddThis = FindDescByPSSMid(pcdd,atoi(aapThis->cCDDid));
+      if (pcddThis) {
+        StrCat(aapThis->long_defline,pcddThis->cCddId);     
+        StrCat(aapThis->long_defline,", ");     
+        StrCat(aapThis->long_defline,pcddThis->cSourc);     
+        StrCat(aapThis->long_defline,", ");     
+        StrCat(aapThis->long_defline,pcddThis->cDescr);
+	aapThis->nmissg = aapThis->nmissg/(Nlm_FloatHi)pcddThis->iPssmLength;
+        fullCDstop = aapThis->mstop + pcddThis->iPssmLength - 1 - aapThis->cmissg;
+        aapThis->cmissg = ((Nlm_FloatHi)pcddThis->iPssmLength-1.0-aapThis->cmissg)/(Nlm_FloatHi)pcddThis->iPssmLength;
+      } else {
+        CddSevError("Failed to retrieve information for a PSSM-Id!");
+      }    
+    }
+    aapThis->bIsProfile = FALSE;
+    if (StringICmp(aapThis->cDatabase,"Smart")==0) {
+      aapThis->red = 255;
+      aapThis->green = aapThis->blue = iColValue;
+      if (StrNCmp(aapThis->cCDDid,"smart0",6) == 0) {
+        cTemp = StringSave(txsp->title);
+        aapThis->cGraphId = StringSave(strtok(cTemp,","));
+	MemFree(cTemp);
+      } else {
+        aapThis->cGraphId = aapThis->cCDDid;
+      }
+    } else if (StringICmp(aapThis->cDatabase,"Pfam") ==0) {
+      aapThis->blue = 255;
+      aapThis->red = aapThis->green = iColValue;
+      cTemp = StringSave(txsp->title);
+      aapThis->cGraphId = StringSave(strtok(cTemp,","));
+      MemFree(cTemp);
+    } else if (StringICmp(aapThis->cDatabase,"scop1.39") ==0) {
+      aapThis->green = 255;
+      aapThis->red = aapThis->blue = iColValue;
+      aapThis->bIsProfile = TRUE;    
+      aapThis->cGraphId = aapThis->cCDDid;
+    } else if (StringICmp(aapThis->cDatabase,"Load") ==0) {
+      aapThis->green = iColValue;
+      aapThis->red = aapThis->blue = 255;    
+      cTemp = StringSave(aapThis->cCDDid);
+      if (strstr(cTemp,":")) {
+        strtok(cTemp,":");
+        aapThis->cGraphId = StringSave(strtok(NULL,":"));
+      } else {
+        strtok(cTemp,"_");
+        aapThis->cGraphId = StringSave(strtok(NULL,"_"));
+      }
+      MemFree(cTemp);
+    } else if (StringCmp(aapThis->cDatabase,"CDD") == 0) {
+      aapThis->pssmid = atoi(aapThis->cCDDid);
+      if (bFull) {
+        cTemp = StringSave(txsp->title);
+        aapThis->cCDDid = StringSave(strtok(cTemp,","));
+        aapThis->cGraphId = StringSave(strtok(NULL,","));
+        if (!aapThis->cGraphId) aapThis->cGraphId = StringSave("obsolete");
+      } else {
+        aapThis->cCDDid = StringSave(pcddThis->cCddId);
+	aapThis->cGraphId = StringSave(pcddThis->cSourc);
+      }
+      if (Nlm_StrNCmp(aapThis->cGraphId," ",1) == 0) aapThis->cGraphId = aapThis->cGraphId+1;
+      CddTruncStringAtFirstPunct(aapThis->cGraphId);
+      CddFillBlanksInString(aapThis->cGraphId);
+    } else if (StringCmp(aapThis->cDatabase,"Cdd") == 0) {
+      cTemp = StringSave(txsp->title);
+      if (Nlm_StrStr(cTemp,",") != NULL) {
+        if (Nlm_StrStr(cTemp,";") == NULL ||
+	    Nlm_StrStr(cTemp,",") < Nlm_StrStr(cTemp,";")) {
+	  aapThis->cGraphId = StringSave(strtok(cTemp,","));
+	} else aapThis->cGraphId = StringSave(strtok(cTemp,";"));
+      } else aapThis->cGraphId = StringSave(strtok(cTemp,";"));
+    } else if (StringCmp(aapThis->cDatabase,"Cog") == 0) {
+      cTemp = StringSave(txsp->title);
+      if (Nlm_StrStr(cTemp,",") != NULL) {
+        if (Nlm_StrStr(cTemp,";") == NULL ||
+	    Nlm_StrStr(cTemp,",") < Nlm_StrStr(cTemp,";")) {
+	  aapThis->cGraphId = StringSave(strtok(cTemp,","));
+	} else aapThis->cGraphId = StringSave(strtok(cTemp,";"));
+      } else aapThis->cGraphId = StringSave(strtok(cTemp,";"));
+    } else {
+      aapThis->green = iColValue;
+      aapThis->red = aapThis->blue = 255;    
+      aapThis->cGraphId = aapThis->cCDDid;
+    }
+    aapThis->bIsArch = FALSE;
+    aapThis->bIsArchComplete = FALSE;
+    if (!bFull && NULL != cDartFam) {
+      for (i=0;i<cDartFamNum;i++) {
+        if (aapThis->pssmid == cDartFam[i]) {
+	  aapThis->bIsArch = TRUE;
+          aapThis->bIsArchComplete = (aapThis->nmissg + aapThis->cmissg < 0.1);
+	  break;
+	}
+      }
+    } else {
+      if (WRPSBHitIsNew(aapThis,aapHead,Connection,cDartFam,cDartFamNum)) {
+        if (!aapThis->bIsArch) {
+          aapThis->colcyc = lastcol + 1;
+          if (aapThis->colcyc >= iNcolors) {
+            aapThis->colcyc -= iNcolors;
+          }
+          lastcol = aapThis->colcyc;
+        } else {
+          aapThis->bIsArchComplete = (aapThis->nmissg + aapThis->cmissg < 0.1);
+        }
+      }
+
+/*
+    if (evalue > 0.01) {
+      aapThis->red   = iDartCol[aapThis->colcyc+iNcolors][0];
+      aapThis->green = iDartCol[aapThis->colcyc+iNcolors][1];
+      aapThis->blue  = iDartCol[aapThis->colcyc+iNcolors][2];
+    
+    } else {
+      aapThis->red   = iDartCol[aapThis->colcyc][0];
+      aapThis->green = iDartCol[aapThis->colcyc][1];
+      aapThis->blue  = iDartCol[aapThis->colcyc][2];
+    }
+*/
+      if (aapThis->bIsArch) {
+        aapThis->colcyc = 255;
+        aapThis->red    = 200;
+        aapThis->green  = 200;
+        aapThis->blue   = 200;
+      } else {
+        aapThis->red   = iDartCol[aapThis->colcyc][0];
+        aapThis->green = iDartCol[aapThis->colcyc][1];
+        aapThis->blue  = iDartCol[aapThis->colcyc][2];
+      }
+      sprintf(aapThis->name,"ali%d",(Int4)random());
+      aapThis->bIsOasis = bDbIsOasis;
+      if (bDbIsOasis) {
+        Nlm_StrCpy(path,cCDDPrefix);
+        if (Nlm_StrNCmp(aapThis->cCDDid,"COG",3) == 0 || Nlm_StrNCmp(aapThis->cCDDid,"KOG",3) == 0) {
+          strcat(path,cCDDefault);
+        } else strcat(path,dbversion);
+        strcat(path,cCDDPost_O);
+        Nlm_StrCpy(hpath,cOASIScgi);
+      } else {
+        Nlm_StrCpy(path,cCDDPrefix);
+        strcat(path,dbversion);
+        strcat(path,cCDDPost_C);
+        Nlm_StrCpy(hpath,cCDDcgi);
+      }
+      strcat(path,"/"); strcat(path,aapThis->cCDDid); strcat(path,cTREextens);
+      strcat(hpath,aapThis->cCDDid);
+      strcat(hpath,"&version=");
+      if (Nlm_StrNCmp(aapThis->cCDDid,"COG",3) == 0 || Nlm_StrNCmp(aapThis->cCDDid,"KOG",3) == 0) {
+        strcat(hpath,CDDefault);
+      } else strcat(hpath,dbversion);
+      aapThis->cHtmlLink = StringSave(hpath);
+/*---------------------------------------------------------------------------*/
+/* Open Cdd tree file and add description to aapThis data structure          */
+/* changed to binary read to get prepared for the v1.00 rollout. Aron 6/12/00*/
+/*---------------------------------------------------------------------------*/
+      pcddt = (CddTreePtr) CddTreeReadFromFile(path,TRUE);
+      aapThis->bHasStructure = FALSE;
+      if (pcddt) {
+        aapThis->description = pcddt->description;
+        description = aapThis->description;
+        while (description) {
+          if (description->choice == CddDescr_comment) {
+            cCurrDesc = description->data.ptrvalue;
+            if (Nlm_StrCmp(cCurrDesc,"linked to 3D-structure")==0) {
+              aapThis->bHasStructure = TRUE;
+              *bAnyPdb = TRUE;
+            }
+          }
+	  if (description->choice == CddDescr_repeats) {
+	    pcdr = (CddRepeatPtr) description->data.ptrvalue;
+	    nindent = pcdr->count - 1;
+	    if (NULL == pcdr->location) {
+	      replen = (fullCDstop - fullCDstart + 1) / (nindent+1);
+	      aapThis->nindents = 0;
+	      aapThis->indents = MemNew(nindent * sizeof(Int4));
+	      for (i=0;i<nindent;i++) {
+	        fullCDstop = ((fullCDstart + (i+1)*replen) * iGraphWidth) / (query_bsp->length - 1);
+                if (fullCDstop > aapThis->gstart && fullCDstop < aapThis->gstop) {
+                  aapThis->indents[aapThis->nindents] = fullCDstop;
+	          aapThis->nindents++;
+	        }
+	      }
+	    } else {
+	      WRPSBIndentsViaSeqAlign(pcdr,aapThis,iGraphWidth,query_bsp->length);
+	    }
+	  }
+          description = description->next;
+        }
+      }
+/*---------------------------------------------------------------------------*/
+/* get the file name for the FASTA-sequence file which stores the subject..  */
+/*---------------------------------------------------------------------------*/
+      aapThis->cSeqFile = MemNew(PATH_MAX*sizeof(Char));
+      if (bDbIsOasis) {
+        Nlm_StrCpy(aapThis->cSeqFile,cCDDPrefix);
+        if (Nlm_StrNCmp(aapThis->cCDDid,"COG",3) == 0 || Nlm_StrNCmp(aapThis->cCDDid,"KOG",3) == 0) {
+          strcat(aapThis->cSeqFile,cCDDefault);
+        } else {
+          strcat(aapThis->cSeqFile,dbversion);
+        }
+        strcat(aapThis->cSeqFile,cCDDPost_O);
+      } else {
+        Nlm_StrCpy(aapThis->cSeqFile,CDDPrefix); strcat(aapThis->cSeqFile,dbversion);
+        strcat(aapThis->cSeqFile,cCDDPost_C);
+      }
+      strcat(aapThis->cSeqFile,"/"); strcat(aapThis->cSeqFile,aapThis->cCDDid);
+      strcat(aapThis->cSeqFile,cSEQextens);
+    }   
+/*---------------------------------------------------------------------------*/
+/* Check for overlaps and determine row number                               */
+/* Check for mutal overlap if condensed graphics is selected                 */
+/*---------------------------------------------------------------------------*/
+    iOvrlap = MemNew(maxrow*sizeof(Int4));
+    iMutual = MemNew(maxrow*sizeof(Int4));
+    for (i=0;i<maxrow;i++) iOvrlap[i]=0;
+    aapThis->row = 1; aapThis->bDrawThisOne = TRUE;
+    if (aapHead) {    
+      aapTmp = aapHead;
+      while (aapTmp) {
+        if (aapTmp->bDrawThisOne) {
+          if (OverlapInterval(aapTmp->mstart,aapTmp->mstop, aapThis->mstart,aapThis->mstop))
+            iOvrlap[aapTmp->row-1] = 1;
+          if (iGraphMode == 1 || iGraphMode == 3) {
+            if (OverlapMutual(aapTmp->mstart,aapTmp->mstop,aapThis->mstart,aapThis->mstop)) {
+              iMutual[aapTmp->row-1] = 1;
+	      if (aapThis->bIsArch) {
+	        if (aapThis->bIsArchComplete) {
+		  if (!aapTmp->bIsArch || !aapTmp->bIsArchComplete) iMutual[aapTmp->row-1] = 0; 
+		}
+	      } else {
+	        if (aapTmp->bIsArch) iMutual[aapTmp->row-1] = 0;
+	      }
+            }
+          }
+        }
+        aapTmp = aapTmp->next;
+      }
+      aapThis->row = 0;
+      for (i=0;i<maxrow;i++) {
+        if (iOvrlap[i]==0) {
+          aapThis->row = i+1;
+          break;
+        }
+      }
+      if (iGraphMode == 1 || iGraphMode == 3) for (i=0;i<maxrow;i++) {
+        if (iMutual[i]==1) {
+          aapThis->bDrawThisOne = FALSE;
+          break;
+        }
+      }
+      if (aapThis->row == 0) aapThis->row = maxrow+1;
+    }
+    MemFree(iMutual);
+    MemFree(iOvrlap);
+    if (aapThis->row > maxrow) maxrow = aapThis->row;
+
+    aapThis->next = NULL;
+
+    if (aapHead==NULL) {
+       aapHead = aapThis;
+       aap = aapHead;
+    } else {
+       aap->next = aapThis;
+       aap = aapThis;
+    }
+/*
+    if (txsp) {
+      txsp->buffer_id = MemFree(txsp->buffer_id);
+      txsp->title = MemFree(txsp->title);
+      txsp->segs_str = MemFree(txsp->segs_str);
+      txsp = MemFree(txsp);
+    }
+*/
+    sap = sap->next;
+  }
+  if (bFull) *mxr = maxrow;
+  return(aapHead);
+}
+
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+/*---------------------------------------------------------------------------*/
+SeqAnnotPtr WRPSBCl3SeqAnnot(AlignmentAbstractPtr aapIn, FILE *table,
+                             Boolean bSeqAlign, Boolean bRetSeqAnnot)
+{
+  AsnIoPtr              aip;
+  AlignmentAbstractPtr  aap;
+  SeqAnnotPtr           sap;
+  SeqLocPtr             slp;
+  SeqFeatPtr            sfp, sfpHead = NULL, sfpTail = NULL;
+  DenseSegPtr           dsp;
+  SeqIdPtr              sipQuery;
+  SeqIntPtr             sintp;
+  DbtagPtr              dbtp;
+  ObjectIdPtr           oidp;
+  Char                  dupstr[PATH_MAX];
+  CharPtr               part1, rest, thispart;
+  UserObjectPtr         uop;
+  UserFieldPtr          ufp, ufpTail;
+  Nlm_FloatHi           evalue, bit_score;
+  Int4                  score, number, i, icnt;
+  Boolean               found_score;
+  AnnotDescPtr          adp, adp2;
+  DatePtr               dp;
+  SeqAlignPtr           salpTail = NULL, salpHead = NULL;
+
+  sap = SeqAnnotNew();
+  if (bSeqAlign) {
+    sap->type = 2; /* Sequence Alignment */
+  } else sap->type = 1; /* feature table */
+  adp = (AnnotDescPtr) ValNodeNew(NULL);
+  adp->choice = Annot_descr_name;
+  adp->data.ptrvalue = StringSave("CDDSearch");
+  sap->desc = adp;
+  adp2 = (AnnotDescPtr) ValNodeNew(NULL);
+  dp = DateCurr();
+  adp2->choice = Annot_descr_create_date;
+  adp2->data.ptrvalue = dp;
+  adp->next = adp2;
+  aap = aapIn;
+  while (aap) {
+    if (aap->bDrawThisOne) {
+      sfp = SeqFeatNew();
+      if (bSeqAlign) {
+        if (!salpHead) {
+	  salpHead = aap->salp;
+	} else salpTail->next = aap->salp;
+	  salpTail = aap->salp;
+	  salpTail->next = NULL;
+      } else {
+        sfp->data.choice = 9;
+        strncpy(dupstr,aap->long_defline,PATH_MAX);
+        part1 = strtok(dupstr," ");
+        if (part1) {
+          rest = dupstr + strlen(part1) + 1;
+        } else {
+          rest = StringSave(aap->long_defline);
+        }
+        icnt = 0;
+        for (i=0;i<Nlm_StrLen(rest);i++) {
+          if (rest[i] == ',') icnt++;
+	  if (icnt > 1) break;
+        }
+        if (icnt > 1) {
+          i = i+2;
+        } else i = 0;
+        thispart = &rest[i];
+        for (i=0;i<Nlm_StrLen(thispart);i++) {
+          if (thispart[i] == '.' || thispart[i] == ';') {
+	    thispart[i] = '\0';
+	    break;
+	  }
+        }
+        sfp->data.value.ptrvalue = StringSave(thispart);
+        sfp->comment = StringSave(aap->cGraphId);   /* comment is short name */
+        if (aap->nmissg >= 0.2 || aap->cmissg >= 0.2) sfp->partial = TRUE;
+        dsp = aap->salp->segs;
+        sipQuery = dsp->ids;
+        slp = (SeqLocPtr) ValNodeNew(NULL); slp->choice = SEQLOC_INT;
+        sintp=SeqIntNew(); sintp->from = aap->mstart; sintp->to = aap->mstop;
+        sintp->id = SeqIdDup(sipQuery); slp->data.ptrvalue = sintp;
+        sfp->location = slp;
+        if (sfp->partial) {
+          SetSeqLocPartial(sfp->location, aap->nmissg >= 0.2, aap->cmissg >= 0.2);
+        }
+        uop = UserObjectNew();
+        oidp = ObjectIdNew();
+        oidp->str = StringSave("cddScoreData");
+        uop->type = oidp;
+        ufp = UserFieldNew();
+        oidp = ObjectIdNew();
+        oidp->str = StringSave("definition");
+        ufp->label = oidp;
+        ufp->choice = 1;
+        ufp->data.ptrvalue =  StringSave(aap->cCDDid);
+        uop->data = ufp;
+        ufpTail = ufp;
+        ufp = UserFieldNew();
+        oidp = ObjectIdNew();
+        oidp->str = StringSave("short_name");
+        ufp->label = oidp;
+        ufp->choice = 1;
+        ufp->data.ptrvalue = StringSave(aap->cGraphId);     
+        ufpTail->next = ufp;
+        ufpTail = ufp;
+        found_score = GetScoreAndEvalue(aap->salp, &score, &bit_score, &evalue, &number);
+        if (found_score) {
+          ufp = UserFieldNew();
+          oidp = ObjectIdNew();
+          oidp->str = StringSave("score");
+          ufp->label = oidp;
+          ufp->choice = 2;
+          ufp->data.intvalue = score;     
+          ufpTail->next = ufp;
+          ufpTail = ufp;
+          ufp = UserFieldNew();
+          oidp = ObjectIdNew();
+          oidp->str = StringSave("evalue");
+          ufp->label = oidp;
+          ufp->choice = 3;
+          ufp->data.realvalue = evalue;     
+          ufpTail->next = ufp;
+          ufpTail = ufp;
+          ufp = UserFieldNew();
+          oidp = ObjectIdNew();
+          oidp->str = StringSave("bit_score");
+          ufp->label = oidp;
+          ufp->choice = 3;
+          ufp->data.realvalue = bit_score;     
+          ufpTail->next = ufp;
+          ufpTail = ufp;
+        }
+        sfp->ext = uop;
+        dbtp = DbtagNew();
+        dbtp->db = StringSave(aap->cDatabase);
+        oidp = ObjectIdNew();
+        oidp->id = aap->pssmid;
+        dbtp->tag = oidp;
+        sfp->dbxref = ValNodeNew(NULL);
+        sfp->dbxref->data.ptrvalue = dbtp;
+        if (!sfpHead) {
+          sfpHead = sfp;
+        } else {
+          sfpTail->next = sfp;
+        }
+        sfpTail = sfp;
+      }
+    }
+    aap = aap->next;
+  }
+  if (bSeqAlign) {
+    sap->data = salpHead;
+  } else sap->data = sfpHead;
+  if (bRetSeqAnnot) return(sap);
+  strcpy(OutputName,GetTempName("wrpsbcl3"));
+  aip = AsnIoOpen(OutputName, "w");
+  SeqAnnotAsnWrite((SeqAnnotPtr) sap, aip, NULL);
+  AsnIoClose(aip);
+  PrintFile(OutputName);
+  RemoveTempFiles();   
+  return(NULL);
+}
+
+AlignmentAbstractPtr AlignmentAbstractSetDestruct(AlignmentAbstractPtr aap)
+{
+  AlignmentAbstractPtr  aapThis, aapNext, aapHead;
+
+  aapThis = aap; aapHead = aap;
+  while (aapThis) {
+    aapNext = aapThis->next;
+    aapThis->long_defline = MemFree(aapThis->long_defline);
+    aapThis->cCDDid = MemFree(aapThis->cCDDid);
+    aapThis->cGraphId = MemFree(aapThis->cGraphId);
+    aapThis->cDatabase = MemFree(aapThis->cDatabase);
+    if (aapThis->defline)  {
+      aapThis->defline->buffer_id = MemFree(aapThis->defline->buffer_id);
+      aapThis->defline->title = MemFree(aapThis->defline->title);
+      aapThis->defline->segs_str = MemFree(aapThis->defline->segs_str);
+      aapThis->defline = MemFree(aapThis->defline);
+    }
+    aapThis = (AlignmentAbstractPtr) MemFree(aapThis);
+    aapThis = aapNext;
+  }
+  return(aapHead);
+}
diff --git a/biostruc/cdd/wrpsbtool.h b/biostruc/cdd/wrpsbtool.h
index 28c39d90..78c6437e 100644
--- a/biostruc/cdd/wrpsbtool.h
+++ b/biostruc/cdd/wrpsbtool.h
@@ -1,4 +1,4 @@
-/* $Id: wrpsbtool.h,v 1.10 2003/10/07 21:16:57 bauer Exp $
+/* $Id: wrpsbtool.h,v 1.11 2003/11/19 14:34:32 bauer Exp $
 *===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
 *
 * Initial Version Creation Date: 4/19/2000
 *
-* $Revision: 1.10 $
+* $Revision: 1.11 $
 *
 * File Description:
 *         header for WWW-RPS BLAST tools
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: wrpsbtool.h,v $
+* Revision 1.11  2003/11/19 14:34:32  bauer
+* changes to support SeqAnnot export
+*
 * Revision 1.10  2003/10/07 21:16:57  bauer
 * support generation of Sequence Annotation from CD-Search results
 *
@@ -94,6 +97,18 @@
 #define DDV_COLOR_MAX 33
 
 #include <gd_io.h>
+#include "dart.h"
+
+#define CDD_MAX_DESCR 3072
+
+typedef struct cdddesc {
+  Int4                iPssmId;
+  Char                cCddId[PATH_MAX];
+  Char                cDescr[CDD_MAX_DESCR];
+  Char                cSourc[PATH_MAX];
+  Int4                iPssmLength;
+  struct cdddesc PNTR next;
+} CddDesc, PNTR CddDescPtr;
 
 typedef struct borkIOCtx {
   gdIOCtx	ctx;
@@ -109,7 +124,7 @@ static     void                   freeBorkCtx(gdIOCtx *ctx);
            Boolean                OverlapInterval(Int4 from1, Int4 to1, Int4 from2, Int4 to2);
            void                   WRPSBSearchHead(CharPtr title, CharPtr banner, Boolean bAnnotOnly, Boolean bNoWrap);
            void                   WRPSBSearchFoot(Boolean bAnnotOnly, Boolean bNoWrap);
-           void                   WRPSBHtmlError(CharPtr cErrTxt); 
+           void                   WRPSBHtmlError(CharPtr cErrTxt, Boolean bAnnotOnly); 
            Int4                   max(Int4 i1, Int4 i2);
            Int4                   min(Int4 i1, Int4 i2);
            Boolean                print_score_eonly(FloatHi evalue, CharPtr buf);
@@ -134,3 +149,38 @@ static     void                   DDV_InitDefSAPdispStyles_BLAST(DDV_Disp_OptPtr
 static     Boolean                DDV_DisplayNewBLAST(SeqAlignPtr sap, ValNodePtr mask,Int4Ptr PNTR matrix,Uint4 disp_format,Pointer disp_data,FILE *fp);
            Boolean                WRPSBDisplayBlastPairList(AlignmentAbstractPtr aap,ValNodePtr mask, FILE *fp,Boolean is_na, Uint4 tx_option,Uint1 ColorSchema,RPSBlastOptionsPtr rpsbop);
            Boolean                WRPSBCl3DisplayBlastPairList(AlignmentAbstractPtr aap,ValNodePtr mask, FILE *fp,Boolean is_na, Uint4 tx_option,Uint1 ColorSchema,BioseqPtr query_bsp, CharPtr dbversion, CharPtr urlcgi);
+static     Boolean                WRPSBHitIsNew(AlignmentAbstractPtr aapThis,
+                                                AlignmentAbstractPtr aapHead,
+			                        Dart_Connect *Connection,
+						Int4 *cDartFam,
+						Int4 cDartFamNum);
+static     void                   WRPSBIndentsViaSeqAlign(CddRepeatPtr pcdr,
+                                                          AlignmentAbstractPtr aap,
+				                          Int4 iGraphWidth,
+				                          Int4 length);
+           AlignmentAbstractPtr   WRPSBCl3AbstractAlignment(BlastPruneSapStructPtr prune,
+                                                            BioseqPtr query_bsp,
+                                                            Int4 iGraphWidth,
+                                                            Int4 *mxr,
+                                                            Int4 iGraphMode,
+                                                            CharPtr dbversion,
+                                                            Boolean *bAnyPdb,
+					                    Dart_Connect *Connection,
+					                    Boolean bFull,
+					                    CharPtr cCDDefault,
+					                    CharPtr cDATApath,
+					                    CharPtr cCDDPrefix,
+					                    CharPtr cCDDPost_C,
+					                    CharPtr cCDDPost_O,
+					                    CharPtr cTREextens,
+					                    CharPtr cSEQextens,
+					                    CharPtr cOASIScgi,
+					                    CharPtr cCDDcgi,
+							    CddDescPtr pcdd,
+					                    Int4 *cDartFam,
+					                    Int4 cDartFamNum,
+							    Boolean bAnnotOnly);
+           SeqAnnotPtr            WRPSBCl3SeqAnnot(AlignmentAbstractPtr aapIn, FILE *table,
+                                                   Boolean bSeqAlign, Boolean bRetSeqAnnot);
+           AlignmentAbstractPtr   AlignmentAbstractSetDestruct(AlignmentAbstractPtr aap);
+
diff --git a/biostruc/mmdbapi1.c b/biostruc/mmdbapi1.c
index 28251534..bd60d93d 100644
--- a/biostruc/mmdbapi1.c
+++ b/biostruc/mmdbapi1.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   03/14/95
 *
-* $Revision: 6.43 $
+* $Revision: 6.44 $
 *
 * File Description: 
 *
@@ -44,6 +44,9 @@
 * 95/08/30 C. Hogue    Minor changes.
 *
 * $Log: mmdbapi1.c,v $
+* Revision 6.44  2003/12/03 02:11:28  kans
+* added defines missing from Mac OS 10.3 headers
+*
 * Revision 6.43  2002/05/10 16:33:18  chenj
 * fix bugs in fnPBSFtoPSA
 *
@@ -289,6 +292,16 @@ NLM_EXTERN void VnpHeapSort PROTO ((ValNodePtr PNTR vnp, int (LIBCALLBACK *compa
 #include <matrix.h>
 #include "prunebsc.h"  
 
+/* Missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+#ifdef __MWERKS__
+#ifdef OS_UNIX_DARWIN
+#ifndef __SCHAR_MAX__
+#define __SCHAR_MAX__ 127
+#endif
+#endif
+#endif
+/* End missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+
 PMBD LIBCALL NewMBD(void)
 {
     PMBD pmbdNew = NULL;
@@ -2691,7 +2704,7 @@ void LIBCALLBACK DoReverseTransform(PFB pfbThis, Int4 iModel, Int4 iIndex, Point
   FloatLoPtr pflvData = NULL;
   FloatLoPtrPtr ppflmData = NULL;
   FloatLoPtrPtr ppflm = NULL;  
-  FloatLo flX,  flY,  flZ;
+  /* FloatLo flX,  flY,  flZ; */
   Int2 i,  j;
   
   if (IsAtomNode(pfbThis))
diff --git a/biostruc/mmdbapi2.c b/biostruc/mmdbapi2.c
index e83075b9..8b405510 100644
--- a/biostruc/mmdbapi2.c
+++ b/biostruc/mmdbapi2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   07/24/95
 *
-* $Revision: 6.8 $
+* $Revision: 6.9 $
 *
 * File Description:
 *
@@ -44,6 +44,9 @@
 * 95/08/30 C. Hogue    Moved globals into mmdbapi2.c.
 *
 * $Log: mmdbapi2.c,v $
+* Revision 6.9  2003/12/03 02:11:28  kans
+* added defines missing from Mac OS 10.3 headers
+*
 * Revision 6.8  2000/08/22 19:47:33  lewisg
 * fix GetMMFromMSDBySeqId
 *
@@ -159,6 +162,16 @@
 #include <mmdbapi2.h>
 #include <sequtil.h>
 
+/* Missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+#ifdef __MWERKS__
+#ifdef OS_UNIX_DARWIN
+#ifndef __SCHAR_MAX__
+#define __SCHAR_MAX__ 127
+#endif
+#endif
+#endif
+/* End missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+
 CharPtr NCBIstdaaUC = "-ABCDEFGHIKLMNPQRSTVWXYZU*";
 CharPtr NCBI4naUC = "-ACMGRSVTUWYHKDBN";
 CharPtr NCBI4naLC = "-acmgrsvtuwyhkdbn";
diff --git a/biostruc/objmmdb3.h b/biostruc/objmmdb3.h
index a986a812..7467fd24 100644
--- a/biostruc/objmmdb3.h
+++ b/biostruc/objmmdb3.h
@@ -627,7 +627,7 @@ NLM_EXTERN RealValuePtr LIBCALL RealValueAsnRead PROTO (( AsnIoPtr, AsnTypePtr))
 NLM_EXTERN Boolean LIBCALL RealValueAsnWrite PROTO (( RealValuePtr , AsnIoPtr, AsnTypePtr));
 
 typedef ValNodePtr MovePtr;
-typedef ValNode Move;
+typedef ValNode Move_t;
 #define Move_rotate 1
 #define Move_translate 2
 
diff --git a/biostruc/strimprt.h b/biostruc/strimprt.h
index f2996877..bf52646b 100644
--- a/biostruc/strimprt.h
+++ b/biostruc/strimprt.h
@@ -28,7 +28,7 @@
 *
 * Version Creation Date:   Circa 1994
 *
-* $Revision: 6.0 $
+* $Revision: 6.1 $
 *
 * File Description: General Header For Extra MMDB Defines
 *
@@ -38,6 +38,9 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: strimprt.h,v $
+* Revision 6.1  2003/12/09 15:55:32  bauer
+* renamed Ascii and Binart to BIOSTRUC_ASCII and BIOSTRUC_BINARY
+*
 * Revision 6.0  1997/08/25 18:11:53  madden
 * Revision changed to 6.0
 *
@@ -74,8 +77,8 @@
 #define ResidueGraphPtr_biostruc 2
 #define ResidueGraphPtr_standard_graphs 3
 
-#define Ascii 0
-#define Binary 1
+#define BIOSTRUC_ASCII 0
+#define BIOSTRUC_BINARY 1
 
 #define PDBSECS 0
 #define NCBISECS 1
diff --git a/checkout.date b/checkout.date
index 7ead1f7b..4cc36caa 100644
--- a/checkout.date
+++ b/checkout.date
@@ -1 +1 @@
-Wed Oct 29 10:58:05 EST 2003
+Sun Feb 1 10:12:30 EST 2004
diff --git a/connect/ncbi_buffer.c b/connect/ncbi_buffer.c
index 1ef34823..404f97c1 100644
--- a/connect/ncbi_buffer.c
+++ b/connect/ncbi_buffer.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_buffer.c,v 6.12 2003/05/14 03:49:53 lavr Exp $
+/*  $Id: ncbi_buffer.c,v 6.13 2003/12/05 17:31:04 ucko Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -60,6 +60,7 @@ typedef struct SBufChunkTag {
 typedef struct BUF_tag {
     size_t     chunk_size; /* this is actually a chunk size unit */
     SBufChunk* list;
+    SBufChunk* last;
 } BUF_struct;
 
 
@@ -71,7 +72,7 @@ extern size_t BUF_SetChunkSize(BUF* pBuf, size_t chunk_size)
         *pBuf = (BUF_struct*) malloc(sizeof(BUF_struct));
         if ( !*pBuf )
             return 0;
-        (*pBuf)->list = 0;
+        (*pBuf)->list = (*pBuf)->last = 0;
     }
 
     /* and set the min. mem. chunk size */
@@ -125,8 +126,7 @@ extern int/*bool*/ BUF_Write(BUF* pBuf, const void* data, size_t size)
         return 0 /* false */;
 
     /* find the last allocated chunk */
-    for (pTail = (*pBuf)->list;  pTail  &&  pTail->next;  pTail = pTail->next)
-        continue;
+    pTail = (*pBuf)->last;
 
     /* write to an unfilled space of the last allocated chunk, if any */
     if (pTail  &&  pTail->size != pTail->alloc_size) {
@@ -153,6 +153,7 @@ extern int/*bool*/ BUF_Write(BUF* pBuf, const void* data, size_t size)
             pTail->next = pChunk;
         else
             (*pBuf)->list = pChunk;
+        (*pBuf)->last = pChunk;
     }
     return 1 /* true */;
 }
@@ -178,6 +179,9 @@ extern int/*bool*/ BUF_PushBack(BUF* pBuf, const void* data, size_t size)
         pChunk->n_skip = pChunk->size = pChunk->alloc_size;
         pChunk->next  = (*pBuf)->list;
         (*pBuf)->list = pChunk;
+        if ( !(*pBuf)->last ) {
+            (*pBuf)->last = pChunk;
+        }
     }
 
     /* write data */
@@ -258,6 +262,9 @@ extern size_t BUF_Read(BUF buf, void* data, size_t size)
         size_t     n_avail = pHead->size - pHead->n_skip;
         if (n_todo >= n_avail) { /* discard the whole chunk */
             buf->list = pHead->next;
+            if ( !buf->list ) {
+                buf->last = 0;
+            }
             free(pHead);
             n_todo -= n_avail;
         } else { /* discard some of the chunk data */
@@ -289,6 +296,10 @@ extern void BUF_Destroy(BUF buf)
 /*
  * ---------------------------------------------------------------------------
  * $Log: ncbi_buffer.c,v $
+ * Revision 6.13  2003/12/05 17:31:04  ucko
+ * Add a tail pointer to BUF_struct to avoid having to walk the entire
+ * list in BUF_Write.
+ *
  * Revision 6.12  2003/05/14 03:49:53  lavr
  * Some indentation; added comment on chunk_size being a chunk size unit
  *
diff --git a/connect/ncbi_connutil.c b/connect/ncbi_connutil.c
index 8f4361bb..8e9d7089 100644
--- a/connect/ncbi_connutil.c
+++ b/connect/ncbi_connutil.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_connutil.c,v 6.60 2003/08/27 16:27:37 lavr Exp $
+/*  $Id: ncbi_connutil.c,v 6.63 2004/01/14 18:52:39 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -1264,6 +1264,8 @@ static const char* s_MIME_SubType[eMIME_Unknown+1] = {
     "x-www-form",
     "html",
     "plain",
+    "xml",
+    "xml+soap",
     "x-unknown"
 };
 
@@ -1460,22 +1462,24 @@ extern size_t HostPortToString(unsigned int   host,
                                char*          buf,
                                size_t         buflen)
 {
-    char abuf[16/*sizeof("255.255.255.255")*/ + 10/*:port*/];
+    char   x_buf[16/*sizeof("255.255.255.255")*/ + 8/*:port*/];
     size_t n;
 
     if (!buf || !buflen)
         return 0;
     if (!host)
-        *abuf = 0;
-    else if (SOCK_ntoa(host, abuf, sizeof(abuf)) != 0)
+        *x_buf = 0;
+    else if (SOCK_ntoa(host, x_buf, sizeof(x_buf)) != 0) {
+        *buf = 0;
         return 0;
+    }
+    n = strlen(x_buf);
     if (port || !host)
-        sprintf(abuf + strlen(abuf), ":%hu", port);
-    n = strlen(abuf);
-    assert(n < sizeof(abuf));
+        n += sprintf(x_buf + n, ":%hu", port);
+    assert(n < sizeof(x_buf));
     if (n >= buflen)
         n = buflen - 1;
-    memcpy(buf, abuf, n);
+    memcpy(buf, x_buf, n);
     buf[n] = 0;
     return n;
 }
@@ -1484,6 +1488,15 @@ extern size_t HostPortToString(unsigned int   host,
 /*
  * --------------------------------------------------------------------------
  * $Log: ncbi_connutil.c,v $
+ * Revision 6.63  2004/01/14 18:52:39  lavr
+ * Recognize eMIME_XmlSoap and corresponding text representation "xml+soap"
+ *
+ * Revision 6.62  2004/01/07 19:23:29  lavr
+ * "xml" added as a MIME subtype
+ *
+ * Revision 6.61  2003/11/12 17:46:12  lavr
+ * HostPortToString() changed to be a little more efficient
+ *
  * Revision 6.60  2003/08/27 16:27:37  lavr
  * Add "Host:" tag to be able to take advantage of Apache VHosts
  *
diff --git a/connect/ncbi_connutil.h b/connect/ncbi_connutil.h
index 87e6ceea..ad8ae01e 100644
--- a/connect/ncbi_connutil.h
+++ b/connect/ncbi_connutil.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_CONNUTIL__H
 #define CONNECT___NCBI_CONNUTIL__H
 
-/*  $Id: ncbi_connutil.h,v 6.33 2003/09/23 21:00:33 lavr Exp $
+/*  $Id: ncbi_connutil.h,v 6.35 2004/01/14 18:51:41 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -530,6 +530,8 @@ typedef enum {
     /* standard MIMEs */
     eMIME_Html,          /* "html"                                     */
     eMIME_Plain,         /* "plain"                                    */
+    eMIME_Xml,           /* "xml"                                      */
+    eMIME_XmlSoap,       /* "xml+soap"                                 */
     /* eMIME_???,           "<subtype>" here go other NCBI subtypes    */
     eMIME_Unknown        /* "x-unknown"     (an arbitrary binary data) */
 } EMIME_SubType;
@@ -640,6 +642,12 @@ extern NCBI_XCONNECT_EXPORT size_t HostPortToString
 /*
  * --------------------------------------------------------------------------
  * $Log: ncbi_connutil.h,v $
+ * Revision 6.35  2004/01/14 18:51:41  lavr
+ * +eMIME_XmlSoap
+ *
+ * Revision 6.34  2004/01/07 19:24:40  lavr
+ * Added MIME subtype eMIME_Xml
+ *
  * Revision 6.33  2003/09/23 21:00:33  lavr
  * Reorder included header files
  *
diff --git a/connect/ncbi_http_connector.c b/connect/ncbi_http_connector.c
index 4127bb7d..848d1a06 100644
--- a/connect/ncbi_http_connector.c
+++ b/connect/ncbi_http_connector.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_http_connector.c,v 6.59 2003/10/29 14:09:08 lavr Exp $
+/*  $Id: ncbi_http_connector.c,v 6.62 2003/11/26 12:57:11 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -265,8 +265,12 @@ static EIO_Status s_ConnectAndSend(SHttpConnector* uuu,int/*bool*/ drop_unread)
         if (status == eIO_Success) {
             assert(uuu->w_len == 0);
             if (!uuu->shut_down) {
-                /* 10/7/03: While this call here is perfectly legal, it could
-                 * cause connection severed by a buggy CISCO load-balancer.*/
+                /* 10/07/03: While this call here is perfectly legal, it could
+                 * cause connection severed by a buggy CISCO load-balancer. */
+                /* 10/28/03: CISCO's beta patch for their LB shows that the
+                 * problem has been fixed; no more 2'30" drops in connections
+                 * that shut down for write.  We still leave this commented
+                 * out to allow unpatched clients work seamlessly... */ 
                 /*SOCK_Shutdown(uuu->sock, eIO_Write);*/
                 uuu->shut_down = 1;
             }
@@ -324,7 +328,7 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
         }
         verify(BUF_Peek(uuu->http, header, size) == size);
         header[size] = '\0';
-        if (strcmp(&header[size - 4], "\r\n\r\n") == 0)
+        if (size >= 4  &&  strcmp(&header[size - 4], "\r\n\r\n") == 0)
             break/*full header captured*/;
         free(header);
 
@@ -408,7 +412,7 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
         free(header);
 
     /* skip & printout the content, if server error was flagged */
-    if (server_error  &&  uuu->net_info->debug_printout) {
+    if (uuu->net_info->debug_printout == eDebugPrintout_Some && server_error) {
         BUF    buf = 0;
         char*  body;
 
@@ -972,6 +976,14 @@ extern CONNECTOR HTTP_CreateConnectorEx
 /*
  * --------------------------------------------------------------------------
  * $Log: ncbi_http_connector.c,v $
+ * Revision 6.62  2003/11/26 12:57:11  lavr
+ * s_ReadHeader(): check header size first before looking for end-of-header
+ *
+ * Revision 6.61  2003/11/03 17:37:42  lavr
+ * Fix previous accidental commit and provide corrent change log info:
+ * 1. Added more notes about SOCK_Shutdown() being left commented out;
+ * 2. Do not print HTTP error body if data trace mode set to "DATA".
+ *
  * Revision 6.59  2003/10/29 14:09:08  lavr
  * Log levels and messages changed in some error reports
  *
diff --git a/connect/ncbi_sendmail.c b/connect/ncbi_sendmail.c
index 769a883e..bf3c4bc8 100644
--- a/connect/ncbi_sendmail.c
+++ b/connect/ncbi_sendmail.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_sendmail.c,v 6.19 2003/04/18 20:59:51 lavr Exp $
+/*  $Id: ncbi_sendmail.c,v 6.22 2004/01/07 19:51:36 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -46,7 +46,7 @@
 #define NCBI_SENDMAIL_TOOLKIT "C"
 #endif
 
-#define MX_MAGIC_NUMBER 0xBABADEDA
+#define MX_MAGIC_NUMBER 0xBA8ADEDA
 #define MX_CRLF         "\r\n"
 
 #define SMTP_READERR    -1      /* Error reading from socket         */
@@ -70,7 +70,7 @@ static int s_SockRead(SOCK sock, char* reply, size_t reply_len)
     size_t n = 0;
     int code = 0;
 
-    if (!reply || !reply_len)
+    if (!reply  ||  !reply_len)
         return 0;
 
     do {
@@ -82,7 +82,7 @@ static int s_SockRead(SOCK sock, char* reply, size_t reply_len)
         if (m != 4)
             return SMTP_REPLYERR;
 
-        if (buf[3] == '-' || (done = isspace((unsigned char)buf[3]))) {
+        if (buf[3] == '-'  ||  (done = isspace((unsigned char) buf[3]))) {
             buf[3] = 0;
             if (!code) {
                 if (!(code = atoi(buf)))
@@ -97,7 +97,7 @@ static int s_SockRead(SOCK sock, char* reply, size_t reply_len)
             if (SOCK_Read(sock,buf,1,&m,eIO_ReadPlain) != eIO_Success  ||  !m)
                 return SMTP_READERR;
 
-            if (buf[0] != '\r' && n < reply_len)
+            if (buf[0] != '\r'  &&  n < reply_len)
                 reply[n++] = buf[0];
         } while (buf[0] != '\n');
 
@@ -116,9 +116,9 @@ static int s_SockRead(SOCK sock, char* reply, size_t reply_len)
 
 
 static int/*bool*/ s_SockReadResponse(SOCK sock, int code, int alt_code,
-                                      char* buffer, size_t buffer_len)
+                                      char* buf, size_t buf_size)
 {
-    int c = s_SockRead(sock, buffer, buffer_len);
+    int c = s_SockRead(sock, buf, buf_size);
     if (c <= 0) {
         const char* message = 0;
         switch (c) {
@@ -145,8 +145,8 @@ static int/*bool*/ s_SockReadResponse(SOCK sock, int code, int alt_code,
             break;
         }
         assert(message);
-        strncpy0(buffer, message, buffer_len - 1);
-    } else if (c == code || (alt_code && c == alt_code))
+        strncpy0(buf, message, buf_size - 1);
+    } else if (c == code  ||  (alt_code  &&  c == alt_code))
         return 1/*success*/;
     return 0/*failure*/;
 }
@@ -157,10 +157,11 @@ static int/*bool*/ s_SockWrite(SOCK sock, const char* buf)
     size_t len = strlen(buf);
     size_t n;
 
-    if (SOCK_Write(sock, buf, len, &n, eIO_WritePersist) != eIO_Success ||
-        n != len)
-        return 0/*failed*/;
-    return 1/*success*/;
+    if (SOCK_Write(sock, buf, len, &n, eIO_WritePersist) == eIO_Success  &&
+        n == len) {
+        return 1/*success*/;
+    }
+    return 0/*failure*/;
 }
 
 
@@ -175,7 +176,7 @@ static char* s_ComposeFrom(char* buf, size_t buf_size)
     if (!login_name) {
         struct passwd* pwd = getpwuid(getuid());
         if (!pwd) {
-            if (!(login_name = getenv("USER")) &&
+            if (!(login_name = getenv("USER"))  &&
                 !(login_name = getenv("LOGNAME"))) {
                 CORE_UNLOCK;
                 return 0;
@@ -186,6 +187,11 @@ static char* s_ComposeFrom(char* buf, size_t buf_size)
 #else
     /* Temporary solution for login name */
     const char* login_name = "anonymous";
+#  ifdef NCBI_OS_MSWIN
+    const char* user_name = getenv("USERNAME");
+    if (user_name)
+        login_name = user_name;
+#  endif
 #endif
     strncpy0(buf, login_name, buf_size - 1);
 #ifdef NCBI_OS_UNIX
@@ -204,16 +210,18 @@ static char* s_ComposeFrom(char* buf, size_t buf_size)
 SSendMailInfo* SendMailInfo_Init(SSendMailInfo* info)
 {
     if (info) {
-        info->magic_number = MX_MAGIC_NUMBER;
-        info->cc = 0;
-        info->bcc = 0;
+        info->magic_number    = MX_MAGIC_NUMBER;
+        info->cc              = 0;
+        info->bcc             = 0;
         if (!s_ComposeFrom(info->from, sizeof(info->from)))
-            info->from[0] = 0;
-        info->header = 0;
-        info->mx_host = MX_HOST;
-        info->mx_port = MX_PORT;
-        info->mx_timeout.sec = MX_TIMEOUT;
+            info->from[0]     = 0;
+        info->header          = 0;
+        info->body_size       = 0;
+        info->mx_host         = MX_HOST;
+        info->mx_port         = MX_PORT;
+        info->mx_timeout.sec  = MX_TIMEOUT;
         info->mx_timeout.usec = 0;
+        info->mx_no_header    = 0/*false*/;
     }
     return info;
 }
@@ -253,6 +261,62 @@ extern const char* CORE_SendMail(const char* to,
            return reason;                                                  \
     } while (0)
 
+
+static const char* s_SendRcpt(SOCK sock, const char* to,
+                              char buf[], size_t buf_size,
+                              const char what[],
+                              const char write_error[],
+                              const char proto_error[])
+{
+    char c;
+    while ((c = *to++) != 0) {
+        char   quote = 0;
+        size_t k = 0;
+        if (isspace((unsigned char) c))
+            continue;
+        while (k < buf_size) {
+            if (quote) {
+                if (c == quote)
+                    quote = 0;
+            } else if (c == '"'  ||  c == '<'  ||  c == '\'') {
+                quote = c == '<' ? '>' : c;
+            } else if (c == ',')
+                break;
+            buf[k++] = c == '\t' ? ' ' : c;
+            if (!(c = *to++))
+                break;
+            if (isspace((unsigned char) c)) {
+                while (isspace((unsigned char)(*to)))
+                    to++;
+            }
+        }
+        if (k >= buf_size)
+            SENDMAIL_RETURN("Recepient address is too long");
+        buf[k] = 0;
+        if (quote) {
+            CORE_LOGF(eLOG_Warning, ("[SendMail]  Ubalanced delimiters in "
+                                     "recepient %s for %s: \"%c\" expected",
+                                     buf, what, quote));
+        }
+        if (!s_SockWrite(sock, "RCPT TO: <")  ||
+            !s_SockWrite(sock, buf)           ||
+            !s_SockWrite(sock, ">" MX_CRLF)) {
+            SENDMAIL_RETURN(write_error);
+        }
+        if (!s_SockReadResponse(sock, 250, 251, buf, buf_size))
+            SENDMAIL_RETURN2(proto_error, buf);
+        if (!c)
+            break;
+    }
+    return 0;
+}
+
+
+#define SENDMAIL_SENDRCPT(what, list, buffer)                              \
+    s_SendRcpt(sock, list, buffer, sizeof(buffer), what,                   \
+               "Write error in RCPT (" what ") command",                   \
+               "Protocol error in RCPT (" what ") command")
+
 #define SENDMAIL_READ_RESPONSE(code, altcode, buffer)                      \
     s_SockReadResponse(sock, code, altcode, buffer, sizeof(buffer))
 
@@ -271,15 +335,17 @@ const char* CORE_SendMailEx(const char*          to,
     if (info->magic_number != MX_MAGIC_NUMBER)
         SENDMAIL_RETURN("Invalid magic number");
 
-    if ((!to || !*to) &&
-        (!info->cc || !*info->cc) &&
-        (!info->bcc || !*info->bcc))
+    if ((!to         ||  !*to)        &&
+        (!info->cc   ||  !*info->cc)  &&
+        (!info->bcc  ||  !*info->bcc)) {
         SENDMAIL_RETURN("At least one message recipient must be specified");
+    }
 
     /* Open connection to sendmail */
     if (SOCK_Create(info->mx_host, info->mx_port, &info->mx_timeout, &sock)
-        != eIO_Success)
+        != eIO_Success) {
         SENDMAIL_RETURN("Cannot connect to sendmail");
+    }
     SOCK_SetTimeout(sock, eIO_ReadWrite, &info->mx_timeout);
 
     /* Follow the protocol conversation, RFC821 */
@@ -288,45 +354,38 @@ const char* CORE_SendMailEx(const char*          to,
 
     if (SOCK_gethostname(buffer, sizeof(buffer)) != 0)
         SENDMAIL_RETURN("Unable to get local host name");
-    if (!s_SockWrite(sock, "HELO ") ||
-        !s_SockWrite(sock, buffer) ||
-        !s_SockWrite(sock, MX_CRLF))
+    if (!s_SockWrite(sock, "HELO ")         ||
+        !s_SockWrite(sock, buffer)          ||
+        !s_SockWrite(sock, MX_CRLF)) {
         SENDMAIL_RETURN("Write error in HELO command");
+    }
     if (!SENDMAIL_READ_RESPONSE(250, 0, buffer))
         SENDMAIL_RETURN2("Protocol error in HELO command", buffer);
 
-    if (!s_SockWrite(sock, "MAIL FROM: <") ||
-        !s_SockWrite(sock, info->from) ||
-        !s_SockWrite(sock, ">" MX_CRLF))
+    if (!s_SockWrite(sock, "MAIL FROM: <")  ||
+        !s_SockWrite(sock, info->from)      ||
+        !s_SockWrite(sock, ">" MX_CRLF)) {
         SENDMAIL_RETURN("Write error in MAIL command");
+    }
     if (!SENDMAIL_READ_RESPONSE(250, 0, buffer))
         SENDMAIL_RETURN2("Protocol error in MAIL command", buffer);
 
     if (to && *to) {
-        if (!s_SockWrite(sock, "RCPT TO: <") ||
-            !s_SockWrite(sock, to) ||
-            !s_SockWrite(sock, ">" MX_CRLF))
-            SENDMAIL_RETURN("Write error in RCPT (To) command");
-        if (!SENDMAIL_READ_RESPONSE(250, 251, buffer))
-            SENDMAIL_RETURN2("Protocol error in RCPT (To) command", buffer);
+        const char* error = SENDMAIL_SENDRCPT("To", to, buffer);
+        if (error)
+            return error;
     }
 
     if (info->cc && *info->cc) {
-        if (!s_SockWrite(sock, "RCPT TO: <") ||
-            !s_SockWrite(sock, info->cc) ||
-            !s_SockWrite(sock, ">" MX_CRLF))
-            SENDMAIL_RETURN("Write error in RCPT (Cc) command");
-        if (!SENDMAIL_READ_RESPONSE(250, 251, buffer))
-            SENDMAIL_RETURN2("Protocol error in RCPT (Cc) command", buffer);
+        const char* error = SENDMAIL_SENDRCPT("Cc", info->cc, buffer);
+        if (error)
+            return error;
     }
 
     if (info->bcc && *info->bcc) {
-        if (!s_SockWrite(sock, "RCPT TO: <") ||
-            !s_SockWrite(sock, info->bcc) ||
-            !s_SockWrite(sock, ">" MX_CRLF))
-            SENDMAIL_RETURN("Write error in RCPT (Bcc) command");
-        if (!SENDMAIL_READ_RESPONSE(250, 251, buffer))
-            SENDMAIL_RETURN2("Protocol error in RCPT (Bcc) command", buffer);
+        const char* error = SENDMAIL_SENDRCPT("Bcc", info->bcc, buffer);
+        if (error)
+            return error;
     }
 
     if (!s_SockWrite(sock, "DATA" MX_CRLF))
@@ -334,37 +393,40 @@ const char* CORE_SendMailEx(const char*          to,
     if (!SENDMAIL_READ_RESPONSE(354, 0, buffer))
         SENDMAIL_RETURN2("Protocol error in DATA command", buffer);
 
-    /* Follow RFC822 to compose message headers. Note that
-     * 'Date:'and 'From:' are both added by sendmail automatically.
-     */ 
-    if (!s_SockWrite(sock, "Subject: ") ||
-        (subject && !s_SockWrite(sock, subject)) ||
-        !s_SockWrite(sock, MX_CRLF))
-        SENDMAIL_RETURN("Write error in sending subject");
-
-    if (to && *to) {
-        if (!s_SockWrite(sock, "To: ") ||
-            !s_SockWrite(sock, to) ||
+    if (!info->mx_no_header) {
+        /* Follow RFC822 to compose message headers. Note that
+         * 'Date:'and 'From:' are both added by sendmail automatically.
+         */ 
+        if (!s_SockWrite(sock, "Subject: ")           ||
+            (subject && !s_SockWrite(sock, subject))  ||
             !s_SockWrite(sock, MX_CRLF))
-            SENDMAIL_RETURN("Write error in sending To");
-    }
+            SENDMAIL_RETURN("Write error in sending subject");
 
-    if (info->cc && *info->cc) {
-        if (!s_SockWrite(sock, "Cc: ") ||
-            !s_SockWrite(sock, info->cc) ||
-            !s_SockWrite(sock, MX_CRLF))
-            SENDMAIL_RETURN("Write error in sending Cc");
-    }
+        if (to && *to) {
+            if (!s_SockWrite(sock, "To: ")            ||
+                !s_SockWrite(sock, to)                ||
+                !s_SockWrite(sock, MX_CRLF))
+                SENDMAIL_RETURN("Write error in sending To");
+        }
+
+        if (info->cc && *info->cc) {
+            if (!s_SockWrite(sock, "Cc: ")            ||
+                !s_SockWrite(sock, info->cc)          ||
+                !s_SockWrite(sock, MX_CRLF))
+                SENDMAIL_RETURN("Write error in sending Cc");
+        }
+    } else if (subject && *subject)
+        CORE_LOG(eLOG_Warning,"[SendMail]  Subject ignored in as-is messages");
 
     if (!s_SockWrite(sock, "X-Mailer: CORE_SendMail (NCBI "
-                           NCBI_SENDMAIL_TOOLKIT " Toolkit)" MX_CRLF))
+                     NCBI_SENDMAIL_TOOLKIT " Toolkit)" MX_CRLF))
         SENDMAIL_RETURN("Write error in sending mailer information");
 
     assert(sizeof(buffer) > sizeof(MX_CRLF) && sizeof(MX_CRLF) >= 3);
 
     if (info->header && *info->header) {
-        int/*bool*/ newline = 0/*false*/;
         size_t n = 0, m = strlen(info->header);
+        int/*bool*/ newline = 0/*false*/;
         while (n < m) {
             size_t k = 0;
             while (k < sizeof(buffer) - sizeof(MX_CRLF)) {
@@ -373,7 +435,8 @@ const char* CORE_SendMailEx(const char*          to,
                     k += sizeof(MX_CRLF) - 1;
                     newline = 1/*true*/;
                 } else {
-                    buffer[k++] = info->header[n];
+                    if (info->header[n] != '\r'  ||  !newline)
+                        buffer[k++] = info->header[n];
                     newline = 0/*false*/;
                 }
                 if (++n >= m)
@@ -381,17 +444,19 @@ const char* CORE_SendMailEx(const char*          to,
             }
             buffer[k] = 0;
             if (!s_SockWrite(sock, buffer))
-                SENDMAIL_RETURN("Write error in sending custom header");
+                SENDMAIL_RETURN("Write error while sending custom header");
         }
         if (!newline && !s_SockWrite(sock, MX_CRLF))
-            SENDMAIL_RETURN("Write error in finalizing custom header");
+            SENDMAIL_RETURN("Write error while finalizing custom header");
     }
 
-    if (body && *body) {
+    if (body) {
+        size_t n = 0, m = info->body_size ? info->body_size : strlen(body);
         int/*bool*/ newline = 0/*false*/;
-        size_t n = 0, m = strlen(body);
-        if (!s_SockWrite(sock, MX_CRLF))
-            SENDMAIL_RETURN("Write error in sending text body delimiter");
+        if (!info->mx_no_header  &&  m) {
+            if (!s_SockWrite(sock, MX_CRLF))
+                SENDMAIL_RETURN("Write error in message body delimiter");
+        }
         while (n < m) {
             size_t k = 0;
             while (k < sizeof(buffer) - sizeof(MX_CRLF)) {
@@ -400,11 +465,13 @@ const char* CORE_SendMailEx(const char*          to,
                     k += sizeof(MX_CRLF) - 1;
                     newline = 1/*true*/;
                 } else {
-                    if (body[n] == '.' && (newline || !n)) {
-                        buffer[k++] = '.';
-                        buffer[k++] = '.';
-                    } else
-                        buffer[k++] = body[n];
+                    if (body[n] != '\r'  ||  !newline) {
+                        if (body[n] == '.'  &&  (newline  ||  !n)) {
+                            buffer[k++] = '.';
+                            buffer[k++] = '.';
+                        } else
+                            buffer[k++] = body[n];
+                    }
                     newline = 0/*false*/;
                 }
                 if (++n >= m)
@@ -412,15 +479,16 @@ const char* CORE_SendMailEx(const char*          to,
             }
             buffer[k] = 0;
             if (!s_SockWrite(sock, buffer))
-                SENDMAIL_RETURN("Write error in sending text body");
+                SENDMAIL_RETURN("Write error while sending message body");
         }
-        if ((!newline && !s_SockWrite(sock, MX_CRLF)) ||
-            !s_SockWrite(sock, "." MX_CRLF))
-            SENDMAIL_RETURN("Write error in finishing text body");
-    } else if (!s_SockWrite(sock, MX_CRLF "." MX_CRLF))
-        SENDMAIL_RETURN("Write error in finishing message");
+        if ((!newline  &&  m  &&  !s_SockWrite(sock, MX_CRLF))
+            ||  !s_SockWrite(sock, "." MX_CRLF)) {
+            SENDMAIL_RETURN("Write error while finalizing message body");
+        }
+    } else if (!s_SockWrite(sock, "." MX_CRLF))
+        SENDMAIL_RETURN("Write error while finalizing message");
     if (!SENDMAIL_READ_RESPONSE(250, 0, buffer))
-        SENDMAIL_RETURN2("Protocol error in sending message body", buffer);
+        SENDMAIL_RETURN2("Protocol error in sending message", buffer);
 
     if (!s_SockWrite(sock, "QUIT" MX_CRLF))
         SENDMAIL_RETURN("Write error in QUIT command");
@@ -432,6 +500,7 @@ const char* CORE_SendMailEx(const char*          to,
 }
 
 #undef SENDMAIL_READ_RESPONSE
+#undef SENDMAIL_SENDRCPT
 #undef SENDMAIL_RETURN2
 #undef SENDMAIL_RETURN
 
@@ -439,6 +508,15 @@ const char* CORE_SendMailEx(const char*          to,
 /*
  * ---------------------------------------------------------------------------
  * $Log: ncbi_sendmail.c,v $
+ * Revision 6.22  2004/01/07 19:51:36  lavr
+ * Try to obtain user name from USERNAME env.var. on Windows, else fallback
+ *
+ * Revision 6.21  2003/12/09 15:38:39  lavr
+ * Take advantage of SSendMailInfo::body_size;  few little makeup changes
+ *
+ * Revision 6.20  2003/12/04 14:55:09  lavr
+ * Extend API with no-header and multiple recipient capabilities
+ *
  * Revision 6.19  2003/04/18 20:59:51  lavr
  * Mixed up SMTP_BADCODE and SMTP_BADREPLY rearranged in order
  *
diff --git a/connect/ncbi_sendmail.h b/connect/ncbi_sendmail.h
index 9d619b02..ef2f3881 100644
--- a/connect/ncbi_sendmail.h
+++ b/connect/ncbi_sendmail.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_SENDMAIL__H
 #define CONNECT___NCBI_SENDMAIL__H
 
-/*  $Id: ncbi_sendmail.h,v 6.14 2003/09/02 20:45:45 lavr Exp $
+/*  $Id: ncbi_sendmail.h,v 6.16 2003/12/09 15:38:02 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -61,9 +61,11 @@ typedef struct {
     const char*  bcc;           /* Blind carbon copy recipient(s)        */
     char         from[1024];    /* Originator address                    */
     const char*  header;        /* Custom header fields ('\n'-separated) */
+    size_t       body_size;     /* Message body size (if specified)      */ 
     const char*  mx_host;       /* Host to contact sendmail at           */
     short        mx_port;       /* Port to contact sendmail at           */
     STimeout     mx_timeout;    /* Timeout for all network transactions  */
+    unsigned     mx_no_header;  /* Boolean whether to complete MX header */
 } SSendMailInfo;
 
 
@@ -72,6 +74,20 @@ typedef struct {
  * can be specified in the form "Name" <address>; recipients should
  * be separated by commas. In case of address-only recipients (no "Name"
  * part above), angle brackets around the address may be omitted.
+ *
+ * NOTE about message body size:
+ * If not specified (0) and by default the message body size is calculated
+ * as strlen() of passed body argument, which must be NUL-terminated.
+ * Otherwise, exactly "body_size" bytes are read from the location pointed
+ * to by "body" parameter and are sent in the message.
+ *
+ * NOTE about MX header:
+ * message header is automatically prepended to a message that has
+ * "mx_no_header" flag cleared (default).  Otherwise, only "header" part
+ * (if any) is sent to the mail exchanger, and the rest of the header and
+ * the message body is passed "as is" following it.
+ * Message header separator and proper message formatting is then
+ * the caller's responsibility.
  */
 
 
@@ -95,7 +111,7 @@ extern NCBI_XCONNECT_EXPORT SSendMailInfo* SendMailInfo_Init
 /* Send a simple message to recipient(s) defined in 'to',
  * and having subject 'subject', which may be empty (both NULL and "" treated
  * equally as empty subjects), and message body 'body' (may be NULL/empty,
- * if not empty, lines are separated by '\n').
+ * if not empty, lines are separated by '\n', must be NUL-terminated).
  * Return value 0 means success; otherwise descriptive error message
  * gets returned. Communicaiton parameters for connection with sendmail
  * are set using default values as described in SendMailInfo_Init().
@@ -110,6 +126,8 @@ extern NCBI_XCONNECT_EXPORT const char* CORE_SendMail
  * all additional parameters of the message and the communication via
  * argument 'info'. In case of 'info' == NULL, the call is completely
  * equivalent to CORE_SendMail().
+ * NB: Body is not neccessarily NUL-terminated if "info" contains non-default
+ * (non-zero) message body size (see SSendMailInfo::body_size above).
  */
 extern NCBI_XCONNECT_EXPORT const char* CORE_SendMailEx
 (const char*          to,
@@ -130,6 +148,12 @@ extern NCBI_XCONNECT_EXPORT const char* CORE_SendMailEx
 /*
  * --------------------------------------------------------------------------
  * $Log: ncbi_sendmail.h,v $
+ * Revision 6.16  2003/12/09 15:38:02  lavr
+ * +SSendMailInfo::body_size and remarks about its use
+ *
+ * Revision 6.15  2003/12/04 14:54:39  lavr
+ * Extend API with no-header and multiple recipient capabilities
+ *
  * Revision 6.14  2003/09/02 20:45:45  lavr
  * -<connect/connect_export.h> -- now included from <connect/ncbi_types.h>
  *
diff --git a/connect/ncbi_service.c b/connect/ncbi_service.c
index 0d5eff97..2ef58545 100644
--- a/connect/ncbi_service.c
+++ b/connect/ncbi_service.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_service.c,v 6.49 2003/09/02 21:17:15 lavr Exp $
+/*  $Id: ncbi_service.c,v 6.50 2004/01/30 14:37:26 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -368,31 +368,18 @@ int/*bool*/ SERV_Update(SERV_ITER iter, const char* text)
 
 char* SERV_Print(SERV_ITER iter)
 {
+    static const char client_revision[] = "Client-Revision: %hu.%hu\r\n";
     static const char accepted_types[] = "Accepted-Server-Types:";
-    static const char client_revision[] = "Client-Revision:";
-    static const char revision[] = "$Revision: 6.49 $";
     char buffer[128], *str;
     TSERV_Type type, t;
     size_t buflen, i;
     BUF buf = 0;
 
     /* Put client version number */
-    buflen = sizeof(client_revision) - 1;
-    memcpy(buffer, client_revision, buflen);
-    for (i = 0; revision[i]; i++)
-        if (isspace((unsigned char) revision[i]))
-            break;
-    while (revision[i] && buflen + 2 < sizeof(buffer)) {
-        if (revision[i] == '$') {
-            if (isspace((unsigned char) revision[i - 1]))
-                --buflen;
-            break;
-        } else
-            buffer[buflen++] = revision[i++];
-    }
-    strcpy(&buffer[buflen], "\r\n");
-    assert(strlen(buffer) == buflen + 2  &&  buflen + 2 < sizeof(buffer));
-    if (!BUF_Write(&buf, buffer, buflen + 2)) {
+    buflen = sprintf(buffer, client_revision,
+                     SERV_CLIENT_REVISION_MAJOR, SERV_CLIENT_REVISION_MINOR);
+    assert(buflen < sizeof(buffer));
+    if (!BUF_Write(&buf, buffer, buflen)) {
         BUF_Destroy(buf);
         return 0;
     }
@@ -481,6 +468,9 @@ double SERV_Preference(double pref, double gap, unsigned int n)
 /*
  * --------------------------------------------------------------------------
  * $Log: ncbi_service.c,v $
+ * Revision 6.50  2004/01/30 14:37:26  lavr
+ * Client revision made independent of CVS revisions
+ *
  * Revision 6.49  2003/09/02 21:17:15  lavr
  * Clean up included headers
  *
diff --git a/connect/ncbi_service.h b/connect/ncbi_service.h
index 7af3d3e2..04c4fe36 100644
--- a/connect/ncbi_service.h
+++ b/connect/ncbi_service.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_SERVICE__H
 #define CONNECT___NCBI_SERVICE__H
 
-/*  $Id: ncbi_service.h,v 6.31 2003/08/11 19:05:54 lavr Exp $
+/*  $Id: ncbi_service.h,v 6.32 2004/01/30 14:37:33 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -39,6 +39,11 @@
 #include <connect/ncbi_host_info.h>
 
 
+/* Revision 6.100 */
+#define SERV_CLIENT_REVISION_MAJOR  6
+#define SERV_CLIENT_REVISION_MINOR  100
+
+
 /** @addtogroup ServiceSupport
  *
  * @{
@@ -194,6 +199,9 @@ extern NCBI_XCONNECT_EXPORT void DISP_SetMessageHook(FDISP_MessageHook);
 /*
  * --------------------------------------------------------------------------
  * $Log: ncbi_service.h,v $
+ * Revision 6.32  2004/01/30 14:37:33  lavr
+ * Client revision made independent of CVS revisions
+ *
  * Revision 6.31  2003/08/11 19:05:54  lavr
  * +DISP_SetMessageHook()
  *
diff --git a/connect/ncbi_socket.c b/connect/ncbi_socket.c
index ff762d0e..b9f3278a 100644
--- a/connect/ncbi_socket.c
+++ b/connect/ncbi_socket.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_socket.c,v 6.137 2003/10/27 16:45:46 ivanov Exp $
+/*  $Id: ncbi_socket.c,v 6.143 2003/11/25 15:08:40 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -33,7 +33,12 @@
  *
  */
 
-#include "ncbi_config.h"
+/* NCBI core headers
+ */
+#include "ncbi_ansi_ext.h"
+#include "ncbi_priv.h"
+/* The next header implicitly includes <connect/ncbi_socket.h> */
+#include <connect/ncbi_connutil.h>
 
 /* OS must be specified in the command-line ("-D....") or in the conf. header
  */
@@ -123,20 +128,10 @@
 #endif /* platform-specific headers (for UNIX, MSWIN, MAC) */
 
 
-/* NCBI core headers
- */
-#include "ncbi_ansi_ext.h"
-#include "ncbi_priv.h"
-/* The next header implicitly includes <connect/ncbi_socket.h> */
-#include <connect/ncbi_connutil.h>
-
-
 /* Portable standard C headers
  */
 #include <errno.h>
 #include <stdlib.h>
-#include <string.h>
-
 
 
 
@@ -158,6 +153,7 @@ typedef SOCKET TSOCK_Handle;
 #  define SOCK_ERRNO          WSAGetLastError()
 #  define SOCK_EINTR          WSAEINTR
 #  define SOCK_EWOULDBLOCK    WSAEWOULDBLOCK
+#  define SOCK_EADDRINUSE     WSAEADDRINUSE
 #  define SOCK_ECONNRESET     WSAECONNRESET
 #  define SOCK_EPIPE          WSAESHUTDOWN
 #  define SOCK_EAGAIN         WSAEINPROGRESS
@@ -183,6 +179,7 @@ typedef int TSOCK_Handle;
 #  define SOCK_ERRNO          errno
 #  define SOCK_EINTR          EINTR
 #  define SOCK_EWOULDBLOCK    EWOULDBLOCK
+#  define SOCK_EADDRINUSE     EADDRINUSE
 #  define SOCK_ECONNRESET     ECONNRESET
 #  define SOCK_EPIPE          EPIPE
 #  define SOCK_EAGAIN         EAGAIN
@@ -230,6 +227,7 @@ typedef int TSOCK_Handle;
 #  endif /*SOCK_ERRNO*/
 #  define SOCK_EINTR          EINTR
 #  define SOCK_EWOULDBLOCK    EWOULDBLOCK
+#  define SOCK_EADDRINUSE     EADDRINUSE
 #  define SOCK_ECONNRESET     ECONNRESET
 #  define SOCK_EPIPE          EPIPE
 #  define SOCK_EAGAIN         EAGAIN
@@ -281,8 +279,8 @@ typedef unsigned   EBSockType;
 #endif
 
 
-#define SET_LISTENING(s) ((s)->r_on_w =  (unsigned) eDefault + 1)
-#define IS_LISTENING(s)  ((s)->r_on_w == (unsigned) eDefault + 1)
+#define SET_LISTENING(s) ((s)->r_on_w  =   (unsigned) eDefault + 1)
+#define IS_LISTENING(s)  ((s)->r_on_w  ==  (unsigned) eDefault + 1)
 
 
 /* Listening socket
@@ -376,16 +374,16 @@ struct SOCK_tag {
  *
  * 5. The following table depicts r_status and eof combinations and their
  *    meanings for stream sockets:
- * -------------------------------+------------------------------------------
+ * -------------------------------+--------------------------------------------
  *              Field             |
  * ---------------+---------------+                  Meaning
  * sock->r_status |   sock->eof   |           (stream sockets only)
- * ---------------+---------------+------------------------------------------
+ * ---------------+---------------+--------------------------------------------
  * eIO_Closed     |       0       |  Socket shut down for reading
  * eIO_Closed     |       1       |  Read severely failed
  * not eIO_Closed |       0       |  Read completed with r_status error
- * not eIO_Closed |       1       |  Read hit EOF and completed with r_status
- * ---------------+---------------+------------------------------------------
+ * not eIO_Closed |       1       |  Read hit EOF (and later r_status)
+ * ---------------+---------------+--------------------------------------------
  */
 
 
@@ -400,18 +398,21 @@ static int/*bool*/ s_Initialized = 0/*false*/;
 static unsigned int s_ID_Counter = 0;
 
 /* Read-while-writing switch */
-static ESwitch s_ReadOnWrite = eOff;       /* no read-on-write by default */
+static ESwitch s_ReadOnWrite = eOff;        /* no read-on-write by default   */
 
 /* Reuse address flag for newly created stream sockets */
-static int/*bool*/ s_ReuseAddress = 0;     /* off by default              */
+static int/*bool*/ s_ReuseAddress = 0;      /* off by default                */
 
 /* I/O restart on signals */
-static ESwitch s_InterruptOnSignal = eOff; /* restart I/O by default      */
+static ESwitch s_InterruptOnSignal = eOff;  /* restart I/O by default        */
 
 /* Data/event logging */
-static ESwitch s_Log = eOff;               /* no logging by default       */
+static ESwitch s_Log = eOff;                /* no logging by default         */
+
+/* Select restart timeout */
+static const struct timeval* s_SelectTimeout = 0; /* =0 (disabled) by default*/
 
-/* Flag to indicate whether API should mask SIGPIPE (during initialization) */
+/* Flag to indicate whether API should mask SIGPIPE (during initialization)  */
 #ifdef NCBI_OS_UNIX
 static int/*bool*/ s_AllowSigPipe = 0/*false - mask SIGPIPE out*/;
 #endif /*NCBI_OS_UNIX*/
@@ -620,6 +621,7 @@ static void s_DoLog
         if (sock->type == eSOCK_Datagram) {
             if ( !sa ) {
                 strcpy(head, "Datagram socket created");
+                *tail = 0;
             } else {
                 const struct sockaddr_in* sin = (const struct sockaddr_in*) sa;
                 if ( !data ) {
@@ -918,7 +920,7 @@ static struct timeval* s_to2tv(const STimeout* to, struct timeval* tv)
 }
 
 
-/* Switch the specified socket i/o between blocking and non-blocking mode
+/* Switch the specified socket I/O between blocking and non-blocking mode
  */
 static int/*bool*/ s_SetNonblock(TSOCK_Handle sock, int/*bool*/ nonblock)
 {
@@ -946,7 +948,7 @@ static int/*bool*/ s_SetReuseAddress(TSOCK_Handle x_sock, int/*bool*/ on_off)
     int  reuse_addr = on_off ? 1 : 0;
 #  endif /*NCBI_OS_MSWIN*/
     return !setsockopt(x_sock, SOL_SOCKET, SO_REUSEADDR, 
-                       (const char*) &reuse_addr, sizeof(reuse_addr));
+                       (char*) &reuse_addr, sizeof(reuse_addr));
 #else
     return 1;
 #endif /*NCBI_OS_UNIX || NCBI_OS_MSWIN*/
@@ -958,11 +960,8 @@ static EIO_Status s_Status(SOCK sock, EIO_Event direction)
     assert(sock  &&  sock->sock != SOCK_INVALID);
     switch ( direction ) {
     case eIO_Read:
-        if (sock->type != eSOCK_Datagram) {
-            return sock->r_status != eIO_Success
-                ? sock->r_status : (sock->eof ? eIO_Closed : eIO_Success);
-        }
-        return sock->r_status;
+        return sock->type != eSOCK_Datagram  &&  sock->eof
+            ? eIO_Closed : sock->r_status;
     case eIO_Write:
         return sock->w_status;
     default:
@@ -974,6 +973,21 @@ static EIO_Status s_Status(SOCK sock, EIO_Event direction)
 }
 
 
+/* compare 2 normialized timeval timeouts: "whether v1 is less than v2" */
+static int/*bool*/ s_Less(const struct timeval* v1, const struct timeval* v2)
+{
+    if (!v1)
+        return 0;
+    if (!v2)
+        return !!v1;
+    if (v1->tv_sec > v2->tv_sec)
+        return 0;
+    if (v1->tv_sec < v2->tv_sec)
+        return 1;
+    return v1->tv_usec < v2->tv_usec;
+}
+
+
 /* Select on the socket I/O (multiple sockets).
  * "Event" field is not considered for entries, whose "sock" field is 0,
  * "revent" for those entries is always "eIO_Open". For all other entries
@@ -990,8 +1004,8 @@ static EIO_Status s_Status(SOCK sock, EIO_Event direction)
  * marked for upread, then returned "revent" may also include "eIO_Read" to
  * indicate that some input is available on that socket.
  * If "eIO_Read" event is inquired on an array (n != 1) including stream
- * socket (n != 1) and some sockets still have connection/data pending,
- * those "revent" field may then include "eIO_Write" to indicate that
+ * socket(s) and some sockets still have connection/data pending, those
+ * "revent" field may then include "eIO_Write" to indicate that
  * connection can be completed/data sent.
  *
  * Return eIO_Success when at least one socket is found either ready 
@@ -1005,16 +1019,20 @@ static EIO_Status s_Select(size_t                n,
                            SSOCK_Poll            polls[],
                            const struct timeval* tv)
 {
-    int/*bool*/ write_only = 1;
-    int/*bool*/ read_only = 1;
-    int/*bool*/ ready = 0;
-    int/*bool*/ bad = 0;
-    fd_set      r_fds, w_fds, e_fds;
-    int         n_fds;
-    size_t      i;
+    int/*bool*/    write_only = 1;
+    int/*bool*/    read_only = 1;
+    int/*bool*/    ready = 0;
+    int/*bool*/    bad = 0;
+    fd_set         r_fds, w_fds, e_fds;
+    int            n_fds;
+    struct timeval x_tv;
+    size_t         i;
+
+    if ( tv )
+        x_tv = *tv;
 
     for (;;) { /* (optionally) auto-resume if interrupted by a signal */
-        struct timeval x_tv;
+        struct timeval xx_tv;
 
         n_fds = 0;
         FD_ZERO(&r_fds);
@@ -1031,7 +1049,8 @@ static EIO_Status s_Select(size_t                n,
             }
             if (polls[i].event  &&
                 (EIO_Event)(polls[i].event | eIO_ReadWrite) == eIO_ReadWrite) {
-                if (polls[i].sock->sock != SOCK_INVALID) {
+                TSOCK_Handle fd = polls[i].sock->sock;
+                if (fd != SOCK_INVALID) {
                     int/*bool*/ ls = IS_LISTENING(polls[i].sock);
                     if (!ls && n != 1 && polls[i].sock->type == eSOCK_Datagram)
                         continue;
@@ -1044,7 +1063,7 @@ static EIO_Status s_Select(size_t                n,
                             if (polls[i].sock->type == eSOCK_Datagram  ||
                                 polls[i].sock->w_status != eIO_Closed) {
                                 read_only = 0;
-                                FD_SET(polls[i].sock->sock, &w_fds);
+                                FD_SET(fd, &w_fds);
                                 if (polls[i].sock->type == eSOCK_Datagram  ||
                                     polls[i].sock->pending)
                                     break;
@@ -1064,7 +1083,7 @@ static EIO_Status s_Select(size_t                n,
                                  polls[i].sock->eof))
                             break;
                         write_only = 0;
-                        FD_SET(polls[i].sock->sock, &r_fds);
+                        FD_SET(fd, &r_fds);
                         if (polls[i].sock->type == eSOCK_Datagram  ||
                             polls[i].event != eIO_Read             ||
                             polls[i].sock->w_status == eIO_Closed  ||
@@ -1072,16 +1091,16 @@ static EIO_Status s_Select(size_t                n,
                                          !polls[i].sock->w_len))
                             break;
                         read_only = 0;
-                        FD_SET(polls[i].sock->sock, &w_fds);
+                        FD_SET(fd, &w_fds);
                         break;
                     default:
                         /* should never get here */
                         assert(0);
                         break;
                     }
-                    FD_SET(polls[i].sock->sock, &e_fds);
-                    if (n_fds < (int) polls[i].sock->sock)
-                        n_fds = (int) polls[i].sock->sock;
+                    FD_SET(fd, &e_fds);
+                    if (n_fds < (int) fd)
+                        n_fds = (int) fd;
                 } else {
                     polls[i].revent = eIO_Close;
                     ready = 1;
@@ -1098,16 +1117,28 @@ static EIO_Status s_Select(size_t                n,
         if ( ready )
             return eIO_Success;
 
-        if ( tv )
-            x_tv = *tv;
+        if (!tv  ||  s_Less(s_SelectTimeout, &x_tv)) {
+            if ( s_SelectTimeout ) {
+                xx_tv = *s_SelectTimeout;
+            }
+        } else
+            xx_tv = x_tv;
 
         n_fds = select(SOCK_NFDS((TSOCK_Handle) n_fds),
                        write_only ? 0 : &r_fds, read_only ? 0 : &w_fds,
-                       &e_fds, tv ? &x_tv : 0);
+                       &e_fds, tv || s_SelectTimeout ? &xx_tv : 0);
 
         /* timeout has expired */
-        if (n_fds == 0)
+        if (n_fds == 0) {
+            if ( !tv )
+                continue;
+            if ( s_Less(s_SelectTimeout, &x_tv) ) {
+                x_tv.tv_sec  -= s_SelectTimeout->tv_sec;
+                x_tv.tv_usec -= s_SelectTimeout->tv_usec;
+                continue;
+            }
             return eIO_Timeout;
+        }
 
         if (n_fds > 0)
             break;
@@ -1133,18 +1164,22 @@ static EIO_Status s_Select(size_t                n,
     n_fds = 0;
     for (i = 0; i < n; i++) {
         if ( polls[i].sock ) {
+            TSOCK_Handle fd = polls[i].sock->sock;
             assert(polls[i].revent == eIO_Open);
-            if ( FD_ISSET(polls[i].sock->sock, &r_fds) )
-                polls[i].revent = eIO_Read;
-            if ( FD_ISSET(polls[i].sock->sock, &w_fds) )
-                polls[i].revent = (EIO_Event)(polls[i].revent | eIO_Write);
-            if (!polls[i].revent  &&  FD_ISSET(polls[i].sock->sock, &e_fds))
+            if (fd != SOCK_INVALID) {
+                if ( FD_ISSET(fd, &r_fds) )
+                    polls[i].revent = eIO_Read;
+                if ( FD_ISSET(fd, &w_fds) )
+                    polls[i].revent = (EIO_Event)(polls[i].revent | eIO_Write);
+                if (!polls[i].revent  &&  FD_ISSET(fd, &e_fds))
+                    polls[i].revent = eIO_Close;
+            } else
                 polls[i].revent = eIO_Close;
             if (polls[i].revent != eIO_Open)
                 n_fds++;
         }
     }
-    assert(n_fds);
+    assert(n_fds != 0);
 
     /* success; can do I/O now */
     return eIO_Success;
@@ -1153,6 +1188,21 @@ static EIO_Status s_Select(size_t                n,
 
 
 /******************************************************************************
+ *  UTILITY
+ */
+
+extern const STimeout* SOCK_SetSelectInternalRestartTimeout(const STimeout* t)
+{
+    static struct timeval  s_NewTmo;
+    static STimeout        s_OldTmo;
+    const  STimeout* retval = s_tv2to(s_SelectTimeout, &s_OldTmo);
+    s_SelectTimeout         = s_to2tv(t,               &s_NewTmo);
+    return retval;
+}
+
+
+
+/******************************************************************************
  *  LISTENING SOCKET
  */
 
@@ -1217,7 +1267,7 @@ extern EIO_Status LSOCK_CreateEx(unsigned short port,
                            ("LSOCK#%u[%u]: [LSOCK::Create]  Failed bind()",
                             x_id, (unsigned int) x_lsock));
         SOCK_CLOSE(x_lsock);
-        return eIO_Unknown;
+        return x_errno == SOCK_EADDRINUSE ? eIO_Closed : eIO_Unknown;
     }
 
     /* listen */
@@ -1278,7 +1328,6 @@ extern EIO_Status LSOCK_Accept(LSOCK           lsock,
         SSOCK_Poll     poll;
         struct timeval tv;
 
-        assert(IS_LISTENING(lsock));
         poll.sock   = (SOCK) lsock;
         poll.event  = eIO_Read;
         poll.revent = eIO_Open;
@@ -1420,7 +1469,7 @@ extern EIO_Status LSOCK_GetOSHandle(LSOCK  lsock,
     }
 
     memcpy(handle, &lsock->sock, handle_size);
-    return eIO_Success;
+    return lsock->sock == SOCK_INVALID ? eIO_Closed : eIO_Success;
 }
 
 
@@ -1531,7 +1580,7 @@ static EIO_Status s_Connect(SOCK            sock,
     }
     sock->sock = x_sock;
 
-    /* set the socket i/o to non-blocking mode */
+    /* set the socket I/O to non-blocking mode */
     if ( !s_SetNonblock(x_sock, 1/*true*/) ) {
         CORE_LOGF(eLOG_Error, ("%s[SOCK::s_Connect] "
                                " Cannot set socket to non-blocking mode",
@@ -1610,11 +1659,9 @@ static EIO_Status s_Connect(SOCK            sock,
         sock->pending = 0/*connected*/;
 
     /* success: do not change any timeouts */
-    sock->host      = x_host;
-    sock->port      = x_port;
-    sock->n_read    = 0;
-    sock->n_written = 0;
-    sock->w_len     = BUF_Size(sock->w_buf);
+    sock->host  = x_host;
+    sock->port  = x_port;
+    sock->w_len = BUF_Size(sock->w_buf);
     return eIO_Success;
 }
 
@@ -1636,7 +1683,7 @@ static int s_Recv(SOCK        sock,
     assert(sock->type != eSOCK_Datagram  &&  !sock->pending);
     if ( !size ) {
         /* internal upread use only */
-        assert(peek  &&  !buffer  &&  sock->r_status != eIO_Closed);
+        assert(sock->r_status != eIO_Closed && !sock->eof && peek && !buffer);
         n_read = 0;
     } else {
         /* read (or peek) from the internal buffer */
@@ -1686,7 +1733,10 @@ static int s_Recv(SOCK        sock,
             if (x_read <= 0) {
                 /* catch EOF/failure */
                 sock->eof = 1/*true*/;
-                sock->r_status = x_read == 0 ? eIO_Success : eIO_Closed;
+                if (x_read == 0)
+                    sock->r_status = eIO_Success;
+                else
+                    sock->r_status = sock->w_status = eIO_Closed;
                 break;
             }
         } else {
@@ -1761,7 +1811,7 @@ static EIO_Status s_SelectStallsafe(size_t                n,
         if (polls[i].revent & polls[i].event)
             break;
         if (polls[i].revent != eIO_Open  &&  !pending) {
-            pending++;
+            pending = 1;
             j = i;
         }
     }
@@ -1923,6 +1973,8 @@ static EIO_Status s_Send(SOCK        sock,
                 break;
             }
             sock->w_status = eIO_Closed;
+            if (x_errno != SOCK_EPIPE)
+                sock->r_status = eIO_Closed;
             if (sock->log == eOn  ||  (sock->log == eDefault && s_Log == eOn))
                 s_DoLog(sock, eIO_Write, 0, 0, 0);
             break;
@@ -2004,8 +2056,8 @@ static EIO_Status s_WritePending(SOCK                  sock,
                                      addr, sizeof(addr));
                 CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
                                    ("%s[SOCK::s_WritePending]  Failed pending "
-                                    "connect() to %s (%s)", s_ID(sock, _id),
-                                    addr, IO_StatusStr(status)));
+                                    "connect() to %s", s_ID(sock, _id), addr));
+                sock->w_status = status;
             }
             return status;
         }
@@ -2048,20 +2100,17 @@ static EIO_Status s_Read(SOCK        sock,
 
     *n_read = 0;
 
-    if (size == 0)
-        return s_Status(sock, eIO_Read);
-
     if (sock->type == eSOCK_Datagram) {
         *n_read = peek ?
             BUF_Peek(sock->r_buf, buf, size) :
             BUF_Read(sock->r_buf, buf, size);
-        sock->r_status = *n_read ? eIO_Success : eIO_Closed;
+        sock->r_status = *n_read || !size ? eIO_Success : eIO_Closed;
         return sock->r_status;
     }
 
     status = s_WritePending(sock, sock->r_timeout, 0);
-    if ( sock->pending )
-        return status;
+    if (sock->pending || !size)
+        return sock->pending ? status : s_Status(sock, eIO_Read);
 
     for (;;) { /* retry if either blocked or interrupted (optional) */
         /* try to read */
@@ -2189,7 +2238,7 @@ static EIO_Status s_Shutdown(SOCK                  sock,
         x_how = SOCK_SHUTDOWN_RD;
         sock->r_status = eIO_Closed;
 #ifdef NCBI_OS_MSWIN
-        /* see comments at the bottom of eIO_Write case */
+        /* see comments at the end of eIO_Write case */
         return eIO_Success;
 #endif /*NCBI_OS_MSWIN*/
         break;
@@ -2244,8 +2293,8 @@ static EIO_Status s_Shutdown(SOCK                  sock,
     if (SOCK_SHUTDOWN(sock->sock, x_how) != 0) {
         int x_errno = SOCK_ERRNO;
         if (
-#if defined(NCBI_OS_LINUX)/*bug in the kernel to report*/  || \
-    defined(NCBI_OS_IRIX)                                  || \
+#if defined(NCBI_OS_LINUX)/*bug in the Linux kernel to report*/  || \
+    defined(NCBI_OS_IRIX)                                        || \
     defined(NCBI_OS_OSF1)
             x_errno != SOCK_ENOTCONN
 #else
@@ -2466,9 +2515,11 @@ extern EIO_Status SOCK_CreateOnTopEx(const void*   handle,
         return eIO_Closed;
 #ifdef NCBI_OS_UNIX
     if (peer.sa.sa_family != AF_INET  &&  peer.sa.sa_family != AF_UNIX)
-#  if defined(NCBI_OS_BSD)  ||  defined(NCBI_OS_DARWIN)  ||  defined(NCBI_OS_IRIX)
+#  if defined(NCBI_OS_BSD)     ||  \
+      defined(NCBI_OS_DARWIN)  ||  \
+      defined(NCBI_OS_IRIX)
         if (peer.sa.sa_family != AF_UNSPEC/*0*/)
-#  endif
+#  endif /*NCBI_OS_???*/
             return eIO_InvalidArg;
 #else
     if (peer.sa.sa_family != AF_INET)
@@ -2477,9 +2528,11 @@ extern EIO_Status SOCK_CreateOnTopEx(const void*   handle,
     
 #ifdef NCBI_OS_UNIX
     if (
-#  if defined(NCBI_OS_BSD)  ||  defined(NCBI_OS_DARWIN)  ||  defined(NCBI_OS_IRIX)
+#  if defined(NCBI_OS_BSD)     ||  \
+      defined(NCBI_OS_DARWIN)  ||  \
+      defined(NCBI_OS_IRIX)
         peer.sa.sa_family == AF_UNSPEC/*0*/  ||
-#  endif
+#  endif /*NCBI_OS_???*/
         peer.sa.sa_family == AF_UNIX) {
         if (!peer.un.sun_path[0]) {
             peerlen = (SOCK_socklen_t) sizeof(peer);
@@ -2598,7 +2651,7 @@ extern EIO_Status SOCK_Reconnect(SOCK            sock,
     if (sock->type & eSOCK_ServerSide) {
         if (!host  ||  !*host  ||  !port) {
             CORE_LOGF(eLOG_Error, ("%s[SOCK::Reconnect]  Attempt to reconnect "
-                                   "server-side socket as client one to "
+                                   "server-side socket as the client one to "
                                    "its peer address", s_ID(sock, _id)));
             return eIO_InvalidArg;
         }
@@ -2607,6 +2660,8 @@ extern EIO_Status SOCK_Reconnect(SOCK            sock,
 
     /* connect */
     sock->id++;
+    sock->n_read    = 0;
+    sock->n_written = 0;
     return s_Connect(sock, host, port, timeout);
 }
 
@@ -2619,8 +2674,7 @@ extern EIO_Status SOCK_Shutdown(SOCK      sock,
     if (sock->sock == SOCK_INVALID) {
         CORE_LOGF(eLOG_Error, ("%s[SOCK::Shutdown] "
                                " Invalid socket", s_ID(sock, _id)));
-        assert(0);
-        return eIO_Unknown;
+        return eIO_Closed;
     }
     if (sock->type == eSOCK_Datagram) {
         CORE_LOGF(eLOG_Error, ("%s[SOCK::Shutdown] "
@@ -2633,18 +2687,26 @@ extern EIO_Status SOCK_Shutdown(SOCK      sock,
 }
 
 
-extern EIO_Status SOCK_Close(SOCK sock)
+extern EIO_Status SOCK_CloseEx(SOCK sock, int/*bool*/ destroy)
 {
     EIO_Status status = sock->sock==SOCK_INVALID ? eIO_Success : s_Close(sock);
-
     assert(sock->sock == SOCK_INVALID);
-    BUF_Destroy(sock->r_buf);
-    BUF_Destroy(sock->w_buf);
-    free(sock);
+
+    if (destroy) {
+        BUF_Destroy(sock->r_buf);
+        BUF_Destroy(sock->w_buf);
+        free(sock);
+    }
     return status;
 }
 
 
+extern EIO_Status SOCK_Close(SOCK sock)
+{
+    return SOCK_CloseEx(sock, 1/*destroy*/);
+}
+
+
 extern EIO_Status SOCK_Wait(SOCK            sock,
                             EIO_Event       event,
                             const STimeout* timeout)
@@ -2654,8 +2716,7 @@ extern EIO_Status SOCK_Wait(SOCK            sock,
     if (sock->sock == SOCK_INVALID) {
         CORE_LOGF(eLOG_Error, ("%s[SOCK::Wait] "
                                " Invalid socket", s_ID(sock, _id)));
-        assert(0);
-        return eIO_Unknown;
+        return eIO_Closed;
     }
 
     /* check against already shutdown socket there */
@@ -2672,7 +2733,7 @@ extern EIO_Status SOCK_Wait(SOCK            sock,
             return eIO_Closed;
         }
         if ( sock->eof )
-            return sock->r_status;
+            return eIO_Closed;
         break;
     case eIO_Write:
         if (sock->type == eSOCK_Datagram)
@@ -2686,17 +2747,20 @@ extern EIO_Status SOCK_Wait(SOCK            sock,
     case eIO_ReadWrite:
         if (sock->type == eSOCK_Datagram  ||  BUF_Size(sock->r_buf) != 0)
             return eIO_Success;
-        if (sock->r_status == eIO_Closed  &&  sock->w_status == eIO_Closed) {
-            CORE_LOGF(eLOG_Warning, ("%s[SOCK::Wait(RW)]  Socket shut down",
-                                     s_ID(sock, _id)));
+        if ((sock->r_status == eIO_Closed  ||  sock->eof)  &&
+            (sock->w_status == eIO_Closed)) {
+            if (sock->r_status == eIO_Closed) {
+                CORE_LOGF(eLOG_Warning, ("%s[SOCK::Wait(RW)]  "
+                                         "Socket shut down", s_ID(sock, _id)));
+            }
             return eIO_Closed;
         }
-        if ( sock->eof )
-            return sock->r_status;
-        if (sock->r_status == eIO_Closed) {
-            CORE_LOGF(eLOG_Note, ("%s[SOCK::Wait(RW)]  Socket %s",
-                                  s_ID(sock, _id), sock->eof
-                                  ? "closed" : "shut down for reading"));
+        if (sock->r_status == eIO_Closed  ||  sock->eof) {
+            if (sock->r_status == eIO_Closed) {
+                CORE_LOGF(eLOG_Note, ("%s[SOCK::Wait(RW)]  Socket %s",
+                                      s_ID(sock, _id), sock->eof
+                                      ? "closed" : "shut down for reading"));
+            }
             event = eIO_Write;
             break;
         }
@@ -2716,9 +2780,9 @@ extern EIO_Status SOCK_Wait(SOCK            sock,
     assert(sock->type != eSOCK_Datagram);
     /* do wait */
     {{
-        struct timeval tv;
-        SSOCK_Poll     poll;
-        EIO_Status     status;
+        struct timeval        tv;
+        SSOCK_Poll            poll;
+        EIO_Status            status;
         const struct timeval* x_tv = s_to2tv(timeout, &tv);
 
         if ((status = s_WritePending(sock, x_tv, 0)) != eIO_Success) {
@@ -2937,9 +3001,8 @@ extern EIO_Status SOCK_Read(SOCK           sock,
     } else {
         CORE_LOGF(eLOG_Error, ("%s[SOCK::Read]  Invalid socket",
                                s_ID(sock, _id)));
-        assert(0);
         x_read = 0;
-        status = eIO_Unknown;
+        status = eIO_Closed;
     }
 
     if ( n_read )
@@ -2956,8 +3019,7 @@ extern EIO_Status SOCK_PushBack(SOCK        sock,
         char _id[32];
         CORE_LOGF(eLOG_Error, ("%s[SOCK::PushBack]  Invalid socket",
                                s_ID(sock, _id)));
-        assert(0);
-        return eIO_Unknown;
+        return eIO_Closed;
     }
 
     return BUF_PushBack(&sock->r_buf, buf, size) ? eIO_Success : eIO_Unknown;
@@ -3004,9 +3066,8 @@ extern EIO_Status SOCK_Write(SOCK            sock,
     } else {
         CORE_LOGF(eLOG_Error, ("%s[SOCK::Write]  Invalid socket",
                                s_ID(sock, _id)));
-        assert(0);
         x_written = 0;
-        status = eIO_Unknown;
+        status = eIO_Closed;
     }
 
     if ( n_written )
@@ -3017,13 +3078,13 @@ extern EIO_Status SOCK_Write(SOCK            sock,
 
 extern EIO_Status SOCK_Abort(SOCK sock)
 {
-    char _id[32];
+    char       _id[32];
+    EIO_Status status;
 
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Abort] "
-                               " Invalid socket", s_ID(sock, _id)));
-        assert(0);
-        return eIO_Unknown;
+        CORE_LOGF(eLOG_Warning, ("%s[SOCK::Abort]  Invalid socket",
+                                 s_ID(sock, _id)));
+        return eIO_Closed;
     }
     if (sock->type == eSOCK_Datagram) {
         CORE_LOGF(eLOG_Error, ("%s[SOCK::Abort]  Called for datagram socket",
@@ -3034,16 +3095,29 @@ extern EIO_Status SOCK_Abort(SOCK sock)
 
     sock->eof = 0;
     sock->w_len = 0;
+    sock->pending = 0;
     sock->r_status = sock->w_status = eIO_Closed;
-    return eIO_Success;
+    if (SOCK_CLOSE(sock->sock) != 0) {
+        int x_errno = SOCK_ERRNO;
+        CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
+                           ("%s[SOCK::Abort]  Failed close()",
+                            s_ID(sock, _id)));
+        status = eIO_Unknown;
+    } else
+        status = eIO_Success;
+    sock->sock = SOCK_INVALID;
+    return status;
 }
 
 
 extern EIO_Status SOCK_Status(SOCK      sock,
                               EIO_Event direction)
 {
-    if (direction != eIO_Read  &&  direction != eIO_Write)
+    if (direction != eIO_Read  &&  direction != eIO_Write) {
+        if (direction == eIO_Open)
+            return sock->sock == SOCK_INVALID ? eIO_Closed  : eIO_Success;
         return eIO_InvalidArg;
+    }
 
     return (sock->sock == SOCK_INVALID ? eIO_Closed :
             sock->pending ? eIO_Timeout : s_Status(sock, direction));
@@ -3096,7 +3170,7 @@ extern EIO_Status SOCK_GetOSHandle(SOCK   sock,
     }
 
     memcpy(handle, &sock->sock, handle_size);
-    return eIO_Success;
+    return sock->sock == SOCK_INVALID ? eIO_Closed : eIO_Success;
 }
 
 
@@ -3232,7 +3306,11 @@ extern EIO_Status DSOCK_Bind(SOCK sock, unsigned short port)
         assert(0);
         return eIO_InvalidArg;
     }
-    assert(sock->sock != SOCK_INVALID);
+    if (sock->sock == SOCK_INVALID) {
+        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Bind] "
+                               " Invalid socket", s_ID(sock, _id)));
+        return eIO_Closed;
+    }
 
     /* bind */
     memset(&addr, 0, sizeof(addr));
@@ -3246,7 +3324,7 @@ extern EIO_Status DSOCK_Bind(SOCK sock, unsigned short port)
         int x_errno = SOCK_ERRNO;
         CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
                            ("%s[DSOCK::Bind]  Failed bind()", s_ID(sock,_id)));
-        return eIO_Unknown;
+        return x_errno == SOCK_EADDRINUSE ? eIO_Closed : eIO_Unknown;
     }
 
     /* statistics & logging */
@@ -3268,7 +3346,11 @@ extern EIO_Status DSOCK_Connect(SOCK sock,
         assert(0);
         return eIO_InvalidArg;
     }
-    assert(sock->sock != SOCK_INVALID);
+    if (sock->sock == SOCK_INVALID) {
+        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Connect] "
+                               " Invalid socket", s_ID(sock, _id)));
+        return eIO_Closed;
+    }
 
     /* drop all pending data */
     s_WipeRBuf(sock);
@@ -3287,7 +3369,7 @@ extern EIO_Status DSOCK_Connect(SOCK sock,
         }
     }
     if (!sock->host || !sock->port) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Connect]  Cannot connect"
+        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Connect]  Cannot connect "
                                "to incomplete address", s_ID(sock, _id)));
         return eIO_InvalidArg;
     }
@@ -3306,7 +3388,7 @@ extern EIO_Status DSOCK_Connect(SOCK sock,
         if (SOCK_ntoa(sock->host, addr, sizeof(addr)) != 0)
             strcpy(addr, "???");
         CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                           ("%s[SOCK::Reconnect]  Cannot connect"
+                           ("%s[DSOCK::Connect]  Cannot connect "
                             "datagram socket to %s:%hu", s_ID(sock, _id),
                             addr, ntohs(sock->port)));
         return eIO_Unknown;
@@ -3339,7 +3421,11 @@ extern EIO_Status DSOCK_SendMsg(SOCK            sock,
         assert(0);
         return eIO_InvalidArg;
     }
-    assert(sock->sock != SOCK_INVALID);
+    if (sock->sock == SOCK_INVALID) {
+        CORE_LOGF(eLOG_Error, ("%s[DSOCK::SendMsg] "
+                               " Invalid socket", s_ID(sock, w)));
+        return eIO_Closed;
+    }
 
     if ( datalen ) {
         s_Write(sock, data, datalen, &x_msgsize);
@@ -3466,7 +3552,11 @@ extern EIO_Status DSOCK_RecvMsg(SOCK            sock,
         assert(0);
         return eIO_InvalidArg;
     }
-    assert(sock->sock != SOCK_INVALID);
+    if (sock->sock == SOCK_INVALID) {
+        CORE_LOGF(eLOG_Error, ("%s[DSOCK::RecvMsg] "
+                               " Invalid socket", s_ID(sock, w)));
+        return eIO_Closed;
+    }
 
     s_WipeRBuf(sock);
     if ( msglen )
@@ -3587,7 +3677,11 @@ extern EIO_Status DSOCK_WaitMsg(SOCK sock, const STimeout* timeout)
         assert(0);
         return eIO_InvalidArg;
     }
-    assert(sock->sock != SOCK_INVALID);
+    if (sock->sock == SOCK_INVALID) {
+        CORE_LOGF(eLOG_Error, ("%s[DSOCK::WaitMsg] "
+                               " Invalid socket", s_ID(sock, _id)));
+        return eIO_Closed;
+    }
 
     poll.sock   = sock;
     poll.event  = eIO_Read;
@@ -3612,7 +3706,11 @@ extern EIO_Status DSOCK_WipeMsg(SOCK sock, EIO_Event direction)
         assert(0);
         return eIO_InvalidArg;
     }
-    assert(sock->sock != SOCK_INVALID);
+    if (sock->sock == SOCK_INVALID) {
+        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Wipe] "
+                               " Invalid socket", s_ID(sock, _id)));
+        return eIO_Closed;
+    }
 
     switch (direction) {
     case eIO_Read:
@@ -3643,7 +3741,11 @@ extern EIO_Status DSOCK_SetBroadcast(SOCK sock, int/*bool*/ broadcast)
         assert(0);
         return eIO_InvalidArg;
     }
-    assert(sock->sock != SOCK_INVALID);
+    if (sock->sock == SOCK_INVALID) {
+        CORE_LOGF(eLOG_Error, ("%s[DSOCK::SetBroadcast] "
+                               " Invalid socket", s_ID(sock, _id)));
+        return eIO_Closed;
+    }
 
 #if defined(NCBI_OS_UNIX)  ||  defined(NCBI_OS_MSWIN)
     /* setsockopt() is not implemented for MAC (in MIT socket emulation lib) */
@@ -3672,19 +3774,19 @@ extern EIO_Status DSOCK_SetBroadcast(SOCK sock, int/*bool*/ broadcast)
 
 extern int/*bool*/ SOCK_IsDatagram(SOCK sock)
 {
-    return sock->type == eSOCK_Datagram;
+    return sock->sock != SOCK_INVALID  &&  sock->type == eSOCK_Datagram;
 }
 
 
 extern int/*bool*/ SOCK_IsClientSide(SOCK sock)
 {
-    return sock->type == eSOCK_ClientSide;
+    return sock->sock != SOCK_INVALID  &&  sock->type == eSOCK_ClientSide;
 }
 
 
 extern int/*bool*/ SOCK_IsServerSide(SOCK sock)
 {
-    return sock->type & eSOCK_ServerSide ? 1 : 0;
+    return sock->sock != SOCK_INVALID  &&  (sock->type & eSOCK_ServerSide);
 }
 
 
@@ -3953,6 +4055,23 @@ extern char* SOCK_gethostbyaddr(unsigned int host,
 /*
  * ===========================================================================
  * $Log: ncbi_socket.c,v $
+ * Revision 6.143  2003/11/25 15:08:40  lavr
+ * DSOCK_Connect(): fix diag messages
+ *
+ * Revision 6.142  2003/11/24 19:21:42  lavr
+ * SOCK_SetSelectInternalRestartTimeout() to accept ptr to STimeout
+ *
+ * Revision 6.141  2003/11/18 20:19:48  lavr
+ * +SOCK_SetSelectInternalRestartTimeout() and restart impl. in s_Select()
+ *
+ * Revision 6.140  2003/11/14 13:05:23  lavr
+ * Eliminate race on socket file descriptors in s_Select() when socket aborted
+ *
+ * Revision 6.138  2003/11/12 17:49:42  lavr
+ * Implement close w/o destruction (SOCK_CloseEx()) and make
+ * corresponding provisions throughout the file.
+ * More consistent return status in SOCK and DSOCK API calls.
+ *
  * Revision 6.137  2003/10/27 16:45:46  ivanov
  * Use workaround for unnamed peer's UNIX sockets on DARWIN also.
  *
diff --git a/connect/ncbi_socket.h b/connect/ncbi_socket.h
index 008058c4..b9019779 100644
--- a/connect/ncbi_socket.h
+++ b/connect/ncbi_socket.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_SOCKET__H
 #define CONNECT___NCBI_SOCKET__H
 
-/*  $Id: ncbi_socket.h,v 6.44 2003/10/24 16:51:11 lavr Exp $
+/*  $Id: ncbi_socket.h,v 6.48 2003/11/25 15:07:12 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -255,6 +255,12 @@ extern NCBI_XCONNECT_EXPORT void SOCK_SetReuseAddress
  */
 
 
+/*
+ */
+extern NCBI_XCONNECT_EXPORT const STimeout*SOCK_SetSelectInternalRestartTimeout
+(const STimeout* timeout);
+
+
 /* By default (on UNIX platforms) the SOCK API functions automagically call
  * "signal(SIGPIPE, SIG_IGN)" on initialization.  To prohibit this feature,
  * you must call SOCK_AllowSigPipeAPI() before you call any other
@@ -428,7 +434,7 @@ extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_Reconnect
  * Cannot be applied to datagram sockets (eIO_InvalidArg results).
  */
 extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_Shutdown
-(SOCK      sock,
+(SOCK      sock, /* [in] handle of the socket to shutdown            */
  EIO_Event how   /* [in] one of:  eIO_Read, eIO_Write, eIO_ReadWrite */
  );
 
@@ -444,6 +450,19 @@ extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_Shutdown
 extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_Close(SOCK sock);
 
 
+/* Close the connection, and conditionally destroy relevant internal data.
+ * NOTE1:  if eIO_Close timeout was specified (or NULL) then it blocks until
+ *         either all unsent data are sent, error flagged, or the timeout
+ *         expires.
+ * NOTE2:  if there is output pending, that output will be flushed.
+ * NOTE3:  SOCK_CloseEx(sock, 1) is equivalent to SOCK_Close(sock);
+ */
+extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_CloseEx
+(SOCK        sock,    /* [in] handle of the socket to close           */
+ int/*bool*/ destroy  /* [in] =1 to destroy handle; =0 to keep handle */
+ );
+
+
 /* Block on the socket until either read/write (dep. on the "event" arg) is
  * available or timeout expires (if "timeout" is NULL then assume it infinite).
  * For a datagram socket, eIO_Closed is returned if the internally latched
@@ -608,11 +627,12 @@ extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_PushBack
  );
 
 
-/* Return (for the specified "direction"):
+/* Return (for the specified "direction" [eIO_Open to check for closed sock]):
  *   eIO_Closed     -- if the connection was shutdown by SOCK_Shutdown(), or
  *                     (for "eIO_Read" only) if EOF was detected
+ *                     if "direction"==eIO_Open, this code means socket closed
  *   eIO_Unknown    -- if an error was detected during the last I/O
- *   eIO_InvalidArg -- if "direction" is not one of:  eIO_Read, eIO_Write
+ *   eIO_InvalidArg -- if "direction" is not one of:  Open, Read, Write
  *   eIO_Timeout    -- if the socket is not yet actually connected
  *   eIO_Success    -- otherwise (incl. eIO_Timeout on last I/O)
  *
@@ -620,11 +640,11 @@ extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_PushBack
  *        as long as there is any unread (buffered) data left.
  *        Thus, when you are "peeking" data instead of actually reading it,
  *        then this is the only "non-destructive" way to check whether EOF
- *        or an error has occurred on read.
+ *        or an error has actually occurred on read.
  */
 extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_Status
 (SOCK      sock,
- EIO_Event direction  /* [in] one of:  eIO_Read, eIO_Write */
+ EIO_Event direction  /* [in] one of:  eIO_Open, eIO_Read, eIO_Write */
  );
 
 
@@ -662,6 +682,7 @@ extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_Write
 
 /* If there is outstanding connection or output data pending, cancel it.
  * Mark the socket as if it has been shut down for both reading and writing.
+ * Break actual connection if any was established.
  * Do not attempt to send anything upon SOCK_Close().
  * This call is available for stream sockets only.
  */
@@ -734,8 +755,8 @@ extern NCBI_XCONNECT_EXPORT ESwitch SOCK_SetReadOnWrite
  *
  *  Datagram socket is created with special DSOCK_Create[Ex] calls but the
  *  resulting object is a SOCK handle. That is, almost all SOCK routines
- *  may be applied to the handle. The only exception is SOCK_Shutdown().
- *  For datagram sockets there are differences in how I/O behaves:
+ *  may be applied to the handle. There are few exceptions, though.
+ *  In datagram sockets I/O differs from how it is done in stream sockets:
  *
  *  SOCK_Write() writes data into an internal message buffer, appending new
  *  data as they come with each SOCK_Write(). When the message is complete,
@@ -937,6 +958,18 @@ extern NCBI_XCONNECT_EXPORT char* SOCK_gethostbyaddr
 /*
  * ---------------------------------------------------------------------------
  * $Log: ncbi_socket.h,v $
+ * Revision 6.48  2003/11/25 15:07:12  lavr
+ * SOCK_Status() to accept eIO_Open
+ *
+ * Revision 6.47  2003/11/24 19:22:24  lavr
+ * SetSelectInternalRestartTimeout() to accept ptr to STimeout
+ *
+ * Revision 6.46  2003/11/18 20:18:49  lavr
+ * +SetSelectInternalRestartTimeout()
+ *
+ * Revision 6.45  2003/11/12 17:43:08  lavr
+ * +SOCK_CloseEx()
+ *
  * Revision 6.44  2003/10/24 16:51:11  lavr
  * GetTimeout(eIO_ReadWrite): return the lesser of eIO_Read and eIO_Write
  *
diff --git a/connect/ncbi_util.c b/connect/ncbi_util.c
index a82546fe..c52964d2 100644
--- a/connect/ncbi_util.c
+++ b/connect/ncbi_util.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_util.c,v 6.29 2003/09/02 21:05:14 lavr Exp $
+/*  $Id: ncbi_util.c,v 6.31 2003/11/14 13:04:38 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -44,9 +44,6 @@
 #  include <time.h>
 #endif
 
-#if defined(OS_MSWIN)  &&  defined(COMP_METRO)
-char *_strtime( char *timestr );
-#endif
 
 /* Static function pre-declarations to avoid C++ compiler warnings
  */
@@ -171,8 +168,7 @@ extern char* LOG_ComposeMessage
 
     /* Pre-calculate total message length */
     if ((format_flags & fLOG_DateTime) != 0) {
-#if  defined(NCBI_OS_MSWIN)  &&  !defined(COMP_METRO) 
-/*Should be compiler-dependent, but C-Toolkit lacks it*/
+#ifdef NCBI_OS_MSWIN /*Should be compiler-dependent but C-Tkit lacks it*/
         _strdate(&datetime[datetime_len]);
         datetime_len += strlen(&datetime[datetime_len]);
         datetime[datetime_len++] = ' ';
@@ -504,6 +500,12 @@ extern const char* CORE_GetPlatform(void)
 /*
  * ---------------------------------------------------------------------------
  * $Log: ncbi_util.c,v $
+ * Revision 6.31  2003/11/14 13:04:38  lavr
+ * Little changes in comments [no code changes]
+ *
+ * Revision 6.30  2003/11/13 19:53:41  rsmith
+ * Took out metrowerks specific #ifdef's (COMP_METRO). Not needed anymore.
+ *
  * Revision 6.29  2003/09/02 21:05:14  lavr
  * Proper indentation of compilation conditionals
  *
diff --git a/connect/ncbi_util.h b/connect/ncbi_util.h
index 28a87f5c..090a571d 100644
--- a/connect/ncbi_util.h
+++ b/connect/ncbi_util.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_UTIL__H
 #define CONNECT___NCBI_UTIL__H
 
-/*  $Id: ncbi_util.h,v 6.20 2003/10/21 11:17:17 lavr Exp $
+/*  $Id: ncbi_util.h,v 6.21 2004/01/27 17:05:59 ucko Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -98,6 +98,11 @@ extern NCBI_XCONNECT_EXPORT MT_LOCK CORE_GetLOCK(void);
 #define LOG_WRITE(lg, level, message) \
   LOG_Write(lg, level, THIS_MODULE, THIS_FILE, __LINE__, message)
 
+/* AIX's <pthread.h> defines LOG_DATA to be an integer constant; we must
+   explicitly drop such definitions to avoid trouble. */
+#ifdef LOG_DATA
+#  undef LOG_DATA
+#endif
 #define LOG_DATA(lg, data, size, message) \
   LOG_Data(lg, eLOG_Trace, THIS_MODULE, THIS_FILE, __LINE__, \
            data, size, message)
@@ -244,6 +249,10 @@ extern NCBI_XCONNECT_EXPORT const char* CORE_GetPlatform(void);
 /*
  * ---------------------------------------------------------------------------
  * $Log: ncbi_util.h,v $
+ * Revision 6.21  2004/01/27 17:05:59  ucko
+ * #undef LOG_DATA if necessary before #defining it with arguments to
+ * avoid trouble on AIX.
+ *
  * Revision 6.20  2003/10/21 11:17:17  lavr
  * Add location information in LOG_DATA()
  *
diff --git a/connect/test/test_ncbi_connutil_misc.c b/connect/test/test_ncbi_connutil_misc.c
index a6105173..48f83bc6 100644
--- a/connect/test/test_ncbi_connutil_misc.c
+++ b/connect/test/test_ncbi_connutil_misc.c
@@ -1,4 +1,4 @@
-/*  $Id: test_ncbi_connutil_misc.c,v 6.11 2002/12/13 21:20:55 lavr Exp $
+/*  $Id: test_ncbi_connutil_misc.c,v 6.13 2004/01/14 18:53:09 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -235,6 +235,8 @@ static void TEST_MIME(void)
                        eMIME_T_NcbiData, eMIME_Unknown, eENCOD_None));
     assert(s_Try_MIME("text/html",
                       eMIME_T_Text, eMIME_Html, eENCOD_None));
+    assert(s_Try_MIME("application/xml+soap",
+                      eMIME_T_Application, eMIME_XmlSoap, eENCOD_None));
     assert(!s_Try_MIME("", eMIME_T_NcbiData, eMIME_Unknown, eENCOD_Unknown));
     assert(!s_Try_MIME(0, eMIME_T_NcbiData, eMIME_Unknown, eENCOD_Unknown));
 }
@@ -300,6 +302,12 @@ int main(void)
 /*
  * ---------------------------------------------------------------------------
  * $Log: test_ncbi_connutil_misc.c,v $
+ * Revision 6.13  2004/01/14 18:53:09  lavr
+ * Use "application/xml+soap" in the test case
+ *
+ * Revision 6.12  2004/01/07 19:24:03  lavr
+ * Added test for MIME content-type "application/xml"
+ *
  * Revision 6.11  2002/12/13 21:20:55  lavr
  * Move log to end
  *
diff --git a/connect/test/test_ncbi_dsock.c b/connect/test/test_ncbi_dsock.c
index cd992fa0..1fa884bb 100644
--- a/connect/test/test_ncbi_dsock.c
+++ b/connect/test/test_ncbi_dsock.c
@@ -1,4 +1,4 @@
-/*  $Id: test_ncbi_dsock.c,v 6.12 2003/10/27 19:00:32 lavr Exp $
+/*  $Id: test_ncbi_dsock.c,v 6.14 2003/12/11 15:34:29 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -32,6 +32,7 @@
 
 #include "../ncbi_ansi_ext.h"
 #include "../ncbi_priv.h"               /* CORE logging facilities */
+#include <connect/ncbi_connutil.h>
 #include <connect/ncbi_socket.h>
 #include <errno.h>
 #include <stdlib.h>
@@ -49,6 +50,9 @@
 #elif defined(NCBI_OS_IRIX)
    /* This has been found experimentally on IRIX64 6.5 04101931 IP25 */
 #  define MAX_DGRAM_SIZE (60*1024)
+#elif defined(NCBI_OS_LINUX)
+/* Larger sizes do not seem to work everywhere */
+#  define MAX_DGRAM_SIZE 65000
 #else
    /* This is the maximal datagram size defined by the UDP standard */
 #  define MAX_DGRAM_SIZE 65535
@@ -96,96 +100,102 @@ static int s_Server(int x_port)
         return 1;
     }
 
-    if ((status = DSOCK_WaitMsg(server, 0/*infinite*/)) != eIO_Success) {
-        CORE_LOGF(eLOG_Error, ("[Server]  Error waiting on DSOCK: %s",
-                               IO_StatusStr(status)));
-        return 1;
-    }
-
-    timeout.sec  = 0;
-    timeout.usec = 0;
-    if ((status= SOCK_SetTimeout(server, eIO_Read, &timeout)) != eIO_Success) {
-        CORE_LOGF(eLOG_Error, ("[Server]  Error setting zero read tmo: %s",
-                               IO_StatusStr(status)));
-        return 1;
-    }
+    for (;;) {
+        if ((status = DSOCK_WaitMsg(server, 0/*infinite*/)) != eIO_Success) {
+            CORE_LOGF(eLOG_Error, ("[Server]  Error waiting on DSOCK: %s",
+                                   IO_StatusStr(status)));
+            break;
+        }
 
-    len = (size_t)(((double) rand()/(double) RAND_MAX)*sizeof(minibuf));
-    if ((status = DSOCK_RecvMsg(server, minibuf, len, 0, &msglen,
-                                &peeraddr, &peerport)) != eIO_Success) {
-        CORE_LOGF(eLOG_Error, ("[Server]  Error reading from DSOCK: %s",
-                               IO_StatusStr(status)));
-        return 1;
-    }
-    if (len > msglen)
-        len = msglen;
+        timeout.sec  = 0;
+        timeout.usec = 0;
+        if ((status = SOCK_SetTimeout(server, eIO_Read, &timeout))
+            != eIO_Success) {
+            CORE_LOGF(eLOG_Error, ("[Server]  Error setting zero read tmo: %s",
+                                   IO_StatusStr(status)));
+            break;
+        }
 
-    if (SOCK_ntoa(peeraddr, addr, sizeof(addr)) != 0)
-        strcpy(addr, "<unknown>");
+        len = (size_t)(((double) rand()/(double) RAND_MAX)*sizeof(minibuf));
+        if ((status = DSOCK_RecvMsg(server, minibuf, len, 0, &msglen,
+                                    &peeraddr, &peerport)) != eIO_Success) {
+            CORE_LOGF(eLOG_Error, ("[Server]  Error reading from DSOCK: %s",
+                                   IO_StatusStr(status)));
+            continue;
+        }
+        if (len > msglen)
+            len = msglen;
 
-    CORE_LOGF(eLOG_Note, ("[Server]  Message received from %s:%hu, %lu bytes",
-                          addr, peerport, (unsigned long) msglen));
+        if (SOCK_ntoa(peeraddr, addr, sizeof(addr)) != 0)
+            strcpy(addr, "<unknown>");
 
-    if (!(buf = (char*) malloc(msglen ? msglen : 1))) {
-        CORE_LOG_ERRNO(eLOG_Error, errno, "[Server]  Cannot alloc msg buf");
-        return 1;
-    }
-    if (len)
-        memcpy(buf, minibuf, len);
+        CORE_LOGF(eLOG_Note, ("[Server]  Message received from %s:%hu, "
+                              "%lu bytes",
+                              addr, peerport, (unsigned long) msglen));
 
-    while (len < msglen) {
-        n = (size_t)(((double) rand()/(double) RAND_MAX)*(msglen - len) + 0.5);
-        if ((status = SOCK_Read(server, buf + len, n, &n, eIO_ReadPlain))
-            != eIO_Success) {
-            CORE_LOGF(eLOG_Error,("[Server]  Error reading msg @ byte %lu: %s",
-                                  (unsigned long) len, IO_StatusStr(status)));
-            return 1;
+        if (!(buf = (char*) malloc(msglen ? msglen : 1))) {
+            CORE_LOG_ERRNO(eLOG_Error, errno,"[Server]  Cannot alloc msg buf");
+            break;
         }
-        len += n;
-    }
-    assert(SOCK_Read(server, 0, 1, &n, eIO_ReadPlain) == eIO_Closed);
+        if (len)
+            memcpy(buf, minibuf, len);
+
+        while (len < msglen) {
+            n = (size_t)(((double)rand()/(double)RAND_MAX)*(msglen-len) + 0.5);
+            if ((status = SOCK_Read(server, buf + len, n, &n, eIO_ReadPlain))
+                != eIO_Success) {
+                CORE_LOGF(eLOG_Error,("[Server]  Error reading msg @ byte %lu:"
+                                      " %s", (unsigned long) len,
+                                      IO_StatusStr(status)));
+                free(buf);
+                continue;
+            }
+            len += n;
+        }
+        assert(SOCK_Read(server, 0, 1, &n, eIO_ReadPlain) == eIO_Closed);
 
-    CORE_LOG(eLOG_Note, "[Server]  Bouncing the message to sender");
+        CORE_LOG(eLOG_Note, "[Server]  Bouncing the message to sender");
 
-    timeout.sec  = 1;
-    timeout.usec = 0;
-    if ((status= SOCK_SetTimeout(server, eIO_Write, &timeout)) != eIO_Success){
-        CORE_LOGF(eLOG_Error, ("[Server]  Error setting write tmo: %s",
-                               IO_StatusStr(status)));
-        return 1;
-    }
+        timeout.sec  = 1;
+        timeout.usec = 0;
+        if ((status = SOCK_SetTimeout(server, eIO_Write, &timeout))
+            != eIO_Success){
+            CORE_LOGF(eLOG_Error, ("[Server]  Error setting write tmo: %s",
+                                   IO_StatusStr(status)));
+            break;
+        }
 
-    for (len = 0; len < msglen; len += n) {
-        n = (size_t)(((double) rand()/(double) RAND_MAX)*(msglen - len) + 0.5);
-        if ((status = SOCK_Write(server, buf + len, n, &n, eIO_WritePlain))
-            != eIO_Success) {
-            CORE_LOGF(eLOG_Error,("[Server]  Error writing msg @ byte %lu: %s",
-                                  (unsigned long) len, IO_StatusStr(status)));
-            return 1;
+        for (len = 0; len < msglen; len += n) {
+            n = (size_t)(((double)rand()/(double)RAND_MAX)*(msglen-len) + 0.5);
+            if ((status = SOCK_Write(server, buf + len, n, &n, eIO_WritePlain))
+                != eIO_Success) {
+                CORE_LOGF(eLOG_Error,("[Server]  Error writing msg @ byte %lu:"
+                                      " %s", (unsigned long) len,
+                                      IO_StatusStr(status)));
+                break;
+            }
         }
-    }
 
-    free(buf);
+        free(buf);
 
-    if ((status = DSOCK_SendMsg(server, addr, peerport, "--Reply--", 9))
-        != eIO_Success) {
-        CORE_LOGF(eLOG_Error, ("[Server]  Error sending to DSOCK: %s",
-                               IO_StatusStr(status)));
-        return 1;
+        if ((status = DSOCK_SendMsg(server, addr, peerport, "--Reply--", 9))
+            != eIO_Success) {
+            CORE_LOGF(eLOG_Error, ("[Server]  Error sending to DSOCK: %s",
+                                   IO_StatusStr(status)));
+            /*continue*/;
+        }
     }
 
+    /* On errors control reaches here */
     if ((status = SOCK_Close(server)) != eIO_Success) {
         CORE_LOGF(eLOG_Error, ("[Server]  Error closing DSOCK: %s",
                                IO_StatusStr(status)));
-        return 1;
     }
-
-    CORE_LOG(eLOG_Note, "[Server]  Completed successfully");
-    return 0;
+    return 1;
 }
 
 
-static int s_Client(int x_port)
+static int s_Client(int x_port, unsigned int max_try)
 {
     size_t         msglen, n;
     STimeout       timeout;
@@ -193,6 +203,8 @@ static int s_Client(int x_port)
     SOCK           client;
     unsigned short port;
     char*          buf;
+    unsigned long  id;
+    unsigned int   m;
 
     if (x_port <= 0) {
         CORE_LOG(eLOG_Error, "[Client]  Port wrongly specified");
@@ -209,6 +221,9 @@ static int s_Client(int x_port)
     }
 
     msglen = (size_t)(((double)rand()/(double)RAND_MAX)*(MAX_DGRAM_SIZE - 10));
+    if (msglen < sizeof(time_t))
+        msglen = sizeof(time_t);
+
     CORE_LOGF(eLOG_Note, ("[Client]  Generating a message %lu bytes long",
                           (unsigned long) msglen));
 
@@ -217,42 +232,71 @@ static int s_Client(int x_port)
         return 1;
     }
 
-    for (n = 0; n < msglen; n++)
+
+    for (n = sizeof(unsigned long); n < msglen; n++)
         buf[n] = rand() % 0xFF;
 
-    if ((status = DSOCK_SendMsg(client, "127.0.0.1", port, buf, msglen))
-        != eIO_Success) {
-        CORE_LOGF(eLOG_Error, ("[Client]  Error sending to DSOCK: %s",
-                               IO_StatusStr(status)));
-        return 1;
-    }
+    id = (unsigned long) time(0);
 
-    timeout.sec  = 1;
-    timeout.usec = 0;
-    if ((status = SOCK_SetTimeout(client, eIO_Read, &timeout)) != eIO_Success){
-        CORE_LOGF(eLOG_Error, ("[Client]  Error setting read tmo: %s",
-                               IO_StatusStr(status)));
-        return 1;
-    }
+    for (m = 1; m <= max_try; m++) {
+        unsigned long tmp;
 
-    if ((status = DSOCK_RecvMsg(client, &buf[msglen], msglen + 9, 0, &n, 0, 0))
-        != eIO_Success) {
-        CORE_LOGF(eLOG_Error, ("[Client]  Error reading from DSOCK: %s",
-                               IO_StatusStr(status)));
-        return 1;
-    }
+        if (m != 1)
+            CORE_LOGF(eLOG_Note, ("[Client]  Attempt #%u", (unsigned int) m));
+        id++;
+
+        *((unsigned long*) buf) = SOCK_htonl((unsigned long) id);
+
+        if ((status = DSOCK_SendMsg(client, "127.0.0.1", port, buf, msglen))
+            != eIO_Success) {
+            CORE_LOGF(eLOG_Error, ("[Client]  Error sending to DSOCK: %s",
+                                   IO_StatusStr(status)));
+            return 1;
+        }
+
+        timeout.sec  = 1;
+        timeout.usec = 0;
+        if ((status = SOCK_SetTimeout(client, eIO_Read, &timeout))
+            != eIO_Success) {
+            CORE_LOGF(eLOG_Error, ("[Client]  Error setting read timeout: %s",
+                                   IO_StatusStr(status)));
+            return 1;
+        }
+
+    again:
+        if ((status = DSOCK_RecvMsg(client, &buf[msglen], msglen+9,0, &n, 0,0))
+            != eIO_Success) {
+            CORE_LOGF(eLOG_Error, ("[Client]  Error reading from DSOCK: %s",
+                                   IO_StatusStr(status)));
+            continue;
+        }
+
+        if (n != msglen + 9) {
+            CORE_LOGF(eLOG_Error, ("[Client]  Received message of wrong size: "
+                                   "%lu", (unsigned long) n));
+            return 1;
+        }
+
+        memcpy(&tmp, &buf[msglen], sizeof(tmp));
+        if (SOCK_ntohl(tmp) != id) {
+            m++;
+            CORE_LOGF(m < max_try ? eLOG_Warning : eLOG_Error,
+                      ("[Client]  Stale message received%s",
+                       m <= max_try ? ", reattempting to fetch" : ""));
+            if (m <= max_try)
+                goto again;
+            break;
+        }
 
-    if (n != msglen + 9) {
-        CORE_LOGF(eLOG_Error, ("[Client]  Received message of wrong size: %lu",
-                               (unsigned long) n));
-        return 1;
-    } else {
         CORE_LOGF(eLOG_Note, ("[Client]  Received the message back, %lu bytes",
                               (unsigned long) n));
+        assert(SOCK_Read(client, 0, 1, &n, eIO_ReadPlain) == eIO_Closed);
+        break;
     }
-    assert(SOCK_Read(client, 0, 1, &n, eIO_ReadPlain) == eIO_Closed);
+    if (m > max_try)
+        return 1;
 
-    for (n = 0; n < msglen; n++) {
+    for (n = sizeof(unsigned long); n < msglen; n++) {
         if (buf[n] != buf[msglen + n])
             break;
     }
@@ -285,6 +329,7 @@ static int s_Client(int x_port)
 int main(int argc, const char* argv[])
 {
     unsigned long seed;
+    unsigned int  max_try = DEF_CONN_MAX_TRY;
     const char*   env = getenv("CONN_DEBUG_PRINTOUT");
 
     CORE_SetLOGFormatFlags(fLOG_None          | fLOG_Level   |
@@ -305,16 +350,19 @@ int main(int argc, const char* argv[])
     CORE_LOGF(eLOG_Note, ("Random SEED = %lu", seed));
     srand(seed);
 
-    if (env && (strcasecmp(env, "1") == 0    ||
-                strcasecmp(env, "yes") == 0  ||
-                strcasecmp(env, "true") == 0 ||
-                strcasecmp(env, "some") == 0 ||
-                strcasecmp(env, "data") == 0)){
+    if (env && (strcasecmp(env, "1") == 0     ||
+                strcasecmp(env, "yes") == 0   ||
+                strcasecmp(env, "true") == 0  ||
+                strcasecmp(env, "some") == 0  ||
+                strcasecmp(env, "data") == 0)) {
         SOCK_SetDataLoggingAPI(eOn);
     }
 
+    if (!(env = getenv("CONN_MAX_TRY"))  ||  !(max_try = atoi(env)))
+        max_try = DEF_CONN_MAX_TRY;
+
     if (strcasecmp(argv[1], "client") == 0)
-        return s_Client(argv[2] ? atoi(argv[2]) : DEFAULT_PORT);
+        return s_Client(argv[2] ? atoi(argv[2]) : DEFAULT_PORT, max_try);
 
     if (strcasecmp(argv[1], "server") == 0)
         return s_Server(argv[2] ? atoi(argv[2]) : DEFAULT_PORT);
@@ -326,6 +374,12 @@ int main(int argc, const char* argv[])
 /*
  * --------------------------------------------------------------------------
  * $Log: test_ncbi_dsock.c,v $
+ * Revision 6.14  2003/12/11 15:34:29  lavr
+ * Lower maximal datagram size for Linux - 65535 didn't seem to work everywhere
+ *
+ * Revision 6.13  2003/12/10 17:24:16  lavr
+ * Reattempt to send/receive a datagram on I/O errors in client
+ *
  * Revision 6.12  2003/10/27 19:00:32  lavr
  * Limit datagram size for Darwin (which is BSD based)
  *
diff --git a/connect/test/test_ncbi_http_connector.c b/connect/test/test_ncbi_http_connector.c
index 4adccbcd..cb5b3b5b 100644
--- a/connect/test/test_ncbi_http_connector.c
+++ b/connect/test/test_ncbi_http_connector.c
@@ -1,4 +1,4 @@
-/*  $Id: test_ncbi_http_connector.c,v 6.13 2003/05/14 03:58:43 lavr Exp $
+/*  $Id: test_ncbi_http_connector.c,v 6.14 2003/11/04 12:26:06 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -57,6 +57,7 @@ extern "C" {
 }
 #endif /* __cplusplus */
 
+/*ARGSUSED*/
 static void s_REG_Get
 (void*       user_data,
  const char* section,
@@ -141,6 +142,9 @@ int main(void)
 /*
  * --------------------------------------------------------------------------
  * $Log: test_ncbi_http_connector.c,v $
+ * Revision 6.14  2003/11/04 12:26:06  lavr
+ * s_GetReg() marked with ARGSUSED, because user_data is not used in there
+ *
  * Revision 6.13  2003/05/14 03:58:43  lavr
  * Match changes in respective APIs of the tests
  *
diff --git a/connect/test/test_ncbi_sendmail.c b/connect/test/test_ncbi_sendmail.c
index 0fe4d776..47f884f6 100644
--- a/connect/test/test_ncbi_sendmail.c
+++ b/connect/test/test_ncbi_sendmail.c
@@ -1,4 +1,4 @@
-/*  $Id: test_ncbi_sendmail.c,v 6.9 2003/05/14 03:58:43 lavr Exp $
+/*  $Id: test_ncbi_sendmail.c,v 6.11 2003/12/09 15:39:30 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -44,6 +44,11 @@
 
 int main(void)
 {
+    const char custom_body[] =
+        "Subject: Custom sized body\n"
+        "\n"
+        "Custom sized body\n"
+        "0123456789\n"; /* these 11 chars to ignore */
     const char* body[] = {
         "This is a simple test",
         "This is a test with\n.",
@@ -62,7 +67,8 @@ int main(void)
     };
     const char* to[] = {
         "lavr",
-        "lavr@pavo"
+        "lavr@pavo",
+        " \"Anton Lavrentiev\"   <lavr@pavo>  , lavr, <lavr>   ",
     };
     size_t i, j, k, n, m;
     const char* mx_host;
@@ -98,10 +104,12 @@ int main(void)
     CORE_LOG(eLOG_Note, "Phase 2 of 2: Testing CORE_SendMailEx");
 
     SendMailInfo_Init(&info);
-    mx_port = info.mx_port;
     mx_host = info.mx_host;
+    mx_port = info.mx_port;
     mx_tmo  = info.mx_timeout;
 
+    info.mx_host = "localhost";
+
     CORE_LOG(eLOG_Note, "Testing bad port");
     info.mx_port = 10;
     retval = CORE_SendMailEx("lavr", "CORE_SendMailEx Test", "Test", &info);
@@ -117,6 +125,7 @@ int main(void)
     CORE_LOGF(eLOG_Note, ("Test passed: %s", retval));
 
     CORE_LOG(eLOG_Note, "Testing timeout");
+    info.mx_host = "www.ncbi.nlm.nih.gov";
     info.mx_timeout.sec = 5;
     info.mx_port = 80;
     retval = CORE_SendMailEx("lavr", "CORE_SendMailEx Test", "Test", &info);
@@ -135,7 +144,7 @@ int main(void)
         CORE_LOG(eLOG_Fatal, "Test failed");
     CORE_LOGF(eLOG_Note, ("Test passed: %s", retval));
 
-    info.mx_host = mx_host;
+    info.mx_host = "localhost";
 
     CORE_LOG(eLOG_Note, "Testing cc");
     info.cc = "vakatov";
@@ -186,13 +195,41 @@ int main(void)
         CORE_LOG(eLOG_Fatal, "Test failed");
     CORE_LOGF(eLOG_Note, ("Test passed: %s", retval));
 
+    CORE_LOG(eLOG_Note, "Testing AS-IS message");
+    info.mx_no_header = 1/*true*/;
+    retval = CORE_SendMailEx("lavr",
+                             "BAD SUBJECT SHOULD NOT APPEAR BUT IGNORED",
+                             "From: yourself\n"
+                             "To: yourself\n"
+                             "Subject: AS-IS message\n"
+                             "\n"
+                             "AS-IS",
+                             &info);
+    if (retval)
+        CORE_LOGF(eLOG_Fatal, ("Test failed: %s", retval));
+    CORE_LOG(eLOG_Note, "Test passed");
+
+    CORE_LOG(eLOG_Note, "Testing AS-IS custom sized message");
+    info.body_size = strlen(custom_body) - 11/*to ignore*/;
+    retval = CORE_SendMailEx("<lavr@pavo>",
+                             "BAD SUBJECT SHOULD NOT APPEAR BUT IGNORED",
+                             custom_body,
+                             &info);
+    if (retval)
+        CORE_LOGF(eLOG_Fatal, ("Test failed: %s", retval));
+    CORE_LOG(eLOG_Note, "Test passed");
+
+    info.body_size = 0;
+    info.mx_no_header = 0;
+    info.mx_host = mx_host;
+
     CORE_LOG(eLOG_Note, "Testing bad from");
     strcpy(info.from, "blahblah@blahblah");
     retval = CORE_SendMailEx("lavr", "CORE_SendMailEx Test", "Test", &info);
     if (!retval)
         CORE_LOG(eLOG_Error, "Test failed");
     else
-        CORE_LOGF(eLOG_Error, ("Test passed: %s", retval));
+        CORE_LOGF(eLOG_Note, ("Test passed: %s", retval));
 
     CORE_LOG(eLOG_Note, "Testing bad magic");
     info.magic_number = 0;
@@ -209,6 +246,12 @@ int main(void)
 /*
  * --------------------------------------------------------------------------
  * $Log: test_ncbi_sendmail.c,v $
+ * Revision 6.11  2003/12/09 15:39:30  lavr
+ * Added new test of custom-sized message body
+ *
+ * Revision 6.10  2003/12/05 18:39:35  lavr
+ * Test multiple recipients and as-is message
+ *
  * Revision 6.9  2003/05/14 03:58:43  lavr
  * Match changes in respective APIs of the tests
  *
diff --git a/corelib/morefile/FullPath.c b/corelib/morefile/FullPath.c
index 99c5bfb8..bb818b85 100644
--- a/corelib/morefile/FullPath.c
+++ b/corelib/morefile/FullPath.c
@@ -40,6 +40,8 @@
      Institutes of Health, Bethesda, Maryland, USA.
 */
 
+/* C++ style comments converted to C comments by NCBI */
+
 
 #ifndef WIN32
 
@@ -174,7 +176,7 @@ pascal	OSErr	FSpGetFullPath(const FSSpec *spec,
 			pb.dirInfo.ioDrDirID = tempSpec.parID;
 			pb.dirInfo.ioFDirIndex = 0;
 			result = PBGetCatInfoSync(&pb);
-			// Allow file/directory name at end of path to not exist.
+			/* Allow file/directory name at end of path to not exist. */
 			realResult = result;
 			if ( (result == noErr) || (result == fnfErr) )
 			{
@@ -218,7 +220,7 @@ pascal	OSErr	FSpGetFullPath(const FSSpec *spec,
 	{
 		/* Return the length */
 		*fullPathLength = GetHandleSize(*fullPath);
-		result = realResult;	// return realResult in case it was fnfErr
+		result = realResult;	/* return realResult in case it was fnfErr */
 	}
 	else
 	{
diff --git a/corelib/ncbifile.c b/corelib/ncbifile.c
index f3ff0336..45cac220 100644
--- a/corelib/ncbifile.c
+++ b/corelib/ncbifile.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   3/4/91
 *
-* $Revision: 6.32 $
+* $Revision: 6.34 $
 *
 * File Description: 
 *     portable file routines
@@ -43,6 +43,12 @@
 * 11-27-94 Ostell      moved includes to ncbiwin.h to avoid conflict MSC
 *
 * $Log: ncbifile.c,v $
+* Revision 6.34  2004/01/23 20:07:16  kans
+* fix to FileGets under Darwin, was losing last character if buffer was shorter than line being read
+*
+* Revision 6.33  2003/11/17 17:17:57  kans
+* changed C++ comments to C comments
+*
 * Revision 6.32  2003/05/05 11:53:37  rsmith
 * Codewarrior compiling for Win32 does not know about setmode or tempnam.
 *
@@ -236,12 +242,12 @@ static char * _this_file = __FILE__;
 
 #ifdef OS_MAC
 #define INLINE_MOREFILES
-//#include "FullPath.h"
-//#include "MoreFilesExtra.h"
+/* #include "FullPath.h" */
+/* #include "MoreFilesExtra.h" */
 #ifdef INLINE_MOREFILES
 
-// MoreFilesExtras.c
-// -----------------
+/* MoreFilesExtras.c */
+/* ----------------- */
 
 /*
 **	Apple Macintosh Developer Technical Support
@@ -441,14 +447,14 @@ static OSErr MacPathname2FSSpec(const char *inPathname, FSSpec *outFSS)
 		return paramErr;
 	}
 	
-	err = HGetVol(NULL, &vRefNum, &dirID);  // default volume and directory
+	err = HGetVol(NULL, &vRefNum, &dirID);  /* default volume and directory */
 	if (err != noErr) return err;
 	
 	len = strlen(inPathname);
 	
 	p = strchr(inPathname, ':');
 	if (p == NULL) {
-		// Partial pathname -- filename only
+		/* Partial pathname -- filename only */
 		Str31 filename;
 		assert(len <= 31);
 		c2pstrcpy(filename, inPathname);
@@ -457,21 +463,21 @@ static OSErr MacPathname2FSSpec(const char *inPathname, FSSpec *outFSS)
 		Str31 name;
 		int nameLen;
 		if (inPathname[0] == ':') {
-			// Relative pathname including directory path
+			/* Relative pathname including directory path */
 			
 		} else {
-			// Absolute pathname
-			//Str31 volName;  // We would use Str28 if it was defined -- 27, plus 1 for ':'.
+			/* Absolute pathname */
+			/* Str31 volName;  We would use Str28 if it was defined -- 27, plus 1 for ':'. */
 			nameLen = p - inPathname;
 			assert(nameLen <= 27);
 			name[0] = nameLen + 1;
-			memcpy(name + 1, inPathname, nameLen + 1);  // Copy the volume name and the colon.
+			memcpy(name + 1, inPathname, nameLen + 1);  /* Copy the volume name and the colon. */
 			err = DetermineVRefNum(name, 0, &vRefNum);
 			if (err != noErr) return err;
 			dirID = 2;
 		}
-		// vRefNum and dirID now specify the directory in which we should descend
-		// the path pointed to by p (pointing to the first colon).
+		/* vRefNum and dirID now specify the directory in which we should descend
+		   the path pointed to by p (pointing to the first colon). */
 		p++;
 		while (p != NULL && *p != '\0') {
 			char *q = strchr(p, ':');
@@ -493,7 +499,7 @@ static OSErr MacPathname2FSSpec(const char *inPathname, FSSpec *outFSS)
 					p = q + 1;
 				}
 			} else {
-				q = strchr(p, '\0');  // go to end of string
+				q = strchr(p, '\0');  /* go to end of string */
 				nameLen = q - p;
 				assert(nameLen > 0);
 				assert(nameLen <= 31);
@@ -521,7 +527,7 @@ static OSErr MacFSSpec2FullPathname(const FSSpec *inFSS, char **outPathname)
 	err = FSpGetFullPath(inFSS, &fullPathLength, &h);
 	if (err != noErr) return err;
 	
-	assert(fullPathLength >= 2);  // An absolute pathname must be at least two chars long
+	assert(fullPathLength >= 2);  /* An absolute pathname must be at least two chars long */
 	fullPath = (char *)Nlm_Malloc(fullPathLength + 1);
 	if (fullPath == NULL) {
 		err = memFullErr;
@@ -755,7 +761,7 @@ NLM_EXTERN char * LIBCALL  Nlm_FileGets (Nlm_CharPtr ptr, size_t size, FILE *fp)
 	ch = fgetc (fp);
 	count = 0;
 	tmp = ptr;
-	while (ch != EOF && ch != '\0' && ch != '\n' && ch != '\r' && count < size - 1) {
+	while (ch != EOF && ch != '\0' && ch != '\n' && ch != '\r' && count < size - 2) {
 	  *tmp = ch;
 	  tmp++;
 	  count++;
@@ -765,6 +771,10 @@ NLM_EXTERN char * LIBCALL  Nlm_FileGets (Nlm_CharPtr ptr, size_t size, FILE *fp)
 	  *tmp = '\n';
 	  tmp++;
 	  count++;
+	} else if (ch != EOF && ch != '\0') {
+	  *tmp = ch;
+	  tmp++;
+	  count++;
 	}
 	*tmp = '\0';
 	if (count < 1)
@@ -1017,14 +1027,14 @@ NLM_EXTERN void LIBCALL Nlm_FileCreate (Nlm_CharPtr fileName, Nlm_CharPtr type,
   if (fileName != NULL && fileName [0] != '\0') {
 
 #ifdef OS_MAC
-    // note: the following assumes either full pathname or that the current
-    // directory is the proper location to find/create the file
+    /* note: the following assumes either full pathname or that the current
+       directory is the proper location to find/create the file */
 
     Nlm_StringNCpy_0(temp, fileName, sizeof(temp));
     Nlm_CtoPstr ( temp);
     fError = FSMakeFSSpec( 0, 0, (StringPtr)temp, &spec);
     
-    // file not found, so create it...
+    /* file not found, so create it... */
     if( fError == fnfErr){
         fType = Nlm_GetOSType (type, 'TEXT');
         fCreator = Nlm_GetOSType (creator, '    ');
diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx
index 6860b066..7aee6e44 100644
--- a/corelib/ncbilcl.lnx
+++ b/corelib/ncbilcl.lnx
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   8/1/94
 *
-* $Revision: 6.8 $
+* $Revision: 6.9 $
 *
 * File Description:
 *		system dependent header
@@ -38,6 +38,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbilcl.lnx,v $
+* Revision 6.9  2004/01/21 22:31:20  ucko
+* Define PROC_X86_64 on x86-64 systems.
+*
 * Revision 6.8  2002/11/22 20:05:04  lavr
 * Configure HAVE_STRDUP and HAVE_STRCASECMP
 *
@@ -100,6 +103,8 @@
 #define PROC_SH /* ? */
 #elif defined(__sparc__) || #cpu(sparc) || #cpu(sparc64) || #machine(sparc) || #machine(sparc64)
 #define PROC_SPARC
+#elif defined(__x86_64__) || #cpu(x86_64)
+#define PROC_X86_64
 #else
 #warning Unknown processor type.  Please define something appropriate.
 #endif
diff --git a/corelib/ncbilcl.met b/corelib/ncbilcl.met
index 5c54087e..20a53eb1 100644
--- a/corelib/ncbilcl.met
+++ b/corelib/ncbilcl.met
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   3/31/94
 *
-* $Revision: 6.10 $
+* $Revision: 6.11 $
 *
 * File Description:
 *		system dependent header
@@ -41,6 +41,9 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: ncbilcl.met,v $
+* Revision 6.11  2003/11/07 18:32:41  rsmith
+* need pascal keyword on Mac builds.
+*
 * Revision 6.10  2003/05/05 15:01:53  rsmith
 * support for targeting Win32 systems with Codewarrior on Mac.
 *
@@ -378,7 +381,6 @@ typedef int (FAR PASCAL *Nlm_FnPtr)();
 #define far
 #define huge
 #define cdecl
-#define pascal
 #define _pascal
 #define _near
 #define _far
diff --git a/corelib/ncbilcl.msw b/corelib/ncbilcl.msw
index d23ef63b..8664f8db 100644
--- a/corelib/ncbilcl.msw
+++ b/corelib/ncbilcl.msw
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.4 $
+* $Revision: 6.5 $
 *
 * File Description:
 *               system dependent header
@@ -39,6 +39,10 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbilcl.msw,v $
+* Revision 6.5  2003/12/24 18:37:55  vakatov
+* More consistent #define of FAR and near (as per D.Sinyakov's request).
+* Also, get rid of all WIN16-related code (it's just not supported nowdays).
+*
 * Revision 6.4  2002/11/22 20:05:04  lavr
 * Configure HAVE_STRDUP and HAVE_STRCASECMP
 *
@@ -97,8 +101,8 @@
 #error MAC applications can be built with MSVC++ compiler only
 #endif
 
-#if !defined(WIN16) && !defined(WIN32) && !defined(_MAC)
-#error You must define one of: WIN16, WIN32, or _MAC 
+#if !defined(WIN32) && !defined(_MAC)
+#  error You must define one of:  WIN32 or _MAC 
 #endif
 
 
@@ -112,36 +116,6 @@
 #define WIN_MSWIN
 
 
-/*================[ Win16 ]===============*/
-#ifdef WIN16
-
-#define PLATFORM_NAME "Win16"
-#define PROC_I80X86
-
-#ifndef PASCAL
-#define PASCAL __pascal
-#define CDECL  __cdecl
-#define EXPORT __export
-#endif
-
-#ifndef FAR
-#define FAR    __far
-#define NEAR   __near
-#endif
-
-typedef signed   long  Nlm_Int4,  FAR * Nlm_Int4Ptr;
-typedef unsigned long  Nlm_Uint4, FAR * Nlm_Uint4Ptr;
-#define Int4           Nlm_Int4
-#define Int4Ptr        Nlm_Int4Ptr
-#define Uint4          Nlm_Uint4
-#define Uint4Ptr       Nlm_Uint4Ptr
-#define INT4_MIN       (-2147483647-1)
-#define INT4_MAX       2147483647
-#define UINT4_MAX      4294967295U
-
-#endif  /* WIN16 */
-
-
 /*================[ Win32 ]===============*/
 #ifdef WIN32
 
@@ -150,6 +124,9 @@ typedef unsigned long  Nlm_Uint4, FAR * Nlm_Uint4Ptr;
 
 #ifndef FAR
 #define FAR
+#endif
+
+#ifndef NEAR
 #define NEAR
 #endif
 
@@ -235,6 +212,8 @@ typedef unsigned long  Nlm_Uint4, FAR * Nlm_Uint4Ptr;
 
 #ifndef FAR
 #define FAR
+#endif
+#ifndef NEAR
 #define NEAR
 #endif
 
diff --git a/corelib/ncbimisc.c b/corelib/ncbimisc.c
index 2ff56458..9abfbf7c 100644
--- a/corelib/ncbimisc.c
+++ b/corelib/ncbimisc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/23/91
 *
-* $Revision: 6.23 $
+* $Revision: 6.24 $
 *
 * File Description: 
 *   	miscellaneous functions
@@ -43,6 +43,9 @@
 * 02-16-94 Epstein     Retired Gestalt functions and definitions
 *
 * $Log: ncbimisc.c,v $
+* Revision 6.24  2003/12/03 02:10:23  kans
+* added defines missing from Mac OS 10.3 headers
+*
 * Revision 6.23  2002/11/06 21:25:10  ucko
 * Don't assume MIPS is IRIX, or HPPA is HP/UX; allow Linux too, for both.
 *
@@ -155,6 +158,16 @@
 #include <TextUtils.h>
 #endif
 
+/* Missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+#ifdef __MWERKS__
+#ifdef OS_UNIX_DARWIN
+#ifndef __CHAR_BIT__
+#define __CHAR_BIT__ 8
+#endif
+#endif
+#endif
+/* End missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+
 /*
 TRIPLE_MARK is the character inserted before the thousands, millions,
 billions, etc. digit positions.  Change TRIPLE_MARK to a period
diff --git a/corelib/ncbistr.c b/corelib/ncbistr.c
index 2ff3b756..e9dc4349 100644
--- a/corelib/ncbistr.c
+++ b/corelib/ncbistr.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   3/4/91
 *
-* $Revision: 6.12 $
+* $Revision: 6.13 $
 *
 * File Description: 
 *   	portable string routines
@@ -37,6 +37,9 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: ncbistr.c,v $
+* Revision 6.13  2003/12/03 02:10:24  kans
+* added defines missing from Mac OS 10.3 headers
+*
 * Revision 6.12  2003/09/15 16:21:32  kans
 * moved StringDoesHaveText from sqnutils3.c
 *
@@ -161,6 +164,16 @@
 #include <ncbi.h>
 #include <ncbiwin.h>
 
+/* Missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+#ifdef __MWERKS__
+#ifdef OS_UNIX_DARWIN
+#ifndef __CHAR_BIT__
+#define __CHAR_BIT__ 8
+#endif
+#endif
+#endif
+/* End missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+
 /* ClearDestString clears the destination string if the source is NULL. */
 static Nlm_CharPtr NEAR Nlm_ClearDestString (Nlm_CharPtr to, size_t max)
 {
diff --git a/corelib/ncbithr.c b/corelib/ncbithr.c
index 522dad84..a4cdd2d3 100644
--- a/corelib/ncbithr.c
+++ b/corelib/ncbithr.c
@@ -1,4 +1,4 @@
-/* $Id: ncbithr.c,v 6.37 2003/09/19 22:58:38 coulouri Exp $ */
+/* $Id: ncbithr.c,v 6.38 2003/12/04 18:02:43 rsmith Exp $ */
 /*****************************************************************************
 
     Name: ncbithr.c
@@ -35,6 +35,9 @@
  Modification History:
 -----------------------------------------------------------------------------
 * $Log: ncbithr.c,v $
+* Revision 6.38  2003/12/04 18:02:43  rsmith
+* Move includes out of definition of NlmCPUNumber.
+*
 * Revision 6.37  2003/09/19 22:58:38  coulouri
 * NetBSD does not (yet?) have pthread_attr_setschedpolicy()
 *
@@ -2562,24 +2565,26 @@ NLM_EXTERN Boolean NlmThreadsAvailable(void)
 }
 
 
-NLM_EXTERN Int4 NlmCPUNumber(void)
-{
 #if defined(OS_UNIX_DARWIN)
-
 #include <mach/mach.h>
 #include <mach/mach_host.h>
-#include <mach/host_info.h>
+#include <mach/host_info.h> 
+#endif
 
-host_basic_info_data_t hinfo;
-mach_msg_type_number_t hinfo_count = HOST_BASIC_INFO_COUNT;
-kern_return_t rc;
+NLM_EXTERN Int4 NlmCPUNumber(void)
+{
+#if defined(OS_UNIX_DARWIN)
 
-rc=host_info( mach_host_self(), HOST_BASIC_INFO, (host_info_t) &hinfo, &hinfo_count);
+  host_basic_info_data_t hinfo;
+  mach_msg_type_number_t hinfo_count = HOST_BASIC_INFO_COUNT;
+  kern_return_t rc;
 
-if (rc!=KERN_SUCCESS)
- return -1;
+  rc=host_info( mach_host_self(), HOST_BASIC_INFO, (host_info_t) &hinfo, &hinfo_count);
+
+  if (rc != KERN_SUCCESS)
+    return -1;
 
-return hinfo.avail_cpus;
+  return hinfo.avail_cpus;
 
 #elif defined(WIN32)
   SYSTEM_INFO sysInfo;
diff --git a/corelib/ncbiwin.h b/corelib/ncbiwin.h
index 1b5b354c..2d070e48 100644
--- a/corelib/ncbiwin.h
+++ b/corelib/ncbiwin.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.8 $
+* $Revision: 6.9 $
 *
 * File Description:
 *               underlying window toolbox import
@@ -37,6 +37,9 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: ncbiwin.h,v $
+* Revision 6.9  2003/11/07 15:54:44  rsmith
+* Remove obsolete and uneeded Macintosh headers Types.h and Windows.h
+*
 * Revision 6.8  2003/05/05 12:00:10  rsmith
 * Change definitions before including windows.h when compiling with Codewarrior for Windows.
 *
@@ -145,8 +148,10 @@
 #include <Quickdraw.h>
 #include <TextEdit.h>
 #include <ToolUtils.h>
+/*
 #include <Types.h>
 #include <Windows.h>
+*/
 #include <Sound.h>
 #include <Folders.h>
 #endif
diff --git a/corelib/tsprintf.c b/corelib/tsprintf.c
index 77bfee49..43dfaedc 100644
--- a/corelib/tsprintf.c
+++ b/corelib/tsprintf.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   07/10/96
 *
-* $Revision: 6.9 $
+* $Revision: 6.10 $
 *
 * File Description:
 *   	Memory- and MT-safe "sprintf()"
@@ -38,6 +38,9 @@
 * --------------------------------------------------------------------------
 *
 * $Log: tsprintf.c,v $
+* Revision 6.10  2003/12/12 23:28:25  dondosha
+* Correction for Opteron, at suggestion from Nicolas Joly
+*
 * Revision 6.9  2002/03/11 16:55:43  ivanov
 * Fixed fp_count() -- error with round-up numbers
 *
@@ -97,6 +100,13 @@
 
 #include <tsprintf.h>
 
+#ifndef va_copy
+# ifdef __va_copy
+#  define va_copy __va_copy
+# else
+#  define va_copy(d,s) ((d) = (s))
+# endif
+#endif
 
 /***********************************************************************
  *  INTERNAL
@@ -473,6 +483,7 @@ NLM_EXTERN const Char PNTR Nlm_TSPrintfArgs(const Char PNTR fmt, va_list args)
   CharPtr temp_buf;
   size_t  cut_fmt;
   char   *x_fmt;
+  va_list save;
 
 #ifdef OS_UNIX_PPCLINUX
 /*
@@ -483,7 +494,9 @@ NLM_EXTERN const Char PNTR Nlm_TSPrintfArgs(const Char PNTR fmt, va_list args)
   parsed_size = 2048;
   cut_fmt = 0;
 #else
-  parsed_size = vsprintf_count_args(fmt, args, &cut_fmt);
+  va_copy(save, args);
+  parsed_size = vsprintf_count_args(fmt, save, &cut_fmt);
+  va_end(save);
   if (parsed_size == 0)
     return NULL;
 #endif
diff --git a/ctools/asn_connection.c b/ctools/asn_connection.c
index b2b97d5b..9b5e0656 100644
--- a/ctools/asn_connection.c
+++ b/ctools/asn_connection.c
@@ -1,4 +1,4 @@
-/*  $Id: asn_connection.c,v 1.4 2002/08/07 16:38:18 lavr Exp $
+/*  $Id: asn_connection.c,v 1.5 2003/11/13 16:01:31 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -33,9 +33,6 @@
 #include <connect/ncbi_service_connector.h>
 #include <ctools/asn_connection.h>
 #include "../connect/ncbi_priv.h"
-#include <assert.h>
-#include <stdio.h>
-#include <stdlib.h>
 
 
 #ifdef __cplusplus
@@ -174,6 +171,9 @@ CONN CreateAsnConn_Service(const char*     service,
 /*
  * --------------------------------------------------------------------------
  * $Log: asn_connection.c,v $
+ * Revision 1.5  2003/11/13 16:01:31  lavr
+ * Included headers revised
+ *
  * Revision 1.4  2002/08/07 16:38:18  lavr
  * EIO_ReadMethod enums changed accordingly; log moved to end
  *
diff --git a/ctools/asn_connection.h b/ctools/asn_connection.h
index f3737dfc..bfeccaa7 100644
--- a/ctools/asn_connection.h
+++ b/ctools/asn_connection.h
@@ -1,7 +1,7 @@
-#ifndef NCBI_ASN_CONNECTION__H
-#define NCBI_ASN_CONNECTION__H
+#ifndef CTOOLS___ASN_CONNECTION__H
+#define CTOOLS___ASN_CONNECTION__H
 
-/*  $Id: asn_connection.h,v 1.7 2003/04/11 17:46:29 siyan Exp $
+/*  $Id: asn_connection.h,v 1.8 2003/11/13 15:58:47 lavr Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -123,6 +123,9 @@ CONN CreateAsnConn_Service
 /*
  * ===========================================================================
  * $Log: asn_connection.h,v $
+ * Revision 1.8  2003/11/13 15:58:47  lavr
+ * Guard macro changed
+ *
  * Revision 1.7  2003/04/11 17:46:29  siyan
  * Added doxygen support
  *
@@ -147,4 +150,4 @@ CONN CreateAsnConn_Service
  * ==========================================================================
  */
 
-#endif /* NCBI_ASN_CONNECTION__H */
+#endif /* CTOOLS___ASN_CONNECTION__H */
diff --git a/data/lineages.txt b/data/lineages.txt
index d126aba2..0b33e23c 100644
--- a/data/lineages.txt
+++ b/data/lineages.txt
@@ -1,107 +1,78 @@
-12
-9	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Buchnera
+13
+9	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Buchnera
 34	Bacteria; Proteobacteria; Deltaproteobacteria; Myxococcales; Cystobacterineae; Myxococcaceae; Myxococcus
 139	Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae; Borrelia; Borrelia burgdorferi group
 160	Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae; Treponema
 173	Bacteria; Spirochaetes; Spirochaetales; Leptospiraceae; Leptospira
 188	Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales; Rhodospirillaceae; Magnetospirillum
-192	Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales; Rhodospirillaceae; Azospirillum
 197	Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae; Campylobacter
 210	Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae; Helicobacter
-266	Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Paracoccus
-271	Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus
+263	Bacteria; Proteobacteria; Gammaproteobacteria; Thiotrichales; Francisellaceae; Francisella
 274	Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus
-285	Bacteria; Proteobacteria; Betaproteobacteria; Comamonadaceae; Comamonas
-287	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadaceae; Pseudomonas
-292	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiaceae; Burkholderia; Burkholderia cepacia complex
-294	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadaceae; Pseudomonas
-303	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadaceae; Pseudomonas
-305	Bacteria; Proteobacteria; Betaproteobacteria; Ralstoniaceae; Ralstonia
-316	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadaceae; Pseudomonas
-317	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadaceae; Pseudomonas
-339	Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadaceae; Xanthomonas
-354	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadaceae; Azotobacter
-358	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium
-359	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium
+287	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+292	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; Burkholderia cepacia complex
+294	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+303	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+305	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Ralstonia
+316	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+317	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+339	Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas
+354	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Azotobacter
+358	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium
 375	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae; Bradyrhizobium
-381	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Phyllobacteriaceae; Mesorhizobium
-382	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Sinorhizobium
-384	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium
-394	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium
-408	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Methylobacteriaceae; Methylobacterium
+382	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium
+384	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium
+394	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium
 446	Bacteria; Proteobacteria; Gammaproteobacteria; Legionellales; Legionellaceae; Legionella
-471	Bacteria; Proteobacteria; Gammaproteobacteria; Moraxellaceae; Acinetobacter
-480	Bacteria; Proteobacteria; Gammaproteobacteria; Moraxellaceae; Moraxella
+480	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Moraxellaceae; Moraxella
 485	Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria
 487	Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria
-510	Bacteria; Proteobacteria; Betaproteobacteria; Ralstoniaceae; Ralstonia
-518	Bacteria; Proteobacteria; Betaproteobacteria; Alcaligenaceae; Bordetella
-520	Bacteria; Proteobacteria; Betaproteobacteria; Alcaligenaceae; Bordetella
-542	Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Zymomonas
-546	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Citrobacter
-548	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Enterobacter
-549	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Pantoea
-550	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Enterobacter
-552	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Erwinia
-554	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Pectobacterium
-556	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Pectobacterium
-562	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Escherichia
-571	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Klebsiella
-573	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Klebsiella
-584	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Proteus
-585	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Proteus
-592	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Salmonella
-601	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Salmonella
-602	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Salmonella
-615	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Serratia
-621	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Shigella
-622	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Shigella
-623	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Shigella
-624	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Shigella
-630	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Yersinia
-632	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Yersinia
-633	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Yersinia
-644	Bacteria; Proteobacteria; Gammaproteobacteria; Aeromonadaceae; Aeromonas
-666	Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionaceae; Vibrio
-669	Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionaceae; Vibrio
-670	Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionaceae; Vibrio
-672	Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionaceae; Vibrio
-714	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellaceae; Actinobacillus
-715	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellaceae; Actinobacillus
-727	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellaceae; Haemophilus
-747	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellaceae; Pasteurella
+518	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Alcaligenaceae; Bordetella
+520	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Alcaligenaceae; Bordetella
+529	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Brucellaceae; Ochrobactrum
+549	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Pantoea
+550	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Enterobacter
+552	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Erwinia
+554	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Pectobacterium
+562	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia
+571	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Klebsiella
+573	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Klebsiella
+602	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella
+615	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Serratia
+623	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Shigella
+630	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Yersinia
+632	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Yersinia
+644	Bacteria; Proteobacteria; Gammaproteobacteria; Aeromonadales; Aeromonadaceae; Aeromonas
+666	Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio
+670	Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio
+672	Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio
+714	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Actinobacillus
+715	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Actinobacillus
+727	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Haemophilus
+731	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Histophilus
+747	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Pasteurella
 770	Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Anaplasma
-777	Bacteria; Proteobacteria; Gammaproteobacteria; Legionellales; Coxiellaceae; Coxiella
-781	Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Rickettsieae; Rickettsia; spotted fever group
 782	Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Rickettsieae; Rickettsia; typhus group
 813	Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; Chlamydia
 817	Bacteria; Bacteroidetes; Bacteroides (class); Bacteroidales; Bacteroidaceae; Bacteroides
 837	Bacteria; Bacteroidetes; Bacteroides (class); Bacteroidales; Porphyromonadaceae; Porphyromonas
-851	Bacteria; Fusobacteria; Fusobacteria (class); Fusobacterales; Fusobacteriaceae; Fusobacterium
-870	Bacteria; Proteobacteria; Gammaproteobacteria; Cardiobacteriaceae; Dichelobacter
-881	Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Desulfovibrio
-915	Bacteria; Proteobacteria; Betaproteobacteria; Nitrosomonadales; Nitrosomonadaceae; Nitrosomonas
-920	Bacteria; Proteobacteria; Gammaproteobacteria; Acidithiobacillus
+851	Bacteria; Fusobacteria; Fusobacterales; Fusobacteriaceae; Fusobacterium
+876	Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Desulfovibrio
+920	Bacteria; Proteobacteria; Gammaproteobacteria; Acidithiobacillales; Acidithiobacillaceae; Acidithiobacillus
 948	Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Anaplasma; phagocytophilum group
-1061	Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Rhodobacter
 1063	Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Rhodobacter
 1085	Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales; Rhodospirillaceae; Rhodospirillum
 1097	Bacteria; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chlorobium
 1108	Bacteria; Chloroflexi; Chloroflexales; Chloroflexaceae; Chloroflexus
 1126	Bacteria; Cyanobacteria; Chroococcales; Microcystis
-1140	Bacteria; Cyanobacteria; Chroococcales; Synechococcus
-1148	Bacteria; Cyanobacteria; Chroococcales; Synechocystis
-1172	Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Anabaena
 1206	Bacteria; Cyanobacteria; Oscillatoriales; Trichodesmium
-1219	Bacteria; Cyanobacteria; Prochlorophytes; Prochlorococcaceae; Prochlorococcus
 1245	Bacteria; Firmicutes; Lactobacillales; Leuconostoc
 1247	Bacteria; Firmicutes; Lactobacillales; Oenococcus
+1265	Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Ruminococcus
 1280	Bacteria; Firmicutes; Bacillales; Staphylococcus
 1282	Bacteria; Firmicutes; Bacillales; Staphylococcus
 1299	Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae; Deinococcus
-1302	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1303	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
-1304	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1307	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1308	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1309	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
@@ -109,153 +80,152 @@
 1313	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1314	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1334	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1336	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1351	Bacteria; Firmicutes; Lactobacillales; Enterococcaceae; Enterococcus
 1352	Bacteria; Firmicutes; Lactobacillales; Enterococcaceae; Enterococcus
 1358	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Lactococcus
-1390	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
 1392	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group
-1393	Bacteria; Firmicutes; Bacillales; Paenibacillaceae; Brevibacillus
 1396	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group
-1397	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
 1402	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
-1404	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
-1421	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
-1422	Bacteria; Firmicutes; Bacillales; Geobacillus
+1422	Bacteria; Firmicutes; Bacillales; Bacillaceae; Geobacillus
 1423	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
 1428	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group
 1488	Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
-1491	Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
 1496	Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
-1501	Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
 1502	Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
 1515	Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
-1582	Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
+1575	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Micrococcineae; Microbacteriaceae; Leifsonia
+1580	Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
 1584	Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
-1587	Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
 1590	Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
-1599	Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
 1639	Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria
 1642	Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria
 1718	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae; Corynebacterium
+1719	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae; Corynebacterium
 1764	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium; Mycobacterium avium complex (MAC)
 1765	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium; Mycobacterium tuberculosis complex
 1769	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium
 1772	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium
 1773	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium; Mycobacterium tuberculosis complex
 1833	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Nocardiaceae; Rhodococcus
-1836	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Pseudonocardineae; Pseudonocardiaceae; Saccharopolyspora
-1895	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces
-1901	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces
 1902	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces
-1911	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces
 1916	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces
-2095	Bacteria; Firmicutes; Mollicutes; Entomoplasmatales; Entomoplasmataceae
-2096	Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
+2095	Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
 2097	Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
 2098	Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
-2104	Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
-2107	Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
 2130	Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Ureaplasma
-2190	Archaea; Euryarchaeota; Methanococci; Methanococcales; Methanocaldococcaceae; Methanocaldococcus
-2208	Archaea; Euryarchaeota; Methanococci; Methanosarcinales; Methanosarcinaceae; Methanosarcina
-2209	Archaea; Euryarchaeota; Methanococci; Methanosarcinales; Methanosarcinaceae; Methanosarcina
-2214	Archaea; Euryarchaeota; Methanococci; Methanosarcinales; Methanosarcinaceae; Methanosarcina
+2208	Archaea; Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae; Methanosarcina
+2209	Archaea; Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae; Methanosarcina
+2214	Archaea; Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae; Methanosarcina
 2234	Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae; Archaeoglobus
 2238	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula
-2242	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobacterium
-2246	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloferax
+2247	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halorubrum
 2261	Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; Pyrococcus
-2285	Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae; Sulfolobus
 2287	Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae; Sulfolobus
-2303	Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales; Thermoplasmataceae; Thermoplasma
-2320	Archaea; Euryarchaeota; Methanopyri; Methanopyrales; Methanopyraceae; Methanopyrus
 2336	Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga
-2371	Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadaceae; Xylella
-2711	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Sapindales; Rutaceae; Citrus
-2762	Eukaryota; Glaucocystophyceae; Cyanophoraceae; Cyanophora
-2771	Eukaryota; Rhodophyta; Bangiophyceae; Porphyridiales; Porphyridiaceae; Cyanidium
+2371	Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xylella
+2711	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Citrus
 2777	Eukaryota; Rhodophyta; Florideophyceae; Gracilariales; Gracilariaceae; Gracilaria
-2787	Eukaryota; Rhodophyta; Bangiophyceae; Bangiales; Bangiaceae; Porphyra
 2788	Eukaryota; Rhodophyta; Bangiophyceae; Bangiales; Bangiaceae; Porphyra
-2839	Eukaryota; stramenopiles; Bacillariophyta; Coscinodiscophyceae; Biddulphiophycidae; Eupodiscales; Eupodiscaceae; Odontella
 2850	Eukaryota; stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Naviculales; Phaeodactylaceae; Phaeodactylum
+2903	Eukaryota; Haptophyceae; Isochrysidales; Emiliania
+2926	Eukaryota; Alveolata; Dinophyceae; Gonyaulacales; Gonyaulacaceae; Alexandrium
+2961	Eukaryota; Alveolata; Dinophyceae; Gymnodiniales; Gymnodiniaceae; Amphidinium
+2972	Eukaryota; Alveolata; Dinophyceae; Pyrocystales; Pyrocystis
 3012	Eukaryota; stramenopiles; Phaeophyceae; Fucales; Fucaceae; Fucus
-3039	Eukaryota; Euglenozoa; Euglenida; Euglenales; Euglena
 3046	Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Volvocales; Dunaliellaceae; Dunaliella
 3055	Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Volvocales; Chlamydomonadaceae; Chlamydomonas
-3067	Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Volvocales; Volvocaceae; Volvox
-3077	Eukaryota; Viridiplantae; Chlorophyta; Trebouxiophyceae; Chlorellales; Chlorellaceae; Chlorella
 3190	Eukaryota; Viridiplantae; Chlorophyta; Prasinophyceae; Chlorodendrales; Chlorodendraceae; Scherffelia
 3197	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Marchantiophyta; Marchantiopsida; Marchantiidae; Marchantiales; Marchantiineae; Marchantiaceae; Marchantia
 3218	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella
 3225	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta; Bryopsida; Dicranidae; Dicranales; Ditrichaceae; Ceratodon
-3240	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Psilotophyta; Psilotales; Psilotaceae; Psilotum
+3311	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Ginkgophyta; Ginkgoales; Ginkgoaceae; Ginkgo
 3329	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Picea
-3349	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
-3350	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
+3347	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
 3352	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
 3357	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pseudotsuga
 3369	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Cupressaceae; Cryptomeria
-3505	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fagales; Betulaceae; Betula
-3544	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllidae; Caryophyllales; Aizoaceae; Mesembryanthemum
-3562	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllidae; Caryophyllales; Chenopodiaceae; Spinacia
-3570	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllidae; Caryophyllales; Caryophyllaceae; Dianthus
-3635	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
-3654	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Cucurbitales; Cucurbitaceae; Citrullus
-3656	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
-3659	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
-3702	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Arabidopsis
-3707	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Brassica
-3708	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Brassica
-3711	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Brassica
-3712	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Brassica
-3726	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Raphanus
-3747	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Rosales; Rosaceae; Rosoideae; Fragaria
-3750	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Rosales; Rosaceae; Maloideae; Malus
-3755	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
-3760	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
-3827	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Cicereae; Cicer
-3847	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
-3873	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Genisteae; Lupinus
-3879	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago
-3880	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago
-3885	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
-3888	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Vicieae; Pisum
-3906	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Vicieae; Vicia
-3917	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
-3981	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Malpighiales; Euphorbiaceae; Hevea
-3983	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Malpighiales; Euphorbiaceae; Manihot
-3988	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Malpighiales; Euphorbiaceae; Ricinus
-3993	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Malpighiales; Euphorbiaceae; Euphorbia
-4039	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; campanulids; Apiales; Apiaceae; Daucus
-4043	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; campanulids; Apiales; Apiaceae; Petroselinum
-4058	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Gentianales; Apocynaceae; Rauvolfioideae; Vinceae; Catharanthus
-4072	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Solanaceae; Capsicum
-4081	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
-4092	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Solanaceae; Nicotiana
-4096	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Solanaceae; Nicotiana
-4097	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Solanaceae; Nicotiana
-4102	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Solanaceae; Petunia
-4113	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Solanaceae; Solanum
-4120	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Convolvulaceae; Ipomoea
-4151	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Lamiales; Antirrhinaceae; Antirrhineae; Antirrhinum
-4232	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
-4236	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; campanulids; Asterales; Asteraceae; Lactuceae; Lactuca
+3382	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Gnetophyta; Gnetopsida; Gnetales; Gnetaceae; Gnetum
+3467	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Ranunculales; Papaveraceae; Eschscholzioideae; Eschscholzia
+3505	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fagales; Betulaceae; Betula
+3544	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Aizoaceae; Mesembryanthemum
+3562	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Amaranthaceae; Spinacia
+3570	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Caryophyllaceae; Dianthus
+3605	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
+3634	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+3635	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+3641	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Byttnerioideae; Theobroma
+3649	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Caricaceae; Carica
+3654	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Citrullus
+3656	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
+3659	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
+3693	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+3695	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+3702	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
+3707	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+3708	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+3711	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+3712	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+3726	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Raphanus
+3747	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Fragaria
+3750	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus
+3755	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
+3760	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
+3818	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Aeschynomeneae; Arachis
+3827	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Cicereae; Cicer
+3847	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
+3870	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Genisteae; Lupinus
+3873	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Genisteae; Lupinus
+3879	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago
+3880	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago
+3885	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
+3886	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
+3888	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Vicieae; Pisum
+3895	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Robinieae; Sesbania
+3899	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
+3906	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Vicieae; Vicia
+3917	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
+3981	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Crotonoideae; Micrandreae; Hevea
+3983	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Crotonoideae; Manihoteae; Manihot
+3988	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
+3993	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Euphorbioideae; Euphorbieae; Euphorbia
+4006	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Linaceae; Linum
+4039	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Apiales; Apiaceae; Apioideae; Scandiceae; Daucinae; Daucus
+4045	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Apiales; Apiaceae; Apioideae; apioid superclade; Apium clade; Apium
+4054	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Apiales; Araliaceae; Panax
+4072	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Capsicum
+4081	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
+4096	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Nicotiana
+4097	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Nicotiana
+4100	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Nicotiana
+4102	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Petunia
+4113	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Solanum
+4120	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Convolvulaceae; Ipomoea
+4146	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Oleaceae; Olea
+4151	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Antirrhinaceae; Antirrhineae; Antirrhinum
+4182	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Pedaliaceae; Sesamum
+4232	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
+4236	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactuca
 4498	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Aveneae; Avena
 4513	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Hordeum
 4530	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Ehrhartoideae; Oryzeae; Oryza
+4543	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Paniceae; Pennisetum
+4547	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Saccharum
 4550	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Secale
-4558	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACC clade; Panicoideae; Andropogoneae; Sorghum
-4560	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACC clade; Panicoideae; Andropogoneae; Sorghum
+4558	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
+4560	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
 4565	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Triticum
 4568	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Triticum
 4571	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Triticum
 4573	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Aegilops
-4577	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACC clade; Panicoideae; Andropogoneae; Zea
+4577	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Zea
 4641	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Zingiberales; Musaceae; Musa
 4679	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Alliaceae; Allium
+4682	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Alliaceae; Allium
+4686	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Asparagaceae; Asparagus
 4754	Eukaryota; Fungi; Ascomycota; Pneumocystidomycetes; Pneumocystidaceae; Pneumocystis
 4787	Eukaryota; stramenopiles; Oomycetes; Pythiales; Pythiaceae; Phytophthora
+4790	Eukaryota; stramenopiles; Oomycetes; Pythiales; Pythiaceae; Phytophthora
 4876	Eukaryota; Fungi; Glomeromycota; Glomeromycetes; Glomerales; Glomeraceae; Glomus
 4896	Eukaryota; Fungi; Ascomycota; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces
 4905	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Pichia
@@ -272,9 +242,10 @@
 5059	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
 5061	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
 5062	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+5068	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
 5085	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
-5141	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariales; Sordariaceae; Neurospora
-5145	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariales; Lasiosphaeriaceae; Podospora
+5116	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Diaporthales; Valsaceae; Cryphonectria-Endothia complex; Cryphonectria
+5141	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Sordariaceae; Neurospora
 5180	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Sclerotinia
 5207	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Heterobasidiomycetes; Tremellomycetidae; Tremellales; Tremellaceae; Filobasidiella
 5270	Eukaryota; Fungi; Basidiomycota; Ustilaginomycetes; Ustilaginomycetidae; Ustilaginales; Ustilaginaceae; Ustilago
@@ -283,6 +254,7 @@
 5322	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Pleurotaceae; Pleurotus
 5334	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Schizophyllaceae; Schizophyllum
 5341	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Agaricaceae; Agaricus
+5346	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Psathyrellaceae; Coprinopsis
 5457	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Phyllachorales; Phyllachoraceae; Glomerella
 5466	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Phyllachorales; Phyllachoraceae; mitosporic Phyllachoraceae; Colletotrichum
 5476	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
@@ -290,24 +262,20 @@
 5482	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
 5499	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes et Chaetothyriomycetes incertae sedis; Mycosphaerellaceae; mitosporic Mycosphaerellaceae; Cladosporium
 5501	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; mitosporic Onygenales; Coccidioides
-5507	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreales; mitosporic Hypocreales; Fusarium; Fusarium oxysporum complex
-5514	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreales; mitosporic Hypocreales; Fusarium
-5518	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreales; Nectriaceae; Gibberella
-5530	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreales; Clavicipitaceae; mitosporic Clavicipitaceae; Metarhizium
-5544	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreales; mitosporic Hypocreales; Trichoderma
-5656	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Crithidia
+5507	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium; Fusarium oxysporum complex
+5514	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium
+5518	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella
+5530	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Clavicipitaceae; mitosporic Clavicipitaceae; Metarhizium
+5544	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
+5660	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania; Leishmania braziliensis species complex
 5661	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
 5664	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
-5665	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
 5671	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
-5689	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania; lizard Leishmania
 5691	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma
 5693	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma; Schizotrypanum
 5722	Eukaryota; Parabasalidea; Trichomonadida; Trichomonadidae; Trichomonadinae; Trichomonas
 5741	Eukaryota; Diplomonadida; Hexamitidae; Giardiinae; Giardia
-5755	Eukaryota; Acanthamoebidae; Acanthamoeba
 5759	Eukaryota; Entamoebidae; Entamoeba
-5791	Eukaryota; Mycetozoa; Myxogastria; Myxogastromycetidae; Physarida; Physarum
 5802	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Eimeriidae; Eimeria
 5807	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Cryptosporidiidae; Cryptosporidium
 5811	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Toxoplasma
@@ -316,13 +284,14 @@
 5833	Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
 5855	Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
 5861	Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
-5874	Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae; Theileria
+5875	Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae; Theileria
 5888	Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Peniculida; Paramecium
-5908	Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Hymenostomatida; Tetrahymenina; Tetrahymena
 5911	Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Hymenostomatida; Tetrahymenina; Tetrahymena
 5932	Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Hymenostomatida; Ophryoglenina; Ichthyophthirius
-6035	Eukaryota; Fungi; Microsporidia; Unikaryonidae; Encephalitozoon
-6087	Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Anthomedusae; Hydridae; Hydra
+5936	Eukaryota; Alveolata; Ciliophora; Spirotrichea; Hypotrichia; Euplotida; Euplotidae; Moneuplotes
+6085	Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Anthomedusae; Hydridae; Hydra
+6100	Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Leptomedusae; Aequoreidae; Aequorea
+6161	Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Seriata; Tricladida; Paludicola; Dugesiidae; Dugesia
 6182	Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Strigeidida; Schistosomatoidea; Schistosomatidae; Schistosoma
 6183	Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Strigeidida; Schistosomatoidea; Schistosomatidae; Schistosoma
 6204	Eukaryota; Metazoa; Platyhelminthes; Cestoda; Eucestoda; Cyclophyllidea; Taeniidae; Taenia
@@ -331,58 +300,64 @@
 6238	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
 6239	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
 6248	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Panagrolaimoidea; Strongyloididae; Strongyloides
+6252	Eukaryota; Metazoa; Nematoda; Chromadorea; Ascaridida; Ascaridoidea; Ascarididae; Ascaris
 6253	Eukaryota; Metazoa; Nematoda; Chromadorea; Ascaridida; Ascaridoidea; Ascarididae; Ascaris
 6265	Eukaryota; Metazoa; Nematoda; Chromadorea; Ascaridida; Ascaridoidea; Toxocaridae; Toxocara
 6279	Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Brugia
 6282	Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Onchocerca
 6287	Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Dirofilaria
 6289	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Haemonchidae; Haemonchinae; Haemonchus
+6293	Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Wuchereria
 6303	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
 6304	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
 6305	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
 6306	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
 6317	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Haemonchidae; Ostertagiinae; Ostertagia
 6334	Eukaryota; Metazoa; Nematoda; Enoplea; Trichocephalida; Trichinellidae; Trichinella
-6421	Eukaryota; Metazoa; Annelida; Clitellata; Hirudinida; Hirudinea; Arynchobdellida; Hirudiniformes; Hirudinidae; Hirudo
 6500	Eukaryota; Metazoa; Mollusca; Gastropoda; Orthogastropoda; Apogastropoda; Heterobranchia; Euthyneura; Opisthobranchia; Anaspidea; Aplysioidea; Aplysiidae; Aplysia
-6523	Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Basommatophora; Lymnaeoidea; Lymnaeidae; Lymnaea
 6526	Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Basommatophora; Lymnaeoidea; Planorbidae; Biomphalaria
 6550	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Mytiloida; Mytiloidea; Mytilidae; Mytilus
+6551	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Mytiloida; Mytiloidea; Mytilidae; Mytilus
 6565	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Ostreoida; Ostreoidea; Ostreidae; Crassostrea
 6661	Eukaryota; Metazoa; Arthropoda; Crustacea; Branchiopoda; Anostraca; Artemiidae; Artemia
 6687	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Penaeus
 6689	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Litopenaeus
-6832	Eukaryota; Metazoa; Arthropoda; Crustacea; Maxillopoda; Copepoda; Harpacticoida; Harpactidae; Tigriopus
+6720	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Pleocyemata; Astacidea; Astacoidea; Astacidae; Pacifastacus
 6941	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodidae; Boophilus
 6943	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodidae; Amblyomma
 6945	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodidae; Ixodes
-7004	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Orthoptera; Caelifera; Acridomorpha; Acridoidea; Acrididae; Oedipodinae; Locusta
+7029	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Macrosiphini; Acyrthosiphon
 7038	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aleyrodiformes; Aleyrodoidea; Aleyrodidae; Aleyrodinae; Bemisia
-7051	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Cantharoidea; Lampyridae; Luciola
 7070	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Tenebrionidae; Tribolium
 7091	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Bombycidae; Bombyx
 7092	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Bombycidae; Bombyx
+7111	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Plusiinae; Trichoplusia
 7121	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Saturniidae; Saturniinae; Saturniini; Antheraea
 7130	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Sphingiodea; Sphingidae; Sphinginae; Manduca
-7154	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Chironomoidea; Chironomidae; Chironominae; Chironomus
-7159	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Aedes
+7159	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Aedes; Stegomyia
 7165	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Anopheles
 7173	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Anopheles
-7200	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Psychodoidea; Psychodidae; Lutzomyia
+7175	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culex; Culex
+7200	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Psychodoidea; Psychodidae; Lutzomyia; Lutzomyia
 7213	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Tephritoidea; Tephritidae; Ceratitis
 7217	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7226	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7227	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7229	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7234	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7237	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7240	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7241	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
-7243	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7244	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7245	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7264	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7368	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Muscoidea; Muscidae; Haematobia
 7370	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Muscoidea; Muscidae; Musca
+7394	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Hippoboscoidea; Glossinidae; Glossina
 7460	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Apis
 7515	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Siphonaptera; Pulicidae; Pulicinae; Ctenocephalides
+7634	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Echinometridae; Heliocidaris
+7650	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Strongylocentrotidae; Hemicentrotus
 7668	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Strongylocentrotidae; Strongylocentrotus
 7719	Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona; Phlebobranchia; Cionidae; Ciona
 7723	Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Stolidobranchia; Styelidae; Polyandrocarpa
@@ -390,55 +365,63 @@
 7739	Eukaryota; Metazoa; Chordata; Cephalochordata; Branchiostomidae; Branchiostoma
 7741	Eukaryota; Metazoa; Chordata; Cephalochordata; Branchiostomidae; Branchiostoma
 7757	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Hyperoartia; Petromyzontiformes; Petromyzontidae; Petromyzon
-7782	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Squalea; Hypnosqualea; Pristiorajea; Batoidea; Rajiformes; Rajidae; Raja
-7792	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Galeomorphii; Heterodontoidea; Heterodontiformes; Heterodontidae; Heterodontus
 7801	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Galeomorphii; Galeoidea; Orectolobiformes; Ginglymostomatidae; Ginglymostoma
-7902	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Chondrostei; Acipenseriformes; Acipenseridae; Acipenser
-7936	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Anguilliformes; Anguillidae; Anguilla
 7937	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Anguilliformes; Anguillidae; Anguilla
 7955	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio
 7957	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Carassius
+7959	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Ctenopharyngodon
 7962	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Cyprinus
 7998	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Siluriformes; Ictaluridae; Ictalurus
 8018	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
-8019	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
 8022	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
+8023	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
 8030	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmo
 8032	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmo
+8036	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salvelinus
 8049	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Paracanthopterygii; Gadiformes; Gadidae; Gadus
 8078	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Cyprinodontiformes; Fundulidae; Fundulus
+8081	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Cyprinodontiformes; Poeciliidae; Poecilia
 8090	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Beloniformes; Adrianichthyidae; Oryziinae; Oryzias
 8128	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei; Cichlidae; Oreochromis
-8161	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Carangidae; Seriola
+8150	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei; Cichlidae; Tropheus
+8161	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Carangoidei; Carangidae; Seriola
+8175	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Sparidae; Sparus
 8222	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Gobioidei; Gobiidae; Gillichthys
 8245	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Scombroidei; Xiphiidae; Xiphias
 8255	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Paralichthyidae; Paralichthys
 8260	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Platichthys
+8262	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Pleuronectes
 8265	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Pseudopleuronectes
+8267	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Hippoglossus
 8296	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Caudata; Salamandroidea; Ambystomatidae; Ambystoma
 8355	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Mesobatrachia; Pipoidea; Pipidae; Xenopodinae; Xenopus
 8364	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Mesobatrachia; Pipoidea; Pipidae; Xenopodinae; Silurana
 8400	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Neobatrachia; Ranoidea; Ranidae; Rana; Aquarana
-8496	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Crocodylidae; Alligatorinae; Alligator
-8616	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; Colubroidea; Elapidae; Bungarinae; Bungarus
 8723	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; Colubroidea; Viperidae; Crotalinae; Bothrops
 8801	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Palaeognathae; Struthioniformes; Struthionidae; Struthio
 8839	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Anseriformes; Anatidae; Anas
 8932	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
 9031	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Gallus
 9091	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Coturnix
-9103	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Meleagrididae; Meleagris
+9103	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Meleagris
+9157	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Paridae; Parus
 9238	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Sphenisciformes; Spheniscidae; Pygoscelis
 9258	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Monotremata; Ornithorhynchidae; Ornithorhynchus
+9315	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Diprotodontia; Macropodidae; Macropus
+9337	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Diprotodontia; Phalangeridae; Trichosurus
+9361	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Edentata; Dasypodidae; Dasypus
+9438	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Chiroptera; Microchiroptera; Molossidae; Tadarida
+9447	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Strepsirhini; Lemuridae; Lemur
 9483	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Callitrichidae; Callithrix
 9490	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Callitrichidae; Saguinus
+9509	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Atelinae; Ateles
 9521	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Cebinae; Saimiri
 9534	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Cercopithecus
 9541	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
+9542	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
 9544	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
 9545	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
 9555	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Papio
-9556	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Papio
 9557	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Papio
 9580	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hylobatidae; Hylobates
 9593	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Gorilla
@@ -450,13 +433,15 @@
 9644	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Fissipedia; Ursidae; Ursus
 9660	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Fissipedia; Mustelidae; Mustelinae; Martes
 9685	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Fissipedia; Felidae; Felis
-9755	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Cetacea; Odontoceti; Physeteridae; Physeter
+9720	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Pinnipedia; Phocidae; Phoca
+9783	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Proboscidea; Elephantidae; Elephas
 9785	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Proboscidea; Elephantidae; Loxodonta
 9796	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Perissodactyla; Equidae; Equus
 9823	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Suina; Suidae; Sus
 9838	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Tylopoda; Camelidae; Camelus
 9844	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Tylopoda; Camelidae; Lama
 9860	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Cervoidea; Cervidae; Cervinae; Cervus
+9870	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Cervoidea; Cervidae; Odocoileinae; Rangifer
 9897	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Aepycerotinae; Aepyceros
 9913	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Bos
 9915	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Bos
@@ -467,66 +452,31 @@
 9995	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Sciuridae; Sciurinae; Marmota
 10029	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Cricetinae; Cricetulus
 10036	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Cricetinae; Mesocricetus
+10041	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Sigmodontinae; Peromyscus
 10042	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Sigmodontinae; Peromyscus
+10047	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Gerbillinae; Meriones
 10090	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus
 10096	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus
 10116	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus
+10117	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus
+10129	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Apodemus
 10141	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Hystricognathi; Caviidae; Cavia
-10243	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Orthopoxvirus
-10244	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Orthopoxvirus
 10245	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Orthopoxvirus
-10255	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Orthopoxvirus
-10261	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Avipoxvirus
-10271	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Leporipoxvirus
-10273	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Leporipoxvirus
-10276	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Suipoxvirus
-10279	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Molluscipoxvirus
 10298	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Simplexvirus
-10310	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Simplexvirus
-10320	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Varicellovirus
-10326	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Varicellovirus
-10331	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Varicellovirus
 10335	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Varicellovirus
 10345	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Varicellovirus
 10359	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae; Cytomegalovirus
-10366	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae; Muromegalovirus
-10368	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae; Roseolovirus
-10372	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae
 10376	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Gammaherpesvirinae; Lymphocryptovirus
-10381	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Gammaherpesvirinae; Rhadinovirus
-10385	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Gammaherpesvirinae
-10386	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Infectious laryngotracheitis-like viruses
-10390	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Marek's disease-like viruses
-10397	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae
-10401	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Ictalurid Herpes-like viruses
 10407	Viruses; Retroid viruses; Hepadnaviridae; Orthohepadnavirus
-10449	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
-10450	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
-10454	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
-10458	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
-10468	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
 10497	Viruses; dsDNA viruses, no RNA stage; Asfarviridae; Asfivirus
-10506	Viruses; dsDNA viruses, no RNA stage; Phycodnaviridae; Chlorovirus
 10566	Viruses; dsDNA viruses, no RNA stage; Papillomaviridae; Papillomavirus
 10581	Viruses; dsDNA viruses, no RNA stage; Papillomaviridae; Papillomavirus
 10632	Viruses; dsDNA viruses, no RNA stage; Polyomaviridae; Polyomavirus
 10633	Viruses; dsDNA viruses, no RNA stage; Polyomaviridae; Polyomavirus
-10665	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae; T4-like viruses
-10677	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae; Mu-like viruses
-10710	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Siphoviridae; Lambda-like viruses
-10724	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Siphoviridae; Lambda-like viruses
-10754	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae; P22-like viruses
-10756	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae; phi-29-like viruses
-10759	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae; T7-like viruses
 10760	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae; T7-like viruses
 10798	Viruses; ssDNA viruses; Parvoviridae; Parvovirinae; Erythrovirus
-10821	Viruses; ssDNA viruses; Geminiviridae; Mastrevirus
-10870	Viruses; ssDNA viruses; Inoviridae; Inovirus
-10927	Viruses; dsRNA viruses; Reoviridae; Rotavirus; unclassified rotaviruses
 10995	Viruses; dsRNA viruses; Birnaviridae; Avibirnavirus
-11021	Viruses; ssRNA positive-strand viruses, no DNA stage; Togaviridae; Alphavirus; EEEV complex
 11034	Viruses; ssRNA positive-strand viruses, no DNA stage; Togaviridae; Alphavirus; WEEV complex
-11036	Viruses; ssRNA positive-strand viruses, no DNA stage; Togaviridae; Alphavirus; VEEV complex
 11041	Viruses; ssRNA positive-strand viruses, no DNA stage; Togaviridae; Rubivirus
 11047	Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Arteriviridae; Arterivirus
 11072	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus; Japanese encephalitis virus group
@@ -534,9 +484,6 @@
 11099	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Pestivirus
 11103	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Hepacivirus
 11120	Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Coronaviridae; Coronavirus
-11128	Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Coronaviridae; Coronavirus; Group 2 species
-11138	Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Coronaviridae; Coronavirus; Group 2 species
-11149	Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Coronaviridae; Coronavirus; Group 1 species
 11161	Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Paramyxovirinae; Rubulavirus
 11176	Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Paramyxovirinae; Rubulavirus
 11234	Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Paramyxovirinae; Morbillivirus
@@ -545,18 +492,17 @@
 11264	Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Pneumovirinae; Metapneumovirus
 11276	Viruses; ssRNA negative-strand viruses; Mononegavirales; Rhabdoviridae; Vesiculovirus
 11292	Viruses; ssRNA negative-strand viruses; Mononegavirales; Rhabdoviridae; Lyssavirus
-11599	Viruses; ssRNA negative-strand viruses; Bunyaviridae; Hantavirus
-11604	Viruses; ssRNA negative-strand viruses; Bunyaviridae; Hantavirus
 11660	Viruses; Retroid viruses; Retroviridae; Lentivirus; Ovine/caprine lentivirus
 11665	Viruses; Retroid viruses; Retroviridae; Lentivirus; Equine lentiviruses
 11673	Viruses; Retroid viruses; Retroviridae; Lentivirus; Feline lentiviruses
 11676	Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
 11709	Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
 11723	Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
+11768	Viruses; Retroid viruses; Retroviridae; Gammaretrovirus
 11786	Viruses; Retroid viruses; Retroviridae; Gammaretrovirus
+11827	Viruses; Retroid viruses; Retroviridae
 11886	Viruses; Retroid viruses; Retroviridae; Alpharetrovirus
 11966	Viruses; Retroid viruses; Retroviridae
-11978	Viruses; ssRNA positive-strand viruses, no DNA stage; Caliciviridae; Vesivirus
 11983	Viruses; ssRNA positive-strand viruses, no DNA stage; Caliciviridae; Norovirus
 12092	Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Hepatovirus
 12111	Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Aphthovirus; Foot-and-mouth disease virus
@@ -565,236 +511,323 @@
 12216	Viruses; ssRNA positive-strand viruses, no DNA stage; Potyviridae; Potyvirus
 12230	Viruses; ssRNA positive-strand viruses, no DNA stage; Potyviridae; Potyvirus
 12232	Viruses; ssRNA positive-strand viruses, no DNA stage; Potyviridae; Potyvirus
-12242	Viruses; ssRNA positive-strand viruses, no DNA stage; Tobamovirus
 12305	Viruses; ssRNA positive-strand viruses, no DNA stage; Bromoviridae; Cucumovirus
-12455	Viruses; ssRNA negative-strand viruses; Mononegavirales; Bornaviridae; Bornavirus
 12461	Viruses; ssRNA positive-strand viruses, no DNA stage; Hepatitis E-like viruses
 12475	Viruses; Deltavirus
-12618	Viruses; ssDNA viruses; Circoviridae; Circovirus
 12637	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus; Dengue virus group
-12643	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Orthopoxvirus
-12702	Viruses; ssRNA positive-strand viruses, no DNA stage; Astroviridae; Astrovirus
+12702	Viruses; ssRNA positive-strand viruses, no DNA stage; Astroviridae; Mamastrovirus
 12721	Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
 12814	Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Pneumovirinae; Pneumovirus
-13443	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
+13323	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Scombroidei; Scombridae; Acanthocybium
+13333	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; stem Magnoliophyta; Amborellaceae; Amborella
+13443	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
+13489	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Moronidae; Dicentrarchus
 13515	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Strepsirhini; Lemuridae; Eulemur
-13563	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Schizophyllaceae; Heterobasidion
+13563	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Schizophyllaceae; Heterobasidion; Heterobasidion annosum species complex
 13616	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Didelphimorphia; Didelphidae; Monodelphis
 13773	Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Pyrobaculum
-23211	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Rosales; Rosaceae; Maloideae; Pyrus
+23211	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Pyrus
 27288	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
 27291	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
 27293	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
 27294	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+27337	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Verticillium
 27405	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Marsupenaeus
 27689	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Chondrostei; Acipenseriformes; Acipenseridae; Acipenser
+27828	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Cooperiidae; Cooperia
 27835	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Heligmonellidae; Nippostrongylinae; Nippostrongylus
+27923	Eukaryota; Metazoa; Ctenophora; Cyclocoela; Lobata; Bolinopsidae; Mnemiopsis
 28037	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
-28289	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Granulovirus
-28304	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae; Muromegalovirus
-28321	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Entomopoxvirinae; Entomopoxvirus B
+28232	Bacteria; Proteobacteria; Deltaproteobacteria; Desulfuromonadales; Geobacteraceae; Geobacter
 28344	Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Arteriviridae; Arterivirus
-28369	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Siphoviridae
-28450	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiaceae; Burkholderia; pseudomallei group
-28451	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Klebsiella
-28526	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
+28450	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+28526	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
+28532	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Cleome
 28610	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Tephritoidea; Tephritidae; Rhagoletis
-28873	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Orthopoxvirus
 28875	Viruses; dsRNA viruses; Reoviridae; Rotavirus
-28901	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Salmonella
-28909	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACC clade; Chloridoideae; Cynodonteae; Cynodon
+28901	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella
+28909	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Chloridoideae; Cynodonteae; Cynodon
 28985	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
 29058	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Heliothinae; Helicoverpa
 29158	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Mytiloida; Mytiloidea; Mytilidae; Mytilus
 29159	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Ostreoida; Ostreoidea; Ostreidae; Crassostrea
 29170	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Ancylostomatoidea; Ancylostomatidae; Ancylostomatinae; Ancylostoma
 29176	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Neospora
-29250	Viruses; unclassified viruses
-29292	Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; Pyrococcus
-29449	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium
+29449	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium
 29459	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Brucellaceae; Brucella
-29488	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Photorhabdus
+29471	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Pectobacterium
+29488	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Photorhabdus
+29501	Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
 29518	Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae; Borrelia; Borrelia burgdorferi group
 29519	Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae; Borrelia; Borrelia burgdorferi group
-29729	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
-29760	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Vitaceae; Vitis
+29546	Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Lawsonia
+29729	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+29730	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+29760	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
 29883	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Tricholomataceae; Laccaria
+30286	Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Stolidobranchia; Molgulidae; Molgula
+30301	Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Stolidobranchia; Botryllidae; Botryllus
 31033	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes; Tetradontoidea; Tetraodontidae; Takifugu
-31175	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Diadematacea; Diadematoida; Diadematidae; Diadema
-31178	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Echinometridae; Echinometra
+31199	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Pectinoida; Pectinoidea; Pectinidae; Argopecten
+31216	Eukaryota; Metazoa; Mollusca; Gastropoda; Orthogastropoda; Apogastropoda; Caenogastropoda; Sorbeoconcha; Hypsogastropoda; Littorinimorpha; Littorinoidea; Littorinidae; Littorina
 31243	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Globodera
-31312	Eukaryota; Viridiplantae; Chlorophyta; Prasinophyceae; Chlorodendrales; Chlorodendraceae; Nephroselmis
-31757	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Siphoviridae; L5-like viruses
-32049	Bacteria; Cyanobacteria; Chroococcales; Synechococcus
 32538	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Fissipedia; Felidae; Leopardus
-33169	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Eremotheciaceae; Eremothecium
-33708	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Gammaherpesvirinae
-33903	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces
-34256	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Lamiales; Lamiaceae; Nepetoideae; Mentheae; Mentha
-34305	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
+33085	Eukaryota; Entamoebidae; Entamoeba
+33169	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Eremothecium
+33178	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+34245	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Zinnia
+34256	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Mentheae; Mentha
+34274	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+34317	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Myrtales; Myrtaceae; Eucalyptus
 34358	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
 34373	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Leotiomycetes; Erysiphales; Erysiphaceae; Blumeria
 34488	Eukaryota; Fungi; Zygomycota; Zygomycetes; Entomophthorales; Ancylistaceae; Conidiobolus
 34506	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Panagrolaimoidea; Strongyloididae; Strongyloides
+34594	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Argasidae; Ornithodoros
 34610	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodidae; Amblyomma
 34740	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Heliconiinae; Heliconius
 34765	Eukaryota; Metazoa; Chordata; Urochordata; Appendicularia; Oikopleuridae; Oikopleura
-35250	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Marek's disease-like viruses
+34816	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Moronidae; Morone
+35520	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Paniceae; Pennisetum
 35632	Eukaryota; Metazoa; Annelida; Clitellata; Oligochaeta; Haplotaxida; Lumbricina; Lumbricidae; Lumbricus
-35938	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Robinieae; Robinia
+35845	Eukaryota; Viridiplantae; Chlorophyta; Ulvophyceae; Dasycladales; Dasycladaceae; Acetabularia
+35876	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Iridaceae; Iris
+35883	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Convolvulaceae; Ipomoea
+35884	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Convolvulaceae; Ipomoea
+35938	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Robinieae; Robinia
 36090	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Globodera
-36427	Viruses; dsRNA viruses; Reoviridae; Rotavirus
 36452	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; unclassified Herpesviridae; stealth viruses
-37108	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Marek's disease-like viruses
+36596	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
+36825	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Phasmatodea; Euphasmida; Phyllioidea; Bacillidae; Bacillus
 37293	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Aotinae; Aotus
 37296	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Gammaherpesvirinae; Rhadinovirus
-37468	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Boletales; Sclerodermataceae; Pisolithus
-37656	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Sapindales; Rutaceae; Citrus
-37657	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllidae; Caryophyllales; Caryophyllaceae; Silene
-37665	Viruses; dsDNA viruses, no RNA stage; Phycodnaviridae; Phaeovirus
+37468	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Boletales; Sclerodermatineae; Pisolithaceae; Pisolithus
+37656	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Citrus
+37657	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Caryophyllaceae; Silene
 37682	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Aegilops
+37690	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Poncirus
 37727	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Penicillium
-39839	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; GBV-C/HGV group
+37769	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Heterobasidiomycetes; Tremellomycetidae; Tremellales; Tremellaceae; Filobasidiella
+38033	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Chaetomiaceae; Chaetomium
+38249	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma
+38666	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Heteromyidae; Perognathinae; Chaetodipus
+38937	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Iguania; Iguanidae; Polychrotinae; Anolis
+39984	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Rhizophoraceae; Bruguiera
 40051	Viruses; dsRNA viruses; Reoviridae; Orbivirus
+40352	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Trichostrongylidae; Trichostrongylinae; Trichostrongylus
 40366	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 40559	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Botryotinia
+40686	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Salix
 40930	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Coccoidea; Pseudococcidae; Planococcus
-41061	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
-41857	Viruses; ssRNA negative-strand viruses; Orthomyxoviridae; Influenza A viruses; Influenzavirus A; Influenza A virus; H3N2 subtype
-41882	Eukaryota; Viridiplantae; Streptophyta; Mesostigmatophyceae; Mesostigmatales; Mesostigmataceae; Mesostigma
+40932	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Aphidini; Rhopalosiphum
+41429	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Anopheles
+42156	Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Litomosoides
+42251	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Pezizomycetes; Pezizales; Tuberaceae; Tuber
+42329	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Cycadophyta; Cycadales; Zamiaceae; Zamia
+42439	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Limnanthaceae; Limnanthes
+42677	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella; Gibberella fujikuroi complex
 42890	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Sarcocystis
-44015	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
-44456	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Myrtales; Onagraceae; Oenothera
+43114	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Caudata; Salamandroidea; Ambystomatidae; Ambystoma
+43425	Eukaryota; Fungi; Glomeromycota; Glomeromycetes; Glomerales; Glomeraceae; Glomus
+43928	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobaculum
+44015	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
 44689	Eukaryota; Mycetozoa; Dictyosteliida; Dictyostelium
-45255	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; GBV-C/HGV group
+45249	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
 45464	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Haemonchidae; Ostertagiinae; Teladorsagia
-45687	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
+45687	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
 45929	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Pratylenchidae; Pratylenchinae; Pratylenchus
-46015	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
-46221	Viruses; ssDNA viruses; Circoviridae; Circovirus
-46242	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
-47664	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Malpighiales; Salicaceae; Populus
+45954	Eukaryota; Metazoa; Mollusca; Bivalvia; Heteroconchia; Veneroida; Dreissenoidea; Dreissenidae; Dreissena
+46761	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Caudata; Salamandroidea; Plethodontidae; Plethodon
+47247	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
+47664	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 47834	Bacteria; Firmicutes; Mollicutes; Entomoplasmatales; Spiroplasmataceae; Spiroplasma
-48154	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Sylviidae; Phylloscopus
+47853	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Micromonosporineae; Micromonosporaceae; Micromonospora
+48215	Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Echinostomida; Echinostomata; Echinostomatidae; Echinostoma
 48935	Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Novosphingobium
 49338	Bacteria; Firmicutes; Clostridia; Clostridiales; Peptococcaceae; Desulfitobacterium
 49351	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Cephaloboidea; Cephalobidae; Zeldia
-49495	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Filicophyta; Filicopsida; Filicales; Pteridaceae; Ceratopteris
-50339	Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales; Thermoplasmataceae; Thermoplasma
+49451	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Nicotiana
+49495	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Moniliformopses; Filicophyta; Filicopsida; Filicales; Pteridaceae; Ceratopteris
 51029	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Heterodera
 51031	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Ancylostomatoidea; Ancylostomatidae; Bunostominae; Necator
-51313	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
-51453	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreales; Hypocreaceae; Hypocrea
-51677	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Granulovirus
-52283	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Sarcoptoidea; Sarcoptidae; Sarcoptes
-53010	Viruses; ssDNA viruses; Geminiviridae; Begomovirus
+51240	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fagales; Juglandaceae; Juglans
+51453	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
+51511	Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona; Phlebobranchia; Cionidae; Ciona
+51657	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
+52283	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Psoroptidia; Sarcoptoidea; Sarcoptidae; Sarcoptes
+52714	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Leymus
+52792	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Turdidae; Luscinia
 53326	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Ancylostomatoidea; Ancylostomatidae; Ancylostomatinae; Ancylostoma
-53413	Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadaceae; Xanthomonas
-53953	Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; Pyrococcus
+53413	Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas
 54126	Eukaryota; Metazoa; Nematoda; Chromadorea; Diplogasterida; Neodiplogasteridae; Pristionchus
+54290	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; GBV-C/HGV group
 54314	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Pestivirus
-54672	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Malpighiales; Euphorbiaceae; Euphorbia
+54672	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Euphorbioideae; Euphorbieae; Euphorbia
 54734	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes et Chaetothyriomycetes incertae sedis; Mycosphaerellaceae; Mycosphaerella
-55188	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Sapindales; Rutaceae; Citrus
+55088	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Phasmatodea; Euphasmida; Phyllioidea; Bacillidae; Bacillus
+55188	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Citrus
 55529	Eukaryota; Cryptophyta; Cryptomonadaceae; Guillardia
-55670	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Stevia
-56141	Eukaryota; Metazoa; Mollusca; Gastropoda; Orthogastropoda; Apogastropoda; Caenogastropoda; Sorbeoconcha; Hypsogastropoda; Littorinimorpha; Rissooidea; Pomatiopsidae; Oncomelania
-56636	Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae; Aeropyrum
+55670	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Eupatorieae; Stevia
+55987	Viruses; ssRNA negative-strand viruses; Orthomyxoviridae; unclassified Orthomyxoviridae
 57667	Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
-59509	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Capripoxvirus
+57870	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Phasmatodea; Euphasmida; Phyllioidea; Bacillidae; Bacillus
+58002	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Phylloxeroidea; Phylloxeridae; Daktulosphaira
+58031	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Cycadophyta; Cycadales; Cycadaceae; Cycas
+59479	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Chiroptera; Microchiroptera; Rhinolophidae; Rhinolophinae; Rhinolophus
+59689	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
+59747	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
 59777	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Lycopodiophyta; Isoetopsida; Selaginellales; Selaginellaceae; Selaginella
-62890	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
-63363	Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex
+59861	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Coregonus
+61147	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Rhizophoraceae; Kandelia
+62324	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Anopheles
+62890	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
+63629	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Ehrhartoideae; Oryzeae; Oryza
 63737	Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Nostoc
 64091	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobacterium
-64093	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Lamiales; Orobanchaceae; Rhinantheae; Triphysaria
+64093	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Orobanchaceae; Rhinantheae; Triphysaria
+64391	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Chrysomeloidea; Chrysomelidae; Bruchinae; Bruchini; Callosobruchus
 64468	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Litopenaeus
+64602	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Natrialba
+64679	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Sciuridae; Sciurinae; Tamias
+64717	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Arvicolinae; Microtus
 65661	Eukaryota; Acanthamoebidae; Acanthamoeba
 66189	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Testudines; Cryptodira; Testudinoidea; Testudinidae; Geochelone
-66797	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Siphoviridae
 66913	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Siluriformes; Ictaluridae; Ictalurus
 67593	Eukaryota; stramenopiles; Oomycetes; Pythiales; Pythiaceae; Phytophthora
-68887	Viruses; ssDNA viruses; unclassified ssDNA viruses
+68887	Viruses; ssDNA viruses; Circoviridae; Anellovirus
+69266	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; Ericales; Ericaceae; Vaccinioideae; Vaccinieae; Vaccinium
 69293	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Gasterosteiformes; Gasterosteidae; Gasterosteus
 70415	Eukaryota; Metazoa; Nematoda; Enoplea; Trichocephalida; Trichuridae; Trichuris
 70448	Eukaryota; Viridiplantae; Chlorophyta; Prasinophyceae; Mamiellales; Mamiellaceae; Ostreococcus
-70600	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
+70863	Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Alteromonadaceae; Shewanella
+71139	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Myrtales; Myrtaceae; Eucalyptus
+71150	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Boletales; Paxilineae; Paxillaceae; Paxillus
 71223	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Cantharoidea; Lampyridae; Pyrocoelia
 71647	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
-72664	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Thellungiella
-73824	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Malpighiales; Salicaceae; Populus
+72088	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Scorpaeniformes; Scorpaenoidei; Scorpaenidae; Sebastes
+73107	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Gruiformes; Otididae; Otis
+73234	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Phasmatodea; Euphasmida; Phyllioidea; Bacillidae; Bacillus
+73275	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
+73304	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
+73824	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+74081	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Scincomorpha; Lacertoidea; Lacertidae; Podarcis
+74649	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Rosa
 74940	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
-75985	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellaceae; Mannheimia
+75846	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Anseriformes; Anatidae; Anas
+75943	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactuca
+76149	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Plumbaginaceae; Plumbago
+76340	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Sciaenidae; Sciaenops
 76593	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Acrossocheilus
+76867	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Cortinariaceae; Hebeloma
+77108	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; stem Magnoliophyta; Nymphaeaceae; Nuphar
 78584	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Strepsirhini; Megaladapidae; Lepilemur
 79327	Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Seriata; Tricladida; Paludicola; Dugesiidae; Schmidtea
+79517	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Timarchini; Timarcha
 79880	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
+79923	Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Opisthorchiida; Opisthorchiata; Opisthorchioidea; Opisthorchiidae; Clonorchis
 80365	Eukaryota; stramenopiles; Phaeophyceae; Laminariales; Laminariaceae; Laminaria
+80379	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Capsicum
+80863	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 82528	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Iridaceae; Crocus
-82927	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Asteridae; lamiids; Lamiales; Acanthaceae; Acanthaceae incertae sedis; Avicennia
-83191	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Entomopoxvirinae; Entomopoxvirus B
+82927	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Acanthaceae; Acanthaceae incertae sedis; Avicennia
+83288	Eukaryota; Rhodophyta; Florideophyceae; Ceramiales; Ceramiaceae; Griffithsia
 83558	Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; Chlamydophila
-83560	Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; Chlamydia
-83912	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Sarcoptoidea; Psoroptidae; Psoroptes
-86304	Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadaceae; Microbulbifer
-86665	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
-89411	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Descurainia
+83675	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Neospora
+83912	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Psoroptidia; Sarcoptoidea; Psoroptidae; Psoroptes
+84072	Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Acoelomorpha; Acoela; Sagittiferidae; Symsagittifera
+85571	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Citrus
+86005	Bacteria; Firmicutes; Bacillales; Alicyclobacillaceae; Pasteuria
+86304	Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Alteromonadaceae; Microbulbifer
+87841	Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Stylommatophora; Sigmurethra; Helicoidea; Bradybaenidae; Euhadra
+89411	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Descurainia
 89462	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Bubalus
-92652	Viruses; dsDNA viruses, no RNA stage; Nimaviridae
+92652	Viruses; dsDNA viruses, no RNA stage; Nimaviridae; Whispovirus
+93678	Viruses; ssDNA viruses; Circoviridae; Anellovirus
 93934	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Coturnix
-96477	Eukaryota; Viridiplantae; Streptophyta; Coleochaetales; Chaetosphaeridiaceae; Chaetosphaeridium
+94289	Eukaryota; Alveolata; Ciliophora; Spirotrichea; Stichotrichia; Stichotrichida; Oxytrichidae; Sterkiella
+94961	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Chiroptera; Microchiroptera; Mystacinidae; Mystacina
+95145	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Paracanthopterygii; Batrachoididae; Opsanus
+96939	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
+97005	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Heterodera
 97393	Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales; Ferroplasmaceae; Ferroplasma
-98038	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Thellungiella
+98038	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Thellungiella
 99878	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Sturnidae; Toxostoma
 99883	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes; Tetradontoidea; Tetraodontidae; Tetraodon
-103690	Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Nostoc
+100452	Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Stylommatophora; Sigmurethra; Helicoidea; Hygromiidae; Candidula
+102803	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Scolytidae; Ips
+103999	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Campanulaceae; Codonopsis
 105358	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Diadematacea; Diadematoida; Diadematidae; Diadema
-105360	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Diadematacea; Diadematoida; Diadematidae; Diadema
-105385	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Neobatrachia; Bufonoidea; Myobatrachidae; Limnodynastes
-107806	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriaceae; Buchnera
+105886	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Apiales; Araliaceae; Acanthopanax
+107832	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Heterobasidiomycetes; Heterobasidiomycetidae; Ceratobasidiales; Ceratobasidiaceae; Thanatephorus
+107907	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Adephaga; Dytiscidae; Colymbetinae; Colymbetini; Meladema
 108098	Viruses; dsDNA viruses, no RNA stage; Adenoviridae; Mastadenovirus
 108607	Eukaryota; Pelobiontida; Mastigamoebidae; Mastigamoeba
-111955	Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae; Sulfolobus
-114186	Bacteria; Proteobacteria; Gammaproteobacteria; Candidatus Carsonella
+110365	Eukaryota; Alveolata; Apicomplexa; Gregarinia; Eugregarinida; Gregarinidae; Gregarina
+112525	Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Basommatophora; Lymnaeoidea; Planorbidae; Biomphalaria
+113636	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+114524	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
 114525	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
 114526	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+117187	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella
+118799	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Adephaga; Carabidae; Carabini; Carabina; Carabus; Carabus
 119072	Bacteria; Firmicutes; Clostridia; Thermoanaerobacteriales; Thermoanaerobacteriaceae; Thermoanaerobacter
-119219	Bacteria; Proteobacteria; Betaproteobacteria; Ralstoniaceae; Ralstonia
+119219	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Ralstonia
+121225	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Phthiraptera; Anoplura; Pediculidae; Pediculus
+121759	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; mitosporic Onygenales; Paracoccidioides
+123226	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Scorpiones; Buthida; Buthoidea; Buthidae; Mesobuthus
 123792	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Sciuridae; Sciurinae; Tamias
 126740	Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga
-126913	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllidae; Caryophyllales; Chenopodiaceae; Suaeda
-128735	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Rosales; Rosaceae; Rosoideae; Rosa
+126913	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Amaranthaceae; Suaeda
+128735	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Rosa
+129883	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Telestes
 129951	Viruses; dsDNA viruses, no RNA stage; Adenoviridae; Mastadenovirus
-130310	Viruses; dsDNA viruses, no RNA stage; Adenoviridae; Mastadenovirus
 131310	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Panagrolaimoidea; Strongyloididae; Parastrongyloides
-132475	Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Yatapoxvirus
-132711	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACC clade; Panicoideae; Andropogoneae; Sorghum
-134537	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiaceae; Burkholderia
+132711	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
+134537	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia
 135974	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Furnariidae; Glyphorynchus
-136966	Viruses; ssDNA viruses; unclassified ssDNA viruses
+136966	Viruses; ssDNA viruses; Circoviridae; Anellovirus
 137523	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Piciformes; Picidae; Dendrocopos
 138948	Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Enterovirus
 138949	Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Enterovirus
 138950	Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Enterovirus
 138953	Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Enterovirus
-140110	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreales; Nectriaceae; Nectria
+140110	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Nectria
 145262	Archaea; Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae; Methanothermobacter
-146786	Bacteria; Cyanobacteria; Chroococcales; Thermosynechococcus
 148305	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Magnaporthaceae; Magnaporthe
-148363	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
+150234	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Adephaga; Cicindelidae; Cicindela; Cicindela
+153471	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 155892	Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Caulobacter
-156889	Bacteria; Proteobacteria; magnetotactic cocci
-157791	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
-161934	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllidae; Caryophyllales; Chenopodiaceae; Beta
+156889	Bacteria; Proteobacteria; Magnetococcus
+157791	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
+160621	Eukaryota; Alveolata; Dinophyceae; Gonyaulacales; Lingulodinium
+161934	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Amaranthaceae; Beta
 162425	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; Emericella
-164405	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Myrtales; Myrtaceae; Melaleuca
-169015	Eukaryota; mixed EST libraries
-169683	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae
-176652	Viruses; dsDNA viruses, no RNA stage; Iridoviridae; Iridovirus
-180816	Viruses; dsDNA viruses, no RNA stage; Caudovirales; Siphoviridae; Lambda-like viruses
-182710	Bacteria; Firmicutes; Bacillales; Oceanobacillus
-188763	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae; Cytomegalovirus
-191492	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
+164405	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Myrtales; Myrtaceae; Melaleuca
+172680	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Gruiformes; Otididae; Chlamydotis
+176275	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Clavicipitaceae; Cordyceps
+178872	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Boletales; Sclerodermatineae; Pisolithaceae; Pisolithus
+180448	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Motacillidae; Motacilla
+182803	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Araneae; Araneomorphae; Entelegynae; Araneoidea; Araneidae; Araneus
+183855	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Myrtales; Myrtaceae; Eucalyptus
+186039	Eukaryota; stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Bacillariales; Bacillariaceae; Fragilariopsis
+189293	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
+189785	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Tamaricaceae; Tamarix
 194440	Viruses; Retroid viruses; Retroviridae; Deltaretrovirus
 194441	Viruses; Retroid viruses; Retroviridae; Deltaretrovirus
-204440	Viruses; dsDNA viruses, no RNA stage; Baculoviridae; Nucleopolyhedrovirus
+197003	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Biphyllidae; Biphyllus
+197009	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Anthribidae; Anthribinae; Platystomini; Platystomus
+197013	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Curculionidae; Curculioninae; Curculionini; Curculio
+197043	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Euhemiptera; Membracoidea; Cicadellidae; Cicadellinae; Homalodisca
+212795	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Serranidae; Epinephelus
+213425	Eukaryota; Metazoa; Mollusca; Gastropoda; Orthogastropoda; Apogastropoda; Caenogastropoda; Sorbeoconcha; Hypsogastropoda; Neogastropoda; Muricoidea; Muricidae; Ocinebrellus
+216816	Bacteria; Actinobacteria; Actinobacteridae; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium
+219666	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Gentianales; Rubiaceae; Rubioideae; Spermacoceae; Hedyotis
+219667	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Gentianales; Rubiaceae; Rubioideae; Spermacoceae; Hedyotis
+219738	Eukaryota; Metazoa; Nematoda; Enoplea; Trichocephalida; Trichuridae; Trichuris
+221420	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Holothuroidea; Aspidochirotacea; Aspidochirotida; Holothuriidae; Holothuria
+223153	Eukaryota; Alveolata; Ciliophora; Litostomatea; Trichostomatia; Vestibuliferida; Isotrichidae; Isotricha
+223852	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Aphidini; Toxoptera
+232323	Eukaryota; Metazoa; Tardigrada; Eutardigrada; Apochela; Hypsibiidae; Hypsibius
+241073	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
+245552	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Alstroemeriaceae; Alstroemeria
+246827	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
diff --git a/data/sequin.hlp b/data/sequin.hlp
index ddeb4c26..3f5be114 100644
--- a/data/sequin.hlp
+++ b/data/sequin.hlp
@@ -5,8 +5,7 @@
   
 <!-- if you use the following meta tags, uncomment them.
  <META NAME="keywords" CONTENT="Sequin">
- <META NAME="description" CONTENT="Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. ">
--->
+ <META NAME="description" CONTENT="Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. "> -->
  <link rel="stylesheet" href="ncbi_sequin.css">
 
 
@@ -2288,7 +2287,7 @@ this location.
 
 #Region containing polycistronic transcript under the control of the same regulatory sequences.
 
-*ori_T
+*oriT
 
 Origin of transfer; region of DNA where transfer is initiated during the process of conjugation or mobilization.
 
@@ -3442,21 +3441,42 @@ added to the sequence. Features are described in more detail in the
 above section entitled
 <A HREF="#Features">
 Features.
-</A>  
-#The seventh option, Publications, allows you to add a Publication Feature
+</A>
+#If you are submitting a set of similar sequences, you can add the same
+feature across the entire span of each by using the Batch Feature Apply
+option.  The feature must span the entire nucleotide sequence of each member;
+you can not annotate specific nucleotide locations using this option (for
+this, see <A HREF="#FeaturePropagate">Feature Propagate</A>).  For each
+feature, you will be prompted to designate whether the feature is 5' or 3'
+partial and whether is is on the plus or minus strand.  You may also add a
+comment of other qualifier to the feature.  The Add Qualifier option allows
+you to add a qualifier to an existing feature.  You must specify the feature
+and qualifier in the Add Qualifier pop-up box.  Source qualifiers can be added
+to all entries using the Add Source Qualifier option.  Qualifiers specific to
+the CDS and gene can be added using Add CDS-Gene-Prot and RNA qualifiers using
+Add RNA Qual.  In each case, a pop-up box appears with qualifier options
+appropriate for that feature.
+
+#The Batch Feature Edit function allows you to edit existing qualifiers.  For
+each menu choice, a pop-up box allows you to select the feature containing the
+qualifier and the specific qualifier to be edited.  You can use the
+Find/Replace text boxes to edit the information contained within the
+qualifier.
+
+#The Publications option allows you to add a Publication Feature
 or Publication Descriptor to the record.  Publications are described in
 more detail in the above section entitled
 <A HREF="#Publications">
 Publications.
 </A>  
-#The eighth option, Descriptors, allows you to add Descriptors to the
+#The Descriptors option allows you to add Descriptors to the
 record.  Descriptors are described in more detail in the section
 entitled
 <A HREF="#Descriptors">
 Descriptors,
 </A>
 above.
-#The ninth option Generate Definition Line, will generate a title for your
+#The Generate Defintion Line option will generate a title for your
 sequence based on the information provided in the record.  This option will
 work
 for single sequences as well as sets of sequences, and can handle complex
@@ -3946,7 +3966,7 @@ ALT="Table of Contents" ALIGN=top BORDER=2></A>
 <P CLASS=medium1><B>Questions or Comments?</B>
 <BR>Write to the <A HREF="mailto:info@ncbi.nlm.nih.gov">NCBI Service
 Desk</A></P>
-<P CLASS=medium1>Revised October 20, 2003
+<P CLASS=medium1>Revised January 30, 2004
 
 </CENTER>
 
diff --git a/data/taxlist.txt b/data/taxlist.txt
index bdc4dada..e90fc914 100644
--- a/data/taxlist.txt
+++ b/data/taxlist.txt
@@ -1,342 +1,375 @@
-12
-Acanthamoeba castellanii		1	4	INV	5755
+13
 Acanthamoeba healyi		1	4	INV	65661
+Acanthocybium solandri		1	2	VRT	13323
+Acanthopanax sessiliflorus		1	1	PLN	105886
+Acetabularia acetabulum		6	1	PLN	35845
 Acidithiobacillus ferrooxidans		11	0	BCT	920
-Acinetobacter calcoaceticus		11	0	BCT	471
 Acipenser baerii	Siberian sturgeon	1	2	VRT	27689
-Acipenser gueldenstaedtii	Russian sturgeon	1	2	VRT	7902
 Acrossocheilus paradoxus		1	2	VRT	76593
 Actinobacillus actinomycetemcomitans		11	0	BCT	714
 Actinobacillus pleuropneumoniae		11	0	BCT	715
+Acyrthosiphon pisum	pea aphid	1	5	INV	7029
 Aedes aegypti	yellow fever mosquito	1	5	INV	7159
 Aegilops speltoides		1	1	PLN	4573
 Aegilops tauschii		1	1	PLN	37682
 Aepyceros melampus	impala	1	2	MAM	9897
+Aequorea victoria		1	4	INV	6100
 Aeromonas hydrophila		11	0	BCT	644
-Aeropyrum pernix		11	0	BCT	56636
 African swine fever virus		1	0	VRL	10497
 Agaricus bisporus		1	4	PLN	5341
 Agrobacterium tumefaciens		11	0	BCT	358
 Aids-associated retrovirus		1	0	VRL	11966
 Ajellomyces capsulatus		1	4	PLN	5037
-Alligator mississippiensis	American alligator	1	2	VRT	8496
+Alexandrium tamarense		1	4	PLN	2926
 Allium cepa	onion	1	1	PLN	4679
+Allium sativum	garlic	1	1	PLN	4682
+Alstroemeria peruviana		1	1	PLN	245552
 Amblyomma americanum		1	5	INV	6943
 Amblyomma variegatum		1	5	INV	34610
+Amborella trichopoda		1	1	PLN	13333
+Ambystoma maculatum	spotted salamander	1	2	VRT	43114
 Ambystoma mexicanum	axolotl	1	2	VRT	8296
-Amsacta moorei entomopoxvirus		1	0	VRL	28321
-Anabaena variabilis		11	0	BCT	1172
+Amphidinium carterae		1	4	PLN	2961
 Anaplasma marginale		11	0	BCT	770
 Anaplasma phagocytophilum		11	0	BCT	948
+Anas fulvigula		1	2	VRT	75846
 Anas platyrhynchos		1	2	VRT	8839
 Ancylostoma caninum	dog hookworm	1	5	INV	29170
 Ancylostoma ceylanicum		1	5	INV	53326
-Anguilla anguilla	European eel	1	2	VRT	7936
 Anguilla japonica	Japanese eel	1	2	VRT	7937
+Anolis sagrei	brown anole	1	2	VRT	38937
 Anopheles arabiensis		1	5	INV	7173
+Anopheles funestus		1	5	INV	62324
 Anopheles gambiae	African malaria mosquito	1	5	INV	7165
+Anopheles maculipennis		1	5	INV	41429
 Antheraea yamamai	Japanese oak silkmoth	1	5	INV	7121
 Antirrhinum majus	snapdragon	1	1	PLN	4151
 Aotus nancymaae	Ma's night monkey	1	2	PRI	37293
-Apis mellifera	honeybee	1	5	INV	7460
+Apis mellifera	honey bee	1	5	INV	7460
+Apium graveolens		1	1	PLN	4045
 Aplysia californica	California sea hare	1	5	INV	6500
-Aquifex aeolicus		11	0	BCT	63363
+Apodemus sylvaticus	European woodmouse	1	2	ROD	10129
+Arabidopsis lyrata		1	1	PLN	59689
+Arabidopsis suecica		1	1	PLN	45249
 Arabidopsis thaliana	thale cress	1	1	PLN	3702
+Arachis hypogaea	peanut	1	1	PLN	3818
+Araneus ventricosus		1	5	INV	182803
 Archaeoglobus fulgidus		11	0	BCT	2234
+Argopecten irradians		1	5	INV	31199
 Artemia franciscana		1	5	INV	6661
+Ascaris lumbricoides	common roundworm	1	5	INV	6252
 Ascaris suum	pig roundworm	1	5	INV	6253
+Ashbya gossypii		1	3	PLN	33169
+Asparagus officinalis	garden asparagus	1	1	PLN	4686
 Aspergillus flavus		1	4	PLN	5059
 Aspergillus fumigatus		1	4	PLN	5085
+Aspergillus nidulans		1	4	PLN	162425
 Aspergillus niger		1	4	PLN	5061
-Aspergillus nomius		1	4	PLN	41061
 Aspergillus oryzae		1	4	PLN	5062
-Autographa californica nucleopolyhedrovirus		1	0	VRL	46015
+Aspergillus terreus		1	4	PLN	33178
+Aspergillus tubingensis		1	4	PLN	5068
+Ateles geoffroyi	black-handed spider monkey	1	2	PRI	9509
 Avena sativa	oat	1	1	PLN	4498
 Avian infectious bronchitis virus		1	0	VRL	11120
 Avicennia marina		1	1	PLN	82927
-Azospirillum brasilense		11	0	BCT	192
 Azotobacter vinelandii		11	0	BCT	354
 B19 virus		1	0	VRL	10798
-Bacillus amyloliquefaciens		11	0	BCT	1390
 Bacillus anthracis		11	0	BCT	1392
+Bacillus atticus		1	5	INV	36825
 Bacillus cereus		11	0	BCT	1396
-Bacillus circulans		11	0	BCT	1397
 Bacillus clausii		11	0	BCT	79880
-Bacillus halodurans		11	0	BCT	86665
+Bacillus grandii		1	5	INV	55088
 Bacillus licheniformis		11	0	BCT	1402
-Bacillus megaterium		11	0	BCT	1404
-Bacillus phage phi29		11	0	PHG	10756
-Bacillus sphaericus		11	0	BCT	1421
+Bacillus lynceorum		1	5	INV	73234
 Bacillus subtilis		11	0	BCT	1423
 Bacillus thuringiensis		11	0	BCT	1428
-Bacteriophage lambda		11	0	PHG	10710
-Bacteriophage SPBc2		11	0	PHG	66797
-Bacteriophage SPP1		11	0	PHG	10724
-Bacteriophage T3		11	0	PHG	10759
+Bacillus whitei		1	5	INV	57870
 Bacteroides fragilis		11	0	BCT	817
+Beauveria bassiana		1	4	PLN	176275
 Bemisia tabaci		1	5	INV	7038
 Beta vulgaris		1	1	PLN	161934
 Betula pendula	European white birch	1	1	PLN	3505
+Bifidobacterium longum		11	0	BCT	216816
 Biomphalaria glabrata	bloodfluke planorb	1	5	INV	6526
+Biomphalaria pfeifferi		1	5	INV	112525
+Biphyllus lunatus		1	5	INV	197003
 Bluetongue virus		1	0	VRL	40051
 Blumeria graminis		1	4	PLN	34373
 Bombyx mandarina	wild silkworm	1	5	INV	7092
 Bombyx mori	domestic silkworm	1	5	INV	7091
-Bombyx mori nuclear polyhedrosis virus		1	0	VRL	10458
 Boophilus microplus	southern cattle tick	1	5	INV	6941
 Bordetella bronchiseptica		11	0	BCT	518
 Bordetella pertussis		11	0	BCT	520
-Borna disease virus		1	0	VRL	12455
 Borrelia afzelii		11	0	BCT	29518
 Borrelia burgdorferi	Lyme disease spirochete	11	0	BCT	139
 Borrelia garinii		11	0	BCT	29519
 Bos indicus	zebu	1	2	MAM	9915
 Bos taurus	cow	1	2	MAM	9913
 Bothrops insularis	island jararaca	1	2	VRT	8723
+Botryllus schlosseri		1	13	INV	30301
 Botryotinia fuckeliana		1	4	PLN	40559
-Bovine coronavirus		1	0	VRL	11128
-Bovine herpesvirus 1		1	0	VRL	10320
-Bovine herpesvirus 4		1	0	VRL	10385
 Bovine respiratory syncytial virus		1	0	VRL	11246
-Bovine rotavirus		1	0	VRL	10927
 Bradyrhizobium japonicum		11	0	BCT	375
 Branchiostoma belcheri		1	5	INV	7741
 Branchiostoma floridae	Florida lancelet	1	5	INV	7739
+Brassica campestris		1	1	PLN	3711
 Brassica juncea		1	1	PLN	3707
 Brassica napus	rape	1	1	PLN	3708
 Brassica oleracea		1	1	PLN	3712
 Brassica rapa		1	1	PLN	3711
-Brevibacillus brevis		11	0	BCT	1393
 Brucella melitensis		11	0	BCT	29459
 Brugia malayi		1	5	INV	6279
+Bruguiera gymnorrhiza		1	1	PLN	39984
 Bubalus bubalis	water buffalo	1	2	MAM	89462
 Buchnera aphidicola		11	0	BCT	9
-Buchnera sp. APS		11	0	BCT	107806
-Bungarus multicinctus	many-banded krait	1	2	VRT	8616
 Burkholderia cepacia		11	0	BCT	292
 Burkholderia fungorum		11	0	BCT	134537
 Burkholderia pseudomallei		11	0	BCT	28450
 Caenorhabditis briggsae		1	5	INV	6238
 Caenorhabditis elegans		1	5	INV	6239
 Callithrix jacchus	white-tufted-ear marmoset	1	2	PRI	9483
-Camelpox virus		1	0	VRL	28873
+Callosobruchus maculatus	cowpea weevil	1	5	INV	64391
 Camelus dromedarius	Arabian camel	1	2	MAM	9838
 Campylobacter jejuni		11	0	BCT	197
 Candida albicans		12	4	PLN	5476
+Candida famata		1	3	PLN	4959
 Candida glabrata		1	3	PLN	5478
 Candida tropicalis		12	3	PLN	5482
-Candidatus Carsonella ruddii		11	0	BCT	114186
+Candidula unifasciata		1	5	INV	100452
 Canis familiaris	dog	1	2	MAM	9615
 Capra hircus	goat	1	2	MAM	9925
 Caprine arthritis-encephalitis virus		1	0	VRL	11660
 Capsicum annuum		1	1	PLN	4072
+Capsicum chinense		1	1	PLN	80379
+Carabus granulatus		1	5	INV	118799
 Carassius auratus	goldfish	1	2	VRT	7957
-Catharanthus roseus	Madagascar periwinkle	1	1	PLN	4058
+Carica papaya	papaya	1	1	PLN	3649
 Caulobacter crescentus		11	0	BCT	155892
+Caulobacter vibrioides		11	0	BCT	155892
 Cavia porcellus	domestic guinea pig	1	2	ROD	10141
 Ceratitis capitata	Mediterranean fruit fly	1	5	INV	7213
 Ceratodon purpureus		1	1	PLN	3225
 Ceratopteris richardii		1	1	PLN	49495
 Cercopithecus aethiops	African green monkey	1	2	PRI	9534
 Cervus elaphus	red deer	1	2	MAM	9860
-Chaetosphaeridium globosum		1	1	PLN	96477
-Chicken anemia virus		1	0	VRL	12618
-Chimpanzee cytomegalovirus		1	0	VRL	188763
-Chironomus thummi		1	5	INV	7154
-Chlamydia muridarum		11	0	BCT	83560
+Chaetodipus intermedius	rock pocket mouse	1	2	ROD	38666
+Chaetomium globosum		1	4	PLN	38033
 Chlamydia trachomatis		11	0	BCT	813
 Chlamydomonas reinhardtii		1	1	PLN	3055
 Chlamydophila pneumoniae		11	0	BCT	83558
-Chlorella vulgaris		1	1	PLN	3077
+Chlamydotis undulata		1	2	VRT	172680
 Chlorobium tepidum		11	0	BCT	1097
 Chloroflexus aurantiacus		11	0	BCT	1108
 Cicer arietinum	chickpea	1	1	PLN	3827
+Cicindela campestris		1	5	INV	150234
 Ciona intestinalis		1	13	INV	7719
-Citrobacter freundii		11	0	BCT	546
+Ciona savignyi		1	13	INV	51511
 Citrullus lanatus	watermelon	1	1	PLN	3654
+Citrus reticulata		1	1	PLN	85571
 Citrus sinensis		1	1	PLN	2711
 Citrus tristeza virus		1	0	VRL	12162
 Citrus unshiu		1	1	PLN	55188
 Citrus x paradisi		1	1	PLN	37656
 Cladosporium fulvum		1	4	PLN	5499
+Cleome hassleriana		1	1	PLN	28532
+Clonorchis sinensis		1	9	INV	79923
 Clostridium acetobutylicum		11	0	BCT	1488
-Clostridium botulinum		11	0	BCT	1491
 Clostridium difficile		11	0	BCT	1496
-Clostridium pasteurianum		11	0	BCT	1501
 Clostridium perfringens		11	0	BCT	1502
 Clostridium thermocellum		11	0	BCT	1515
 Coccidioides immitis		1	4	PLN	5501
+Codonopsis lanceolata		1	1	PLN	103999
 Coffea arabica	coffee	1	1	PLN	13443
+Colletotrichum gloeosporioides		1	4	PLN	5457
 Colletotrichum trifolii		1	4	PLN	5466
 Columba livia	domestic pigeon	1	2	VRT	8932
-Comamonas testosteroni		11	0	BCT	285
 Conidiobolus coronatus		1	4	PLN	34488
+Cooperia oncophora		1	5	INV	27828
+Coprinopsis cinerea		1	4	PLN	5346
+Coprinus cinereus		1	4	PLN	5346
+Cordyceps bassiana		1	4	PLN	176275
+Coregonus clupeaformis		1	2	VRT	59861
 Corynebacterium glutamicum		11	0	BCT	1718
-Cotton leaf curl virus		1	0	VRL	53010
+Corynebacterium pseudotuberculosis		11	0	BCT	1719
 Coturnix coturnix	common quail	1	2	VRT	9091
 Coturnix japonica	Japanese quail	1	2	VRT	93934
-Cowpox virus		1	0	VRL	10243
-Coxiella burnetii		11	0	BCT	777
 Crassostrea gigas	Pacific oyster	1	5	INV	29159
 Crassostrea virginica	eastern oyster	1	5	INV	6565
 Cricetulus griseus	Chinese hamster	1	2	ROD	10029
-Crithidia fasciculata		1	4	INV	5656
 Crocus sativus		1	1	PLN	82528
+Cryphonectria parasitica		1	4	PLN	5116
+Cryptococcus bacillisporus		1	4	PLN	37769
+Cryptococcus neoformans		1	4	PLN	5207
 Cryptomeria japonica	Japanese cedar	1	1	PLN	3369
 Cryptosporidium parvum		1	4	INV	5807
 Ctenocephalides felis	cat flea	1	5	INV	7515
+Ctenopharyngodon idella	grass carp	1	2	VRT	7959
 Cucumber mosaic virus	cucumber mosaic cucumovirus	1	0	VRL	12305
 Cucumis melo	muskmelon	1	1	PLN	3656
 Cucumis sativus	cucumber	1	1	PLN	3659
-Cyanidium caldarium		1	1	PLN	2771
-Cyanophora paradoxa		1	1	PLN	2762
-Cydia pomonella granulovirus		1	0	VRL	28289
+Culex pipiens	house mosquito	1	5	INV	7175
+Curculio glandium		1	5	INV	197013
+Cycas rumphii		1	1	PLN	58031
 Cynodon dactylon	Bermuda grass	1	1	PLN	28909
 Cyprinus carpio	common carp	1	2	VRT	7962
+Daktulosphaira vitifoliae	grape phylloxera	1	5	INV	58002
 Danio rerio	zebrafish	1	2	VRT	7955
+Dasypus novemcinctus	nine-banded armadillo	1	2	MAM	9361
 Daucus carota	carrot	1	1	PLN	4039
 Debaryomyces hansenii		1	3	PLN	4959
 Deinococcus radiodurans		11	0	BCT	1299
+Delacroixia coronata		1	4	PLN	34488
 Dendrocopos major		1	2	VRT	137523
 Dengue virus		1	0	VRL	12637
 Descurainia sophia		1	1	PLN	89411
 Desulfitobacterium hafniense		11	0	BCT	49338
-Desulfovibrio vulgaris		11	0	BCT	881
+Desulfovibrio desulfuricans		11	0	BCT	876
 Diadema antillarum		1	9	INV	105358
-Diadema savignyi		1	9	INV	105360
-Diadema setosum		1	9	INV	31175
 Dianthus caryophyllus	clove pink	1	1	PLN	3570
-Dichelobacter nodosus		11	0	BCT	870
+Dicentrarchus labrax	European sea bass	1	2	VRT	13489
 Dictyostelium discoideum		1	1	INV	44689
-Dirofilaria immitis		1	5	INV	6287
+Dirofilaria immitis	dog heartworm nematode	1	5	INV	6287
+Dreissena polymorpha		1	5	INV	45954
 Drosophila americana		1	5	INV	40366
 Drosophila ananassae		1	5	INV	7217
+Drosophila buzzatii		1	5	INV	7264
 Drosophila mauritiana		1	5	INV	7226
 Drosophila melanogaster	fruit fly	1	5	INV	7227
+Drosophila miranda		1	5	INV	7229
 Drosophila persimilis		1	5	INV	7234
 Drosophila pseudoobscura		1	5	INV	7237
 Drosophila simulans		1	5	INV	7240
 Drosophila subobscura		1	5	INV	7241
-Drosophila teissieri		1	5	INV	7243
 Drosophila virilis		1	5	INV	7244
 Drosophila yakuba		1	5	INV	7245
+Dugesia japonica		1	9	INV	6161
 Dunaliella salina		1	1	PLN	3046
-Eastern equine encephalitis virus		1	0	VRL	11021
 Echinococcus granulosus		1	9	INV	6210
 Echinococcus multilocularis		1	9	INV	6211
-Echinometra mathaei		1	9	INV	31178
-Ectocarpus siliculosus virus		1	0	VRL	37665
-Ectromelia virus		1	0	VRL	12643
+Echinostoma paraensei		1	14	INV	48215
 Eimeria tenella		1	4	INV	5802
+Elephas maximus	Asiatic elephant	1	2	MAM	9783
 Emericella nidulans		1	4	PLN	162425
-Encephalitozoon cuniculi		1	1	INV	6035
+Emiliania huxleyi		1	4	PLN	2903
 Entamoeba histolytica		1	1	INV	5759
-Enterobacter aerogenes		11	0	BCT	548
+Entamoeba invadens		1	1	INV	33085
 Enterobacter cloacae		11	0	BCT	550
-Enterobacteria phage M13		11	0	PHG	10870
-Enterobacteria phage Mu		11	0	PHG	10677
-Enterobacteria phage P22		11	0	PHG	10754
-Enterobacteria phage T4		11	0	PHG	10665
 Enterobacteria phage T7		11	0	PHG	10760
 Enterococcus faecalis		11	0	BCT	1351
 Enterococcus faecium		11	0	BCT	1352
-Epiphyas postvittana nucleopolyhedrovirus		1	0	VRL	70600
+Epinephelus quernus	Hawaiian grouper	1	2	VRT	212795
 Equine arteritis virus		1	0	VRL	11047
-Equine herpesvirus 1		1	0	VRL	10326
-Equine herpesvirus 4		1	0	VRL	10331
 Equine infectious anemia virus		1	0	VRL	11665
 Equus caballus	horse	1	2	MAM	9796
 Eremothecium gossypii		1	3	PLN	33169
 Erwinia amylovora		11	0	BCT	552
-Erwinia chrysanthemi		11	0	BCT	556
 Escherichia coli		11	0	BCT	562
-Euglena gracilis		1	4	PLN	3039
+Eschscholzia californica	California poppy	1	1	PLN	3467
+Eucalyptus globulus		1	1	PLN	34317
+Eucalyptus grandis		1	1	PLN	71139
+Eucalyptus tereticornis		1	1	PLN	183855
+Euhadra peliomphala		1	5	INV	87841
 Eulemur fulvus	brown lemur	1	2	PRI	13515
 Euphorbia esula	leafy spurge	1	1	PLN	3993
 Euphorbia lagascae		1	1	PLN	54672
-Feline calicivirus		1	0	VRL	11978
 Feline immunodeficiency virus		1	0	VRL	11673
+Feline leukemia virus		1	0	VRL	11768
 Felis catus	cat	1	2	MAM	9685
 Ferroplasma acidarmanus		11	0	BCT	97393
+Filobasidiella bacillispora		1	4	PLN	37769
 Filobasidiella neoformans		1	4	PLN	5207
 Foot-and-mouth disease virus A		1	0	VRL	12111
 Foot-and-mouth disease virus O		1	0	VRL	12118
-Fowlpox virus		1	0	VRL	10261
 Fragaria x ananassa		1	1	PLN	3747
+Fragilariopsis cylindrus		1	1	PLN	186039
+Francisella tularensis		11	0	BCT	263
 Fucus distichus		1	1	PLN	3012
+Fugu rubripes		1	2	VRT	31033
 Fundulus heteroclitus	killifish	1	2	VRT	8078
 Fusarium oxysporum		1	4	PLN	5507
 Fusarium sporotrichioides		1	4	PLN	5514
+Fusarium subglutinans		1	4	PLN	42677
 Fusobacterium nucleatum		11	0	BCT	851
 Gadus morhua	Atlantic cod	1	2	VRT	8049
-Gallid herpesvirus 1		1	0	VRL	10386
-Gallid herpesvirus 2		1	0	VRL	10390
-Gallid herpesvirus 3		1	0	VRL	35250
 Gallus gallus	chicken	1	2	VRT	9031
 Gasterosteus aculeatus	three spined stickleback	1	2	VRT	69293
+GB virus C/Hepatitis G virus	Hepatitis GB virus C / Hepatitis G virus	1	0	VRL	54290
 Geobacillus stearothermophilus		11	0	BCT	1422
+Geobacter metallireducens		11	0	BCT	28232
 Geochelone nigra		1	2	VRT	66189
 Giardia intestinalis		1	0	INV	5741
+Giardia lamblia		1	0	INV	5741
+Gibberella moniliformis		1	4	PLN	117187
 Gibberella zeae		1	4	PLN	5518
 Gillichthys mirabilis	long-jawed mudsucker	1	2	VRT	8222
 Ginglymostoma cirratum	nurse shark	1	2	VRT	7801
+Ginkgo biloba	maidenhair tree	1	1	PLN	3311
 Globodera pallida		1	5	INV	36090
 Globodera rostochiensis		1	5	INV	31243
 Glomerella cingulata		1	4	PLN	5457
 Glomus intraradices		1	4	PLN	4876
+Glomus versiforme		1	4	PLN	43425
+Glossina morsitans		1	5	INV	7394
 Glycine clandestina		1	1	PLN	45687
 Glycine max	soybean	1	1	PLN	3847
 Glycine tomentella		1	1	PLN	44015
 Glyphorynchus spirurus	wedge-billed woodcreeper	1	2	VRT	135974
+Gnetum gnemon		1	1	PLN	3382
 Gorilla gorilla	gorilla	1	2	PRI	9593
 Gossypium arboreum		1	1	PLN	29729
+Gossypium barbadense	sea-island cotton	1	1	PLN	3634
+Gossypium herbaceum		1	1	PLN	34274
 Gossypium hirsutum	upland cotton	1	1	PLN	3635
+Gossypium raimondii		1	1	PLN	29730
 Gracilaria gracilis		1	4	PLN	2777
+Gregarina niphandrodes		1	4	INV	110365
+Griffithsia japonica		1	1	PLN	83288
 Guillardia theta		1	1	PLN	55529
+Haematobia irritans	horn fly	1	5	INV	7368
 Haemonchus contortus		1	5	INV	6289
 Haemophilus influenzae		11	0	BCT	727
 Haloarcula marismortui		11	0	BCT	2238
-Halobacterium salinarum		11	0	BCT	2242
 Halobacterium sp. NRC-1		11	0	BCT	64091
+Halobaculum gomorrense		11	0	BCT	43928
 Halocynthia roretzi		1	13	INV	7729
-Haloferax volcanii		11	0	BCT	2246
-Hantaan virus		1	0	VRL	11599
+Halorubrum lacusprofundi		11	0	BCT	2247
+Hebeloma cylindrosporum		1	4	PLN	76867
+Hedyotis centranthoides		1	1	PLN	219666
+Hedyotis terminalis		1	1	PLN	219667
 Helianthus annuus	common sunflower	1	1	PLN	4232
+Helianthus argophyllus		1	1	PLN	73275
+Helianthus paradoxus		1	1	PLN	73304
 Helicobacter pylori		11	0	BCT	210
 Heliconius melpomene		1	5	INV	34740
 Helicoverpa armigera	cotton bollworm	1	5	INV	29058
-Helicoverpa armigera nuclear polyhedrosis virus		1	0	VRL	51313
-Helicoverpa zea single nucleocapsid nucleopolyhedrovirus		1	0	VRL	10468
-Heliocoverpa armigera nucleopolyhedrovirus G4		1	0	VRL	148363
-Heliothis zea virus 1		1	0	VRL	29250
+Heliocidaris erythrogramma		1	9	INV	7634
+Hemicentrotus pulcherrimus		1	9	INV	7650
 Hepatitis A virus		1	0	VRL	12092
 Hepatitis B virus		1	0	VRL	10407
 Hepatitis C virus		1	0	VRL	11103
 Hepatitis D virus		1	0	VRL	12475
 Hepatitis E virus		1	0	VRL	12461
-Hepatitis G virus		1	0	VRL	45255
-Hepatitis GB virus C		1	0	VRL	39839
 Heterobasidion annosum		1	4	PLN	13563
 Heterodera glycines		1	5	INV	51029
-Heterodontus francisci	horn shark	1	2	VRT	7792
+Heterodera schachtii		1	5	INV	97005
 Hevea brasiliensis	Para rubber tree	1	1	PLN	3981
-Hirudo medicinalis	medicinal leech	1	5	INV	6421
+Hippoglossus hippoglossus	Atlantic halibut	1	2	VRT	8267
+Histophilus somni		11	0	BCT	731
+Holothuria nobilis		1	9	INV	221420
+Homalodisca coagulata	glassy-winged sharpshooter	1	5	INV	197043
 Homo sapiens	human	1	2	PRI	9606
 Hordeum vulgare		1	1	PLN	4513
 Human adenovirus B		1	0	VRL	108098
 Human adenovirus C		1	0	VRL	129951
-Human adenovirus D		1	0	VRL	130310
 Human astrovirus		1	0	VRL	12702
+Human endogenous retrovirus		1	0	VRL	11827
 Human enterovirus A		1	0	VRL	138948
 Human enterovirus B		1	0	VRL	138949
 Human enterovirus C		1	0	VRL	138950
 Human herpesvirus 1		1	0	VRL	10298
-Human herpesvirus 2		1	0	VRL	10310
 Human herpesvirus 3		1	0	VRL	10335
 Human herpesvirus 4	Epstein-Barr virus	1	0	VRL	10376
 Human herpesvirus 5		1	0	VRL	10359
-Human herpesvirus 6		1	0	VRL	10368
-Human herpesvirus 7		1	0	VRL	10372
 Human herpesvirus 8	Kaposi's sarcoma-associated herpesvirus - Human herpesvirus 8	1	0	VRL	37296
 Human immunodeficiency virus		1	0	VRL	12721
 Human immunodeficiency virus 1		1	0	VRL	11676
@@ -344,77 +377,85 @@ Human immunodeficiency virus 2		1	0	VRL	11709
 Human papillomavirus		1	0	VRL	10566
 Human papillomavirus type 16		1	0	VRL	10581
 Human respiratory syncytial virus		1	0	VRL	11250
-Hydra vulgaris		1	4	INV	6087
+Hydra magnipapillata		1	4	INV	6085
 Hylobates lar	common gibbon	1	2	PRI	9580
 Hypocrea jecorina		1	4	PLN	51453
+Hypocrea lixii		1	4	PLN	5544
+Hypsibius dujardini		1	5	INV	232323
 Ichthyophthirius multifiliis		6	4	INV	5932
-Ictalurid herpesvirus 1		1	0	VRL	10401
 Ictalurus furcatus		1	2	VRT	66913
 Ictalurus punctatus	channel catfish	1	2	VRT	7998
 Infectious bursal disease virus	Gumboro virus	1	0	VRL	10995
-Influenza A virus H3N2		1	0	VRL	41857
-Invertebrate iridescent virus 6		1	0	VRL	176652
+Infectious salmon anemia virus		1	0	VRL	55987
 Ipomoea batatas	sweet potato	1	1	PLN	4120
+Ipomoea nil	Japanese morning glory	1	1	PLN	35883
+Ipomoea trifida		1	1	PLN	35884
+Ips pini	North American pine engraver	1	5	INV	102803
+Iris hollandica		1	1	PLN	35876
+Isotricha sp. BBF-2003		1	4	INV	223153
 Ixodes scapularis	black-legged tick	1	5	INV	6945
 Japanese encephalitis virus		1	0	VRL	11072
 JC virus		1	0	VRL	10632
-Klebsiella aerogenes		11	0	BCT	28451
+Juglans regia	English walnut	1	1	PLN	51240
+Kandelia candel		1	1	PLN	61147
 Klebsiella oxytoca		11	0	BCT	571
 Klebsiella pneumoniae		11	0	BCT	573
+Kluyveromyces delphensis		1	3	PLN	51657
 Kluyveromyces lactis		1	3	PLN	28985
 Kluyveromyces marxianus		1	3	PLN	4911
 Kluyveromyces thermotolerans		1	3	PLN	4916
 Laccaria bicolor		1	4	PLN	29883
-Lactobacillus casei		11	0	BCT	1582
+Lactobacillus brevis		11	0	BCT	1580
 Lactobacillus delbrueckii		11	0	BCT	1584
-Lactobacillus helveticus		11	0	BCT	1587
 Lactobacillus plantarum		11	0	BCT	1590
-Lactobacillus sakei		11	0	BCT	1599
 Lactococcus lactis		11	0	BCT	1358
 Lactuca sativa		1	1	PLN	4236
+Lactuca serriola		1	1	PLN	75943
 Lama glama	llama	1	2	MAM	9844
 Laminaria digitata		1	1	PLN	80365
+Lawsonia intracellularis		11	0	BCT	29546
 Legionella pneumophila		11	0	BCT	446
+Leifsonia xyli		11	0	BCT	1575
+Leishmania braziliensis		1	4	INV	5660
 Leishmania donovani		1	4	INV	5661
 Leishmania infantum		1	4	INV	5671
 Leishmania major		1	4	INV	5664
-Leishmania mexicana		1	4	INV	5665
-Leishmania tarentolae		1	4	INV	5689
+Lemur catta	ring-tailed lemur	1	2	PRI	9447
 Leopardus pardalis	ocelot	1	2	MAM	32538
 Lepilemur septentrionalis	northern sportive lemur	1	2	PRI	78584
 Leptospira interrogans		11	0	BCT	173
 Leuconostoc mesenteroides		11	0	BCT	1245
-Limnodynastes tasmaniensis		1	2	VRT	105385
+Leymus chinensis		1	1	PLN	52714
+Limnanthes alba	white meadowfoam	1	1	PLN	42439
+Lingulodinium polyedrum		1	4	PLN	160621
+Linum usitatissimum	flax	1	1	PLN	4006
 Listeria innocua		11	0	BCT	1642
 Listeria monocytogenes		11	0	BCT	1639
+Litomosoides sigmodontis		1	5	INV	42156
 Litopenaeus setiferus	white shrimp	1	5	INV	64468
 Litopenaeus vannamei	Pacific white shrimp	1	5	INV	6689
-Locusta migratoria	migratory locust	1	5	INV	7004
-Lotus japonicus		1	1	PLN	34305
+Littorina littorea		1	5	INV	31216
+Lotus corniculatus		1	1	PLN	47247
 Loxodonta africana	African savanna elephant	1	2	MAM	9785
-Luciola cruciata	Japanese firefly	1	5	INV	7051
 Lumbricus rubellus	humus earthworm	1	5	INV	35632
-Lumpy skin disease virus		1	0	VRL	59509
+Lupinus albus	white lupine	1	1	PLN	3870
 Lupinus luteus	yellow lupine	1	1	PLN	3873
+Luscinia svecica		1	2	VRT	52792
 Lutzomyia longipalpis		1	5	INV	7200
 Lycopersicon esculentum	tomato	1	1	PLN	4081
 Lycopersicon hirsutum		1	1	PLN	62890
 Lycopersicon pennellii		1	1	PLN	28526
-Lymantria dispar nucleopolyhedrovirus		1	0	VRL	10449
-Lymnaea stagnalis	great pond snail	1	5	INV	6523
 Macaca fascicularis	crab-eating macaque	1	2	PRI	9541
+Macaca fuscata	Japanese macaque	1	2	PRI	9542
 Macaca mulatta	rhesus monkey	1	2	PRI	9544
 Macaca nemestrina	pig-tailed macaque	1	2	PRI	9545
+Macropus eugenii	tammar wallaby	1	2	MAM	9315
 Magnaporthe grisea		1	4	PLN	148305
 Magnetococcus sp. MC-1		11	0	BCT	156889
 Magnetospirillum magnetotacticum		11	0	BCT	188
-Maize streak virus		1	0	VRL	10821
 Malus x domestica	apple tree	1	1	PLN	3750
-Mamestra configurata nucleopolyhedrovirus		1	0	VRL	191492
-Mamestra configurata nucleopolyhedrovirus B		1	0	VRL	204440
 Manduca sexta	tobacco hornworm	1	5	INV	7130
 Manihot esculenta	cassava	1	1	PLN	3983
-Mannheimia haemolytica		11	0	BCT	75985
 Marchantia polymorpha	liverwort	1	1	PLN	3197
 Marmota monax	woodchuck	1	2	ROD	9995
 Marsupenaeus japonicus		1	5	INV	27405
@@ -423,137 +464,144 @@ Mastigamoeba balamuthi		1	1	INV	108607
 Measles virus		1	0	VRL	11234
 Medicago sativa		1	1	PLN	3879
 Medicago truncatula	barrel medic	1	1	PLN	3880
+Meladema coriacea		1	5	INV	107907
 Melaleuca alternifolia	tea tree	1	1	PLN	164405
-Melanoplus sanguinipes entomopoxvirus		1	0	VRL	83191
-Meleagrid herpesvirus 1	herpesvirus of turkeys	1	0	VRL	37108
 Meleagris gallopavo	turkey	1	2	VRT	9103
 Meloidogyne arenaria		1	5	INV	6304
+Meloidogyne chitwoodi		1	5	INV	59747
 Meloidogyne hapla		1	5	INV	6305
 Meloidogyne incognita	southern root-knot nematode	1	5	INV	6306
 Meloidogyne javanica	root-knot nematode	1	5	INV	6303
+Meloidogyne paranaensis		1	5	INV	189293
 Mentha x piperita	peppermint	1	1	PLN	34256
+Meriones unguiculatus	Mongolian gerbil	1	2	ROD	10047
 Mesembryanthemum crystallinum	common iceplant	1	1	PLN	3544
+Mesobuthus gibbosus		1	5	INV	123226
 Mesocricetus auratus	golden hamster	1	2	ROD	10036
-Mesorhizobium loti		11	0	BCT	381
-Mesostigma viride		1	1	PLN	41882
 Metarhizium anisopliae		1	4	PLN	5530
-Methanocaldococcus jannaschii		11	0	BCT	2190
-Methanopyrus kandleri		11	0	BCT	2320
 Methanosarcina acetivorans		11	0	BCT	2214
 Methanosarcina barkeri		11	0	BCT	2208
 Methanosarcina mazei		11	0	BCT	2209
 Methanothermobacter thermautotrophicus		11	0	BCT	145262
-Methylobacterium extorquens		11	0	BCT	408
 Microbotryum violaceum		1	4	PLN	5272
 Microbulbifer degradans		11	0	BCT	86304
 Microcystis aeruginosa		11	0	BCT	1126
-Molluscum contagiosum virus		1	0	VRL	10279
-Monkeypox virus		1	0	VRL	10244
-Monodelphis domestica	South American short-tailed grey opossum	1	2	MAM	13616
+Micromonospora carbonacea		11	0	BCT	47853
+Microtus oeconomus	tundra vole	1	2	ROD	64717
+Mnemiopsis leidyi		1	4	INV	27923
+Molgula tectiformis		1	13	INV	30286
+Moneuplotes crassus		10	4	INV	5936
+Monodelphis domestica	gray short-tailed opossum	1	2	MAM	13616
 Moraxella catarrhalis		11	0	BCT	480
-Mouse cytomegalovirus 1		1	0	VRL	10366
+Morone saxatilis	striped sea-bass	1	2	VRT	34816
+Motacilla flava		1	2	VRT	180448
 Mumps virus		1	0	VRL	11161
-Murid herpesvirus 4		1	0	VRL	33708
-Murine hepatitis virus		1	0	VRL	11138
 Murine leukemia virus		1	0	VRL	11786
 Mus musculus	house mouse	1	2	ROD	10090
 Mus spretus	western wild mouse	1	2	ROD	10096
 Musa acuminata		1	1	PLN	4641
 Musca domestica	house fly	1	5	INV	7370
-Mycobacteriophage D29		11	0	PHG	28369
 Mycobacterium avium		11	0	BCT	1764
 Mycobacterium bovis		11	0	BCT	1765
 Mycobacterium leprae		11	0	BCT	1769
-Mycobacterium phage L5		11	0	PHG	31757
 Mycobacterium smegmatis		11	0	BCT	1772
 Mycobacterium tuberculosis		11	0	BCT	1773
 Mycoplasma capricolum		4	0	BCT	2095
-Mycoplasma gallisepticum		4	0	BCT	2096
 Mycoplasma genitalium		4	0	BCT	2097
+Mycoplasma haemofelis		4	0	BCT	29501
 Mycoplasma hominis		4	0	BCT	2098
-Mycoplasma pneumoniae		4	0	BCT	2104
-Mycoplasma pulmonis		4	0	BCT	2107
 Mycosphaerella graminicola		1	4	PLN	54734
+Mystacina tuberculata	New Zealand lesser short-tailed bat	1	2	MAM	94961
 Mytilus edulis		1	5	INV	6550
 Mytilus galloprovincialis	Mediterranean mussel	1	5	INV	29158
+Mytilus trossulus	common blue mussel	1	5	INV	6551
 Myxococcus xanthus		11	0	BCT	34
-Myxoma virus		1	0	VRL	10273
+Natrialba asiatica		11	0	BCT	64602
 Necator americanus		1	5	INV	51031
 Nectria haematococca		1	4	PLN	140110
 Neisseria gonorrhoeae		11	0	BCT	485
 Neisseria meningitidis		11	0	BCT	487
 Neospora caninum		1	4	INV	29176
-Nephroselmis olivacea		1	1	PLN	31312
+Neospora hughesi		1	4	INV	83675
 Neurospora crassa		1	4	PLN	5141
 Newcastle disease virus		1	0	VRL	11176
-Nicotiana plumbaginifolia	curled-leaved tobacco	1	1	PLN	4092
+Nicotiana attenuata		1	1	PLN	49451
+Nicotiana benthamiana		1	1	PLN	4100
 Nicotiana sylvestris	wood tobacco	1	1	PLN	4096
 Nicotiana tabacum	common tobacco	1	1	PLN	4097
 Nippostrongylus brasiliensis		1	5	INV	27835
-Nitrosomonas europaea		11	0	BCT	915
 Norwalk virus		1	0	VRL	11983
 Nostoc punctiforme		11	0	BCT	63737
-Nostoc sp. PCC 7120		11	0	BCT	103690
 Novosphingobium aromaticivorans		11	0	BCT	48935
-Oceanobacillus iheyensis		11	0	BCT	182710
-Odontella sinensis		1	1	PLN	2839
+Nuphar advena		1	1	PLN	77108
+Ochrobactrum anthropi		11	0	BCT	529
+Ocinebrellus inornatus	Asian drill	1	5	INV	213425
 Oenococcus oeni		11	0	BCT	1247
-Oenothera elata		1	1	PLN	44456
 Oikopleura dioica		1	5	INV	34765
+Olea europaea	common olive	1	1	PLN	4146
 Onchocerca volvulus		1	5	INV	6282
-Oncomelania hupensis		1	5	INV	56141
 Oncorhynchus keta	chum salmon	1	2	VRT	8018
-Oncorhynchus kisutch	coho salmon	1	2	VRT	8019
 Oncorhynchus mykiss	rainbow trout	1	2	VRT	8022
+Oncorhynchus nerka	sockeye salmon	1	2	VRT	8023
 Oncorhynchus tshawytscha	Chinook salmon	1	2	VRT	74940
+Opsanus beta		1	2	VRT	95145
 Oreochromis niloticus	Nile tilapia	1	2	VRT	8128
-Orgyia pseudotsugata single capsid nuclear polyhedrosis virus		1	0	VRL	10450
+Ornithodoros porcinus		1	5	INV	34594
 Ornithorhynchus anatinus	platypus	1	2	MAM	9258
 Oryctolagus cuniculus	rabbit	1	2	MAM	9986
+Oryza minuta		1	1	PLN	63629
 Oryza sativa		1	1	PLN	4530
 Oryzias latipes	Japanese medaka	1	2	VRT	8090
 Ostertagia ostertagi		1	5	INV	6317
 Ostreococcus tauri		1	1	PLN	70448
+Otis tarda		1	2	VRT	73107
 Ovis aries	sheep	1	2	MAM	9940
+Oxytricha trifallax		6	4	INV	94289
+Pacifastacus leniusculus	signal crayfish	1	5	INV	6720
 Pan paniscus	pygmy chimpanzee	1	2	PRI	9597
 Pan troglodytes	chimpanzee	1	2	PRI	9598
+Panax ginseng		1	1	PLN	4054
 Pantoea agglomerans		11	0	BCT	549
 Papio anubis	olive baboon	1	2	PRI	9555
-Papio cynocephalus	yellow baboon	1	2	PRI	9556
 Papio hamadryas	hamadryas baboon	1	2	PRI	9557
-Paracoccus denitrificans		11	0	BCT	266
+Paracoccidioides brasiliensis		1	4	PLN	121759
 Paralichthys olivaceus	bastard halibut	1	2	VRT	8255
-Paramecium bursaria Chlorella virus 1		1	0	VRL	10506
 Paramecium tetraurelia		6	4	INV	5888
 Parastrongyloides trichosuri		1	5	INV	131310
+Parus major		1	2	VRT	9157
 Pasteurella multocida		11	0	BCT	747
+Pasteuria penetrans		11	0	BCT	86005
+Paxillus involutus		1	4	PLN	71150
+Pectobacterium atrosepticum		11	0	BCT	29471
 Pectobacterium carotovorum		11	0	BCT	554
+Pediculus humanus	human lice	1	5	INV	121225
 Penaeus monodon	black tiger shrimp	1	5	INV	6687
 Penicillium marneffei		1	4	PLN	37727
+Pennisetum ciliare	buffelgrass	1	1	PLN	35520
+Pennisetum glaucum		1	1	PLN	4543
+Peromyscus leucopus	white-footed mouse	1	2	ROD	10041
 Peromyscus maniculatus	deer mouse	1	2	ROD	10042
 Pestivirus type 1		1	0	VRL	11099
 Pestivirus type 2		1	0	VRL	54314
 Petromyzon marinus	sea lamprey	1	2	VRT	7757
-Petroselinum crispum	parsley	1	1	PLN	4043
 Petunia x hybrida		1	1	PLN	4102
 Phaeodactylum tricornutum		1	1	PLN	2850
 Phanerochaete chrysosporium		1	4	PLN	5306
+Phaseolus coccineus		1	1	PLN	3886
 Phaseolus vulgaris		1	1	PLN	3885
+Phoca vitulina	harbor seal	1	2	MAM	9720
 Photorhabdus luminescens		11	0	BCT	29488
-Phylloscopus trochiloides		1	2	VRT	48154
-Physarum polycephalum	slime mold	1	1	INV	5791
 Physcomitrella patens		1	1	PLN	3218
-Physeter catodon	sperm whale	1	2	MAM	9755
 Phytophthora infestans	potato late blight agent	1	1	PLN	4787
+Phytophthora nicotianae		1	1	PLN	4790
 Phytophthora sojae		1	1	PLN	67593
 Picea abies	Norway spruce	1	1	PLN	3329
 Pichia angusta		1	3	PLN	4905
 Pichia farinosa		1	3	PLN	4920
 Pinus pinaster		1	1	PLN	71647
-Pinus sylvestris	Scots pine	1	1	PLN	3349
-Pinus sylvestris/Heterobasidion annosum		1	1	INV	169015
+Pinus radiata	Monterey pine	1	1	PLN	3347
 Pinus taeda	loblolly pine	1	1	PLN	3352
-Pinus thunbergii	Japanese black pine	1	1	PLN	3350
+Pisolithus microcarpus		1	4	PLN	178872
 Pisolithus tinctorius		1	4	PLN	37468
 Pisum sativum	pea	1	1	PLN	3888
 Planococcus lilacinus	lilac mealybug	1	5	INV	40930
@@ -563,17 +611,26 @@ Plasmodium falciparum	malaria parasite P. falciparum	1	4	INV	5833
 Plasmodium vivax	malaria parasite P. vivax	1	4	INV	5855
 Plasmodium yoelii		1	4	INV	5861
 Platichthys flesus	European flounder	1	2	VRT	8260
+Platystomus albinus		1	5	INV	197009
+Plethodon elongatus	Del Norte salamander	1	2	VRT	46761
+Pleuronectes platessa	plaice	1	2	VRT	8262
 Pleurotus ostreatus	oyster mushroom	1	4	PLN	5322
+Plumbago zeylanica		1	1	PLN	76149
 Pneumocystis carinii		1	4	PLN	4754
-Podospora anserina		1	4	PLN	5145
+Podarcis hispanica		1	2	VRT	74081
+Poecilia reticulata	guppy	1	2	VRT	8081
 Poliovirus		1	0	VRL	138953
 Polyandrocarpa misakiensis		1	13	INV	7723
+Poncirus trifoliata		1	1	PLN	37690
 Pongo pygmaeus	orangutan	1	2	PRI	9600
+Populus alba x Populus glandulosa		1	1	PLN	153471
+Populus alba x Populus tremula		1	1	PLN	80863
 Populus balsamifera		1	1	PLN	73824
+Populus balsamifera subsp. trichocarpa x Populus deltoides		1	1	PLN	3695
+Populus tremula		1	1	PLN	113636
 Populus tremula x Populus tremuloides		1	1	PLN	47664
-Porcine circovirus		1	0	VRL	46221
+Populus tremuloides	quaking aspen	1	1	PLN	3693
 Porcine reproductive and respiratory syndrome virus		1	0	VRL	28344
-Porphyra purpurea		1	4	PLN	2787
 Porphyra yezoensis		1	4	PLN	2788
 Porphyromonas gingivalis		11	0	BCT	837
 Potato virus Y		1	0	VRL	12216
@@ -581,79 +638,75 @@ Pratylenchus penetrans		1	5	INV	45929
 Primate T-lymphotropic virus 1		1	0	VRL	194440
 Primate T-lymphotropic virus 2		1	0	VRL	194441
 Pristionchus pacificus		1	5	INV	54126
-Prochlorococcus marinus		11	0	BCT	1219
-Proteus mirabilis		11	0	BCT	584
-Proteus vulgaris		11	0	BCT	585
+Prunus armeniaca	apricot	1	1	PLN	36596
 Prunus dulcis	almond	1	1	PLN	3755
 Prunus persica	peach	1	1	PLN	3760
 Pseudomonas aeruginosa		11	0	BCT	287
 Pseudomonas fluorescens		11	0	BCT	294
-Pseudomonas phage phiKZ		11	0	PHG	169683
 Pseudomonas putida		11	0	BCT	303
 Pseudomonas stutzeri		11	0	BCT	316
 Pseudomonas syringae		11	0	BCT	317
 Pseudopleuronectes americanus	winter flounder	1	2	VRT	8265
-Pseudorabies virus		1	0	VRL	10345
 Pseudotsuga menziesii	Douglas fir	1	1	PLN	3357
-Psilotum nudum		1	1	PLN	3240
+Psoroptes equi var. ovis	sheep scab mite	1	5	INV	83912
 Psoroptes ovis	sheep scab mite	1	5	INV	83912
-Puumala virus		1	0	VRL	11604
 Pygoscelis adeliae	Adelie penguin	1	2	VRT	9238
+Pyricularia grisea		1	4	PLN	148305
 Pyrobaculum aerophilum		11	0	BCT	13773
-Pyrococcus abyssi		11	0	BCT	29292
 Pyrococcus furiosus		11	0	BCT	2261
-Pyrococcus horikoshii		11	0	BCT	53953
 Pyrocoelia rufa		1	5	INV	71223
+Pyrocystis lunula		1	4	PLN	2972
 Pyrus communis	pear	1	1	PLN	23211
-Rabbit fibroma virus		1	0	VRL	10271
 Rabies virus		1	0	VRL	11292
-Raja erinacea	little skate	1	2	VRT	7782
-Ralstonia eutropha		11	0	BCT	510
 Ralstonia metallidurans		11	0	BCT	119219
 Ralstonia solanacearum		11	0	BCT	305
 Rana catesbeiana	bullfrog	1	2	VRT	8400
+Rangifer tarandus	reindeer	1	2	MAM	9870
 Raphanus sativus	radish	1	1	PLN	3726
-Rat cytomegalovirus		1	0	VRL	28304
 Rattus norvegicus	Norway rat	1	2	ROD	10116
+Rattus rattus	black rat	1	2	ROD	10117
 Respiratory syncytial virus		1	0	VRL	12814
 Rhagoletis pomonella	apple maggot	1	5	INV	28610
+Rhinolophus ferrumequinum	greater horseshoe bat	1	2	MAM	59479
 Rhizobium etli		11	0	BCT	29449
 Rhizobium leguminosarum		11	0	BCT	384
-Rhizobium rhizogenes		11	0	BCT	359
+Rhizobium meliloti		11	0	BCT	382
+Rhizobium radiobacter		11	0	BCT	358
 Rhizobium sp. NGR234		11	0	BCT	394
-Rhodobacter capsulatus		11	0	BCT	1061
+Rhizoctonia solani		1	4	PLN	107832
 Rhodobacter sphaeroides		11	0	BCT	1063
 Rhodococcus erythropolis		11	0	BCT	1833
 Rhodospirillum rubrum		11	0	BCT	1085
+Rhopalosiphum padi	bird cherry-oat aphid	1	5	INV	40932
 Ricinus communis	castor bean	1	1	PLN	3988
-Rickettsia conorii		11	0	BCT	781
 Rickettsia prowazekii		11	0	BCT	782
 Robinia pseudoacacia		1	1	PLN	35938
+Rosa chinensis		1	1	PLN	74649
 Rosa hybrid cultivar		1	1	PLN	128735
 Rotavirus A		1	0	VRL	28875
-Rotavirus C		1	0	VRL	36427
 Rous sarcoma virus		1	0	VRL	11886
 Rubella virus		1	0	VRL	11041
+Ruminococcus flavefaciens		11	0	BCT	1265
 Saccharomyces bayanus		1	3	PLN	4931
 Saccharomyces cariocanus		1	3	PLN	114526
 Saccharomyces castellii		1	3	PLN	27288
 Saccharomyces cerevisiae	baker's yeast	1	3	PLN	4932
 Saccharomyces exiguus		1	3	PLN	34358
 Saccharomyces kluyveri		1	3	PLN	4934
+Saccharomyces kudriavzevii		1	3	PLN	114524
 Saccharomyces mikatae		1	3	PLN	114525
 Saccharomyces paradoxus		1	3	PLN	27291
 Saccharomyces servazzii		1	3	PLN	27293
 Saccharomyces unisporus		1	3	PLN	27294
-Saccharopolyspora erythraea		11	0	BCT	1836
+Saccharum officinarum		1	1	PLN	4547
 Saguinus oedipus	cotton-top tamarin	1	2	PRI	9490
 Saimiri sciureus	common squirrel monkey	1	2	PRI	9521
-Saimiriine herpesvirus 2		1	0	VRL	10381
+Salix viminalis	osier	1	1	PLN	40686
 Salmo salar	Atlantic salmon	1	2	VRT	8030
 Salmo trutta	brown trout	1	2	VRT	8032
 Salmonella enterica		11	0	BCT	28901
-Salmonella enteritidis		11	0	BCT	592
-Salmonella typhi		11	0	BCT	601
 Salmonella typhimurium		11	0	BCT	602
+Salvelinus alpinus	Arctic char	1	2	VRT	8036
 Sarcocystis neurona		1	4	INV	42890
 Sarcoptes scabiei		1	5	INV	52283
 Scherffelia dubia		1	1	PLN	3190
@@ -662,16 +715,18 @@ Schistosoma mansoni		1	9	INV	6183
 Schizophyllum commune		1	4	PLN	5334
 Schizosaccharomyces pombe	fission yeast	1	4	PLN	4896
 Schmidtea mediterranea		1	9	INV	79327
+Sciaenops ocellatus		1	2	VRT	76340
 Sclerotinia sclerotiorum		1	4	PLN	5180
+Sebastes mystinus		1	2	VRT	72088
 Secale cereale	rye	1	1	PLN	4550
 Selaginella lepidophylla		1	1	PLN	59777
 SEN virus		1	0	VRL	136966
 Seriola quinqueradiata	five-ray yellowtail	1	2	VRT	8161
 Serratia marcescens		11	0	BCT	615
-Shigella boydii		11	0	BCT	621
-Shigella dysenteriae		11	0	BCT	622
+Sesamum indicum	sesame	1	1	PLN	4182
+Sesbania rostrata		1	1	PLN	3895
+Shewanella oneidensis		11	0	BCT	70863
 Shigella flexneri		11	0	BCT	623
-Shigella sonnei		11	0	BCT	624
 Shrimp white spot syndrome virus		1	0	VRL	92652
 Silene latifolia		1	1	PLN	37657
 Silurana tropicalis	western clawed frog	1	2	VRT	8364
@@ -684,117 +739,119 @@ Solanum tuberosum	potato	1	1	PLN	4113
 Sorghum bicolor	sorghum	1	1	PLN	4558
 Sorghum halepense		1	1	PLN	4560
 Sorghum propinquum		1	1	PLN	132711
+Sparus aurata	gilthead seabream	1	2	VRT	8175
+Sphingomonas aromaticivorans		11	0	BCT	48935
 Spinacia oleracea	spinach	1	1	PLN	3562
 Spiroplasma kunkelii		4	0	BCT	47834
-Spodoptera exigua nucleopolyhedrovirus		1	0	VRL	10454
-Spodoptera litura nucleopolyhedrovirus		1	0	VRL	46242
+Sporotrichum pruinosum		1	4	PLN	5306
 Staphylococcus aureus		11	0	BCT	1280
 Staphylococcus epidermidis		11	0	BCT	1282
 Stealth virus 1		1	0	VRL	36452
+Sterkiella histriomuscorum		6	4	INV	94289
 Stevia rebaudiana		1	1	PLN	55670
 Streptococcus agalactiae		11	0	BCT	1311
 Streptococcus dysgalactiae		11	0	BCT	1334
-Streptococcus gordonii		11	0	BCT	1302
+Streptococcus equi		11	0	BCT	1336
 Streptococcus mitis		11	0	BCT	28037
 Streptococcus mutans		11	0	BCT	1309
 Streptococcus oralis		11	0	BCT	1303
 Streptococcus pneumoniae		11	0	BCT	1313
 Streptococcus pyogenes		11	0	BCT	1314
-Streptococcus salivarius		11	0	BCT	1304
 Streptococcus suis		11	0	BCT	1307
 Streptococcus thermophilus		11	0	BCT	1308
-Streptomyces avermitilis		11	0	BCT	33903
-Streptomyces avidinii		11	0	BCT	1895
-Streptomyces clavuligerus		11	0	BCT	1901
 Streptomyces coelicolor		11	0	BCT	1902
-Streptomyces griseus		11	0	BCT	1911
 Streptomyces lividans		11	0	BCT	1916
 Strongylocentrotus purpuratus		1	9	INV	7668
 Strongyloides ratti		1	5	INV	34506
 Strongyloides stercoralis		1	5	INV	6248
 Struthio camelus	ostrich	1	2	VRT	8801
-Stx2 converting bacteriophage I		11	0	PHG	180816
 Suaeda maritima		1	1	PLN	126913
-Sulfolobus acidocaldarius		11	0	BCT	2285
+Suid herpesvirus 1		1	0	VRL	10345
 Sulfolobus solfataricus		11	0	BCT	2287
-Sulfolobus tokodaii		11	0	BCT	111955
 Sus scrofa	pig	1	2	MAM	9823
-Swinepox virus		1	0	VRL	10276
+Symsagittifera roscofensis		1	5	INV	84072
 Syncerus caffer	African buffalo	1	2	MAM	9970
-Synechococcus sp. PCC 7002		11	0	BCT	32049
-Synechococcus sp. PCC 7942		11	0	BCT	1140
-Synechocystis sp. PCC 6803		11	0	BCT	1148
+Tadarida brasiliensis	Brazilian free-tailed bat	1	2	MAM	9438
 Taenia solium	pork tapeworm	1	9	INV	6204
 Takifugu rubripes		1	2	VRT	31033
+Tamarix androssowii		1	1	PLN	189785
+Tamias amoenus	yellow-pine chipmunk	1	2	ROD	64679
 Tamias ruficaudus	red-tailed chipmunk	1	2	ROD	123792
 Teladorsagia circumcincta		1	5	INV	45464
-Tetrahymena pyriformis		6	4	INV	5908
+Telestes souffia		1	2	VRT	129883
 Tetrahymena thermophila		6	4	INV	5911
 Tetraodon nigroviridis		1	2	VRT	99883
-Theileria annulata		1	4	INV	5874
+Thanatephorus cucumeris		1	4	PLN	107832
+Theileria parva		1	4	INV	5875
 Thellungiella halophila		1	1	PLN	98038
-Thellungiella salsuginea		1	1	PLN	72664
+Theobroma cacao	cacao	1	1	PLN	3641
 Thermoanaerobacter tengcongensis		11	0	BCT	119072
-Thermoplasma acidophilum		11	0	BCT	2303
-Thermoplasma volcanium		11	0	BCT	50339
-Thermosynechococcus elongatus		11	0	BCT	146786
 Thermotoga maritima		11	0	BCT	2336
 Thermotoga sp. RQ2		11	0	BCT	126740
-Thermus aquaticus		11	0	BCT	271
 Thermus thermophilus		11	0	BCT	274
-Tigriopus californicus		1	5	INV	6832
-Tobacco mosaic virus		1	0	VRL	12242
+Timarcha balearica		1	5	INV	79517
 Toxocara canis		1	5	INV	6265
 Toxoplasma gondii		1	4	INV	5811
+Toxoptera citricida	brown citrus aphid	1	5	INV	223852
 Toxostoma curvirostre		1	2	VRT	99878
-Transmissible gastroenteritis virus		1	0	VRL	11149
 Treponema pallidum		11	0	BCT	160
 Tribolium castaneum	red flour beetle	1	5	INV	7070
 Trichinella spiralis		1	5	INV	6334
 Trichoderma harzianum		1	4	PLN	5544
+Trichoderma reesei		1	4	PLN	51453
 Trichodesmium erythraeum		11	0	BCT	1206
 Trichomonas vaginalis		1	0	INV	5722
+Trichoplusia ni	cabbage looper	1	5	INV	7111
+Trichostrongylus vitrinus		1	5	INV	40352
+Trichosurus vulpecula	silver-gray brushtail possum	1	2	MAM	9337
 Trichuris muris		1	5	INV	70415
+Trichuris vulpis		1	5	INV	219738
+Trifolium repens	white clover	1	1	PLN	3899
 Triphysaria versicolor		1	1	PLN	64093
 Triticum aestivum	bread wheat	1	1	PLN	4565
 Triticum monococcum		1	1	PLN	4568
 Triticum turgidum		1	1	PLN	4571
+Tropheus moorii	blunthead cichlid	1	2	VRT	8150
 Trypanosoma brucei		1	4	INV	5691
+Trypanosoma carassii		1	4	INV	38249
 Trypanosoma cruzi		1	4	INV	5693
 TT virus		1	0	VRL	68887
-Tupaia herpesvirus		1	0	VRL	10397
+TTV-like mini virus		1	0	VRL	93678
+Tuber borchii	whitish truffle	1	4	PLN	42251
 Turkey rhinotracheitis virus		1	0	VRL	11264
 Turnip mosaic virus		1	0	VRL	12230
 Ureaplasma urealyticum		4	0	BCT	2130
 Ursus arctos	brown bear	1	2	MAM	9644
 Ustilago maydis		1	4	PLN	5270
 Vaccinia virus		1	0	VRL	10245
-Variola virus		1	0	VRL	10255
-Venezuelan equine encephalitis virus		1	0	VRL	11036
+Vaccinium corymbosum		1	1	PLN	69266
+Verticillium dahliae		1	4	PLN	27337
 Vesicular stomatitis virus		1	0	VRL	11276
 Vibrio cholerae		11	0	BCT	666
-Vibrio harveyi		11	0	BCT	669
 Vibrio parahaemolyticus		11	0	BCT	670
 Vibrio vulnificus		11	0	BCT	672
 Vicia faba	fava bean	1	1	PLN	3906
 Vigna radiata		1	1	PLN	157791
 Vigna unguiculata	cowpea	1	1	PLN	3917
+Vitis aestivalis		1	1	PLN	3605
+Vitis hybrid cultivar		1	1	PLN	241073
+Vitis riparia		1	1	PLN	96939
+Vitis shuttleworthii		1	1	PLN	246827
 Vitis vinifera		1	1	PLN	29760
-Volvox carteri		1	1	PLN	3067
 West Nile virus		1	0	VRL	11082
+Wuchereria bancrofti		1	5	INV	6293
 Xanthomonas axonopodis		11	0	BCT	53413
 Xanthomonas campestris		11	0	BCT	339
 Xenopus laevis	African clawed frog	1	2	VRT	8355
-Xestia c-nigrum granulovirus		1	0	VRL	51677
+Xenopus tropicalis	western clawed frog	1	2	VRT	8364
 Xiphias gladius	swordfish	1	2	VRT	8245
 Xylella fastidiosa		11	0	BCT	2371
-Yaba-like disease virus		1	0	VRL	132475
 Yarrowia lipolytica		1	3	PLN	4952
 Yersinia enterocolitica		11	0	BCT	630
 Yersinia pestis		11	0	BCT	632
-Yersinia pseudotuberculosis		11	0	BCT	633
+Zamia furfuracea		1	1	PLN	42329
 Zea mays		1	1	PLN	4577
 Zeldia punctata		1	5	INV	49351
+Zinnia elegans		1	1	PLN	34245
 Zucchini yellow mosaic virus		1	0	VRL	12232
 Zygosaccharomyces rouxii		1	3	PLN	4956
-Zymomonas mobilis		11	0	BCT	542
diff --git a/demo/blast_driver.c b/demo/blast_driver.c
index 8249d58f..65befc58 100644
--- a/demo/blast_driver.c
+++ b/demo/blast_driver.c
@@ -1,4 +1,4 @@
-/* $Id: blast.c,v 1.9 2003/10/23 20:15:37 dondosha Exp $
+/* $Id: blast_driver.c,v 1.16 2004/01/07 14:40:20 papadopo Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,10 +32,10 @@ Author: Ilya Dondoshansky
 Contents: Main function for running BLAST
 
 ******************************************************************************
- * $Revision: 1.9 $
+ * $Revision: 1.16 $
  * */
 
-static char const rcsid[] = "$Id: blast.c,v 1.9 2003/10/23 20:15:37 dondosha Exp $";
+static char const rcsid[] = "$Id: blast_driver.c,v 1.16 2004/01/07 14:40:20 papadopo Exp $";
 
 #include <ncbi.h>
 #include <sqnutils.h>
@@ -45,9 +45,9 @@ static char const rcsid[] = "$Id: blast.c,v 1.9 2003/10/23 20:15:37 dondosha Exp
 #include <algo/blast/core/blast_message.h>
 #include <algo/blast/core/blast_util.h>
 #include <algo/blast/core/blast_engine.h>
-#include "blast_seqalign.h"
-#include "blast_format.h"
-#include "seqsrc_readdb.h"
+#include <algo/blast/api/blast_seqalign.h>
+#include <algo/blast/api/blast_format.h>
+#include <algo/blast/api/seqsrc_readdb.h>
 
 #define NUMARG (sizeof(myargs)/sizeof(myargs[0]))
 
@@ -147,8 +147,9 @@ static Args myargs[] = {
       "0", NULL, NULL, FALSE, 'y', ARG_INT, 0.0, 0, NULL},
    { "Do only ungapped alignment (always TRUE for tblastx)",/*ARG_UNGAPPED*/
      "F", NULL, NULL, FALSE, 'u', ARG_BOOLEAN, 0.0, 0, NULL},
-   { "Use greedy algorithm for gapped extensions", /* ARG_GREEDY */
-     "F", NULL, NULL, FALSE, 'g', ARG_BOOLEAN, 0.0, 0, NULL},
+   { "Use greedy algorithm for gapped extensions:\n      0 no, 1 one-step, "
+     "2 two-step, 3 two-step with ungapped", /* ARG_GREEDY */
+     "F", NULL, NULL, FALSE, 'g', ARG_INT, 0.0, 0, NULL},
    { "Gap open penalty (default: non-affine if greedy; 5 if dyn. prog.)", 
      "0", NULL, NULL, FALSE, 'G', ARG_INT, 0.0, 0, NULL}, /* ARG_GAPOPEN */
    { "Gap extension penalty (default: non-affine if greedy; 2 otherwise)",
@@ -256,6 +257,14 @@ BLAST_FillOptions(LookupTableOptions* lookup_options,
 
    if (myargs[ARG_STRIDE].intvalue)
       lookup_options->scan_step = myargs[ARG_STRIDE].intvalue;
+   
+   if (myargs[ARG_PHI].strvalue) {
+      lookup_options->phi_pattern = strdup(myargs[ARG_PHI].strvalue);
+      lookup_options->lut_type = 
+          ((program_number == blast_type_blastn) ? 
+           PHI_NA_LOOKUP : PHI_AA_LOOKUP);
+      hit_options->phi_align = TRUE;
+   }
 
    BLAST_FillQuerySetUpOptions(query_setup_options, program_number, 
       myargs[ARG_FILTER].strvalue, myargs[ARG_STRAND].intvalue);
@@ -272,6 +281,25 @@ BLAST_FillOptions(LookupTableOptions* lookup_options,
    BLAST_FillExtensionOptions(ext_options, program_number, greedy_extension, 
       myargs[ARG_XDROP].intvalue, myargs[ARG_XDROP_FINAL].intvalue);
 
+   if (greedy_extension) {
+       switch (myargs[ARG_GREEDY].intvalue) {
+       case 1:
+           ext_options->algorithm_type = EXTEND_GREEDY;
+           word_options->ungapped_extension = FALSE;
+           break;
+       case 2:
+           ext_options->algorithm_type = EXTEND_GREEDY_NO_TRACEBACK;
+           word_options->ungapped_extension = FALSE;
+           break;
+       case 3:
+           ext_options->algorithm_type = EXTEND_GREEDY_NO_TRACEBACK;
+           word_options->ungapped_extension = TRUE;
+           break;
+       default:
+           break;
+       }
+   }
+
    BLAST_FillScoringOptions(score_options, program_number, greedy_extension, 
       myargs[ARG_MISMATCH].intvalue, myargs[ARG_MATCH].intvalue,
       myargs[ARG_MATRIX].strvalue, myargs[ARG_GAPOPEN].intvalue,
@@ -304,10 +332,10 @@ BLAST_FillOptions(LookupTableOptions* lookup_options,
    BLAST_FillEffectiveLengthsOptions(eff_len_options, 
       numseqs, totlen, (Int8) myargs[ARG_SEARCHSP].floatvalue);
 
-   if (myargs[ARG_DBGENCODE].intvalue && db_options &&
-       (program_number == blast_type_tblastn ||
-        program_number == blast_type_tblastx)) {
-      db_options->genetic_code = myargs[ARG_DBGENCODE].intvalue;
+   if (db_options && (program_number == blast_type_tblastn ||
+                      program_number == blast_type_tblastx)) {
+      if (myargs[ARG_DBGENCODE].intvalue)
+         db_options->genetic_code = myargs[ARG_DBGENCODE].intvalue;
       if ((status = BLAST_GeneticCodeFind(db_options->genetic_code, 
                        &db_options->gen_code_string)))
          return status;
@@ -338,13 +366,13 @@ Int2 Nlm_Main(void)
    Int2 status;
    QuerySetUpOptions* query_options=NULL;	
    BlastEffectiveLengthsOptions* eff_len_options=NULL;
-   BlastMask* lcase_mask = NULL;
-   BlastMask* filter_loc=NULL;	/* All masking locations */
+   BlastMaskLoc* lcase_mask = NULL;
+   BlastMaskLoc* filter_loc=NULL;	/* All masking locations */
    SeqLoc* query_slp = NULL;
    BlastScoreBlk* sbp = NULL;
    FILE *infp, *outfp;
    BlastQueryInfo* query_info;
-   BlastResults* results = NULL;
+   BlastHSPResults* results = NULL;
    Blast_Message* blast_message = NULL;
    SeqAlign* seqalign;
    BlastFormattingOptions* format_options;
@@ -413,6 +441,8 @@ Int2 Nlm_Main(void)
       readdb_args = (ReaddbNewArgs*) malloc(sizeof(ReaddbNewArgs));
       readdb_args->dbname = dbname = myargs[ARG_DB].strvalue;
       readdb_args->is_protein = !db_is_na;
+      readdb_args->first_db_seq = 0;
+      readdb_args->final_db_seq = 0;
       
       bssn_info.constructor = &ReaddbSeqSrcNew;
       bssn_info.ctor_argument = (void*) readdb_args;
@@ -460,7 +490,7 @@ Int2 Nlm_Main(void)
       }
 
       if (translated_query) {
-         BlastMaskDNAToProtein(&lcase_mask, query_slp);
+         BlastMaskLocDNAToProtein(&lcase_mask, query_slp);
       }
 
       status = BLAST_SetUpQuery(program_number, query_slp, 
@@ -476,7 +506,7 @@ Int2 Nlm_Main(void)
       if (translated_query) {
          /* Filter locations were returned in protein coordinates; convert them
             back to nucleotide here */
-         BlastMaskProteinToDNA(&filter_loc, query_slp);
+         BlastMaskLocProteinToDNA(&filter_loc, query_slp);
       }
 
       if (status) {
@@ -490,8 +520,6 @@ Int2 Nlm_Main(void)
       LookupTableWrapInit(query, lookup_options, 
                           lookup_segments, sbp, &lookup_wrap);
     
-      return_stats = (BlastReturnStat*) calloc(1, sizeof(BlastReturnStat));
-
       if (bssp) {
          BLAST_DatabaseSearchEngine(program_number, query, query_info, 
             bssp, sbp, score_options, lookup_wrap, 
@@ -512,7 +540,7 @@ Int2 Nlm_Main(void)
 
       /* Convert results to the SeqAlign form */
       BLAST_ResultsToSeqAlign(program_number, results, query_slp, bssp, 
-         subject_slp, score_options, sbp, hit_options->gapped_calculation,
+         subject_slp, score_options, sbp, score_options->gapped_calculation,
          &seqalign);
 
       results = BLAST_ResultsFree(results);
@@ -530,6 +558,8 @@ Int2 Nlm_Main(void)
                   blast_program, query_info->num_queries, query_slp,
                   filter_loc, format_options, score_options->is_ooframe);
 
+      BlastMaskLocFree(filter_loc);
+
       PrintOutputFooter(program_number, format_options, score_options, sbp, 
          lookup_options, word_options, ext_options, hit_options, query_info, 
          readdb_args, return_stats);
@@ -540,7 +570,9 @@ Int2 Nlm_Main(void)
       query_slp = SeqLocSetFree(query_slp);
    } /* End loop on sets of queries */
    
+   sfree(readdb_args);
    subject = BlastSequenceBlkFree(subject);
+   subject_slp = SeqLocSetFree(subject_slp);
    sfree(return_stats);
    LookupTableOptionsFree(lookup_options);
    BlastQuerySetUpOptionsFree(query_options);
diff --git a/demo/blastall.c b/demo/blastall.c
index 6f56f52f..41fcf1b7 100644
--- a/demo/blastall.c
+++ b/demo/blastall.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: blastall.c,v 6.135 2003/08/21 15:37:54 dondosha Exp $";
+static char const rcsid[] = "$Id: blastall.c,v 6.136 2003/11/05 22:28:06 dondosha Exp $";
 
-/* $Id: blastall.c,v 6.135 2003/08/21 15:37:54 dondosha Exp $
+/* $Id: blastall.c,v 6.136 2003/11/05 22:28:06 dondosha Exp $
 **************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -28,6 +28,9 @@ static char const rcsid[] = "$Id: blastall.c,v 6.135 2003/08/21 15:37:54 dondosh
 ************************************************************************** 
  * 
  * $Log: blastall.c,v $
+ * Revision 6.136  2003/11/05 22:28:06  dondosha
+ * No need to shift subsequence coordinates in tabular output, since they are already shifted in the seqalign
+ *
  * Revision 6.135  2003/08/21 15:37:54  dondosha
  * Corrections for out-of-frame tabular output and megablast XML output
  *
@@ -1571,7 +1574,7 @@ Int2 Main (void)
 	         BlastPrintTabularResults(curr_seqalign, query_bsp, slp, 
                number_of_alignments, blast_program, 
                !options->gapped_calculation, options->is_ooframe,
-               believe_query, from, 0, global_fp, NULL, (align_view == 9));
+               believe_query, 0, 0, global_fp, NULL, (align_view == 9));
 
 	         SeqAlignSetFree(curr_seqalign);
 	      }
diff --git a/demo/copymat.c b/demo/copymat.c
index 08231e58..adbdd1e8 100644
--- a/demo/copymat.c
+++ b/demo/copymat.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: copymat.c,v 6.25 2003/05/30 17:31:09 coulouri Exp $";
+static char const rcsid[] = "$Id: copymat.c,v 6.30 2004/01/30 20:34:45 coulouri Exp $";
 
 /*
 * ===========================================================================
@@ -36,6 +36,22 @@ Contents: main routines for copymatrices program to convert
 score matrices output by makematrices into a single byte-encoded file.
    
 $Log: copymat.c,v $
+Revision 6.30  2004/01/30 20:34:45  coulouri
+fix minor nit to FileWrite call
+
+Revision 6.29  2004/01/26 19:40:48  coulouri
+* Correct buffer overrun
+* Use offset rather than pointer in LookupBackboneCell
+
+Revision 6.28  2003/11/24 18:18:47  coulouri
+Correction to previous fix for 64-bit irix
+
+Revision 6.27  2003/11/21 18:01:15  ivanov
+Added extern definition for impalaMakeFileNames()
+
+Revision 6.26  2003/11/20 15:44:32  camacho
+Tom Madden's changes to use lookup table contruction code from algo/blast.
+
 Revision 6.25  2003/05/30 17:31:09  coulouri
 add rcsid
 
@@ -107,10 +123,39 @@ Changed a little format of RPS lookup tables file.
 #include <sequtil.h>
 #include <seqport.h>
 #include <tofasta.h>
-#include <blast.h>
-#include <blastpri.h>
-#include <posit.h>
-#include <profiles.h>
+
+#ifndef MAXLINELEN
+#   define MAXLINELEN 2000
+#endif
+#ifndef MAX_NAME_LENGTH
+#   define MAX_NAME_LENGTH 500
+#endif
+#ifndef PRO_ALPHABET_SIZE
+#   define PRO_ALPHABET_SIZE  26
+#endif
+#ifndef SORT_THRESHOLD
+#   define SORT_THRESHOLD 20
+#endif
+#ifndef RPS_MAGIC_NUMBER
+#   define RPS_MAGIC_NUMBER 7702
+#endif
+/*factor used to multiply the gapped K parameter to make it
+  more accurate in most cases*/
+#ifndef PRO_K_MULTIPLIER
+#   define PRO_K_MULTIPLIER 1.2
+#endif
+#include <algo/blast/core/blast_lookup.h>
+#include <algo/blast/core/blast_options.h>
+
+typedef Int4 ScoreRow[PRO_ALPHABET_SIZE];
+extern Boolean LIBCALL 
+IMPALAPrintHelp PROTO((Boolean html, Int4 line_length, Char * programName, 
+                       FILE *outfp));
+extern void  LIBCALL
+impalaMakeFileNames PROTO((Char * matrixDbName, Char * auxiliaryFileName,
+                           Char * mmapFileName, Char * seqFileName,
+                           Char *matrixFileName, Char * ckptFileName,
+                           Char *directoryPrefix));
 
 #define NUMARG (sizeof(myargs)/sizeof(myargs[0]))
 
@@ -333,6 +378,40 @@ static Int4 findTotalLength(FILE *matrixAuxiliaryFile, Int4 numProfiles,
     return(totalLength);
 }
 
+static Boolean RPSUpdateOffsets(LookupTable *lookup)
+{
+    Uint4 len;
+    Int4 index;
+    Int4 num_used;
+    Int4 offset_diff;
+
+    len = lookup->backbone_size;
+    offset_diff = lookup->wordsize - 1;
+
+    /* Walk through table, copying info into mod_lt[] */
+    for(index = 0; index < len; index++) {
+        
+        if((num_used=lookup->thick_backbone[index].num_used) <= 3)
+        {
+            while (num_used > 0)
+            {
+                num_used--;
+            	lookup->thick_backbone[index].payload.entries[num_used] += offset_diff;
+            }
+        }
+        else
+        {
+            while (num_used > 0)
+            {
+                 num_used--;
+                 lookup->overflow [ lookup->thick_backbone[index].payload.overflow_cursor + num_used] += offset_diff;
+            }
+        }
+    }
+    return TRUE;
+}
+
+
 /* #define RPS_THRESHOLD 11 */
 /* #define RPS_WORDSIZE  3 */
 
@@ -341,50 +420,44 @@ static Int4 findTotalLength(FILE *matrixAuxiliaryFile, Int4 numProfiles,
    pointers relative to the start of "mod_lookup_table_memory" chunk 
    RPS Blast will calculate real pointers in run time using these values
 */
-Boolean RPSUpdatePointers(LookupTablePtr lookup)
+Boolean RPSUpdatePointers(LookupTable *lookup, Uint4 *new_overflow, Uint4 *new_overflow_size)
 {
-    ModLAEntry * mod_lt;
     Uint4 len;
     Int4 index;
-    ModLookupPositionPtr start_address;
+    Uint4 *start_address;
     long mlpp_address;
-    ModLookupPositionPtr *lpp;
+    Uint4 *new_overflow_cursor;
+    Int4 *src;
+    Int4 first_hit;
+
+    len = lookup->backbone_size;
 
-    len = lookup->array_size;
-    mod_lt=lookup->mod_lt;
-    start_address = (ModLookupPositionPtr) lookup->mod_lookup_table_memory;
+    start_address = new_overflow_cursor = new_overflow;
 
     /* Walk through table, copying info into mod_lt[] */
     for(index = 0; index < len; index++) {
         
-        if(mod_lt[index].num_used <= 3)
+        if(lookup->thick_backbone[index].num_used <= 3)
             continue;
 
-#if 1
+        src = &(lookup->overflow[lookup->thick_backbone[index].payload.overflow_cursor]);
+        MemCpy(new_overflow_cursor, &src[1], sizeof(Uint4)*(lookup->thick_backbone[index].num_used-1));
+
+        mlpp_address = (long) new_overflow_cursor;
+
+	new_overflow_cursor += lookup->thick_backbone[index].num_used-1;
+	first_hit = src[0];
 
-        /* Taking pointer to 4/8 bytes address */        
-        lpp= (ModLookupPositionPtr *) &mod_lt[index].entries[1];
-        
-        mlpp_address = (long) *lpp;
         mlpp_address -= (long) start_address;
         
         /* Now this is new relative address - usually small  */
-        *lpp  = (ModLookupPositionPtr) mlpp_address;
-
-#if defined(OS_UNIX_IRIX)
-        if(sizeof(ModLookupPositionPtr) == 8) { /* 64bit build */
-            mlpp_address = mod_lt[index].entries[1];
-            mod_lt[index].entries[1] = mod_lt[index].entries[2];
-            mod_lt[index].entries[2] = mlpp_address;
-        }
-#endif
-        
-#else
-        mod_lt[index].entries[1] -= (int) start_address;
-        mod_lt[index].entries[2] = 0; /* Not used */
-#endif
+        lookup->thick_backbone[index].payload.entries[1] = (Int4) mlpp_address;
+        lookup->thick_backbone[index].payload.entries[0] = first_hit;
 
     }
+
+    *new_overflow_size = new_overflow_cursor - new_overflow;
+
     return TRUE;
 }
 
@@ -392,17 +465,24 @@ Boolean RPSUpdatePointers(LookupTablePtr lookup)
    Write lookup table to the disk into file "*.loo", which will be
    used memory-mapped during RPS Blast search 
 */
-Boolean RPSDumpLookupTable(LookupTablePtr lookup, FILE *fd)
+Boolean RPSDumpLookupTable(LookupTable *lookup, FILE *fd)
 {
+    Uint4 *new_overflow;
+    Uint4 new_overflow_size;
 
-    RPSUpdatePointers(lookup);
+    RPSUpdateOffsets(lookup);
 
-    FileWrite(lookup->mod_lt, sizeof(ModLAEntry), 1+lookup->array_size, fd);
-    if(lookup->mod_lookup_table_size) {
-        FileWrite(lookup->mod_lookup_table_memory, 
-                  lookup->mod_lookup_table_size, 
-                  sizeof(ModLookupPosition), fd);
-    }
+    new_overflow = malloc(lookup->overflow_size*sizeof(Uint4)); 
+    RPSUpdatePointers(lookup, new_overflow, &new_overflow_size);
+
+    FileWrite(lookup->thick_backbone, sizeof(LookupBackboneCell), lookup->backbone_size, fd);
+    if(new_overflow_size)
+        FileWrite(new_overflow,
+                  sizeof(Uint4),
+                  new_overflow_size,
+                  fd);
+
+    sfree(new_overflow);
     
     return TRUE;
 }
@@ -415,25 +495,63 @@ Boolean RPSCreateLookupFile(ScoreRow *combinedMatrix, Int4 numProfiles,
                             Int4Ptr seqlens, CharPtr filename, 
                             Nlm_FloatHi scalingFactor)
 {
-    LookupTablePtr lookup;
-    BlastAllWordPtr all_words;
-    Int4 start, i, header_size, all_length, magicNumber;
+    BlastScoreBlk *sbp;
+    DoubleInt *double_int;
     FILE *fd;
+    Int4  **posMatrix;
+    Int4 start, i, header_size, all_length, magicNumber;
     Int4Ptr offsets;
-    BLAST_ScorePtr PNTR posMatrix;
     Int4 num_lookups;
+    ListNode *lookup_segment=NULL;
+    LookupTable *lookup;
+    LookupTableWrap* lookup_wrap_ptr=NULL;
+    LookupTableOptions* lookup_options;
+   
 
     if((fd = FileOpen(filename, "wb")) == NULL)
         return FALSE;
     
     num_lookups = 1; /* Single lookup table for all set */
-    lookup = lookup_new(PRO_ALPHABET_SIZE, 3, 0);
 
-    all_words = BlastPopulateAllWordArrays(3, PRO_ALPHABET_SIZE);
+    all_length = seqlens[numProfiles] - seqlens[0];
+    
+    posMatrix = MemNew((all_length + 1) * sizeof(Int4 *));
+    for (i = 0; i < all_length; i++) {
+        posMatrix[i] = (Int4 *) &(combinedMatrix[i][0]);
+    }
+    
+    /* Last row is necessary */
+    posMatrix[all_length] = MemNew(sizeof(Int4) * PRO_ALPHABET_SIZE);
+
+    for(i = 0; i < PRO_ALPHABET_SIZE; i++) {
+        posMatrix[all_length][i] = -INT2_MAX;
+    }
+
+    sbp = BlastScoreBlkNew(BLASTAA_SEQ_CODE, 1);
+    sbp->posMatrix = posMatrix;
+    LookupTableOptionsNew(blast_type_blastp, &lookup_options);
+    BLAST_FillLookupTableOptions(lookup_options, blast_type_blastp, FALSE, 
+	(Int4) (myargs[3].floatvalue*scalingFactor), myargs[4].intvalue, FALSE, FALSE, TRUE);  /* add last arg for psi-blast?? */
+
+
+    double_int = (DoubleInt*) calloc(1, sizeof(DoubleInt));
+    double_int->i1 = 0;
+    double_int->i2 = all_length;
+
+    ListNodeAddPointer(&lookup_segment, 0, double_int);
+
+    /* Need query for psi-blast??  where to put the PSSM? */
+    LookupTableWrapInit(NULL, lookup_options, lookup_segment, sbp, &lookup_wrap_ptr);
+   
+    sbp->posMatrix = NULL;
+    sbp = BlastScoreBlkFree(sbp);
+    lookup_options = LookupTableOptionsFree(lookup_options);
+    lookup_segment = ListNodeFreeData(lookup_segment);
+
+    lookup = (LookupTable*) lookup_wrap_ptr->lut;
 
     /* Only Uint4 maximum length for lookup file allowed in current
        implementation */
-
     header_size = (numProfiles+1)*sizeof(Int4) + 8*sizeof(Int4);
     
     /* Beginning of file will be allocated for lookup offsets */
@@ -441,32 +559,11 @@ Boolean RPSCreateLookupFile(ScoreRow *combinedMatrix, Int4 numProfiles,
     
     offsets = MemNew(sizeof(Int4) * (num_lookups + 1));
     
-    all_length = seqlens[numProfiles] - seqlens[0];
-    
-    posMatrix = MemNew((all_length + 1) * sizeof(BLAST_Score *));
-    for (i = 0; i < all_length; i++) {
-        posMatrix[i] = (BLAST_Score *) &(combinedMatrix[i][0]);
-    }
-    
-    /* Last row is necessary */
-    posMatrix[all_length] = MemNew(sizeof(BLAST_Score) * PRO_ALPHABET_SIZE);
-    for(i = 0; i < PRO_ALPHABET_SIZE; i++) {
-        posMatrix[all_length][i] = -INT2_MAX;
-    }
 
     offsets[0] = ftell(fd);
     
     start = seqlens[0]; /* 0 */
     
-    if(BlastNewFindWordsEx(lookup, &posMatrix[start], 0, all_length, 
-                           all_words, (Int4) (myargs[3].floatvalue*scalingFactor), 
-                           myargs[4].intvalue, 0) < 0) {
-        ErrPostEx(SEV_ERROR, 0,0, "Failure to create llokup table");
-        return FALSE;
-    }
-    
-    lookup_position_aux_destruct(lookup);
-    
     RPSDumpLookupTable(lookup, fd);
     
     i = 1;
@@ -477,9 +574,9 @@ Boolean RPSCreateLookupFile(ScoreRow *combinedMatrix, Int4 numProfiles,
     magicNumber = RPS_MAGIC_NUMBER;
     FileWrite(&magicNumber, sizeof(Int4), 1, fd); /* header[0] */
     FileWrite(&num_lookups, sizeof(Int4), 1, fd); /* header[1] */
-    FileWrite(&lookup->num_pos_added, sizeof(Int4), 1, fd); /* header[2] */
-    FileWrite(&lookup->num_unique_pos_added, sizeof(Int4), 1, fd); /* header[3] */
-    FileWrite(&lookup->mod_lookup_table_size, sizeof(Int4), 1, fd); /* header[4] */
+    FileWrite(&lookup->neighbor_matches, sizeof(Int4), 1, fd); /* header[2] */
+    FileWrite(&lookup->neighbor_matches, sizeof(Int4), 1, fd); /* header[3] */
+    FileWrite(&lookup->overflow_size, sizeof(Int4), 1, fd); /* header[4] */
     
     /* Now writing recorded offsets in the beginning of the file */
     
@@ -487,27 +584,14 @@ Boolean RPSCreateLookupFile(ScoreRow *combinedMatrix, Int4 numProfiles,
     FileWrite(offsets, sizeof(Int4), num_lookups + 1, fd);
     FileClose(fd);
     
-/* comment out for now, why is this here?
-    if (scalingFactor != 1.0) {
-        for(j = 0; j < all_length; j++) {
-            for(i = 0; i < PRO_ALPHABET_SIZE; i++) {
-                combinedMatrix[j][i] /= scalingFactor;
-            }
-        }
-    }
-*/
-
     /* Final memory cleenup */
     
-    lookup = lookup_destruct(lookup);
-    
     MemFree(posMatrix[all_length]);
     MemFree(posMatrix);
 
-    BlastAllWordDestruct(all_words);
-    
     return TRUE;
 }
+
 /* -- SSH --
    Create file <database_name> (without extention), which is concatenation
    of all FASTA files used. Used by RPS Blast.
diff --git a/demo/debruijn.c b/demo/debruijn.c
index 732745b0..c287351c 100644
--- a/demo/debruijn.c
+++ b/demo/debruijn.c
@@ -1,72 +1,107 @@
-#include <stdio.h>
-#include <util.h>
+/* $Id: debruijn.c,v 1.3 2004/01/05 20:44:55 coulouri Exp $
+
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's offical duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+
+*/
+
+static char const rcsid[] = "$Id: debruijn.c,v 1.3 2004/01/05 20:44:55 coulouri Exp $";
 
 /*
  * example driver for de Bruijn sequences.
  *
  * this code generates all n-mers over a protein
- * or dna alphabet. useful for creating fasta test sequences.
+ * or dna alphabet. useful for creating test sequences.
  */
 
-/* k = 22 */
-char proteinalphabet[] = "arndcqeghilkmfpstwyvbz";
+#include <ncbi.h>
+#include <algo/blast/core/lookup_util.h>
+
+static Args myargs[] = {
+  { "word size",
+    NULL, NULL, NULL, FALSE, 'n', ARG_INT, 0.0, 0, NULL },
+  { "alphabet\n"
+    "(supply 'ncbistdaa' or 'ncbi2na' for standard\n"
+    "alphabets, or supply your own alphabet)\n",
+    NULL, NULL, NULL, FALSE, 'a', ARG_STRING, 0.0, 0, NULL },
+};
 
-/* k = 4 */
-char dnaalphabet[] = "acgt";
+Uint1 ncbistdaa[] = "-abcdefghiklmnpqrstvwxyzu*";
+Uint1 ncbi2na[] = "acgt";
 
-int main(int argc, char *argv[])
+Int2 Main(void)
 {
-  int i;
-  int n, k;
-  char *output;
-  int outputsize;
-  char *alphabet;
+  Int4 i;
+  Int4 n, k;
+  Uint1 *output;
+  Int4 outputsize;
+  Uint1 *alphabet=NULL;
+  
+  if ( ! GetArgs("debruijn", sizeof(myargs)/sizeof(myargs[0]), myargs) )
+   return 1;
+  
+  n = myargs[0].intvalue;
 
-  if (argc != 4)
+  if (n < 1)
     {
-      fprintf(stderr, "usage: %s n k prot-or-dna\n", argv[0]);
-      fprintf(stderr, "where prot-or-dna = 0 for protein, 1 for dna\n");
-      fprintf(stderr, "example: %s 3 22 0\n",argv[0]);
-      fprintf(stderr, "example: %s 11 4 1\n",argv[0]);
-      exit(1);
+      fprintf(stderr,"n must be greater than one.\n");
+      return 1;
     }
-  
-  n = atoi(argv[1]);
-  k = atoi(argv[2]);
-  
-  if (atoi(argv[3]) == 0)
-    alphabet = proteinalphabet;
-  else
-    alphabet = dnaalphabet;
 
+  alphabet = myargs[1].strvalue;
+
+  if (strcmp("ncbistdaa", myargs[1].strvalue) == 0)
+    alphabet = ncbistdaa;
+
+  if (strcmp("ncbi2na", myargs[1].strvalue) == 0)
+    alphabet = ncbi2na;
+
+  k = strlen(alphabet);
+  
   /* output array needs:
    * k^n bytes - to store the de Bruijn sequence
    * n-1 bytes - to unwrap (see below)
    * 1   byte  - for the terminating NUL
    */
 
-  outputsize = iexp(k,n) + (n-1) + 1;
-  output = (char *) calloc( outputsize, sizeof(char));
+  outputsize = iexp(k,n) + (n-1);
+  output = (char *) malloc(outputsize + 1);
 
   /* compute the (n,k) de Bruijn sequence */  
   debruijn(n,k,output,alphabet);
   
-  /* but, we don't want a true cyclical de Bruijn sequence, we want
-   * all words in a straight line. so we copy the first n-1 letters
+  /* We don't want a true cyclical de Bruijn sequence; we want
+   * all words in a straight line- copy the first n-1 letters
    * to the end.
    */
 
   for(i=0;i<(n-1);i++)
-    output[outputsize-((n-1)+1)+i] = output[i];
-
-  /* don't forget to NUL-terminate it */
+    output[outputsize-n+1+i] = output[i];
 
-  output[outputsize-1] = '\0';
+  /* Terminate the string. */
 
-  fprintf(stderr,"n (word size) = %d\n",n);
-  fprintf(stderr,"k (alphabet size) = %d\n",k);
-  fprintf(stderr,"output size = k^n + (n-1) + 1 = %d + %d + 1 = %d\n",iexp(k,n),n-1,outputsize);
-  fprintf(stderr,"naive size would have been %d\n",n * iexp(k,n));
+  output[outputsize+1] = '\0';
 
   puts(output);
 
diff --git a/demo/formatdb.c b/demo/formatdb.c
index 37e7a8ed..9a2143fe 100644
--- a/demo/formatdb.c
+++ b/demo/formatdb.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: formatdb.c,v 6.91 2003/10/01 18:59:56 camacho Exp $";
+static char const rcsid[] = "$Id: formatdb.c,v 6.92 2004/01/29 14:56:44 camacho Exp $";
 
 /*****************************************************************************
 
@@ -32,11 +32,14 @@ static char const rcsid[] = "$Id: formatdb.c,v 6.91 2003/10/01 18:59:56 camacho
    
    Version Creation Date: 10/01/96
 
-   $Revision: 6.91 $
+   $Revision: 6.92 $
 
    File Description:  formats FASTA databases for use by BLAST
 
    $Log: formatdb.c,v $
+   Revision 6.92  2004/01/29 14:56:44  camacho
+   Removed -A option, FORMATDB_VER_TEXT no longer supported
+
    Revision 6.91  2003/10/01 18:59:56  camacho
    Fix to creation of custom databases using a gi list and alias files when the
    source database spans multiple volumes.
@@ -418,8 +421,6 @@ Args dump_args[] = {
       "F", NULL, NULL, TRUE, 's', ARG_BOOLEAN, 0.0, 0, NULL},
     { "Verbose: check for non-unique string ids in the database",
       "F", NULL, NULL, TRUE, 'V', ARG_BOOLEAN, 0.0, 0, NULL},
-    { "Create ASN.1 structured deflines",
-      "T", NULL, NULL, TRUE, 'A', ARG_BOOLEAN, 0.0, 0, NULL},
     { "Create an alias file with this name\n"
       "        use the gifile arg (below) if set to calculate db size\n"
       "        use the BLAST db specified with -i (above)", 
@@ -452,7 +453,6 @@ enum {
     dbsize_arg,
     sparse_arg,
     nonunique_arg,
-    asn1_deflines_arg,
     alias_fn_arg,
     gifile_arg,
     bin_gifile_arg,
@@ -669,9 +669,7 @@ Int2 Main(void)
                             dump_args[basename_arg].strvalue,
                             dump_args[alias_fn_arg].strvalue,
                             ((Int8)dump_args[dbsize_arg].intvalue)*1000000, 0,
-                            dump_args[asn1_deflines_arg].intvalue ?
-                                FORMATDB_VER : FORMATDB_VER_TEXT ,
-                            FALSE, 0);
+                            FORMATDB_VER, FALSE, 0);
     if (options == NULL)
         return 1;
 
diff --git a/demo/megablast.c b/demo/megablast.c
index 2fa5beb6..7db38590 100644
--- a/demo/megablast.c
+++ b/demo/megablast.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: megablast.c,v 6.107 2003/05/30 17:31:09 coulouri Exp $";
+static char const rcsid[] = "$Id: megablast.c,v 6.111 2004/01/27 20:47:18 dondosha Exp $";
 
-/* $Id: megablast.c,v 6.107 2003/05/30 17:31:09 coulouri Exp $
+/* $Id: megablast.c,v 6.111 2004/01/27 20:47:18 dondosha Exp $
 **************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -28,6 +28,18 @@ static char const rcsid[] = "$Id: megablast.c,v 6.107 2003/05/30 17:31:09 coulou
 ************************************************************************** 
  * $Revision 6.13$ *  
  * $Log: megablast.c,v $
+ * Revision 6.111  2004/01/27 20:47:18  dondosha
+ * Set no_traceback option to 2 for -D4, 1 for -D0, 0 for others
+ *
+ * Revision 6.110  2003/11/05 22:28:06  dondosha
+ * No need to shift subsequence coordinates in tabular output, since they are already shifted in the seqalign
+ *
+ * Revision 6.109  2003/10/30 17:30:49  dondosha
+ * Fixed error in previous commit - output file pointer has to be set for all cases
+ *
+ * Revision 6.108  2003/10/29 17:48:15  dondosha
+ * Added -D4 option for 2-stage greedy gapped extension with format identical to -D2
+ *
  * Revision 6.107  2003/05/30 17:31:09  coulouri
  * add rcsid
  *
@@ -396,7 +408,8 @@ enum {
    MBLAST_ENDPOINTS = 0,
    MBLAST_SEGMENTS,
    MBLAST_ALIGNMENTS,
-   MBLAST_ALIGN_INFO
+   MBLAST_ALIGN_INFO,
+   MBLAST_DELAYED_TRACEBACK
 };
 
 static int LIBCALLBACK
@@ -912,6 +925,7 @@ Int2 Main (void)
    Boolean lcase_masking;
    BlastOutputPtr boutp = NULL;
    MBXmlPtr mbxp = NULL;
+   Boolean traditional_formatting;
    
     StringCpy(buf, "megablast ");
     StringNCat(buf, BlastGetVersionNumber(), sizeof(buf)-StringLen(buf)-1);
@@ -947,14 +961,17 @@ Int2 Main (void)
 	}
 
 	align_type = BlastGetTypes(blast_program, &query_is_na, &db_is_na);
- 
+   traditional_formatting = 
+      (myargs[12].intvalue == MBLAST_ALIGNMENTS ||
+       myargs[12].intvalue == MBLAST_DELAYED_TRACEBACK);
+
         if (myargs[15].strvalue) {
            if (myargs[15].strvalue[0] == 'f' || myargs[15].strvalue[0] == 'F' ||
                myargs[15].strvalue[0] == '0')
               believe_query = FALSE;
            else
               believe_query = TRUE;
-        } else if (myargs[12].intvalue == MBLAST_ALIGNMENTS && 
+        } else if (traditional_formatting && 
                    !myargs[14].strvalue)
            believe_query = FALSE;
         else
@@ -1058,9 +1075,11 @@ Int2 Main (void)
 	   options->gifile = StringSave(myargs[22].strvalue);
    
 	if (myargs[12].intvalue == MBLAST_ENDPOINTS)
-	   options->no_traceback = TRUE;
+      options->no_traceback = 1;
+   else if (myargs[12].intvalue == MBLAST_DELAYED_TRACEBACK)
+	   options->no_traceback = 2;
 	else
-	   options->no_traceback = FALSE;
+	   options->no_traceback = 0;
 
 	options->megablast_full_deflines = (Boolean) myargs[27].intvalue;
         options->perc_identity = (FloatLo) myargs[30].floatvalue;
@@ -1077,10 +1096,9 @@ Int2 Main (void)
 	StrCpy(prefix, "");
 
 	global_fp = outfp;
-        if (myargs[12].intvalue != MBLAST_ALIGNMENTS)
-           options->output = outfp;
+        options->output = outfp;
 
-	if (myargs[12].intvalue==MBLAST_ALIGNMENTS) {
+	if (traditional_formatting) {
 	   if (align_view < 7) {
               if (html) {
                  fprintf(outfp, "<HTML>\n<TITLE>MEGABLAST Search Results</TITLE>\n");
@@ -1233,7 +1251,7 @@ Int2 Main (void)
            }
               
               
-	   if (myargs[12].intvalue==MBLAST_ALIGNMENTS) {
+	   if (traditional_formatting) {
 	      dbinfo = NULL;
 	      ka_params = NULL;
 	      ka_params_gap = NULL;
@@ -1333,7 +1351,7 @@ Int2 Main (void)
                        BlastPrintTabulatedResults(seqalign, 
                           query_bsp_array[index], NULL, number_of_alignments,
                           blast_program, !options->gapped_calculation, 
-                          believe_query, options->required_start, 0, 
+                          believe_query, 0, 0, 
                           global_fp, (align_view == 9));
 
                        SeqAlignSetFree(seqalign);
diff --git a/demo/rtestval.c b/demo/rtestval.c
index 6752bbe7..1a3bd194 100644
--- a/demo/rtestval.c
+++ b/demo/rtestval.c
@@ -5,7 +5,7 @@
 *       check for stop codons
 *       Check for and fix non 3.0 asn spec things
 *
-* $Id: rtestval.c,v 1.10 2003/05/13 16:02:42 coulouri Exp $
+* $Id: rtestval.c,v 1.11 2003/11/14 18:07:54 kans Exp $
 *
 *****************************************************************************/
 #include <accid1.h>
@@ -158,6 +158,10 @@ Int2 Main(void)
 	vsp->cutoff = (Int2)(myargs[10].intvalue);
 	vsp->useSeqMgrIndexes = (Boolean)(myargs[12].intvalue); /* indexed validate */
 	vsp->validateAlignments = (Boolean)(myargs[13].intvalue);
+	if (vsp->validateAlignments) {
+      vsp->alignFindRemoteBsp = TRUE;
+      vsp->doSeqHistAssembly = TRUE;
+	}
 	vsp->farIDsInAlignments = (Boolean)(myargs[13].intvalue);
 	vsp->alwaysRequireIsoJTA = (Boolean)(myargs[14].intvalue);
 	vsp->farFetchCDSproducts = (Boolean) (myargs[15].intvalue && myargs[16].intvalue);
diff --git a/demo/tbl2asn.c b/demo/tbl2asn.c
index 1b36b887..a969f40e 100644
--- a/demo/tbl2asn.c
+++ b/demo/tbl2asn.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   5/5/00
 *
-* $Revision: 6.71 $
+* $Revision: 6.79 $
 *
 * File Description: 
 *
@@ -61,7 +61,7 @@
 #include <simple.h>
 #include <aliparse.h>
 
-#define TBL2ASN_APP_VER "2.5"
+#define TBL2ASN_APP_VER "2.8"
 
 CharPtr TBL2ASN_APPLICATION = TBL2ASN_APP_VER;
 
@@ -162,6 +162,7 @@ static void ValidateOneFile (
   if (vsp != NULL) {
     vsp->useSeqMgrIndexes = TRUE;
     vsp->suppressContext = TRUE;
+    vsp->seqSubmitParent = TRUE;
     oldErrSev = ErrSetMessageLevel (SEV_NONE);
     ValidateSeqEntry (sep, vsp);
     ValidStructFree (vsp);
@@ -552,6 +553,16 @@ static OrgStuff commonOrgStuff [] = {
     "PLN", 1, 1, 39947
   },
   {
+    "Aspergillus nidulans FGSC A4", "",
+    "Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; Emericella",
+    "PLN", 1, 4, 227321
+  },
+  {
+    "environmental sequence", "",
+    "unclassified; environmental samples",
+    "UNA", 1, 2, 256318
+  },
+  {
     NULL, NULL, NULL, NULL, 0, 0, 0
   }
 };
@@ -778,42 +789,62 @@ static BioseqPtr AttachSeqAnnotEntity (Uint2 entityID, SeqAnnotPtr sap, Boolean
   return bsp;
 }
 
-static CharPtr TrimBracketsFromString (CharPtr str)
+static CharPtr TrimBracketsFromString (CharPtr str, SqnTagPtr stp)
 
 {
   Uchar    ch;	/* to use 8bit characters in multibyte languages */
+  Int2     count;
   CharPtr  dst;
   CharPtr  ptr;
 
-  if (StringHasNoText (str)) return str;
+  if (StringHasNoText (str) || stp == NULL) return str;
 
   /* remove bracketed fields */
 
+  count = 0;
   dst = str;
   ptr = str;
   ch = *ptr;
   while (ch != '\0') {
     if (ch == '[') {
-      ptr++;
-      ch = *ptr;
-      while (ch != '\0' && ch != ']' && ch != '"') {
+      if (count < stp->num_tags && (! stp->used [count])) {
+        *dst = ch;
+        dst++;
         ptr++;
         ch = *ptr;
-      }
-      if (ch == '"') {
+        while (ch != '\0' && ch != ']') {
+          *dst = ch;
+          dst++;
+          ptr++;
+          ch = *ptr;
+        }
+        *dst = ch;
+        dst++;
+        ptr++;
+        ch = *ptr;
+      } else {
         ptr++;
         ch = *ptr;
-        while (ch != '\0' && ch != '"') {
+        while (ch != '\0' && ch != ']' && ch != '"') {
+          ptr++;
+          ch = *ptr;
+        }
+        if (ch == '"') {
+          ptr++;
+          ch = *ptr;
+          while (ch != '\0' && ch != '"') {
+            ptr++;
+            ch = *ptr;
+          }
+        }
+        while (ch != '\0' && ch != ']') {
           ptr++;
           ch = *ptr;
         }
-      }
-      while (ch != '\0' && ch != ']') {
         ptr++;
         ch = *ptr;
       }
-      ptr++;
-      ch = *ptr;
+      count++;
     } else {
       *dst = ch;
       dst++;
@@ -1037,16 +1068,16 @@ static void ProcessOneNuc (
     }
   }
 
-  if (stp != NULL) {
-    SqnTagFree (stp);
-  }
-
-  TrimBracketsFromString (ttl);
+  TrimBracketsFromString (ttl, stp);
   if (! StringHasNoText (ttl)) {
     str = StringSave (ttl);
     SeqDescrAddPointer (&(bsp->descr), Seq_descr_title, (Pointer) str);
   }
 
+  if (stp != NULL) {
+    SqnTagFree (stp);
+  }
+
   ValNodeFreeData (vnp);
 }
 
@@ -1179,6 +1210,60 @@ static void ReplaceOnePeptide (
   MemFree (str2);
 }
 
+static void ReplaceOneRNA (
+  SimpleSeqPtr ssp,
+  Boolean conflict
+)
+
+{
+  ByteStorePtr  bs;
+  BioseqPtr     bsp;
+  SeqIdPtr      sip;
+  CharPtr       str1, str2;
+
+  if (ssp == NULL || ssp->numid < 1) return;
+
+  sip = MakeSeqID (ssp->id [0]);
+  bsp = BioseqFind (sip);
+  SeqIdFree (sip);
+  if (bsp == NULL || bsp->repr != Seq_repr_raw) return;
+
+  /* remove trailing X and * */
+
+  bs = ssp->seq;
+  ssp->seqlen = BSLen (bs);
+
+  str1 = BSMerge (ssp->seq, NULL);
+  str2 = GetSequenceByBsp (bsp);
+
+  if (StringCmp (str1, str2) != 0) {
+
+    /* swap sequence byte stores */
+
+    bs = bsp->seq_data;
+    bsp->seq_data = ssp->seq;
+    ssp->seq = bs;
+    bsp->length = BSLen (bsp->seq_data);
+    bsp->seq_data_type = Seq_code_iupacna;
+
+    /*
+    mrna = SeqMgrGetRNAgivenProduct (bsp, NULL);
+    if (mrna != NULL) {
+
+      if (conflict) {
+        mrna->excpt = TRUE;
+        if (StringHasNoText (mrna->except_text)) {
+          mrna->except_text = StringSave ("RNA editing");
+        }
+      }
+    }
+    */
+  }
+
+  MemFree (str1);
+  MemFree (str2);
+}
+
 static Uint2 ProcessOneAsn (
   FILE* fp,
   BioSourcePtr src,
@@ -2128,6 +2213,29 @@ static void ProcessOneRecord (
     FileClose (fp);
   }
 
+  /* read one or more feature tables from .rna file */
+
+  fp = OpenOneFile (directory, base, ".rna");
+  if (fp != NULL) {
+
+    /* indexing needed to find mRNA from transcript product to set RNA editing exception */
+
+    SeqMgrIndexFeatures (entityID, NULL);
+
+    while ((dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE)) != NULL) {
+      if (datatype == OBJ_FASTA) {
+
+        ssp = (SimpleSeqPtr) dataptr;
+        ReplaceOneRNA (ssp, tbl->conflict);
+        SimpleSeqFree (ssp);
+
+      } else {
+        ObjMgrFree (datatype, dataptr);
+      }
+    }
+    FileClose (fp);
+  }
+
   /* read one or more quality score blocks from .qvl file */
 
   fp = OpenOneFile (directory, base, ".qvl");
@@ -2222,7 +2330,11 @@ static void ProcessOneRecord (
     if (! tbl->genprodset) {
       VisitFeaturesInSep (sep, NULL, ClearRnaProducts);
     }
-    InstantiateProteinTitles (entityID, NULL);
+    if (SeqMgrFeaturesAreIndexed (entityID)) {
+      InstantiateProteinTitles (entityID, NULL);
+    } else {
+      Message (MSG_POSTERR, "Unable to instantiate protein titles due to dropped index");
+    }
     if (tbl->genprodset) {
       /* need to reindex before instantiating mRNA titles */
       SeqMgrIndexFeatures (entityID, NULL);
diff --git a/desktop/biosrc.c b/desktop/biosrc.c
index 5483b797..b52f139a 100644
--- a/desktop/biosrc.c
+++ b/desktop/biosrc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.42 $
+* $Revision: 6.43 $
 *
 * File Description: 
 *
@@ -109,10 +109,10 @@ ENUM_ALIST(subsource_subtype_alist)
   {"Plasmid-name",          19},
   {"Plastid-name",          22},
   {"Pop-variant",           17},
+  {"Rearranged",            15},
   {"Segment",               24},
   {"Sex",                    7},
   {"Subclone",               4},
-  {"Rearranged",            15},
   {"Tissue-lib",            18},
   {"Tissue-type",           10},
   {"Transgenic",            26},
diff --git a/desktop/cdrgn.c b/desktop/cdrgn.c
index f30c029e..587ced29 100644
--- a/desktop/cdrgn.c
+++ b/desktop/cdrgn.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.55 $
+* $Revision: 6.57 $
 *
 * File Description: 
 *
@@ -4696,7 +4696,7 @@ static ENUM_ALIST(rna_type_alist)
   {"snRNA",        5},
   {"scRNA",        6},
   {"snoRNA",       7},
-  {"Other RNA",  255},
+  {"misc_RNA",   255},
 END_ENUM_ALIST
 
 static Uint1 check_rna_type (Uint1 type)
@@ -4818,6 +4818,7 @@ static void RnaRefPtrToRnaPage (DialoG d, Pointer data)
 
   rpp = (RnaPagePtr) GetObjectExtra (d);
   rrp = (RnaRefPtr) data;
+
   if (rpp != NULL) {
     SetEnumPopup (rpp->type, rna_type_alist,
                   (UIEnum) check_rna_type (rrp->type));
@@ -4885,6 +4886,12 @@ static void RnaRefPtrToRnaPage (DialoG d, Pointer data)
             head = NULL;
             for (j = 0; j < 6; j++) {
               if (trna->codon [j] < 64) {
+				/* Note - it is important to set the fourth character in the codon array to NULL
+				 * because CodonForIndex only fills in the three characters of actual codon,
+				 * so if you StringCpy the codon array and the NULL character is not found after
+				 * the three codon characters, you will write in memory you did not intend to.
+				 */
+				codon [3] = 0;
                 if (CodonForIndex (trna->codon [j], Seq_code_iupacna, codon)) {
                   StringCpy (str, (CharPtr) codon);
                   str [3] = '\0';
diff --git a/desktop/dlgutil1.c b/desktop/dlgutil1.c
index afa78016..9cd7b606 100644
--- a/desktop/dlgutil1.c
+++ b/desktop/dlgutil1.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.40 $
+* $Revision: 6.42 $
 *
 * File Description: 
 *
@@ -515,6 +515,7 @@ static Boolean GeneGatherFunc (GatherContextPtr gcp)
 {
   FeatureFormPtr  ffp;
   GeneGatherPtr   ggp;
+  GeneRefPtr      grp;
   ObjMgrTypePtr   omtp;
   SeqFeatPtr      sfp;
   Char            thislabel [41];
@@ -548,6 +549,22 @@ static Boolean GeneGatherFunc (GatherContextPtr gcp)
         }
         if (vnp != NULL) {
           vnp->data.ptrvalue = StringSave (thislabel);
+          grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+          if (grp != NULL) {
+            if (grp->locus != NULL) {
+              vnp->choice = 1;
+            } else if (grp->desc != NULL) {
+              vnp->choice = 2;
+            } else if (grp->locus_tag != NULL) {
+              vnp->choice = 3;
+            } else if (grp->syn != NULL) {
+              vnp->choice = 4;
+            } else if (grp->db != NULL) {
+              vnp->choice = 5;
+            } else if (grp->maploc != NULL) {
+              vnp->choice = 6;
+            }
+          }
         }
       }
     }
@@ -648,11 +665,21 @@ static Boolean GeneMatchFunc (GatherContextPtr gcp)
         genexref = ggp->genexref;
         if (genexref != NULL) {
           grp = (GeneRefPtr) sfp->data.value.ptrvalue;
-          if (StringICmp (genexref->locus, grp->locus) == 0) {
-            ggp->val = ggp->idx;
-            ggp->xrefmatch = TRUE;
-            if (ffp != NULL) {
-              SetValue (ffp->useGeneXref, 2);
+          if (! StringHasNoText (genexref->locus)) {
+            if (StringICmp (genexref->locus, grp->locus) == 0) {
+              ggp->val = ggp->idx;
+              ggp->xrefmatch = TRUE;
+              if (ffp != NULL) {
+                SetValue (ffp->useGeneXref, 2);
+              }
+            }
+          } else if (! StringHasNoText (genexref->locus_tag)) {
+            if (StringICmp (genexref->locus_tag, grp->locus_tag) == 0) {
+              ggp->val = ggp->idx;
+              ggp->xrefmatch = TRUE;
+              if (ffp != NULL) {
+                SetValue (ffp->useGeneXref, 2);
+              }
             }
           }
         }
@@ -1127,7 +1154,14 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
               i--;
             }
             if (vnp != NULL) {
-              grp = CreateNewGeneRef ((CharPtr) vnp->data.ptrvalue, NULL, NULL, FALSE);
+              if (vnp->choice == 1) {
+                grp = CreateNewGeneRef ((CharPtr) vnp->data.ptrvalue, NULL, NULL, FALSE);
+              } else if (vnp->choice == 3) {
+                grp = GeneRefNew ();
+                if (grp != NULL) {
+                  grp->locus_tag = StringSave ((CharPtr) vnp->data.ptrvalue);
+                }
+              }
             }
           }
           if (grp != NULL) {
@@ -2965,7 +2999,7 @@ static void SeqLocPtrToIntervalPage (DialoG d, Pointer data)
 static Pointer IntervalPageToSeqLocPtr (DialoG d)
 
 {
-  BioseqPtr        bsp;
+  BioseqPtr        bsp, prev_bsp;
   Char             ch;
   SeqLocPtr        firstSlp;
   Int4             from;
@@ -2992,7 +3026,7 @@ static Pointer IntervalPageToSeqLocPtr (DialoG d)
   SeqIntPtr        sip;
   SeqLocPtr        slp;
   SeqPntPtr        spp;
-  Int2             strand;
+  Int2             strand, prev_strand;
   TagListPtr       tlp;
   Int4             tmp;
   SeqLocPtr        tmploc1;
@@ -3008,6 +3042,8 @@ static Pointer IntervalPageToSeqLocPtr (DialoG d)
   tlp = GetObjectExtra (ipp->ivals);
   if (tlp == NULL) return NULL;
 
+  prev_bsp = NULL;
+  prev_strand = Seq_strand_unknown;
   slp = NULL;
   sfp = SeqFeatNew ();
   if (sfp != NULL) {
@@ -3119,10 +3155,9 @@ static Pointer IntervalPageToSeqLocPtr (DialoG d)
             if (strand > Seq_strand_both_rev) {
               strand = Seq_strand_other;
             }
+            prev_strand = strand;
           } else {
-            /*
-            okay = FALSE;
-            */
+            strand = prev_strand;
           }
           MemFree (txt);
         }
@@ -3136,10 +3171,24 @@ static Pointer IntervalPageToSeqLocPtr (DialoG d)
         bsp = NULL;
         txt = ExtractTagListColumn ((CharPtr) vnp->data.ptrvalue, ipp->nucsOK ? 3 : 2);
         if (txt != NULL) {
-          if (StrToInt (txt, &val2) && val2 > 0 && val2 <= ipp->count) {
+          if (! StrToInt (txt, &val2) || val2 <= 0)
+          {
+            if (prev_bsp != NULL)
+            {
+              bsp = prev_bsp;
+            }
+            else
+            {
+              okay = FALSE;
+            }
+          }
+          else if (val2 <= ipp->count)
+          {
             sep = ipp->bsptr [val2];
-            if (sep != NULL && sep->choice == 1) {
+            if (sep != NULL && sep->choice == 1)
+            {
               bsp = (BioseqPtr) sep->data.ptrvalue;
+              prev_bsp = bsp;
             } else {
               okay = FALSE;
             }
diff --git a/desktop/dlgutil2.c b/desktop/dlgutil2.c
index 9e10333b..aa89ad9c 100644
--- a/desktop/dlgutil2.c
+++ b/desktop/dlgutil2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.39 $
+* $Revision: 6.42 $
 *
 * File Description: 
 *
@@ -1297,6 +1297,10 @@ static void GeneXrefWarn (GrouP g)
 
 {
   Int2  val;
+  Boolean indexerVersion;
+
+  indexerVersion = (Boolean) (GetAppProperty ("InternalNcbiSequin") != NULL);
+  if (indexerVersion) return;
 
   val = GetValue (g);
   if (val == 2) {
@@ -1670,10 +1674,17 @@ extern Boolean FileToScrollText (TexT t, CharPtr path)
 
   if (t != NULL && path != NULL && *path != '\0') {
     len = FileLength (path);
+    max = (Int4) INT2_MAX;
 #ifdef WIN_MOTIF
     max = INT4_MAX;
-#else
-    max = (Int4) INT2_MAX;
+#endif
+#ifdef WIN_MSWIN
+    max = INT4_MAX;
+#endif
+#ifdef WIN_MAC
+#ifdef OS_UNIX_DARWIN
+    max = INT4_MAX;
+#endif
 #endif
     if (len > 0 && len < max - 4) {
       str = MemNew (sizeof (char) * (len + 3));
diff --git a/desktop/e2docsum.c b/desktop/e2docsum.c
index 8f502c81..00b0d6e3 100644
--- a/desktop/e2docsum.c
+++ b/desktop/e2docsum.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/30/01
 *
-* $Revision: 6.46 $
+* $Revision: 6.47 $
 *
 * File Description: 
 *
@@ -2480,11 +2480,12 @@ static Int4Ptr GetCheckedUids (SummFormPtr sfp, Int2Ptr nump)
 static void LaunchMedlineViewer (Int4 uid)
 
 {
-  Pointer         dataptr;
-  Uint2           datatype;
-  Uint2           entityID;
-  Int2            handled;
-  PubmedEntryPtr  pep;
+  Pointer          dataptr;
+  Uint2            datatype;
+  Uint2            entityID;
+  Int2             handled;
+  MedlineEntryPtr  mep;
+  PubmedEntryPtr   pep;
 
   WatchCursor ();
   Update ();
@@ -2496,7 +2497,11 @@ static void LaunchMedlineViewer (Int4 uid)
     return;
   }
   datatype = OBJ_MEDLINE_ENTRY;
-  dataptr = (Pointer) (MedlineEntryPtr) pep->medent;
+  mep = (MedlineEntryPtr) pep->medent;
+  if (mep != NULL && mep->uid == 0) {
+    mep->uid = uid;
+  }
+  dataptr = (Pointer) mep;
   entityID = ObjMgrRegister (datatype, dataptr);
   if (dataptr == NULL || entityID == 0) {
     ArrowCursor ();
diff --git a/desktop/gbfview.c b/desktop/gbfview.c
index c368cc39..e3d03dd3 100644
--- a/desktop/gbfview.c
+++ b/desktop/gbfview.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   2/5/97
 *
-* $Revision: 6.70 $
+* $Revision: 6.71 $
 *
 * File Description: 
 *
@@ -568,6 +568,7 @@ typedef struct lookforids {
   Boolean isNTorNW;
   Boolean isNC;
   Boolean isTPA;
+  Boolean isAEorCH;
 } LookForIDs, PNTR LookForIDsPtr;
 
 static void LookForSeqIDs (BioseqPtr bsp, Pointer userdata)
@@ -584,6 +585,14 @@ static void LookForSeqIDs (BioseqPtr bsp, Pointer userdata)
       case SEQID_EMBL :
       case SEQID_DDBJ :
         lfip->isGED = TRUE;
+        tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+        if (tsip != NULL) {
+          if (StringNCmp (tsip->accession, "AE", 2) == 0) {
+            lfip->isAEorCH = TRUE;
+          } else if (StringNCmp (tsip->accession, "CH", 2) == 0) {
+            lfip->isAEorCH = TRUE;
+          }
+        }
         break;
       case SEQID_TPG :
       case SEQID_TPE :
@@ -613,7 +622,8 @@ static void LookForGEDetc (
   BoolPtr isGED,
   BoolPtr isNTorNW,
   BoolPtr isNC,
-  BoolPtr isTPA
+  BoolPtr isTPA,
+  BoolPtr isAEorCH
 )
 
 {
@@ -625,6 +635,7 @@ static void LookForGEDetc (
   *isNTorNW = lfi.isNTorNW;
   *isNC = lfi.isNC;
   *isTPA = lfi.isTPA;
+  *isAEorCH = lfi.isAEorCH;
 }
 
 static void LookForNonLocalID (BioseqPtr bsp, Pointer userdata)
@@ -894,6 +905,7 @@ static void PopulateFlatFile (BioseqViewPtr bvp, FmtType format, FlgType flags)
   FILE             *fp;
   Boolean          hastpaaligns;
   Int2             into;
+  Boolean          isAEorCH;
   Boolean          isGED;
   Boolean          isNTorNW;
   Boolean          isNC;
@@ -964,7 +976,7 @@ static void PopulateFlatFile (BioseqViewPtr bvp, FmtType format, FlgType flags)
   bsp = bvp->bsp;
   entityID = ObjMgrGetEntityIDForPointer (bsp);
   topsep = GetTopSeqEntryForEntityID (entityID);
-  LookForGEDetc (topsep, &isGED, &isNTorNW, &isNC, &isTPA);
+  LookForGEDetc (topsep, &isGED, &isNTorNW, &isNC, &isTPA, &isAEorCH);
 
   if ((flags & SHOW_CONTIG_FEATURES) != 0 || (flags & SHOW_CONTIG_SOURCES) != 0) {
     if (isNTorNW || isTPA) {
@@ -1067,6 +1079,8 @@ static void PopulateFlatFile (BioseqViewPtr bvp, FmtType format, FlgType flags)
       flags |= ONLY_NEAR_FEATURES;
     } else if (isNC) {
       flags |= NEAR_FEATURES_SUPPRESS;
+    } else if (isAEorCH) {
+      flags |= NEAR_FEATURES_SUPPRESS;
     }
   }
   if (bvp->useScrollText) {
diff --git a/desktop/salogif.c b/desktop/salogif.c
index dd913e65..91a50c59 100644
--- a/desktop/salogif.c
+++ b/desktop/salogif.c
@@ -1,4 +1,4 @@
-/*  $RCSfile: salogif.c,v $  $Revision: 6.3 $  $Date: 2003/07/15 14:36:31 $
+/*  $RCSfile: salogif.c,v $  $Revision: 6.6 $  $Date: 2004/01/23 22:48:57 $
 * ==========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -25,13 +25,22 @@
 *
 * Author:	Jinghui Zhang
 *
-* $Revision: 6.3 $
+* $Revision: 6.6 $
 *
 * File Description:
 *	 The Blast Search result visualization utilities  
 *
 * --------------------------------------------------------------------------
 * $Log: salogif.c,v $
+* Revision 6.6  2004/01/23 22:48:57  jianye
+* restore seqid in PrintOneAlignmentOverview and initialize some varialbes
+*
+* Revision 6.5  2003/11/20 18:36:08  dondosha
+* Added function PrintOneAlignmentOverview to create an overview gif for one of the multiple query sequences
+*
+* Revision 6.4  2003/10/31 02:51:14  dondosha
+* Always use first seqid for master (query) sequence instead of "best" id in ModMaxAlign
+*
 * Revision 6.3  2003/07/15 14:36:31  dondosha
 * Added #defines for substitutes to fprintf and fflush, needed for gzip compression of Web BLAST results
 *
@@ -244,7 +253,7 @@ static Boolean print_defline_for_sequence
 static Boolean PrintImageMapForGlobal
 (GlobalDrawPtr g_draw, Int4 pntX, Int4 pntY, 
  Int4 scale, CharPtr title_buf, SeqAlignPtr align,
- FILE *fp, const Char* formname)
+ FILE *fp, const Char* formname, int query_index)
 {
   AlignRegionPtr arp;
   ValNodePtr curr;
@@ -262,7 +271,7 @@ static Boolean PrintImageMapForGlobal
       if(gbp->has_fish_align == FALSE && gbp->arp_list != NULL)
         {
           if(retval == FALSE)
-            fprintf(fp, "<map name=img_map>\n"); 
+            fprintf(fp, "<map name=img_map%d>\n", query_index); 
           for(curr = gbp->arp_list; curr != NULL; curr = curr->next)
             {
               arp = (AlignRegionPtr)curr->data.ptrvalue;
@@ -343,7 +352,7 @@ static Boolean alignment_is_redundant
   Int4 c_len, r_len;
   Boolean load;
   Int2 i;
-  Int4 start, stop;
+  Int4 start = 0 , stop = 0;
   SeqIdPtr sip;
 
   len = 0;
@@ -441,7 +450,7 @@ static void update_redundant_val
   Int4 c_len;
   Boolean load;
   Int2 i;
-  Int4 start, stop;
+  Int4 start = 0, stop = 0;
 
   switch(align->segtype) {
   case 3:
@@ -629,7 +638,7 @@ static SeqAlignPtr ModMaxAlign
     return (*h_align);
   if(*h_align == NULL || m_bsp == NULL)
     return (*h_align); 
-  m_sip = SeqIdFindBest(m_bsp->id, 0);
+  m_sip = m_bsp->id;
 
   val = (Uint1Ptr)MemNew((size_t)m_bsp->length * sizeof(Int1));
   curr = *h_align;
@@ -684,6 +693,19 @@ NLM_EXTERN Boolean PrintAlignmentOverview
  const Char* gif_name,
  const Char* title)
 {
+   return PrintOneAlignmentOverview(h_annot, fp, formname, href, gif_name, 
+                                    title, 1);
+}
+
+NLM_EXTERN Boolean PrintOneAlignmentOverview
+(SeqAnnotPtr h_annot,
+ FILE*       fp,
+ const Char* formname,
+ const Char* href,
+ const Char* gif_name,
+ const Char* title,
+ int query_index)
+{
   SeqEntryPtr sep;
   Boolean is_new_sep;
   SeqAnnotPtr sap, annot, prev;
@@ -699,6 +721,7 @@ NLM_EXTERN Boolean PrintAlignmentOverview
   FILE *gif_fp;
   Int4 align_num;
   Char title_buf[201], tmpbuf[64];
+  SeqIdPtr idtemp;
 
   if(h_annot == NULL || fp == NULL)
     return FALSE;
@@ -710,6 +733,8 @@ NLM_EXTERN Boolean PrintAlignmentOverview
   if(master_bsp == NULL)
     return FALSE;
   bsp = master_bsp;
+  idtemp= bsp->id->next;
+  bsp->id->next = NULL;
   sep = SeqEntryFind(bsp->id);
   if(sep == NULL)
     {
@@ -770,7 +795,8 @@ NLM_EXTERN Boolean PrintAlignmentOverview
 
     /*print out the image map*/
     if(!PrintImageMapForGlobal(g_draw, pBox.left, pBox.top, 1, title_buf,
-                               (SeqAlignPtr)(annot->data), fp, formname))
+                               (SeqAlignPtr)(annot->data), fp, formname,
+                               query_index))
       printf("Fail to print the image map\n");
     fflush(fp);
 
@@ -797,9 +823,9 @@ NLM_EXTERN Boolean PrintAlignmentOverview
     ExitMuskStyles();
     fprintf(fp, "<CENTER>\n");
 
-    fprintf(fp, "<IMG WIDTH=%d HEIGHT=%d USEMAP=#img_map BORDER=1 "
+    fprintf(fp, "<IMG WIDTH=%d HEIGHT=%d USEMAP=#img_map%d ORDER=1 "
             "SRC=\"%s%s\" ISMAP>", 
-            (int)width, (int)height, href, gif_name);
+            (int)width, (int)height, query_index, href, gif_name);
 
     fprintf(fp, "</CENTER>\n");
     fprintf(fp, "<HR>\n<PRE>\n");
@@ -829,7 +855,7 @@ NLM_EXTERN Boolean PrintAlignmentOverview
   else
     prev->next = NULL;
   SeqAnnotFree(sap);
-
+  master_bsp->id->next = idtemp;  /*restore seqid*/
   BioseqUnlock(master_bsp);
 
   return retval;
diff --git a/desktop/salogif.h b/desktop/salogif.h
index e3e4c351..8c8b086f 100644
--- a/desktop/salogif.h
+++ b/desktop/salogif.h
@@ -1,7 +1,7 @@
 #ifndef SALOGIF__H
 #define SALOGIF__H
 
-/*  $RCSfile: salogif.h,v $  $Revision: 6.1 $  $Date: 2000/03/20 19:00:28 $
+/*  $RCSfile: salogif.h,v $  $Revision: 6.2 $  $Date: 2003/11/20 18:36:08 $
 * ==========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -33,6 +33,9 @@
 *
 * --------------------------------------------------------------------------
 * $Log: salogif.h,v $
+* Revision 6.2  2003/11/20 18:36:08  dondosha
+* Added function PrintOneAlignmentOverview to create an overview gif for one of the multiple query sequences
+*
 * Revision 6.1  2000/03/20 19:00:28  shavirin
 * Initial revision in the new location.
 *
@@ -71,6 +74,20 @@ NLM_EXTERN Boolean PrintAlignmentOverview
  const Char* title      /* title printed at the top of generated HTML output */
  );
 
+/* Shows alignments gif image for one query 
+ * from a set of multiple queries. 
+ */
+NLM_EXTERN Boolean PrintOneAlignmentOverview
+(SeqAnnotPtr h_annot,   /* output of blast search */
+ FILE*       fp,        /* file where output goes to */
+ const Char* formname,  /* it is needed to specify name of embeded HTML form,
+                           * create this form before if there is no one */
+ const Char* href,      /* hyperlink location of the GIF file */
+ const Char* gif_name,  /* GIF file name */
+ const Char* title,     /* title printed at the top of generated HTML output */
+ int query_index        /* Index of this query in the set of queries */
+ );
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/desktop/smdlg2.c b/desktop/smdlg2.c
index 8d237f1d..bfac9ecc 100644
--- a/desktop/smdlg2.c
+++ b/desktop/smdlg2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   8/10/95
 *
-* $Revision: 6.0 $
+* $Revision: 6.1 $
 *
 * File Description: 
 *
@@ -182,7 +182,7 @@ static void
 }
 
 static void
-/*FCN*/UpdateControls (
+/*FCN*/UpdateDlgControls (
   void
 ){
   if ( totalFeatures == 0 ){
@@ -322,7 +322,7 @@ static void
   FillGroupList(TRUE);
   SetGroupValue ( curGroupInd );
   SaveGroupArray();
-  UpdateControls();
+  UpdateDlgControls();
 }
 
 static void
@@ -347,7 +347,7 @@ static void
   FillGroupList(TRUE);
   SetGroupValue ( curGroupInd );
   SaveGroupArray();
-  UpdateControls();
+  UpdateDlgControls();
 }
 
 static void
@@ -382,7 +382,7 @@ static void
     curFeatureInd = 0;
     SetFeatValue ( curFeatureInd );
   }
-  UpdateControls();
+  UpdateDlgControls();
   SaveGroupArray();
 }
 
@@ -436,7 +436,7 @@ static void
       SetFeatValue ( curFeatureInd );
     }
     SaveGroupArray();
-    UpdateControls();
+    UpdateDlgControls();
   }
 }
 
@@ -457,7 +457,7 @@ static void
   FillGroupList(TRUE);
   SetGroupValue ( curGroupInd );
   SaveGroupArray();
-  UpdateControls();
+  UpdateDlgControls();
 }
 
 static void
@@ -491,7 +491,7 @@ static void
     curFeatureInd = 0;
     SetFeatValue ( curFeatureInd );
   }
-  UpdateControls();
+  UpdateDlgControls();
 }
 
 static void
@@ -504,7 +504,7 @@ static void
     curFeatureInd = GetValue ( featList ) - 1;
   }
   if ( curFeatureInd > nHideFeatures ) curFeatureInd--;
-  UpdateControls();
+  UpdateDlgControls();
 }
 
 static void
@@ -521,7 +521,7 @@ static void
   FillFeatList(TRUE);
   SetFeatValue ( curFeatureInd );
   SaveFeatureArray();
-  UpdateControls();
+  UpdateDlgControls();
 }
 
 static void
@@ -546,7 +546,7 @@ static void
   FillFeatList(TRUE);
   SetFeatValue ( curFeatureInd );
   SaveFeatureArray();
-  UpdateControls();
+  UpdateDlgControls();
 }
 
 static void
@@ -581,7 +581,7 @@ static void
   FillFeatList(TRUE);
   SetFeatValue ( curFeatureInd );
   SaveFeatureArray();
-  UpdateControls();
+  UpdateDlgControls();
 }
 
 static void
@@ -601,7 +601,7 @@ static void
   FillFeatList(TRUE);
   SetFeatValue ( curFeatureInd );
   SaveFeatureArray();
-  UpdateControls();
+  UpdateDlgControls();
 }
 
 static void 
@@ -694,7 +694,7 @@ GrouP
   FillGroupList(FALSE);
   SetGroupValue (curGroupInd);
   FillFeatPopup(FALSE);
-  UpdateControls ();
+  UpdateDlgControls ();
   return g;
 }
 
diff --git a/desktop/smdlg3.c b/desktop/smdlg3.c
index e6100192..f51dcc48 100644
--- a/desktop/smdlg3.c
+++ b/desktop/smdlg3.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   8/10/95
 *
-* $Revision: 6.0 $
+* $Revision: 6.1 $
 *
 * File Description: 
 *
@@ -319,7 +319,7 @@ static void
 }
 
 static void
-/*FCN*/UpdateControls ( 
+/*FCN*/UpdateDlgControls ( 
   Boolean panel,
   Boolean other
 ){
@@ -617,7 +617,7 @@ static void
     Nlm_SetMuskCParamEd( curClass, inClipSchema[i].subClass,
                          inClipSchema[i].pType, inClipBoard[i] );
   }
-  UpdateControls(TRUE,TRUE);
+  UpdateDlgControls(TRUE,TRUE);
 }
 
 static void
@@ -702,7 +702,7 @@ static void
 ){
   LoadFeatAr ();
   FillFetureList(TRUE);
-  UpdateControls(TRUE,TRUE);
+  UpdateDlgControls(TRUE,TRUE);
   UpdateTools();
 }
 
@@ -711,7 +711,7 @@ static void
   LisT l
 ){
   curExtraInd = GetValue (l) - 1;
-  UpdateControls(TRUE,TRUE);
+  UpdateDlgControls(TRUE,TRUE);
   UpdateTools();
 }
 
@@ -758,7 +758,7 @@ static void
       Enable ( applayButton );
     }
   }
-  UpdateControls(TRUE,TRUE);
+  UpdateDlgControls(TRUE,TRUE);
   UpdateTools();
 }
 
@@ -782,7 +782,7 @@ static void
   if ( GetStatus(b) ) val = (BigScalar)TRUE;
   else val = (BigScalar)FALSE;
   Nlm_SetMuskCParamEd(curClass,MSM_SEG_BORD,MSM_TRUEFALSE,val);
-  UpdateControls(TRUE,FALSE);
+  UpdateDlgControls(TRUE,FALSE);
 }
 
 static void
@@ -804,7 +804,7 @@ static void
   }
   val = (BigScalar)(GetValue(g)-1);
   Nlm_SetMuskCParamEd(curClass,MSM_FGAP,MSM_STYLE,val);
-  UpdateControls(TRUE,FALSE);
+  UpdateDlgControls(TRUE,FALSE);
 }
 
 static void
@@ -846,7 +846,7 @@ static void
     }
   }
   Nlm_SetMuskCParamEd(curClass,curSubClass,MSM_STYLE,val);
-  UpdateControls(TRUE,FALSE);
+  UpdateDlgControls(TRUE,FALSE);
 }
 
 static void
@@ -882,7 +882,7 @@ static void
     if ( GetStatus (orientCheckBox[curDlg]) ) val |= MSM_SEG_SHOWORIENT;
   }
   Nlm_SetMuskCParamEd(curClass,MSM_SEGMENT, MSM_STYLE, val);
-  UpdateControls(TRUE,FALSE);
+  UpdateDlgControls(TRUE,FALSE);
   UpdateTools ();
 }
 
@@ -905,7 +905,7 @@ static void
   }
   val = (BigScalar)GetValue(p) * 2 + 2;
   Nlm_SetMuskCParamEd(curClass,MSM_SEGMENT, MSM_HEIGHT, val);
-  UpdateControls(TRUE,FALSE);
+  UpdateDlgControls(TRUE,FALSE);
 }
 
 static void
@@ -1236,7 +1236,7 @@ static GrouP
                    NULL );
   }
   curSubDlg[curDlg] = 0;
-  UpdateControls (FALSE,TRUE);
+  UpdateDlgControls (FALSE,TRUE);
   return gRet;
 } /* End of CreateDlgFeatures () */
 
@@ -1308,7 +1308,7 @@ static void
       Nlm_SetMuskCParamEd(curClass,curSubClass,MSM_HEIGHT,fsize);
     }
   }
-  UpdateControls ( TRUE, TRUE );
+  UpdateDlgControls ( TRUE, TRUE );
 }
 
 static void  Nlm_SetTDef (
@@ -1322,7 +1322,7 @@ static void  Nlm_SetTDef (
     Show ( featPopuP );
     LoadFeatAr();
     FillFetureList (TRUE);
-    UpdateControls (TRUE,TRUE);
+    UpdateDlgControls (TRUE,TRUE);
   }
   UpdateTools();
 }
diff --git a/doc/blast.txt b/doc/blast.txt
index 44141b4f..944b2c49 100644
--- a/doc/blast.txt
+++ b/doc/blast.txt
@@ -1,18 +1,20 @@
 README for stand-alone BLAST
 
-$Date: 2003/06/30 16:30:18 $
+$Date: 2004/01/30 21:13:06 $
 
 This document provides information on stand-alone BLAST.  Topics covered are
 setting up stand-alone BLAST, command-line options for stand-alone BLAST,
 and a release history of the different versions.
 
+NCBI provides binaries for the following platforms:
+
 Apple MacOS 9 (powerpc)
 Apple MacOS X (powerpc)
 DEC/Compaq/HP OSF1 5.1 (alpha)
 FreeBSD 4.5 (ia32)
 HP HPUX 11 (hppa, ia64)
 IBM AIX 5.1 (power4, powerpc)
-Linux (kernel 2.4, glibc 2.2.4) (ia32, ia64)
+Linux (kernel 2.4, glibc 2.2.4) (ia32, ia64, amd64)
 Microsoft Windows 2000 (ia32)
 SGI IRIX 6.5 (mips)
 Sun Solaris 7 (ia32)
diff --git a/doc/dispatcher.html b/doc/dispatcher.html
index 64955714..a7c1832f 100644
--- a/doc/dispatcher.html
+++ b/doc/dispatcher.html
@@ -392,18 +392,6 @@ Firewall Port        IP Address
 </pre>
 
 <p>
-Please also note obsolescent settings that still should be provided
-but will be removed in the nearest future:
-
-<p align="center">
-<pre>
-Firewall Port        IP Address
---------------------------------
-    5811            130.14.22.32
-    5812            130.14.22.31
-</pre>
-
-<p>
 If your firewall is not transparent, the firewall port number
 should be mapped to the same port number on the external host.
 
@@ -559,7 +547,7 @@ you have a question, please contact <a href="mailto:info@ncbi.nlm.nih.gov">
 <p>
 <hr>
 <table border="0" cellspasing="0">
-<tr><td>Source: distrib/doc/dispatcher.html</td><td>$Date: 2003/09/29 15:04:00 $</td><td>$Revision: 6.23 $</td></tr>
+<tr><td>Source: distrib/doc/dispatcher.html</td><td>$Date: 2004/01/16 19:03:44 $</td><td>$Revision: 6.24 $</td></tr>
 </table>
 
 
diff --git a/doc/firewall.html b/doc/firewall.html
index 763e656b..3733e603 100644
--- a/doc/firewall.html
+++ b/doc/firewall.html
@@ -48,7 +48,7 @@
       <p>&nbsp;</p>
 
 			 <p>
-				<i>Last modified:</i> $Date: 2003/09/29 15:04:00 $<br>
+				<i>Last modified:</i> $Date: 2004/01/16 19:03:44 $<br>
 				<i>Latest version: </i>
 				<a href="http://www.ncbi.nlm.nih.gov/cpp/network/firewall.html">
 				  http://www.ncbi.nlm.nih.gov/cpp/network/firewall.html</a>
@@ -120,17 +120,6 @@ Firewall Port        IP Address
     5845            130.14.22.12  (cannot be accessed from outside NCBI!)
 </pre>
 
-Please also note obsolescent settings that still should be provided
-but will be removed in the nearest future:
-
-<p align="center">
-<pre>
-Firewall Port        IP Address
---------------------------------
-    5811            130.14.22.32
-    5812            130.14.22.31
-</pre>
-
 <p>
 If your firewall is not transparent, the firewall port number
 should be mapped to the same port number on the external host.
diff --git a/doc/formatdb.txt b/doc/formatdb.txt
index 1ef831f7..75beccdb 100644
--- a/doc/formatdb.txt
+++ b/doc/formatdb.txt
@@ -3,24 +3,24 @@ Formatdb README
 
 Table of Contents
 
-	Introduction
+    Introduction
  
-	Command Line Options
+    Command Line Options
 
     Configuration File
  
-	Formatdb Notes/Troubleshooting
-	  
-    		A The -o option and identifiers
-    		B "SORTFiles failed" message
-    		C Formatting large FASTA files
-    		D Piping a database to formatdb without uncompressing
-    		E Creating custom databases.
-    		F General troubleshooting tips.
-    		G "SeqIdParse Failure" error
-    		H "FileOpen" error
+    Formatdb Notes/Troubleshooting
+      
+            A The -o option and identifiers
+            B "SORTFiles failed" message
+            C Formatting large FASTA files
+            D Piping a database to formatdb without uncompressing
+            E Creating custom databases.
+            F General troubleshooting tips.
+            G "SeqIdParse Failure" error
+            H "FileOpen" error
 
-	Appendix 1: The Files Produced by Formatdb 	 
+    Appendix 1: The Files Produced by Formatdb      
 
 
 
@@ -46,143 +46,133 @@ Command Line Options
 A list of the command line options and the current version for formatdb may 
 be obtained by executing formatdb without options, as in:
 
-	formatdb -
+    formatdb -
 
 The formatdb options are summarized below:
 
 formatdb 2.2.5 arguments:
 
-	-t  Title for database file [String]  
-	    Optional
-	-i  Input file(s) for formatting (this parameter must be set)
-	    [File In]
-	-l  Logfile name: [File Out]  
-	    Optional
+    -t  Title for database file [String]  
+        Optional
+    -i  Input file(s) for formatting (this parameter must be set)
+        [File In]
+    -l  Logfile name: [File Out]  
+        Optional
             default = formatdb.log
-	-p  Type of file
-	    T - protein
-	    F - nucleotide [T/F]  Optional
-	    default = T
+    -p  Type of file
+        T - protein
+        F - nucleotide [T/F]  Optional
+        default = T
 
-	-o  Parse options
-	    T - True: Parse SeqId and create indexes.
-	    F - False: Do not parse SeqId. Do not create indexes.
-	    [T/F]  Optional default = F
+    -o  Parse options
+        T - True: Parse SeqId and create indexes.
+        F - False: Do not parse SeqId. Do not create indexes.
+        [T/F]  Optional default = F
 
-	If the "-o" option is TRUE (and the source database is in FASTA
-	format), then the database identifiers in the FASTA definition
-	line must follow the convention of the FASTA Defline Format.
-	Please see section "F Note on creating custom databases"
-	below.
+    If the "-o" option is TRUE (and the source database is in FASTA
+    format), then the database identifiers in the FASTA definition
+    line must follow the convention of the FASTA Defline Format.
+    Please see section "F Note on creating custom databases"
+    below.
 
-	-a  Input file is database in ASN.1 format (otherwise FASTA is expected)
-	    T - True,
-	    F - False.
-	    [T/F]  Optional default = F
+    -a  Input file is database in ASN.1 format (otherwise FASTA is expected)
+        T - True,
+        F - False.
+        [T/F]  Optional default = F
 
-	-b  ASN.1 database in binary mode
-	    T - binary,
-	    F - text mode.
-	    [T/F]  Optional default = F
+    -b  ASN.1 database in binary mode
+        T - binary,
+        F - text mode.
+        [T/F]  Optional default = F
 
-	A source ASN.1 database may be represented in two formats -
-	ascii text and binary. The "-b" option, if TRUE, specifies that
-	input ASN.1 database is in binary format. The option is ignored
-	in case of FASTA input database.
+    A source ASN.1 database may be represented in two formats -
+    ascii text and binary. The "-b" option, if TRUE, specifies that
+    input ASN.1 database is in binary format. The option is ignored
+    in case of FASTA input database.
 
 
-	-e  Input is a Seq-entry [T/F]  
-	    Optional
-	    default = F
+    -e  Input is a Seq-entry [T/F]  
+        Optional
+        default = F
 
-	A source ASN.1 database (either text ascii or binary) may
-	contain a Bioseq-set or just one Bioseq. In the latter case the
-	"-e" switch should be set to TRUE.
+    A source ASN.1 database (either text ascii or binary) may
+    contain a Bioseq-set or just one Bioseq. In the latter case the
+    "-e" switch should be set to TRUE.
 
-	-n  Base name for BLAST files [String]  
-	    Optional
+    -n  Base name for BLAST files [String]  
+        Optional
 
-	This options allows one to produce BLAST databases with a
-	different name than that of the original FASTA file.  For
-	instance, one could have a file named 'ecoli.nuc.txt' and and
-	format it as 'ecoli':
+    This options allows one to produce BLAST databases with a
+    different name than that of the original FASTA file.  For
+    instance, one could have a file named 'ecoli.nuc.txt' and and
+    format it as 'ecoli':
 
-	    formatdb -i ecoli.nuc.txt -p F -o T -n ecoli
+        formatdb -i ecoli.nuc.txt -p F -o T -n ecoli
 
-	    uncompress -c nr.z | formatdb -i stdin -o T -n nr
+        uncompress -c nr.z | formatdb -i stdin -o T -n nr
 
-	This can be used in situations where the original FASTA file is
-	not required other than by formatdb.  This can help in a
-	situation where disk-space is tight.
+    This can be used in situations where the original FASTA file is
+    not required other than by formatdb.  This can help in a
+    situation where disk-space is tight.
 
-	-v  Database volume size in millions of letters [Integer] Optional
-	    default = 0
+    -v  Database volume size in millions of letters [Integer] Optional
+        default = 0
         range from 0 to <NULL>
 
-	This option breaks up large FASTA files into 'volumes' (each
-	with a maximum  size of 2 billion letters).  As part of the
-	creation of a volume formatdb  writes a new type of BLAST
-	database file, called an  alias file, with the  extension 'nal'
-	or 'pal'.
+    This option breaks up large FASTA files into 'volumes' (each
+    with a maximum  size of 2 billion letters).  As part of the
+    creation of a volume formatdb  writes a new type of BLAST
+    database file, called an  alias file, with the  extension 'nal'
+    or 'pal'.
 
-	-s  Create indexes limited only to accessions - sparse [T/F]  
-	    Optional
-	    default = F
+    -s  Create indexes limited only to accessions - sparse [T/F]  
+        Optional
+        default = F
 
-	This option limits the indices for the string identifiers (used
-	by formatdb)  to accessions (i.e., no locus names).  This is
-	especially useful for sequences sets  like the EST's where the
-	accession and locus names are identical.  Formatdb runs  faster
-	and produces smaller temporary files if this option is used.
-	It is strongly  recommended for EST's, STS's, GSS's, and
-	HTGS's.
+    This option limits the indices for the string identifiers (used
+    by formatdb)  to accessions (i.e., no locus names).  This is
+    especially useful for sequences sets  like the EST's where the
+    accession and locus names are identical.  Formatdb runs  faster
+    and produces smaller temporary files if this option is used.
+    It is strongly  recommended for EST's, STS's, GSS's, and
+    HTGS's.
 
-	-A  Create ASN.1 structured deflines [T/F]  
-	    Optional
-	    default = T
+    -L  Create an alias file with this name
+        use the gifile arg (below) if set to calculate db size
+        use the BLAST db specified with -i (above) [File Out]  Optional
 
-	This option produces a new BLAST database format (version 4).  
-    The BLAST programs can read this format as well as the current format.  
-	The program automatically identifies which version it should work 
-	with.  This new format stores the sequence definition lines in 
-	a structured manner (as ASN.1), this will allow future versions of 
-	BLAST to better present taxonomic information as well as information 
-	about other resources (e.g., UniGene, LocusLink) for a database sequence.
+    This option produces a BLAST database alias file using a specified
+    database, but limiting the sequences searched to those in the GI list
+    given by the -F argument.  See the section "Note on creating an alias file 
+    for a GI list" for more information.
 
-  	-L  Create an alias file with this name
-        	use the gifile arg (below) if set to calculate db size
-        	use the BLAST db specified with -i (above) [File Out]  Optional
+    -F  Gifile (file containing list of gi's) [File In]  Optional
 
-	This option produces a BLAST database alias file using a specified
-	database, but limiting the sequences searched to those in the GI list
-	given by the -F argument.  See the section "Note on creating an alias file 
-	for a GI list" for more information.
+    This option can be used to specify the GI list for the alias file
+    construction (-L option above) or to produce a binary GI list if
+    the -B option (below) is set.
 
-  	-F  Gifile (file containing list of gi's) [File In]  Optional
+    -B  Binary Gifile produced from the Gifile specified above [File Out]  Optional
 
-	This option can be used to specify the GI list for the alias file
-	construction (-L option above) or to produce a binary GI list if
-	the -B option (below) is set.
-
-  	-B  Binary Gifile produced from the Gifile specified above [File Out]  Optional
-
-	This option specifies the name of a binary GI list file.  This option should
-	be used with the -F option.  A text GI list may be specified with the -F
-	option and the -B option will produce that GI list in binary format.  The
-	binary file is smaller and BLAST does not need to convert it, so it can
-	be read faster.  
+    This option specifies the name of a binary GI list file.  This option should
+    be used with the -F option.  A text GI list may be specified with the -F
+    option and the -B option will produce that GI list in binary format.  The
+    binary file is smaller and BLAST does not need to convert it, so it can
+    be read faster.  
 
 
 Configuration File
 ------------------
 Starting from formatdb version 4, we have added a configuration file to allow
 flexibility in specifying the membership and link bits to set in the ASN.1
-defline structures. The membership bit arrays are used to help distinguish
-sequences that belong to a subset database (e.g.: pdb, swissprot) in a
-non-redundant database (e.g.: nr). The link bit arrays are used to indentify
-which sequences should have a user specified "link out" in the blast (html) 
-report. These features are still under development and useful within NCBI
-only. A sample configuration file follows:
+defline structures. This feature is available by recompiling the formatdb
+binary with the following compile time flag: -DSET_ASN1_DEFLINE_BITS.
+The membership bit arrays are used to help distinguish sequences that belong 
+to a subset database (e.g.: pdb, swissprot) in a non-redundant database 
+(e.g.: nr). The link bit arrays are used to indentify which sequences should 
+have a user specified "link out" in the blast (html) report. These features 
+are still under development and useful within NCBI only. A sample 
+configuration file follows:
 
 ; .formatdbrc: formatdb configuration file
 ;
@@ -465,6 +455,7 @@ contain at most about 4 billion bases.  The new databases allows that to
 be much larger.
 
 
+PLEASE NOTE THAT VERSION 3 OF THE BLAST DATABASES WILL NO LONGER BE SUPPORTED.
 
 
 The new databases keep the sequence descriptors in a structured format
@@ -499,18 +490,18 @@ the identifiers for the databases from which the sequences were derived.
 
   Database Name                         Identifier Syntax
 
-  GenBank				gb|accession|locus
-  EMBL Data Library			emb|accession|locus
-  DDBJ, DNA Database of Japan		dbj|accession|locus
-  NBRF PIR				pir||entry
-  Protein Research Foundation		prf||name
-  SWISS-PROT				sp|accession|entry name
-  Brookhaven Protein Data Bank		pdb|entry|chain
-  Patents				pat|country|number 
-  GenInfo Backbone Id			bbs|number 
-  General database identifier		gnl|database|identifier
-  NCBI Reference Sequence		ref|accession|locus
-  Local Sequence identifier		lcl|identifier
+  GenBank                               gb|accession|locus
+  EMBL Data Library                     emb|accession|locus
+  DDBJ, DNA Database of Japan           dbj|accession|locus
+  NBRF PIR                              pir||entry
+  Protein Research Foundation           prf||name
+  SWISS-PROT                            sp|accession|entry name
+  Brookhaven Protein Data Bank          pdb|entry|chain
+  Patents                               pat|country|number 
+  GenInfo Backbone Id                   bbs|number 
+  General database identifier           gnl|database|identifier
+  NCBI Reference Sequence               ref|accession|locus
+  Local Sequence identifier             lcl|identifier
  
 
 For example, an identifier might be "gb|M73307|AGMA13GT", where the "gb" tag
@@ -682,37 +673,38 @@ BLASTDB=LabMac:blast:data
 Appendix 1: The Files Produced by Formatdb
 ------------------------------------------
 Using formatdb without the "-o T" indexing option results in three
-BLAST database files (.nhr, .nin, ,nsq).  Using the "-o T" option will result in 
-additional files. 
-If gi's are present in the FASTA definition lines of the source file, there will 
-be four additional files created (.nsd, nsi, nni, nnd). These are ISAM indices for 
-mapping a sequence identifier to a particular sequence in the BLAST database If 
-gi's are not use there will be only two additional files created (.nsd, .nsi).  
-These files are listed below for both an example nucleotide and a protein sequence 
-database.  The actual sequence data is stored in the files with extension "nsq" or 
-"psq".  The compression ratio for these files is about 4:1 for nucleotides and 1:1 
-for protein sequence source files.
-
-Extension	Content		Format		
+BLAST database files (.nhr, .nin, ,nsq).  Using the "-o T" option will result 
+in additional files. 
+If gi's are present in the FASTA definition lines of the source file, there 
+will be four additional files created (.nsd, nsi, nni, nnd). These are 
+ISAM indices for mapping a sequence identifier to a particular sequence in 
+the BLAST database. If gi's are not use there will be only two additional 
+files created (.nsd, .nsi).  
+These files are listed below for both an example nucleotide and a protein 
+sequence database. The actual sequence data is stored in the files with 
+extension "nsq" or "psq".  The compression ratio for these files is 
+about 4:1 for nucleotides and 1:1 for protein sequence source files.
+
+Extension    Content        Format        
 ---------------------------------------------
 Nucleotide database formatted without "-o T"
-						
-nhr  		deflines	binary	
-					
-nin            	indices		binary   	
+                        
+nhr          deflines       binary    
+                    
+nin          indices        binary       
 
-nsq		sequence data	binary		
+nsq        sequence data    binary        
 
 
 Nucleotide database formatted with "-o T" add these ISAM files:
 
-nnd            	GI data		binary    	
+nnd          GI data        binary        
 
-nni            	GI indices 	binary    	
+nni          GI indices     binary        
 
-nsd  		non-GI data	binary		
-		
-nsi  		non-GI indices  binary		
+nsd          non-GI data    binary        
+        
+nsi         non-GI indices  binary        
 
 The formatdb index files involving deflines are small relative to the
 source database due to entries such as the one below in which the
@@ -731,25 +723,25 @@ GCTTAGCCACGCCCCCACGGGACACAGCAGTGATAAAAATTAAGCTATAAACGAAAGTTCGACTAAGTCATGTTAATTTA
 ....16398 bp total
 
 
-Extension	Content		Format			
+Extension    Content        Format            
 ------------------------------------------
 Protein database formatted without "-o T
 
-phr  		deflines	binary	
-					
-pin            	indices		binary   	
+phr        deflines         binary    
+                    
+pin        indices          binary       
 
-psq		sequence data	binary		
+psq        sequence data    binary        
 
 Protein database formatted with "-o T" add these ISAM files:
 
-pnd            	GI data		binary    	
+pnd        GI data          binary        
 
-pni            	GI indices 	binary    	
+pni        GI indices       binary        
 
-psd  		non-GI data	binary		
-		
-psi  		non-GI indices  binary		
+psd        non-GI data      binary        
+        
+psi        non-GI indices   binary        
 
 The formatdb index files involving deflines are large relative to the
 source database due to entries such as the one below in which the
@@ -768,4 +760,4 @@ used to extract data from the BLAST databases.  Readdb is part
 of the the NCBI toolkit (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/),
 readdb.h contains a list of supported function calls.  
 
-Last updated April 02 2001
+Last updated January 30 2004
diff --git a/doc/fwd_check.sh b/doc/fwd_check.sh
index 3bc0306e..8dc7480e 100755
--- a/doc/fwd_check.sh
+++ b/doc/fwd_check.sh
@@ -1,5 +1,5 @@
 #! /bin/sh
-# $Id: fwd_check.sh,v 1.14 2003/09/29 14:04:45 lavr Exp $
+# $Id: fwd_check.sh,v 1.15 2004/01/16 19:03:45 lavr Exp $
 # Author:   Denis Vakatov (vakatov@ncbi,nlm.nih.gov)
 # Modified: Anton Lavrentiev (lavr@ncbi.nlm.nih.gov)
 #
@@ -20,8 +20,8 @@ cat <<EOF
 ;130.14.22.2	5859	RETIRED
 ;130.14.22.8	5840	RETIRED
 ;130.14.22.30	5810	RETIRED
-130.14.22.31	5812	OBSOLESCENT
-130.14.22.32	5811	OBSOLESCENT
+130.14.22.31	5812	RETIRED
+130.14.22.32	5811	RETIRED
 130.14.22.12	5845	INTERNAL
 130.14.29.112	5860	RESERVED
 130.14.29.112	5861	OK
diff --git a/doc/images/seqn01.png b/doc/images/seqn01.png
index 0436eafa..11c5aba1 100644
--- a/doc/images/seqn01.png
+++ b/doc/images/seqn01.png
diff --git a/doc/images/seqn02.png b/doc/images/seqn02.png
index 409423c5..1f9f82e9 100644
--- a/doc/images/seqn02.png
+++ b/doc/images/seqn02.png
diff --git a/doc/images/seqn03.png b/doc/images/seqn03.png
index 4ae67e56..751776b4 100644
--- a/doc/images/seqn03.png
+++ b/doc/images/seqn03.png
diff --git a/doc/images/seqn04.png b/doc/images/seqn04.png
index 2f620327..e40337e2 100644
--- a/doc/images/seqn04.png
+++ b/doc/images/seqn04.png
diff --git a/doc/images/seqn05.png b/doc/images/seqn05.png
index 85349391..e85d2536 100644
--- a/doc/images/seqn05.png
+++ b/doc/images/seqn05.png
diff --git a/doc/images/seqn06.png b/doc/images/seqn06.png
index 8d216689..84859cbd 100644
--- a/doc/images/seqn06.png
+++ b/doc/images/seqn06.png
diff --git a/doc/images/seqn07.png b/doc/images/seqn07.png
index 9c41ff75..5a172e28 100644
--- a/doc/images/seqn07.png
+++ b/doc/images/seqn07.png
diff --git a/doc/images/seqn08.png b/doc/images/seqn08.png
index adb4f3ba..bea5944a 100644
--- a/doc/images/seqn08.png
+++ b/doc/images/seqn08.png
diff --git a/doc/images/seqn09.png b/doc/images/seqn09.png
index 5995f5ec..405444da 100644
--- a/doc/images/seqn09.png
+++ b/doc/images/seqn09.png
diff --git a/doc/images/seqn10.png b/doc/images/seqn10.png
index 0d35480a..00556348 100644
--- a/doc/images/seqn10.png
+++ b/doc/images/seqn10.png
diff --git a/doc/images/seqn11.png b/doc/images/seqn11.png
index a5dafc3d..27d86887 100644
--- a/doc/images/seqn11.png
+++ b/doc/images/seqn11.png
diff --git a/doc/images/seqn12.png b/doc/images/seqn12.png
index c12857f8..32c2c1a4 100644
--- a/doc/images/seqn12.png
+++ b/doc/images/seqn12.png
diff --git a/doc/images/seqn13.png b/doc/images/seqn13.png
index 77cd5ba5..3deafbaf 100644
--- a/doc/images/seqn13.png
+++ b/doc/images/seqn13.png
diff --git a/doc/images/seqn14.png b/doc/images/seqn14.png
index 9ef673b6..3974a791 100644
--- a/doc/images/seqn14.png
+++ b/doc/images/seqn14.png
diff --git a/doc/images/seqn15.png b/doc/images/seqn15.png
index 6bd95104..44cf7c1c 100644
--- a/doc/images/seqn15.png
+++ b/doc/images/seqn15.png
diff --git a/doc/images/seqn16.png b/doc/images/seqn16.png
index 090ae0a5..54e5c201 100644
--- a/doc/images/seqn16.png
+++ b/doc/images/seqn16.png
diff --git a/doc/images/seqn17.png b/doc/images/seqn17.png
index aac50041..6b192dd0 100644
--- a/doc/images/seqn17.png
+++ b/doc/images/seqn17.png
diff --git a/doc/images/seqn18.png b/doc/images/seqn18.png
index 9350c0ac..2324eeb3 100644
--- a/doc/images/seqn18.png
+++ b/doc/images/seqn18.png
diff --git a/doc/images/seqn19.png b/doc/images/seqn19.png
index 75dbbeb3..d6e8a0cc 100644
--- a/doc/images/seqn19.png
+++ b/doc/images/seqn19.png
diff --git a/doc/images/seqn20.png b/doc/images/seqn20.png
index a9d0df70..ca8b83f8 100644
--- a/doc/images/seqn20.png
+++ b/doc/images/seqn20.png
diff --git a/doc/images/seqn21.png b/doc/images/seqn21.png
index c07f458b..240aa84c 100644
--- a/doc/images/seqn21.png
+++ b/doc/images/seqn21.png
diff --git a/doc/images/seqn22.png b/doc/images/seqn22.png
index d4532f07..8d595a59 100644
--- a/doc/images/seqn22.png
+++ b/doc/images/seqn22.png
diff --git a/doc/man/asn2gb.1 b/doc/man/asn2gb.1
index 7986d22b..78e4d2aa 100644
--- a/doc/man/asn2gb.1
+++ b/doc/man/asn2gb.1
@@ -1,4 +1,4 @@
-.TH ASN2GB 1 2003-04-27 NCBI "NCBI Tools User's Manual"
+.TH ASN2GB 1 2003-11-10 NCBI "NCBI Tools User's Manual"
 .SH NAME
 asn2gb \- convert ASN.1 biological data to a GenBank-style flat format
 .SH SYNOPSIS
@@ -23,12 +23,12 @@ asn2gb \- convert ASN.1 biological data to a GenBank-style flat format
 [\|\fB\-s\fP\ \fIstyle\fP\|]
 [\|\fB\-t\fP\ \fIN\fP\|]
 [\|\fB\-u\fP\ \fIN\fP\|]
-[\|\fB\-x\fP\ \fIacc\fP\|]
+.\" [\|\fB\-x\fP\ \fIacc\fP\|] \" disabled
 [\|\fB\-y\fP\ \fIN\fP\|]
 .SH DESCRIPTION
-\fBasn2ff\fP converts descriptions of biological sequences from NCBI's
+\fBasn2gb\fP converts descriptions of biological sequences from NCBI's
 ASN.1 format to one of several flat-file formats, and is the successor
-to \fBasn2gb\fP(1).
+to \fBasn2ff\fP(1).
 .SH OPTIONS
 A summary of options is included below.
 .TP
@@ -182,9 +182,9 @@ Hide most imported features
 Hide SNP features
 .PD
 .RE
-.TP
-\fB\-x\fP\ \fIacc\fP
-Accession to extract
+.\" .TP
+.\" \fB\-x\fP\ \fIacc\fP
+.\" Accession to extract
 .TP
 \fB\-y\fP\ \fIN\fP
 Feature itemID
diff --git a/doc/man/blast.1 b/doc/man/blast.1
index 8c7ec8cf..0f58ced1 100644
--- a/doc/man/blast.1
+++ b/doc/man/blast.1
@@ -1,4 +1,4 @@
-.TH BLAST 1 2003-04-27 NCBI "NCBI Tools User's Manual"
+.TH BLAST 1 2003-11-10 NCBI "NCBI Tools User's Manual"
 .SH NAME
 bl2seq, blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop \- Basic Local Alignment Search Tool
 .SH SYNOPSIS
@@ -626,7 +626,8 @@ Do not perform gapped alignment (N/A for tblastx)
 Generate words for every base of the database (default is every 4th)
 .TP
 \fB\-h\fP\ \fIX\fP (blastpgp, impala)
-e-value threshold for inclusion in multipass model (default = 0.005)
+e-value threshold for inclusion in multipass model (default = 0.002
+for blastpgp, 0.005 for impala)
 .TP
 \fB\-i\fP\ \fIfilename\fP
 Read (first) sequence from \fIfilename\fP (default is stdin)
diff --git a/doc/man/fastacmd.1 b/doc/man/fastacmd.1
index 588cfe33..d17795dd 100644
--- a/doc/man/fastacmd.1
+++ b/doc/man/fastacmd.1
@@ -1,4 +1,4 @@
-.TH FASTACMD 1 2003-04-27 NCBI "NCBI Tools User's Manual"
+.TH FASTACMD 1 2003-11-10 NCBI "NCBI Tools User's Manual"
 .SH NAME
 fastacmd \- retrieve FASTA sequences from a BLAST database
 .SH SYNOPSIS
@@ -96,6 +96,21 @@ commas
 .TP
 \fB\-t\fP
 Definition line should contain target GI only
+.SH EXIT STATUS
+.RS
+.PD 0
+.IP 0
+Completed successfully.
+.IP 1
+An error (other than those below) occurred.
+.IP 2
+The BLAST database was not found.
+.IP 3
+A search (accession, GI, or taxonomy info) failed.
+.IP 4
+No taxonomy database was found.
+.PD
+.RE
 .SH AUTHOR
 The National Center for Biotechnology Information.
 .SH SEE ALSO
diff --git a/doc/man/tbl2asn.1 b/doc/man/tbl2asn.1
index 3798b8e0..f60ec5d5 100644
--- a/doc/man/tbl2asn.1
+++ b/doc/man/tbl2asn.1
@@ -1,4 +1,4 @@
-.TH TBL2ASN 1 2003-04-27 NCBI "NCBI Tools User's Manual"
+.TH TBL2ASN 1 2003-11-10 NCBI "NCBI Tools User's Manual"
 .SH NAME
 tbl2asn \- prepare a GenBank submission using an ASCII feature table
 .SH SYNOPSIS
@@ -9,10 +9,13 @@ tbl2asn \- prepare a GenBank submission using an ASCII feature table
 [\|\fB\-c\fP\|]
 [\|\fB\-d\fP\|]
 [\|\fB\-g\fP\|]
-[\|\fB\-f\fP\ \fIfilename\fP\|]
+[\|\fB\-i\fP\ \fIfilename\fP\|]
+[\|\fB\-j\fP\ \fIstr\fP\|]
 [\|\fB\-k\fP\|]
+[\|\fB\-l\fP\|]
 [\|\fB\-m\fP\|]
 [\|\fB\-n\fP\ \fIstr\fP\|]
+[\|\fB\-o\fP\ \fIfilename\fP\|]
 [\|\fB\-p\fP\ \fIstr\fP\|]
 [\|\fB\-q\fP\|]
 [\|\fB\-r\fP\ \fIstr\fP\|]
@@ -20,6 +23,7 @@ tbl2asn \- prepare a GenBank submission using an ASCII feature table
 [\|\fB\-t\fP\ \fIfilename\fP\|]
 [\|\fB\-v\fP\|]
 [\|\fB\-x\fP\ \fIstr\fP\|]
+[\|\fB\-y\fP\ \fIstr\fP\|]
 .SH DESCRIPTION
 \fBtbl2asn\fP reads a template along with sequence and table files,
 and outputs ASN.1 for submission to GenBank. Thus, the submitter does
@@ -45,21 +49,30 @@ Annotate longest ORF
 \fB\-d\fP
 Read FASTAs as Delta
 .TP
-\fB\-f\fP\ \fIfilename\fP
-Read only this file
-.TP
 \fB\-g\fP
 Input is a genomic product set
 .TP
+\fB\-i\fP\ \fIfilename\fP
+Single input file
+.TP
+\fB\-j\fP\ \fIstr\fP
+Source qualifiers
+.TP
 \fB\-k\fP
 Set conflict on mismatch
 .TP
+\fB\-l\fP
+Read FASTA+Gap Alignment
+.TP
 \fB\-m\fP
 Allow alternative starts
 .TP
 \fB\-n\fP\ \fIstr\fP
 Organism name
 .TP
+\fB\-o\fP\ \fIfilename\fP
+Single output file
+.TP
 \fB\-p\fP\ \fIstr\fP
 Path to files
 .TP
@@ -80,6 +93,9 @@ Validate
 .TP
 \fB\-x\fP\ \fIstr\fP
 Suffix (default = \fB.fsa\fP)
+.TP
+\fB\-y\fP\ \fIstr\fP
+Comment
 .SH AUTHOR
 The National Center for Biotechnology Information.
 .SH SEE ALSO
diff --git a/doc/sequin.htm b/doc/sequin.htm
index cbd52165..41267466 100644
--- a/doc/sequin.htm
+++ b/doc/sequin.htm
@@ -48,7 +48,7 @@ A Quick Guide</b>
 
 <hr>
 
-<! use img src="http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/image##.gif" align=bottom>
+<! use img src="http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/image##.png" align=bottom>
 
 <p align="left">
 <font size=4>
@@ -312,7 +312,7 @@ save Sequin information templates for each sequence.
 
 <br>
 <p align="center">
-<img src="images/seqn01.gif" align=bottom alt="Welcome to Sequin form has
+<img src="images/seqn01.png" align=bottom alt="Welcome to Sequin form has
 push buttons to Start New Submission, Read Existing Record, Show Help, and
 Quit Program.">
 <br>
@@ -348,7 +348,7 @@ to release the record immediately into the public databases.
 
 <br>
 <p align="center">
-<img src="images/seqn02.gif" align=bottom alt="Submission page defaults
+<img src="images/seqn02.png" align=bottom alt="Submission page defaults
 allow immediate release of the record.">
 <br>
 
@@ -364,7 +364,7 @@ it is not necessary to type periods after initials or suffixes.
 
 <br>
 <p align="center">
-<img src="images/seqn03.gif" align=bottom alt="Contact page has fields for
+<img src="images/seqn03.png" align=bottom alt="Contact page has fields for
 contact person's Name, Phone, Fax, and Email.">
 <br>
 
@@ -382,7 +382,7 @@ or Sr.), not academic degrees.
 
 <br>
 <p align="center">
-<img src="images/seqn04.gif" align=bottom alt="Authors page has a spreadsheet
+<img src="images/seqn04.png" align=bottom alt="Authors page has a spreadsheet
 for entering an arbitrary number of authors.">
 <br>
 
@@ -392,7 +392,7 @@ primary author.
 
 <br>
 <p align="center">
-<img src="images/seqn05.gif" align=bottom alt="Affiliation page has fields
+<img src="images/seqn05.png" align=bottom alt="Affiliation page has fields
 for institutional mailing address.">
 <br>
 
@@ -429,7 +429,7 @@ unrelated sequences, where no alignment is present or should be calculated.
 
 <br>
 <p align="center">
-<img src="images/seqn06.gif" align=bottom alt="Sequence Format form has controls
+<img src="images/seqn06.png" align=bottom alt="Sequence Format form has controls
 for choosing the submission type and sequence data format.">
 <br>
 
@@ -472,7 +472,7 @@ GenBank.)
 
 <br>
 <p align="center">
-<img src="images/seqn07.gif" align=bottom alt="Organism page has fields for
+<img src="images/seqn07.png" align=bottom alt="Organism page has fields for
 Scientific Name, Location of Sequence, and Genetic Code for Translation">
 <br>
 
@@ -522,7 +522,7 @@ The format for annotating the nucleotide FASTA definition line is shown below:
 
 <br>
 <p align="center">
-<img src="images/seqn08.gif" align=bottom alt="Nucleotide page has controls
+<img src="images/seqn08.png" align=bottom alt="Nucleotide page has controls
 for Molecule, Topology, and Incomplete at 5 prime or 3 prime end.">
 <br>
 
@@ -555,7 +555,7 @@ The format for annotating the protein FASTA definition line is shown below:
 
 <br>
 <p align="center">
-<img src="images/seqn09.gif" align=bottom alt="Proteins page has controls
+<img src="images/seqn09.png" align=bottom alt="Proteins page has controls
 for Incomplete at amino or carboxy end.">
 <br>
 
@@ -578,7 +578,7 @@ sequence after the record is constructed.
 
 <br>
 <p align="center">
-<img src="images/seqn10.gif" align=bottom alt="Annotation page has controls
+<img src="images/seqn10.png" align=bottom alt="Annotation page has controls
 for adding Gene, rRNA, or CDS features to all sequences.">
 <br>
 
@@ -621,7 +621,7 @@ the missing information manually.
 
 <br>
 <p align="center">
-<img src="images/seqn11.gif" align=bottom alt="Product form has fields for
+<img src="images/seqn11.png" align=bottom alt="Product form has fields for
 Sequence ID, Title, Gene Symbol, Protein Name, and Comment.">
 <br>
 
@@ -656,7 +656,7 @@ form.
 
 <br>
 <p align="center">
-<img src="images/seqn12.gif" align=bottom alt="Source Modifiers form has a
+<img src="images/seqn12.png" align=bottom alt="Source Modifiers form has a
 spreadsheet for entering modifiers to each individual sequence.">
 <br>
 
@@ -679,7 +679,7 @@ EMBL as the database for submission in the first form).
 
 <br>
 <p align="center">
-<img src="images/seqn13.gif" align=bottom alt="View form has controls for
+<img src="images/seqn13.png" align=bottom alt="View form has controls for
 Target Sequence and Display format. Default format is GenBank flatfile.">
 <br>
 
@@ -717,7 +717,7 @@ products are spatially related to each other.
 
 <br>
 <p align="center">
-<img src="images/seqn14.gif" align=bottom alt="Graphical view has additional
+<img src="images/seqn14.png" align=bottom alt="Graphical view has additional
 controls for Style and Scale, and displays a drawing of feature locations on
 the sequence coordinate.">
 <br>
@@ -743,7 +743,7 @@ protein translations are shown as a series of tilde&nbsp;(~)&nbsp;characters.
 
 <br>
 <p align="center">
-<img src="images/seqn15.gif" align=bottom alt="Sequence format displays
+<img src="images/seqn15.png" align=bottom alt="Sequence format displays
 feature locations on the actual sequence letters.">
 <br>
 
@@ -822,7 +822,7 @@ large contig.
 
 <br>
 <p align="center">
-<img src="images/seqn16.gif" align=bottom alt="Update Sequence form
+<img src="images/seqn16.png" align=bottom alt="Update Sequence form
 displays information on how the old and new sequences align.">
 <br>
 
@@ -896,7 +896,7 @@ genetic codes, mismatched amino acids, and non-consensus splice sites.
 
 <br>
 <p align="center">
-<img src="images/seqn17.gif" align=bottom alt="Validator form has controls for
+<img src="images/seqn17.png" align=bottom alt="Validator form has controls for
 Message verbosity, Severity, message Filter, and a display of error messages.">
 <br>
 
@@ -960,7 +960,7 @@ tRNA, or completion of a stop codon by poly-adenylation of an mRNA.
 
 <br>
 <p align="center">
-<img src="images/seqn18.gif" align=bottom alt="Coding Region page has small
+<img src="images/seqn18.png" align=bottom alt="Coding Region page has small
 folder tabs for Product, Protein, Exceptions, and Misc. Product subpage has
 controls for Genetic Code, Predict Interval, and Translate Product.">
 <br>
@@ -1011,7 +1011,7 @@ database staff.
 
 <br>
 <p align="center">
-<img src="images/seqn19.gif" align=bottom alt="Properties page has small
+<img src="images/seqn19.png" align=bottom alt="Properties page has small
 folder tabs for General, Comment, Citations, and Cross-Refs. General page
 has controls for Partial, Pseudo, Evidence, Exception, and Explanation.">
 <br>
@@ -1031,7 +1031,7 @@ locations.
 
 <br>
 <p align="center">
-<img src="images/seqn20.gif" align=bottom alt="Location page has controls for
+<img src="images/seqn20.png" align=bottom alt="Location page has controls for
 5 prime Partial and 3 partial Partial, and a spreadsheet for entering an arbitrary
 number of intervals.">
 <br>
@@ -1085,7 +1085,7 @@ both the nucleotide and protein sequences.
 
 <br>
 <p align="center">
-<img src="images/seqn21.gif" align=bottom alt="NCBI DeskTop window displays a
+<img src="images/seqn21.png" align=bottom alt="NCBI DeskTop window displays a
 Venn Diagram of the internal structure of a record in the NCBI Data Model.">
 <br>
 
@@ -1136,7 +1136,7 @@ sequence record.
 
 <br>
 <p align="center">
-<img src="images/seqn22.gif" align=bottom alt="Network Configuration form has
+<img src="images/seqn22.png" align=bottom alt="Network Configuration form has
 buttons for Normal, Firewall, or No Connection.">
 <br>
 
@@ -1477,7 +1477,7 @@ genomic records are available at
 <CENTER>
 <P CLASS=medium1><B>Questions or Comments?</B>
 <BR>Write to the <A HREF="mailto:info@ncbi.nlm.nih.gov">NCBI Service Desk</A></P>
-<P CLASS=medium1>Revised April 14, 2003
+<P CLASS=medium1>Revised January 20, 2004
 
 </CENTER>
 
diff --git a/errmsg/valid.msg b/errmsg/valid.msg
index a7923795..bc138e16 100644
--- a/errmsg/valid.msg
+++ b/errmsg/valid.msg
@@ -159,6 +159,13 @@ $^   SeqLitGapLength0, 43
 A SeqLit component of a delta Bioseq can specify a gap, but it should not be a gap
 of 0 length.
 
+$^   TpaAssmeblyProblem, 44
+Third party annotation records should have a TpaAssembly user object and a
+Seq-hist.assembly alignment for the PRIMARY block.
+
+$^   SeqLocLength, 45
+A SeqLoc component of a delta Bioseq is suspiciously small.
+
 $$ SEQ_DESCR, 2
 
 $^   BioSourceMissing, 1
@@ -334,6 +341,9 @@ A feature location should refer to the accession or gi number, not a local or ge
 $^   ArchaicFeatureProduct, 14
 A feature product should refer to the accession or gi number, not a local or general ID.
 
+$^   GraphPackagingProblem, 15
+A graph should be packaged on its bioseq, or on a set containing the Bioseq.
+
 $$ SEQ_FEAT, 5
 
 $^   InvalidForType, 1
@@ -608,6 +618,17 @@ the inheritance by overlap.
 $^   UTRdoesNotAbutCDS, 66
 The 5'UTR and 3'UTR features should exactly abut the CDS feature.
 
+$^   BadConflictFlag, 67
+The coding region conflict flag is set, but the translated product is the
+same as the instantiated product Bioseq.
+
+$^   ConflictFlagSet, 68
+The coding region conflict flag is appropriately set, but this record should
+be brought to the attention of the source database for possible correction.
+
+$^   LocusTagProblem, 69
+A gene locus_tag should be a single token, with no spaces.
+
 $$ SEQ_ALIGN, 6
 
 $^   SeqIdProblem, 1
diff --git a/link/macmet/ApplicationStationery.mcp b/link/macmet/ApplicationStationery.mcp
index 7e7b3ee3..aa77f0f5 100644
--- a/link/macmet/ApplicationStationery.mcp
+++ b/link/macmet/ApplicationStationery.mcp
diff --git a/link/macmet/LibraryStationery.mcp b/link/macmet/LibraryStationery.mcp
index af6ead50..70f03339 100644
--- a/link/macmet/LibraryStationery.mcp
+++ b/link/macmet/LibraryStationery.mcp
diff --git a/make/makeApps.met b/make/makeApps.met
index 469f8202..80784322 100755
--- a/make/makeApps.met
+++ b/make/makeApps.met
@@ -20,9 +20,8 @@ property pCreateMachOTargets : true
 property pCreateCarbonTargets : false
 property pCreateWinTargets : false
 
-property pCreateDebugTargets : true
 property pCreateOptimizedTargets : true
-
+property pCreateDebugTargets : false
 property pCreateProfiledTargets : false
 
 -- Whether to have the projects use CVS or not.
@@ -35,7 +34,8 @@ property pShouldBuild : true
 
 property pStationeryName : "ApplicationStationery"
 
-property pTargetKeyWords : "Mach-O Carbon Win32 Debug Final"
+-- the handler GetTargetSpecs should change if these do.
+property pTargetKeyWords : "Mach-O Carbon Win32 Debug Final Profile"
 
 
 global gProjectData
@@ -46,19 +46,16 @@ on SimpleProjectData(projName, features)
 		set projName to characters 1 through 25 of projName as string
 	end if
 	
-	tell application "CodeWarrior IDE"
-		
-		if features does not contain "C" and features does not contain "C++" then
-			--error "Project " & projName & "'s default language (a feature) must be C or C++."
-			copy "C" to end of features
-		end if
-		set myFeatures to features
-		return {name:projName, features:myFeatures, rsrcs:{"ncbilogo.r", "Info.plc"}, settings:Â
-			{Prefix File:"", ppcProject:{}}, projLibs:Â
-			{"ncbi", "ncbiconn", "ncbiobj", "vibrant", "ncbimmdb", "ncbitool"}, fileData:Â
-			{{projPath:"demo:", fileList:{projName & ".c"}}}}
-		
-	end tell
+	if features does not contain "C" and features does not contain "C++" then
+		--error "Project " & projName & "'s default language (a feature) must be C or C++."
+		copy "C" to end of features
+	end if
+	set myFeatures to features
+	return {name:projName, features:myFeatures, rsrcs:{"ncbilogo.r", "Info.plc"}, settings:Â
+		{prefixFile:"", ppcProject:{}}, projLibs:Â
+		{"ncbi", "ncbiconn", "ncbiobj", "vibrant", "ncbimmdb", "ncbitool"}, fileData:Â
+		{{projPath:"demo:", fileList:{projName & ".c"}}}}
+	
 end SimpleProjectData
 
 on AddProject(projData)
@@ -76,12 +73,12 @@ on SetProjectData()
 		set myName to "Sequin"
 		set myFeatures to {"sockets"}
 		set mySettings to Â
-			{Prefix File:"", creator:"SEQN", ppcProject:{Preferred Heap Size:32000, Min Heap Size:6000}} Â
+			{prefixFile:"", creator:"SEQN", ppcProject:{Preferred Heap Size:32000, Min Heap Size:6000}} Â
 				
 		set myRsrcs to {"sequin.r", "InfoSequin.plc"}
 		set myLibs to {"ncbi", "ncbiconn", "ncbiobj", "ncbicdr", "vibrant", "ncbidesk", Â
 			"ncbimmdb", "ncbitool", "netcli", "netentr", "ncbibls3", "ncbimla", Â
-			"ncbitxc2", "ncbiid1", "vibnet"}
+			"ncbitxc2", "ncbiid1", "ncbispell", "vibnet"}
 		set myFiles to Â
 			{{projPath:"cdromlib:", fileList:{"accentr.c", "accutils.c"}}, Â
 				{projPath:"sequin:", fileList:{"sequin1.c", "sequin2.c", "sequin3.c", "sequin4.c", "sequin5.c", Â
@@ -93,7 +90,7 @@ on SetProjectData()
 		-- Entrez
 		set myName to "Entrez"
 		set myFeatures to {"sockets"}
-		set mySettings to {Prefix File:"", creator:"ENTZ", ppcProject:{}}
+		set mySettings to {prefixFile:"", creator:"ENTZ", ppcProject:{}}
 		set myRsrcs to {"entrez.r", "Info.plc"}
 		set myLibs to {"ncbi", "ncbiconn", "ncbiobj", "ncbicdr", "vibrant", "ncbidesk", "ncbimmdb", Â
 			"ncbitool", "netcli", "netentr", "ncbibls3", "ncbiid1", "vibnet"}
@@ -107,7 +104,7 @@ on SetProjectData()
 		-- Entrez2
 		set myName to "Entrez2"
 		set myFeatures to {"sockets"}
-		set mySettings to {Prefix File:"", creator:"ENTZ", ppcProject:{}}
+		set mySettings to {prefixFile:"", creator:"ENTZ", ppcProject:{}}
 		set myRsrcs to {"entrez.r", "Info.plc"}
 		set myLibs to {"ncbi", "ncbiconn", "ncbiobj", "ncbimmdb", "ncbitool", "vibrant", "ncbidesk"}
 		set myFiles to Â
@@ -119,7 +116,7 @@ on SetProjectData()
 		-- BlastCL3
 		set myName to "blastcl3"
 		set myFeatures to {"sockets"}
-		set mySettings to {Prefix File:"blastcl3.pfx", ppcProject:{}}
+		set mySettings to {prefixFile:"blastcl3.pfx", ppcProject:{}}
 		set myRsrcs to {"ncbilogo.r", "Info.plc"}
 		set myLibs to {"ncbi", "ncbiconn", "ncbiobj", "vibrant", "ncbitool", "netcli", "ncbibls3"}
 		set myFiles to Â
@@ -131,7 +128,7 @@ on SetProjectData()
 		-- Bl2seq
 		set myName to "bl2seq"
 		set myFeatures to {"sockets"}
-		set mySettings to {Prefix File:"", ppcProject:{}}
+		set mySettings to {prefixFile:"", ppcProject:{}}
 		set myRsrcs to {"ncbilogo.r", "Info.plc"}
 		set myLibs to {"ncbi", "ncbiconn", "ncbiobj", "vibrant", "ncbitool", "netcli", "ncbibls3", "ncbiid1"}
 		set myFiles to Â
@@ -147,7 +144,7 @@ on SetProjectData()
 		-- Spidey
 		set myName to "spidey"
 		set myFeatures to {"sockets"}
-		set mySettings to {Prefix File:"", ppcProject:{}}
+		set mySettings to {prefixFile:"", ppcProject:{}}
 		set myRsrcs to {"ncbilogo.r", "Info.plc"}
 		set myLibs to {"ncbi", "ncbiconn", "ncbiobj", "vibrant", "ncbitool", "netcli", "ncbiid1"}
 		set myFiles to Â
@@ -272,14 +269,11 @@ end stripVolName
 
 on HomeDir()
 	tell application "Finder"
-		
 		if my IsOSX() then
 			return the home as string
-			-- return my stripVolName(home as string)
 		else
 			return gStartupDisk
 		end if
-		
 	end tell
 end HomeDir
 
@@ -294,15 +288,6 @@ on ModuleRoot()
 	return modRoot
 end ModuleRoot
 
-on AccessRoot()
-	if my IsOSX() then
-		-- strip off the volume name at the front.
-		return my stripVolName(gDistribRoot)
-	else
-		return gDistribRoot
-	end if
-end AccessRoot
-
 on GetMyPath()
 	set myPath to path to me as string
 	if myPath contains "Script Editor" or Â
@@ -313,7 +298,7 @@ on GetMyPath()
 		return gDistribRoot & "make:"
 	else
 		tell application "Finder"
-			return container of myPath
+			return container of myPath as string
 		end tell
 	end if
 end GetMyPath
@@ -325,9 +310,7 @@ on SetGlobals()
 		
 		set gStartupDisk to startup disk as string
 		set gHomeDir to my HomeDir()
-		
 		set gDistribRoot to my ModuleRoot()
-		set gAccessRoot to my AccessRoot()
 		
 		set gIncludeDir to gDistribRoot & "include:"
 		set gSourceDir to gDistribRoot
@@ -388,20 +371,35 @@ on UpdateRenameHeader(canonicalName, canonicalDir, dotHName, dotHDir)
 	end tell
 end UpdateRenameHeader
 
-on SetUserPaths()
+
+on AppendAccessPath(aPath, isRecursive, isUserPath)
 	tell application "CodeWarrior IDE"
+		if (aPath does not end with ":") then set aPath to aPath & ":"
 		
-		set pathsToAdd to {}
-		-- Put the ncbi root, recursively at the end of the user paths.
-		copy {name:gAccessRoot, recursive:true, origin:absolute} to end of pathsToAdd
-		Set Preferences of panel "Access Paths" to {User Paths:pathsToAdd}
-		
+		set aPath to POSIX path of aPath
+		set pathsToAdd to {{name:aPath, recursive:isRecursive, origin:root relative, root:"OS X Volume", format:Unix Path}}
+		if isUserPath then
+			Set Preferences of panel "Access Paths" to {User Paths:pathsToAdd}
+		else
+			Set Preferences of panel "Access Paths" to {System Paths:pathsToAdd}
+		end if
 	end tell
-end SetUserPaths
+end AppendAccessPath
 
-on SetSysPaths()
-	-- This was all done in the Stationery project.
-end SetSysPaths
+
+on AppendPrefixFile(filename)
+	tell application "CodeWarrior IDE"
+		try -- CW ver. 8
+			Set Preferences of panel "C/C++ Compiler" to {Prefix File:prefixFile}
+		end try
+		try -- CW ver. 9
+			set oldtext to Get Preferences of {Prefix Text} from panel "C/C++ Preprocessor"
+			set oldtext to (Prefix Text of oldtext)
+			set prefixFileInclude to (oldtext & return & "#include \"" & filename & "\"")
+			Set Preferences of panel "C/C++ Preprocessor" to {Prefix Text:prefixFileInclude}
+		end try
+	end tell
+end AppendPrefixFile
 
 
 on SetupTarget(proj, targetIndex)
@@ -419,11 +417,10 @@ on SetupTarget(proj, targetIndex)
 		
 		if targetName contains "Debug" then
 			set targetDebug to true
-			if pCreateProfiledTargets then
-				set targetProfile to true
-			else
-				set targetProfile to false
-			end if
+			set targetProfile to false
+		else if targetName contains "Profile" then
+			set targetDebug to false
+			set targetProfile to true
 		else -- if targeName contains "Final" then
 			set targetDebug to false
 			set targetProfile to false
@@ -465,14 +462,16 @@ on SetupTarget(proj, targetIndex)
 		end if
 		
 		-- Debug or not.
-		if not targetDebug then
-			set fileNameSuffix to fileNameSuffix & "_O" -- for Optimized.
-		else
+		if targetDebug then
 			set fileNameSuffix to fileNameSuffix & "_D"
+		else if targetProfile then
+			set fileNameSuffix to fileNameSuffix & "_P"
+		else
+			set fileNameSuffix to fileNameSuffix & "_O" -- for Optimized.
 		end if
 		
 		-- non debug targets get different output names.
-		if not targetDebug then
+		if not targetDebug and not targetProfile then
 			if targetAPI is "Mach-O" then
 				set targetFilename to projName & "OSX" -- Mach adds OSX on the end.
 			else
@@ -518,8 +517,12 @@ on SetupTarget(proj, targetIndex)
 			end try
 		end if
 		
-		my SetUserPaths()
-		-- my SetSysPaths() -- done in the stationery project.
+		
+		if targetAPI is "Mach-O" then
+			my AppendAccessPath(gDistribRoot, true, false) -- end of system paths.
+		else
+			my AppendAccessPath(gDistribRoot, true, true) -- end of user paths.
+		end if
 		
 		-- Add per-project system paths.
 		set pathsToAdd to {}
@@ -530,7 +533,7 @@ on SetupTarget(proj, targetIndex)
 			Set Preferences of panel "Access Paths" to {System Paths:pathsToAdd}
 		
 		-- Set the appropriate prefix file.
-		set prefixFile to Prefix File of projSettings
+		set prefixFile to prefixFile of projSettings
 		if targetAPI is "Win32" and projFeatures contains "winprefix" then
 			set prefixFile to "Win32Headers.pch"
 		else
@@ -541,13 +544,7 @@ on SetupTarget(proj, targetIndex)
 			end if
 		end if
 		if prefixFile is not "" then
-			try -- CW ver. 8
-				Set Preferences of panel "C/C++ Compiler" to {Prefix File:prefixFile}
-			end try
-			try -- CW ver. 9
-				set prefixFileInclude to "#include \"" & prefixFile & "\""
-				Set Preferences of panel "C/C++ Preprocessor" to {Prefix Text:prefixFileInclude}
-			end try
+			my AppendPrefixFile(prefixFile)
 		end if
 		
 	end tell
@@ -579,7 +576,7 @@ on SetupTarget(proj, targetIndex)
 	tell application "CodeWarrior IDE"
 		
 		-- take care of debugging and profiling settings
-		if targetDebug then
+		if targetDebug or targetProfile then
 			set the debug of every target file of target targetIndex Â
 				of project document 1 to true
 		end if
@@ -605,7 +602,9 @@ on SetupTarget(proj, targetIndex)
 			end if
 		end if
 		repeat with i in projLibs
-			copy gLibsDir & i & fileNameSuffix & ".lib" to end of filesToAdd
+			if exists file (gLibsDir & i & fileNameSuffix & ".lib") of application "Finder" then
+				copy gLibsDir & i & fileNameSuffix & ".lib" to end of filesToAdd
+			end if
 		end repeat
 		
 		try
@@ -687,11 +686,6 @@ on UpdateTarget(proj, targetIndex)
 		-- Grab the fields of our project record and store them in local variables.
 		set projName to proj's name
 		
-		-- mitsock library isn't needed (and won't compile) except under Carbon.
-		if projName is "mitsock" and targetAPI is not "Carbon" then
-			return
-		end if
-		
 		set targetName to name of target targetIndex of project document 1
 		
 		set the current target of project document 1 to target targetIndex of project document 1
@@ -854,19 +848,23 @@ on GetTargetSpecs()
 		end if
 	end repeat
 	-- no Build files? match what the script parameters say to match.
-	-- NOTE: This is dependent on pTargetKeyWords
+	-- NOTE: This is dependent on pTargetKeyWords and the target names in the stationery.
 	if (count items of targetSpecs) is 0 then
-		if pCreateDebugTargets or pCreateOptimizedTargets then
-			if pCreateDebugTargets and pCreateOptimizedTargets then
-				set debugspec to ""
-			else if pCreateDebugTargets then
-				set debugspec to "Debug"
-			else if pCreateOptimizedTargets then
-				set debugspec to "Final"
-			end if
-			if pCreateMachOTargets then copy ("Mach-O" & " " & debugspec) to end of targetSpecs
-			if pCreateCarbonTargets then copy ("Carbon" & " " & debugspec) to end of targetSpecs
-			if pCreateWinTargets then copy ("Win32" & " " & debugspec) to end of targetSpecs
+		set debugspec to ""
+		if pCreateDebugTargets then
+			if pCreateMachOTargets then copy ("Mach-O Debug") to end of targetSpecs
+			if pCreateCarbonTargets then copy ("Carbon Debug") to end of targetSpecs
+			if pCreateWinTargets then copy ("Win32 Debug") to end of targetSpecs
+		end if
+		if pCreateProfiledTargets then
+			if pCreateMachOTargets then copy ("Mach-O Profile") to end of targetSpecs
+			if pCreateCarbonTargets then copy ("Carbon Profile") to end of targetSpecs
+			if pCreateWinTargets then copy ("Win32 Profile") to end of targetSpecs
+		end if
+		if pCreateOptimizedTargets then
+			if pCreateMachOTargets then copy ("Mach-O Final") to end of targetSpecs
+			if pCreateCarbonTargets then copy ("Carbon Final") to end of targetSpecs
+			if pCreateWinTargets then copy ("Win32 Final") to end of targetSpecs
 		end if
 	end if
 	return targetSpecs
@@ -904,7 +902,6 @@ on BuildProject(projName, targetSpecs)
 		if the name of window 1 is "Project Messages" then
 			close first window -- "close window 1" becomes "Close Window 1" (different event)
 		end if
-		
 		repeat with i from 1 to (count targets of project document 1)
 			-- do we want to build this target?
 			set thisTarget to name of target i of project document 1
diff --git a/make/makeLibs.met b/make/makeLibs.met
index 8cef04df..6debd3ad 100755
--- a/make/makeLibs.met
+++ b/make/makeLibs.met
@@ -14,15 +14,15 @@ property pSaveContinueOnErrors : false
 
 -- Whether to recreate existing project files.
 property pAlwaysCreateProjects : false
+
 -- Which targets to build.
 -- All of the targets are populated all the time. These affect what is compiled & built.
 property pCreateMachOTargets : true
 property pCreateCarbonTargets : false
 property pCreateWinTargets : false
 
-property pCreateDebugTargets : true
 property pCreateOptimizedTargets : true
-
+property pCreateDebugTargets : false
 property pCreateProfiledTargets : false
 
 -- Whether to have the projects use CVS or not.
@@ -34,13 +34,12 @@ property pShouldBuild : true
 property pStationeryName : "LibraryStationery"
 
 -- the handler GetTargetSpecs should change if these do.
-property pTargetKeyWords : "Mach-O Carbon Win32 Debug Final"
+property pTargetKeyWords : "Mach-O Carbon Win32 Debug Final Profile"
 
 
 global gStartupDisk
 global gHomeDir
 global gDistribRoot
-global gAccessRoot
 global gProjectsDir
 global gSourceDir
 global gIncludeDir
@@ -55,18 +54,15 @@ on ProjectData(projName, features, aFileData)
 		set projName to characters 1 through 25 of projName as string
 	end if
 	
-	tell application "CodeWarrior IDE"
-		
-		if features does not contain "C" and features does not contain "C++" then
-			copy "C" to end of features
-		end if
-		set myFeatures to features
-		
-		return {name:projName, features:myFeatures, rsrcs:{}, settings:Â
-			{Prefix File:"", ppcProject:{}}, projLibs:{}, sysPaths:{}, fileData:Â
-			aFileData}
-		
-	end tell
+	if features does not contain "C" and features does not contain "C++" then
+		copy "C" to end of features
+	end if
+	set myFeatures to features
+	
+	return {name:projName, features:myFeatures, rsrcs:{}, settings:Â
+		{prefixFile:"", ppcProject:{}}, projLibs:{}, sysPaths:{}, fileData:Â
+		aFileData}
+	
 end ProjectData
 
 on AddProject(projData)
@@ -115,7 +111,7 @@ end mkFileDataExceptFiles
 on DataPlusPrefixFile(dataRec, prefix)
 	tell application "CodeWarrior IDE"
 		
-		set the Prefix File of dataRec's settings to prefix
+		set the prefixFile of dataRec's settings to prefix
 		return dataRec
 		
 	end tell
@@ -140,8 +136,8 @@ end EndsWith
 
 on SetProjectData()
 	
-	-- Not Okay under Mach-O
-	--AddSimpleProject("mitsock", {}, "connect:mitsock")
+	-- Only needed for Carbon
+	AddSimpleProject("mitsock", {}, "connect:mitsock")
 	
 	AddProject(ProjectData("ncbi", {"winprefix"}, {Â
 		mkFileDataExceptFiles("corelib:", {"drwnflpt.c", "drwnfspc.c", "drwnmfls.c", "ncbiargs.c", "ncbimain.c"}), Â
@@ -156,6 +152,8 @@ on SetProjectData()
 		mkFileData("api:"), Â
 		mkFileDataExceptFiles("ddv:", {"ddvmain.c"})}))
 	
+	AddSimpleProject("vibrant", {"winprefix"}, "vibrant")
+	
 	AddSimpleProjectExceptFiles("ncbicdr", {}, "cdromlib", {"acccn3ds.c", "accentr.c", "accmmdbs.c", "accutils.c"})
 	
 	AddSimpleProjectExceptFiles("ncbidesk", {}, "desktop", {"sdisplay.c"})
@@ -199,8 +197,6 @@ on SetProjectData()
 		mkFileDataExceptFiles("network:taxon1:taxon2:", {"txcproc.c"}), Â
 		mkFileDataExceptFiles("network:taxon1:common:", {"checkid.c"})}), "tax2.pfx"))
 	
-	AddSimpleProject("vibrant", {"winprefix"}, "vibrant")
-	
 	AddSimpleProjectListFiles("ncbiconn", {"winprefix"}, "connect", Â
 		{"ncbi_buffer", "ncbi_socket", "ncbi_core", "ncbi_core_c", "ncbi_util", "ncbi_priv", Â
 			"ncbi_ansi_ext", "ncbi_connection", "ncbi_connector", "ncbi_connutil", Â
@@ -211,6 +207,12 @@ on SetProjectData()
 	
 	AddSimpleProjectExceptFiles("netcli", {}, "network:nsclilib", {"ni_encr.c", "ni_list.c", "ni_lib.c"})
 	
+	AddSimpleProject("ncbispell", {}, "network:spell:client")
+
+	AddSimpleProject("ncbiblast", {}, "algo:blast:core")
+	
+	AddSimpleProject("ncbiblastapi", {}, "algo:blast:api")
+	
 end SetProjectData
 
 --
@@ -267,15 +269,6 @@ on ModuleRoot()
 	return modRoot
 end ModuleRoot
 
-on AccessRoot()
-	if my IsOSX() then
-		-- strip off the volume name at the front.
-		return my stripVolName(gDistribRoot)
-	else
-		return gDistribRoot
-	end if
-end AccessRoot
-
 on GetMyPath()
 	set myPath to path to me as string
 	if myPath contains "Script Editor" or Â
@@ -299,7 +292,6 @@ on SetGlobals()
 		set gStartupDisk to startup disk as string
 		set gHomeDir to my HomeDir()
 		set gDistribRoot to my ModuleRoot()
-		set gAccessRoot to my AccessRoot()
 		
 		set gIncludeDir to gDistribRoot & "include:"
 		set gSourceDir to gDistribRoot
@@ -369,20 +361,35 @@ on CopyHeaders()
 	end tell
 end CopyHeaders
 
-on SetUserPaths()
+
+on AppendAccessPath(aPath, isRecursive, isUserPath)
 	tell application "CodeWarrior IDE"
+		if (aPath does not end with ":") then set aPath to aPath & ":"
 		
-		set pathsToAdd to {}
-		-- Put the ncbi root, recursively at the end of the user paths.
-		copy {name:gAccessRoot, recursive:true, origin:absolute} to end of pathsToAdd
-		Set Preferences of panel "Access Paths" to {User Paths:pathsToAdd}
-		
+		set aPath to POSIX path of aPath
+		set pathsToAdd to {{name:aPath, recursive:isRecursive, origin:root relative, root:"OS X Volume", format:Unix Path}}
+		if isUserPath then
+			Set Preferences of panel "Access Paths" to {User Paths:pathsToAdd}
+		else
+			Set Preferences of panel "Access Paths" to {System Paths:pathsToAdd}
+		end if
 	end tell
-end SetUserPaths
+end AppendAccessPath
 
-on SetSysPaths()
-	-- This was all done in the Stationery project.
-end SetSysPaths
+
+on AppendPrefixFile(filename)
+	tell application "CodeWarrior IDE"
+		try -- CW ver. 8
+			Set Preferences of panel "C/C++ Compiler" to {Prefix File:prefixFile}
+		end try
+		try -- CW ver. 9
+			set oldtext to Get Preferences of {Prefix Text} from panel "C/C++ Preprocessor"
+			set oldtext to (Prefix Text of oldtext)
+			set prefixFileInclude to (oldtext & return & "#include \"" & filename & "\"")
+			Set Preferences of panel "C/C++ Preprocessor" to {Prefix Text:prefixFileInclude}
+		end try
+	end tell
+end AppendPrefixFile
 
 
 on SetupTarget(proj, targetIndex)
@@ -400,11 +407,10 @@ on SetupTarget(proj, targetIndex)
 		
 		if targetName contains "Debug" then
 			set targetDebug to true
-			if pCreateProfiledTargets then
-				set targetProfile to true
-			else
-				set targetProfile to false
-			end if
+			set targetProfile to false
+		else if targetName contains "Profile" then
+			set targetDebug to false
+			set targetProfile to true
 		else -- if targeName contains "Final" then
 			set targetDebug to false
 			set targetProfile to false
@@ -451,10 +457,12 @@ on SetupTarget(proj, targetIndex)
 		end if
 		
 		-- Debug or not.
-		if not targetDebug then
-			set targetFilename to targetFilename & "_O" -- for Optimized.
-		else
+		if targetDebug then
 			set targetFilename to targetFilename & "_D"
+		else if targetProfile then
+			set targetFilename to targetFilename & "_P"
+		else
+			set targetFilename to targetFilename & "_O" -- for Optimized.
 		end if
 		
 		set targetFilename to targetFilename & ".lib"
@@ -479,8 +487,12 @@ on SetupTarget(proj, targetIndex)
 			Set Preferences of panel targetPanelName to ppcProject of projSettings
 		end if
 		
-		my SetUserPaths()
-		-- my SetSysPaths() -- done in the stationery project.
+		
+		if targetAPI is "Mach-O" then
+			my AppendAccessPath(gDistribRoot, true, false) -- end of system paths.
+		else
+			my AppendAccessPath(gDistribRoot, true, true) -- end of user paths.
+		end if
 		
 		-- Add per-project system paths.
 		set pathsToAdd to {}
@@ -491,7 +503,7 @@ on SetupTarget(proj, targetIndex)
 			Set Preferences of panel "Access Paths" to {System Paths:pathsToAdd}
 		
 		-- Set the appropriate prefix file.
-		set prefixFile to Prefix File of projSettings
+		set prefixFile to prefixFile of projSettings
 		if targetAPI is "Win32" and projFeatures contains "winprefix" then
 			set prefixFile to "Win32Headers.pch"
 		else
@@ -502,13 +514,7 @@ on SetupTarget(proj, targetIndex)
 			end if
 		end if
 		if prefixFile is not "" then
-			try -- CW ver. 8
-				Set Preferences of panel "C/C++ Compiler" to {Prefix File:prefixFile}
-			end try
-			try -- CW ver. 9
-				set prefixFileInclude to "#include \"" & prefixFile & "\""
-				Set Preferences of panel "C/C++ Preprocessor" to {Prefix Text:prefixFileInclude}
-			end try
+			my AppendPrefixFile(prefixFile)
 		end if
 		
 	end tell
@@ -540,7 +546,7 @@ on SetupTarget(proj, targetIndex)
 	tell application "CodeWarrior IDE"
 		
 		-- take care of debugging and profiling settings
-		if targetDebug then
+		if targetDebug or targetProfile then
 			set the debug of every target file of target targetIndex Â
 				of project document 1 to true
 		end if
@@ -572,6 +578,7 @@ on SetupTarget(proj, targetIndex)
 	end tell
 end SetupTarget
 
+
 on GetTargetFiles(i)
 	tell application "CodeWarrior IDE"
 		-- get the target
@@ -789,19 +796,23 @@ on GetTargetSpecs()
 		end if
 	end repeat
 	-- no Build files? match what the script parameters say to match.
-	-- NOTE: This is dependent on pTargetKeyWords
+	-- NOTE: This is dependent on pTargetKeyWords and the target names in the stationery.
 	if (count items of targetSpecs) is 0 then
-		if pCreateDebugTargets or pCreateOptimizedTargets then
-			if pCreateDebugTargets and pCreateOptimizedTargets then
-				set debugspec to ""
-			else if pCreateDebugTargets then
-				set debugspec to "Debug"
-			else if pCreateOptimizedTargets then
-				set debugspec to "Final"
-			end if
-			if pCreateMachOTargets then copy ("Mach-O" & " " & debugspec) to end of targetSpecs
-			if pCreateCarbonTargets then copy ("Carbon" & " " & debugspec) to end of targetSpecs
-			if pCreateWinTargets then copy ("Win32" & " " & debugspec) to end of targetSpecs
+		set debugspec to ""
+		if pCreateDebugTargets then
+			if pCreateMachOTargets then copy ("Mach-O Debug") to end of targetSpecs
+			if pCreateCarbonTargets then copy ("Carbon Debug") to end of targetSpecs
+			if pCreateWinTargets then copy ("Win32 Debug") to end of targetSpecs
+		end if
+		if pCreateProfiledTargets then
+			if pCreateMachOTargets then copy ("Mach-O Profile") to end of targetSpecs
+			if pCreateCarbonTargets then copy ("Carbon Profile") to end of targetSpecs
+			if pCreateWinTargets then copy ("Win32 Profile") to end of targetSpecs
+		end if
+		if pCreateOptimizedTargets then
+			if pCreateMachOTargets then copy ("Mach-O Final") to end of targetSpecs
+			if pCreateCarbonTargets then copy ("Carbon Final") to end of targetSpecs
+			if pCreateWinTargets then copy ("Win32 Final") to end of targetSpecs
 		end if
 	end if
 	return targetSpecs
diff --git a/make/makeall.dos b/make/makeall.dos
index aa41aa90..b3fc1690 100644
--- a/make/makeall.dos
+++ b/make/makeall.dos
@@ -1,4 +1,4 @@
-# $Id: makeall.dos,v 6.158 2003/01/07 22:11:29 lavr Exp $
+# $Id: makeall.dos,v 6.159 2003/11/28 15:19:09 camacho Exp $
 ##################################################
 ###  Makefile for non-network-based libraries + asntool
 #####
@@ -106,7 +106,7 @@ OBJ23 = +csim.obj +db_slist.obj +dust.obj +falign.obj +g_any.obj \
 	+urkutil.obj +urkpcc.obj +urkptpf.obj \
 	+urkepi.obj +urkfltr.obj +urkdust.obj +urksigu.obj +seg.obj \
 	+urkbias.obj +urkcnsrt.obj +urktree.obj +pseed3.obj +pattern1.obj \
-	+impatool.obj +posit2.obj +newkar.obj +mbalign.obj \
+	+impatool.obj +posit2.obj +mbalign.obj \
 	+vecscrn.obj +mblast.obj +rpsutil.obj +kappa.obj  \
 	+xmlblast.obj +bxmlobj.obj +dotseq.obj +spidey.obj +motif.obj
 
diff --git a/make/makeall.met b/make/makeall.met
deleted file mode 100644
index 524441cb..00000000
--- a/make/makeall.met
+++ /dev/null
@@ -1 +0,0 @@
--- C libs --

--
-- Properties
--

property pUsingCPlusPlus : false
property pProjectFileExtension : ".mcp"

-- Whether to recreate existing project files.
property pAlwaysCreateProjects : false

-- Which targets to create.
-- If these are changed you must recreate the project files.  There is no direct effect on building.
property pCreateBlueTargets : true -- 'Blue' was codename for System 7, here it means pre-Carbon.
property pCreateCarbonTargets : true
property pCreateDebugTargets : true
property pCreateProfiledTargets : false
property pCreateOptimizedTargets : true

-- Whether to compile everything.
property pShouldBuild : true

property pDirsToCreate : {Â
	{relPath:"", name:"include"}, Â
	{relPath:"", name:"lib"}}

property pLinkExecutables : false

--
-- Routines specific to this project
--

on ProjectData(projName, features, fileData)
	
	if (count characters of projName) > 18 then
		set projName to characters 1 through 18 of projName as string
	end if
	
	tell application "CodeWarrior IDE"
		
		if features does not contain "C" and features does not contain "C++" then
			--error "Project " & projName & "'s default language (a feature) must be C or C++."
			copy "C" to end of features
		end if
		set myFeatures to features
		--copy "BNDL" to end of myFeatures
		return {name:projName, features:myFeatures, rsrcs:{}, settings:Â
			{Prefix File:"", ppcProject:{}}, projLibs:{}, sysPaths:{}, fileData:Â
			fileData}
		
	end tell
end ProjectData

on SimpleProjectData(projName, features, section, fileList)
	
	set myPath to section & ":"
	return ProjectData(projName, features, {{projPath:myPath, fileList:fileList}})
	
end SimpleProjectData

on AddSimpleProject(projName, features, section, fileList)
	
	AddProject(SimpleProjectData(projName, features, section, fileList))
	
end AddSimpleProject

on DataPlusPrefixFile(dataRec, prefix)
	tell application "CodeWarrior IDE"
		
		set the Prefix File of dataRec's settings to prefix
		return dataRec
		
	end tell
end DataPlusPrefixFile

on SetProjectData()
	
	AddSimpleProject("mitsock", {}, "connect:mitsock", Â
		{"OTSocketInternal", "OTErrno", "OTSockets", "OTidle", "OTNetdbServices", "OTnetdb"})
	
	AddProject(ProjectData("ncbi", {}, {Â
		Â
			{projPath:"corelib:", fileList:{Â
				"ncbibs", "ncbienv", "ncbierr", "ncbifile", "ncbimath", "ncbimem", "ncbimisc", Â
				"ncbimsg", "ncbiprop", "ncbisgml", "ncbistr", "ncbitime", "ncbilang", "gifgen", Â
				"togif", "ncbithr", "tsprintf", "tree", "wwwutils", "matrix", "binary", "regex"}}, Â
		Â
			{projPath:"corelib:morefile:", fileList:{Â
				"FullPath", "FSpCompat", "MoreFilesX"}}, Â
		Â
			{projPath:"connect:", fileList:{Â
				"ncbibuf", "ncbisock", "connection", "urlquery"}}, Â
		Â
			{projPath:"ctools:", fileList:{Â
				"asn_connection"}}, Â
		Â
			{projPath:"asnlib:", fileList:{Â
				"asnbufo", "asndebin", "asnenbin", "asngen", "asngenob", "asnio", "asnlex", Â
				"asnlext", "asnout", "asnprint", "asntypes"}}}))
	
	AddSimpleProject("ncbiconn", {}, "connect", Â
		{"ncbi_buffer", "ncbi_socket", "ncbi_core", "ncbi_core_c", "ncbi_util", "ncbi_priv", Â
			"ncbi_ansi_ext", "ncbi_connection", "ncbi_connector", "ncbi_connutil", Â
			"ncbi_file_connector", "ncbi_host_info.c", "ncbi_http_connector", Â
			"ncbi_memory_connector", "ncbi_server_info", "ncbi_service", Â
			"ncbi_service_connector", "ncbi_dispd", "ncbi_lbsmd_stub", Â
			"ncbi_socket_connector", "ncbi_sendmail"})
	
	AddProject(ProjectData("ncbiobj", {}, {Â
		Â
			{projPath:"object:", fileList:{Â
				"objacces", "objalign", "objall", "objbibli", "objblock", "objcode", "objfdef", Â
				"objfeat", "objgen", "objloc", "objmdrs", "objmedli", "objproj", Â
				"objprt", "objpub", "objpubme", "objres", "objseq", "objsset", "objalignloc", Â
				"objsub", "objgbseq", "objtseq"}}, Â
		Â
			{projPath:"access:", fileList:{Â
				"objent2", "ent2api", "pmfapi", "qblastapi", "vecscnapi", "objmim", Â
				"mimapi"}}, Â
		Â
			{projPath:"api:", fileList:{Â
				"asn2ff1", "asn2ff2", "asn2ff3", "asn2ff4", "asn2ff5", "asn2ff6", "asn2gnbk", "codon", Â
				"edutil", "ffprint", "findrepl", "ftusrstr", "gather", "gbfeat", "gbftglob", "gbparint", Â
				"jzcoll", "jzmisc", "lsqfetch", "maputil", "mconsist", "objmgr", "prtutil", "satutil", Â
				"seqmgr", "seqport", "sequtil", "simple", "sqnutil1", "sqnutil2", "sqnutil3", Â
				"subutil", "tofasta", "tofile", "tomedlin", "utilpars", "utilpub", "salpstat", Â
				"salpedit", "valid", "alignmgr", "alignmgr2", "aliparse", "aliread", "alignval", Â
				"wprint", "salpacc", "salprop", "salsap", "salstruc", "salutil", "udvseq", "blocks", Â
				"pgppop", "samutil", "ddvcolor", "viewmgr", "jsavlt", "needleman", "fdlobj", "txalign"}}, Â
		Â
			{projPath:"ddv:", fileList:{Â
				"ddvcreate"}}}))
	
	AddSimpleProject("ncbicdr", {}, "cdromlib", Â
		{"casn", "cdconfig", "cdentrez", "cdnewlib", "cdromlib", "objentr"})
	
	AddSimpleProject("vibrant", {}, "vibrant", Â
		{"ncbidraw", "vibbutns", "vibextra", "vibfiles", "vibforms", "vibgroup", "viblists", Â
			"vibmenus", "vibprmpt", "vibsbars", "vibslate", "vibtexts", "vibutils", Â
			"vibwndws", "document", "drawing", "mapping", "palette", "picture", "table", Â
			"viewer", "diagnost", "image", "pictur3d", "prim3d1", "prim3d2", "prim3d3", Â
			"prim3d4", "prim3d5", "viewer3d", "vibmouse", "imagelst", "treeview", "shim3d", Â
			"odlbox"})
	
	AddSimpleProject("ncbidesk", {}, "desktop", Â
		{"asn2graphic", "biosrc", "bspview", "cdrgn", "dlgutil1", "dlgutil2", "dotmatrx", "drawseq", Â
			"e2trmlst", "e2docsum", "fea2seg", "fstyle", "glbpic", "gbfview", "gphview", "gphdraw", Â
			"gxydraw", "gtrdraw", "seqpanel", "ingengraph", "ingenext", "ingenwin", "import", "layout", "mapgene", Â
			"medview", "prtgene", "pubdesc", "saldist", "saled", "salfiles", "salpanel", "salparam", Â
			"salsa", "seqsub", "seqfltr", "seqgraph", "seqgrphx", "seqmtrx", "seqpcc", "seqanal", Â
			"aacomp", "seqscrl", "smdlg1", "smdlg2", "smdlg3", "smtools", "styleman", "stylemui", Â
			"vsm", "vsmfile", "vsmutil", "udvgraph", "udvopen", "udvpanel", "salogif", Â
			"dotvibrant"})
	
	AddSimpleProject("ddvlib", {}, "ddv", Â
		{"ddvclick", "ddvgraph", "ddvopen", "ddvpanel"})
	
	AddSimpleProject("ncbitool", {}, "tools", Â
		{"csim", "db_slist", "dust", "falign", "g_any", "pobutil", "stsutil", "sec", "sim2", Â
			"sim3", "sim4", "simutil", "slist", "suggadj", "suggest", "suggslp", "tfuns", Â
			"toasn3", "toporg", "blast", "blastconcat", "blastutl", "blastool", "splutil", "actutils", Â
			"gapxdrop", "bandalg0", "bandalg1", "bandalg2", "bandalg3", "bandalg4", "bandalg5", Â
			"bandalgn", "blastkar", "lookup", "posit", "readdb", "ncbisam", "ncbisort", "salign", Â
			"salptool", "urkutil", "urkpcc", "urkptpf", "urkepi", "urkfltr", "urkdust", Â
			"urksigu", "seg", "urkbias", "urkcnsrt", "urktree", "pattern1", "pseed3", Â
			"impatool", "posit2", "newkar", "mbalign", "mblast", "vecscrn", Â
			"rpsutil", "kappa", "xmlblast", "bxmlobj", "dotseq", "spidey", "motif"})
	
	AddProject(DataPlusPrefixFile(ProjectData("ncbimmdb", {}, {Â
		Â
			{projPath:"biostruc:", fileList:{Â
				"corematx", "dvncode", "objmmdb1", "objmmdb2", "objmmdb3", "mmdbapi", Â
				"mmdbapi1", "mmdbapi2", "mmdbapi3", "mmdbapi4", "mmdbentr", "vastsubs", Â
				"prunebsc"}}, Â
		Â
			{projPath:"object:", fileList:{Â
				"objmime"}}, Â
		Â
			{projPath:"access:", fileList:{Â
				"strucapi"}}, Â
		Â
			{projPath:"biostruc:cn3d:", fileList:{Â
				"objcn3d"}}, Â
		Â
			{projPath:"biostruc:cdd:", fileList:{Â
				"objcdd", "cddutil", "cddposutil", Â
				"thrdalgs", "thrdatd", "thrdbwfi", "thrdcpal", Â
				"thrdcpll", "thrdcprl", "thrdcxei", "thrddgri", "thrdrsmp", Â
				"thrdsal0", "thrdsalr", "thrdsalu", "thrdsgoi", "thrdslo0", Â
				"thrdslor", "thrdslou", "thrdspci", "thrdspea", "thrdspel", Â
				"thrdspni", "thrdttb0", "thrdttbi", "thrdzsc"}}}), "gif.pfx"))
	
	AddSimpleProject("ncbiNacc", {}, "cdromlib", Â
		{"accentr", "accutils", "accmmdbs", "acccn3ds"})
	
	AddSimpleProject("netentr", {}, "network:entrez:client", Â
		{"netentr", "netlib", "objneten"})
	
	AddSimpleProject("netcli", {}, "network:nsclilib", Â
		{"ncbicli", "ncbiurl", "ni_disp", "ni_encrs", "ni_service", "ni_error", "ni_lib_", Â
			"ni_macdv", "ni_msg", "ni_www", "ni_debug"})
	
	AddSimpleProject("ncbibls3", {}, "network:blast3:client", Â
		{"netblap3", "objblst3"})
	
	AddSimpleProject("ncbiid1", {}, "network:id1arch", Â
		{"id1gen", "id1arch", "accid1"})
	
	AddSimpleProject("ncbimla", {}, "network:medarch:client", Â
		{"medarch", "medutil", "objmla"})
	
	AddProject(DataPlusPrefixFile(ProjectData("ncbitxc2", {}, {Â
		Â
			{projPath:"network:taxon1:taxon2:", fileList:{Â
				"parttree", "taxcs", "tc2proc", "txcdproc"}}, Â
		Â
			{projPath:"network:taxon1:common:", fileList:{Â
				"objtax1", "taxutil"}}}), "tax2.pfx"))
	
	AddSimpleProject("vibnet", {}, "network:vibnet", Â
		{"netcnfg", "trmlst", "docsum"})
	
end SetProjectData

--
-- Global variables
--

global gStartupDisk
global gHomeDir
global gMWroot
global gMWCWfolder
global gMacLibs
global gStubLibs
global gPPCLibs
global gMSLPPCLibs

global gDistribRoot
global gAccessRoot

global gProjectsDir
global gSourceDir
global gIncludeDir
global gLibsDir
global gRsrcsDir
global gOutputDir
global gSourcePath
global gIncludePath
global gLibsPath
global gRsrcsPath

global gProjectData

on CopyHeaders()
	tell application "Finder"
		
		set corelibFolder to folder (gDistribRoot & "corelib")
		
		my UpdateRenameHeader("ncbilcl.met", corelibFolder, "ncbilcl.h", "")
		
	end tell
end CopyHeaders

on AddProject(projData)
	
	copy projData to end of gProjectData
	
end AddProject

on ResolveAlias(pathname)
	tell application "Finder"
		--if the last character of pathname is ":" then error "Don't use a trailing colon with ResolveAlias."
		if exists folder pathname then return pathname & ":"
		if exists alias file pathname then return the original item of alias file pathname as string
		error "The folder (or alias) '" & pathname & "' doesn't exist."
	end tell
end ResolveAlias

on IsOSX()
	tell application "Finder"
		
		set vers to the version as text
		
		if second character of vers is equal to "." then
			set vers to "0" & vers
		end if
		
		return vers > 10 or vers = 10
		
	end tell
end IsOSX

on HomeDir()
	tell application "Finder"
		
		if my IsOSX() then
			-- return the home as string
			set hm to home as string
			set wd to words of hm
			set rs to rest of wd
			set text item delimiters of AppleScript to ":"
			set nw to (rs as string) & ":"
			set text item delimiters of AppleScript to ""
			return nw
		else
			return gStartupDisk
		end if
		
	end tell
end HomeDir

on CToolkitRoot()
	
	try
		set modRoot to ResolveAlias(gMWroot & "ncbi")
	on error
		try
			set modRoot to ResolveAlias(gStartupDisk & gHomeDir & "ncbi")
		end try
	end try
	
	return modRoot
	
end CToolkitRoot

on CPlusPlusToolkitRoot()
	
	try
		set modRoot to ResolveAlias(gMWroot & "cxx")
	on error
		try
			set modRoot to ResolveAlias(gStartupDisk & gHomeDir & "cxx")
		end try
	end try
	
	return modRoot
	
end CPlusPlusToolkitRoot

on ModuleRoot()
	
	if pUsingCPlusPlus then
		return CPlusPlusToolkitRoot()
	else
		return CToolkitRoot()
	end if
	
end ModuleRoot

on AccessRoot()
	if my IsOSX() then
		set wd to words of gDistribRoot
		set rs to rest of wd
		set text item delimiters of AppleScript to ":"
		set nw to (rs as string) & ":"
		set text item delimiters of AppleScript to ""
		return nw
	else
		return gDistribRoot
	end if
end AccessRoot

on MWRootDir()
	
	set mwRoot to ""
	set mwLocations to {gStartupDisk, gStartupDisk & "Applications:", gStartupDisk & "Applications (Mac OS 9):", Â
		gStartupDisk & gHomeDir, gStartupDisk & gHomeDir & "Applications:", gStartupDisk & gHomeDir & "Applications (Mac OS 9):"}
	repeat with mwVersion from 8 to 9
		set dirName to "Metrowerks CodeWarrior " & mwVersion & ".0"
		repeat with mwLoc in mwLocations
			try
				set mwRoot to ResolveAlias(mwLoc & dirName)
				return mwRoot
			end try
		end repeat
	end repeat
	
	error "Can't find the Metrowerks CodeWarrior folder."
	
end MWRootDir

on SetGlobals()
	tell application "Finder"
		
		set gProjectData to {}
		
		set gStartupDisk to startup disk as string
		set gHomeDir to my HomeDir()
		set gMWroot to my MWRootDir()
		set gMWCWfolder to gMWroot & "Metrowerks CodeWarrior:"
		set gMacLibs to gMWCWfolder & "MacOS Support:Universal:Libraries:"
		set gStubLibs to gMacLibs & "StubLibraries:"
		set gPPCLibs to gMacLibs & "PPCLibraries:"
		set gMSLPPCLibs to gMWCWfolder & "MSL:MSL_C:MSL_MacOS:Lib:PPC:"
		
		set gDistribRoot to my ModuleRoot()
		set gAccessRoot to my AccessRoot()
		
		set gIncludeDir to gDistribRoot & "include:"
		set gIncludePath to gAccessRoot & "include:"
		if pUsingCPlusPlus then
			set gSourceDir to gDistribRoot & "src:"
			set gLibsDir to gDistribRoot & "compilers:mac_prj:lib:"
			set gOutputDir to gDistribRoot & "compilers:mac_prj:bin:"
			set gProjectsDir to gOutputDir
		else
			set gSourceDir to gDistribRoot
			set gLibsDir to gDistribRoot & "lib:"
			set gOutputDir to gDistribRoot & "build:"
			set gRsrcsDir to gDistribRoot & "link:macmet:"
			set gSourcePath to gAccessRoot
			set gLibsPath to gAccessRoot & "lib:"
			set gOutputPath to gAccessRoot & "build:"
			set gRsrcsPath to gAccessRoot & "link:macmet:"
		end if
		
		if pLinkExecutables then
			set gProjectsDir to gOutputDir
		else
			set gProjectsDir to gLibsDir
		end if
		
	end tell
end SetGlobals

on HeaderExists(header, headerDir)
	tell application "Finder"
		
		if headerDir is "" then set headerDir to folder gIncludeDir
		return exists file header of headerDir
		
	end tell
end HeaderExists

on IsOlderThan(fileA, fileB)
	tell application "Finder"
		
		return (the modification date of fileA < the modification date of fileB)
		
	end tell
end IsOlderThan

on UpdateRenameHeader(canonicalName, canonicalDir, dotHName, dotHDir)
	tell application "Finder"
		
		set needRename to (dotHName is not "")
		if not needRename then set dotHName to canonicalName
		if dotHDir is "" then set dotHDir to folder gIncludeDir
		
		-- This file is only present if the script was interrupted.
		if needRename and my HeaderExists(canonicalName, dotHDir) then
			delete file canonicalName of dotHDir
		end if
		
		-- The native config file.
		-- If it's missing, assume this is a prepared distribution and the header is already up-to-date.
		if not my HeaderExists(canonicalName, canonicalDir) then return
		set canonicalFile to file canonicalName of canonicalDir
		
		set needCopy to true
		if my HeaderExists(dotHName, dotHDir) then
			set dotHFile to file dotHName of dotHDir
			if my IsOlderThan(dotHFile, canonicalFile) then
				delete dotHFile
			else
				set needCopy to false
			end if
		end if
		
		if needCopy then
			duplicate canonicalFile to dotHDir
			if needRename then set name of file canonicalName of dotHDir to dotHName
		end if
		
	end tell
end UpdateRenameHeader

on SetDebugSettings(shouldDebug, shouldProfile)
	tell application "CodeWarrior IDE"
		
		if shouldDebug then
			(* ===== Panel PPC Global Optimizer =====  *)
			Set Preferences of panel "PPC Global Optimizer" to Â
				{Optimize For:code_Speed, Level:0}
			(* ===== Panel PPC Linker ===== *)
			Set Preferences of panel "PPC Linker" to Â
				{Generate SYM File:true Â
					, Suppress Warnings:false}
			(* ===== Panel C/C++ Language =====  *)
			Set Preferences of panel "C/C++ Compiler" to Â
				{Inlining:inline_none Â
					, AutoInlining:false}
		else
			(* ==== optimized/release settings ==== *)
			(* ===== Panel PPC Global Optimizer =====  *)
			Set Preferences of panel "PPC Global Optimizer" to Â
				{Optimize For:code_Speed, Level:4}
			(* ===== Panel PPC Linker ===== *)
			Set Preferences of panel "PPC Linker" to Â
				{Generate SYM File:false Â
					, Suppress Warnings:true}
			(* ===== Panel C/C++ Language =====  *)
			Set Preferences of panel "C/C++ Compiler" to Â
				{Inlining:inline_smart Â
					, AutoInlining:true}
		end if
		
		if shouldProfile then
			(* ===== Panel PPC Processor ===== *)
			Set Preferences of panel "PPC CodeGen" to Â
				{Use Profiler:true}
		else
			(* ===== Panel PPC Processor ===== *)
			Set Preferences of panel "PPC CodeGen" to Â
				{Use Profiler:false}
		end if
		
	end tell
end SetDebugSettings

on SetPreferences()
	tell application "CodeWarrior IDE"
		
		(* ===== Section "Target" ===== *)
		
		-- Panel "Target Settings"
		Set Preferences of panel "Target Settings" to {Linker:"MacOS PPC Linker"}
		
		-- Panel "PPC Target"
		if pLinkExecutables then
			Set Preferences of panel "PPC Project" to Â
				{Project Type:standard application, SIZE Flags:22720, File Creator:"NCBI", File Type:"APPL", Preferred Size:8000, Minimum Size:5000, Stack Size:64}
		else
			Set Preferences of panel "PPC Project" to {Project Type:library}
		end if
		(* ===== Section "Language Settings" ===== *)
		
		-- Panel "C/C++ Language"
		Set Preferences of panel "C/C++ Compiler" to Â
			{Activate CPlusPlus:false Â
				, ARM Conformance:false Â
				, Exception Handling:true Â
				, RTTI:true Â
				, Pool Strings:true Â
				, Dont Reuse Strings:false Â
				, Require Function Prototypes:true Â
				, ANSI Strict:false Â
				, ANSI Keywords Only:false Â
				, Expand Trigraph Sequences:false Â
				, MPW Newlines:false Â
				, MPW Pointer Type Rules:false Â
				, Enums Always Ints:false}
		
		-- Panel "C/C++ Warnings"
		Set Preferences of panel "C/C++ Warnings" to Â
			{Treat Warnings As Errors:false Â
				, Illegal Pragmas:true Â
				, Empty Declarations:true Â
				, Possible Errors:true Â
				, Unused Variables:true Â
				, Unused Arguments:false Â
				, Extra Commas:true Â
				, Extended Error Checking:true Â
				, Hidden Virtual Functions:true Â
				, Implicit Arithmetic Conversions:false Â
				, NonInlined Functions:false Â
				, Inconsistent Class Struct:true}
		
		(* ===== Section "Code Generation" ===== *)
		
		-- Panel "PPC Processor"
		Set Preferences of panel "PPC CodeGen" to Â
			{Struct Alignment:Align_PPC Â
				, Make Strings ReadOnly:true Â
				, Store Data in TOC:true Â
				, Use FMADD Instructions:false Â
				, Use Profiler:false Â
				, Traceback Tables:TB_Inline Â
				, Schedule:false Â
				, Peephole Optimizer:true}
		
		(* ===== Section "Linker" ===== *)
		
		-- Panel "PPC Linker"
		Set Preferences of panel "PPC Linker" to Â
			{Generate SYM File:true Â
				, Full Path In SYM Files:true Â
				, Generate Link Map:false Â
				, Link Mode:fast Â
				, Initialization Name:Â
				"", Main Name:Â
				"__start", Termination Name:""} Â
				
		-- Panel "PPC PEF"
		Set Preferences of panel "PPC PEF" to Â
			{Export Symbols:none Â
				, Old Definition:0 Â
				, Old Implementation:0 Â
				, Current Version:0 Â
				, Code Sorting:nosort Â
				, Share Data Section:false Â
				, Expand Uninitialized Data:false Â
				, Fragment Name:""}
		
		(* ===== Section "Debugger" ===== *)
		
		-- Panel "Debugger Settings"
		Set Preferences of panel "Debugger Target" to Â
			{Log System Messages:false}
		
		my SetPaths1()
		
	end tell
end SetPreferences

on SetPaths1()
	tell application "CodeWarrior IDE"
		
		(* ===== Panel Access Paths ===== *)
		-- We need to be able to move the default system compiler folder to the end of the list
		-- because certain files like "all.h" and "all" are defined by both Metrowerks and NCBI.
		-- We want to find the NCBI "all.h" first.
		Set Preferences of panel "Access Paths" to {System Paths:{}} -- This removes the compiler default folder
		
		Set Preferences of panel "Access Paths" to {Always Full Search:true, Convert Paths:true}
		
	end tell
end SetPaths1

on SetPaths2()
	tell application "CodeWarrior IDE"
		
		-- Add recursive include dir AFTER source dirs to avoid major performance hit
		set pathsToAdd to {}
		-- gDistribRoot & "link:macmet:", 
		repeat with i in {gAccessRoot, gLibsPath, gIncludePath}
			copy {name:i, recursive:false, origin:absolute} to end of pathsToAdd
		end repeat
		if not pUsingCPlusPlus then
			copy {name:gAccessRoot & "link:macmet:", recursive:true, origin:absolute} to end of pathsToAdd
		end if
		Set Preferences of panel "Access Paths" to {User Paths:pathsToAdd}
		
		set pathsToAdd to {{name:gIncludePath, recursive:true, origin:absolute}}
		if not pUsingCPlusPlus then
			copy {name:gAccessRoot, recursive:true, origin:absolute} to end of pathsToAdd
		end if
		
		-- After we have added all paths, reinsert compiler default at end of list
		set dirsToAdd to {Â
			":MacOS Support:", Â
			":MSL:"}
		-- if gPNGpresent ...
		
		repeat with i in dirsToAdd
			copy {name:i, recursive:true, origin:shell relative} to end of pathsToAdd
		end repeat
		Set Preferences of panel "Access Paths" to {System Paths:pathsToAdd}
		
	end tell
end SetPaths2

on AddFeatures(features, flags)
	tell application "CodeWarrior IDE"
		
		if features contains "BNDL" then
			Set Preferences of panel "Output Flags" to {Has Bundle:true}
		end if
		
		if features contains "sockets" and flags does not contain "Carbon" then
			set libsToAdd to {Â
				gStubLibs & "ThreadsLib", Â
				gStubLibs & "OpenTransportLib", Â
				gStubLibs & "OpenTptInternetLib", Â
				gStubLibs & "InternetConfigLib", Â
				gPPCLibs & "OpenTptInetPPC.o", Â
				gPPCLibs & "OpenTransportAppPPC.o"}
			
			Add Files libsToAdd
			
		end if
		
	end tell
end AddFeatures

on SetupTarget(proj, flags)
	tell application "CodeWarrior IDE"
		
		-- initialize variables
		set projRsrcs to {}
		set projFeatures to {}
		set sysPaths to {}
		
		-- Grab the fields of our project record and store them in local variables.
		set projName to proj's name
		set projSettings to proj's settings
		try
			set projFeatures to proj's features
		end try
		try
			set sysPaths to proj's sysPaths
		end try
		try
			set projRsrcs to proj's rsrcs
		end try
		set projLibs to proj's projLibs
		set projFileData to proj's fileData
		
		-- Figure out what our output file and input libraries will be named.
		if flags contains "Carbon" then
			set targetAPI to "C2"
		else
			set targetAPI to "Mac"
		end if
		if flags contains "debug" then
			set targetDebug to "dbg"
		else
			if flags contains "profile" then
				set targetDebug to "prf"
			else
				set targetDebug to ""
			end if
		end if
		set targetName to projName & " " & targetAPI
		set libNameSuffix to "-" & targetAPI
		if targetDebug is not "" then
			set targetName to targetName & " " & targetDebug
			set libNameSuffix to libNameSuffix & "-" & targetDebug
		end if
		if pLinkExecutables then
			set targetFilename to targetName
		else
			set targetFilename to projName & libNameSuffix & ".lib"
		end if
		
		-- Make the new target, and set the current target to be it.
		make new target at project document 1 with properties {name:targetName}
		set the current target of project document 1 to the result
		
		-- Set default settings.  do this BEFORE setting per-project settings!
		my SetPreferences()
		
		-- Set the name of the output file (the application)
		Set Preferences of panel "PPC Project" to {File Name:targetFilename}
		
		-- If we have any per-project override settings, set them.
		if (count ppcProject of projSettings) > 0 then
			Set Preferences of panel "PPC Project" to ppcProject of projSettings
		end if
		--Set Preferences of panel "Access Paths" to {User Paths:{{name:NCBISOURCE & projPath, origin:absolute}}}
		my SetPaths2()
		
		-- Add per-project system paths.
		set pathsToAdd to {}
		repeat with i in sysPaths
			copy {name:i, recursive:true, origin:absolute} to end of pathsToAdd
		end repeat
		if (count pathsToAdd) > 0 then Â
			Set Preferences of panel "Access Paths" to {System Paths:pathsToAdd}
		
		-- Set the appropriate prefix file.
		set prefixFile to Prefix File of projSettings
		if flags contains "Carbon" then
			if prefixFile is "" then
				set prefixFile to "CarbonPrefix.h"
			else
				set prefixFile to "Carbon-" & prefixFile
			end if
		end if
		Set Preferences of panel "C/C++ Compiler" to {Prefix File:prefixFile}
		
		-- Are we assuming a .c or a .cpp extension?
		if projFeatures contains "C++" then
			set fileExtension to pCPlusPlusExtension
		else
			set fileExtension to ".c"
		end if
		
		-- Add source files.
		repeat with group in projFileData
			set projPath to projPath of group
			Set Preferences of panel "Access Paths" to Â
				{User Paths:{{name:gSourcePath & projPath, origin:absolute}}}
			set fileList to group's fileList
			set filesToAdd to {}
			repeat with i in fileList
				if i does not contain "." then set i to i & fileExtension
				copy gSourceDir & projPath & i to end of filesToAdd
			end repeat
			Add Files filesToAdd
		end repeat
		
		if flags contains "debug" or flags contains "profile" then
			set the debug of every target file of target (count targets of project document 1) Â
				of project document 1 to true
			if flags contains "profile" then
				my SetDebugSettings(true, true)
			else
				my SetDebugSettings(true, false)
			end if
		else
			my SetDebugSettings(false, false)
		end if
		
		-- Add appropriate system libraries.
		if pLinkExecutables then
			if flags contains "Carbon" then
				if flags contains "profile" then
					my AddCarbonLibs(true)
				else
					my AddCarbonLibs(false)
				end if
			else
				if flags contains "profile" then
					my AddBlueLibs(true)
				else
					my AddBlueLibs(false)
				end if
			end if
		end if
		my AddFeatures(projFeatures, flags)
		
		set filesToAdd to {}
		
		-- Add user libraries.
		if projFeatures contains "sockets" then
			if projLibs does not contain "mitsock" then
				copy "mitsock" to beginning of projLibs
			end if
		end if
		repeat with i in projLibs
			copy gLibsDir & i & libNameSuffix & ".lib" to end of filesToAdd
		end repeat
		
		-- Add resources.
		repeat with i in projRsrcs
			copy gRsrcsDir & i to end of filesToAdd
		end repeat
		
		Add Files filesToAdd
		
		Reset File Paths
		
	end tell
end SetupTarget

on CreateFolders()
	tell application "Finder"
		
		repeat with i in pDirsToCreate
			set pth to relPath of i
			if pth is not "" then set pth to pth & ":"
			if not (exists folder (gDistribRoot & pth & i's name)) then
				make new folder at folder (gDistribRoot & pth) with properties {name:i's name}
			end if
		end repeat
		
	end tell
end CreateFolders

on CreateProject(proj)
	tell application "CodeWarrior IDE"
		
		-- This statement doesn't work, because AppleScript is broken.
		if proj is {} then return
		
		try
			get proj's name
		on error
			return
		end try
		
		set projFilename to proj's name & pProjectFileExtension
		set projPathname to gProjectsDir & projFilename
		if pAlwaysCreateProjects or not (exists file projPathname of application "Finder") then
			
			try
				close (the first project document whose name is projFilename)
			end try
			
			Create Project {projPathname}
			
			if pCreateBlueTargets and pCreateDebugTargets then
				my SetupTarget(proj, "Blue debug")
			end if
			
			if pCreateBlueTargets and pCreateProfiledTargets then
				my SetupTarget(proj, "Blue profile")
			end if
			
			if pCreateBlueTargets and pCreateOptimizedTargets then
				my SetupTarget(proj, "Blue")
			end if
			
			if pCreateCarbonTargets and pCreateDebugTargets then
				my SetupTarget(proj, "Carbon debug")
			end if
			
			if pCreateCarbonTargets and pCreateProfiledTargets then
				my SetupTarget(proj, "Carbon profile")
			end if
			
			if pCreateCarbonTargets and pCreateOptimizedTargets then
				my SetupTarget(proj, "Carbon")
			end if
			
			set the current target of project document 1 to target 1 of project document 1
			
			Close Project
			
		end if
		
	end tell
end CreateProject

on CreateAllProjects()
	
	repeat with proj in gProjectData
		CreateProject(proj)
	end repeat
	
end CreateAllProjects

on BuildProject(projName)
	tell application "CodeWarrior IDE"
		open (gProjectsDir & projName & pProjectFileExtension)
		repeat with i from 2 to (count targets of project document 1)
			set the current target of project document 1 to target i of project document 1
			Make Project
			-- If there were compiler warnings, then a compiler window will be in front.
			-- For whatever reason, this causes the next "set the current target..." to fail.
			-- An easy way to make the window go away without having to know if it's there or not 
			-- is to build again, which, because everything is already compiled, finishes instantly
			-- and produces no warnings.
			--Make Project
			-- An even better way is to check for the window and close it.
			if the name of window 1 is "Errors & Warnings" then
				close first window -- "close window 1" becomes "Close Window 1" (different event)
			end if
		end repeat
		set the current target of project document 1 to target 1 of project document 1
		Close Project
	end tell
end BuildProject

on BuildAllProjects()
	
	repeat with proj in gProjectData
		try
			set projName to proj's name
		on error
			set projName to ""
		end try
		-- This statement doesn't work, because AppleScript is broken.
		if proj is not {} then
			if projName is not "" then
				BuildProject(projName)
			end if
		end if
	end repeat
	
end BuildAllProjects

on SignalCompletion()
	
	beep
	
end SignalCompletion

with timeout of 60000 seconds
	
	SetGlobals()
	
	SetProjectData()
	
	CreateFolders()
	CopyHeaders()
	
	tell application "CodeWarrior IDE" to activate
	
	CreateAllProjects()
	
	if pShouldBuild then
		BuildAllProjects()
	end if
	
	SignalCompletion()
	
end timeout

\ No newline at end of file
diff --git a/make/makeall.unx b/make/makeall.unx
index fe7fb7d9..b4dce566 100644
--- a/make/makeall.unx
+++ b/make/makeall.unx
@@ -1,6 +1,6 @@
 #	makefile for asntool and ncbi core routines,
 #
-#	$Id: makeall.unx,v 6.215 2003/10/09 16:41:32 beloslyu Exp $
+#	$Id: makeall.unx,v 6.222 2003/12/30 20:55:03 kans Exp $
 #
 #	cdromlib data access functions, vibrant, and entrez
 #	SunOS with unbundled ANSI compiler [ make LCL=acc RAN=ranlib CC=acc ]
@@ -120,7 +120,8 @@ ULIB39 = libideochr.a
 LIB39= $(ULIB39)
 LIB39 =
 LIB50 = libregexp.a
-
+LIB60 = libblast.a
+LIB61 = libblastapi.a
 #
 # Pseudo-dummy targets when Vibrant is not used
 #
@@ -192,7 +193,8 @@ SRC2 =	objacces.c objalign.c objall.c objbibli.c \
 	sequtil.c prtutil.c simple.c tofasta.c tofile.c tomedlin.c \
 	valid.c alignmgr.c aliparse.c aliread.c alignval.c sqnutil1.c sqnutil2.c sqnutil3.c \
 	subutil.c edutil.c asn2ff1.c asn2ff2.c asn2ff3.c asn2ff4.c \
-	asn2ff5.c asn2ff6.c asn2gnbk.c ftusrstr.c gbfeat.c gbftglob.c \
+	asn2ff5.c asn2ff6.c asn2gnb1.c asn2gnb2.c asn2gnb3.c asn2gnb4.c \
+	asn2gnb5.c asn2gnb6.c ftusrstr.c gbfeat.c gbftglob.c \
 	gbparint.c utilpars.c utilpub.c ffprint.c wprint.c satutil.c \
 	seqmgr.c objmgr.c gather.c accmmdbs.c acccn3ds.c lsqfetch.c findrepl.c \
 	codon.c jzcoll.c jzmisc.c maputil.c mconsist.c \
@@ -252,7 +254,7 @@ SRC23 = csim.c db_slist.c dust.c falign.c g_any.c sim2.c sim3.c sim4.c \
 	actutils.c posit.c lookup.c readdb.c ncbisam.c ncbisort.c \
 	salign.c salptool.c urkutil.c urkpcc.c urkptpf.c urkepi.c \
 	urkfltr.c urkdust.c urksigu.c seg.c urkbias.c urkcnsrt.c urktree.c \
-	pseed3.c pattern1.c impatool.c posit2.c newkar.c mbalign.c \
+	pseed3.c pattern1.c impatool.c posit2.c mbalign.c \
 	vecscrn.c mblast.c rpsutil.c kappa.c xmlblast.c bxmlobj.c objscoremat.c \
 	dotseq.c spidey.c motif.c
 
@@ -278,6 +280,17 @@ SRC39 = ideochrow.c humchrom_dat.c mschrom_dat.c ideochrom.c ideoorgs.c \
 
 SRC50 = chartables.c get.c maketables.c pcre.c pcreposix.c study.c
 
+SRC60 = aa_ungapped.c blast_dust.c blast_engine.c blast_extend.c \
+    blast_filter.c blast_gapalign.c blast_hits.c blast_lookup.c \
+    blast_message.c blast_options.c blast_seg.c blast_seqsrc.c \
+    blast_setup.c blast_stat.c blast_traceback.c blast_util.c \
+    gapinfo.c greedy_align.c link_hsps.c lookup_wrap.c mb_lookup.c \
+    ncbi_math.c ncbi_std.c pattern.c phi_extend.c phi_lookup.c \
+    lookup_util.c
+
+SRC61 = blast_input.c blast_seq.c blast_seqalign.c seqsrc_readdb.c \
+    blast_format.c
+
 # objects needed for versions of asntool and entrez
 
 THR_OBJ = ncbithr.o
@@ -310,7 +323,8 @@ OBJ2 =	objacces.o objalign.o objall.o objbibli.o \
 	sequtil.o prtutil.o simple.o tofasta.o tofile.o tomedlin.o \
 	valid.o alignmgr.o aliparse.o aliread.o alignval.o sqnutil1.o sqnutil2.o sqnutil3.o \
 	subutil.o edutil.o asn2ff1.o asn2ff2.o asn2ff3.o asn2ff4.o \
-	asn2ff5.o asn2ff6.o asn2gnbk.o ftusrstr.o gbfeat.o gbftglob.o \
+	asn2ff5.o asn2ff6.o asn2gnb1.o asn2gnb2.o asn2gnb3.o asn2gnb4.o \
+	asn2gnb5.o asn2gnb6.o ftusrstr.o gbfeat.o gbftglob.o \
 	gbparint.o utilpars.o utilpub.o ffprint.o wprint.o satutil.o \
 	seqmgr.o objmgr.o gather.o accmmdbs.o acccn3ds.o lsqfetch.o findrepl.o \
 	codon.o jzcoll.o jzmisc.o maputil.o mconsist.o \
@@ -382,7 +396,7 @@ OBJ23 = csim.o db_slist.o dust.o falign.o g_any.o sim2.o sim3.o sim4.o \
 	actutils.o posit.o lookup.o readdb.o ncbisam.o ncbisort.o \
 	salign.o salptool.o urkutil.o urkpcc.o urkptpf.o urkepi.o \
 	urkfltr.o urkdust.o urksigu.o seg.o urkbias.o urkcnsrt.o urktree.o \
-	pseed3.o pattern1.o impatool.o posit2.o newkar.o mbalign.o \
+	pseed3.o pattern1.o impatool.o posit2.o mbalign.o \
 	vecscrn.o mblast.o rpsutil.o kappa.o xmlblast.o bxmlobj.o objscoremat.o \
 	dotseq.o spidey.o motif.o
 
@@ -413,6 +427,18 @@ OBJ39 = ideochrow.o humchrom_dat.o mschrom_dat.o ideochrom.o ideoorgs.o \
 
 OBJ50 = chartables.o get.o maketables.o pcre.o pcreposix.o study.o
 
+OBJ60 = aa_ungapped.o blast_dust.o blast_engine.o blast_extend.o \
+    blast_filter.o blast_gapalign.o blast_hits.o blast_lookup.o \
+    blast_message.o blast_options.o blast_seg.o blast_seqsrc.o \
+    blast_setup.o blast_stat.o blast_traceback.o blast_util.o \
+    gapinfo.o greedy_align.o link_hsps.o lookup_wrap.o mb_lookup.o \
+    ncbi_math.o ncbi_std.o pattern.o phi_extend.o phi_lookup.o \
+    lookup_util.o
+
+OBJ61 = blast_input.o blast_seq.o blast_seqalign.o seqsrc_readdb.o \
+    blast_format.o
+
+
 # NOTE: if you enter an object file to an OBJxx greater than 30, you have to explicitly
 # enter the make actions below (e.g. ddvclick.o).  This is because the
 # implicit make rule for opengl objects (.glo) somehow causes the default make rule for .o
@@ -430,10 +456,10 @@ ln-if-absent:	../make/ln-if-absent
 
 nocopy : sources $(THR_OBJ) $(LIB1) $(LIB2) $(LIB3) $(DLIB4) $(DLIB400) \
 	$(LIB5) $(DLIB20) $(DLIB45) $(LIB22) $(LIB23) $(DLIB28) $(DLIB30) $(DLIB3000) \
-	$(DLIB34) $(DLIB37) $(DLIB38) $(LIB50) $(NCBI_SHLIBS)
+	$(DLIB34) $(DLIB37) $(DLIB38) $(LIB50) $(LIB60) $(LIB61) $(NCBI_SHLIBS)
 
 sources : $(THR_SRC) $(SRC1) $(SRC2) $(SRC3) $(SRC4) $(SRC5) $(SRC20) $(SRC22) \
-    $(SRC23) $(SRC28) $(SRC30) $(SRC50)
+    $(SRC23) $(SRC28) $(SRC30) $(SRC50) $(SRC60) $(SRC61)
 
 ## To clean out the directory without removing make
 ##
@@ -707,6 +733,12 @@ copy :
 	$(SRCCOPY) ../network/nsclilib/*.h ../include
 	$(SRCCOPY) ../network/blast3/client/*.h ../include
 	$(SRCCOPY) ../network/id1arch/*.h ../include
+	- mkdir -p ../include/algo/blast/core
+	$(SRCCOPY) ../algo/blast/core/*.c .
+	cp -fp ../algo/blast/core/*.h ../include/algo/blast/core
+	- mkdir -p ../include/algo/blast/api
+	$(SRCCOPY) ../algo/blast/api/*.c .
+	cp -fp ../algo/blast/api/*.h ../include/algo/blast/api
 	- chmod -R ug+rw,o+r .
 
 
@@ -871,6 +903,17 @@ $(LIB50) : $(OBJ50)
 	$(LIBCOPY) $(LIB50) $(NCBI_LIBDIR)
 	$(RAN) $(NCBI_LIBDIR)/$(LIB50)
 
+$(LIB60) : $(OBJ60)
+	- $(RM_LIB) $(LIB60)
+	$(AR) cru $(LIB60) $(OBJ60)
+	$(LIBCOPY) $(LIB60) $(NCBI_LIBDIR)
+	$(RAN) $(NCBI_LIBDIR)/$(LIB60)
+
+$(LIB61) : $(OBJ61)
+	- $(RM_LIB) $(LIB61)
+	$(AR) cru $(LIB61) $(OBJ61)
+	$(LIBCOPY) $(LIB61) $(NCBI_LIBDIR)
+	$(RAN) $(NCBI_LIBDIR)/$(LIB61)
 
 ## make asntool application
 ##  This is ALWAYS the command line version
diff --git a/make/makeallchives b/make/makeallchives
index 2feb2847..76b97196 100755
--- a/make/makeallchives
+++ b/make/makeallchives
@@ -1,6 +1,6 @@
 #!/bin/sh
 #
-# $Id: makeallchives,v 1.63 2003/06/03 16:40:51 beloslyu Exp $
+# $Id: makeallchives,v 1.68 2004/01/06 17:13:48 coulouri Exp $
 #
 #
 # Creates all archives from a directory above 'ncbi'
@@ -92,13 +92,13 @@ EOF
 		;;
 	blast)
 		f="blastall blastpgp seedtop formatdb fastacmd copymat makemat \
-impala megablast blastclust rpsblast bl2seq ../doc/README.imp \
-../doc/README.bls ../doc/README.mbl ../doc/README.bcl ../doc/README.rps \
-../doc/README.formatdb ../doc/README.fastacmd ../doc/README-qm"
+impala megablast blastclust rpsblast bl2seq ../doc/impala.txt \
+../doc/blast.txt ../doc/megablast.txt ../doc/blastclust.txt ../doc/rpsblast.txt \
+../doc/formatdb.txt ../doc/fastacmd.txt ../doc/README-qm"
 		rm -f archive/blast/data/sequin.hlp
 		;;
 	netblast)
-		f="blastcl3 ../doc/firewall.html ../doc/README.nbl"
+		f="blastcl3 ../doc/firewall.html ../doc/netblast.txt"
 		;;
 	*)
 		;;
@@ -265,4 +265,30 @@ do
 	#and remove it
 	rm -fr $A
 done
+
+# build wwwblast archive
+
+# cd archive && cvs export -d blast -r HEAD distrib/network/wwwblast && cd ..
+
+mkdir blast
+
+cp -r ../ncbi/network/wwwblast/* blast 
+
+find blast -type d -name CVS | xargs rm -rf
+find blast -type d -name Src | xargs rm -rf
+
+for file in psiblast.REAL psiblast_cs.REAL blast.REAL blast_cs.REAL wblast2.REAL wblast2_cs.REAL bl2bag.cgi nph-viewgif.cgi
+do
+cp ../ncbi/build/$file blast
+done
+
+mkdir -p blast/TmpGifs
+chmod 777 blast/TmpGifs
+chmod 666 blast/*.log
+
+tar -cpf wwwblast-$platform.tar blast
+gzip wwwblast-$platform.tar
+
+rm -rf blast
+
 exit 0
diff --git a/make/makedemo.met b/make/makedemo.met
deleted file mode 100644
index 32688a12..00000000
--- a/make/makedemo.met
+++ /dev/null
@@ -1 +0,0 @@
--- C demos --

--
-- Properties
--

property pUsingCPlusPlus : false
property pProjectFileExtension : ".mcp"

-- Whether to recreate existing project files.
property pAlwaysCreateProjects : false

-- Which targets to create.
-- If these are changed you must recreate the project files.  There is no direct effect on building.
property pCreateBlueTargets : true -- 'Blue' was codename for System 7, here it means pre-Carbon.
property pCreateCarbonTargets : true
property pCreateDebugTargets : true
property pCreateProfiledTargets : false
property pCreateOptimizedTargets : true

-- Whether to compile everything.
property pShouldBuild : true

property pDirsToCreate : {{relPath:"", name:"build"}}

property pLinkExecutables : true

--
-- Routines specific to this project
--

on SimpleProjectData(projName, features)
	
	if (count characters of projName) > 18 then
		set projName to characters 1 through 18 of projName as string
	end if
	
	tell application "CodeWarrior IDE"
		
		if features does not contain "C" and features does not contain "C++" then
			--error "Project " & projName & "'s default language (a feature) must be C or C++."
			copy "C" to end of features
		end if
		set myFeatures to features
		copy "BNDL" to end of myFeatures
		return {name:projName, features:myFeatures, rsrcs:{"ncbilogo.r"}, settings:Â
			{Prefix File:"", ppcProject:{}}, projLibs:Â
			{"mitsock", "ncbi", "ncbiconn", "ncbiobj", "vibrant", "ncbitool"}, fileData:Â
			{{projPath:"demo:", fileList:{projName}}}}
		
	end tell
end SimpleProjectData

on AddSimpleProject(projName, features)
	
	AddProject(SimpleProjectData(projName, features))
	
end AddSimpleProject

on SetProjectData()
	tell application "CodeWarrior IDE"
		
		-- Entrez
		set myName to "Entrez"
		set myFeatures to {"sockets", "BNDL"}
		set mySettings to {Prefix File:"net.pfx", ppcProject:{File Creator:"ENTZ"}}
		set myRsrcs to {"entrez.r"}
		set myLibs to {"mitsock", "ncbi", "ncbiconn", "ncbiobj", "ncbicdr", "vibrant", "ncbidesk", "ncbimmdb", Â
			"ncbitool", "netcli", "netentr", "ncbibls3", "ncbiid1", "vibnet"}
		set myFiles to Â
			{{projPath:"cdromlib:", fileList:{"accentr", "accutils"}}, Â
				{projPath:"demo:", fileList:{"entrez"}}}
		set entrezData to Â
			{name:myName, features:myFeatures, settings:mySettings, rsrcs:myRsrcs, projLibs:Â
				myLibs, fileData:myFiles}
		
		-- Entrez2
		set myName to "Entrez2"
		set myFeatures to {"sockets", "BNDL"}
		set mySettings to {Prefix File:"net.pfx", ppcProject:{File Creator:"ENTZ"}}
		set myRsrcs to {"entrez.r"}
		set myLibs to {"mitsock", "ncbi", "ncbiconn", "ncbiobj", "ncbimmdb", "ncbitool", "vibrant", "ncbidesk"}
		set myFiles to Â
			{{projPath:"demo:", fileList:{"entrez2"}}}
		set entrez2Data to Â
			{name:myName, features:myFeatures, settings:mySettings, rsrcs:myRsrcs, projLibs:Â
				myLibs, fileData:myFiles}
		
		-- Sequin
		set myName to "Sequin"
		set myFeatures to {"sockets", "BNDL"}
		set mySettings to Â
			{Prefix File:"net.pfx", ppcProject:Â
				{File Creator:"SEQN", Preferred Size:32000, Minimum Size:6000}}
		set myRsrcs to {"sequin.r"}
		set myLibs to {"mitsock", "ncbi", "ncbiconn", "ncbiobj", "ncbicdr", "vibrant", "ncbidesk", Â
			"ncbimmdb", "ncbitool", "netcli", "netentr", "ncbibls3", "ncbimla", Â
			"ncbitxc2", "ncbiid1", "vibnet"}
		set myFiles to Â
			{{projPath:"cdromlib:", fileList:{"accentr", "accutils"}}, Â
				{projPath:"sequin:", fileList:{"sequin1", "sequin2", "sequin3", "sequin4", "sequin5", Â
					"sequin6", "sequin7", "sequin8", "sequin9", "sequinx"}}}
		set sequinData to Â
			{name:myName, features:myFeatures, settings:mySettings, rsrcs:myRsrcs, projLibs:Â
				myLibs, fileData:myFiles}
		
		-- BlastCL3
		set myName to "blastcl3"
		set myFeatures to {"sockets", "BNDL"}
		set mySettings to {Prefix File:"blastcl3.pfx", ppcProject:{}}
		set myRsrcs to {"ncbilogo.r"}
		set myLibs to {"mitsock", "ncbi", "ncbiconn", "ncbiobj", "vibrant", "ncbitool", "netcli", "ncbibls3"}
		set myFiles to Â
			{{projPath:"demo:", fileList:{"blastall"}}}
		set blastcl3Data to Â
			{name:myName, features:myFeatures, settings:mySettings, rsrcs:myRsrcs, projLibs:Â
				myLibs, fileData:myFiles}
		
		-- Bl2seq
		set myName to "bl2seq"
		set myFeatures to {"sockets", "BNDL"}
		set mySettings to {Prefix File:"net.pfx", ppcProject:{}}
		set myRsrcs to {"ncbilogo.r"}
		set myLibs to {"mitsock", "ncbi", "ncbiconn", "ncbiobj", "vibrant", "ncbitool", "netcli", "ncbibls3", "ncbiid1"}
		set myFiles to Â
			{{projPath:"demo:", fileList:{"bl2seq"}}}
		set bl2seqData to Â
			{name:myName, features:myFeatures, settings:mySettings, rsrcs:myRsrcs, projLibs:Â
				myLibs, fileData:myFiles}
		
		-- Impala
		set impalaData to my SimpleProjectData("impala", {})
		set item 1 of fileList of item 1 of fileData of impalaData to "profiles"
		
	end tell
	
	AddProject(sequinData)
	AddProject(entrezData)
	AddProject(entrez2Data)
	AddSimpleProject("tbl2asn", {})
	AddSimpleProject("formatdb", {})
	AddSimpleProject("fastacmd", {})
	AddProject(bl2seqData)
	AddSimpleProject("blastall", {})
	AddSimpleProject("blastpgp", {})
	AddProject(blastcl3Data)
	AddSimpleProject("megablast", {})
	AddSimpleProject("blastclust", {})
	AddSimpleProject("rpsblast", {})
	AddSimpleProject("seedtop", {})
	AddSimpleProject("copymat", {})
	AddSimpleProject("makemat", {})
	AddProject(impalaData)
	
end SetProjectData

--
-- Global variables
--

global gStartupDisk
global gHomeDir
global gMWroot
global gMWCWfolder
global gMacLibs
global gStubLibs
global gPPCLibs
global gMSLPPCLibs

global gDistribRoot
global gAccessRoot

global gProjectsDir
global gSourceDir
global gIncludeDir
global gLibsDir
global gRsrcsDir
global gOutputDir
global gSourcePath
global gIncludePath
global gLibsPath
global gRsrcsPath

global gProjectData

on AddProject(projData)
	
	copy projData to end of gProjectData
	
end AddProject

on ResolveAlias(pathname)
	tell application "Finder"
		--if the last character of pathname is ":" then error "Don't use a trailing colon with ResolveAlias."
		if exists folder pathname then return pathname & ":"
		if exists alias file pathname then return the original item of alias file pathname as string
		error "The folder (or alias) '" & pathname & "' doesn't exist."
	end tell
end ResolveAlias

on IsOSX()
	tell application "Finder"
		
		set vers to the version as text
		
		if second character of vers is equal to "." then
			set vers to "0" & vers
		end if
		
		return vers > 10 or vers = 10
		
	end tell
end IsOSX

on HomeDir()
	tell application "Finder"
		
		if my IsOSX() then
			-- return the home as string
			set hm to home as string
			set wd to words of hm
			set rs to rest of wd
			set text item delimiters of AppleScript to ":"
			set nw to (rs as string) & ":"
			set text item delimiters of AppleScript to ""
			return nw
		else
			return gStartupDisk
		end if
		
	end tell
end HomeDir

on CToolkitRoot()
	
	try
		set modRoot to ResolveAlias(gMWroot & "ncbi")
	on error
		try
			set modRoot to ResolveAlias(gStartupDisk & gHomeDir & "ncbi")
		end try
	end try
	
	return modRoot
	
end CToolkitRoot

on CPlusPlusToolkitRoot()
	
	try
		set modRoot to ResolveAlias(gMWroot & "cxx")
	on error
		try
			set modRoot to ResolveAlias(gStartupDisk & gHomeDir & "cxx")
		end try
	end try
	
	return modRoot
	
end CPlusPlusToolkitRoot

on ModuleRoot()
	
	if pUsingCPlusPlus then
		return CPlusPlusToolkitRoot()
	else
		return CToolkitRoot()
	end if
	
end ModuleRoot

on AccessRoot()
	if my IsOSX() then
		set wd to words of gDistribRoot
		set rs to rest of wd
		set text item delimiters of AppleScript to ":"
		set nw to (rs as string) & ":"
		set text item delimiters of AppleScript to ""
		return nw
	else
		return gDistribRoot
	end if
end AccessRoot

on MWRootDir()
	
	set mwRoot to ""
	set mwLocations to {gStartupDisk, gStartupDisk & "Applications:", gStartupDisk & "Applications (Mac OS 9):", Â
		gStartupDisk & gHomeDir, gStartupDisk & gHomeDir & "Applications:", gStartupDisk & gHomeDir & "Applications (Mac OS 9):"}
	repeat with mwVersion from 8 to 9
		set dirName to "Metrowerks CodeWarrior " & mwVersion & ".0"
		repeat with mwLoc in mwLocations
			try
				set mwRoot to ResolveAlias(mwLoc & dirName)
				return mwRoot
			end try
		end repeat
	end repeat
	
	error "Can't find the Metrowerks CodeWarrior folder."
	
end MWRootDir

on SetGlobals()
	tell application "Finder"
		
		set gProjectData to {}
		
		set gStartupDisk to startup disk as string
		set gHomeDir to my HomeDir()
		set gMWroot to my MWRootDir()
		set gMWCWfolder to gMWroot & "Metrowerks CodeWarrior:"
		set gMacLibs to gMWCWfolder & "MacOS Support:Universal:Libraries:"
		set gStubLibs to gMacLibs & "StubLibraries:"
		set gPPCLibs to gMacLibs & "PPCLibraries:"
		set gMSLPPCLibs to gMWCWfolder & "MSL:MSL_C:MSL_MacOS:Lib:PPC:"
		
		set gDistribRoot to my ModuleRoot()
		set gAccessRoot to my AccessRoot()
		
		set gIncludeDir to gDistribRoot & "include:"
		set gIncludePath to gAccessRoot & "include:"
		if pUsingCPlusPlus then
			set gSourceDir to gDistribRoot & "src:"
			set gLibsDir to gDistribRoot & "compilers:mac_prj:lib:"
			set gOutputDir to gDistribRoot & "compilers:mac_prj:bin:"
			set gProjectsDir to gOutputDir
		else
			set gSourceDir to gDistribRoot
			set gLibsDir to gDistribRoot & "lib:"
			set gOutputDir to gDistribRoot & "build:"
			set gRsrcsDir to gDistribRoot & "link:macmet:"
			set gSourcePath to gAccessRoot
			set gLibsPath to gAccessRoot & "lib:"
			set gOutputPath to gAccessRoot & "build:"
			set gRsrcsPath to gAccessRoot & "link:macmet:"
		end if
		
		if pLinkExecutables then
			set gProjectsDir to gOutputDir
		else
			set gProjectsDir to gLibsDir
		end if
		
	end tell
end SetGlobals

on SetDebugSettings(shouldDebug, shouldProfile)
	tell application "CodeWarrior IDE"
		
		if shouldDebug then
			(* ===== Panel PPC Global Optimizer =====  *)
			Set Preferences of panel "PPC Global Optimizer" to Â
				{Optimize For:code_Speed, Level:0}
			(* ===== Panel PPC Linker ===== *)
			Set Preferences of panel "PPC Linker" to Â
				{Generate SYM File:true Â
					, Suppress Warnings:false}
			(* ===== Panel C/C++ Language =====  *)
			Set Preferences of panel "C/C++ Compiler" to Â
				{Inlining:inline_none Â
					, AutoInlining:false}
		else
			(* ==== optimized/release settings ==== *)
			(* ===== Panel PPC Global Optimizer =====  *)
			Set Preferences of panel "PPC Global Optimizer" to Â
				{Optimize For:code_Speed, Level:4}
			(* ===== Panel PPC Linker ===== *)
			Set Preferences of panel "PPC Linker" to Â
				{Generate SYM File:false Â
					, Suppress Warnings:true}
			(* ===== Panel C/C++ Language =====  *)
			Set Preferences of panel "C/C++ Compiler" to Â
				{Inlining:inline_smart Â
					, AutoInlining:true}
		end if
		
		if shouldProfile then
			(* ===== Panel PPC Processor ===== *)
			Set Preferences of panel "PPC CodeGen" to Â
				{Use Profiler:true}
		else
			(* ===== Panel PPC Processor ===== *)
			Set Preferences of panel "PPC CodeGen" to Â
				{Use Profiler:false}
		end if
		
	end tell
end SetDebugSettings

on SetPreferences()
	tell application "CodeWarrior IDE"
		
		(* ===== Section "Target" ===== *)
		
		-- Panel "Target Settings"
		Set Preferences of panel "Target Settings" to {Linker:"MacOS PPC Linker"}
		
		-- Panel "PPC Target"
		if pLinkExecutables then
			Set Preferences of panel "PPC Project" to Â
				{Project Type:standard application, SIZE Flags:22720, File Creator:"NCBI", File Type:"APPL", Preferred Size:8000, Minimum Size:5000, Stack Size:64}
		else
			Set Preferences of panel "PPC Project" to {Project Type:library}
		end if
		(* ===== Section "Language Settings" ===== *)
		
		-- Panel "C/C++ Language"
		Set Preferences of panel "C/C++ Compiler" to Â
			{Activate CPlusPlus:false Â
				, ARM Conformance:false Â
				, Exception Handling:true Â
				, RTTI:true Â
				, Pool Strings:true Â
				, Dont Reuse Strings:false Â
				, Require Function Prototypes:true Â
				, ANSI Strict:false Â
				, ANSI Keywords Only:false Â
				, Expand Trigraph Sequences:false Â
				, MPW Newlines:false Â
				, MPW Pointer Type Rules:false Â
				, Enums Always Ints:false}
		
		-- Panel "C/C++ Warnings"
		Set Preferences of panel "C/C++ Warnings" to Â
			{Treat Warnings As Errors:false Â
				, Illegal Pragmas:true Â
				, Empty Declarations:true Â
				, Possible Errors:true Â
				, Unused Variables:true Â
				, Unused Arguments:false Â
				, Extra Commas:true Â
				, Extended Error Checking:true Â
				, Hidden Virtual Functions:true Â
				, Implicit Arithmetic Conversions:false Â
				, NonInlined Functions:false Â
				, Inconsistent Class Struct:true}
		
		(* ===== Section "Code Generation" ===== *)
		
		-- Panel "PPC Processor"
		Set Preferences of panel "PPC CodeGen" to Â
			{Struct Alignment:Align_PPC Â
				, Make Strings ReadOnly:true Â
				, Store Data in TOC:true Â
				, Use FMADD Instructions:false Â
				, Use Profiler:false Â
				, Traceback Tables:TB_Inline Â
				, Schedule:false Â
				, Peephole Optimizer:true}
		
		(* ===== Section "Linker" ===== *)
		
		-- Panel "PPC Linker"
		Set Preferences of panel "PPC Linker" to Â
			{Generate SYM File:true Â
				, Full Path In SYM Files:true Â
				, Generate Link Map:false Â
				, Link Mode:fast Â
				, Initialization Name:Â
				"", Main Name:Â
				"__start", Termination Name:""} Â
				
		-- Panel "PPC PEF"
		Set Preferences of panel "PPC PEF" to Â
			{Export Symbols:none Â
				, Old Definition:0 Â
				, Old Implementation:0 Â
				, Current Version:0 Â
				, Code Sorting:nosort Â
				, Share Data Section:false Â
				, Expand Uninitialized Data:false Â
				, Fragment Name:""}
		
		(* ===== Section "Debugger" ===== *)
		
		-- Panel "Debugger Settings"
		Set Preferences of panel "Debugger Target" to Â
			{Log System Messages:false}
		
		my SetPaths1()
		
	end tell
end SetPreferences

on SetPaths1()
	tell application "CodeWarrior IDE"
		
		(* ===== Panel Access Paths ===== *)
		-- We need to be able to move the default system compiler folder to the end of the list
		-- because certain files like "all.h" and "all" are defined by both Metrowerks and NCBI.
		-- We want to find the NCBI "all.h" first.
		Set Preferences of panel "Access Paths" to {System Paths:{}} -- This removes the compiler default folder
		
		Set Preferences of panel "Access Paths" to {Always Full Search:true, Convert Paths:true}
		
	end tell
end SetPaths1

on SetPaths2()
	tell application "CodeWarrior IDE"
		
		-- Add recursive include dir AFTER source dirs to avoid major performance hit
		set pathsToAdd to {}
		-- gDistribRoot & "link:macmet:", 
		repeat with i in {gAccessRoot, gLibsPath, gIncludePath}
			copy {name:i, recursive:false, origin:absolute} to end of pathsToAdd
		end repeat
		if not pUsingCPlusPlus then
			copy {name:gAccessRoot & "link:macmet:", recursive:true, origin:absolute} to end of pathsToAdd
		end if
		Set Preferences of panel "Access Paths" to {User Paths:pathsToAdd}
		
		set pathsToAdd to {{name:gIncludePath, recursive:true, origin:absolute}}
		if not pUsingCPlusPlus then
			copy {name:gAccessRoot, recursive:true, origin:absolute} to end of pathsToAdd
		end if
		
		-- After we have added all paths, reinsert compiler default at end of list
		set dirsToAdd to {Â
			":MacOS Support:", Â
			":MSL:"}
		-- if gPNGpresent ...
		
		repeat with i in dirsToAdd
			copy {name:i, recursive:true, origin:shell relative} to end of pathsToAdd
		end repeat
		Set Preferences of panel "Access Paths" to {System Paths:pathsToAdd}
		
	end tell
end SetPaths2

on SetWeakLink(libName)
	tell application "CodeWarrior IDE"
		
		set the weak link of Â
			every target file of target (count targets of project document 1) of project document 1 Â
			whose path ends with ":" & libName Â
			to true
		
	end tell
end SetWeakLink

on AddBlueLibs(shouldProfile)
	tell application "CodeWarrior IDE"
		
		set libsToAdd to {Â
			gMSLPPCLibs & "MSL C.PPC.Lib", Â
			gMSLPPCLibs & "MSL C++.PPC.Lib", Â
			gMSLPPCLibs & "MSL SIOUX.PPC.Lib", Â
			gMWCWfolder & "MacOS Support:Libraries:Runtime:Runtime PPC:MSL RuntimePPC.Lib", Â
			gMSLPPCLibs & "MSL_C_PPC.Lib", Â
			gMSLPPCLibs & "MSL_C++_PPC.Lib", Â
			gMSLPPCLibs & "MSL_SIOUX_PPC.Lib", Â
			gMSLPPCLibs & "MSL_Extras_PPC.Lib", Â
			gMWCWfolder & "MacOS Support:Libraries:Runtime:Libs:MSL_Runtime_PPC.Lib", Â
			gStubLibs & "InterfaceLib", Â
			gStubLibs & "AppearanceLib", Â
			gStubLibs & "NavigationLib", Â
			gStubLibs & "MathLib", Â
			gStubLibs & "TextCommon", Â
			gStubLibs & "UnicodeConverter", Â
			gStubLibs & "UTCUtils", Â
			gPPCLibs & "CarbonAccessors.o"}
		
		if shouldProfile then
			copy gMWCWfolder & "MacOS Support:Profiler:Profiler PPC:Profiler PPC.Lib" to end of libsToAdd
		end if
		
		Add Files libsToAdd
		
		my SetWeakLink("AppearanceLib")
		my SetWeakLink("NavigationLib")
		
	end tell
end AddBlueLibs

on AddCarbonLibs(shouldProfile)
	tell application "CodeWarrior IDE"
		
		set libsToAdd to {Â
			gMSLPPCLibs & "MSL C.Carbon.Lib", Â
			gMSLPPCLibs & "MSL C++.PPC.Lib", Â
			gMSLPPCLibs & "MSL SIOUX.Carbon.Lib", Â
			gMWCWfolder & "MacOS Support:Libraries:Runtime:Runtime PPC:MSL RuntimePPC.Lib", Â
			gMSLPPCLibs & "MSL_C_Carbon.Lib", Â
			gMSLPPCLibs & "MSL_C++_PPC.Lib", Â
			gMSLPPCLibs & "MSL_SIOUX_Carbon.Lib", Â
			gMSLPPCLibs & "MSL_Extras_Carbon.Lib", Â
			gMWCWfolder & "MacOS Support:Libraries:Runtime:Libs:MSL_Runtime_PPC.Lib", Â
			gStubLibs & "CarbonLib"}
		
		if shouldProfile then
			copy gMWCWfolder & "MacOS Support:Profiler:Profiler PPC:Profiler Carbon.Lib" to end of libsToAdd
		end if
		
		Add Files libsToAdd
		
	end tell
end AddCarbonLibs

on AddFeatures(features, flags)
	tell application "CodeWarrior IDE"
		
		if features contains "BNDL" then
			Set Preferences of panel "Output Flags" to {Has Bundle:true}
		end if
		
		if features contains "sockets" and flags does not contain "Carbon" then
			set libsToAdd to {Â
				gStubLibs & "ThreadsLib", Â
				gStubLibs & "OpenTransportLib", Â
				gStubLibs & "OpenTptInternetLib", Â
				gStubLibs & "InternetConfigLib", Â
				gPPCLibs & "OpenTptInetPPC.o", Â
				gPPCLibs & "OpenTransportAppPPC.o"}
			
			Add Files libsToAdd
			
		end if
		
	end tell
end AddFeatures

on SetupTarget(proj, flags)
	tell application "CodeWarrior IDE"
		
		-- initialize variables
		set projRsrcs to {}
		set projFeatures to {}
		set sysPaths to {}
		
		-- Grab the fields of our project record and store them in local variables.
		set projName to proj's name
		set projSettings to proj's settings
		try
			set projFeatures to proj's features
		end try
		try
			set sysPaths to proj's sysPaths
		end try
		try
			set projRsrcs to proj's rsrcs
		end try
		set projLibs to proj's projLibs
		set projFileData to proj's fileData
		
		-- Figure out what our output file and input libraries will be named.
		if flags contains "Carbon" then
			set targetAPI to "C2"
		else
			set targetAPI to "Mac"
		end if
		if flags contains "debug" then
			set targetDebug to "dbg"
		else
			if flags contains "profile" then
				set targetDebug to "prf"
			else
				set targetDebug to ""
			end if
		end if
		set targetName to projName & " " & targetAPI
		set libNameSuffix to "-" & targetAPI
		if targetDebug is not "" then
			set targetName to targetName & " " & targetDebug
			set libNameSuffix to libNameSuffix & "-" & targetDebug
		end if
		if pLinkExecutables then
			set targetFilename to targetName
		else
			set targetFilename to projName & libNameSuffix & ".lib"
		end if
		
		-- Make the new target, and set the current target to be it.
		make new target at project document 1 with properties {name:targetName}
		set the current target of project document 1 to the result
		
		-- Set default settings.  do this BEFORE setting per-project settings!
		my SetPreferences()
		
		-- Set the name of the output file (the application)
		Set Preferences of panel "PPC Project" to {File Name:targetFilename}
		
		-- If we have any per-project override settings, set them.
		if (count ppcProject of projSettings) > 0 then
			Set Preferences of panel "PPC Project" to ppcProject of projSettings
		end if
		--Set Preferences of panel "Access Paths" to {User Paths:{{name:NCBISOURCE & projPath, origin:absolute}}}
		my SetPaths2()
		
		-- Add per-project system paths.
		set pathsToAdd to {}
		repeat with i in sysPaths
			copy {name:i, recursive:true, origin:absolute} to end of pathsToAdd
		end repeat
		if (count pathsToAdd) > 0 then Â
			Set Preferences of panel "Access Paths" to {System Paths:pathsToAdd}
		
		-- Set the appropriate prefix file.
		set prefixFile to Prefix File of projSettings
		if flags contains "Carbon" then
			if prefixFile is "" then
				set prefixFile to "CarbonPrefix.h"
			else
				set prefixFile to "Carbon-" & prefixFile
			end if
		end if
		Set Preferences of panel "C/C++ Compiler" to {Prefix File:prefixFile}
		
		-- Are we assuming a .c or a .cpp extension?
		if projFeatures contains "C++" then
			set fileExtension to pCPlusPlusExtension
		else
			set fileExtension to ".c"
		end if
		
		-- Add source files.
		repeat with group in projFileData
			set projPath to projPath of group
			Set Preferences of panel "Access Paths" to Â
				{User Paths:{{name:gSourcePath & projPath, origin:absolute}}}
			set fileList to group's fileList
			set filesToAdd to {}
			repeat with i in fileList
				if i does not contain "." then set i to i & fileExtension
				copy gSourceDir & projPath & i to end of filesToAdd
			end repeat
			Add Files filesToAdd
		end repeat
		
		if flags contains "debug" or flags contains "profile" then
			set the debug of every target file of target (count targets of project document 1) Â
				of project document 1 to true
			if flags contains "profile" then
				my SetDebugSettings(true, true)
			else
				my SetDebugSettings(true, false)
			end if
		else
			my SetDebugSettings(false, false)
		end if
		
		-- Add appropriate system libraries.
		if pLinkExecutables then
			if flags contains "Carbon" then
				if flags contains "profile" then
					my AddCarbonLibs(true)
				else
					my AddCarbonLibs(false)
				end if
			else
				if flags contains "profile" then
					my AddBlueLibs(true)
				else
					my AddBlueLibs(false)
				end if
			end if
		end if
		my AddFeatures(projFeatures, flags)
		
		set filesToAdd to {}
		
		-- Add user libraries.
		if projFeatures contains "sockets" then
			if projLibs does not contain "mitsock" then
				copy "mitsock" to beginning of projLibs
			end if
		end if
		repeat with i in projLibs
			copy gLibsDir & i & libNameSuffix & ".lib" to end of filesToAdd
		end repeat
		
		-- Add resources.
		repeat with i in projRsrcs
			copy gRsrcsDir & i to end of filesToAdd
		end repeat
		if flags contains "Carbon" then
			copy gRsrcsDir & "Carbon.r" to end of filesToAdd
		end if
		
		Add Files filesToAdd
		
		Reset File Paths
		
	end tell
end SetupTarget

on CreateFolders()
	tell application "Finder"
		
		repeat with i in pDirsToCreate
			set pth to relPath of i
			if pth is not "" then set pth to pth & ":"
			if not (exists folder (gDistribRoot & pth & i's name)) then
				make new folder at folder (gDistribRoot & pth) with properties {name:i's name}
			end if
		end repeat
		
	end tell
end CreateFolders

on CreateProject(proj)
	tell application "CodeWarrior IDE"
		
		-- This statement doesn't work, because AppleScript is broken.
		if proj is {} then return
		
		try
			get proj's name
		on error
			return
		end try
		
		set projFilename to proj's name & pProjectFileExtension
		set projPathname to gProjectsDir & projFilename
		if pAlwaysCreateProjects or not (exists file projPathname of application "Finder") then
			
			try
				close (the first project document whose name is projFilename)
			end try
			
			Create Project {projPathname}
			
			if pCreateBlueTargets and pCreateDebugTargets then
				my SetupTarget(proj, "Blue debug")
			end if
			
			if pCreateBlueTargets and pCreateProfiledTargets then
				my SetupTarget(proj, "Blue profile")
			end if
			
			if pCreateBlueTargets and pCreateOptimizedTargets then
				my SetupTarget(proj, "Blue")
			end if
			
			if pCreateCarbonTargets and pCreateDebugTargets then
				my SetupTarget(proj, "Carbon debug")
			end if
			
			if pCreateCarbonTargets and pCreateProfiledTargets then
				my SetupTarget(proj, "Carbon profile")
			end if
			
			if pCreateCarbonTargets and pCreateOptimizedTargets then
				my SetupTarget(proj, "Carbon")
			end if
			
			set the current target of project document 1 to target 1 of project document 1
			
			Close Project
			
		end if
		
	end tell
end CreateProject

on CreateAllProjects()
	
	repeat with proj in gProjectData
		CreateProject(proj)
	end repeat
	
end CreateAllProjects

on BuildProject(projName)
	tell application "CodeWarrior IDE"
		open (gProjectsDir & projName & pProjectFileExtension)
		repeat with i from 2 to (count targets of project document 1)
			set the current target of project document 1 to target i of project document 1
			Make Project
			-- If there were compiler warnings, then a compiler window will be in front.
			-- For whatever reason, this causes the next "set the current target..." to fail.
			-- An easy way to make the window go away without having to know if it's there or not 
			-- is to build again, which, because everything is already compiled, finishes instantly
			-- and produces no warnings.
			--Make Project
			-- An even better way is to check for the window and close it.
			if the name of window 1 is "Errors & Warnings" then
				close first window -- "close window 1" becomes "Close Window 1" (different event)
			end if
		end repeat
		set the current target of project document 1 to target 1 of project document 1
		Close Project
	end tell
end BuildProject

on BuildAllProjects()
	
	repeat with proj in gProjectData
		try
			set projName to proj's name
		on error
			set projName to ""
		end try
		-- This statement doesn't work, because AppleScript is broken.
		if proj is not {} then
			if projName is not "" then
				BuildProject(projName)
			end if
		end if
	end repeat
	
end BuildAllProjects

on SignalCompletion()
	
	beep
	
end SignalCompletion

with timeout of 60000 seconds
	
	SetGlobals()
	
	SetProjectData()
	
	CreateFolders()
	
	tell application "CodeWarrior IDE" to activate
	
	CreateAllProjects()
	
	if pShouldBuild then
		BuildAllProjects()
	end if
	
	SignalCompletion()
	
end timeout

\ No newline at end of file
diff --git a/make/makedemo.unx b/make/makedemo.unx
index 16f1fa25..5d256fea 100644
--- a/make/makedemo.unx
+++ b/make/makedemo.unx
@@ -1,6 +1,6 @@
 #	makefile for demo programs
 #
-#	$Id: makedemo.unx,v 6.64 2003/01/16 22:39:47 dondosha Exp $
+#	$Id: makedemo.unx,v 6.68 2004/01/02 22:05:16 coulouri Exp $
 #
 #	Sun with unbundled ANSI compiler [ make CC=acc ]
 #	Sun with Gnu C [ make CC=gcc ]
@@ -73,6 +73,8 @@ LIB20 =
 LIB22 = -lncbimmdb
 LIB23 = -lncbitool
 LIB50 = -lregexp
+LIB60 = -lblast
+LIB61 = -lblastapi
 NCBI_INCDIR = ../include
 NCBI_LIBDIR = ../lib
 NCBI_LINKINGLIBDIR = $(NCBI_LIBDIR)
@@ -94,20 +96,20 @@ EXE1 = testcore makeset \
     getmesh indexpub getpub testobj seqtest \
 	dosimple asn2ff getseq getfeat checksub asndhuff \
 	entrcmd errhdr cdscan findspl \
-	ncbisort fa2htgs fastacmd formatdb blastall blastpgp \
+	ncbisort fa2htgs fastacmd formatdb blast blastall blastpgp \
 	testval seedtop fmerge makemat copymat impala \
 	megablast vecscreen gil2bin tbl2asn blastclust rpsblast \
-	asn2xml \
+	asn2xml debruijn \
 	test_regexp demo_regexp demo_regexp_grep
 
 SRC1 = testcore.c makeset.c \
     getmesh.c indexpub.c getpub.c testobj.c seqtest.c dosimple.c asn2ff.c \
     getseq.c getfeat.c checksub.c asndhuff.c \
     entrcmd.c errhdr.c cdscan.c findspl.c \
-    ncbisort.c fa2htgs.c fastacmd.c formatdb.c blastall.c blastpgp.c \
-    testval.c seedtop.c fmerge.c makemat.c copymat.c profiles.c \
+    ncbisort.c fa2htgs.c fastacmd.c formatdb.c blast_driver.c blastall.c \
+    blastpgp.c testval.c seedtop.c fmerge.c makemat.c copymat.c profiles.c \
 	megablast.c vecscreen.c gil2bin.c tbl2asn.c blastclust.c rpsblast.c \
-	asn2xml.c \
+	asn2xml.c debruijn.c \
 	pcretest.c pcredemo.c pcregrep.c
 
 INTERNAL = testgen
@@ -274,6 +276,13 @@ formatdb : formatdb.c
 fmerge : fmerge.c
 	$(CC) -o fmerge $(LDFLAGS) fmerge.c $(LIB23) $(LIB2) $(LIB1) $(OTHERLIBS)
 
+# blast (reincarnation of blastall from algo/blast sources)
+
+blast : blast_driver.c
+	$(CC) -o blast $(LDFLAGS) blast_driver.c $(LIB61) $(LIB60) $(LIB23) $(LIB2) $(LIB1) $(OTHERLIBS)
+
+debruijn : debruijn.c
+	$(CC) -o debruijn $(LDFLAGS) debruijn.c $(LIB60) $(LIB1) $(OTHERLIBS)
 # blastall
 
 blastall : blastall.c $(THREAD_OBJ)
@@ -297,7 +306,7 @@ makemat : makemat.c $(THREAD_OBJ)
 # copymat
 
 copymat : copymat.c $(THREAD_OBJ)
-	$(CC) -o copymat $(LDFLAGS) copymat.c $(THREAD_OBJ) $(LIB23) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)
+	$(CC) -o copymat $(LDFLAGS) copymat.c $(THREAD_OBJ) $(LIB60) $(LIB23) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)
 
 # impala
 
diff --git a/make/makedis.csh b/make/makedis.csh
index 8fb5164a..e5680363 100755
--- a/make/makedis.csh
+++ b/make/makedis.csh
@@ -1,6 +1,6 @@
 #!/bin/csh -f
 #
-# $Id: makedis.csh,v 1.89 2003/09/05 19:22:18 beloslyu Exp $
+# $Id: makedis.csh,v 1.94 2004/01/22 19:56:15 ucko Exp $
 #
 ##                            PUBLIC DOMAIN NOTICE                          
 #               National Center for Biotechnology Information
@@ -155,6 +155,9 @@ case Linux:
 	case "parisc":
 		set platform=hppalinux
 		breaksw
+	case "i?86":
+		set platform=linux-x86
+		breaksw
 	default:
 		set platform=linux
 		breaksw
@@ -312,8 +315,9 @@ else
     set PNG_LIBS=""
 endif
 
-set WWWBLAST=(psiblast.REAL psiblast_cs.REAL blast.REAL blast_cs.REAL \
-nph-viewgif.cgi wblast2_cs.REAL bl2bag.cgi)
+set VIBWWWBLAST=(psiblast.REAL psiblast_cs.REAL blast.REAL blast_cs.REAL)
+set NONVIBWWWBLAST=(nph-viewgif.cgi wblast2.REAL wblast2_cs.REAL bl2bag.cgi)
+set WWWBLAST=($VIBWWWBLAST $NONVIBWWWBLAST)
 
 if ( "$HAVE_MOTIF" == 1 ) then
 	set ALL_VIB=(LIB30=libncbicn3d.a \
@@ -335,7 +339,7 @@ if ( "$HAVE_MOTIF" == 1 ) then
 		OGLLIBS=\"$OGL_LIBS $PNG_LIBS\" \
 		VIBFLAG=\"$NCBI_VIBFLAG\" \
 		VIB=\"Psequin Nentrez udv ddv blastcl3 \
-		idfetch bl2seq asn2xml asn2gb entrez2 gbseqget \
+		idfetch bl2seq asn2gb entrez2 gbseqget \
 		$WWWBLAST $OGL_TARGETS\") 
 else if ( "$HAVE_MAC" == 1 ) then
 	set ALL_VIB=(LIB30=libncbicn3d.a \
@@ -357,7 +361,7 @@ else if ( "$HAVE_MAC" == 1 ) then
 		OGLLIBS=\"$OGL_LIBS $PNG_LIBS\" \
 		VIBFLAG=\"$NCBI_VIBFLAG\" \
 		VIB=\"Psequin udv ddv blastcl3 \
-		idfetch bl2seq asn2xml asn2gb entrez2 gbseqget $WWWBLAST \") 
+		idfetch bl2seq asn2gb entrez2 gbseqget $WWWBLAST \") 
 else # no Motif, build only ascii-based applications
     set OGL_NCBI_LIBS=""
     set OGL_INCLUDE=""
@@ -366,7 +370,7 @@ else # no Motif, build only ascii-based applications
 
 	set ALL_VIB=()
 	set DEMO_VIB=()
-	set NET_VIB=(VIB=\"blastcl3 idfetch bl2seq asn2xml asn2gb $WWWBLAST \") 
+	set NET_VIB=(VIB=\"blastcl3 idfetch bl2seq asn2gb $NONVIBWWWBLAST \") 
 endif
 
 set CMD='make $MFLG \
@@ -464,7 +468,7 @@ else
 	getpub getseq gil2bin idfetch impala indexpub makemat makeset \
 	megablast ncbisort netentcf rpsblast seedtop seqtest sequin entrez2 \
 	tbl2asn test_regexp testcore testobj testval udv vecscreen Cn3D \
-	$WWWBLAST )
+	blast debruijn $WWWBLAST )
 	if ( -x ./$i ) then
 		rm -f ../bin/$i
 		if ( $os == "Darwin" ) then
diff --git a/make/makenet.unx b/make/makenet.unx
index 44fce382..41c99e10 100644
--- a/make/makenet.unx
+++ b/make/makenet.unx
@@ -1,6 +1,6 @@
 #   makefile for network demo programs and network entrez
 #
-#	$Id: makenet.unx,v 6.159 2003/09/03 14:41:54 kans Exp $
+#	$Id: makenet.unx,v 6.162 2003/12/16 19:05:13 kimelman Exp $
 #   test, ignore
 #
 #   Sun with unbundled ANSI compiler [ make CC=acc RAN=ranlib ]
@@ -130,6 +130,8 @@ BLIB44 =
 
 BLIB45 = libddvlib.a
 
+BLIB46 = libncbiid2.a
+
 #
 # Pseudo-dummy targets when Vibrant is not used
 #
@@ -196,9 +198,11 @@ LIB38 = -lncbiprsn
 LIB40 = -lncbitxc2
 LIB41 = -lncbiid1
 LIB42 = -lctutils
+LIB_PS = -lctutils -lz
 LIB43 = -losutils
 LIB44 = -lidload
 LIB45 = -lddvlib
+LIB46 = -lncbiid2
 
 ##
 ## encryption of network services
@@ -331,6 +335,8 @@ SRC43 = os_mtutils.c already_running.c
 
 SRC44 = idload_lib.c
 
+SRC46 = id2.c
+
 #NET_LIBS_SRC = $(SRC6) $(SRC6_) $(SRC7) $(SRC8) $(SRC9)
 NET_LIBS_SRC = $(SRC6) $(SRC7) $(SRC8) $(SRC9)
 
@@ -398,6 +404,8 @@ OBJ43 = os_mtutils.o already_running.o
 
 OBJ44 = idload_lib.o
 
+OBJ46 = id2.o
+
 # objects & sources needed for versions of network demo programs
 
 OBJVCLIENT =	vclient.o
@@ -523,7 +531,7 @@ S : $(BLIB16)
 ES : $(BLIB17)
 
 
-others : $(BLIB11) $(BLIB12) $(BLIB13) $(BLIB19) $(BLIB25) $(BLIB27) $(BLIB35) $(BLIB36) $(BLIB38) $(BLIB40) $(NCBI_SHLIBS).alt $(BLIB41) $(BLIB42) $(BLIB43) $(BLIB44)
+others : $(BLIB11) $(BLIB12) $(BLIB13) $(BLIB19) $(BLIB25) $(BLIB27) $(BLIB35) $(BLIB36) $(BLIB38) $(BLIB40) $(NCBI_SHLIBS).alt $(BLIB41) $(BLIB42) $(BLIB43) $(BLIB44) $(BLIB46)
 
 
 ## To clean out the directory without removing make
@@ -598,6 +606,8 @@ copy :
 	-$(SRCCOPY) ../network/id0arch/client/*.c .
 	-$(SRCCOPY) ../network/id1arch/*.h ../include
 	-$(SRCCOPY) ../network/id1arch/*.c .
+	-$(SRCCOPY) ../network/id2arch/*.h ../include
+	-$(SRCCOPY) ../network/id2arch/*.c .
 	-$(SRCCOPY) ../network/spell/client/*.h ../include
 	-$(SRCCOPY) ../network/spell/client/*.c .
 	-$(SRCCOPY) ../network/suggest/client/*.h ../include
@@ -736,6 +746,8 @@ accid1.o: accid1.c
 	$(CC) $(CFLAGS) accid1.c
 id1arch.o: id1arch.c
 	$(CC) $(CFLAGS) id1arch.c
+id2.o: id2.c
+	$(CC) $(CFLAGS) id2.c
 objbl1p1.o : objbl1p1.c
 	$(CC) $(CFLAGS) objbl1p1.c
 objbl1p2.o : objbl1p2.c
@@ -973,6 +985,11 @@ $(BLIB41) : $(OBJ41)
 	$(LIBCOPY) $(BLIB41) $(NCBI_LIBDIR)
 	$(RAN) $(NCBI_LIBDIR)/$(BLIB41)
 
+$(BLIB46) : $(OBJ46)
+	- rm -f $(BLIB46)
+	$(AR) cru $(BLIB46) $(OBJ46)
+	$(LIBCOPY) $(BLIB46) $(NCBI_LIBDIR)
+	$(RAN) $(NCBI_LIBDIR)/$(BLIB46)
 
 #
 # Dummy target used when Vibrant is not used
@@ -1154,7 +1171,7 @@ asn2gb :	asn2gb.c
 # asn2gb_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqfetchEnable
 # should be used only internally within NCBI.
 asn2gb_psf :	asn2gb.c
-	$(CC) -DINTERNAL_NCBI_ASN2GB -g -o asn2gb_psf $(LDFLAGS) asn2gb.c $(LIB42) -lnlmzip $(LIB23) $(LIB2) $(LIB1) $(NCBI_SYBLIBS_CT) $(OTHERLIBS)
+	$(CC) -DINTERNAL_NCBI_ASN2GB -g -o asn2gb_psf $(LDFLAGS) asn2gb.c $(LIB_PS) $(LIB23) $(LIB2) $(LIB1) $(NCBI_SYBLIBS_CT) $(OTHERLIBS)
 
 # gbseqget program (gbseqget)
 gbseqget :	gbseqget.c
@@ -1202,7 +1219,7 @@ fetchent : fetchent.c
 
 # demo program (condense)
 condense :	condense.c
-	$(CC) $(IN_HOUSE_CFLAGS) -o condense $(LDFLAGS) condense.c $(LIB42) $(LIB2) $(LIB1) $(NCBI_SYBLIBS_CT) -lnlmzip $(OTHERLIBS)
+	$(CC) $(IN_HOUSE_CFLAGS) -o condense $(LDFLAGS) condense.c $(LIB_PS) $(LIB2) $(LIB1) $(NCBI_SYBLIBS_CT) $(OTHERLIBS)
 
 # test client for the id0 network service
 
diff --git a/make/msvc_prj/blast/blast.dsp b/make/msvc_prj/blast/blast.dsp
new file mode 100644
index 00000000..88181360
--- /dev/null
+++ b/make/msvc_prj/blast/blast.dsp
@@ -0,0 +1,293 @@
+# Microsoft Developer Studio Project File - Name="blast" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Static Library" 0x0104
+
+CFG=blast - Win32 DebugDLL
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "blast.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "blast.mak" CFG="blast - Win32 DebugDLL"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "blast - Win32 DebugDLL" (based on "Win32 (x86) Static Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+RSC=rc.exe
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "DebugDLL"
+# PROP BASE Intermediate_Dir "DebugDLL"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "DebugDLL"
+# PROP Intermediate_Dir "DebugDLL"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MDd /W3 /Gm /GX /ZI /Od /I "..\..\.." /I "..\..\..\corelib" /I "..\..\..\asnstat" /I "..\..\..\asnlib" /I "..\..\..\tools" /I "..\..\..\object" /I "..\..\..\api" /I "..\..\..\ddv" /I "..\..\..\cdromlib" /I "..\..\..\biostruc" /I "..\..\..\vibrant" /I "..\..\..\desktop" /I "..\..\..\network\taxon1\common" /I "..\..\..\network\taxon1\taxon2" /I "..\..\..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ  /c
+# ADD CPP /nologo /MDd /W3 /Gm /GX /ZI /Od /I "..\..\.." /I "..\..\..\corelib" /I "..\..\..\asnstat" /I "..\..\..\asnlib" /I "..\..\..\tools" /I "..\..\..\object" /I "..\..\..\api" /I "..\..\..\ddv" /I "..\..\..\cdromlib" /I "..\..\..\biostruc" /I "..\..\..\vibrant" /I "..\..\..\desktop" /I "..\..\..\network\taxon1\common" /I "..\..\..\network\taxon1\taxon2" /I "..\..\..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ  /c
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+# Begin Target
+
+# Name "blast - Win32 DebugDLL"
+# Begin Group "core"
+
+# PROP Default_Filter ""
+# Begin Group "src"
+
+# PROP Default_Filter ""
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\aa_ungapped.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_dust.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_engine.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_extend.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_filter.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_gapalign.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_hits.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_lookup.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_message.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_options.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_seg.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_seqsrc.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_setup.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_stat.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_traceback.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_util.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\gapinfo.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\greedy_align.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\link_hsps.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\lookup_util.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\lookup_wrap.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\mb_lookup.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\ncbi_math.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\ncbi_std.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\pattern.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\phi_extend.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\phi_lookup.c
+# End Source File
+# End Group
+# Begin Group "include"
+
+# PROP Default_Filter ""
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\aa_ungapped.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_def.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_dust.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_engine.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_extend.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_filter.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_gapalign.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_hits.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_lookup.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_message.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_options.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_seg.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_seqsrc.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_setup.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_stat.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_traceback.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\blast_util.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\gapinfo.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\greedy_align.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\link_hsps.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\lnfact.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\lookup_util.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\lookup_wrap.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\mb_lookup.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\ncbi_config.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\ncbi_math.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\ncbi_std.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\pattern.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\phi_extend.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\algo\blast\core\phi_lookup.h
+# End Source File
+# End Group
+# End Group
+# End Target
+# End Project
diff --git a/make/msvc_prj/install.sh b/make/msvc_prj/install.sh
index 03b06531..0068ee4c 100644
--- a/make/msvc_prj/install.sh
+++ b/make/msvc_prj/install.sh
@@ -1,5 +1,5 @@
 #! /bin/sh
-# $Id: install.sh,v 1.29 2003/10/09 18:46:48 ivanov Exp $
+# $Id: install.sh,v 1.33 2004/01/29 16:18:37 ivanov Exp $
 # Authors:  Denis Vakatov    (vakatov@ncbi.nlm.nih.gov)
 #           Vladimir Ivanov  (ivanov@ncbi.nlm.nih.gov)
 #           Anton Lavrentiev (lavr@ncbi.nlm.nih.gov)
@@ -10,7 +10,7 @@
 # Cmd.-line args  -- source and destination
 script="$0"
 builddir="${1:-//u/coremake/ncbi}"
-target="${2:-//u/coremake/public/ncbi}"
+target="${2:-//u/coremake/public/ncbi.last}"
 
 if test -n "$3" ; then
   echo "USAGE:  `basename $script` [build_dir] [install_dir]"
@@ -39,11 +39,14 @@ incdir="$target"/include
 srcdir="$target"/src
 bindir="$target"/bin
 datdir="$target"/data
+errdir="$target"/errmsg
 
 # Alternate dirs (mirrors)
 srcdir_a="$target"/altsrc
 dbgdir_a="$target"/dbglib
 libdir_a="$target"/lib
+datdir_a="$target"/../c/data
+errdir_a="$target"/../c/errmsg
 
 
 # Check
@@ -92,9 +95,12 @@ makedir "$srcdir"/tools
 makedir "$srcdir"/vibrant
 makedir "$bindir"   -p
 makedir "$datdir"   -p
+makedir "$errdir"   -p
 makedir "$srcdir_a" -p
 makedir "$dbgdir_a" -p
 makedir "$libdir_a" -p
+makedir "$datdir_a" -p
+makedir "$errdir_a" -p
 
 
 # Copy files
@@ -207,6 +213,9 @@ done
 
 # Data
 cp -pr "$builddir"/data/* "$datdir"
+cp -pr "$builddir"/data/* "$datdir_a"
+cp -pr "$builddir"/errmsg/* "$errdir"
+cp -pr "$builddir"/errmsg/* "$errdir_a"
 
 
 # Fill alt source tree
diff --git a/make/msvc_prj/internal/all_internal.dsp b/make/msvc_prj/internal/all_internal.dsp
new file mode 100644
index 00000000..1bc23e4f
--- /dev/null
+++ b/make/msvc_prj/internal/all_internal.dsp
@@ -0,0 +1,48 @@
+# Microsoft Developer Studio Project File - Name="all_internal" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Generic Project" 0x010a
+
+CFG=all_internal - Win32 DebugDLL
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "all_internal.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "all_internal.mak" CFG="all_internal - Win32 DebugDLL"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "all_internal - Win32 DebugDLL" (based on "Win32 (x86) Generic Project")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+MTL=midl.exe
+
+!IF  "$(CFG)" == "all_internal - Win32 DebugDLL"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "DebugDLL"
+# PROP BASE Intermediate_Dir "DebugDLL"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "DebugDLL"
+# PROP Intermediate_Dir "DebugDLL"
+# PROP Target_Dir ""
+
+!ENDIF 
+
+# Begin Target
+
+# Name "all_internal - Win32 DebugDLL"
+# End Target
+# End Project
diff --git a/make/msvc_prj/internal/smart/smartnet/smartnet.dsp b/make/msvc_prj/internal/smart/smartnet/smartnet.dsp
new file mode 100644
index 00000000..0c2104ff
--- /dev/null
+++ b/make/msvc_prj/internal/smart/smartnet/smartnet.dsp
@@ -0,0 +1,70 @@
+# Microsoft Developer Studio Project File - Name="smartnet" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Static Library" 0x0104
+
+CFG=smartnet - Win32 DebugDLL
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "smartnet.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "smartnet.mak" CFG="smartnet - Win32 DebugDLL"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "smartnet - Win32 DebugDLL" (based on "Win32 (x86) Static Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+RSC=rc.exe
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "DebugDLL"
+# PROP BASE Intermediate_Dir "DebugDLL"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "DebugDLL"
+# PROP Intermediate_Dir "DebugDLL"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MDd /W3 /GX /Z7 /Od /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# SUBTRACT BASE CPP /Fr
+# ADD CPP /nologo /MDd /W3 /GR /Z7 /Od /I "..\..\..\..\.." /I "..\..\..\..\..\api" /I "..\..\..\..\..\corelib" /I "..\..\..\..\..\vibrant" /I "..\..\..\..\..\internal\smart\smartnet" /D "WIN32" /D "_DEBUG" /YX /FD /GZ /c
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+# Begin Target
+
+# Name "smartnet - Win32 DebugDLL"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=..\..\..\..\..\internal\smart\smartnet\smartnet_win32.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=..\..\..\..\..\internal\smart\smartnet\smartnet.h
+# End Source File
+# End Group
+# End Target
+# End Project
diff --git a/make/msvc_prj/ncbi.dsw b/make/msvc_prj/ncbi.dsw
index 25502ae1..f5379186 100644
--- a/make/msvc_prj/ncbi.dsw
+++ b/make/msvc_prj/ncbi.dsw
@@ -293,8 +293,23 @@ Package=<4>
     Begin Project Dependency
     Project_Dep_Name exe_sequin
     End Project Dependency
+}}}
+
+###############################################################################
+
+Project: "all_internal"=.\internal\all_internal.dsp - Package Owner=<4>
+
+Package=<5>
+{{{
+}}}
+
+Package=<4>
+{{{
+    Begin Project Dependency
+    Project_Dep_Name exe_ssequin
+    End Project Dependency
     Begin Project Dependency
-    Project_Dep_Name exe_sequin_ogl
+    Project_Dep_Name smartnet
     End Project Dependency
 }}}
 
@@ -377,6 +392,9 @@ Package=<4>
     Begin Project Dependency
     Project_Dep_Name regexp
     End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name blast
+    End Project Dependency
 }}}
 
 ###############################################################################
@@ -398,6 +416,21 @@ Package=<4>
     Begin Project Dependency
     Project_Dep_Name all_lib
     End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name all_internal
+    End Project Dependency
+}}}
+
+###############################################################################
+
+Project: "blast"=.\blast\blast.dsp - Package Owner=<4>
+
+Package=<5>
+{{{
+}}}
+
+Package=<4>
+{{{
 }}}
 
 ###############################################################################
@@ -950,6 +983,9 @@ Package=<4>
     Begin Project Dependency
     Project_Dep_Name ncbimain
     End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name blast
+    End Project Dependency
 }}}
 
 ###############################################################################
@@ -2046,9 +2082,6 @@ Package=<4>
     Project_Dep_Name ncbitool
     End Project Dependency
     Begin Project Dependency
-    Project_Dep_Name vibrant
-    End Project Dependency
-    Begin Project Dependency
     Project_Dep_Name ncbinacc
     End Project Dependency
     Begin Project Dependency
@@ -2448,9 +2481,6 @@ Package=<4>
     Project_Dep_Name vibnet
     End Project Dependency
     Begin Project Dependency
-    Project_Dep_Name ncbicn3d
-    End Project Dependency
-    Begin Project Dependency
     Project_Dep_Name netblast
     End Project Dependency
     Begin Project Dependency
@@ -2463,15 +2493,9 @@ Package=<4>
     Project_Dep_Name ncbidesk
     End Project Dependency
     Begin Project Dependency
-    Project_Dep_Name ddvlib
-    End Project Dependency
-    Begin Project Dependency
     Project_Dep_Name ncbitxc2
     End Project Dependency
     Begin Project Dependency
-    Project_Dep_Name ncbiid1
-    End Project Dependency
-    Begin Project Dependency
     Project_Dep_Name medarch
     End Project Dependency
     Begin Project Dependency
@@ -2499,7 +2523,7 @@ Package=<4>
 
 ###############################################################################
 
-Project: "exe_sequin_ogl"=.\sequin\sequin_ogl\exe_sequin_ogl.dsp - Package Owner=<4>
+Project: "exe_ssequin"=.\sequin\ssequin\exe_ssequin.dsp - Package Owner=<4>
 
 Package=<5>
 {{{
@@ -2508,10 +2532,10 @@ Package=<5>
 Package=<4>
 {{{
     Begin Project Dependency
-    Project_Dep_Name vibnet
+    Project_Dep_Name smartnet
     End Project Dependency
     Begin Project Dependency
-    Project_Dep_Name ncbicn3d_ogl
+    Project_Dep_Name vibnet
     End Project Dependency
     Begin Project Dependency
     Project_Dep_Name netblast
@@ -2526,15 +2550,9 @@ Package=<4>
     Project_Dep_Name ncbidesk
     End Project Dependency
     Begin Project Dependency
-    Project_Dep_Name ddvlib
-    End Project Dependency
-    Begin Project Dependency
     Project_Dep_Name ncbitxc2
     End Project Dependency
     Begin Project Dependency
-    Project_Dep_Name ncbiid1
-    End Project Dependency
-    Begin Project Dependency
     Project_Dep_Name medarch
     End Project Dependency
     Begin Project Dependency
@@ -2558,6 +2576,9 @@ Package=<4>
     Begin Project Dependency
     Project_Dep_Name ncbi
     End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbispel
+    End Project Dependency
 }}}
 
 ###############################################################################
@@ -2721,6 +2742,18 @@ Package=<4>
 
 ###############################################################################
 
+Project: "ncbispel"=.\network\spell\client\ncbispel.dsp - Package Owner=<4>
+
+Package=<5>
+{{{
+}}}
+
+Package=<4>
+{{{
+}}}
+
+###############################################################################
+
 Project: "ncbitool"=.\tools\ncbitool.dsp - Package Owner=<4>
 
 Package=<5>
@@ -2793,6 +2826,18 @@ Package=<4>
 
 ###############################################################################
 
+Project: "smartnet"=.\internal\smart\smartnet\smartnet.dsp - Package Owner=<4>
+
+Package=<5>
+{{{
+}}}
+
+Package=<4>
+{{{
+}}}
+
+###############################################################################
+
 Project: "socket_io_bouncer"=.\connect\test\socket_io_bouncer\socket_io_bouncer.dsp - Package Owner=<4>
 
 Package=<5>
diff --git a/make/msvc_prj/network/spell/client/ncbispel.dsp b/make/msvc_prj/network/spell/client/ncbispel.dsp
new file mode 100644
index 00000000..471bad36
--- /dev/null
+++ b/make/msvc_prj/network/spell/client/ncbispel.dsp
@@ -0,0 +1,78 @@
+# Microsoft Developer Studio Project File - Name="ncbispel" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Static Library" 0x0104
+
+CFG=ncbispel - Win32 DebugDLL
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "ncbispel.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "ncbispel.mak" CFG="ncbispel - Win32 DebugDLL"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "ncbispel - Win32 DebugDLL" (based on "Win32 (x86) Static Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+RSC=rc.exe
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "DebugDLL"
+# PROP BASE Intermediate_Dir "DebugDLL"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "DebugDLL"
+# PROP Intermediate_Dir "DebugDLL"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MDd /W3 /GX /Z7 /Od /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# SUBTRACT BASE CPP /Fr
+# ADD CPP /nologo /MDd /W3 /GR /Z7 /Od /I "..\..\..\..\.." /I "..\..\..\..\..\network\spell\client" /I "..\..\..\..\..\asnlib" /I "..\..\..\..\..\asnstat" /I "..\..\..\..\..\corelib" /I "..\..\..\..\..\network\nsclilib" /D "WIN32" /D "_DEBUG" /YX /FD /GZ /c
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+# Begin Target
+
+# Name "ncbispel - Win32 DebugDLL"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=..\..\..\..\..\network\spell\client\objspell.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\..\network\spell\client\spellapi.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=..\..\..\..\..\network\spell\client\objspell.h
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\..\network\spell\client\spellapi.h
+# End Source File
+# End Group
+# End Target
+# End Project
diff --git a/make/msvc_prj/object/ncbiobj.dsp b/make/msvc_prj/object/ncbiobj.dsp
index 80f31333..76d45955 100644
--- a/make/msvc_prj/object/ncbiobj.dsp
+++ b/make/msvc_prj/object/ncbiobj.dsp
@@ -109,7 +109,27 @@ SOURCE=..\..\..\api\asn2ff6.c
 # End Source File
 # Begin Source File
 
-SOURCE=..\..\..\api\asn2gnbk.c
+SOURCE=..\..\..\api\asn2gnb1.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\api\asn2gnb2.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\api\asn2gnb3.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\api\asn2gnb4.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\api\asn2gnb5.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\api\asn2gnb6.c
 # End Source File
 # Begin Source File
 
diff --git a/make/msvc_prj/sequin/ssequin/exe_ssequin.dsp b/make/msvc_prj/sequin/ssequin/exe_ssequin.dsp
new file mode 100644
index 00000000..09fde287
--- /dev/null
+++ b/make/msvc_prj/sequin/ssequin/exe_ssequin.dsp
@@ -0,0 +1,119 @@
+# Microsoft Developer Studio Project File - Name="exe_ssequin" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Application" 0x0101
+
+CFG=exe_ssequin - Win32 DebugDLL
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "exe_ssequin.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "exe_ssequin.mak" CFG="exe_ssequin - Win32 DebugDLL"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "exe_ssequin - Win32 DebugDLL" (based on "Win32 (x86) Application")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "DebugDLL"
+# PROP BASE Intermediate_Dir "DebugDLL"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "DebugDLL"
+# PROP Intermediate_Dir "DebugDLL"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+LIB32=link.exe -lib
+# ADD BASE CPP /nologo /MDd /W3 /GX /Z7 /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# ADD CPP /nologo /MDd /W3 /GR /Z7 /Od /I "..\..\..\.." /I "..\..\..\..\api" /I "..\..\..\..\asnstat" /I "..\..\..\..\ddv" /I "..\..\..\..\access" /I "..\..\..\..\desktop" /I "..\..\..\..\object" /I "..\..\..\..\asnlib" /I "..\..\..\..\vibrant" /I "..\..\..\..\network\vibnet" /I "..\..\..\..\cdromlib" /I "..\..\..\..\tools" /I "..\..\..\..\connect" /I "..\..\..\..\corelib" /I "..\..\..\..\network\taxon1\taxon2" /I "..\..\..\..\network\nsclilib" /I "..\..\..\..\network\blast3\client" /I "..\..\..\..\network\taxon1\common" /I "..\..\..\..\network\medarch\client" /I "..\..\..\..\network\id1arch" /I "..\..\..\..\network\spell\client" /I "..\..\..\..\biostruc" /I "..\..\..\..\internal\smart\smartnet" /D "WIN32" /D "_DEBUG" /D "INTERNAL_NCBI_SEQUIN" /D "USE_SMARTNET" /YX /FD /GZ /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /pdb:none /debug /machine:I386
+# ADD LINK32 oldnames.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib wsock32.lib /nologo /subsystem:windows /debug /machine:I386 /out:"DebugDLL/ssequin.exe" /pdbtype:sept
+# SUBTRACT LINK32 /pdb:none /nodefaultlib
+# Begin Target
+
+# Name "exe_ssequin - Win32 DebugDLL"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=..\..\..\..\link\mswin\sequin.rc
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin1.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin10.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin2.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin3.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin4.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin5.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin6.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin7.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin8.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin9.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequinx.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=..\..\..\..\sequin\sequin.h
+# End Source File
+# End Group
+# End Target
+# End Project
diff --git a/make/msvc_prj/tools/ncbitool.dsp b/make/msvc_prj/tools/ncbitool.dsp
index 3a8ddd8a..bb060556 100644
--- a/make/msvc_prj/tools/ncbitool.dsp
+++ b/make/msvc_prj/tools/ncbitool.dsp
@@ -171,10 +171,6 @@ SOURCE=..\..\..\tools\ncbisort.c
 # End Source File
 # Begin Source File
 
-SOURCE=..\..\..\tools\newkar.c
-# End Source File
-# Begin Source File
-
 SOURCE=..\..\..\tools\objscoremat.c
 # End Source File
 # Begin Source File
diff --git a/make/readme.dos b/make/readme.dos
index 0d1855f6..7a1ff79c 100644
--- a/make/readme.dos
+++ b/make/readme.dos
@@ -1,4 +1,4 @@
-# $Id: readme.dos,v 6.12 2002/04/29 18:12:06 vakatov Exp $
+# $Id: readme.dos,v 6.13 2004/01/26 17:04:53 vakatov Exp $
 # By Denis Vakatov, NCBI
 
 
@@ -31,6 +31,8 @@ Building the NCBI C Toolkit
       "all - Win32 Release"
       "all - Win32 DebugMT"
       "all - Win32 ReleaseMT"
+      "all - Win32 DebugDLL"
+      "all - Win32 ReleaseDLL"
 3.2) Or, you can choose to build any library(es) or application(s)
      in any configuration by using either the list of
      project configuration here or "ClassView" (or "FileView") frame.
diff --git a/network/blast3/client/netblap3.c b/network/blast3/client/netblap3.c
index 191d5b13..0748f819 100644
--- a/network/blast3/client/netblap3.c
+++ b/network/blast3/client/netblap3.c
@@ -34,6 +34,9 @@
 *
 * RCS Modification History:
 * $Log: netblap3.c,v $
+* Revision 1.105  2004/01/27 20:53:12  dondosha
+* Value of no_traceback megablast option is now Uint1 instead of Boolean
+*
 * Revision 1.104  2003/01/13 18:08:26  bealer
 * - Replace nonstandard snprintf() function with strcpy/strcat/strlen.
 *
@@ -800,7 +803,7 @@ BlastOptionsToParameters (BLAST_OptionsBlkPtr options)
         parameters->smith_waterman = options->smith_waterman;
         parameters->is_megablast = options->is_megablast_search;
         parameters->query_lcase_mask = (ValNodePtr) options->query_lcase_mask;
-        parameters->endpoint_results = options->no_traceback;
+        parameters->endpoint_results = (Boolean) options->no_traceback;
         parameters->percent_identity = (FloatHi) options->perc_identity;
         parameters->first_db_seq = options->first_db_seq;
         parameters->final_db_seq = options->final_db_seq;
@@ -2768,7 +2771,8 @@ parametersToOptions (BlastParametersPtr parameters, CharPtr program, ValNodePtr
 		options->is_megablast_search = parameters->is_megablast;
                 options->query_lcase_mask = 
                    (SeqLocPtr) parameters->query_lcase_mask;
-                options->no_traceback = parameters->endpoint_results;
+                if (parameters->endpoint_results)
+                   options->no_traceback = 1; 
                 options->perc_identity = (FloatLo) parameters->percent_identity;
                 options->first_db_seq = parameters->first_db_seq;
                 options->final_db_seq = parameters->final_db_seq;
diff --git a/network/id1arch/idfetch.c b/network/id1arch/idfetch.c
index ce439e7a..5d9afa05 100644
--- a/network/id1arch/idfetch.c
+++ b/network/id1arch/idfetch.c
@@ -25,6 +25,12 @@
  * Author Karl Sirotkin
  *
  $Log: idfetch.c,v $
+ Revision 1.29  2003/12/17 20:35:38  kans
+ initialize status, send NORMAL_STYLE to SeqEntrytoGnbk instead of 0 (also fixed in asn2gnbk), pass lookup flags
+
+ Revision 1.28  2003/11/19 16:35:19  yaschenk
+ relaxing ranges for -g and -c
+
  Revision 1.27  2003/03/28 18:48:39  yaschenk
  tuning ObjMgr, adding STREAM_SEQ_PORT_FIRST to SeqEntryToGnbk
 
@@ -190,14 +196,14 @@ Args myargs[] = {
 2 - get SeqIds\n\t\t\t\
 3 - get gi historyn (sequence change only)\n\t\t\t\
 4 - get gi revision history (any change to asn.1)\n", "0","0","4",TRUE,'i',ARG_INT,0.0,0,NULL},
-	{"GI id for single Entity to dump" ,"0","0","99999999",TRUE,'g',ARG_INT,0.0,0,NULL},
+	{"GI id for single Entity to dump" ,"0","0","999999999",TRUE,'g',ARG_INT,0.0,0,NULL},
 	{"File with list of gi's, accessions, accession.version's, fasta seqid's to dump",NULL,NULL,NULL,TRUE,'G',ARG_FILE_IN,0.0,0,NULL},
 	{"Max complexity:\t\
 0 - get the whole blob\n\t\t\t\
 1 - get the bioseq of interest\n\t\t\t\
 2 - get the minimal bioseq-set containing the bioseq of interest\n\t\t\t\
 3 - get the minimal nuc-prot containing the bioseq of interest\n\t\t\t\
-4 - get the minimal pub-set containing the bioseq of interest\n" ,"0","0","4",TRUE,'c',ARG_INT,0.0,0,NULL},
+4 - get the minimal pub-set containing the bioseq of interest\n" ,"0",NULL,NULL,TRUE,'c',ARG_INT,0.0,0,NULL},
  	{"flaTtened SeqId, format: \n		\'type(name,accession,release,version)\'\n			as \'5(HUMHBB)\' or \n		type=accession, or \n		type:number ",
 		NULL,NULL,NULL,TRUE,'f',ARG_STRING,0.0,0,NULL},
  	{"Fasta style SeqId ENCLOSED IN QUOTES:\n\t\t\t\
@@ -857,7 +863,7 @@ static Boolean ProcessOneDocSum (Int4 num, Int4Ptr uids)
 static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex)
 {
   SeqEntryPtr	sep=NULL;
-  Int4		status,gi_state;
+  Int4		status = 0,gi_state;
   SeqIdPtr	sip_ret=NULL;
   SeqId		si={SEQID_GI,0,0};
   ID1SeqHistPtr	ishp=NULL;
@@ -991,7 +997,8 @@ static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex)
       if(!SeqEntryToFlat(sep, fp, GENBANK_FMT, RELEASE_MODE)){
 #else 
       AssignIDsInEntity(0,OBJ_SEQENTRY,sep);
-      if(!SeqEntryToGnbk(sep,NULL,GENBANK_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES,STREAM_SEQ_PORT_FIRST,0,NULL,fp)){
+      if(!SeqEntryToGnbk(sep,NULL,GENBANK_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES,
+         LOOKUP_FAR_COMPONENTS|LOOKUP_FAR_LOCATIONS|LOOKUP_FAR_PRODUCTS|LOOKUP_FAR_HISTORY|STREAM_SEQ_PORT_FIRST,0,NULL,fp)){
 #endif
         ErrPostEx(SEV_WARNING,0,0,
                   "GenBank Format does not exist for this sequence ");
@@ -1004,7 +1011,8 @@ static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex)
       if(!SeqEntryToFlat(sep, fp, GENPEPT_FMT, RELEASE_MODE))
 #else 
       AssignIDsInEntity(0,OBJ_SEQENTRY,sep);
-      if(!SeqEntryToGnbk(sep,NULL,GENPEPT_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES,STREAM_SEQ_PORT_FIRST,0,NULL,fp))
+      if(!SeqEntryToGnbk(sep,NULL,GENPEPT_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES,
+        LOOKUP_FAR_COMPONENTS|LOOKUP_FAR_LOCATIONS|LOOKUP_FAR_PRODUCTS|LOOKUP_FAR_HISTORY|STREAM_SEQ_PORT_FIRST,0,NULL,fp))
 #endif
       {
         ErrPostEx(SEV_WARNING,0,0,
diff --git a/network/id2arch/id2.asn b/network/id2arch/id2.asn
new file mode 100644
index 00000000..f85764af
--- /dev/null
+++ b/network/id2arch/id2.asn
@@ -0,0 +1,341 @@
+--$Revision: 1.6 $
+--********************************************************************
+--
+--  Network Id server network access
+--  Vasilchenko 2003
+--
+--
+--*********************************************************************
+--
+--  ID2.asn
+--
+--     messages for id server network access
+--
+--*********************************************************************
+
+NCBI-ID2Access DEFINITIONS ::=
+BEGIN
+
+IMPORTS Seq-id, Seq-loc FROM NCBI-Seqloc
+        ID2S-Chunk-Id   FROM NCBI-Seq-split;
+
+
+----------------------------------------------------------------------------
+-- request types
+----------------------------------------------------------------------------
+
+ID2-Request-Packet ::= SEQUENCE OF ID2-Request
+
+
+ID2-Request ::= SEQUENCE {
+        -- request's serial number, can be used in asynchronic clients
+        -- server should copy it to corresponding field in reply
+        serial-number  INTEGER OPTIONAL,
+
+        params          ID2-Params OPTIONAL,
+
+        request CHOICE {
+                init            NULL,
+                get-packages    ID2-Request-Get-Packages,
+                string-to-gi    ID2-Request-String-To-Gi,
+                seq-id-to-gi    ID2-Request-Seq-id-To-Gi,
+                gi-to-tse-id    ID2-Request-Gi-To-TSE-Id,
+                get-tse         ID2-Request-Get-TSE,
+                reget-tse       ID2-Request-ReGet-TSE,
+                get-chunks      ID2S-Request-Get-Chunks
+        }
+}
+
+
+ID2-Request-Get-Packages ::= SEQUENCE {
+        -- return known packages from this list
+        -- if unset - return all known packages
+        names           SEQUENCE OF VisibleString OPTIONAL,
+
+        -- return packages' names only
+        no-contents     NULL OPTIONAL
+}
+
+
+ID2-Request-String-To-Gi ::= SEQUENCE {
+        -- requested sequence ID, can be any string
+        id              VisibleString
+}
+
+
+ID2-Request-Seq-id-To-Gi ::= SEQUENCE {
+        -- requested sequence ID, can be any ID
+        seq-id          Seq-id
+}
+
+
+ID2-Request-Gi-To-TSE-Id ::= SEQUENCE {
+        -- id can be supplied by inner request
+        gi              CHOICE {
+                gi              INTEGER,
+                string          ID2-Request-String-To-Gi,
+                seq-id          ID2-Request-Seq-id-To-Gi
+        },
+
+        -- return id of tse with sequence
+        sources         SET OF VisibleString OPTIONAL,
+
+        -- return TSE-Ids with external references to this gi
+        external        NULL OPTIONAL,
+
+        -- return in addition list of gis also resolving to this tse
+        current-gis     NULL OPTIONAL
+}
+
+
+ID2-Request-Get-TSE ::= SEQUENCE {
+        -- id can be supplied by inner request
+        tse-id          CHOICE {
+                tse-id          ID2-TSE-Id,
+                gi      SEQUENCE {
+                        request         ID2-Request-Gi-To-TSE-Id,
+
+                        -- if this field is set, then server will not send
+                        -- tses listed here
+                        exclude-tses    SET OF ID2-TSE-Id OPTIONAL
+                }
+        },
+
+        -- level of details requested immediately
+        -- server will send relevant chunks if TSE is splitted
+        details         ID2-Get-TSE-Details OPTIONAL
+}
+
+
+ID2-Request-ReGet-TSE ::= SEQUENCE {
+        tse-id          ID2-TSE-Id,
+
+        -- level of details requested
+        details         ID2-Get-TSE-Details OPTIONAL,
+
+        -- start offset of data to get
+        offset          INTEGER
+}
+
+
+ID2S-Request-Get-Chunks ::= SEQUENCE {
+        tse-id          ID2-TSE-Id,
+
+        -- requests for specific chunks of splitted blob
+        chunks          SET OF ID2S-Chunk-Id
+}
+
+
+ID2-Get-TSE-Details ::= SEQUENCE {
+        location        Seq-loc,
+
+        seq-class-level INTEGER DEFAULT 1,
+
+        descr-level     INTEGER DEFAULT 1,
+
+        descr-type-mask INTEGER DEFAULT 0,
+        
+        annot-type-mask INTEGER DEFAULT 0,
+
+        feat-type-mask  INTEGER DEFAULT 0,
+
+        sequence-level  ENUMERATED {
+                none     (0) ,
+                seq-map  (1) ,
+                seq-data (2)
+        } DEFAULT none
+}
+
+
+----------------------------------------------------------------------------
+-- reply types
+----------------------------------------------------------------------------
+
+
+ID2-Reply ::= SEQUENCE {
+        -- request's serial number, copy from request
+        serial-number   INTEGER OPTIONAL,
+
+        params          ID2-Params OPTIONAL,
+
+        reply CHOICE {
+                init            NULL,
+                get-package     ID2-Reply-Get-Package,
+                -- string-to-gi    ID2-Reply-String-To-Gi,
+                seq-id-to-gi    ID2-Reply-Seq-id-To-Gi,
+                gi-to-tse-id    ID2-Reply-Gi-To-TSE-Id,
+                get-tse         ID2-Reply-Get-TSE,
+                get-tse-info    ID2S-Reply-Get-TSE-Info,
+                get-chunk       ID2S-Reply-Get-Chunk
+        },
+
+        error           SEQUENCE OF ID2-Error OPTIONAL,
+
+        -- true if this reply is the last one for the request
+        -- false if more replies will follow
+        end-of-reply    BOOLEAN
+}
+
+
+ID2-Error ::= SEQUENCE {
+        severity        ENUMERATED {
+                -- nothing harmful happened
+                warning             (1) ,
+
+                -- command cannot be completed this time
+                failed-command      (2) ,
+
+                -- connection cannot be reused, reconnect is required
+                failed-connection   (3) ,
+
+                -- server cannot be used for a while
+                failed-server       (4) ,
+
+                -- resolve request gives no data
+                -- probably temporarily (see retry-delay field)
+                no-data             (5) ,
+
+                -- data exists but client doesn't have permission to get it
+                restricted-data     (6) ,
+
+                -- this request type is not supported by server
+                unsupported-command (7) ,
+
+                -- error in request packet, cannot retry
+                invalid-arguments   (8)
+        },
+
+        -- client may retry the request after specified time in seconds 
+        retry-delay INTEGER OPTIONAL,
+
+        message VisibleString OPTIONAL
+}
+
+
+ID2-Reply-Get-Package ::= SEQUENCE {
+        name            VisibleString,
+
+        params          ID2-Params OPTIONAL
+}
+
+
+ID2-Reply-Seq-id-To-Gi ::= SEQUENCE {
+        -- request sequence ID, copy from request
+        seq-id          Seq-id,
+
+        -- gi of requested Seq-id
+        -- not set if error occured
+        gi              INTEGER OPTIONAL
+}
+
+
+ID2-Reply-Gi-To-TSE-Id ::= SEQUENCE {
+        gi              INTEGER,
+
+        -- source name of this tse set
+        -- "" for native tse - tse with sequence
+        source          VisibleString DEFAULT "",
+
+        -- tse set with requested gi
+        -- not set if error occured
+        tses            SET OF ID2-TSE-Id-Info OPTIONAL
+}
+
+
+ID2-TSE-Id-Info ::= SEQUENCE {
+        tse-id          ID2-TSE-Id,
+
+        -- version of split data
+        -- (0 for non split)
+        split-version   INTEGER DEFAULT 0
+}
+
+
+ID2-Reply-Get-TSE ::= SEQUENCE {
+        tse-id          ID2-TSE-Id,
+
+        -- whole tse or tse skeleton
+        -- not set if error occured
+        data            ID2-Reply-Data OPTIONAL
+}
+
+
+ID2S-Reply-Get-TSE-Info ::= SEQUENCE {
+        tse-id          ID2-TSE-Id,
+
+        -- version of split data
+        split-version   INTEGER,
+
+        -- tse split info
+        -- not set if error occured
+        info            ID2-Reply-Data OPTIONAL
+}
+
+
+ID2S-Reply-Get-Chunk ::= SEQUENCE {
+        tse-id          ID2-TSE-Id,
+
+        chunk-id        ID2S-Chunk-Id,
+
+        -- chunk data
+        -- not set if error occured
+        data            ID2-Reply-Data OPTIONAL
+}
+
+
+ID2-Reply-Data ::= SEQUENCE {
+        data-type       INTEGER, -- index of negotiated types
+        -- recommended types
+        --   Seq-entry,
+        --   ID2S-Split-Info,
+        --   ID2S-Chunk
+
+        -- serialization format (ASN.1 binary, ASN.1 text)
+        data-format             INTEGER, -- index of negotiated formats
+
+        -- post serialization compression (plain, gzip, etc.)
+        data-compression        INTEGER, -- index of negotiated formats
+
+        -- data blob
+        data                    SEQUENCE OF OCTET STRING
+}
+
+
+----------------------------------------------------------------------------
+-- utility types
+----------------------------------------------------------------------------
+
+
+ID2-TSE-Id ::= SEQUENCE {
+        sat             INTEGER,
+        sat-key         INTEGER
+}
+
+
+ID2-Params ::= SEQUENCE OF ID2-Param
+
+
+ID2-Param ::= SEQUENCE {
+        name    VisibleString,
+        value   SEQUENCE OF VisibleString OPTIONAL,
+        type    ENUMERATED {
+                -- no response expected
+                set-value   (1) ,
+
+                -- this option is for client only
+                -- server replies with its value of param if known
+                -- server omits this param in reply if unknown to server
+                get-value   (2) ,
+
+                -- no direct response expected,
+                -- but if the param or its value is not supported
+                -- an error is reported and the request is not be completed
+                force-value (3) ,
+
+                -- use named package
+                -- value should be unset
+                use-package (4)
+        } DEFAULT set-value
+}
+
+END
diff --git a/network/id2arch/id2.c b/network/id2arch/id2.c
new file mode 100644
index 00000000..8a96fe8d
--- /dev/null
+++ b/network/id2arch/id2.c
@@ -0,0 +1,8013 @@
+#include <asn.h>
+
+#define NLM_GENERATED_CODE_PROTO
+
+#include <id2map.h>
+#include <id2gen.h>
+
+static Boolean loaded = FALSE;
+
+#include <id2.h>
+
+#ifndef NLM_EXTERN_LOADS
+#define NLM_EXTERN_LOADS {}
+#endif
+
+NLM_EXTERN Boolean LIBCALL
+id2genAsnLoad(void)
+{
+
+   if ( ! loaded) {
+      NLM_EXTERN_LOADS
+
+      if ( ! AsnLoad ())
+      return FALSE;
+      loaded = TRUE;
+   }
+
+   return TRUE;
+}
+
+
+
+/**************************************************
+*    Generated object loaders for Module NCBI-ID2Access
+*    Generated using ASNCODE Revision: 6.0 at Dec 15, 2003  5:08 PM
+*
+**************************************************/
+
+
+/**************************************************
+*
+*    ID2RequestPacketFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestPacketPtr LIBCALL
+ID2RequestPacketFree(ID2RequestPacketPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr,  (AsnOptFreeFunc) ID2RequestFree);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    ID2RequestPacketAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestPacketPtr LIBCALL
+ID2RequestPacketAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2RequestPacketPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2RequestPacket ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_PACKET);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_PACKET);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2RequestAsnRead, (AsnOptFreeFunc) ID2RequestFree);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2RequestPacketFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestPacketAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2RequestPacketAsnWrite(ID2RequestPacketPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REQUEST_PACKET);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericUserSeqOfAsnWrite(ptr , (AsnWriteFunc) ID2RequestAsnWrite, aip, atp, ID2_REQUEST_PACKET_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestPtr LIBCALL
+ID2RequestNew(void)
+{
+   ID2RequestPtr ptr = MemNew((size_t) sizeof(ID2Request));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2RequestFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestPtr LIBCALL
+ID2RequestFree(ID2RequestPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2ParamsFree(ptr -> params);
+   Request_requestFree(ptr -> Request_request);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    Request_requestFree()
+*
+**************************************************/
+static 
+Request_requestPtr LIBCALL
+Request_requestFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case Request_request_get_packages:
+      ID2RequestGetPackagesFree(anp -> data.ptrvalue);
+      break;
+   case Request_request_string_to_gi:
+      ID2RequestStringToGiFree(anp -> data.ptrvalue);
+      break;
+   case Request_request_seq_id_to_gi:
+      ID2RequestSeqIdToGiFree(anp -> data.ptrvalue);
+      break;
+   case Request_request_gi_to_tse_id:
+      ID2RequestGiToTSEIdFree(anp -> data.ptrvalue);
+      break;
+   case Request_request_get_tse:
+      ID2RequestGetTSEFree(anp -> data.ptrvalue);
+      break;
+   case Request_request_reget_tse:
+      ID2RequestReGetTSEFree(anp -> data.ptrvalue);
+      break;
+   case Request_request_get_chunks:
+      ID2SRequestGetChunksFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ID2RequestAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestPtr LIBCALL
+ID2RequestAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2RequestPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2Request ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2RequestNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REQUEST_serial_number) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> serial_number = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REQUEST_params) {
+      ptr -> params = ID2ParamsAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REQUEST_request) {
+      ptr -> Request_request = Request_requestAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2RequestFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    Request_requestAsnRead()
+*
+**************************************************/
+static 
+Request_requestPtr LIBCALL
+Request_requestAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* Request_request ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_request);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_request);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == ID2_REQUEST_request_init) {
+      choice = Request_request_init;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == REQUEST_request_get_packages) {
+      choice = Request_request_get_packages;
+      func = (AsnReadFunc) ID2RequestGetPackagesAsnRead;
+   }
+   else if (atp == REQUEST_request_string_to_gi) {
+      choice = Request_request_string_to_gi;
+      func = (AsnReadFunc) ID2RequestStringToGiAsnRead;
+   }
+   else if (atp == REQUEST_request_seq_id_to_gi) {
+      choice = Request_request_seq_id_to_gi;
+      func = (AsnReadFunc) ID2RequestSeqIdToGiAsnRead;
+   }
+   else if (atp == REQUEST_request_gi_to_tse_id) {
+      choice = Request_request_gi_to_tse_id;
+      func = (AsnReadFunc) ID2RequestGiToTSEIdAsnRead;
+   }
+   else if (atp == ID2_REQUEST_request_get_tse) {
+      choice = Request_request_get_tse;
+      func = (AsnReadFunc) ID2RequestGetTSEAsnRead;
+   }
+   else if (atp == ID2_REQUEST_request_reget_tse) {
+      choice = Request_request_reget_tse;
+      func = (AsnReadFunc) ID2RequestReGetTSEAsnRead;
+   }
+   else if (atp == ID2_REQUEST_request_get_chunks) {
+      choice = Request_request_get_chunks;
+      func = (AsnReadFunc) ID2SRequestGetChunksAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ID2RequestAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2RequestAsnWrite(ID2RequestPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REQUEST);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> serial_number;
+   retval = AsnWrite(aip, ID2_REQUEST_serial_number,  &av);
+   if (ptr -> params != NULL) {
+      if ( ! ID2ParamsAsnWrite(ptr -> params, aip, ID2_REQUEST_params)) {
+         goto erret;
+      }
+   }
+   if (ptr -> Request_request != NULL) {
+      if ( ! Request_requestAsnWrite(ptr -> Request_request, aip, ID2_REQUEST_request)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    Request_requestAsnWrite()
+*
+**************************************************/
+static Boolean LIBCALL 
+Request_requestAsnWrite(Request_requestPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, ID2_REQUEST_request);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case Request_request_init:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, ID2_REQUEST_request_init, &av);
+      break;
+   case Request_request_get_packages:
+      writetype = REQUEST_request_get_packages;
+      func = (AsnWriteFunc) ID2RequestGetPackagesAsnWrite;
+      break;
+   case Request_request_string_to_gi:
+      writetype = REQUEST_request_string_to_gi;
+      func = (AsnWriteFunc) ID2RequestStringToGiAsnWrite;
+      break;
+   case Request_request_seq_id_to_gi:
+      writetype = REQUEST_request_seq_id_to_gi;
+      func = (AsnWriteFunc) ID2RequestSeqIdToGiAsnWrite;
+      break;
+   case Request_request_gi_to_tse_id:
+      writetype = REQUEST_request_gi_to_tse_id;
+      func = (AsnWriteFunc) ID2RequestGiToTSEIdAsnWrite;
+      break;
+   case Request_request_get_tse:
+      writetype = ID2_REQUEST_request_get_tse;
+      func = (AsnWriteFunc) ID2RequestGetTSEAsnWrite;
+      break;
+   case Request_request_reget_tse:
+      writetype = ID2_REQUEST_request_reget_tse;
+      func = (AsnWriteFunc) ID2RequestReGetTSEAsnWrite;
+      break;
+   case Request_request_get_chunks:
+      writetype = ID2_REQUEST_request_get_chunks;
+      func = (AsnWriteFunc) ID2SRequestGetChunksAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ID2ParamsFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ParamsPtr LIBCALL
+ID2ParamsFree(ID2ParamsPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr,  (AsnOptFreeFunc) ID2ParamFree);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    ID2ParamsAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ParamsPtr LIBCALL
+ID2ParamsAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2ParamsPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2Params ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_PARAMS);
+   } else {
+      atp = AsnLinkType(orig, ID2_PARAMS);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2ParamAsnRead, (AsnOptFreeFunc) ID2ParamFree);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2ParamsFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2ParamsAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2ParamsAsnWrite(ID2ParamsPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_PARAMS);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericUserSeqOfAsnWrite(ptr , (AsnWriteFunc) ID2ParamAsnWrite, aip, atp, ID2_PARAMS_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestGetPackagesNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestGetPackagesPtr LIBCALL
+ID2RequestGetPackagesNew(void)
+{
+   ID2RequestGetPackagesPtr ptr = MemNew((size_t) sizeof(ID2RequestGetPackages));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2RequestGetPackagesFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestGetPackagesPtr LIBCALL
+ID2RequestGetPackagesFree(ID2RequestGetPackagesPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericBaseSeqOfFree(ptr -> names ,ASNCODE_PTRVAL_SLOT);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2RequestGetPackagesAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestGetPackagesPtr LIBCALL
+ID2RequestGetPackagesAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2RequestGetPackagesPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2RequestGetPackages ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_GET_PACKAGES);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_GET_PACKAGES);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2RequestGetPackagesNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REQUEST_GET_PACKAGES_names) {
+      ptr -> names = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_PTRVAL_SLOT, &isError);
+      if (isError && ptr -> names == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == GET_PACKAGES_no_contents) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> no_contents = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2RequestGetPackagesFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestGetPackagesAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2RequestGetPackagesAsnWrite(ID2RequestGetPackagesPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REQUEST_GET_PACKAGES);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> names ,ASNCODE_PTRVAL_SLOT, aip, ID2_REQUEST_GET_PACKAGES_names, REQUEST_GET_PACKAGES_names_E);
+   av.boolvalue = ptr -> no_contents;
+   retval = AsnWrite(aip, GET_PACKAGES_no_contents,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestStringToGiNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestStringToGiPtr LIBCALL
+ID2RequestStringToGiNew(void)
+{
+   ID2RequestStringToGiPtr ptr = MemNew((size_t) sizeof(ID2RequestStringToGi));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2RequestStringToGiFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestStringToGiPtr LIBCALL
+ID2RequestStringToGiFree(ID2RequestStringToGiPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> id);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2RequestStringToGiAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestStringToGiPtr LIBCALL
+ID2RequestStringToGiAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2RequestStringToGiPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2RequestStringToGi ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_STRING_TO_GI);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_STRING_TO_GI);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2RequestStringToGiNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REQUEST_STRING_TO_GI_id) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> id = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2RequestStringToGiFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestStringToGiAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2RequestStringToGiAsnWrite(ID2RequestStringToGiPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REQUEST_STRING_TO_GI);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> id != NULL) {
+      av.ptrvalue = ptr -> id;
+      retval = AsnWrite(aip, ID2_REQUEST_STRING_TO_GI_id,  &av);
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestSeqIdToGiNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestSeqIdToGiPtr LIBCALL
+ID2RequestSeqIdToGiNew(void)
+{
+   ID2RequestSeqIdToGiPtr ptr = MemNew((size_t) sizeof(ID2RequestSeqIdToGi));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2RequestSeqIdToGiFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestSeqIdToGiPtr LIBCALL
+ID2RequestSeqIdToGiFree(ID2RequestSeqIdToGiPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   SeqIdFree(ptr -> seq_id);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2RequestSeqIdToGiAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestSeqIdToGiPtr LIBCALL
+ID2RequestSeqIdToGiAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2RequestSeqIdToGiPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2RequestSeqIdToGi ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_SEQ_ID_TO_GI);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_SEQ_ID_TO_GI);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2RequestSeqIdToGiNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REQUEST_SEQ_ID_TO_GI_seq_id) {
+      ptr -> seq_id = SeqIdAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2RequestSeqIdToGiFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestSeqIdToGiAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2RequestSeqIdToGiAsnWrite(ID2RequestSeqIdToGiPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REQUEST_SEQ_ID_TO_GI);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> seq_id != NULL) {
+      if ( ! SeqIdAsnWrite(ptr -> seq_id, aip, ID2_REQUEST_SEQ_ID_TO_GI_seq_id)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestGiToTSEIdNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestGiToTSEIdPtr LIBCALL
+ID2RequestGiToTSEIdNew(void)
+{
+   ID2RequestGiToTSEIdPtr ptr = MemNew((size_t) sizeof(ID2RequestGiToTSEId));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2RequestGiToTSEIdFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestGiToTSEIdPtr LIBCALL
+ID2RequestGiToTSEIdFree(ID2RequestGiToTSEIdPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   Gi_giFree(ptr -> Gi_gi);
+   AsnGenericBaseSeqOfFree(ptr -> sources ,ASNCODE_PTRVAL_SLOT);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    Gi_giFree()
+*
+**************************************************/
+static 
+Gi_giPtr LIBCALL
+Gi_giFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case Gi_gi_string:
+      ID2RequestStringToGiFree(anp -> data.ptrvalue);
+      break;
+   case Gi_gi_seq_id:
+      ID2RequestSeqIdToGiFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ID2RequestGiToTSEIdAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestGiToTSEIdPtr LIBCALL
+ID2RequestGiToTSEIdAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2RequestGiToTSEIdPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2RequestGiToTSEId ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_GI_TO_TSE_ID);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_GI_TO_TSE_ID);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2RequestGiToTSEIdNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REQUEST_GI_TO_TSE_ID_gi) {
+      ptr -> Gi_gi = Gi_giAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == REQUEST_GI_TO_TSE_ID_sources) {
+      ptr -> sources = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_PTRVAL_SLOT, &isError);
+      if (isError && ptr -> sources == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == REQUEST_GI_TO_TSE_ID_external) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> external = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == GI_TO_TSE_ID_current_gis) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> current_gis = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2RequestGiToTSEIdFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    Gi_giAsnRead()
+*
+**************************************************/
+static 
+Gi_giPtr LIBCALL
+Gi_giAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* Gi_gi ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_GI_TO_TSE_ID_gi);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_GI_TO_TSE_ID_gi);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == ID2_REQUEST_GI_TO_TSE_ID_gi_gi) {
+      choice = Gi_gi_gi;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == REQUEST_GI_TO_TSE_ID_gi_string) {
+      choice = Gi_gi_string;
+      func = (AsnReadFunc) ID2RequestStringToGiAsnRead;
+   }
+   else if (atp == REQUEST_GI_TO_TSE_ID_gi_seq_id) {
+      choice = Gi_gi_seq_id;
+      func = (AsnReadFunc) ID2RequestSeqIdToGiAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ID2RequestGiToTSEIdAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2RequestGiToTSEIdAsnWrite(ID2RequestGiToTSEIdPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REQUEST_GI_TO_TSE_ID);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> Gi_gi != NULL) {
+      if ( ! Gi_giAsnWrite(ptr -> Gi_gi, aip, ID2_REQUEST_GI_TO_TSE_ID_gi)) {
+         goto erret;
+      }
+   }
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> sources ,ASNCODE_PTRVAL_SLOT, aip, REQUEST_GI_TO_TSE_ID_sources, REQUEST_GI_TO_TSE_ID_sources_E);
+   av.boolvalue = ptr -> external;
+   retval = AsnWrite(aip, REQUEST_GI_TO_TSE_ID_external,  &av);
+   av.boolvalue = ptr -> current_gis;
+   retval = AsnWrite(aip, GI_TO_TSE_ID_current_gis,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    Gi_giAsnWrite()
+*
+**************************************************/
+static Boolean LIBCALL 
+Gi_giAsnWrite(Gi_giPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, ID2_REQUEST_GI_TO_TSE_ID_gi);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case Gi_gi_gi:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, ID2_REQUEST_GI_TO_TSE_ID_gi_gi, &av);
+      break;
+   case Gi_gi_string:
+      writetype = REQUEST_GI_TO_TSE_ID_gi_string;
+      func = (AsnWriteFunc) ID2RequestStringToGiAsnWrite;
+      break;
+   case Gi_gi_seq_id:
+      writetype = REQUEST_GI_TO_TSE_ID_gi_seq_id;
+      func = (AsnWriteFunc) ID2RequestSeqIdToGiAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ID2RequestGetTSENew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestGetTSEPtr LIBCALL
+ID2RequestGetTSENew(void)
+{
+   ID2RequestGetTSEPtr ptr = MemNew((size_t) sizeof(ID2RequestGetTSE));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    TseId_giNew()
+*
+**************************************************/
+static 
+TseId_giPtr LIBCALL
+TseId_giNew(void)
+{
+   TseId_giPtr ptr = MemNew((size_t) sizeof(TseId_gi));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2RequestGetTSEFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestGetTSEPtr LIBCALL
+ID2RequestGetTSEFree(ID2RequestGetTSEPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   TseId_tse_idFree(ptr -> TseId_tse_id);
+   ID2GetTSEDetailsFree(ptr -> details);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    TseId_tse_idFree()
+*
+**************************************************/
+static 
+TseId_tse_idPtr LIBCALL
+TseId_tse_idFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case TseId_tse_id_tse_id:
+      ID2TSEIdFree(anp -> data.ptrvalue);
+      break;
+   case TseId_tse_id_TseId_Gi:
+      TseId_giFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    TseId_giFree()
+*
+**************************************************/
+static 
+TseId_giPtr LIBCALL
+TseId_giFree(TseId_giPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2RequestGiToTSEIdFree(ptr -> request);
+   AsnGenericUserSeqOfFree(ptr -> exclude_tses, (AsnOptFreeFunc) ID2TSEIdFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2RequestGetTSEAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestGetTSEPtr LIBCALL
+ID2RequestGetTSEAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2RequestGetTSEPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2RequestGetTSE ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_GET_TSE);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_GET_TSE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2RequestGetTSENew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REQUEST_GET_TSE_tse_id) {
+      ptr -> TseId_tse_id = TseId_tse_idAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REQUEST_GET_TSE_details) {
+      ptr -> details = ID2GetTSEDetailsAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2RequestGetTSEFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    TseId_tse_idAsnRead()
+*
+**************************************************/
+static 
+TseId_tse_idPtr LIBCALL
+TseId_tse_idAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* TseId_tse_id ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_GET_TSE_tse_id);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_GET_TSE_tse_id);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == REQUEST_GET_TSE_tse_id_tse_id) {
+      choice = TseId_tse_id_tse_id;
+      func = (AsnReadFunc) ID2TSEIdAsnRead;
+   }
+   else if (atp == ID2_REQUEST_GET_TSE_tse_id_gi) {
+      choice = TseId_tse_id_TseId_Gi;
+      func = (AsnReadFunc) TseId_giAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    TseId_giAsnRead()
+*
+**************************************************/
+static 
+TseId_giPtr LIBCALL
+TseId_giAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   TseId_giPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* TseId_gi ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_GET_TSE_tse_id_gi);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_GET_TSE_tse_id_gi);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = TseId_giNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == GET_TSE_tse_id_gi_request) {
+      ptr -> request = ID2RequestGiToTSEIdAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == GET_TSE_tse_id_gi_exclude_tses) {
+      ptr -> exclude_tses = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2TSEIdAsnRead, (AsnOptFreeFunc) ID2TSEIdFree);
+      if (isError && ptr -> exclude_tses == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = TseId_giFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestGetTSEAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2RequestGetTSEAsnWrite(ID2RequestGetTSEPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REQUEST_GET_TSE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> TseId_tse_id != NULL) {
+      if ( ! TseId_tse_idAsnWrite(ptr -> TseId_tse_id, aip, ID2_REQUEST_GET_TSE_tse_id)) {
+         goto erret;
+      }
+   }
+   if (ptr -> details != NULL) {
+      if ( ! ID2GetTSEDetailsAsnWrite(ptr -> details, aip, ID2_REQUEST_GET_TSE_details)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    TseId_tse_idAsnWrite()
+*
+**************************************************/
+static Boolean LIBCALL 
+TseId_tse_idAsnWrite(TseId_tse_idPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, ID2_REQUEST_GET_TSE_tse_id);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case TseId_tse_id_tse_id:
+      writetype = REQUEST_GET_TSE_tse_id_tse_id;
+      func = (AsnWriteFunc) ID2TSEIdAsnWrite;
+      break;
+   case TseId_tse_id_TseId_Gi:
+      writetype = ID2_REQUEST_GET_TSE_tse_id_gi;
+      func = (AsnWriteFunc) TseId_giAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    TseId_giAsnWrite()
+*
+**************************************************/
+static Boolean LIBCALL 
+TseId_giAsnWrite(TseId_giPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REQUEST_GET_TSE_tse_id_gi);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> request != NULL) {
+      if ( ! ID2RequestGiToTSEIdAsnWrite(ptr -> request, aip, GET_TSE_tse_id_gi_request)) {
+         goto erret;
+      }
+   }
+   AsnGenericUserSeqOfAsnWrite(ptr -> exclude_tses, (AsnWriteFunc) ID2TSEIdAsnWrite, aip, GET_TSE_tse_id_gi_exclude_tses, TSE_tse_id_gi_exclude_tses_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestReGetTSENew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestReGetTSEPtr LIBCALL
+ID2RequestReGetTSENew(void)
+{
+   ID2RequestReGetTSEPtr ptr = MemNew((size_t) sizeof(ID2RequestReGetTSE));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2RequestReGetTSEFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestReGetTSEPtr LIBCALL
+ID2RequestReGetTSEFree(ID2RequestReGetTSEPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2TSEIdFree(ptr -> tse_id);
+   ID2GetTSEDetailsFree(ptr -> details);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2RequestReGetTSEAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2RequestReGetTSEPtr LIBCALL
+ID2RequestReGetTSEAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2RequestReGetTSEPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2RequestReGetTSE ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REQUEST_REGET_TSE);
+   } else {
+      atp = AsnLinkType(orig, ID2_REQUEST_REGET_TSE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2RequestReGetTSENew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REQUEST_REGET_TSE_tse_id) {
+      ptr -> tse_id = ID2TSEIdAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REQUEST_REGET_TSE_details) {
+      ptr -> details = ID2GetTSEDetailsAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REQUEST_REGET_TSE_offset) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> offset = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2RequestReGetTSEFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2RequestReGetTSEAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2RequestReGetTSEAsnWrite(ID2RequestReGetTSEPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REQUEST_REGET_TSE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> tse_id != NULL) {
+      if ( ! ID2TSEIdAsnWrite(ptr -> tse_id, aip, ID2_REQUEST_REGET_TSE_tse_id)) {
+         goto erret;
+      }
+   }
+   if (ptr -> details != NULL) {
+      if ( ! ID2GetTSEDetailsAsnWrite(ptr -> details, aip, ID2_REQUEST_REGET_TSE_details)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> offset;
+   retval = AsnWrite(aip, ID2_REQUEST_REGET_TSE_offset,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SRequestGetChunksNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SRequestGetChunksPtr LIBCALL
+ID2SRequestGetChunksNew(void)
+{
+   ID2SRequestGetChunksPtr ptr = MemNew((size_t) sizeof(ID2SRequestGetChunks));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SRequestGetChunksFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SRequestGetChunksPtr LIBCALL
+ID2SRequestGetChunksFree(ID2SRequestGetChunksPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2TSEIdFree(ptr -> tse_id);
+   AsnGenericBaseSeqOfFree(ptr -> chunks ,ASNCODE_INTVAL_SLOT);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SRequestGetChunksAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SRequestGetChunksPtr LIBCALL
+ID2SRequestGetChunksAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SRequestGetChunksPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SRequestGetChunks ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_REQUEST_GET_CHUNKS);
+   } else {
+      atp = AsnLinkType(orig, ID2S_REQUEST_GET_CHUNKS);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SRequestGetChunksNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_REQUEST_GET_CHUNKS_tse_id) {
+      ptr -> tse_id = ID2TSEIdAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_REQUEST_GET_CHUNKS_chunks) {
+      ptr -> chunks = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_INTVAL_SLOT, &isError);
+      if (isError && ptr -> chunks == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SRequestGetChunksFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SRequestGetChunksAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SRequestGetChunksAsnWrite(ID2SRequestGetChunksPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_REQUEST_GET_CHUNKS);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> tse_id != NULL) {
+      if ( ! ID2TSEIdAsnWrite(ptr -> tse_id, aip, ID2S_REQUEST_GET_CHUNKS_tse_id)) {
+         goto erret;
+      }
+   }
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> chunks ,ASNCODE_INTVAL_SLOT, aip, ID2S_REQUEST_GET_CHUNKS_chunks, REQUEST_GET_CHUNKS_chunks_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2TSEIdNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2TSEIdPtr LIBCALL
+ID2TSEIdNew(void)
+{
+   ID2TSEIdPtr ptr = MemNew((size_t) sizeof(ID2TSEId));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2TSEIdFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2TSEIdPtr LIBCALL
+ID2TSEIdFree(ID2TSEIdPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2TSEIdAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2TSEIdPtr LIBCALL
+ID2TSEIdAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2TSEIdPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2TSEId ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_TSE_ID);
+   } else {
+      atp = AsnLinkType(orig, ID2_TSE_ID);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2TSEIdNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_TSE_ID_sat) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> sat = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_TSE_ID_sat_key) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> sat_key = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2TSEIdFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2TSEIdAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2TSEIdAsnWrite(ID2TSEIdPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_TSE_ID);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> sat;
+   retval = AsnWrite(aip, ID2_TSE_ID_sat,  &av);
+   av.intvalue = ptr -> sat_key;
+   retval = AsnWrite(aip, ID2_TSE_ID_sat_key,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2GetTSEDetailsNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2GetTSEDetailsPtr LIBCALL
+ID2GetTSEDetailsNew(void)
+{
+   ID2GetTSEDetailsPtr ptr = MemNew((size_t) sizeof(ID2GetTSEDetails));
+
+   ptr -> seq_class_level = 1;
+   ptr -> descr_level = 1;
+   ptr -> descr_type_mask = 0;
+   ptr -> annot_type_mask = 0;
+   ptr -> feat_type_mask = 0;
+   ptr -> sequence_level = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2GetTSEDetailsFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2GetTSEDetailsPtr LIBCALL
+ID2GetTSEDetailsFree(ID2GetTSEDetailsPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2SeqLocFree(ptr -> location);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2GetTSEDetailsAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2GetTSEDetailsPtr LIBCALL
+ID2GetTSEDetailsAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2GetTSEDetailsPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2GetTSEDetails ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_GET_TSE_DETAILS);
+   } else {
+      atp = AsnLinkType(orig, ID2_GET_TSE_DETAILS);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2GetTSEDetailsNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_GET_TSE_DETAILS_location) {
+      ptr -> location = ID2SeqLocAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == TSE_DETAILS_seq_class_level) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> seq_class_level = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_GET_TSE_DETAILS_descr_level) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> descr_level = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == TSE_DETAILS_descr_type_mask) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> descr_type_mask = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == TSE_DETAILS_annot_type_mask) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> annot_type_mask = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == GET_TSE_DETAILS_feat_type_mask) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> feat_type_mask = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == GET_TSE_DETAILS_sequence_level) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> sequence_level = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2GetTSEDetailsFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2GetTSEDetailsAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2GetTSEDetailsAsnWrite(ID2GetTSEDetailsPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_GET_TSE_DETAILS);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> location != NULL) {
+      if ( ! ID2SeqLocAsnWrite(ptr -> location, aip, ID2_GET_TSE_DETAILS_location)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> seq_class_level;
+   retval = AsnWrite(aip, TSE_DETAILS_seq_class_level,  &av);
+   av.intvalue = ptr -> descr_level;
+   retval = AsnWrite(aip, ID2_GET_TSE_DETAILS_descr_level,  &av);
+   av.intvalue = ptr -> descr_type_mask;
+   retval = AsnWrite(aip, TSE_DETAILS_descr_type_mask,  &av);
+   av.intvalue = ptr -> annot_type_mask;
+   retval = AsnWrite(aip, TSE_DETAILS_annot_type_mask,  &av);
+   av.intvalue = ptr -> feat_type_mask;
+   retval = AsnWrite(aip, GET_TSE_DETAILS_feat_type_mask,  &av);
+   av.intvalue = ptr -> sequence_level;
+   retval = AsnWrite(aip, GET_TSE_DETAILS_sequence_level,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SeqLocFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SeqLocPtr LIBCALL
+ID2SeqLocFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case ID2SeqLoc_int__:
+      ID2IntervalFree(anp -> data.ptrvalue);
+      break;
+   case ID2SeqLoc_int_set:
+      ID2PackedSeqIntsFree(anp -> data.ptrvalue);
+      break;
+   case ID2SeqLoc_whole_range:
+      ID2IdRangeFree(anp -> data.ptrvalue);
+      break;
+   case ID2SeqLoc_loc_set:
+      AsnGenericChoiceSeqOfFree((Pointer) pnt, (AsnOptFreeFunc) ID2SeqLocFree);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ID2SeqLocAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SeqLocPtr LIBCALL
+ID2SeqLocAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SeqLoc ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_SEQ_LOC);
+   } else {
+      atp = AsnLinkType(orig, ID2_SEQ_LOC);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == ID2_SEQ_LOC_whole) {
+      choice = ID2SeqLoc_whole;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == ID2_SEQ_LOC_int__) {
+      choice = ID2SeqLoc_int__;
+      func = (AsnReadFunc) ID2IntervalAsnRead;
+   }
+   else if (atp == ID2_SEQ_LOC_int_set) {
+      choice = ID2SeqLoc_int_set;
+      func = (AsnReadFunc) ID2PackedSeqIntsAsnRead;
+   }
+   else if (atp == ID2_SEQ_LOC_whole_range) {
+      choice = ID2SeqLoc_whole_range;
+      func = (AsnReadFunc) ID2IdRangeAsnRead;
+   }
+   else if (atp == ID2_SEQ_LOC_loc_set) {
+      choice = ID2SeqLoc_loc_set;
+      anp -> data.ptrvalue =
+      AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SeqLocAsnRead,             (AsnOptFreeFunc) ID2SeqLocFree);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ID2SeqLocAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SeqLocAsnWrite(ID2SeqLocPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, ID2_SEQ_LOC);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case ID2SeqLoc_whole:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, ID2_SEQ_LOC_whole, &av);
+      break;
+   case ID2SeqLoc_int__:
+      writetype = ID2_SEQ_LOC_int__;
+      func = (AsnWriteFunc) ID2IntervalAsnWrite;
+      break;
+   case ID2SeqLoc_int_set:
+      writetype = ID2_SEQ_LOC_int_set;
+      func = (AsnWriteFunc) ID2PackedSeqIntsAsnWrite;
+      break;
+   case ID2SeqLoc_whole_range:
+      writetype = ID2_SEQ_LOC_whole_range;
+      func = (AsnWriteFunc) ID2IdRangeAsnWrite;
+      break;
+   case ID2SeqLoc_loc_set:
+      retval = AsnGenericChoiceSeqOfAsnWrite((Pointer) pnt, (AsnWriteFunc) ID2SeqLocAsnWrite, aip, ID2_SEQ_LOC_loc_set, ID2_SEQ_LOC_loc_set_E);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ID2ReplyNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyPtr LIBCALL
+ID2ReplyNew(void)
+{
+   ID2ReplyPtr ptr = MemNew((size_t) sizeof(ID2Reply));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2ReplyFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyPtr LIBCALL
+ID2ReplyFree(ID2ReplyPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2ParamsFree(ptr -> params);
+   Reply_replyFree(ptr -> Reply_reply);
+   AsnGenericUserSeqOfFree(ptr -> error, (AsnOptFreeFunc) ID2ErrorFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    Reply_replyFree()
+*
+**************************************************/
+static 
+Reply_replyPtr LIBCALL
+Reply_replyFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case Reply_reply_get_package:
+      ID2ReplyGetPackageFree(anp -> data.ptrvalue);
+      break;
+   case Reply_reply_seq_id_to_gi:
+      ID2ReplySeqIdToGiFree(anp -> data.ptrvalue);
+      break;
+   case Reply_reply_gi_to_tse_id:
+      ID2ReplyGiToTSEIdFree(anp -> data.ptrvalue);
+      break;
+   case Reply_reply_get_tse:
+      ID2ReplyGetTSEFree(anp -> data.ptrvalue);
+      break;
+   case Reply_reply_get_tse_info:
+      ID2SReplyGetTSEInfoFree(anp -> data.ptrvalue);
+      break;
+   case Reply_reply_get_chunk:
+      ID2SReplyGetChunkFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ID2ReplyAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyPtr LIBCALL
+ID2ReplyAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2ReplyPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2Reply ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REPLY);
+   } else {
+      atp = AsnLinkType(orig, ID2_REPLY);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2ReplyNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REPLY_serial_number) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> serial_number = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_params) {
+      ptr -> params = ID2ParamsAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_reply) {
+      ptr -> Reply_reply = Reply_replyAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_error) {
+      ptr -> error = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2ErrorAsnRead, (AsnOptFreeFunc) ID2ErrorFree);
+      if (isError && ptr -> error == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_end_of_reply) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> end_of_reply = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2ReplyFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    Reply_replyAsnRead()
+*
+**************************************************/
+static 
+Reply_replyPtr LIBCALL
+Reply_replyAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* Reply_reply ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REPLY_reply);
+   } else {
+      atp = AsnLinkType(orig, ID2_REPLY_reply);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == ID2_REPLY_reply_init) {
+      choice = Reply_reply_init;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == ID2_REPLY_reply_get_package) {
+      choice = Reply_reply_get_package;
+      func = (AsnReadFunc) ID2ReplyGetPackageAsnRead;
+   }
+   else if (atp == ID2_REPLY_reply_seq_id_to_gi) {
+      choice = Reply_reply_seq_id_to_gi;
+      func = (AsnReadFunc) ID2ReplySeqIdToGiAsnRead;
+   }
+   else if (atp == ID2_REPLY_reply_gi_to_tse_id) {
+      choice = Reply_reply_gi_to_tse_id;
+      func = (AsnReadFunc) ID2ReplyGiToTSEIdAsnRead;
+   }
+   else if (atp == ID2_REPLY_reply_get_tse) {
+      choice = Reply_reply_get_tse;
+      func = (AsnReadFunc) ID2ReplyGetTSEAsnRead;
+   }
+   else if (atp == ID2_REPLY_reply_get_tse_info) {
+      choice = Reply_reply_get_tse_info;
+      func = (AsnReadFunc) ID2SReplyGetTSEInfoAsnRead;
+   }
+   else if (atp == ID2_REPLY_reply_get_chunk) {
+      choice = Reply_reply_get_chunk;
+      func = (AsnReadFunc) ID2SReplyGetChunkAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ID2ReplyAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2ReplyAsnWrite(ID2ReplyPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REPLY);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> serial_number;
+   retval = AsnWrite(aip, ID2_REPLY_serial_number,  &av);
+   if (ptr -> params != NULL) {
+      if ( ! ID2ParamsAsnWrite(ptr -> params, aip, ID2_REPLY_params)) {
+         goto erret;
+      }
+   }
+   if (ptr -> Reply_reply != NULL) {
+      if ( ! Reply_replyAsnWrite(ptr -> Reply_reply, aip, ID2_REPLY_reply)) {
+         goto erret;
+      }
+   }
+   AsnGenericUserSeqOfAsnWrite(ptr -> error, (AsnWriteFunc) ID2ErrorAsnWrite, aip, ID2_REPLY_error, ID2_REPLY_error_E);
+   av.boolvalue = ptr -> end_of_reply;
+   retval = AsnWrite(aip, ID2_REPLY_end_of_reply,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    Reply_replyAsnWrite()
+*
+**************************************************/
+static Boolean LIBCALL 
+Reply_replyAsnWrite(Reply_replyPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, ID2_REPLY_reply);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case Reply_reply_init:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, ID2_REPLY_reply_init, &av);
+      break;
+   case Reply_reply_get_package:
+      writetype = ID2_REPLY_reply_get_package;
+      func = (AsnWriteFunc) ID2ReplyGetPackageAsnWrite;
+      break;
+   case Reply_reply_seq_id_to_gi:
+      writetype = ID2_REPLY_reply_seq_id_to_gi;
+      func = (AsnWriteFunc) ID2ReplySeqIdToGiAsnWrite;
+      break;
+   case Reply_reply_gi_to_tse_id:
+      writetype = ID2_REPLY_reply_gi_to_tse_id;
+      func = (AsnWriteFunc) ID2ReplyGiToTSEIdAsnWrite;
+      break;
+   case Reply_reply_get_tse:
+      writetype = ID2_REPLY_reply_get_tse;
+      func = (AsnWriteFunc) ID2ReplyGetTSEAsnWrite;
+      break;
+   case Reply_reply_get_tse_info:
+      writetype = ID2_REPLY_reply_get_tse_info;
+      func = (AsnWriteFunc) ID2SReplyGetTSEInfoAsnWrite;
+      break;
+   case Reply_reply_get_chunk:
+      writetype = ID2_REPLY_reply_get_chunk;
+      func = (AsnWriteFunc) ID2SReplyGetChunkAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ID2ReplyGetPackageNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyGetPackagePtr LIBCALL
+ID2ReplyGetPackageNew(void)
+{
+   ID2ReplyGetPackagePtr ptr = MemNew((size_t) sizeof(ID2ReplyGetPackage));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2ReplyGetPackageFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyGetPackagePtr LIBCALL
+ID2ReplyGetPackageFree(ID2ReplyGetPackagePtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> name);
+   ID2ParamsFree(ptr -> params);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2ReplyGetPackageAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyGetPackagePtr LIBCALL
+ID2ReplyGetPackageAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2ReplyGetPackagePtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2ReplyGetPackage ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REPLY_GET_PACKAGE);
+   } else {
+      atp = AsnLinkType(orig, ID2_REPLY_GET_PACKAGE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2ReplyGetPackageNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REPLY_GET_PACKAGE_name) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> name = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_GET_PACKAGE_params) {
+      ptr -> params = ID2ParamsAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2ReplyGetPackageFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2ReplyGetPackageAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2ReplyGetPackageAsnWrite(ID2ReplyGetPackagePtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REPLY_GET_PACKAGE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> name != NULL) {
+      av.ptrvalue = ptr -> name;
+      retval = AsnWrite(aip, ID2_REPLY_GET_PACKAGE_name,  &av);
+   }
+   if (ptr -> params != NULL) {
+      if ( ! ID2ParamsAsnWrite(ptr -> params, aip, ID2_REPLY_GET_PACKAGE_params)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2ReplySeqIdToGiNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplySeqIdToGiPtr LIBCALL
+ID2ReplySeqIdToGiNew(void)
+{
+   ID2ReplySeqIdToGiPtr ptr = MemNew((size_t) sizeof(ID2ReplySeqIdToGi));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2ReplySeqIdToGiFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplySeqIdToGiPtr LIBCALL
+ID2ReplySeqIdToGiFree(ID2ReplySeqIdToGiPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   SeqIdFree(ptr -> seq_id);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2ReplySeqIdToGiAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplySeqIdToGiPtr LIBCALL
+ID2ReplySeqIdToGiAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2ReplySeqIdToGiPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2ReplySeqIdToGi ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REPLY_SEQ_ID_TO_GI);
+   } else {
+      atp = AsnLinkType(orig, ID2_REPLY_SEQ_ID_TO_GI);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2ReplySeqIdToGiNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REPLY_SEQ_ID_TO_GI_seq_id) {
+      ptr -> seq_id = SeqIdAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_SEQ_ID_TO_GI_gi) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> gi = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2ReplySeqIdToGiFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2ReplySeqIdToGiAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2ReplySeqIdToGiAsnWrite(ID2ReplySeqIdToGiPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REPLY_SEQ_ID_TO_GI);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> seq_id != NULL) {
+      if ( ! SeqIdAsnWrite(ptr -> seq_id, aip, ID2_REPLY_SEQ_ID_TO_GI_seq_id)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> gi;
+   retval = AsnWrite(aip, ID2_REPLY_SEQ_ID_TO_GI_gi,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2ReplyGiToTSEIdNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyGiToTSEIdPtr LIBCALL
+ID2ReplyGiToTSEIdNew(void)
+{
+   ID2ReplyGiToTSEIdPtr ptr = MemNew((size_t) sizeof(ID2ReplyGiToTSEId));
+
+   ptr -> source = "0";
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2ReplyGiToTSEIdFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyGiToTSEIdPtr LIBCALL
+ID2ReplyGiToTSEIdFree(ID2ReplyGiToTSEIdPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> source);
+   AsnGenericUserSeqOfFree(ptr -> tses, (AsnOptFreeFunc) ID2TSEIdInfoFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2ReplyGiToTSEIdAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyGiToTSEIdPtr LIBCALL
+ID2ReplyGiToTSEIdAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2ReplyGiToTSEIdPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2ReplyGiToTSEId ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REPLY_GI_TO_TSE_ID);
+   } else {
+      atp = AsnLinkType(orig, ID2_REPLY_GI_TO_TSE_ID);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2ReplyGiToTSEIdNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REPLY_GI_TO_TSE_ID_gi) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> gi = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_GI_TO_TSE_ID_source) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> source = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_GI_TO_TSE_ID_tses) {
+      ptr -> tses = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2TSEIdInfoAsnRead, (AsnOptFreeFunc) ID2TSEIdInfoFree);
+      if (isError && ptr -> tses == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2ReplyGiToTSEIdFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2ReplyGiToTSEIdAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2ReplyGiToTSEIdAsnWrite(ID2ReplyGiToTSEIdPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REPLY_GI_TO_TSE_ID);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> gi;
+   retval = AsnWrite(aip, ID2_REPLY_GI_TO_TSE_ID_gi,  &av);
+   if (ptr -> source != NULL) {
+      av.ptrvalue = ptr -> source;
+      retval = AsnWrite(aip, ID2_REPLY_GI_TO_TSE_ID_source,  &av);
+   }
+   AsnGenericUserSeqOfAsnWrite(ptr -> tses, (AsnWriteFunc) ID2TSEIdInfoAsnWrite, aip, ID2_REPLY_GI_TO_TSE_ID_tses, ID2_REPLY_GI_TO_TSE_ID_tses_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2ReplyGetTSENew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyGetTSEPtr LIBCALL
+ID2ReplyGetTSENew(void)
+{
+   ID2ReplyGetTSEPtr ptr = MemNew((size_t) sizeof(ID2ReplyGetTSE));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2ReplyGetTSEFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyGetTSEPtr LIBCALL
+ID2ReplyGetTSEFree(ID2ReplyGetTSEPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2TSEIdFree(ptr -> tse_id);
+   ID2ReplyDataFree(ptr -> data);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2ReplyGetTSEAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyGetTSEPtr LIBCALL
+ID2ReplyGetTSEAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2ReplyGetTSEPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2ReplyGetTSE ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REPLY_GET_TSE);
+   } else {
+      atp = AsnLinkType(orig, ID2_REPLY_GET_TSE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2ReplyGetTSENew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REPLY_GET_TSE_tse_id) {
+      ptr -> tse_id = ID2TSEIdAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_GET_TSE_data) {
+      ptr -> data = ID2ReplyDataAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2ReplyGetTSEFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2ReplyGetTSEAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2ReplyGetTSEAsnWrite(ID2ReplyGetTSEPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REPLY_GET_TSE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> tse_id != NULL) {
+      if ( ! ID2TSEIdAsnWrite(ptr -> tse_id, aip, ID2_REPLY_GET_TSE_tse_id)) {
+         goto erret;
+      }
+   }
+   if (ptr -> data != NULL) {
+      if ( ! ID2ReplyDataAsnWrite(ptr -> data, aip, ID2_REPLY_GET_TSE_data)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SReplyGetTSEInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SReplyGetTSEInfoPtr LIBCALL
+ID2SReplyGetTSEInfoNew(void)
+{
+   ID2SReplyGetTSEInfoPtr ptr = MemNew((size_t) sizeof(ID2SReplyGetTSEInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SReplyGetTSEInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SReplyGetTSEInfoPtr LIBCALL
+ID2SReplyGetTSEInfoFree(ID2SReplyGetTSEInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2TSEIdFree(ptr -> tse_id);
+   ID2ReplyDataFree(ptr -> info);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SReplyGetTSEInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SReplyGetTSEInfoPtr LIBCALL
+ID2SReplyGetTSEInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SReplyGetTSEInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SReplyGetTSEInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_REPLY_GET_TSE_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_REPLY_GET_TSE_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SReplyGetTSEInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_REPLY_GET_TSE_INFO_tse_id) {
+      ptr -> tse_id = ID2TSEIdAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == GET_TSE_INFO_split_version) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> split_version = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_REPLY_GET_TSE_INFO_info) {
+      ptr -> info = ID2ReplyDataAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SReplyGetTSEInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SReplyGetTSEInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SReplyGetTSEInfoAsnWrite(ID2SReplyGetTSEInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_REPLY_GET_TSE_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> tse_id != NULL) {
+      if ( ! ID2TSEIdAsnWrite(ptr -> tse_id, aip, ID2S_REPLY_GET_TSE_INFO_tse_id)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> split_version;
+   retval = AsnWrite(aip, GET_TSE_INFO_split_version,  &av);
+   if (ptr -> info != NULL) {
+      if ( ! ID2ReplyDataAsnWrite(ptr -> info, aip, ID2S_REPLY_GET_TSE_INFO_info)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SReplyGetChunkNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SReplyGetChunkPtr LIBCALL
+ID2SReplyGetChunkNew(void)
+{
+   ID2SReplyGetChunkPtr ptr = MemNew((size_t) sizeof(ID2SReplyGetChunk));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SReplyGetChunkFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SReplyGetChunkPtr LIBCALL
+ID2SReplyGetChunkFree(ID2SReplyGetChunkPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2TSEIdFree(ptr -> tse_id);
+   ID2ReplyDataFree(ptr -> data);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SReplyGetChunkAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SReplyGetChunkPtr LIBCALL
+ID2SReplyGetChunkAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SReplyGetChunkPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SReplyGetChunk ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_REPLY_GET_CHUNK);
+   } else {
+      atp = AsnLinkType(orig, ID2S_REPLY_GET_CHUNK);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SReplyGetChunkNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_REPLY_GET_CHUNK_tse_id) {
+      ptr -> tse_id = ID2TSEIdAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_REPLY_GET_CHUNK_chunk_id) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> chunk_id = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_REPLY_GET_CHUNK_data) {
+      ptr -> data = ID2ReplyDataAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SReplyGetChunkFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SReplyGetChunkAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SReplyGetChunkAsnWrite(ID2SReplyGetChunkPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_REPLY_GET_CHUNK);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> tse_id != NULL) {
+      if ( ! ID2TSEIdAsnWrite(ptr -> tse_id, aip, ID2S_REPLY_GET_CHUNK_tse_id)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> chunk_id;
+   retval = AsnWrite(aip, ID2S_REPLY_GET_CHUNK_chunk_id,  &av);
+   if (ptr -> data != NULL) {
+      if ( ! ID2ReplyDataAsnWrite(ptr -> data, aip, ID2S_REPLY_GET_CHUNK_data)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2ErrorNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ErrorPtr LIBCALL
+ID2ErrorNew(void)
+{
+   ID2ErrorPtr ptr = MemNew((size_t) sizeof(ID2Error));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2ErrorFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ErrorPtr LIBCALL
+ID2ErrorFree(ID2ErrorPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> message);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2ErrorAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ErrorPtr LIBCALL
+ID2ErrorAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2ErrorPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2Error ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_ERROR);
+   } else {
+      atp = AsnLinkType(orig, ID2_ERROR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2ErrorNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_ERROR_severity) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> severity = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_ERROR_retry_delay) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> retry_delay = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_ERROR_message) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> message = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2ErrorFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2ErrorAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2ErrorAsnWrite(ID2ErrorPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_ERROR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> severity;
+   retval = AsnWrite(aip, ID2_ERROR_severity,  &av);
+   av.intvalue = ptr -> retry_delay;
+   retval = AsnWrite(aip, ID2_ERROR_retry_delay,  &av);
+   if (ptr -> message != NULL) {
+      av.ptrvalue = ptr -> message;
+      retval = AsnWrite(aip, ID2_ERROR_message,  &av);
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2TSEIdInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2TSEIdInfoPtr LIBCALL
+ID2TSEIdInfoNew(void)
+{
+   ID2TSEIdInfoPtr ptr = MemNew((size_t) sizeof(ID2TSEIdInfo));
+
+   ptr -> split_version = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2TSEIdInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2TSEIdInfoPtr LIBCALL
+ID2TSEIdInfoFree(ID2TSEIdInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2TSEIdFree(ptr -> tse_id);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2TSEIdInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2TSEIdInfoPtr LIBCALL
+ID2TSEIdInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2TSEIdInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2TSEIdInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_TSE_ID_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2_TSE_ID_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2TSEIdInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_TSE_ID_INFO_tse_id) {
+      ptr -> tse_id = ID2TSEIdAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_TSE_ID_INFO_split_version) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> split_version = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2TSEIdInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2TSEIdInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2TSEIdInfoAsnWrite(ID2TSEIdInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_TSE_ID_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> tse_id != NULL) {
+      if ( ! ID2TSEIdAsnWrite(ptr -> tse_id, aip, ID2_TSE_ID_INFO_tse_id)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> split_version;
+   retval = AsnWrite(aip, ID2_TSE_ID_INFO_split_version,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2ReplyDataNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyDataPtr LIBCALL
+ID2ReplyDataNew(void)
+{
+   ID2ReplyDataPtr ptr = MemNew((size_t) sizeof(ID2ReplyData));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2ReplyDataFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyDataPtr LIBCALL
+ID2ReplyDataFree(ID2ReplyDataPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericBaseSeqOfFree(ptr -> data ,ASNCODE_BYTEVAL_SLOT);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2ReplyDataAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ReplyDataPtr LIBCALL
+ID2ReplyDataAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2ReplyDataPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2ReplyData ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_REPLY_DATA);
+   } else {
+      atp = AsnLinkType(orig, ID2_REPLY_DATA);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2ReplyDataNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_REPLY_DATA_data_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> data_type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_DATA_data_format) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> data_format = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_DATA_data_compression) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> data_compression = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_REPLY_DATA_data) {
+      ptr -> data = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_BYTEVAL_SLOT, &isError);
+      if (isError && ptr -> data == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2ReplyDataFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2ReplyDataAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2ReplyDataAsnWrite(ID2ReplyDataPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_REPLY_DATA);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> data_type;
+   retval = AsnWrite(aip, ID2_REPLY_DATA_data_type,  &av);
+   av.intvalue = ptr -> data_format;
+   retval = AsnWrite(aip, ID2_REPLY_DATA_data_format,  &av);
+   av.intvalue = ptr -> data_compression;
+   retval = AsnWrite(aip, ID2_REPLY_DATA_data_compression,  &av);
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> data ,ASNCODE_BYTEVAL_SLOT, aip, ID2_REPLY_DATA_data, ID2_REPLY_DATA_data_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSplitInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSplitInfoPtr LIBCALL
+ID2SSplitInfoNew(void)
+{
+   ID2SSplitInfoPtr ptr = MemNew((size_t) sizeof(ID2SSplitInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SSplitInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSplitInfoPtr LIBCALL
+ID2SSplitInfoFree(ID2SSplitInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr -> bioseqs_info, (AsnOptFreeFunc) ID2SBioseqsInfoFree);
+   AsnGenericUserSeqOfFree(ptr -> chunks, (AsnOptFreeFunc) ID2SChunkInfoFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SSplitInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSplitInfoPtr LIBCALL
+ID2SSplitInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SSplitInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SSplitInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_SPLIT_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_SPLIT_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SSplitInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_SPLIT_INFO_bioseqs_info) {
+      ptr -> bioseqs_info = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SBioseqsInfoAsnRead, (AsnOptFreeFunc) ID2SBioseqsInfoFree);
+      if (isError && ptr -> bioseqs_info == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_SPLIT_INFO_chunks) {
+      ptr -> chunks = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SChunkInfoAsnRead, (AsnOptFreeFunc) ID2SChunkInfoFree);
+      if (isError && ptr -> chunks == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SSplitInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSplitInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SSplitInfoAsnWrite(ID2SSplitInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_SPLIT_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   AsnGenericUserSeqOfAsnWrite(ptr -> bioseqs_info, (AsnWriteFunc) ID2SBioseqsInfoAsnWrite, aip, ID2S_SPLIT_INFO_bioseqs_info, ID2S_SPLIT_INFO_bioseqs_info_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> chunks, (AsnWriteFunc) ID2SChunkInfoAsnWrite, aip, ID2S_SPLIT_INFO_chunks, ID2S_SPLIT_INFO_chunks_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SBioseqsInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SBioseqsInfoPtr LIBCALL
+ID2SBioseqsInfoNew(void)
+{
+   ID2SBioseqsInfoPtr ptr = MemNew((size_t) sizeof(ID2SBioseqsInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SBioseqsInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SBioseqsInfoPtr LIBCALL
+ID2SBioseqsInfoFree(ID2SBioseqsInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2SBioseqInfoFree(ptr -> info);
+   ID2IdRangeFree(ptr -> bioseqs);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SBioseqsInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SBioseqsInfoPtr LIBCALL
+ID2SBioseqsInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SBioseqsInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SBioseqsInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_BIOSEQS_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_BIOSEQS_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SBioseqsInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_BIOSEQS_INFO_info) {
+      ptr -> info = ID2SBioseqInfoAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_BIOSEQS_INFO_bioseqs) {
+      ptr -> bioseqs = ID2IdRangeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SBioseqsInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SBioseqsInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SBioseqsInfoAsnWrite(ID2SBioseqsInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_BIOSEQS_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> info != NULL) {
+      if ( ! ID2SBioseqInfoAsnWrite(ptr -> info, aip, ID2S_BIOSEQS_INFO_info)) {
+         goto erret;
+      }
+   }
+   if (ptr -> bioseqs != NULL) {
+      if ( ! ID2IdRangeAsnWrite(ptr -> bioseqs, aip, ID2S_BIOSEQS_INFO_bioseqs)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SChunkInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkInfoPtr LIBCALL
+ID2SChunkInfoNew(void)
+{
+   ID2SChunkInfoPtr ptr = MemNew((size_t) sizeof(ID2SChunkInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SChunkInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkInfoPtr LIBCALL
+ID2SChunkInfoFree(ID2SChunkInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericChoiceSeqOfFree(ptr -> content, (AsnOptFreeFunc) ID2SChunkContentFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SChunkInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkInfoPtr LIBCALL
+ID2SChunkInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SChunkInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SChunkInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_CHUNK_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_CHUNK_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SChunkInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_CHUNK_INFO_id) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> id = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_CHUNK_INFO_content) {
+      ptr -> content = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SChunkContentAsnRead, (AsnOptFreeFunc) ID2SChunkContentFree);
+      if (isError && ptr -> content == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SChunkInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SChunkInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SChunkInfoAsnWrite(ID2SChunkInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_CHUNK_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> id;
+   retval = AsnWrite(aip, ID2S_CHUNK_INFO_id,  &av);
+   AsnGenericChoiceSeqOfAsnWrite(ptr -> content, (AsnWriteFunc) ID2SChunkContentAsnWrite, aip, ID2S_CHUNK_INFO_content, ID2S_CHUNK_INFO_content_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SBioseqInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SBioseqInfoPtr LIBCALL
+ID2SBioseqInfoNew(void)
+{
+   ID2SBioseqInfoPtr ptr = MemNew((size_t) sizeof(ID2SBioseqInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SBioseqInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SBioseqInfoPtr LIBCALL
+ID2SBioseqInfoFree(ID2SBioseqInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID2SSequenceSplitInfoFree(ptr -> sequence_split);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SBioseqInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SBioseqInfoPtr LIBCALL
+ID2SBioseqInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SBioseqInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SBioseqInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_BIOSEQ_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_BIOSEQ_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SBioseqInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_BIOSEQ_INFO_gap_count) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> gap_count = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == BIOSEQ_INFO_seq_map_has_ref) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> seq_map_has_ref = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_BIOSEQ_INFO_sequence_split) {
+      ptr -> sequence_split = ID2SSequenceSplitInfoAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SBioseqInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SBioseqInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SBioseqInfoAsnWrite(ID2SBioseqInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_BIOSEQ_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> gap_count;
+   retval = AsnWrite(aip, ID2S_BIOSEQ_INFO_gap_count,  &av);
+   av.boolvalue = ptr -> seq_map_has_ref;
+   retval = AsnWrite(aip, BIOSEQ_INFO_seq_map_has_ref,  &av);
+   if (ptr -> sequence_split != NULL) {
+      if ( ! ID2SSequenceSplitInfoAsnWrite(ptr -> sequence_split, aip, ID2S_BIOSEQ_INFO_sequence_split)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2IdRangeNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2IdRangePtr LIBCALL
+ID2IdRangeNew(void)
+{
+   ID2IdRangePtr ptr = MemNew((size_t) sizeof(ID2IdRange));
+
+   ptr -> count = 1;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2IdRangeFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2IdRangePtr LIBCALL
+ID2IdRangeFree(ID2IdRangePtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2IdRangeAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2IdRangePtr LIBCALL
+ID2IdRangeAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2IdRangePtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2IdRange ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_ID_RANGE);
+   } else {
+      atp = AsnLinkType(orig, ID2_ID_RANGE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2IdRangeNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_ID_RANGE_start) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> start = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_ID_RANGE_count) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> count = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2IdRangeFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2IdRangeAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2IdRangeAsnWrite(ID2IdRangePtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_ID_RANGE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> start;
+   retval = AsnWrite(aip, ID2_ID_RANGE_start,  &av);
+   av.intvalue = ptr -> count;
+   retval = AsnWrite(aip, ID2_ID_RANGE_count,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSequenceSplitInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSequenceSplitInfoPtr LIBCALL
+ID2SSequenceSplitInfoNew(void)
+{
+   ID2SSequenceSplitInfoPtr ptr = MemNew((size_t) sizeof(ID2SSequenceSplitInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SSequenceSplitInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSequenceSplitInfoPtr LIBCALL
+ID2SSequenceSplitInfoFree(ID2SSequenceSplitInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericBaseSeqOfFree(ptr -> chunk_blocks ,ASNCODE_INTVAL_SLOT);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SSequenceSplitInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSequenceSplitInfoPtr LIBCALL
+ID2SSequenceSplitInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SSequenceSplitInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SSequenceSplitInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_SEQUENCE_SPLIT_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_SEQUENCE_SPLIT_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SSequenceSplitInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == SEQUENCE_SPLIT_INFO_block_size) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> block_size = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SPLIT_INFO_chunk_start) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> chunk_start = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SPLIT_INFO_chunk_blocks) {
+      ptr -> chunk_blocks = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_INTVAL_SLOT, &isError);
+      if (isError && ptr -> chunk_blocks == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SSequenceSplitInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSequenceSplitInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SSequenceSplitInfoAsnWrite(ID2SSequenceSplitInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_SEQUENCE_SPLIT_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> block_size;
+   retval = AsnWrite(aip, SEQUENCE_SPLIT_INFO_block_size,  &av);
+   av.intvalue = ptr -> chunk_start;
+   retval = AsnWrite(aip, SPLIT_INFO_chunk_start,  &av);
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> chunk_blocks ,ASNCODE_INTVAL_SLOT, aip, SPLIT_INFO_chunk_blocks, SPLIT_INFO_chunk_blocks_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SChunkContentFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkContentPtr LIBCALL
+ID2SChunkContentFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case ID2SChunkContent_seq_descr:
+      ID2SSeqDescrInfoFree(anp -> data.ptrvalue);
+      break;
+   case ID2SChunkContent_seq_annot:
+      ID2SSeqAnnotInfoFree(anp -> data.ptrvalue);
+      break;
+   case ID2SChunkContent_seq_assembly:
+      ID2SSeqAssemblyInfoFree(anp -> data.ptrvalue);
+      break;
+   case ID2SChunkContent_seq_map:
+      ID2SeqLocFree(anp -> data.ptrvalue);
+      break;
+   case ID2SChunkContent_seq_data:
+      ID2SeqLocFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ID2SChunkContentAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkContentPtr LIBCALL
+ID2SChunkContentAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SChunkContent ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_CHUNK_CONTENT);
+   } else {
+      atp = AsnLinkType(orig, ID2S_CHUNK_CONTENT);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == ID2S_CHUNK_CONTENT_seq_descr) {
+      choice = ID2SChunkContent_seq_descr;
+      func = (AsnReadFunc) ID2SSeqDescrInfoAsnRead;
+   }
+   else if (atp == ID2S_CHUNK_CONTENT_seq_annot) {
+      choice = ID2SChunkContent_seq_annot;
+      func = (AsnReadFunc) ID2SSeqAnnotInfoAsnRead;
+   }
+   else if (atp == ID2S_CHUNK_CONTENT_seq_assembly) {
+      choice = ID2SChunkContent_seq_assembly;
+      func = (AsnReadFunc) ID2SSeqAssemblyInfoAsnRead;
+   }
+   else if (atp == ID2S_CHUNK_CONTENT_seq_map) {
+      choice = ID2SChunkContent_seq_map;
+      func = (AsnReadFunc) ID2SeqLocAsnRead;
+   }
+   else if (atp == ID2S_CHUNK_CONTENT_seq_data) {
+      choice = ID2SChunkContent_seq_data;
+      func = (AsnReadFunc) ID2SeqLocAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ID2SChunkContentAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SChunkContentAsnWrite(ID2SChunkContentPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, ID2S_CHUNK_CONTENT);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case ID2SChunkContent_seq_descr:
+      writetype = ID2S_CHUNK_CONTENT_seq_descr;
+      func = (AsnWriteFunc) ID2SSeqDescrInfoAsnWrite;
+      break;
+   case ID2SChunkContent_seq_annot:
+      writetype = ID2S_CHUNK_CONTENT_seq_annot;
+      func = (AsnWriteFunc) ID2SSeqAnnotInfoAsnWrite;
+      break;
+   case ID2SChunkContent_seq_assembly:
+      writetype = ID2S_CHUNK_CONTENT_seq_assembly;
+      func = (AsnWriteFunc) ID2SSeqAssemblyInfoAsnWrite;
+      break;
+   case ID2SChunkContent_seq_map:
+      writetype = ID2S_CHUNK_CONTENT_seq_map;
+      func = (AsnWriteFunc) ID2SeqLocAsnWrite;
+      break;
+   case ID2SChunkContent_seq_data:
+      writetype = ID2S_CHUNK_CONTENT_seq_data;
+      func = (AsnWriteFunc) ID2SeqLocAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ID2SSeqDescrInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSeqDescrInfoPtr LIBCALL
+ID2SSeqDescrInfoNew(void)
+{
+   ID2SSeqDescrInfoPtr ptr = MemNew((size_t) sizeof(ID2SSeqDescrInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SSeqDescrInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSeqDescrInfoPtr LIBCALL
+ID2SSeqDescrInfoFree(ID2SSeqDescrInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr -> bioseqs, (AsnOptFreeFunc) ID2IdRangeFree);
+   AsnGenericUserSeqOfFree(ptr -> bioseq_sets, (AsnOptFreeFunc) ID2IdRangeFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SSeqDescrInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSeqDescrInfoPtr LIBCALL
+ID2SSeqDescrInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SSeqDescrInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SSeqDescrInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_SEQ_DESCR_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_SEQ_DESCR_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SSeqDescrInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_SEQ_DESCR_INFO_type_mask) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type_mask = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_SEQ_DESCR_INFO_bioseqs) {
+      ptr -> bioseqs = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2IdRangeAsnRead, (AsnOptFreeFunc) ID2IdRangeFree);
+      if (isError && ptr -> bioseqs == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_SEQ_DESCR_INFO_bioseq_sets) {
+      ptr -> bioseq_sets = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2IdRangeAsnRead, (AsnOptFreeFunc) ID2IdRangeFree);
+      if (isError && ptr -> bioseq_sets == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SSeqDescrInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSeqDescrInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SSeqDescrInfoAsnWrite(ID2SSeqDescrInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_SEQ_DESCR_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> type_mask;
+   retval = AsnWrite(aip, ID2S_SEQ_DESCR_INFO_type_mask,  &av);
+   AsnGenericUserSeqOfAsnWrite(ptr -> bioseqs, (AsnWriteFunc) ID2IdRangeAsnWrite, aip, ID2S_SEQ_DESCR_INFO_bioseqs, ID2S_SEQ_DESCR_INFO_bioseqs_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> bioseq_sets, (AsnWriteFunc) ID2IdRangeAsnWrite, aip, ID2S_SEQ_DESCR_INFO_bioseq_sets, SEQ_DESCR_INFO_bioseq_sets_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSeqAnnotInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSeqAnnotInfoPtr LIBCALL
+ID2SSeqAnnotInfoNew(void)
+{
+   ID2SSeqAnnotInfoPtr ptr = MemNew((size_t) sizeof(ID2SSeqAnnotInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SSeqAnnotInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSeqAnnotInfoPtr LIBCALL
+ID2SSeqAnnotInfoFree(ID2SSeqAnnotInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> name);
+   AsnGenericUserSeqOfFree(ptr -> feat, (AsnOptFreeFunc) ID2SFeatTypeInfoFree);
+   ID2SeqLocFree(ptr -> seq_loc);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SSeqAnnotInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSeqAnnotInfoPtr LIBCALL
+ID2SSeqAnnotInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SSeqAnnotInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SSeqAnnotInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_SEQ_ANNOT_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_SEQ_ANNOT_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SSeqAnnotInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_SEQ_ANNOT_INFO_name) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> name = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_SEQ_ANNOT_INFO_align) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> align = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_SEQ_ANNOT_INFO_graph) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> graph = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_SEQ_ANNOT_INFO_feat) {
+      ptr -> feat = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SFeatTypeInfoAsnRead, (AsnOptFreeFunc) ID2SFeatTypeInfoFree);
+      if (isError && ptr -> feat == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_SEQ_ANNOT_INFO_seq_loc) {
+      ptr -> seq_loc = ID2SeqLocAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SSeqAnnotInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSeqAnnotInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SSeqAnnotInfoAsnWrite(ID2SSeqAnnotInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_SEQ_ANNOT_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> name != NULL) {
+      av.ptrvalue = ptr -> name;
+      retval = AsnWrite(aip, ID2S_SEQ_ANNOT_INFO_name,  &av);
+   }
+   av.boolvalue = ptr -> align;
+   retval = AsnWrite(aip, ID2S_SEQ_ANNOT_INFO_align,  &av);
+   av.boolvalue = ptr -> graph;
+   retval = AsnWrite(aip, ID2S_SEQ_ANNOT_INFO_graph,  &av);
+   AsnGenericUserSeqOfAsnWrite(ptr -> feat, (AsnWriteFunc) ID2SFeatTypeInfoAsnWrite, aip, ID2S_SEQ_ANNOT_INFO_feat, ID2S_SEQ_ANNOT_INFO_feat_E);
+   if (ptr -> seq_loc != NULL) {
+      if ( ! ID2SeqLocAsnWrite(ptr -> seq_loc, aip, ID2S_SEQ_ANNOT_INFO_seq_loc)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSeqAssemblyInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSeqAssemblyInfoPtr LIBCALL
+ID2SSeqAssemblyInfoNew(void)
+{
+   ID2SSeqAssemblyInfoPtr ptr = MemNew((size_t) sizeof(ID2SSeqAssemblyInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SSeqAssemblyInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSeqAssemblyInfoPtr LIBCALL
+ID2SSeqAssemblyInfoFree(ID2SSeqAssemblyInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr -> bioseqs, (AsnOptFreeFunc) ID2IdRangeFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SSeqAssemblyInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSeqAssemblyInfoPtr LIBCALL
+ID2SSeqAssemblyInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SSeqAssemblyInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SSeqAssemblyInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_SEQ_ASSEMBLY_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_SEQ_ASSEMBLY_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SSeqAssemblyInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_SEQ_ASSEMBLY_INFO_bioseqs) {
+      ptr -> bioseqs = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2IdRangeAsnRead, (AsnOptFreeFunc) ID2IdRangeFree);
+      if (isError && ptr -> bioseqs == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SSeqAssemblyInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSeqAssemblyInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SSeqAssemblyInfoAsnWrite(ID2SSeqAssemblyInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_SEQ_ASSEMBLY_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   AsnGenericUserSeqOfAsnWrite(ptr -> bioseqs, (AsnWriteFunc) ID2IdRangeAsnWrite, aip, ID2S_SEQ_ASSEMBLY_INFO_bioseqs, SEQ_ASSEMBLY_INFO_bioseqs_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SFeatTypeInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SFeatTypeInfoPtr LIBCALL
+ID2SFeatTypeInfoNew(void)
+{
+   ID2SFeatTypeInfoPtr ptr = MemNew((size_t) sizeof(ID2SFeatTypeInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SFeatTypeInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SFeatTypeInfoPtr LIBCALL
+ID2SFeatTypeInfoFree(ID2SFeatTypeInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericBaseSeqOfFree(ptr -> subtypes ,ASNCODE_INTVAL_SLOT);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SFeatTypeInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SFeatTypeInfoPtr LIBCALL
+ID2SFeatTypeInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SFeatTypeInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SFeatTypeInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_FEAT_TYPE_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_FEAT_TYPE_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SFeatTypeInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_FEAT_TYPE_INFO_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_FEAT_TYPE_INFO_subtypes) {
+      ptr -> subtypes = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_INTVAL_SLOT, &isError);
+      if (isError && ptr -> subtypes == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SFeatTypeInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SFeatTypeInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SFeatTypeInfoAsnWrite(ID2SFeatTypeInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_FEAT_TYPE_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, ID2S_FEAT_TYPE_INFO_type,  &av);
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> subtypes ,ASNCODE_INTVAL_SLOT, aip, ID2S_FEAT_TYPE_INFO_subtypes, ID2S_FEAT_TYPE_INFO_subtypes_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SChunkNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkPtr LIBCALL
+ID2SChunkNew(void)
+{
+   ID2SChunkPtr ptr = MemNew((size_t) sizeof(ID2SChunk));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SChunkFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkPtr LIBCALL
+ID2SChunkFree(ID2SChunkPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr -> data, (AsnOptFreeFunc) ID2SChunkDataFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SChunkAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkPtr LIBCALL
+ID2SChunkAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SChunkPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SChunk ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_CHUNK);
+   } else {
+      atp = AsnLinkType(orig, ID2S_CHUNK);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SChunkNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_CHUNK_data) {
+      ptr -> data = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SChunkDataAsnRead, (AsnOptFreeFunc) ID2SChunkDataFree);
+      if (isError && ptr -> data == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SChunkFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SChunkAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SChunkAsnWrite(ID2SChunkPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_CHUNK);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   AsnGenericUserSeqOfAsnWrite(ptr -> data, (AsnWriteFunc) ID2SChunkDataAsnWrite, aip, ID2S_CHUNK_data, ID2S_CHUNK_data_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SChunkDataNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkDataPtr LIBCALL
+ID2SChunkDataNew(void)
+{
+   ID2SChunkDataPtr ptr = MemNew((size_t) sizeof(ID2SChunkData));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SChunkDataFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkDataPtr LIBCALL
+ID2SChunkDataFree(ID2SChunkDataPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   Id_idFree(ptr -> Id_id);
+   AsnGenericChoiceSeqOfFree(ptr -> descrs, (AsnOptFreeFunc) SeqDescrFree);
+   AsnGenericUserSeqOfFree(ptr -> annots, (AsnOptFreeFunc) SeqAnnotFree);
+   AsnGenericUserSeqOfFree(ptr -> assembly, (AsnOptFreeFunc) SeqAlignFree);
+   AsnGenericUserSeqOfFree(ptr -> seq_map, (AsnOptFreeFunc) SeqLiteralFree);
+   AsnGenericUserSeqOfFree(ptr -> seq_data, (AsnOptFreeFunc) SeqLiteralFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    Id_idFree()
+*
+**************************************************/
+static 
+Id_idPtr LIBCALL
+Id_idFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ID2SChunkDataAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SChunkDataPtr LIBCALL
+ID2SChunkDataAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SChunkDataPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SChunkData ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_CHUNK_DATA);
+   } else {
+      atp = AsnLinkType(orig, ID2S_CHUNK_DATA);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SChunkDataNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_CHUNK_DATA_id) {
+      ptr -> Id_id = Id_idAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_CHUNK_DATA_descrs) {
+      ptr -> descrs = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqDescrAsnRead, (AsnOptFreeFunc) SeqDescrFree);
+      if (isError && ptr -> descrs == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_CHUNK_DATA_annots) {
+      ptr -> annots = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqAnnotAsnRead, (AsnOptFreeFunc) SeqAnnotFree);
+      if (isError && ptr -> annots == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_CHUNK_DATA_assembly) {
+      ptr -> assembly = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqAlignAsnRead, (AsnOptFreeFunc) SeqAlignFree);
+      if (isError && ptr -> assembly == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_CHUNK_DATA_seq_map) {
+      ptr -> seq_map = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqLiteralAsnRead, (AsnOptFreeFunc) SeqLiteralFree);
+      if (isError && ptr -> seq_map == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_CHUNK_DATA_seq_data) {
+      ptr -> seq_data = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqLiteralAsnRead, (AsnOptFreeFunc) SeqLiteralFree);
+      if (isError && ptr -> seq_data == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SChunkDataFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    Id_idAsnRead()
+*
+**************************************************/
+static 
+Id_idPtr LIBCALL
+Id_idAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* Id_id ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_CHUNK_DATA_id);
+   } else {
+      atp = AsnLinkType(orig, ID2S_CHUNK_DATA_id);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == ID2S_CHUNK_DATA_id_bioseq_set) {
+      choice = Id_id_bioseq_set;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == ID2S_CHUNK_DATA_id_gi) {
+      choice = Id_id_gi;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ID2SChunkDataAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SChunkDataAsnWrite(ID2SChunkDataPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_CHUNK_DATA);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> Id_id != NULL) {
+      if ( ! Id_idAsnWrite(ptr -> Id_id, aip, ID2S_CHUNK_DATA_id)) {
+         goto erret;
+      }
+   }
+   AsnGenericChoiceSeqOfAsnWrite(ptr -> descrs, (AsnWriteFunc) SeqDescrAsnWrite, aip, ID2S_CHUNK_DATA_descrs, ID2S_CHUNK_DATA_descrs_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> annots, (AsnWriteFunc) SeqAnnotAsnWrite, aip, ID2S_CHUNK_DATA_annots, ID2S_CHUNK_DATA_annots_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> assembly, (AsnWriteFunc) SeqAlignAsnWrite, aip, ID2S_CHUNK_DATA_assembly, ID2S_CHUNK_DATA_assembly_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> seq_map, (AsnWriteFunc) SeqLiteralAsnWrite, aip, ID2S_CHUNK_DATA_seq_map, ID2S_CHUNK_DATA_seq_map_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> seq_data, (AsnWriteFunc) SeqLiteralAsnWrite, aip, ID2S_CHUNK_DATA_seq_data, ID2S_CHUNK_DATA_seq_data_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    Id_idAsnWrite()
+*
+**************************************************/
+static Boolean LIBCALL 
+Id_idAsnWrite(Id_idPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, ID2S_CHUNK_DATA_id);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case Id_id_bioseq_set:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, ID2S_CHUNK_DATA_id_bioseq_set, &av);
+      break;
+   case Id_id_gi:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, ID2S_CHUNK_DATA_id_gi, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ID2IntervalNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2IntervalPtr LIBCALL
+ID2IntervalNew(void)
+{
+   ID2IntervalPtr ptr = MemNew((size_t) sizeof(ID2Interval));
+
+   ptr -> length = 1;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2IntervalFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2IntervalPtr LIBCALL
+ID2IntervalFree(ID2IntervalPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2IntervalAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2IntervalPtr LIBCALL
+ID2IntervalAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2IntervalPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2Interval ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_INTERVAL);
+   } else {
+      atp = AsnLinkType(orig, ID2_INTERVAL);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2IntervalNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_INTERVAL_gi) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> gi = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_INTERVAL_start) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> start = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_INTERVAL_length) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> length = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2IntervalFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2IntervalAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2IntervalAsnWrite(ID2IntervalPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_INTERVAL);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> gi;
+   retval = AsnWrite(aip, ID2_INTERVAL_gi,  &av);
+   av.intvalue = ptr -> start;
+   retval = AsnWrite(aip, ID2_INTERVAL_start,  &av);
+   av.intvalue = ptr -> length;
+   retval = AsnWrite(aip, ID2_INTERVAL_length,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2PackedSeqIntsNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2PackedSeqIntsPtr LIBCALL
+ID2PackedSeqIntsNew(void)
+{
+   ID2PackedSeqIntsPtr ptr = MemNew((size_t) sizeof(ID2PackedSeqInts));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2PackedSeqIntsFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2PackedSeqIntsPtr LIBCALL
+ID2PackedSeqIntsFree(ID2PackedSeqIntsPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr -> ints, (AsnOptFreeFunc) ID2SeqRangeFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2PackedSeqIntsAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2PackedSeqIntsPtr LIBCALL
+ID2PackedSeqIntsAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2PackedSeqIntsPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2PackedSeqInts ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_PACKED_SEQ_INTS);
+   } else {
+      atp = AsnLinkType(orig, ID2_PACKED_SEQ_INTS);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2PackedSeqIntsNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_PACKED_SEQ_INTS_gi) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> gi = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_PACKED_SEQ_INTS_ints) {
+      ptr -> ints = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SeqRangeAsnRead, (AsnOptFreeFunc) ID2SeqRangeFree);
+      if (isError && ptr -> ints == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2PackedSeqIntsFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2PackedSeqIntsAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2PackedSeqIntsAsnWrite(ID2PackedSeqIntsPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_PACKED_SEQ_INTS);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> gi;
+   retval = AsnWrite(aip, ID2_PACKED_SEQ_INTS_gi,  &av);
+   AsnGenericUserSeqOfAsnWrite(ptr -> ints, (AsnWriteFunc) ID2SeqRangeAsnWrite, aip, ID2_PACKED_SEQ_INTS_ints, ID2_PACKED_SEQ_INTS_ints_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SeqRangeNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SeqRangePtr LIBCALL
+ID2SeqRangeNew(void)
+{
+   ID2SeqRangePtr ptr = MemNew((size_t) sizeof(ID2SeqRange));
+
+   ptr -> length = 1;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SeqRangeFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SeqRangePtr LIBCALL
+ID2SeqRangeFree(ID2SeqRangePtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SeqRangeAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SeqRangePtr LIBCALL
+ID2SeqRangeAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SeqRangePtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SeqRange ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_SEQ_RANGE);
+   } else {
+      atp = AsnLinkType(orig, ID2_SEQ_RANGE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SeqRangeNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_SEQ_RANGE_start) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> start = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_SEQ_RANGE_length) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> length = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SeqRangeFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SeqRangeAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SeqRangeAsnWrite(ID2SeqRangePtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_SEQ_RANGE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> start;
+   retval = AsnWrite(aip, ID2_SEQ_RANGE_start,  &av);
+   av.intvalue = ptr -> length;
+   retval = AsnWrite(aip, ID2_SEQ_RANGE_length,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2ParamNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ParamPtr LIBCALL
+ID2ParamNew(void)
+{
+   ID2ParamPtr ptr = MemNew((size_t) sizeof(ID2Param));
+
+   ptr -> type = 1;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2ParamFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ParamPtr LIBCALL
+ID2ParamFree(ID2ParamPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> name);
+   AsnGenericBaseSeqOfFree(ptr -> value ,ASNCODE_PTRVAL_SLOT);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2ParamAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2ParamPtr LIBCALL
+ID2ParamAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2ParamPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2Param ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_PARAM);
+   } else {
+      atp = AsnLinkType(orig, ID2_PARAM);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2ParamNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2_PARAM_name) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> name = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_PARAM_value) {
+      ptr -> value = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_PTRVAL_SLOT, &isError);
+      if (isError && ptr -> value == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2_PARAM_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2ParamFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2ParamAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2ParamAsnWrite(ID2ParamPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_PARAM);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> name != NULL) {
+      av.ptrvalue = ptr -> name;
+      retval = AsnWrite(aip, ID2_PARAM_name,  &av);
+   }
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> value ,ASNCODE_PTRVAL_SLOT, aip, ID2_PARAM_value, ID2_PARAM_value_E);
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, ID2_PARAM_type,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
diff --git a/network/id2arch/id2.h b/network/id2arch/id2.h
new file mode 100644
index 00000000..affa3533
--- /dev/null
+++ b/network/id2arch/id2.h
@@ -0,0 +1,519 @@
+/***********************************************************************
+*
+**
+*        Automatic header module from ASNTOOL
+*
+************************************************************************/
+
+#ifndef _ASNTOOL_
+#include <asn.h>
+#endif
+
+static char * asnfilename = "id2.h14";
+static AsnValxNode avnx[27] = {
+    {20,"set-value" ,1,0.0,&avnx[1] } ,
+    {20,"get-value" ,2,0.0,&avnx[2] } ,
+    {20,"force-value" ,3,0.0,&avnx[3] } ,
+    {20,"use-package" ,4,0.0,NULL } ,
+    {3,NULL,1,0.0,NULL } ,
+    {3,NULL,1,0.0,NULL } ,
+    {3,NULL,1,0.0,NULL } ,
+    {3,NULL,1,0.0,NULL } ,
+    {3,NULL,1,0.0,NULL } ,
+    {3,NULL,1,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"none" ,0,0.0,&avnx[14] } ,
+    {20,"seq-map" ,1,0.0,&avnx[15] } ,
+    {20,"seq-data" ,2,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {1,"" ,0,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"warning" ,1,0.0,&avnx[20] } ,
+    {20,"failed-command" ,2,0.0,&avnx[21] } ,
+    {20,"failed-connection" ,3,0.0,&avnx[22] } ,
+    {20,"failed-server" ,4,0.0,&avnx[23] } ,
+    {20,"no-data" ,5,0.0,&avnx[24] } ,
+    {20,"restricted-data" ,6,0.0,&avnx[25] } ,
+    {20,"unsupported-command" ,7,0.0,&avnx[26] } ,
+    {20,"invalid-arguments" ,8,0.0,NULL } };
+
+static AsnType atx[217] = {
+  {401, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1]} ,
+  {402, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[2]} ,
+  {403, "Seq-descr" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[3]} ,
+  {404, "Seq-literal" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[4]} ,
+  {405, "Seq-align" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[5]} ,
+  {406, "ID2-Request-Packet" ,1,0,0,0,0,0,0,0,NULL,&atx[18],&atx[6],0,&atx[7]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[7],NULL,0,NULL} ,
+  {407, "ID2-Request" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[8],0,&atx[11]} ,
+  {0, "serial-number" ,128,0,0,1,0,0,0,0,NULL,&atx[9],NULL,0,&atx[10]} ,
+  {302, "INTEGER" ,0,2,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "params" ,128,1,0,1,0,0,0,0,NULL,&atx[11],NULL,0,&atx[22]} ,
+  {408, "ID2-Params" ,1,0,0,0,0,0,0,0,NULL,&atx[18],&atx[12],0,&atx[26]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[13],NULL,0,NULL} ,
+  {448, "ID2-Param" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[14],0,NULL} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[15],NULL,0,&atx[16]} ,
+  {323, "VisibleString" ,0,26,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "value" ,128,1,0,1,0,0,0,0,NULL,&atx[18],&atx[17],0,&atx[19]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[15],NULL,0,NULL} ,
+  {312, "SEQUENCE OF" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "type" ,128,2,0,0,1,0,0,0,&avnx[4],&atx[20],&avnx[0],0,NULL} ,
+  {310, "ENUMERATED" ,0,10,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {311, "SEQUENCE" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "request" ,128,2,0,0,0,0,0,0,NULL,&atx[42],&atx[23],0,NULL} ,
+  {0, "init" ,128,0,0,0,0,0,0,0,NULL,&atx[24],NULL,0,&atx[25]} ,
+  {305, "NULL" ,0,5,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "get-packages" ,128,1,0,0,0,0,0,0,NULL,&atx[26],NULL,0,&atx[30]} ,
+  {409, "ID2-Request-Get-Packages" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[27],0,&atx[31]} ,
+  {0, "names" ,128,0,0,1,0,0,0,0,NULL,&atx[18],&atx[28],0,&atx[29]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[15],NULL,0,NULL} ,
+  {0, "no-contents" ,128,1,0,1,0,0,0,0,NULL,&atx[24],NULL,0,NULL} ,
+  {0, "string-to-gi" ,128,2,0,0,0,0,0,0,NULL,&atx[31],NULL,0,&atx[33]} ,
+  {410, "ID2-Request-String-To-Gi" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[32],0,&atx[34]} ,
+  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[15],NULL,0,NULL} ,
+  {0, "seq-id-to-gi" ,128,3,0,0,0,0,0,0,NULL,&atx[34],NULL,0,&atx[36]} ,
+  {411, "ID2-Request-Seq-id-To-Gi" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[35],0,&atx[37]} ,
+  {0, "seq-id" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,NULL} ,
+  {0, "gi-to-tse-id" ,128,4,0,0,0,0,0,0,NULL,&atx[37],NULL,0,&atx[48]} ,
+  {412, "ID2-Request-Gi-To-TSE-Id" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[38],0,&atx[49]} ,
+  {0, "gi" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&atx[39],0,&atx[43]} ,
+  {0, "gi" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[40]} ,
+  {0, "string" ,128,1,0,0,0,0,0,0,NULL,&atx[31],NULL,0,&atx[41]} ,
+  {0, "seq-id" ,128,2,0,0,0,0,0,0,NULL,&atx[34],NULL,0,NULL} ,
+  {315, "CHOICE" ,0,-1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "sources" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[44],0,&atx[46]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[15],NULL,0,NULL} ,
+  {314, "SET OF" ,0,17,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "external" ,128,2,0,1,0,0,0,0,NULL,&atx[24],NULL,0,&atx[47]} ,
+  {0, "current-gis" ,128,3,0,1,0,0,0,0,NULL,&atx[24],NULL,0,NULL} ,
+  {0, "get-tse" ,128,5,0,0,0,0,0,0,NULL,&atx[49],NULL,0,&atx[89]} ,
+  {413, "ID2-Request-Get-TSE" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[50],0,&atx[90]} ,
+  {0, "tse-id" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&atx[51],0,&atx[59]} ,
+  {0, "tse-id" ,128,0,0,0,0,0,0,0,NULL,&atx[52],NULL,0,&atx[55]} ,
+  {416, "ID2-TSE-Id" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[53],0,&atx[60]} ,
+  {0, "sat" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[54]} ,
+  {0, "sat-key" ,128,1,0,0,0,0,0,0,NULL,&atx[9],NULL,0,NULL} ,
+  {0, "gi" ,128,1,0,0,0,0,0,0,NULL,&atx[21],&atx[56],0,NULL} ,
+  {0, "request" ,128,0,0,0,0,0,0,0,NULL,&atx[37],NULL,0,&atx[57]} ,
+  {0, "exclude-tses" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[58],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[52],NULL,0,NULL} ,
+  {0, "details" ,128,1,0,1,0,0,0,0,NULL,&atx[60],NULL,0,NULL} ,
+  {417, "ID2-Get-TSE-Details" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[61],0,&atx[99]} ,
+  {0, "location" ,128,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[83]} ,
+  {419, "ID2-Seq-loc" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&atx[63],0,&atx[100]} ,
+  {0, "whole" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[64]} ,
+  {0, "int" ,128,1,0,0,0,0,0,0,NULL,&atx[65],NULL,0,&atx[69]} ,
+  {445, "ID2-Interval" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[66],0,&atx[70]} ,
+  {0, "gi" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[67]} ,
+  {0, "start" ,128,1,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[68]} ,
+  {0, "length" ,128,2,0,0,1,0,0,0,&avnx[5],&atx[9],NULL,0,NULL} ,
+  {0, "int-set" ,128,2,0,0,0,0,0,0,NULL,&atx[70],NULL,0,&atx[77]} ,
+  {446, "ID2-Packed-Seq-ints" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[71],0,&atx[74]} ,
+  {0, "gi" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[72]} ,
+  {0, "ints" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[73],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[74],NULL,0,NULL} ,
+  {447, "ID2-Seq-range" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[75],0,&atx[13]} ,
+  {0, "start" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[76]} ,
+  {0, "length" ,128,1,0,0,1,0,0,0,&avnx[6],&atx[9],NULL,0,NULL} ,
+  {0, "whole-range" ,128,3,0,0,0,0,0,0,NULL,&atx[78],NULL,0,&atx[81]} ,
+  {434, "ID2-Id-Range" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[79],0,&atx[160]} ,
+  {0, "start" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[80]} ,
+  {0, "count" ,128,1,0,0,1,0,0,0,&avnx[7],&atx[9],NULL,0,NULL} ,
+  {0, "loc-set" ,128,4,0,0,0,0,0,0,NULL,&atx[45],&atx[82],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} ,
+  {0, "seq-class-level" ,128,1,0,0,1,0,0,0,&avnx[8],&atx[9],NULL,0,&atx[84]} ,
+  {0, "descr-level" ,128,2,0,0,1,0,0,0,&avnx[9],&atx[9],NULL,0,&atx[85]} ,
+  {0, "descr-type-mask" ,128,3,0,0,1,0,0,0,&avnx[10],&atx[9],NULL,0,&atx[86]} ,
+  {0, "annot-type-mask" ,128,4,0,0,1,0,0,0,&avnx[11],&atx[9],NULL,0,&atx[87]} ,
+  {0, "feat-type-mask" ,128,5,0,0,1,0,0,0,&avnx[12],&atx[9],NULL,0,&atx[88]} ,
+  {0, "sequence-level" ,128,6,0,0,1,0,0,0,&avnx[16],&atx[20],&avnx[13],0,NULL} ,
+  {0, "reget-tse" ,128,6,0,0,0,0,0,0,NULL,&atx[90],NULL,0,&atx[94]} ,
+  {414, "ID2-Request-ReGet-TSE" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[91],0,&atx[95]} ,
+  {0, "tse-id" ,128,0,0,0,0,0,0,0,NULL,&atx[52],NULL,0,&atx[92]} ,
+  {0, "details" ,128,1,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[93]} ,
+  {0, "offset" ,128,2,0,0,0,0,0,0,NULL,&atx[9],NULL,0,NULL} ,
+  {0, "get-chunks" ,128,7,0,0,0,0,0,0,NULL,&atx[95],NULL,0,NULL} ,
+  {415, "ID2S-Request-Get-Chunks" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[96],0,&atx[52]} ,
+  {0, "tse-id" ,128,0,0,0,0,0,0,0,NULL,&atx[52],NULL,0,&atx[97]} ,
+  {0, "chunks" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[98],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[99],NULL,0,NULL} ,
+  {418, "ID2S-Chunk-Id" ,1,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[62]} ,
+  {420, "ID2-Reply" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[101],0,&atx[106]} ,
+  {0, "serial-number" ,128,0,0,1,0,0,0,0,NULL,&atx[9],NULL,0,&atx[102]} ,
+  {0, "params" ,128,1,0,1,0,0,0,0,NULL,&atx[11],NULL,0,&atx[103]} ,
+  {0, "reply" ,128,2,0,0,0,0,0,0,NULL,&atx[42],&atx[104],0,&atx[143]} ,
+  {0, "init" ,128,0,0,0,0,0,0,0,NULL,&atx[24],NULL,0,&atx[105]} ,
+  {0, "get-package" ,128,1,0,0,0,0,0,0,NULL,&atx[106],NULL,0,&atx[109]} ,
+  {421, "ID2-Reply-Get-Package" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[107],0,&atx[110]} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[15],NULL,0,&atx[108]} ,
+  {0, "params" ,128,1,0,1,0,0,0,0,NULL,&atx[11],NULL,0,NULL} ,
+  {0, "seq-id-to-gi" ,128,2,0,0,0,0,0,0,NULL,&atx[110],NULL,0,&atx[113]} ,
+  {422, "ID2-Reply-Seq-id-To-Gi" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[111],0,&atx[114]} ,
+  {0, "seq-id" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[112]} ,
+  {0, "gi" ,128,1,0,1,0,0,0,0,NULL,&atx[9],NULL,0,NULL} ,
+  {0, "gi-to-tse-id" ,128,3,0,0,0,0,0,0,NULL,&atx[114],NULL,0,&atx[122]} ,
+  {423, "ID2-Reply-Gi-To-TSE-Id" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[115],0,&atx[123]} ,
+  {0, "gi" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[116]} ,
+  {0, "source" ,128,1,0,0,1,0,0,0,&avnx[17],&atx[15],NULL,0,&atx[117]} ,
+  {0, "tses" ,128,2,0,1,0,0,0,0,NULL,&atx[45],&atx[118],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[119],NULL,0,NULL} ,
+  {428, "ID2-TSE-Id-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[120],0,&atx[126]} ,
+  {0, "tse-id" ,128,0,0,0,0,0,0,0,NULL,&atx[52],NULL,0,&atx[121]} ,
+  {0, "split-version" ,128,1,0,0,1,0,0,0,&avnx[18],&atx[9],NULL,0,NULL} ,
+  {0, "get-tse" ,128,4,0,0,0,0,0,0,NULL,&atx[123],NULL,0,&atx[133]} ,
+  {424, "ID2-Reply-Get-TSE" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[124],0,&atx[134]} ,
+  {0, "tse-id" ,128,0,0,0,0,0,0,0,NULL,&atx[52],NULL,0,&atx[125]} ,
+  {0, "data" ,128,1,0,1,0,0,0,0,NULL,&atx[126],NULL,0,NULL} ,
+  {429, "ID2-Reply-Data" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[127],0,&atx[151]} ,
+  {0, "data-type" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[128]} ,
+  {0, "data-format" ,128,1,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[129]} ,
+  {0, "data-compression" ,128,2,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[130]} ,
+  {0, "data" ,128,3,0,0,0,0,0,0,NULL,&atx[18],&atx[131],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[132],NULL,0,NULL} ,
+  {304, "OCTET STRING" ,0,4,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "get-tse-info" ,128,5,0,0,0,0,0,0,NULL,&atx[134],NULL,0,&atx[138]} ,
+  {425, "ID2S-Reply-Get-TSE-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[135],0,&atx[139]} ,
+  {0, "tse-id" ,128,0,0,0,0,0,0,0,NULL,&atx[52],NULL,0,&atx[136]} ,
+  {0, "split-version" ,128,1,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[137]} ,
+  {0, "info" ,128,2,0,1,0,0,0,0,NULL,&atx[126],NULL,0,NULL} ,
+  {0, "get-chunk" ,128,6,0,0,0,0,0,0,NULL,&atx[139],NULL,0,NULL} ,
+  {426, "ID2S-Reply-Get-Chunk" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[140],0,&atx[145]} ,
+  {0, "tse-id" ,128,0,0,0,0,0,0,0,NULL,&atx[52],NULL,0,&atx[141]} ,
+  {0, "chunk-id" ,128,1,0,0,0,0,0,0,NULL,&atx[99],NULL,0,&atx[142]} ,
+  {0, "data" ,128,2,0,1,0,0,0,0,NULL,&atx[126],NULL,0,NULL} ,
+  {0, "error" ,128,3,0,1,0,0,0,0,NULL,&atx[18],&atx[144],0,&atx[149]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[145],NULL,0,NULL} ,
+  {427, "ID2-Error" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[146],0,&atx[119]} ,
+  {0, "severity" ,128,0,0,0,0,0,0,0,NULL,&atx[20],&avnx[19],0,&atx[147]} ,
+  {0, "retry-delay" ,128,1,0,1,0,0,0,0,NULL,&atx[9],NULL,0,&atx[148]} ,
+  {0, "message" ,128,2,0,1,0,0,0,0,NULL,&atx[15],NULL,0,NULL} ,
+  {0, "end-of-reply" ,128,4,0,0,0,0,0,0,NULL,&atx[150],NULL,0,NULL} ,
+  {301, "BOOLEAN" ,0,1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {430, "ID2S-Split-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[152],0,&atx[154]} ,
+  {0, "bioseqs-info" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[153],0,&atx[166]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[154],NULL,0,NULL} ,
+  {431, "ID2S-Bioseqs-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[155],0,&atx[168]} ,
+  {0, "info" ,128,0,0,0,0,0,0,0,NULL,&atx[156],NULL,0,&atx[165]} ,
+  {433, "ID2S-Bioseq-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[157],0,&atx[78]} ,
+  {0, "gap-count" ,128,0,0,1,0,0,0,0,NULL,&atx[9],NULL,0,&atx[158]} ,
+  {0, "seq-map-has-ref" ,128,1,0,1,0,0,0,0,NULL,&atx[150],NULL,0,&atx[159]} ,
+  {0, "sequence-split" ,128,2,0,1,0,0,0,0,NULL,&atx[160],NULL,0,NULL} ,
+  {435, "ID2S-Sequence-Split-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[161],0,&atx[172]} ,
+  {0, "block-size" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[162]} ,
+  {0, "chunk-start" ,128,1,0,0,0,0,0,0,NULL,&atx[99],NULL,0,&atx[163]} ,
+  {0, "chunk-blocks" ,128,2,0,0,0,0,0,0,NULL,&atx[18],&atx[164],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[9],NULL,0,NULL} ,
+  {0, "bioseqs" ,128,1,0,0,0,0,0,0,NULL,&atx[78],NULL,0,NULL} ,
+  {0, "chunks" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[167],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[168],NULL,0,NULL} ,
+  {432, "ID2S-Chunk-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[169],0,&atx[156]} ,
+  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[99],NULL,0,&atx[170]} ,
+  {0, "content" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[171],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[172],NULL,0,NULL} ,
+  {436, "ID2S-Chunk-Content" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&atx[173],0,&atx[174]} ,
+  {0, "seq-descr" ,128,0,0,0,0,0,0,0,NULL,&atx[174],NULL,0,&atx[180]} ,
+  {437, "ID2S-Seq-descr-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[175],0,&atx[181]} ,
+  {0, "type-mask" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[176]} ,
+  {0, "bioseqs" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[177],0,&atx[178]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[78],NULL,0,NULL} ,
+  {0, "bioseq-sets" ,128,2,0,1,0,0,0,0,NULL,&atx[45],&atx[179],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[78],NULL,0,NULL} ,
+  {0, "seq-annot" ,128,1,0,0,0,0,0,0,NULL,&atx[181],NULL,0,&atx[192]} ,
+  {438, "ID2S-Seq-annot-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[182],0,&atx[193]} ,
+  {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[15],NULL,0,&atx[183]} ,
+  {0, "align" ,128,1,0,1,0,0,0,0,NULL,&atx[24],NULL,0,&atx[184]} ,
+  {0, "graph" ,128,2,0,1,0,0,0,0,NULL,&atx[24],NULL,0,&atx[185]} ,
+  {0, "feat" ,128,3,0,1,0,0,0,0,NULL,&atx[45],&atx[186],0,&atx[191]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[187],NULL,0,NULL} ,
+  {442, "ID2S-Feat-type-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[188],0,&atx[200]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[189]} ,
+  {0, "subtypes" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[190],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[9],NULL,0,NULL} ,
+  {0, "seq-loc" ,128,4,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} ,
+  {0, "seq-assembly" ,128,2,0,0,0,0,0,0,NULL,&atx[193],NULL,0,&atx[196]} ,
+  {439, "ID2S-Seq-assembly-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[194],0,&atx[197]} ,
+  {0, "bioseqs" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[195],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[78],NULL,0,NULL} ,
+  {0, "seq-map" ,128,3,0,0,0,0,0,0,NULL,&atx[197],NULL,0,&atx[198]} ,
+  {440, "ID2S-Seq-map-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[199]} ,
+  {0, "seq-data" ,128,4,0,0,0,0,0,0,NULL,&atx[199],NULL,0,NULL} ,
+  {441, "ID2S-Seq-data-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[187]} ,
+  {443, "ID2S-Chunk" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[201],0,&atx[203]} ,
+  {0, "data" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[202],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[203],NULL,0,NULL} ,
+  {444, "ID2S-Chunk-Data" ,1,0,0,0,0,0,0,0,NULL,&atx[21],&atx[204],0,&atx[65]} ,
+  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&atx[205],0,&atx[207]} ,
+  {0, "bioseq-set" ,128,0,0,0,0,0,0,0,NULL,&atx[9],NULL,0,&atx[206]} ,
+  {0, "gi" ,128,1,0,0,0,0,0,0,NULL,&atx[9],NULL,0,NULL} ,
+  {0, "descrs" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[208],0,&atx[209]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "annots" ,128,2,0,1,0,0,0,0,NULL,&atx[45],&atx[210],0,&atx[211]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1],NULL,0,NULL} ,
+  {0, "assembly" ,128,3,0,1,0,0,0,0,NULL,&atx[45],&atx[212],0,&atx[213]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[4],NULL,0,NULL} ,
+  {0, "seq-map" ,128,4,0,1,0,0,0,0,NULL,&atx[18],&atx[214],0,&atx[215]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[3],NULL,0,NULL} ,
+  {0, "seq-data" ,128,5,0,1,0,0,0,0,NULL,&atx[18],&atx[216],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[3],NULL,0,NULL} };
+
+static AsnModule ampx[1] = {
+  { "NCBI-ID2Access" , "id2.h14",&atx[0],NULL,NULL,0,0} };
+
+static AsnValxNodePtr avn = avnx;
+static AsnTypePtr at = atx;
+static AsnModulePtr amp = ampx;
+
+
+
+/**************************************************
+*
+*    Defines for Module NCBI-ID2Access
+*
+**************************************************/
+
+#define ID2_REQUEST_PACKET &at[5]
+#define ID2_REQUEST_PACKET_E &at[6]
+
+#define ID2_REQUEST &at[7]
+#define ID2_REQUEST_serial_number &at[8]
+#define ID2_REQUEST_params &at[10]
+#define ID2_REQUEST_request &at[22]
+#define ID2_REQUEST_request_init &at[23]
+#define REQUEST_request_get_packages &at[25]
+#define REQUEST_request_string_to_gi &at[30]
+#define REQUEST_request_seq_id_to_gi &at[33]
+#define REQUEST_request_gi_to_tse_id &at[36]
+#define ID2_REQUEST_request_get_tse &at[48]
+#define ID2_REQUEST_request_reget_tse &at[89]
+#define ID2_REQUEST_request_get_chunks &at[94]
+
+#define ID2_PARAMS &at[11]
+#define ID2_PARAMS_E &at[12]
+
+#define ID2_REQUEST_GET_PACKAGES &at[26]
+#define ID2_REQUEST_GET_PACKAGES_names &at[27]
+#define REQUEST_GET_PACKAGES_names_E &at[28]
+#define GET_PACKAGES_no_contents &at[29]
+
+#define ID2_REQUEST_STRING_TO_GI &at[31]
+#define ID2_REQUEST_STRING_TO_GI_id &at[32]
+
+#define ID2_REQUEST_SEQ_ID_TO_GI &at[34]
+#define ID2_REQUEST_SEQ_ID_TO_GI_seq_id &at[35]
+
+#define ID2_REQUEST_GI_TO_TSE_ID &at[37]
+#define ID2_REQUEST_GI_TO_TSE_ID_gi &at[38]
+#define ID2_REQUEST_GI_TO_TSE_ID_gi_gi &at[39]
+#define REQUEST_GI_TO_TSE_ID_gi_string &at[40]
+#define REQUEST_GI_TO_TSE_ID_gi_seq_id &at[41]
+#define REQUEST_GI_TO_TSE_ID_sources &at[43]
+#define REQUEST_GI_TO_TSE_ID_sources_E &at[44]
+#define REQUEST_GI_TO_TSE_ID_external &at[46]
+#define GI_TO_TSE_ID_current_gis &at[47]
+
+#define ID2_REQUEST_GET_TSE &at[49]
+#define ID2_REQUEST_GET_TSE_tse_id &at[50]
+#define REQUEST_GET_TSE_tse_id_tse_id &at[51]
+#define ID2_REQUEST_GET_TSE_tse_id_gi &at[55]
+#define GET_TSE_tse_id_gi_request &at[56]
+#define GET_TSE_tse_id_gi_exclude_tses &at[57]
+#define TSE_tse_id_gi_exclude_tses_E &at[58]
+#define ID2_REQUEST_GET_TSE_details &at[59]
+
+#define ID2_REQUEST_REGET_TSE &at[90]
+#define ID2_REQUEST_REGET_TSE_tse_id &at[91]
+#define ID2_REQUEST_REGET_TSE_details &at[92]
+#define ID2_REQUEST_REGET_TSE_offset &at[93]
+
+#define ID2S_REQUEST_GET_CHUNKS &at[95]
+#define ID2S_REQUEST_GET_CHUNKS_tse_id &at[96]
+#define ID2S_REQUEST_GET_CHUNKS_chunks &at[97]
+#define REQUEST_GET_CHUNKS_chunks_E &at[98]
+
+#define ID2_TSE_ID &at[52]
+#define ID2_TSE_ID_sat &at[53]
+#define ID2_TSE_ID_sat_key &at[54]
+
+#define ID2_GET_TSE_DETAILS &at[60]
+#define ID2_GET_TSE_DETAILS_location &at[61]
+#define TSE_DETAILS_seq_class_level &at[83]
+#define ID2_GET_TSE_DETAILS_descr_level &at[84]
+#define TSE_DETAILS_descr_type_mask &at[85]
+#define TSE_DETAILS_annot_type_mask &at[86]
+#define GET_TSE_DETAILS_feat_type_mask &at[87]
+#define GET_TSE_DETAILS_sequence_level &at[88]
+
+#define ID2S_CHUNK_ID &at[99]
+
+#define ID2_SEQ_LOC &at[62]
+#define ID2_SEQ_LOC_whole &at[63]
+#define ID2_SEQ_LOC_int &at[64]
+#define ID2_SEQ_LOC_int_set &at[69]
+#define ID2_SEQ_LOC_whole_range &at[77]
+#define ID2_SEQ_LOC_loc_set &at[81]
+#define ID2_SEQ_LOC_loc_set_E &at[82]
+
+#define ID2_REPLY &at[100]
+#define ID2_REPLY_serial_number &at[101]
+#define ID2_REPLY_params &at[102]
+#define ID2_REPLY_reply &at[103]
+#define ID2_REPLY_reply_init &at[104]
+#define ID2_REPLY_reply_get_package &at[105]
+#define ID2_REPLY_reply_seq_id_to_gi &at[109]
+#define ID2_REPLY_reply_gi_to_tse_id &at[113]
+#define ID2_REPLY_reply_get_tse &at[122]
+#define ID2_REPLY_reply_get_tse_info &at[133]
+#define ID2_REPLY_reply_get_chunk &at[138]
+#define ID2_REPLY_error &at[143]
+#define ID2_REPLY_error_E &at[144]
+#define ID2_REPLY_end_of_reply &at[149]
+
+#define ID2_REPLY_GET_PACKAGE &at[106]
+#define ID2_REPLY_GET_PACKAGE_name &at[107]
+#define ID2_REPLY_GET_PACKAGE_params &at[108]
+
+#define ID2_REPLY_SEQ_ID_TO_GI &at[110]
+#define ID2_REPLY_SEQ_ID_TO_GI_seq_id &at[111]
+#define ID2_REPLY_SEQ_ID_TO_GI_gi &at[112]
+
+#define ID2_REPLY_GI_TO_TSE_ID &at[114]
+#define ID2_REPLY_GI_TO_TSE_ID_gi &at[115]
+#define ID2_REPLY_GI_TO_TSE_ID_source &at[116]
+#define ID2_REPLY_GI_TO_TSE_ID_tses &at[117]
+#define ID2_REPLY_GI_TO_TSE_ID_tses_E &at[118]
+
+#define ID2_REPLY_GET_TSE &at[123]
+#define ID2_REPLY_GET_TSE_tse_id &at[124]
+#define ID2_REPLY_GET_TSE_data &at[125]
+
+#define ID2S_REPLY_GET_TSE_INFO &at[134]
+#define ID2S_REPLY_GET_TSE_INFO_tse_id &at[135]
+#define GET_TSE_INFO_split_version &at[136]
+#define ID2S_REPLY_GET_TSE_INFO_info &at[137]
+
+#define ID2S_REPLY_GET_CHUNK &at[139]
+#define ID2S_REPLY_GET_CHUNK_tse_id &at[140]
+#define ID2S_REPLY_GET_CHUNK_chunk_id &at[141]
+#define ID2S_REPLY_GET_CHUNK_data &at[142]
+
+#define ID2_ERROR &at[145]
+#define ID2_ERROR_severity &at[146]
+#define ID2_ERROR_retry_delay &at[147]
+#define ID2_ERROR_message &at[148]
+
+#define ID2_TSE_ID_INFO &at[119]
+#define ID2_TSE_ID_INFO_tse_id &at[120]
+#define ID2_TSE_ID_INFO_split_version &at[121]
+
+#define ID2_REPLY_DATA &at[126]
+#define ID2_REPLY_DATA_data_type &at[127]
+#define ID2_REPLY_DATA_data_format &at[128]
+#define ID2_REPLY_DATA_data_compression &at[129]
+#define ID2_REPLY_DATA_data &at[130]
+#define ID2_REPLY_DATA_data_E &at[131]
+
+#define ID2S_SPLIT_INFO &at[151]
+#define ID2S_SPLIT_INFO_bioseqs_info &at[152]
+#define ID2S_SPLIT_INFO_bioseqs_info_E &at[153]
+#define ID2S_SPLIT_INFO_chunks &at[166]
+#define ID2S_SPLIT_INFO_chunks_E &at[167]
+
+#define ID2S_BIOSEQS_INFO &at[154]
+#define ID2S_BIOSEQS_INFO_info &at[155]
+#define ID2S_BIOSEQS_INFO_bioseqs &at[165]
+
+#define ID2S_CHUNK_INFO &at[168]
+#define ID2S_CHUNK_INFO_id &at[169]
+#define ID2S_CHUNK_INFO_content &at[170]
+#define ID2S_CHUNK_INFO_content_E &at[171]
+
+#define ID2S_BIOSEQ_INFO &at[156]
+#define ID2S_BIOSEQ_INFO_gap_count &at[157]
+#define BIOSEQ_INFO_seq_map_has_ref &at[158]
+#define ID2S_BIOSEQ_INFO_sequence_split &at[159]
+
+#define ID2_ID_RANGE &at[78]
+#define ID2_ID_RANGE_start &at[79]
+#define ID2_ID_RANGE_count &at[80]
+
+#define ID2S_SEQUENCE_SPLIT_INFO &at[160]
+#define SEQUENCE_SPLIT_INFO_block_size &at[161]
+#define SPLIT_INFO_chunk_start &at[162]
+#define SPLIT_INFO_chunk_blocks &at[163]
+#define SPLIT_INFO_chunk_blocks_E &at[164]
+
+#define ID2S_CHUNK_CONTENT &at[172]
+#define ID2S_CHUNK_CONTENT_seq_descr &at[173]
+#define ID2S_CHUNK_CONTENT_seq_annot &at[180]
+#define ID2S_CHUNK_CONTENT_seq_assembly &at[192]
+#define ID2S_CHUNK_CONTENT_seq_map &at[196]
+#define ID2S_CHUNK_CONTENT_seq_data &at[198]
+
+#define ID2S_SEQ_DESCR_INFO &at[174]
+#define ID2S_SEQ_DESCR_INFO_type_mask &at[175]
+#define ID2S_SEQ_DESCR_INFO_bioseqs &at[176]
+#define ID2S_SEQ_DESCR_INFO_bioseqs_E &at[177]
+#define ID2S_SEQ_DESCR_INFO_bioseq_sets &at[178]
+#define SEQ_DESCR_INFO_bioseq_sets_E &at[179]
+
+#define ID2S_SEQ_ANNOT_INFO &at[181]
+#define ID2S_SEQ_ANNOT_INFO_name &at[182]
+#define ID2S_SEQ_ANNOT_INFO_align &at[183]
+#define ID2S_SEQ_ANNOT_INFO_graph &at[184]
+#define ID2S_SEQ_ANNOT_INFO_feat &at[185]
+#define ID2S_SEQ_ANNOT_INFO_feat_E &at[186]
+#define ID2S_SEQ_ANNOT_INFO_seq_loc &at[191]
+
+#define ID2S_SEQ_ASSEMBLY_INFO &at[193]
+#define ID2S_SEQ_ASSEMBLY_INFO_bioseqs &at[194]
+#define SEQ_ASSEMBLY_INFO_bioseqs_E &at[195]
+
+#define ID2S_SEQ_MAP_INFO &at[197]
+
+#define ID2S_SEQ_DATA_INFO &at[199]
+
+#define ID2S_FEAT_TYPE_INFO &at[187]
+#define ID2S_FEAT_TYPE_INFO_type &at[188]
+#define ID2S_FEAT_TYPE_INFO_subtypes &at[189]
+#define ID2S_FEAT_TYPE_INFO_subtypes_E &at[190]
+
+#define ID2S_CHUNK &at[200]
+#define ID2S_CHUNK_data &at[201]
+#define ID2S_CHUNK_data_E &at[202]
+
+#define ID2S_CHUNK_DATA &at[203]
+#define ID2S_CHUNK_DATA_id &at[204]
+#define ID2S_CHUNK_DATA_id_bioseq_set &at[205]
+#define ID2S_CHUNK_DATA_id_gi &at[206]
+#define ID2S_CHUNK_DATA_descrs &at[207]
+#define ID2S_CHUNK_DATA_descrs_E &at[208]
+#define ID2S_CHUNK_DATA_annots &at[209]
+#define ID2S_CHUNK_DATA_annots_E &at[210]
+#define ID2S_CHUNK_DATA_assembly &at[211]
+#define ID2S_CHUNK_DATA_assembly_E &at[212]
+#define ID2S_CHUNK_DATA_seq_map &at[213]
+#define ID2S_CHUNK_DATA_seq_map_E &at[214]
+#define ID2S_CHUNK_DATA_seq_data &at[215]
+#define ID2S_CHUNK_DATA_seq_data_E &at[216]
+
+#define ID2_INTERVAL &at[65]
+#define ID2_INTERVAL_gi &at[66]
+#define ID2_INTERVAL_start &at[67]
+#define ID2_INTERVAL_length &at[68]
+
+#define ID2_PACKED_SEQ_INTS &at[70]
+#define ID2_PACKED_SEQ_INTS_gi &at[71]
+#define ID2_PACKED_SEQ_INTS_ints &at[72]
+#define ID2_PACKED_SEQ_INTS_ints_E &at[73]
+
+#define ID2_SEQ_RANGE &at[74]
+#define ID2_SEQ_RANGE_start &at[75]
+#define ID2_SEQ_RANGE_length &at[76]
+
+#define ID2_PARAM &at[13]
+#define ID2_PARAM_name &at[14]
+#define ID2_PARAM_value &at[16]
+#define ID2_PARAM_value_E &at[17]
+#define ID2_PARAM_type &at[19]
diff --git a/network/id2arch/id2gen.h b/network/id2arch/id2gen.h
new file mode 100644
index 00000000..c17237b4
--- /dev/null
+++ b/network/id2arch/id2gen.h
@@ -0,0 +1,968 @@
+#ifndef _id2gen_ 
+#define _id2gen_ 
+
+#undef NLM_EXTERN
+#ifdef NLM_IMPORT
+#define NLM_EXTERN NLM_IMPORT
+#else
+#define NLM_EXTERN extern
+#endif
+
+
+#ifdef __cplusplus
+extern "C" { /* } */
+#endif
+
+
+/**************************************************
+*
+*    Generated objects for Module NCBI-ID2Access
+*    Generated using ASNCODE Revision: 6.0 at Dec 15, 2003  5:08 PM
+*
+**************************************************/
+
+NLM_EXTERN Boolean LIBCALL
+id2genAsnLoad PROTO((void));
+
+
+/**************************************************
+*
+*    ID2RequestPacket
+*
+**************************************************/
+typedef struct struct_ID2Request ID2RequestPacket;
+typedef struct struct_ID2Request PNTR ID2RequestPacketPtr;
+#define ID2RequestPacketNew() ID2RequestNew() 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN ID2RequestPacketPtr LIBCALL ID2RequestPacketFree PROTO ((ID2RequestPacketPtr ));
+NLM_EXTERN ID2RequestPacketPtr LIBCALL ID2RequestPacketNew PROTO (( void ));
+NLM_EXTERN ID2RequestPacketPtr LIBCALL ID2RequestPacketAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2RequestPacketAsnWrite PROTO (( ID2RequestPacketPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    ID2Request
+*
+**************************************************/
+typedef struct struct_ID2_Request {
+   struct struct_ID2_Request PNTR next;
+   Int4   serial_number;
+   struct struct_ID2_Param PNTR   params;
+   ValNodePtr   Request_request;
+} ID2Request, PNTR ID2RequestPtr;
+
+
+NLM_EXTERN ID2RequestPtr LIBCALL ID2RequestFree PROTO ((ID2RequestPtr ));
+NLM_EXTERN ID2RequestPtr LIBCALL ID2RequestNew PROTO (( void ));
+NLM_EXTERN ID2RequestPtr LIBCALL ID2RequestAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2RequestAsnWrite PROTO (( ID2RequestPtr , AsnIoPtr, AsnTypePtr));
+
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+typedef ValNodePtr Request_requestPtr;
+typedef ValNode Request_request;
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+#define Request_request_init 1
+#define Request_request_get_packages 2
+#define Request_request_string_to_gi 3
+#define Request_request_seq_id_to_gi 4
+#define Request_request_gi_to_tse_id 5
+#define Request_request_get_tse 6
+#define Request_request_reget_tse 7
+#define Request_request_get_chunks 8
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+static Request_requestPtr LIBCALL Request_requestFree PROTO ((Request_requestPtr ));
+static Request_requestPtr LIBCALL Request_requestAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+static Boolean LIBCALL Request_requestAsnWrite PROTO (( Request_requestPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    ID2Params
+*
+**************************************************/
+typedef struct struct_ID2Param ID2Params;
+typedef struct struct_ID2Param PNTR ID2ParamsPtr;
+#define ID2ParamsNew() ID2ParamNew() 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN ID2ParamsPtr LIBCALL ID2ParamsFree PROTO ((ID2ParamsPtr ));
+NLM_EXTERN ID2ParamsPtr LIBCALL ID2ParamsNew PROTO (( void ));
+NLM_EXTERN ID2ParamsPtr LIBCALL ID2ParamsAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2ParamsAsnWrite PROTO (( ID2ParamsPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    ID2RequestGetPackages
+*
+**************************************************/
+typedef struct struct_ID2_Request_Get_Packages {
+   ValNodePtr   names;
+   Uint1   no_contents;
+} ID2RequestGetPackages, PNTR ID2RequestGetPackagesPtr;
+
+
+NLM_EXTERN ID2RequestGetPackagesPtr LIBCALL ID2RequestGetPackagesFree PROTO ((ID2RequestGetPackagesPtr ));
+NLM_EXTERN ID2RequestGetPackagesPtr LIBCALL ID2RequestGetPackagesNew PROTO (( void ));
+NLM_EXTERN ID2RequestGetPackagesPtr LIBCALL ID2RequestGetPackagesAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2RequestGetPackagesAsnWrite PROTO (( ID2RequestGetPackagesPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2RequestStringToGi
+*
+**************************************************/
+typedef struct struct_ID2_Request_String_To_Gi {
+   CharPtr   id;
+} ID2RequestStringToGi, PNTR ID2RequestStringToGiPtr;
+
+
+NLM_EXTERN ID2RequestStringToGiPtr LIBCALL ID2RequestStringToGiFree PROTO ((ID2RequestStringToGiPtr ));
+NLM_EXTERN ID2RequestStringToGiPtr LIBCALL ID2RequestStringToGiNew PROTO (( void ));
+NLM_EXTERN ID2RequestStringToGiPtr LIBCALL ID2RequestStringToGiAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2RequestStringToGiAsnWrite PROTO (( ID2RequestStringToGiPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2RequestSeqIdToGi
+*
+**************************************************/
+typedef struct struct_ID2_Request_Seq_id_To_Gi {
+   ValNodePtr   seq_id;
+} ID2RequestSeqIdToGi, PNTR ID2RequestSeqIdToGiPtr;
+
+
+NLM_EXTERN ID2RequestSeqIdToGiPtr LIBCALL ID2RequestSeqIdToGiFree PROTO ((ID2RequestSeqIdToGiPtr ));
+NLM_EXTERN ID2RequestSeqIdToGiPtr LIBCALL ID2RequestSeqIdToGiNew PROTO (( void ));
+NLM_EXTERN ID2RequestSeqIdToGiPtr LIBCALL ID2RequestSeqIdToGiAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2RequestSeqIdToGiAsnWrite PROTO (( ID2RequestSeqIdToGiPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2RequestGiToTSEId
+*
+**************************************************/
+typedef struct struct_ID2_Request_Gi_To_TSE_Id {
+   ValNodePtr   Gi_gi;
+   ValNodePtr   sources;
+   Uint1   external;
+   Uint1   current_gis;
+} ID2RequestGiToTSEId, PNTR ID2RequestGiToTSEIdPtr;
+
+
+NLM_EXTERN ID2RequestGiToTSEIdPtr LIBCALL ID2RequestGiToTSEIdFree PROTO ((ID2RequestGiToTSEIdPtr ));
+NLM_EXTERN ID2RequestGiToTSEIdPtr LIBCALL ID2RequestGiToTSEIdNew PROTO (( void ));
+NLM_EXTERN ID2RequestGiToTSEIdPtr LIBCALL ID2RequestGiToTSEIdAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2RequestGiToTSEIdAsnWrite PROTO (( ID2RequestGiToTSEIdPtr , AsnIoPtr, AsnTypePtr));
+
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+typedef ValNodePtr Gi_giPtr;
+typedef ValNode Gi_gi;
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+#define Gi_gi_gi 1
+#define Gi_gi_string 2
+#define Gi_gi_seq_id 3
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+static Gi_giPtr LIBCALL Gi_giFree PROTO ((Gi_giPtr ));
+static Gi_giPtr LIBCALL Gi_giAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+static Boolean LIBCALL Gi_giAsnWrite PROTO (( Gi_giPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    ID2RequestGetTSE
+*
+**************************************************/
+typedef struct struct_ID2_Request_Get_TSE {
+   ValNodePtr   TseId_tse_id;
+   struct struct_ID2_Get_TSE_Details PNTR   details;
+} ID2RequestGetTSE, PNTR ID2RequestGetTSEPtr;
+
+
+NLM_EXTERN ID2RequestGetTSEPtr LIBCALL ID2RequestGetTSEFree PROTO ((ID2RequestGetTSEPtr ));
+NLM_EXTERN ID2RequestGetTSEPtr LIBCALL ID2RequestGetTSENew PROTO (( void ));
+NLM_EXTERN ID2RequestGetTSEPtr LIBCALL ID2RequestGetTSEAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2RequestGetTSEAsnWrite PROTO (( ID2RequestGetTSEPtr , AsnIoPtr, AsnTypePtr));
+
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+typedef ValNodePtr TseId_tse_idPtr;
+typedef ValNode TseId_tse_id;
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+#define TseId_tse_id_tse_id 1
+#define TseId_tse_id_TseId_Gi 2
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+static TseId_tse_idPtr LIBCALL TseId_tse_idFree PROTO ((TseId_tse_idPtr ));
+static TseId_tse_idPtr LIBCALL TseId_tse_idAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+static Boolean LIBCALL TseId_tse_idAsnWrite PROTO (( TseId_tse_idPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    TseId_gi
+*
+**************************************************/
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+typedef struct struct_TseId_Gi {
+   struct struct_ID2_Request_Gi_To_TSE_Id PNTR   request;
+   struct struct_ID2_TSE_Id PNTR   exclude_tses;
+} TseId_gi, PNTR TseId_giPtr;
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+static TseId_giPtr LIBCALL TseId_giFree PROTO ((TseId_giPtr ));
+static TseId_giPtr LIBCALL TseId_giNew PROTO (( void ));
+static TseId_giPtr LIBCALL TseId_giAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+static Boolean LIBCALL TseId_giAsnWrite PROTO (( TseId_giPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    ID2RequestReGetTSE
+*
+**************************************************/
+typedef struct struct_ID2_Request_ReGet_TSE {
+   struct struct_ID2_TSE_Id PNTR   tse_id;
+   struct struct_ID2_Get_TSE_Details PNTR   details;
+   Int4   offset;
+} ID2RequestReGetTSE, PNTR ID2RequestReGetTSEPtr;
+
+
+NLM_EXTERN ID2RequestReGetTSEPtr LIBCALL ID2RequestReGetTSEFree PROTO ((ID2RequestReGetTSEPtr ));
+NLM_EXTERN ID2RequestReGetTSEPtr LIBCALL ID2RequestReGetTSENew PROTO (( void ));
+NLM_EXTERN ID2RequestReGetTSEPtr LIBCALL ID2RequestReGetTSEAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2RequestReGetTSEAsnWrite PROTO (( ID2RequestReGetTSEPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SRequestGetChunks
+*
+**************************************************/
+typedef struct struct_ID2S_Request_Get_Chunks {
+   struct struct_ID2_TSE_Id PNTR   tse_id;
+   ValNodePtr   chunks;
+} ID2SRequestGetChunks, PNTR ID2SRequestGetChunksPtr;
+
+
+NLM_EXTERN ID2SRequestGetChunksPtr LIBCALL ID2SRequestGetChunksFree PROTO ((ID2SRequestGetChunksPtr ));
+NLM_EXTERN ID2SRequestGetChunksPtr LIBCALL ID2SRequestGetChunksNew PROTO (( void ));
+NLM_EXTERN ID2SRequestGetChunksPtr LIBCALL ID2SRequestGetChunksAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SRequestGetChunksAsnWrite PROTO (( ID2SRequestGetChunksPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2TSEId
+*
+**************************************************/
+typedef struct struct_ID2_TSE_Id {
+   struct struct_ID2_TSE_Id PNTR next;
+   Int4   sat;
+   Int4   sat_key;
+} ID2TSEId, PNTR ID2TSEIdPtr;
+
+
+NLM_EXTERN ID2TSEIdPtr LIBCALL ID2TSEIdFree PROTO ((ID2TSEIdPtr ));
+NLM_EXTERN ID2TSEIdPtr LIBCALL ID2TSEIdNew PROTO (( void ));
+NLM_EXTERN ID2TSEIdPtr LIBCALL ID2TSEIdAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2TSEIdAsnWrite PROTO (( ID2TSEIdPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2GetTSEDetails
+*
+**************************************************/
+typedef struct struct_ID2_Get_TSE_Details {
+   ValNodePtr   location;
+   Int4   seq_class_level;
+   Int4   descr_level;
+   Int4   descr_type_mask;
+   Int4   annot_type_mask;
+   Int4   feat_type_mask;
+   Uint2   sequence_level;
+   /* following #defines are for enumerated type, not used by object loaders */
+#define ID2_Get_TSE_Details_sequence_level_none 0
+#define ID2_Get_TSE_Details_sequence_level_seq_map 1
+#define ID2_Get_TSE_Details_sequence_level_seq_data 2
+
+} ID2GetTSEDetails, PNTR ID2GetTSEDetailsPtr;
+
+
+NLM_EXTERN ID2GetTSEDetailsPtr LIBCALL ID2GetTSEDetailsFree PROTO ((ID2GetTSEDetailsPtr ));
+NLM_EXTERN ID2GetTSEDetailsPtr LIBCALL ID2GetTSEDetailsNew PROTO (( void ));
+NLM_EXTERN ID2GetTSEDetailsPtr LIBCALL ID2GetTSEDetailsAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2GetTSEDetailsAsnWrite PROTO (( ID2GetTSEDetailsPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr ID2SeqLocPtr;
+typedef ValNode ID2SeqLoc;
+#define ID2SeqLoc_whole 1
+#define ID2SeqLoc_int__ 2
+#define ID2SeqLoc_int_set 3
+#define ID2SeqLoc_whole_range 4
+#define ID2SeqLoc_loc_set 5
+
+
+NLM_EXTERN ID2SeqLocPtr LIBCALL ID2SeqLocFree PROTO ((ID2SeqLocPtr ));
+NLM_EXTERN ID2SeqLocPtr LIBCALL ID2SeqLocAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SeqLocAsnWrite PROTO (( ID2SeqLocPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2Reply
+*
+**************************************************/
+typedef struct struct_ID2_Reply {
+   Int4   serial_number;
+   struct struct_ID2_Param PNTR   params;
+   ValNodePtr   Reply_reply;
+   struct struct_ID2_Error PNTR   error;
+   Uint1   end_of_reply;
+} ID2Reply, PNTR ID2ReplyPtr;
+
+
+NLM_EXTERN ID2ReplyPtr LIBCALL ID2ReplyFree PROTO ((ID2ReplyPtr ));
+NLM_EXTERN ID2ReplyPtr LIBCALL ID2ReplyNew PROTO (( void ));
+NLM_EXTERN ID2ReplyPtr LIBCALL ID2ReplyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2ReplyAsnWrite PROTO (( ID2ReplyPtr , AsnIoPtr, AsnTypePtr));
+
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+typedef ValNodePtr Reply_replyPtr;
+typedef ValNode Reply_reply;
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+#define Reply_reply_init 1
+#define Reply_reply_get_package 2
+#define Reply_reply_seq_id_to_gi 3
+#define Reply_reply_gi_to_tse_id 4
+#define Reply_reply_get_tse 5
+#define Reply_reply_get_tse_info 6
+#define Reply_reply_get_chunk 7
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+static Reply_replyPtr LIBCALL Reply_replyFree PROTO ((Reply_replyPtr ));
+static Reply_replyPtr LIBCALL Reply_replyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+static Boolean LIBCALL Reply_replyAsnWrite PROTO (( Reply_replyPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    ID2ReplyGetPackage
+*
+**************************************************/
+typedef struct struct_ID2_Reply_Get_Package {
+   CharPtr   name;
+   struct struct_ID2_Param PNTR   params;
+} ID2ReplyGetPackage, PNTR ID2ReplyGetPackagePtr;
+
+
+NLM_EXTERN ID2ReplyGetPackagePtr LIBCALL ID2ReplyGetPackageFree PROTO ((ID2ReplyGetPackagePtr ));
+NLM_EXTERN ID2ReplyGetPackagePtr LIBCALL ID2ReplyGetPackageNew PROTO (( void ));
+NLM_EXTERN ID2ReplyGetPackagePtr LIBCALL ID2ReplyGetPackageAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2ReplyGetPackageAsnWrite PROTO (( ID2ReplyGetPackagePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2ReplySeqIdToGi
+*
+**************************************************/
+typedef struct struct_ID2_Reply_Seq_id_To_Gi {
+   ValNodePtr   seq_id;
+   Int4   gi;
+} ID2ReplySeqIdToGi, PNTR ID2ReplySeqIdToGiPtr;
+
+
+NLM_EXTERN ID2ReplySeqIdToGiPtr LIBCALL ID2ReplySeqIdToGiFree PROTO ((ID2ReplySeqIdToGiPtr ));
+NLM_EXTERN ID2ReplySeqIdToGiPtr LIBCALL ID2ReplySeqIdToGiNew PROTO (( void ));
+NLM_EXTERN ID2ReplySeqIdToGiPtr LIBCALL ID2ReplySeqIdToGiAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2ReplySeqIdToGiAsnWrite PROTO (( ID2ReplySeqIdToGiPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2ReplyGiToTSEId
+*
+**************************************************/
+typedef struct struct_ID2_Reply_Gi_To_TSE_Id {
+   Int4   gi;
+   CharPtr   source;
+   struct struct_ID2_TSE_Id_Info PNTR   tses;
+} ID2ReplyGiToTSEId, PNTR ID2ReplyGiToTSEIdPtr;
+
+
+NLM_EXTERN ID2ReplyGiToTSEIdPtr LIBCALL ID2ReplyGiToTSEIdFree PROTO ((ID2ReplyGiToTSEIdPtr ));
+NLM_EXTERN ID2ReplyGiToTSEIdPtr LIBCALL ID2ReplyGiToTSEIdNew PROTO (( void ));
+NLM_EXTERN ID2ReplyGiToTSEIdPtr LIBCALL ID2ReplyGiToTSEIdAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2ReplyGiToTSEIdAsnWrite PROTO (( ID2ReplyGiToTSEIdPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2ReplyGetTSE
+*
+**************************************************/
+typedef struct struct_ID2_Reply_Get_TSE {
+   struct struct_ID2_TSE_Id PNTR   tse_id;
+   struct struct_ID2_Reply_Data PNTR   data;
+} ID2ReplyGetTSE, PNTR ID2ReplyGetTSEPtr;
+
+
+NLM_EXTERN ID2ReplyGetTSEPtr LIBCALL ID2ReplyGetTSEFree PROTO ((ID2ReplyGetTSEPtr ));
+NLM_EXTERN ID2ReplyGetTSEPtr LIBCALL ID2ReplyGetTSENew PROTO (( void ));
+NLM_EXTERN ID2ReplyGetTSEPtr LIBCALL ID2ReplyGetTSEAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2ReplyGetTSEAsnWrite PROTO (( ID2ReplyGetTSEPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SReplyGetTSEInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Reply_Get_TSE_Info {
+   struct struct_ID2_TSE_Id PNTR   tse_id;
+   Int4   split_version;
+   struct struct_ID2_Reply_Data PNTR   info;
+} ID2SReplyGetTSEInfo, PNTR ID2SReplyGetTSEInfoPtr;
+
+
+NLM_EXTERN ID2SReplyGetTSEInfoPtr LIBCALL ID2SReplyGetTSEInfoFree PROTO ((ID2SReplyGetTSEInfoPtr ));
+NLM_EXTERN ID2SReplyGetTSEInfoPtr LIBCALL ID2SReplyGetTSEInfoNew PROTO (( void ));
+NLM_EXTERN ID2SReplyGetTSEInfoPtr LIBCALL ID2SReplyGetTSEInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SReplyGetTSEInfoAsnWrite PROTO (( ID2SReplyGetTSEInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SReplyGetChunk
+*
+**************************************************/
+typedef struct struct_ID2S_Reply_Get_Chunk {
+   struct struct_ID2_TSE_Id PNTR   tse_id;
+   Int4   chunk_id;
+   struct struct_ID2_Reply_Data PNTR   data;
+} ID2SReplyGetChunk, PNTR ID2SReplyGetChunkPtr;
+
+
+NLM_EXTERN ID2SReplyGetChunkPtr LIBCALL ID2SReplyGetChunkFree PROTO ((ID2SReplyGetChunkPtr ));
+NLM_EXTERN ID2SReplyGetChunkPtr LIBCALL ID2SReplyGetChunkNew PROTO (( void ));
+NLM_EXTERN ID2SReplyGetChunkPtr LIBCALL ID2SReplyGetChunkAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SReplyGetChunkAsnWrite PROTO (( ID2SReplyGetChunkPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2Error
+*
+**************************************************/
+typedef struct struct_ID2_Error {
+   struct struct_ID2_Error PNTR next;
+   Uint2   severity;
+   /* following #defines are for enumerated type, not used by object loaders */
+#define ID2_Error_severity_warning 1
+#define ID2_Error_severity_failed_command 2
+#define ID2_Error_severity_failed_connection 3
+#define ID2_Error_severity_failed_server 4
+#define ID2_Error_severity_no_data 5
+#define ID2_Error_severity_restricted_data 6
+#define ID2_Error_severity_unsupported_command 7
+#define ID2_Error_severity_invalid_arguments 8
+
+   Int4   retry_delay;
+   CharPtr   message;
+} ID2Error, PNTR ID2ErrorPtr;
+
+
+NLM_EXTERN ID2ErrorPtr LIBCALL ID2ErrorFree PROTO ((ID2ErrorPtr ));
+NLM_EXTERN ID2ErrorPtr LIBCALL ID2ErrorNew PROTO (( void ));
+NLM_EXTERN ID2ErrorPtr LIBCALL ID2ErrorAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2ErrorAsnWrite PROTO (( ID2ErrorPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2TSEIdInfo
+*
+**************************************************/
+typedef struct struct_ID2_TSE_Id_Info {
+   struct struct_ID2_TSE_Id_Info PNTR next;
+   struct struct_ID2_TSE_Id PNTR   tse_id;
+   Int4   split_version;
+} ID2TSEIdInfo, PNTR ID2TSEIdInfoPtr;
+
+
+NLM_EXTERN ID2TSEIdInfoPtr LIBCALL ID2TSEIdInfoFree PROTO ((ID2TSEIdInfoPtr ));
+NLM_EXTERN ID2TSEIdInfoPtr LIBCALL ID2TSEIdInfoNew PROTO (( void ));
+NLM_EXTERN ID2TSEIdInfoPtr LIBCALL ID2TSEIdInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2TSEIdInfoAsnWrite PROTO (( ID2TSEIdInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2ReplyData
+*
+**************************************************/
+typedef struct struct_ID2_Reply_Data {
+   Int4   data_type;
+   Int4   data_format;
+   Int4   data_compression;
+   ValNodePtr   data;
+} ID2ReplyData, PNTR ID2ReplyDataPtr;
+
+
+NLM_EXTERN ID2ReplyDataPtr LIBCALL ID2ReplyDataFree PROTO ((ID2ReplyDataPtr ));
+NLM_EXTERN ID2ReplyDataPtr LIBCALL ID2ReplyDataNew PROTO (( void ));
+NLM_EXTERN ID2ReplyDataPtr LIBCALL ID2ReplyDataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2ReplyDataAsnWrite PROTO (( ID2ReplyDataPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SSplitInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Split_Info {
+   struct struct_ID2S_Bioseqs_Info PNTR   bioseqs_info;
+   struct struct_ID2S_Chunk_Info PNTR   chunks;
+} ID2SSplitInfo, PNTR ID2SSplitInfoPtr;
+
+
+NLM_EXTERN ID2SSplitInfoPtr LIBCALL ID2SSplitInfoFree PROTO ((ID2SSplitInfoPtr ));
+NLM_EXTERN ID2SSplitInfoPtr LIBCALL ID2SSplitInfoNew PROTO (( void ));
+NLM_EXTERN ID2SSplitInfoPtr LIBCALL ID2SSplitInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SSplitInfoAsnWrite PROTO (( ID2SSplitInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SBioseqsInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Bioseqs_Info {
+   struct struct_ID2S_Bioseqs_Info PNTR next;
+   struct struct_ID2S_Bioseq_Info PNTR   info;
+   struct struct_ID2_Id_Range PNTR   bioseqs;
+} ID2SBioseqsInfo, PNTR ID2SBioseqsInfoPtr;
+
+
+NLM_EXTERN ID2SBioseqsInfoPtr LIBCALL ID2SBioseqsInfoFree PROTO ((ID2SBioseqsInfoPtr ));
+NLM_EXTERN ID2SBioseqsInfoPtr LIBCALL ID2SBioseqsInfoNew PROTO (( void ));
+NLM_EXTERN ID2SBioseqsInfoPtr LIBCALL ID2SBioseqsInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SBioseqsInfoAsnWrite PROTO (( ID2SBioseqsInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SChunkInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Chunk_Info {
+   struct struct_ID2S_Chunk_Info PNTR next;
+   Int4   id;
+   ValNodePtr   content;
+} ID2SChunkInfo, PNTR ID2SChunkInfoPtr;
+
+
+NLM_EXTERN ID2SChunkInfoPtr LIBCALL ID2SChunkInfoFree PROTO ((ID2SChunkInfoPtr ));
+NLM_EXTERN ID2SChunkInfoPtr LIBCALL ID2SChunkInfoNew PROTO (( void ));
+NLM_EXTERN ID2SChunkInfoPtr LIBCALL ID2SChunkInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SChunkInfoAsnWrite PROTO (( ID2SChunkInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SBioseqInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Bioseq_Info {
+   Int4   gap_count;
+   Uint1   seq_map_has_ref;
+   struct struct_ID2S_Sequence_Split_Info PNTR   sequence_split;
+} ID2SBioseqInfo, PNTR ID2SBioseqInfoPtr;
+
+
+NLM_EXTERN ID2SBioseqInfoPtr LIBCALL ID2SBioseqInfoFree PROTO ((ID2SBioseqInfoPtr ));
+NLM_EXTERN ID2SBioseqInfoPtr LIBCALL ID2SBioseqInfoNew PROTO (( void ));
+NLM_EXTERN ID2SBioseqInfoPtr LIBCALL ID2SBioseqInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SBioseqInfoAsnWrite PROTO (( ID2SBioseqInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2IdRange
+*
+**************************************************/
+typedef struct struct_ID2_Id_Range {
+   struct struct_ID2_Id_Range PNTR next;
+   Int4   start;
+   Int4   count;
+} ID2IdRange, PNTR ID2IdRangePtr;
+
+
+NLM_EXTERN ID2IdRangePtr LIBCALL ID2IdRangeFree PROTO ((ID2IdRangePtr ));
+NLM_EXTERN ID2IdRangePtr LIBCALL ID2IdRangeNew PROTO (( void ));
+NLM_EXTERN ID2IdRangePtr LIBCALL ID2IdRangeAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2IdRangeAsnWrite PROTO (( ID2IdRangePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SSequenceSplitInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Sequence_Split_Info {
+   Int4   block_size;
+   Int4   chunk_start;
+   ValNodePtr   chunk_blocks;
+} ID2SSequenceSplitInfo, PNTR ID2SSequenceSplitInfoPtr;
+
+
+NLM_EXTERN ID2SSequenceSplitInfoPtr LIBCALL ID2SSequenceSplitInfoFree PROTO ((ID2SSequenceSplitInfoPtr ));
+NLM_EXTERN ID2SSequenceSplitInfoPtr LIBCALL ID2SSequenceSplitInfoNew PROTO (( void ));
+NLM_EXTERN ID2SSequenceSplitInfoPtr LIBCALL ID2SSequenceSplitInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SSequenceSplitInfoAsnWrite PROTO (( ID2SSequenceSplitInfoPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr ID2SChunkContentPtr;
+typedef ValNode ID2SChunkContent;
+#define ID2SChunkContent_seq_descr 1
+#define ID2SChunkContent_seq_annot 2
+#define ID2SChunkContent_seq_assembly 3
+#define ID2SChunkContent_seq_map 4
+#define ID2SChunkContent_seq_data 5
+
+
+NLM_EXTERN ID2SChunkContentPtr LIBCALL ID2SChunkContentFree PROTO ((ID2SChunkContentPtr ));
+NLM_EXTERN ID2SChunkContentPtr LIBCALL ID2SChunkContentAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SChunkContentAsnWrite PROTO (( ID2SChunkContentPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SSeqDescrInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Seq_descr_Info {
+   Int4   type_mask;
+   struct struct_ID2_Id_Range PNTR   bioseqs;
+   struct struct_ID2_Id_Range PNTR   bioseq_sets;
+} ID2SSeqDescrInfo, PNTR ID2SSeqDescrInfoPtr;
+
+
+NLM_EXTERN ID2SSeqDescrInfoPtr LIBCALL ID2SSeqDescrInfoFree PROTO ((ID2SSeqDescrInfoPtr ));
+NLM_EXTERN ID2SSeqDescrInfoPtr LIBCALL ID2SSeqDescrInfoNew PROTO (( void ));
+NLM_EXTERN ID2SSeqDescrInfoPtr LIBCALL ID2SSeqDescrInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SSeqDescrInfoAsnWrite PROTO (( ID2SSeqDescrInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SSeqAnnotInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Seq_annot_Info {
+   CharPtr   name;
+   Uint1   align;
+   Uint1   graph;
+   struct struct_ID2S_Feat_type_Info PNTR   feat;
+   ValNodePtr   seq_loc;
+} ID2SSeqAnnotInfo, PNTR ID2SSeqAnnotInfoPtr;
+
+
+NLM_EXTERN ID2SSeqAnnotInfoPtr LIBCALL ID2SSeqAnnotInfoFree PROTO ((ID2SSeqAnnotInfoPtr ));
+NLM_EXTERN ID2SSeqAnnotInfoPtr LIBCALL ID2SSeqAnnotInfoNew PROTO (( void ));
+NLM_EXTERN ID2SSeqAnnotInfoPtr LIBCALL ID2SSeqAnnotInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SSeqAnnotInfoAsnWrite PROTO (( ID2SSeqAnnotInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SSeqAssemblyInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Seq_assembly_Info {
+   struct struct_ID2_Id_Range PNTR   bioseqs;
+} ID2SSeqAssemblyInfo, PNTR ID2SSeqAssemblyInfoPtr;
+
+
+NLM_EXTERN ID2SSeqAssemblyInfoPtr LIBCALL ID2SSeqAssemblyInfoFree PROTO ((ID2SSeqAssemblyInfoPtr ));
+NLM_EXTERN ID2SSeqAssemblyInfoPtr LIBCALL ID2SSeqAssemblyInfoNew PROTO (( void ));
+NLM_EXTERN ID2SSeqAssemblyInfoPtr LIBCALL ID2SSeqAssemblyInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SSeqAssemblyInfoAsnWrite PROTO (( ID2SSeqAssemblyInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SSeqMapInfo
+*
+**************************************************/
+#define ID2SSeqMapInfo  ValNode
+#define ID2SSeqMapInfoPtr  ValNodePtr
+#define ID2SSeqMapInfoFree  ValNodeFree
+#define ID2SSeqMapInfoNew  ValNodeNew
+#define ID2SSeqMapInfoAsnRead  ValNodeAsnRead
+#define ID2SSeqMapInfoAsnWrite  ValNodeAsnWrite
+
+
+/**************************************************
+*
+*    ID2SSeqDataInfo
+*
+**************************************************/
+#define ID2SSeqDataInfo  ValNode
+#define ID2SSeqDataInfoPtr  ValNodePtr
+#define ID2SSeqDataInfoFree  ValNodeFree
+#define ID2SSeqDataInfoNew  ValNodeNew
+#define ID2SSeqDataInfoAsnRead  ValNodeAsnRead
+#define ID2SSeqDataInfoAsnWrite  ValNodeAsnWrite
+
+
+/**************************************************
+*
+*    ID2SFeatTypeInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Feat_type_Info {
+   struct struct_ID2S_Feat_type_Info PNTR next;
+   Int4   type;
+   ValNodePtr   subtypes;
+} ID2SFeatTypeInfo, PNTR ID2SFeatTypeInfoPtr;
+
+
+NLM_EXTERN ID2SFeatTypeInfoPtr LIBCALL ID2SFeatTypeInfoFree PROTO ((ID2SFeatTypeInfoPtr ));
+NLM_EXTERN ID2SFeatTypeInfoPtr LIBCALL ID2SFeatTypeInfoNew PROTO (( void ));
+NLM_EXTERN ID2SFeatTypeInfoPtr LIBCALL ID2SFeatTypeInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SFeatTypeInfoAsnWrite PROTO (( ID2SFeatTypeInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SChunk
+*
+**************************************************/
+typedef struct struct_ID2S_Chunk {
+   struct struct_ID2S_Chunk_Data PNTR   data;
+} ID2SChunk, PNTR ID2SChunkPtr;
+
+
+NLM_EXTERN ID2SChunkPtr LIBCALL ID2SChunkFree PROTO ((ID2SChunkPtr ));
+NLM_EXTERN ID2SChunkPtr LIBCALL ID2SChunkNew PROTO (( void ));
+NLM_EXTERN ID2SChunkPtr LIBCALL ID2SChunkAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SChunkAsnWrite PROTO (( ID2SChunkPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SChunkData
+*
+**************************************************/
+typedef struct struct_ID2S_Chunk_Data {
+   struct struct_ID2S_Chunk_Data PNTR next;
+   ValNodePtr   Id_id;
+   ValNodePtr   descrs;
+   struct struct_Seq_annot PNTR   annots;
+   struct struct_Seq_align PNTR   assembly;
+   struct struct_Seq_literal PNTR   seq_map;
+   struct struct_Seq_literal PNTR   seq_data;
+} ID2SChunkData, PNTR ID2SChunkDataPtr;
+
+
+NLM_EXTERN ID2SChunkDataPtr LIBCALL ID2SChunkDataFree PROTO ((ID2SChunkDataPtr ));
+NLM_EXTERN ID2SChunkDataPtr LIBCALL ID2SChunkDataNew PROTO (( void ));
+NLM_EXTERN ID2SChunkDataPtr LIBCALL ID2SChunkDataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SChunkDataAsnWrite PROTO (( ID2SChunkDataPtr , AsnIoPtr, AsnTypePtr));
+
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+typedef ValNodePtr Id_idPtr;
+typedef ValNode Id_id;
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+#define Id_id_bioseq_set 1
+#define Id_id_gi 2
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+static Id_idPtr LIBCALL Id_idFree PROTO ((Id_idPtr ));
+static Id_idPtr LIBCALL Id_idAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+static Boolean LIBCALL Id_idAsnWrite PROTO (( Id_idPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    ID2Interval
+*
+**************************************************/
+typedef struct struct_ID2_Interval {
+   Int4   gi;
+   Int4   start;
+   Int4   length;
+} ID2Interval, PNTR ID2IntervalPtr;
+
+
+NLM_EXTERN ID2IntervalPtr LIBCALL ID2IntervalFree PROTO ((ID2IntervalPtr ));
+NLM_EXTERN ID2IntervalPtr LIBCALL ID2IntervalNew PROTO (( void ));
+NLM_EXTERN ID2IntervalPtr LIBCALL ID2IntervalAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2IntervalAsnWrite PROTO (( ID2IntervalPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2PackedSeqInts
+*
+**************************************************/
+typedef struct struct_ID2_Packed_Seq_ints {
+   Int4   gi;
+   struct struct_ID2_Seq_range PNTR   ints;
+} ID2PackedSeqInts, PNTR ID2PackedSeqIntsPtr;
+
+
+NLM_EXTERN ID2PackedSeqIntsPtr LIBCALL ID2PackedSeqIntsFree PROTO ((ID2PackedSeqIntsPtr ));
+NLM_EXTERN ID2PackedSeqIntsPtr LIBCALL ID2PackedSeqIntsNew PROTO (( void ));
+NLM_EXTERN ID2PackedSeqIntsPtr LIBCALL ID2PackedSeqIntsAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2PackedSeqIntsAsnWrite PROTO (( ID2PackedSeqIntsPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2SeqRange
+*
+**************************************************/
+typedef struct struct_ID2_Seq_range {
+   struct struct_ID2_Seq_range PNTR next;
+   Int4   start;
+   Int4   length;
+} ID2SeqRange, PNTR ID2SeqRangePtr;
+
+
+NLM_EXTERN ID2SeqRangePtr LIBCALL ID2SeqRangeFree PROTO ((ID2SeqRangePtr ));
+NLM_EXTERN ID2SeqRangePtr LIBCALL ID2SeqRangeNew PROTO (( void ));
+NLM_EXTERN ID2SeqRangePtr LIBCALL ID2SeqRangeAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SeqRangeAsnWrite PROTO (( ID2SeqRangePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2Param
+*
+**************************************************/
+typedef struct struct_ID2_Param {
+   struct struct_ID2_Param PNTR next;
+   CharPtr   name;
+   ValNodePtr   value;
+   Uint2   type;
+   /* following #defines are for enumerated type, not used by object loaders */
+#define ID2_Param_type_set_value 1
+#define ID2_Param_type_get_value 2
+#define ID2_Param_type_force_value 3
+#define ID2_Param_type_use_package 4
+
+} ID2Param, PNTR ID2ParamPtr;
+
+
+NLM_EXTERN ID2ParamPtr LIBCALL ID2ParamFree PROTO ((ID2ParamPtr ));
+NLM_EXTERN ID2ParamPtr LIBCALL ID2ParamNew PROTO (( void ));
+NLM_EXTERN ID2ParamPtr LIBCALL ID2ParamAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2ParamAsnWrite PROTO (( ID2ParamPtr , AsnIoPtr, AsnTypePtr));
+
+#ifdef __cplusplus
+/* { */ }
+#endif
+
+#endif /* _id2gen_ */
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
diff --git a/network/id2arch/id2map.h b/network/id2arch/id2map.h
new file mode 100644
index 00000000..937324db
--- /dev/null
+++ b/network/id2arch/id2map.h
@@ -0,0 +1,10 @@
+#include <objsset.h>
+
+#define NLM_EXTERN_LOADS {if (! SeqSetAsnLoad())return FALSE; \
+                          }
+#define struct_Seq_hist seqhist
+#define SeqLiteralAsnRead  SeqLitAsnRead
+#define SeqLiteralAsnWrite SeqLitAsnWrite
+#define SeqLiteralFree     SeqLitFree
+#define struct_ID2Param    struct_ID2_Param
+#define ID2_SEQ_LOC_int__  ID2_SEQ_LOC_int
diff --git a/network/nsclilib/readme b/network/nsclilib/readme
index c68748ad..2e716917 100644
--- a/network/nsclilib/readme
+++ b/network/nsclilib/readme
@@ -87,9 +87,9 @@ Value:
 | SRV_PROXY_HOST:5859       --> 130.14.22.2:5859  RETIRED  -- DO NOT USE!
 | SRV_PROXY_HOST:5840       --> 130.14.22.8:5840  RETIRED  -- DO NOT USE!
 | SRV_PROXY_HOST:5810       --> 130.14.22.30:5810 RETIRED  -- DO NOT USE!
+| SRV_PROXY_HOST:5812       --> 130.14.22.31:5812 RETIRED  -- DO NOT USE!
+| SRV_PROXY_HOST:5811       --> 130.14.22.32:5811 RETIRED  -- DO NOT USE!
 | SRV_PROXY_HOST:5845       --> 130.14.22.12:5845 INTERNAL
-| SRV_PROXY_HOST:5812       --> 130.14.22.31:5812 OBSOLESCENT
-| SRV_PROXY_HOST:5811       --> 130.14.22.32:5811 OBSOLESCENT
 | SRV_PROXY_HOST:5850..5860 --> 130.14.29.112:5850..5860
 | 
 | NOTE:  It's pretty rare (if ever) when you have to use
@@ -189,4 +189,4 @@ Solaris or IRIX. Then, the client must run on the host that:
 a) belongs to one of NCBI subnets and
 b) has "lbdaemon"(load-balance daemon) application running on it.
 
-$Date: 2003/09/29 15:05:10 $
+$Date: 2004/01/16 19:03:45 $
diff --git a/network/spell/client/objspell.c b/network/spell/client/objspell.c
new file mode 100644
index 00000000..5c7a496b
--- /dev/null
+++ b/network/spell/client/objspell.c
@@ -0,0 +1,425 @@
+/*
+*
+*
+* RCS Modification History:
+* $Log: objspell.c,v $
+* Revision 6.0  1997/08/25 18:40:24  madden
+* Revision changed to 6.0
+*
+* Revision 4.0  1995/07/26 13:55:42  ostell
+* force revision to 4.0
+*
+ * Revision 1.2  1995/05/17  17:59:51  epstein
+ * add RCS log revision history
+ *
+*/
+
+#include <asn.h>
+
+#define NLM_GENERATED_CODE_PROTO
+
+#include "objspell.h"
+
+static Boolean loaded = FALSE;
+
+#include "spell.h"
+
+#ifndef NLM_EXTERN_LOADS
+#define NLM_EXTERN_LOADS {}
+#endif
+
+static Boolean
+objspellAsnLoad(void)
+{
+
+   if ( ! loaded) {
+      NLM_EXTERN_LOADS
+
+      if ( ! AsnLoad ())
+      return FALSE;
+      loaded = TRUE;
+   }
+
+   return TRUE;
+}
+
+
+
+/**************************************************
+*    Generated object loaders for Module NCBI-SPELL
+*
+**************************************************/
+
+
+/**************************************************
+*
+*    SpellRequestFree()
+*
+**************************************************/
+
+SpellRequestPtr LIBCALL
+SpellRequestFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case SpellRequest_spelltext:
+      MemFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    SpellRequestAsnRead()
+*
+**************************************************/
+
+SpellRequestPtr LIBCALL
+SpellRequestAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objspellAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SpellRequest ::= (self contained) */
+      atp = AsnReadId(aip, amp, SPELL_REQUEST);
+   } else {
+      atp = AsnLinkType(orig, SPELL_REQUEST);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == SPELL_REQUEST_init) {
+      choice = SpellRequest_init;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == SPELL_REQUEST_spelltext) {
+      choice = SpellRequest_spelltext;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.ptrvalue = av.ptrvalue;
+   }
+   else if (atp == SPELL_REQUEST_fini) {
+      choice = SpellRequest_fini;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    SpellRequestAsnWrite()
+*
+**************************************************/
+Boolean LIBCALL 
+SpellRequestAsnWrite(SpellRequestPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objspellAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, SPELL_REQUEST);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   av.intvalue = anp->data.intvalue;
+   switch (anp->choice)
+   {
+   case SpellRequest_init:
+      retval = AsnWrite(aip, SPELL_REQUEST_init, &av);
+      break;
+   case SpellRequest_spelltext:
+      retval = AsnWrite(aip, SPELL_REQUEST_spelltext, &av);
+      break;
+   case SpellRequest_fini:
+      retval = AsnWrite(aip, SPELL_REQUEST_fini, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    SpellResponseFree()
+*
+**************************************************/
+
+SpellResponsePtr LIBCALL
+SpellResponseFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case SpellResponse_spelltext:
+      AsnGenericBaseSeqOfFree((ValNodePtr) pnt,ASNCODE_PTRVAL_SLOT);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    SpellResponseAsnRead()
+*
+**************************************************/
+
+SpellResponsePtr LIBCALL
+SpellResponseAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objspellAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SpellResponse ::= (self contained) */
+      atp = AsnReadId(aip, amp, SPELL_RESPONSE);
+   } else {
+      atp = AsnLinkType(orig, SPELL_RESPONSE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == SPELL_RESPONSE_error) {
+      choice = SpellResponse_error;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == SPELL_RESPONSE_init) {
+      choice = SpellResponse_init;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == SPELL_RESPONSE_spelltext) {
+      choice = SpellResponse_spelltext;
+      anp -> data.ptrvalue = 
+      AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_PTRVAL_SLOT, &isError);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   else if (atp == SPELL_RESPONSE_fini) {
+      choice = SpellResponse_fini;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    SpellResponseAsnWrite()
+*
+**************************************************/
+Boolean LIBCALL 
+SpellResponseAsnWrite(SpellResponsePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objspellAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, SPELL_RESPONSE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   av.intvalue = anp->data.intvalue;
+   switch (anp->choice)
+   {
+   case SpellResponse_error:
+      retval = AsnWrite(aip, SPELL_RESPONSE_error, &av);
+      break;
+   case SpellResponse_init:
+      retval = AsnWrite(aip, SPELL_RESPONSE_init, &av);
+      break;
+   case SpellResponse_spelltext:
+      retval = AsnGenericBaseSeqOfAsnWrite((Pointer) pnt,ASNCODE_PTRVAL_SLOT, aip, SPELL_RESPONSE_spelltext, SPELL_RESPONSE_spelltext_E);            break;
+   case SpellResponse_fini:
+      retval = AsnWrite(aip, SPELL_RESPONSE_fini, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
diff --git a/network/spell/client/objspell.h b/network/spell/client/objspell.h
new file mode 100644
index 00000000..607d3c6d
--- /dev/null
+++ b/network/spell/client/objspell.h
@@ -0,0 +1,57 @@
+/*
+*
+*
+* RCS Modification History:
+* $Log: objspell.h,v $
+* Revision 6.0  1997/08/25 18:40:26  madden
+* Revision changed to 6.0
+*
+* Revision 4.0  1995/07/26 13:55:42  ostell
+* force revision to 4.0
+*
+ * Revision 1.2  1995/05/17  17:59:53  epstein
+ * add RCS log revision history
+ *
+*/
+
+#ifndef _objspell_ 
+#define _objspell_ 
+
+#ifdef __cplusplus
+extern "C" { /* } */
+#endif
+
+
+/**************************************************
+*
+*    Generated objects for Module NCBI-SPELL
+*
+**************************************************/
+typedef ValNodePtr SpellRequestPtr;
+typedef ValNode SpellRequest;
+#define SpellRequest_init 1
+#define SpellRequest_spelltext 2
+#define SpellRequest_fini 3
+
+
+SpellRequestPtr LIBCALL SpellRequestFree PROTO ((SpellRequestPtr ));
+SpellRequestPtr LIBCALL SpellRequestAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+Boolean LIBCALL SpellRequestAsnWrite PROTO (( SpellRequestPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr SpellResponsePtr;
+typedef ValNode SpellResponse;
+#define SpellResponse_error 1
+#define SpellResponse_init 2
+#define SpellResponse_spelltext 3
+#define SpellResponse_fini 4
+
+
+SpellResponsePtr LIBCALL SpellResponseFree PROTO ((SpellResponsePtr ));
+SpellResponsePtr LIBCALL SpellResponseAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+Boolean LIBCALL SpellResponseAsnWrite PROTO (( SpellResponsePtr , AsnIoPtr, AsnTypePtr));
+
+#ifdef __cplusplus
+/* { */ }
+#endif
+
+#endif
diff --git a/network/spell/client/spell.asn b/network/spell/client/spell.asn
new file mode 100644
index 00000000..af69260e
--- /dev/null
+++ b/network/spell/client/spell.asn
@@ -0,0 +1,27 @@
+--
+--********************************************************************
+--
+--  Spell checker for MEDLINE
+--  Jonathan Epstein
+--  June 1994
+--
+--
+--********************************************************************
+
+NCBI-SPELL DEFINITIONS ::=
+BEGIN
+
+Spell-request ::= CHOICE {
+    init NULL ,
+    spelltext VisibleString ,
+    fini NULL
+}
+
+Spell-response ::= CHOICE {
+    error INTEGER ,
+    init NULL ,
+    spelltext SEQUENCE OF VisibleString ,
+    fini NULL
+}
+
+END
diff --git a/network/spell/client/spellapi.c b/network/spell/client/spellapi.c
new file mode 100644
index 00000000..42fadaad
--- /dev/null
+++ b/network/spell/client/spellapi.c
@@ -0,0 +1,453 @@
+/*
+*
+*
+* RCS Modification History:
+* $Log: spellapi.c,v $
+* Revision 6.1  1998/02/03 16:51:12  shavirin
+* Removed some memory leaks.
+*
+* Revision 6.0  1997/08/25 18:40:31  madden
+* Revision changed to 6.0
+*
+* Revision 4.0  1995/07/26 13:55:42  ostell
+* force revision to 4.0
+*
+ * Revision 1.7  1995/05/31  21:12:10  ostell
+ * added SpellCheckData() to return user supplied data ptr and eliminate
+ * the need for global static variables by calling functions
+ *
+ * Revision 1.6  1995/05/17  17:59:56  epstein
+ * add RCS log revision history
+ *
+*/
+
+#include <ncbinet.h>
+#include "spellapi.h"
+#include "objspell.h"
+
+static SpellResponsePtr NetSpellReadAsn PROTO((void));
+static Boolean ReestablishNetSpell PROTO((void));
+static Boolean NetInit PROTO((void));
+static Boolean ForceNetInit PROTO((void));
+static Boolean NetFini PROTO((void));
+static Boolean GenericReestablishNet PROTO((CharPtr svcName, Boolean showErrs)); 
+static NI_HandPtr svcp = NULL;
+static AsnIoPtr   asnin = NULL;
+static AsnIoPtr   asnout = NULL;
+SpellRequestPtr sprp;
+SpellResponsePtr spbp;
+static Boolean num_attached = 0;
+static Boolean reallyFinal = TRUE;
+static NI_DispatcherPtr dispatcher;
+static Boolean (*myNetInit) PROTO((void));
+
+ 
+  
+
+/*****************************************************************************
+*
+*   SpellInit ()
+*
+*****************************************************************************/
+
+Boolean SpellInit (void)
+
+{
+    DataVal    av;
+
+    myNetInit = SpellInit;
+
+    if (! NetInit())
+        return FALSE;
+
+    svcp = NI_GenericGetService(dispatcher, NULL, "SPELL", "Spell", TRUE);
+    if (svcp == NULL)
+    {
+        ErrPostEx(SEV_ERROR, 0, 0, "NI_ServiceGet [%s] (%s)", ni_errlist[ni_errno], ni_errtext);
+        SpellFini();
+        return FALSE;
+    }
+
+    asnin = svcp->raip;
+    asnout = svcp->waip;
+
+    /**********************************************************/
+
+    sprp = ValNodeNew(NULL);
+    sprp->choice = SpellRequest_init;
+    SpellRequestAsnWrite (sprp, asnout, NULL);
+    AsnIoReset(asnout);
+    SpellRequestFree (sprp);
+
+    if ((spbp = NetSpellReadAsn()) == NULL)
+    {
+        return FALSE;
+    }
+    else
+    {
+        spbp->data.ptrvalue = NULL;
+        SpellResponseFree (spbp);
+        return TRUE;
+    }
+}
+
+/*****************************************************************************
+*
+*   SpellFini ()
+*
+*****************************************************************************/
+
+static Boolean s_SpellFini (void)
+
+{
+    Boolean retval = TRUE;
+
+    if (asnout != NULL && asnin != NULL)
+    {
+        sprp = ValNodeNew(NULL);
+        sprp->choice = SpellRequest_fini;
+        SpellRequestAsnWrite (sprp, asnout, NULL);
+        AsnIoReset(asnout);
+        SpellRequestFree (sprp);
+
+        if ((spbp = NetSpellReadAsn()) == NULL)
+        {
+            retval = FALSE;
+        }
+        else
+        {
+            spbp->data.ptrvalue = NULL;
+            SpellResponseFree (spbp);
+            retval = TRUE;
+        }
+    }
+
+    NetFini();
+    return retval;
+}
+
+/* the only thing done here is to suppress errors */
+
+Boolean SpellFini (void)
+
+{
+    short erract;
+    ErrDesc err;
+    Boolean retval;
+
+    ErrGetOpts(&erract, NULL);
+    ErrSetOpts(ERR_IGNORE, 0);
+    ErrFetch(&err);
+
+    retval = s_SpellFini();
+
+    ErrSetOpts(erract, 0);
+    ErrFetch(&err);
+
+    return retval;
+}
+
+static ValNodePtr
+s_SpellCheck(CharPtr str)
+{
+    SpellRequestPtr sprp;
+    ValNodePtr retval;
+
+    sprp = ValNodeNew(NULL);
+    sprp->choice = SpellRequest_spelltext;
+    sprp->data.ptrvalue = str;
+    SpellRequestAsnWrite(sprp, asnout, NULL);
+    AsnIoReset(asnout);
+    sprp->data.ptrvalue = NULL;
+
+    if ((spbp = NetSpellReadAsn()) == NULL )
+        return NULL;
+
+    if (spbp->choice != SpellResponse_spelltext)
+    {
+        SpellResponseFree( sprp );
+        return NULL;
+    }
+    retval = (ValNodePtr) spbp->data.ptrvalue;
+    spbp->data.ptrvalue = NULL;
+
+    SpellResponseFree(sprp);
+    SpellResponseFree(spbp);
+ 
+    return retval;
+}
+
+int SpellCheck(CharPtr str, void (*CallBack)(CharPtr))
+{
+    Int4 i;
+    short erract;
+    ErrDesc err;
+    ValNodePtr vnp = NULL;
+    ValNodePtr v;
+    int retval = 0;
+    CharPtr p;
+    CharPtr str2;
+
+    if (str == NULL)
+        return 0;
+
+    /* convert the string, converting characters which may not appear in */
+    /* a VisibleString to blanks                                         */
+    str2 = StringSave(str);
+    for (p = str2; *p; p++)
+    {
+        if (*p < ' ' || *p >= 0x7f)
+            *p = ' ';
+    }
+
+    for (i = 0; i < SPELL_SERV_RETRIES; i++)
+    {
+        if (i > 0)
+        {
+            if (! ReestablishNetSpell())
+                break;
+        }
+    
+        ErrGetOpts(&erract, NULL);
+        ErrSetOpts(ERR_IGNORE, 0);
+        ErrFetch(&err);
+
+        vnp = s_SpellCheck(str2);
+
+        ErrSetOpts(erract, 0);
+        if (! ErrFetch(&err))
+            break; /* success */
+    }
+
+    for (v = vnp; v != NULL; v = v->next)
+    {
+        if (CallBack != NULL)
+            CallBack((CharPtr) v->data.ptrvalue);
+        retval++;
+    }
+    ValNodeFreeData(vnp);
+
+    MemFree(str2);
+
+    return retval;
+}
+
+int SpellCheckData(CharPtr str, void (*CallBack)(CharPtr, Pointer), Pointer userdata)
+{
+    Int4 i;
+    short erract;
+    ErrDesc err;
+    ValNodePtr vnp = NULL;
+    ValNodePtr v;
+    int retval = 0;
+    CharPtr p;
+    CharPtr str2;
+
+    if (str == NULL)
+        return 0;
+
+    /* convert the string, converting characters which may not appear in */
+    /* a VisibleString to blanks                                         */
+    str2 = StringSave(str);
+    for (p = str2; *p; p++)
+    {
+        if (*p < ' ' || *p >= 0x7f)
+            *p = ' ';
+    }
+
+    for (i = 0; i < SPELL_SERV_RETRIES; i++)
+    {
+        if (i > 0)
+        {
+            if (! ReestablishNetSpell())
+                break;
+        }
+    
+        ErrGetOpts(&erract, NULL);
+        ErrSetOpts(ERR_IGNORE, 0);
+        ErrFetch(&err);
+
+        vnp = s_SpellCheck(str2);
+
+        ErrSetOpts(erract, 0);
+        if (! ErrFetch(&err))
+            break; /* success */
+    }
+
+    for (v = vnp; v != NULL; v = v->next)
+    {
+        if (CallBack != NULL)
+            CallBack((CharPtr) v->data.ptrvalue, userdata);
+        retval++;
+    }
+    ValNodeFreeData(vnp);
+
+    return retval;
+}
+
+int StringInMedline(CharPtr String, void (*CallBack)(CharPtr))
+{
+    int retval;
+
+    if (! SpellInit())
+    {
+        return 0;
+    }
+    retval = SpellCheck(String, CallBack);
+    SpellFini();
+
+    return retval;
+}
+
+
+/*****************************************************************************
+*
+*   NetSpellReadAsn ()
+*
+*****************************************************************************/
+
+static SpellResponsePtr NetSpellReadAsn(void)
+{
+    SpellResponsePtr spbp;
+    short erract;
+    ErrDesc err;
+
+    ErrGetOpts(&erract, NULL);
+    ErrSetOpts(ERR_IGNORE, 0);
+    ErrFetch(&err); /* clear any pending error */
+
+    spbp = SpellResponseAsnRead(asnin, NULL);
+
+    if (ErrFetch(&err))
+    {
+        ErrPost(CTX_UNKNOWN, 1, "Null message read from server");
+    }
+    ErrSetOpts(erract, 0);
+
+    return spbp;
+}
+
+/*****************************************************************************
+*
+*   ReestablishNetSpell ()
+*
+*****************************************************************************/
+
+static Boolean ReestablishNetSpell(void)
+{
+    return GenericReestablishNet("Spell", TRUE);
+}
+
+/*****************************************************************************
+*
+*   GenericReestablishNet ()
+*
+*****************************************************************************/
+
+static Boolean GenericReestablishNet(CharPtr svcName, Boolean showErrs)
+{
+    Handle mon = NULL;
+    Boolean retval;
+    CharPtr buf;
+
+    buf = MemNew(2 * StrLen(svcName) + 60);
+
+    if (showErrs) {
+        sprintf (buf, "Re-establishing %s Service", svcName);
+        mon = MonitorStrNew(buf, 40);
+        sprintf (buf, "Requesting %s service", svcName);
+        MonitorStrValue(mon, buf);
+    }
+    NetFini();
+    retval = TRUE;
+
+    if (! myNetInit())
+    {
+        sprintf (buf, "%s get failed; re-contacting dispatcher", svcName);
+        MonitorStrValue(mon, buf);
+        retval = FALSE;
+        if (ForceNetInit())
+        { /* successfully established contact w/dispatcher */
+            sprintf (buf, "%s get failed; re-requesting %s service",
+                     svcName, svcName);
+            MonitorStrValue(mon, buf);
+            retval = myNetInit();
+        }
+        else {
+            ErrPost(CTX_UNKNOWN, 1, "Unable to re-contact dispatcher");
+            if (showErrs) {
+                ErrShow();
+            }
+        }
+    }
+
+    MonitorFree(mon);
+
+    if (! retval )
+    {
+        sprintf (buf, "Unable to re-establish %s service", svcName);
+        ErrPost(CTX_UNKNOWN, 1, buf);
+        if (showErrs) {
+            ErrShow();
+        }
+    }
+
+    MemFree(buf);
+    return retval;
+}
+
+/*****************************************************************************
+*
+*   NetInit ()
+*
+*****************************************************************************/
+
+static Boolean
+NetInit(void)
+{
+    if (num_attached++ > 0)
+        return TRUE;
+
+    return ((dispatcher = NI_GenericInit(NULL, NULL, TRUE, NULL, 0)) != NULL);
+}
+
+
+/*****************************************************************************
+*
+*   ForceNetInit ()
+*
+*****************************************************************************/
+
+static Boolean ForceNetInit(void)
+{
+    Boolean retval;
+
+    reallyFinal = FALSE;
+    num_attached = 0; /* force re-attempt to contact dispatcher */
+    retval = NetInit();
+    reallyFinal = TRUE;
+
+    return retval;
+}
+
+/*****************************************************************************
+*
+*   NetFini ()
+*
+*****************************************************************************/
+
+static Boolean NetFini(void)
+{
+   if (num_attached > 0)
+        num_attached--;
+
+    if (num_attached == 0)
+    {
+        NI_ServiceDisconnect(svcp);
+        svcp = NULL;
+        NI_EndServices (dispatcher);
+        dispatcher = NULL;
+    }
+
+    return TRUE;
+}
diff --git a/network/spell/client/spellapi.h b/network/spell/client/spellapi.h
new file mode 100644
index 00000000..6c2ce0e5
--- /dev/null
+++ b/network/spell/client/spellapi.h
@@ -0,0 +1,27 @@
+/*
+*
+*
+* RCS Modification History:
+* $Log: spellapi.h,v $
+* Revision 6.0  1997/08/25 18:40:34  madden
+* Revision changed to 6.0
+*
+* Revision 4.0  1995/07/26 13:55:42  ostell
+* force revision to 4.0
+*
+ * Revision 1.3  1995/05/31  21:12:10  ostell
+ * added SpellCheckData() to return user supplied data ptr and eliminate
+ * the need for global static variables by calling functions
+ *
+ * Revision 1.2  1995/05/17  17:59:58  epstein
+ * add RCS log revision history
+ *
+*/
+
+Boolean SpellInit PROTO((void));
+Boolean SpellFini PROTO((void));
+int SpellCheck PROTO((CharPtr String, void (*CallBack)(CharPtr)));
+int SpellCheckData PROTO((CharPtr String, void (*CallBack)(CharPtr,Pointer), Pointer userdata));
+int StringInMedline PROTO((CharPtr String, void (*CallBack)(CharPtr)));
+
+#define SPELL_SERV_RETRIES 2
diff --git a/network/spell/server/fmspell.c b/network/spell/server/fmspell.c
new file mode 100644
index 00000000..ce5e21c4
--- /dev/null
+++ b/network/spell/server/fmspell.c
@@ -0,0 +1,136 @@
+/* $Id: fmspell.c,v 1.1 1998/02/24 21:01:22 shavirin Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: fmspell.c,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 02/24/1998
+*
+* $Revision: 1.1 $
+*
+* File Description:
+*        Database formatter for NCBI SPELL Service
+*
+* $Log: fmspell.c,v $
+* Revision 1.1  1998/02/24 21:01:22  shavirin
+* Initial revision
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <ncbisort.h>
+#include <ncbisam.h>
+
+#define NUMARG 3
+
+Args fmspell_args[NUMARG] = {
+    { "Input file name for spell database", 
+      "termlist", NULL, NULL, FALSE, 'd', ARG_STRING, 0.0, 0, NULL},
+    {"Input file anme for stop words",
+     "stopwords", NULL,NULL,FALSE,'s',ARG_FILE_IN, 0.0,0,NULL},
+    {"Logfile name:",
+     "fmspell.log", NULL,NULL,TRUE,'l',ARG_FILE_OUT, 0.0,0,NULL}
+};
+
+#define DB_filename    (CharPtr) fmspell_args[0].strvalue 
+#define STOP_filename  (CharPtr) fmspell_args[1].strvalue 
+#define LogFileName    (CharPtr) fmspell_args[2].strvalue  
+
+static Boolean FMSpellCreateIndex(CharPtr db_name)
+{
+    SORTObjectPtr sop;
+    Char filenamebuf[FILENAME_MAX], DBName[FILENAME_MAX];
+    Char ext1[8], ext2[8], ext3[8], ext4[8];
+    FILE *fd_out;
+    CharPtr files;
+    ISAMErrorCode error;
+    ISAMObjectPtr isamp;
+
+    /*  object for unique sorting */
+    
+    if((sop = SORTObjectNew(NULL, '\0', 0,
+                            FALSE, TRUE)) == NULL) { 
+        ErrPostEx(SEV_ERROR, 0, 0, "Failed to create SORT Object");
+        return FALSE;
+    }
+    
+    sprintf(filenamebuf, "%s.tmp", db_name); 
+    
+    if((fd_out = FileOpen(filenamebuf, "w")) == NULL)
+        return FALSE;
+    
+    files = db_name;
+    
+    SORTFiles(&files, 1, fd_out, sop);
+    SORTObjectFree(sop);
+    
+    FileClose(fd_out);
+    FileRename(filenamebuf, db_name);
+    
+    sprintf(filenamebuf, "%s.idx", db_name); 
+    
+    if((isamp = ISAMObjectNew(ISAMString, db_name, 
+                              filenamebuf)) == NULL) {
+        ErrPostEx(SEV_ERROR, 0, 0, "Creating of ISAM object failed");
+        return FALSE;
+    }
+    
+    if((error = ISAMMakeIndex(isamp, 0)) != ISAMNoError) {
+        ErrPostEx(SEV_ERROR, 0, 0, "Creating of index failed with "
+                  "error code %ld\n", (long) error);
+        ISAMObjectFree(isamp);
+        return FALSE;
+    } 
+    
+    ISAMObjectFree(isamp);
+    
+    return TRUE;
+}
+
+Int2 Main(void)
+{
+
+    if ( !GetArgs ("fmspell", NUMARG, fmspell_args) ) {
+        return -1;
+    }
+    if ( !ErrSetLog (LogFileName) ) {
+        ErrShow();
+    } else {
+        ErrSetOpts (ERR_CONTINUE, ERR_LOG_ON);
+    }
+    
+    if(!FMSpellCreateIndex(DB_filename))
+        return 1;
+    
+    if(!FMSpellCreateIndex(STOP_filename))
+        return 1;
+    
+    ErrPostEx(SEV_INFO, 0, 0, "Formating finished successfuly");
+
+    return 0;
+}
diff --git a/network/spell/server/spellsrv.c b/network/spell/server/spellsrv.c
new file mode 100644
index 00000000..fcc169d2
--- /dev/null
+++ b/network/spell/server/spellsrv.c
@@ -0,0 +1,414 @@
+/* $Id: spellsrv.c,v 1.2 1998/02/25 19:33:01 shavirin Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: spellsrv.c,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 02/24/1998
+*
+* $Revision: 1.2 $
+*
+* File Description:
+*        Main file for NCBI SPELL Service
+*
+* $Log: spellsrv.c,v $
+* Revision 1.2  1998/02/25 19:33:01  shavirin
+* Added additional filtering of words.
+*
+*
+* ==========================================================================
+*/
+#include <ncbi.h>
+#include <ncbinet.h>
+#include <objspell.h>
+#include <ncbisam.h>
+
+#define SPELL_MAX_WORD_SIZE 512
+#define NUMARG 5
+
+#define IS_VALID(c) (isalnum(c) || ((c) == '-') || ((c) == '+') || ((c) == '_') || ((c) == '&') || ((c) == '\'') || ((c) == '`'))
+
+Args spellsrv_args[NUMARG] = {
+    { "Input file name for spell database", 
+      "termlist", NULL, NULL, TRUE, 't', ARG_STRING, 0.0, 0, NULL},
+    {"Input file anme for stop words",
+     "stopwords", NULL,NULL, TRUE,'s',ARG_FILE_IN, 0.0,0,NULL},
+    {"Logfile name:",
+     "/dev/null", NULL,NULL,TRUE,'l',ARG_FILE_OUT, 0.0,0,NULL},
+    {"Debug mode",
+     NULL, NULL,NULL,TRUE,'d',ARG_BOOLEAN, 0.0,0,NULL},
+    {"Standalone mode",
+     NULL, NULL,NULL,TRUE,'z',ARG_BOOLEAN, 0.0,0,NULL}
+};
+
+#define DB_filename    (CharPtr) spellsrv_args[0].strvalue 
+#define STOP_filename  (CharPtr) spellsrv_args[1].strvalue 
+#define LogFileName    (CharPtr) spellsrv_args[2].strvalue  
+#define DebugMode      (CharPtr) spellsrv_args[3].intvalue  
+#define StandAlone     (CharPtr) spellsrv_args[4].intvalue  
+
+typedef struct SPELLData
+{
+    ISAMObjectPtr term_isamp;
+    ISAMObjectPtr stop_isamp;
+} SPELLData, PNTR SPELLDataPtr;
+
+Boolean SPELLSendResponse(Pointer ptr, AsnIoPtr asnout, Int4 error)
+{
+    SpellResponsePtr srp;
+    
+    srp = ValNodeNew(NULL);
+    
+    if (error != NULL) {
+        srp->choice = SpellResponse_error;
+        srp->data.intvalue = error;
+    } else {
+    	srp->choice = SpellResponse_spelltext;
+    	srp->data.ptrvalue = ptr;
+    }
+    
+    SpellResponseAsnWrite(srp, asnout, NULL);
+    
+    srp->data.ptrvalue = NULL;
+    SpellResponseFree(srp);
+}
+
+static Int4 SPELLFindWord(SPELLDataPtr spellp, CharPtr word)
+{
+    Uint4 index;
+    ISAMErrorCode error;
+    
+    if((error = SISAMSearch(spellp->stop_isamp, word, 0, NULL,
+                            NULL, &index)) < 0) {
+        ErrPostEx(SEV_FATAL, 0, 0, "Failed to search string index "
+                  "ISAM Error code is %d\n", error);
+        return error;
+    }
+    
+    /* If word found in "stopwords" - skip main search */
+    
+    if(error == ISAMNoError)
+        return 1;
+    
+    if((error = SISAMSearch(spellp->term_isamp, word, 0, NULL,
+                            NULL, &index)) < 0) {
+        ErrPostEx(SEV_FATAL, 0, 0, "Failed to search string index "
+                  "ISAM Error code is %d\n", error);
+        return error;
+    }
+    
+    if(error == ISAMNoError)
+        return 1;
+    
+    return 0;
+}
+
+static void SPELLGetWord(CharPtr word, CharPtr line, Int4 wordsize) 
+{
+    Int4 x = 0, y = 0;
+    
+    /* Looking for alphanumeric in the beginning of the word */
+
+    for(x = 0; line[x] && !isalnum(line[x]); x++)
+        continue;
+    
+    while(TRUE && y < wordsize) {
+        if(!(word[y] = line[x]))
+            break;
+        if(!IS_VALID(line[x]))
+            break;
+        ++y; ++x;
+    }
+    
+    word[y] = '\0';
+
+    while(line[x] && !isalnum(line[x])) ++x;
+    
+    for(y=0;(line[y] = line[x]);++x,++y);
+}
+
+Boolean SPELLFixWord(CharPtr word)
+{
+    Int4 i, len;
+
+    StrLower(word);
+    len = StringLen(word);
+    
+    /* Testing for all numerics and accessions */
+
+    if(len == 1)
+        return FALSE;
+    
+    if(isdigit(*word)) {
+        for(i = 1; i < len; i++) {
+            if(!(isdigit(word[i]) || ispunct(word[i])))
+                break;
+        }
+
+        if(i == len) return FALSE; /* This is number */
+
+    }
+    
+    /* Testing, that this is 6 length accession */
+    
+    if(len == 6 && isalpha(word[0])) {
+        for(i = 1; i < len; i++) {
+            if(!isdigit(word[i]))
+                break;
+        }
+
+        if (i == len) return FALSE; /* This is accession */
+
+    }
+    
+    if(len == 8 && isalpha(word[0])  && isalpha(word[1])) {
+        for(i = 2; i < len; i++) {
+            if(!isdigit(word[i])) {
+                break;
+            }
+        }
+        
+        if (i == len) return FALSE; /* This is accession */
+        
+    }
+
+    return TRUE;
+}
+
+static ValNodePtr SPELLCheckString(SPELLDataPtr spellp, CharPtr string)
+{
+    Int4 len, i, result;
+    Char word[SPELL_MAX_WORD_SIZE];
+    CharPtr p, chptr, strtmp;
+    ValNodePtr head = NULL, vnp, vnp_l;
+    
+    chptr = strtmp = StringSave(string);
+
+    /* Some usefull filtering */
+    
+    for (p = strtmp; *p; p++) {
+        if (*p < ' ' || *p >= 0x7f)
+            *p = ' ';
+    }
+
+    /* Removing punctuation in the end of the string */
+
+    do {
+        SPELLGetWord(word, strtmp, SPELL_MAX_WORD_SIZE);
+
+        if(!SPELLFixWord(word)) /* FALSE will filter the word */
+            continue;
+
+        if((result = SPELLFindWord(spellp, word)) == 0) { /* not found */
+            if(head == NULL) {
+                head = ValNodeNew(NULL);
+                head->data.ptrvalue = StringSave(word);
+                vnp_l = head;
+            } else {
+                vnp = ValNodeNew(NULL);
+                vnp->data.ptrvalue = StringSave(word);
+                vnp_l->next = vnp;
+                vnp_l = vnp;
+            }
+        } else if(result < 0) {
+            break;
+        } else {
+            continue;
+        }
+    } while (*strtmp != NULLB);
+    
+    MemFree(chptr);
+
+    return head;
+}
+
+static SPELLDataPtr SPELLInit(CharPtr db_name, CharPtr stop_name)
+{
+    SPELLDataPtr spellp;
+    Char buffer[PATH_MAX], buffer1[PATH_MAX];
+    CharPtr path;
+
+    spellp = MemNew(sizeof(SPELLData));
+    
+    if((path = getenv("SPELLCHECKDIR")) == NULL)
+        path = ".";
+    
+    /* Initializing termlist */
+    
+    
+    sprintf(buffer1, "%s/%s", path, db_name);      
+    sprintf(buffer,  "%s/%s.idx", path, db_name);      
+    
+    if(FileLength(buffer) != 0 && FileLength(buffer1) != 0) {
+        if((spellp->term_isamp = ISAMObjectNew(ISAMString, 
+                                               buffer1, buffer)) == NULL) {
+            ErrPostEx(SEV_ERROR, 993, 1, "Failed to create SISAM object");
+            return NULL;
+        }
+    } else {
+        ErrPostEx(SEV_ERROR, 993, 1, 
+                  "Database or index term files do not exists");
+        return NULL;
+    }
+    /* Initializing stopwords list */
+
+    sprintf(buffer1, "%s/%s", path, stop_name);      
+    sprintf(buffer,  "%s/%s.idx", path, stop_name);
+    if(FileLength(buffer) != 0 && FileLength(buffer1) != 0) {
+        if((spellp->stop_isamp = ISAMObjectNew(ISAMString, 
+                                               buffer1, buffer)) == NULL) {
+            ErrPostEx(SEV_ERROR, 993, 1, "Failed to create SISAM object");
+            return NULL;
+        }
+    } else {
+        ErrPostEx(SEV_ERROR, 993, 1, 
+                  "Database or index term files do not exists");
+        return NULL;
+    }
+
+    return spellp;
+}
+static void SPELLFree(SPELLDataPtr spellp)
+{
+    ISAMObjectFree(spellp->term_isamp);
+    ISAMObjectFree(spellp->stop_isamp);
+    
+    MemFree(spellp);
+    return;
+}
+
+Int2 Main(void)
+{
+    SpellRequestPtr splrp;
+    SpellResponsePtr splbp;
+    Boolean done = FALSE;
+    short erract;
+    ErrDesc err;
+    NI_HandPtr hp;
+    Char buf[100];
+    AsnIoPtr asnin;
+    AsnIoPtr asnout;
+    int read_timeout;
+    SPELLDataPtr spellp;
+    ValNodePtr vnp;
+    
+    if (!GetArgs ("spellsrv", NUMARG, spellsrv_args) ) {
+        return -1;
+    }
+    if (!ErrSetLog (LogFileName) ) {
+        ErrShow();
+    } else {
+        ErrSetOpts (ERR_CONTINUE, ERR_LOG_ON);
+    }    
+    
+    if((spellp = SPELLInit(DB_filename, STOP_filename)) == NULL)
+        return 1;
+    
+    if (!StandAlone && !DebugMode) {
+        NI_ServerACK();
+        
+        hp = NI_OpenASNIO();
+        
+        /* this read-timeout is effectively an idle timeout for */
+        /* the server process; the process will terminate upon  */
+        /* read-timeout                                         */
+        GetAppParam("NCBI", "NET_SERV", "SERV_INACT_TIMER", "10",
+                    buf, sizeof buf);
+        read_timeout = atoi(buf) * 60; /* param is minutes */
+        MsgSetReadTimeout(hp, read_timeout);
+        
+        asnin = hp->raip;
+        asnout = hp->waip;
+    } else if (StandAlone) {
+        asnin = AsnIoNew(ASNIO_BIN_IN, stdin, NULL, NULL, NULL);
+        asnout = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);        
+    } else {
+        asnin = AsnIoOpen("spellserv.inp", "r");
+        asnout = AsnIoOpen("spellserv.out", "w");
+    }
+
+    while (!done) {
+        /* encountering EOF on reading is a "normal" occurrence, */
+        /* and does not merit an error message                   */
+        ErrGetOpts(&erract, NULL);
+        ErrSetOpts(ERR_IGNORE, 0);
+        ErrFetch(&err); /* clear any pending error, which can be ignored */
+
+        splrp = SpellRequestAsnRead(asnin, NULL);
+        
+        if (ErrFetch(&err))
+        {
+	    done = TRUE;
+            Message(MSG_POST, "Error encountered on AsnReadId %d", err);
+            break; /* client terminated */
+        }
+        ErrSetOpts(erract, 0);
+
+        if (splrp == NULL)
+        {
+	    done = TRUE;
+            Message(MSG_POST, "Null AsnReadId");
+            break; /* client terminated */
+        }
+
+        switch (splrp->choice) {
+
+        case SpellRequest_init:
+
+            splbp = ValNodeNew(NULL);
+            splbp->choice = SpellResponse_init;
+            splbp->data.ptrvalue = NULL;
+            SpellResponseAsnWrite (splbp, asnout, NULL);
+            SpellResponseFree (splbp);
+            splrp->data.ptrvalue = NULL;
+            break;
+
+        case SpellRequest_spelltext:
+
+            vnp =  SPELLCheckString(spellp, (CharPtr) splrp->data.ptrvalue);
+	    SPELLSendResponse((Pointer) vnp, asnout, 0);
+	    break;
+
+        case SpellRequest_fini:
+
+            done = TRUE;
+            splbp = ValNodeNew(NULL);
+            splbp->choice = SpellResponse_fini;
+            splbp->data.ptrvalue = NULL;
+
+            SpellResponseAsnWrite (splbp, asnout, NULL);
+            SpellResponseFree (splbp);
+            splrp->data.ptrvalue = NULL;
+            break;
+        }
+
+        AsnIoReset (asnout);
+        SpellRequestFree (splrp);
+    }
+
+    AsnIoClose (asnin);
+    AsnIoClose (asnout);
+}
diff --git a/network/taxon1/taxon2/txcdproc.c b/network/taxon1/taxon2/txcdproc.c
index 2aab690f..f8055068 100644
--- a/network/taxon1/taxon2/txcdproc.c
+++ b/network/taxon1/taxon2/txcdproc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   07/15/97
 *
-* $Revision: 1.15 $
+* $Revision: 1.16 $
 *
 * File Description: 
 *       API for Taxonomy service
@@ -44,6 +44,9 @@
 *
 * RCS Modification History:
 * $Log: txcdproc.c,v $
+* Revision 1.16  2003/11/04 17:13:58  soussov
+* adds NetFini() call if service can not start properly
+*
 * Revision 1.15  2003/06/12 16:46:25  soussov
 * changes severity for AsnRead failures
 *
@@ -215,6 +218,7 @@ static Boolean TaxServInit(void)
     Taxon1ReqFree (taxrp);
 
     if((taxbp = NetTaxArchReadAsn()) == NULL) {
+        NetFini();
         return FALSE;
     }
     else  {
diff --git a/network/vibnet/docsum.c b/network/vibnet/docsum.c
index e2b282a0..be09ca80 100644
--- a/network/vibnet/docsum.c
+++ b/network/vibnet/docsum.c
@@ -29,13 +29,16 @@
 *
 * Version Creation Date:   9/13/96
 *
-* $Revision: 6.55 $
+* $Revision: 6.56 $
 *
 * File Description: 
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: docsum.c,v $
+* Revision 6.56  2003/12/02 20:42:06  kans
+* fixed sprintf calls in SetDefaultFailureMessae
+*
 * Revision 6.55  2002/11/06 21:30:57  ucko
 * ChangeViewerLinkData: when extracting a string from vnp->data, use
 * ptrvalue rather than intvalue (which may be the wrong width)
@@ -672,16 +675,16 @@ static CharPtr SetDefaultFailureMessage (SummFormPtr sfp, Int2 item, CharPtr pre
   } else if (sfp->simple != NULL && sfp->uids == NULL) {
     ssp = sfp->simple [item - 1];
     if (ssp == NULL) {
-      sprintf ("%sIncorrect seq-entry for database %s", prefix, dbname);
+      sprintf (tmp, "%sIncorrect seq-entry for database %s", prefix, dbname);
     } else {
       StringCpy (buf, "?");
       if (ssp->numid > 0 && ssp->bestid < ssp->numid) {
         StringNCpy_0 (buf, ssp->id [ssp->bestid], sizeof (buf));
       }
-      sprintf ("%sProblem with sequence %s in %s database", prefix, buf, dbname);
+      sprintf (tmp, "%sProblem with sequence %s in %s database", prefix, buf, dbname);
     }
   } else {
-    sprintf ("%sInternal confusion for database %s", prefix, dbname);
+    sprintf (tmp, "%sInternal confusion for database %s", prefix, dbname);
   }
   return StringSave (tmp);
 }
diff --git a/network/wwwblast/Src/Makefile b/network/wwwblast/Src/Makefile
index 8ea0c4c3..62186b24 100644
--- a/network/wwwblast/Src/Makefile
+++ b/network/wwwblast/Src/Makefile
@@ -14,10 +14,9 @@ THREAD_LIBS = -lpthread
 #NCBI_OTHERLIBS += -lposix4 -lresolv -lsocket -lrpcsvc -lnsl -lgen
 # Solaris Sparc
 #NCBI_OTHERLIBS += -lposix4 -lresolv -lsocket -lrpcsvc -lnsl
-# Darwin
+# MacOS
 #NCBI_OTHERLIBS = -lc
 #THREAD_LIBS =
-#DEFINE = -DDARWIN
 
 #
 CC=cc 
@@ -46,6 +45,8 @@ DEBUG_FLAG = -g
 #OPTIMIZED compilation
 LIBS = $(NCBI_LIBDIR)
 DEBUG_FLAG = -O
+# For MacOS, use the following line:
+#DEBUG_FLAG = -O2 -g
 
 OBJ_FILES = wwwbutl.c $(LIBS)/ncbithr.o
 
@@ -60,49 +61,58 @@ INCDIR = -I. -I$(NCBI_INCDIR)
 #BLASTQUE = /home/dondosha/BlastQueue
 #INCDIR = -I$(BLASTQUE)/Client -I$(BLASTQUE)/ASN.1 -I. -I$(NCBI_INCDIR)
 
+CFLAGS = -c $(DEBUG_FLAG) $(INCDIR)
+#For MacOS, add the following line:
+#CFLAGS += -no-cpp-precomp -Wno-long-double
+ 
 # For standalone model
-CFLAGS=  $(DEBUG_FLAG) $(INCDIR)
+LDFLAGS = $(DEBUG_FLAG) $(INCDIR)
+#For MacOS, add the following line:
+#LDFLAGS += -framework CoreServices
 
 # Use client/server for gi/accession lookups
-CFLAGS_CS = $(DEBUG_FLAG) $(INCDIR) -DNCBI_ENTREZ_CLIENT
+LDFLAGS_CS = $(DEBUG_FLAG) $(INCDIR) -DNCBI_ENTREZ_CLIENT
+#For MacOS, add the following line:
+#LDFLAGS_CS += -framework CoreServices 
 
 # For full NCBI Client-server model
-#CFLAGS_FCS= -c $(DEBUG_FLAG) $(INCDIR) -DNCBI_CLIENT_SERVER
+#CFLAGS += -DNCBI_CLIENT_SERVER
+#LDFLAGS_CS += -DNCBI_CLIENT_SERVER
 
 .c.o:   Makefile
-	$(CC) -c $(CFLAGS) $<
+	$(CC) $(CFLAGS) $<
 
 all: psiblast.REAL psiblast_cs.REAL  blast.REAL blast_cs.REAL nph-viewgif.cgi wblast2.REAL wblast2_cs.REAL bl2bag.cgi 
 
 blast.REAL: wwwblast.c $(OBJ_FILES) Makefile
-	$(CC)  $(CFLAGS) wwwblast.c $(OBJ_FILES) \
+	$(CC) $(LDFLAGS) wwwblast.c $(OBJ_FILES) \
 	-L$(LIBS) $(ALL_LIBS) -o ./blast.REAL
 	mv ./blast.REAL ..
 blast_cs.REAL: wwwblast.c $(OBJ_FILES) Makefile
-	$(CC) $(CFLAGS_CS) wwwblast.c $(OBJ_FILES) \
+	$(CC) $(LDFLAGS_CS) wwwblast.c $(OBJ_FILES) \
 	-L$(LIBS) $(ALL_LIBS_CS) -o ./blast_cs.REAL
 	mv ./blast_cs.REAL ..
 psiblast.REAL: psiblast.o $(OBJ_FILES) Makefile
-	$(CC) $(CFLAGS) psiblast.o $(OBJ_FILES) \
+	$(CC) $(LDFLAGS) psiblast.o $(OBJ_FILES) \
 	-L$(LIBS) $(ALL_LIBS) -o ./psiblast.REAL
 	mv ./psiblast.REAL ../psiblast.REAL
 psiblast_cs.REAL: psiblast.o $(OBJ_FILES) Makefile
-	$(CC) $(CFLAGS_CS) psiblast.o $(OBJ_FILES) \
+	$(CC) $(LDFLAGS_CS) psiblast.o $(OBJ_FILES) \
 	-L$(LIBS) $(ALL_LIBS_CS) -o ./psiblast_cs.REAL
 	mv ./psiblast_cs.REAL ../psiblast_cs.REAL
 nph-viewgif.cgi: viewgif.o
 	$(CC) viewgif.o -o nph-viewgif.cgi
 	mv nph-viewgif.cgi ..
 wblast2.REAL : wblast2.c 
-	$(CC) $(CFLAGS) $(BL2_DEFINE) wblast2.c \
+	$(CC) $(LDFLAGS) $(BL2_DEFINE) wblast2.c \
 	-L$(LIBS) $(BL2_LIBS) -o ./wblast2.REAL
 	mv wblast2.REAL ..
 wblast2_cs.REAL : wblast2.c $(BL2_OBJ)
-	$(CC) $(CFLAGS_CS) $(BL2_DEFINE) wblast2.c $(BL2_OBJ) \
+	$(CC) $(LDFLAGS_CS) $(BL2_DEFINE) wblast2.c $(BL2_OBJ) \
 	-L$(LIBS) $(BL2_LIBS_CS) -o ./wblast2_cs.REAL
 	mv wblast2_cs.REAL ..
 bl2bag.cgi : bl2bag.o
-	$(CC) bl2bag.o -L$(LIBS) -lncbi -lm -o bl2bag.cgi
+	$(CC) $(LDFLAGS) bl2bag.o -L$(LIBS) -lncbi -lm -o bl2bag.cgi
 	mv bl2bag.cgi ..
 
 xml:
diff --git a/network/wwwblast/Src/XML/Makefile b/network/wwwblast/Src/XML/Makefile
index 8e2d221c..ddfc14c4 100644
--- a/network/wwwblast/Src/XML/Makefile
+++ b/network/wwwblast/Src/XML/Makefile
@@ -24,7 +24,7 @@ LDFLAGS = -I./ -I$(INCPATH) $(OPTFLAGS) -L$(LIBPATH) $(VIBFLAG) $(NEWASN2FF) -g
 bxmlobj.c: $(NCBI_ASNALL) blstxml.asn
 	$(ASNTOOL) -m blstxml.asn -M $(NCBI_ASNALL) -B bxmlobj -G -w100 -Z
 	$(ASNTOOL) -m blstxml.asn -o blstxml.h -w 100 -Z
-	$(ASNTOOL) -m blstxml.asn -X NCBI_BlastOutput.mod
+#	$(ASNTOOL) -m blstxml.asn -X NCBI_BlastOutput.mod
 #	mv bxmlobj.c ..
 #	mv blstxml.h ..
 #	mv bxmlobj.h ..
diff --git a/network/wwwblast/Src/psiblast.c b/network/wwwblast/Src/psiblast.c
index c192d0a3..b316a80e 100644
--- a/network/wwwblast/Src/psiblast.c
+++ b/network/wwwblast/Src/psiblast.c
@@ -1,4 +1,4 @@
-/* $Id: psiblast.c,v 1.3 2003/07/15 19:57:11 coulouri Exp $
+/* $Id: psiblast.c,v 1.4 2003/11/21 17:51:32 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,12 +29,15 @@
 *
 * Initial Version Creation Date: 04/21/2000
 *
-* $Revision: 1.3 $
+* $Revision: 1.4 $
 *
 * File Description:
 *         WWW PSI BLAST Main file
 *
 * $Log: psiblast.c,v $
+* Revision 1.4  2003/11/21 17:51:32  dondosha
+* Minor bug fix
+*
 * Revision 1.3  2003/07/15 19:57:11  coulouri
 * use sigaction()
 *
@@ -349,7 +352,7 @@ Int2 Main (void)
     }
     
     fprintf(stdout, "<FORM NAME=\"PSI_BLAST\" METHOD=\"POST\" "
-            "ACTION=\"%s/step%d\" ENCTYPE= \"multipart/form-data\">\n", 
+            "ACTION=\"%s?step%d\" ENCTYPE= \"multipart/form-data\">\n", 
             getenv("SCRIPT_NAME") == NULL ? "" : getenv("SCRIPT_NAME"),
             /* WWWGetPort(theInfo->info), */ psidata->StepNumber);
     
diff --git a/network/wwwblast/Src/wblast2.c b/network/wwwblast/Src/wblast2.c
index e0270302..95fbbf20 100644
--- a/network/wwwblast/Src/wblast2.c
+++ b/network/wwwblast/Src/wblast2.c
@@ -1,4 +1,4 @@
-/* $Id: wblast2.c,v 1.7 2003/07/14 18:43:17 dondosha Exp $
+/* $Id: wblast2.c,v 1.8 2003/12/19 18:12:37 coulouri Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -27,12 +27,15 @@
 *
 * Initial Creation Date: 10/23/2000
 *
-* $Revision: 1.7 $
+* $Revision: 1.8 $
 *
 * File Description:
 *        BLAST 2 Sequences CGI program
 *
 * $Log: wblast2.c,v $
+* Revision 1.8  2003/12/19 18:12:37  coulouri
+* fix name collision in aix
+*
 * Revision 1.7  2003/07/14 18:43:17  dondosha
 * Changed Entrez references syntax
 *
@@ -452,7 +455,7 @@ static Boolean run_status;
 /* Flag to indicate which signals were received */ 
 static Uint8 sigflag = 0;
 /* set of signal masks */
-static Uint8 sigmask[64];
+static Uint8 wb2_sigmask[64];
 
 #define WBLAST2_SEARCH 0
 #define WBLAST2_FORMAT 1
@@ -463,7 +466,7 @@ void PrepareSigmask(void)
 {
    int ii;
    for( ii = 0; ii < 64; ii++ ) {
-      sigmask[ii] = 1 << ii;
+      wb2_sigmask[ii] = 1 << ii;
    }
 }
 
@@ -472,7 +475,7 @@ static int GetSignal()
 {
    int ii;
    for( ii = 0; ii < 64; ii++ ) {
-      if( sigflag & sigmask[ii] ) {
+      if( sigflag & wb2_sigmask[ii] ) {
          break;
       }
    }
@@ -483,7 +486,7 @@ static int GetSignal()
 /** set signal flag */
 static void sighandler(int sig)
 {
-   sigflag |= sigmask[sig];
+   sigflag |= wb2_sigmask[sig];
 }
 
 static void	Blast2SeqMainPage(CharPtr warning, CharPtr seq1, CharPtr seq2, CharPtr one, CharPtr two, ValNodePtr error, Boolean is_prot, BLAST_OptionsBlkPtr options, Int2 mtrx, Int4 from, Int4 to, Int4 ffrom, Int4 tto, Int2 filter, Int2 pagecount) {
diff --git a/network/wwwblast/Src/wwwblast.c b/network/wwwblast/Src/wwwblast.c
index 9582e926..504c6527 100644
--- a/network/wwwblast/Src/wwwblast.c
+++ b/network/wwwblast/Src/wwwblast.c
@@ -1,4 +1,4 @@
-/* $Id: wwwblast.c,v 1.8 2003/06/04 16:12:51 dondosha Exp $
+/* $Id: wwwblast.c,v 1.13 2004/01/16 17:35:20 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,12 +29,27 @@
 *
 * Initial Creation Date: 03/15/2000
 *
-* $Revision: 1.8 $
+* $Revision: 1.13 $
 *
 * File Description:
 *        Standalone WWW Blast CGI program.
 *
 * $Log: wwwblast.c,v $
+* Revision 1.13  2004/01/16 17:35:20  dondosha
+* Fixed mouseover problems
+*
+* Revision 1.12  2003/11/20 22:19:35  dondosha
+* Pass www_root_path to the PrintDefLines... function
+*
+* Revision 1.11  2003/11/20 20:10:52  dondosha
+* Decide whether to print header only after the output type is determined
+*
+* Revision 1.10  2003/11/20 19:10:33  dondosha
+* Do not print progress messages if XML output requested
+*
+* Revision 1.9  2003/11/05 22:40:28  dondosha
+* Do not shift coordinates for tabular output if query is a subsequence - they are already shifted in the seqalign
+*
 * Revision 1.8  2003/06/04 16:12:51  dondosha
 * Set db genetic code for formatting
 *
@@ -179,6 +194,19 @@ static int LIBCALLBACK WWWTickCallback(Int4 sequence_number,
     
     return 1;
 }
+
+/* Callback in case of XML output should not print anything to the stdout */
+static int LIBCALLBACK WWWXMLTickCallback(Int4 sequence_number, 
+                                          Int4 number_of_positive_hits)
+{
+   if(!TestSTDOut()) {
+      return -1;
+   }
+   fflush(stdout);
+   
+   return 1;
+}
+
 static Int4 get_number_alignment(SeqAlignPtr align)
 {
     Int4 num = 0;
@@ -378,10 +406,11 @@ TraditionalBlastReportEngineWithImage(SeqLocPtr slp, BioseqPtr bsp, BlastNet3Hpt
                                   theInfo->number_of_alignments,
                                   program, 
                                   !theInfo->options->gapped_calculation,
-                                  FALSE, SeqLocStart(slp), 0, stdout,
+                                  FALSE, 0, 0, stdout,
                                   (theInfo->align_view == HitTableWithHeader));
        SeqAlignSetFree(seqalign);
     } else {
+    Int4 query_number = 1;
     while (seqalign) {
         if (!options->is_megablast_search)
             next_seqalign = NULL;
@@ -430,7 +459,7 @@ TraditionalBlastReportEngineWithImage(SeqLocPtr slp, BioseqPtr bsp, BlastNet3Hpt
             seqannot->data = seqalign;
             
             if(theInfo->show_overview) {
-                Char f_name[64], title[1024], href[64];
+                Char f_name[64], title[1024], href[64], form_name[16];
                 Int4 align_num;       
                 
                 sprintf(f_name, "%ld%ld.gif", (long)random(), (long)getpid());
@@ -443,18 +472,23 @@ TraditionalBlastReportEngineWithImage(SeqLocPtr slp, BioseqPtr bsp, BlastNet3Hpt
                         "</H3>\n", theInfo->www_root_path, (long)align_num);
                 
                 /* Open HTML form */
-                fprintf(stdout, "<FORM NAME=\"BLASTFORM\">\n");
+                sprintf(form_name, "BLASTFORM%ld", query_number);
+                fprintf(stdout, "<FORM NAME=\"%s\">\n", form_name);
                 fflush(stdout);
                 
-                PrintAlignmentOverview(seqannot, stdout, 
-                                       "BLASTFORM", href, f_name, title); 
+                PrintOneAlignmentOverview(seqannot, stdout, form_name, href, f_name,
+                                          title, query_number);
+                ++query_number;
             }
             
             prune = BlastPruneHitsFromSeqAlign(seqalign, theInfo->number_of_descriptions, NULL);
             ObjMgrSetHold();
             init_buff_ex(85);
             
-            PrintDefLinesFromSeqAlignEx2(prune->sap, 80, stdout, theInfo->print_options, FIRST_PASS, NULL, theInfo->number_of_descriptions, database, theInfo->www_blast_type);
+            PrintDefLinesFromSeqAlignWithPath(prune->sap, 80, stdout, 
+               theInfo->print_options, FIRST_PASS, NULL, 
+               theInfo->number_of_descriptions, database, 
+               theInfo->www_blast_type, theInfo->www_root_path);
             free_buff();
             
             prune = BlastPruneHitsFromSeqAlign(seqalign, theInfo->number_of_alignments, prune);
@@ -504,7 +538,7 @@ TraditionalBlastReportEngineWithImage(SeqLocPtr slp, BioseqPtr bsp, BlastNet3Hpt
         if (seqannot)
             seqannot = SeqAnnotFree(seqannot);
         seqalign = next_seqalign;
-        fprintf(stdout, "<PRE>\n");
+        fprintf(stdout, "<PRE>\n</form>\n");
     }
     } /* End if not hit table */ 
     if (!done) { /* seqalign == NULL */
@@ -768,6 +802,8 @@ Boolean WWWBlastDoSearch(WWWBlastInfoPtr theInfo)
     Boolean tabular_output = (theInfo->align_view == HitTable || 
                               theInfo->align_view == HitTableWithHeader);
     MBXmlPtr mbxp = NULL;
+    int LIBCALLBACK (*callback)(Int4, Int4);
+    Int4 query_number;
 
     if(theInfo == NULL)
 	return FALSE;
@@ -805,8 +841,12 @@ Boolean WWWBlastDoSearch(WWWBlastInfoPtr theInfo)
         other_returns = NULL;
         error_returns = NULL;
         
-        if(!theInfo->xml_output)
+        if(!theInfo->xml_output) {
             printf("</PRE>\n");
+            callback = WWWTickCallback;
+        } else {
+            callback = WWWXMLTickCallback;
+        }
 
         if (!is_megablast) {
             if (SeqIdComp(SeqLocId(lcase_mask), SeqLocId(query_slp)) == 
@@ -817,15 +857,15 @@ Boolean WWWBlastDoSearch(WWWBlastInfoPtr theInfo)
                 lcase_mask = lcase_mask->next;
             }
             if (query_slp) {
-                seqalign = BioseqBlastEngineByLocEx(query_slp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, WWWTickCallback, NULL, theInfo->gi_list, theInfo->gi_list_total);
+                seqalign = BioseqBlastEngineByLocEx(query_slp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, callback, NULL, theInfo->gi_list, theInfo->gi_list_total);
             } else {
-                seqalign = BioseqBlastEngineEx(theInfo->fake_bsp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, WWWTickCallback, NULL, theInfo->gi_list, theInfo->gi_list_total);
+                seqalign = BioseqBlastEngineEx(theInfo->fake_bsp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, callback, NULL, theInfo->gi_list, theInfo->gi_list_total);
             }
         } else {
            if (options->no_traceback)
-            seqalignp = BioseqMegaBlastEngineByLoc(query_slp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, WWWTickCallback, NULL, theInfo->gi_list, theInfo->gi_list_total, AppendMegaBlastHit);
+            seqalignp = BioseqMegaBlastEngineByLoc(query_slp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, callback, NULL, theInfo->gi_list, theInfo->gi_list_total, AppendMegaBlastHit);
            else
-            seqalignp = BioseqMegaBlastEngineByLoc(query_slp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, WWWTickCallback, NULL, theInfo->gi_list, theInfo->gi_list_total, NULL);
+            seqalignp = BioseqMegaBlastEngineByLoc(query_slp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, callback, NULL, theInfo->gi_list, theInfo->gi_list_total, NULL);
         }
 
         if(!theInfo->xml_output)
@@ -904,6 +944,7 @@ Boolean WWWBlastDoSearch(WWWBlastInfoPtr theInfo)
         }
 
         ReadDBBioseqSetDbGeneticCode(theInfo->options->db_genetic_code);
+        query_number = 1;
 
         for (index=0; !done; index++) {
             if (is_megablast)
@@ -943,8 +984,8 @@ Boolean WWWBlastDoSearch(WWWBlastInfoPtr theInfo)
                         query_slp, theInfo->number_of_alignments, 
                         theInfo->program, 
                         !theInfo->options->gapped_calculation, FALSE, 
-                        (query_slp ? SeqLocStart(query_slp) : 0), 0, 
-                        stdout, (theInfo->align_view == HitTableWithHeader));
+                        0, 0, stdout, 
+                        (theInfo->align_view == HitTableWithHeader));
                 } else {
                     seqannot = SeqAnnotNew();
                     seqannot->type = 2;
@@ -969,7 +1010,7 @@ Boolean WWWBlastDoSearch(WWWBlastInfoPtr theInfo)
                     /* Now printing nice gif with alignment overview */
                     
                     if(theInfo->show_overview) {
-                        Char f_name[64], title[1024], href[64];
+                        Char f_name[64], title[1024], href[64], form_name[16];
                         Int4 align_num;
                         
                         sprintf(f_name, "%ld%ld.gif", (long)random(), (long)getpid());
@@ -984,19 +1025,21 @@ Boolean WWWBlastDoSearch(WWWBlastInfoPtr theInfo)
                         
                         
                         /* Open HTML form */
-                        fprintf(stdout, "<FORM NAME=\"BLASTFORM\">\n");
+                        sprintf(form_name, "BLASTFORM%ld", query_number);
+                        fprintf(stdout, "<FORM NAME=\"%s\">\n", form_name);
                         fflush(stdout);
                         
-                        PrintAlignmentOverview(seqannot, stdout, 
-                                               "BLASTFORM", href, f_name, title); 
+                        PrintOneAlignmentOverview(seqannot, stdout, form_name, href, 
+                                                  f_name, title, query_number); 
+                        ++query_number;
                     }
                     
                     prune = BlastPruneHitsFromSeqAlign(seqalign, theInfo->number_of_descriptions, NULL);
                     ObjMgrSetHold();
                     init_buff_ex(85);
-                    PrintDefLinesFromSeqAlignEx2(prune->sap, 80, stdout, 
+                    PrintDefLinesFromSeqAlignWithPath(prune->sap, 80, stdout, 
                        theInfo->print_options, FIRST_PASS, NULL, -1,
-                       NULL, theInfo->www_blast_type);
+                       NULL, theInfo->www_blast_type, theInfo->www_root_path);
                     free_buff();
                     
                     prune = BlastPruneHitsFromSeqAlign(seqalign, theInfo->number_of_alignments, prune);
@@ -1080,6 +1123,7 @@ Boolean WWWBlastDoSearch(WWWBlastInfoPtr theInfo)
             }
             if(!theInfo->xml_output && seqannot != NULL)
                 seqannot = SeqAnnotFree(seqannot);
+            fprintf(stdout, "</form>\n");
         }
         
         matrix = BLAST_MatrixDestruct(matrix);
@@ -1184,7 +1228,7 @@ static void WWWBlastPrintTopHeader(WWWBlastInfoPtr theInfo)
     
     fprintf(stdout, "<BODY BGCOLOR=\"#FFFFFF\" LINK=\"#0000FF\" "
             "VLINK=\"#660099\" ALINK=\"#660099\">\n");
-    fprintf(stdout, "<map name=img_map1>\n");
+    fprintf(stdout, "<map name=img_map0>\n");
     fprintf(stdout, "<area shape=rect coords=2,1,48,21 "
             "href=\"http://www.ncbi.nlm.nih.gov\">\n");
     fprintf(stdout, "<area shape=rect coords=385,1,435,21 "
@@ -1194,7 +1238,7 @@ static void WWWBlastPrintTopHeader(WWWBlastInfoPtr theInfo)
     fprintf(stdout, "<area shape=rect coords=487,1,508,21 "
             "href=\"%s/blast/docs/blast_help.html\">\n", theInfo->www_root_path);
     fprintf(stdout, "</map>\n"); 
-    fprintf(stdout, "<IMG USEMAP=#img_map1 WIDTH=509 HEIGHT=22 "
+    fprintf(stdout, "<IMG USEMAP=#img_map0 WIDTH=509 HEIGHT=22 "
             "SRC=\"%s/blast/images/blast_results.gif\" ISMAP> \n", 
             theInfo->www_root_path);
 }
@@ -1241,14 +1285,14 @@ Int2 Main(void)
     if((theInfo = WWWBlastReadArgs(NULL)) == NULL)
         return 1;
     
-    if (!theInfo->xml_output) 
-       WWWBlastPrintTopHeader(theInfo);
-
     /* Read options into structure */
     if(!WWWCreateSearchOptions(theInfo)) {
         return 1;
     }
     
+    if (!theInfo->xml_output) 
+       WWWBlastPrintTopHeader(theInfo);
+
     /* validate them */
     if(!WWWValidateOptions(theInfo)) {
         return 1;
diff --git a/network/wwwblast/Src/wwwbutl.c b/network/wwwblast/Src/wwwbutl.c
index 9f734288..94387037 100644
--- a/network/wwwblast/Src/wwwbutl.c
+++ b/network/wwwblast/Src/wwwbutl.c
@@ -1,4 +1,4 @@
-/* $Id: wwwbutl.c,v 1.18 2003/08/13 14:35:33 dondosha Exp $
+/* $Id: wwwbutl.c,v 1.21 2004/01/16 17:35:20 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,12 +29,21 @@
 *
 * Initial Version Creation Date: 04/21/2000
 *
-* $Revision: 1.18 $
+* $Revision: 1.21 $
 *
 * File Description:
 *         WWW BLAST/PSI/PHI utilities
 *
 * $Log: wwwbutl.c,v $
+* Revision 1.21  2004/01/16 17:35:20  dondosha
+* Fixed mouseover problems
+*
+* Revision 1.20  2003/11/20 22:19:35  dondosha
+* Pass www_root_path to the PrintDefLines... function
+*
+* Revision 1.19  2003/11/20 19:10:01  dondosha
+* Never print header for XML output
+*
 * Revision 1.18  2003/08/13 14:35:33  dondosha
 * When no percent identity cutoff, default value for mismatch penalty is -3 for blastn
 *
@@ -1920,7 +1929,7 @@ static void PrintRequestHeader(WWWBlastInfoPtr theInfo)
     printf("</HEAD>\n");
     printf("<BODY BGCOLOR=\"#FFFFFF\" LINK=\"#0000FF\" "
            "VLINK=\"#660099\" ALINK=\"#660099\">\n");
-    fprintf(stdout, "<map name=img_map1>\n");
+    fprintf(stdout, "<map name=img_map0>\n");
     fprintf(stdout, "<area shape=rect coords=2,1,48,21 "
             "href=\"http://www.ncbi.nlm.nih.gov\">\n");
     fprintf(stdout, "<area shape=rect coords=385,1,435,21 "
@@ -1930,7 +1939,7 @@ static void PrintRequestHeader(WWWBlastInfoPtr theInfo)
     fprintf(stdout, "<area shape=rect coords=487,1,508,21 "
             "href=\"%s/blast/docs/blast_help.html\">\n", theInfo->www_root_path);
     fprintf(stdout, "</map>\n"); 
-    fprintf(stdout, "<IMG USEMAP=#img_map1 WIDTH=509 HEIGHT=22 "
+    fprintf(stdout, "<IMG USEMAP=#img_map0 WIDTH=509 HEIGHT=22 "
             "SRC=\"%s/blast/images/psi_blast.gif\" ISMAP> \n", 
             theInfo->www_root_path);
     printf("<BR><BR><PRE>\n");
@@ -2336,7 +2345,9 @@ BLASTPrintDataPtr PSIBlastSearch(WWWBlastInfoPtr theInfo)
     if(theInfo == NULL)
 	return NULL;
 
-    PrintRequestHeader(theInfo); 
+    if (!theInfo->xml_output)
+       PrintRequestHeader(theInfo); 
+
     print_data = (BLASTPrintDataPtr) MemNew(sizeof(BLASTPrintData));
     
     psidata = MemNew(sizeof(PSIData));
@@ -2480,7 +2491,9 @@ BLASTPrintDataPtr PHIBlastSearch(WWWBlastInfoPtr theInfo)
     if(theInfo == NULL)
 	return NULL;
     
-    PrintRequestHeader(theInfo); 
+    if (!theInfo->xml_output)
+       PrintRequestHeader(theInfo); 
+
     print_data = (BLASTPrintDataPtr) MemNew(sizeof(BLASTPrintData));
     
     psidata = MemNew(sizeof(PSIData));
@@ -2742,8 +2755,11 @@ the alignment was checked on the previous iteration \
         
         fflush(stdout);
         print_options += TXALIGN_CHECK_BOX_CHECKED;
-        PrintDefLinesFromSeqAlignEx(GoodSeqAlignments, 80, stdout, print_options, FIRST_PASS, marks, theInfo->number_of_descriptions);
-        
+        PrintDefLinesFromSeqAlignWithPath(GoodSeqAlignments, 80, stdout,
+           print_options, FIRST_PASS, marks,
+           theInfo->number_of_descriptions, theInfo->database,
+           theInfo->www_blast_type, theInfo->www_root_path);
+
         print_options -= TXALIGN_CHECK_BOX_CHECKED;
         
         if (print_data->psidata->StepNumber == 0)
@@ -2757,7 +2773,11 @@ the alignment was checked on the previous iteration \
                    "Sequences with pattern at position %d and E-value WORSE than threshold</FONT></b></CENTER>\n", 
                    SeqLocStart(seqloc)+1);
             
-            PrintDefLinesFromSeqAlignEx(BadSeqAlignments, 80, stdout, print_options, FIRST_PASS, &marks[countGood], theInfo->number_of_descriptions - countGood);
+            PrintDefLinesFromSeqAlignWithPath(BadSeqAlignments, 80, stdout,
+               print_options, FIRST_PASS, &marks[countGood], 
+               theInfo->number_of_descriptions - countGood, 
+               theInfo->database, theInfo->www_blast_type, 
+               theInfo->www_root_path);
         }
 
         marks = MemFree(marks);
@@ -2979,8 +2999,9 @@ the alignment was checked on the previous iteration \
         printf("                          (bits) Value\n\n");
     }
     
-    PrintDefLinesFromSeqAlignEx(GoodSeqAlignments, 80, stdout, 
-                                print_options, FIRST_PASS, marks, theInfo->number_of_descriptions);
+    PrintDefLinesFromSeqAlignWithPath(GoodSeqAlignments, 80, stdout, 
+       print_options, FIRST_PASS, marks, theInfo->number_of_descriptions,
+       theInfo->database, theInfo->www_blast_type, theInfo->www_root_path);
     
     print_options -= TXALIGN_CHECK_BOX_CHECKED;
     
@@ -2995,7 +3016,10 @@ the alignment was checked on the previous iteration \
         printf("<HR><CENTER><b><FONT color=\"green\">"
                "Sequences with E-value WORSE than threshold </FONT></b></CENTER>\n");
     
-        PrintDefLinesFromSeqAlignEx(BadSeqAlignments, 80, stdout, print_options, FIRST_PASS, &marks[countGood], theInfo->number_of_descriptions - countGood);
+        PrintDefLinesFromSeqAlignWithPath(BadSeqAlignments, 80, stdout, 
+           print_options, FIRST_PASS, &marks[countGood], 
+           theInfo->number_of_descriptions - countGood, theInfo->database,
+           theInfo->www_blast_type, theInfo->www_root_path);
     }
 
     if (theInfo->number_of_descriptions) {
diff --git a/network/wwwblast/readme.html b/network/wwwblast/readme.html
index 114e70a2..c23b298f 100644
--- a/network/wwwblast/readme.html
+++ b/network/wwwblast/readme.html
@@ -1,4 +1,4 @@
-<!-- $Id: readme.html,v 1.9 2003/06/24 21:53:54 dondosha Exp $ -->
+<!-- $Id: readme.html,v 1.11 2004/01/30 22:29:05 dondosha Exp $ -->
 <HTML>
 <HEAD>
 <TITLE>Introduction to the Standalone WWW Blast server</TITLE>
@@ -29,12 +29,34 @@
 </UL>
 
 <H3><A NAME="Inroduction">Introduction</A> </H3>
-<P>This standalone WWW BLAST server suite of programs was designed similar to the regular NCBI BLAST server and such command-line NCBI BLAST programs like "blastall", "blastpgp", "rpsblast" and "megablast". It incorporates most features, which exist in NCBI BLAST programs and should be relatively easy to use. This server does not support any request queuing and load balancing. As soon as the user hits a "Search" button, BLAST starts immediately if entered information is valid. So, this server is not intended to handle large load, which may exist in public service. Such queueing and loadbalancing however may be implemented using such products as Load Sharing Facility - "LSF" from <a href="http://www.platform.com">Platform Computing Corporation</a>. Interface to "LSF" was implemented in NCBI, however this was not included in this suite. Standalone server assumes that users have their own BLAST or RPS-BLAST database(s), that should be searched and want to have a simple WWW interface to such search. It is STRONLY recommended that user has experience in installation and running standalone NCBI BLAST programs. </P>
-<P>After files are uncompressed, server is ready to be used immediately. Any customizations to the program are welcomed and may be done by experienced programmers using source code, which is also provided. <P>Recompilation of the server executables requires that programmer has compiled NCBI toolkit libraries. This toolkit can be downloaded from the NCBI FTP web site: <A HREF="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/README.htm">ftp://ftp.ncbi.nih.gov</A> <BR>After the NCBI toolkit is compiled, user needs to edit the Makefile in the blast/Src directory, and define the NCBI variable in the top line of the Makefile, so it points to the root directory where the NCBI toolkit is located.</P>
+<P>This standalone WWW BLAST server suite of programs was designed similar to the regular NCBI BLAST server and such command-line NCBI BLAST programs like "blastall", "blastpgp", "rpsblast" and "megablast". It incorporates most features, which exist in NCBI BLAST programs and should be relatively easy to use. This server does not support any request queuing and load balancing. As soon as the user hits a "Search" button, BLAST starts immediately if entered information is valid. So, this server is not intended to handle large load, which may exist in public service. Such queueing and loadbalancing however may be implemented using such products as Load Sharing Facility - "LSF" from <a href="http://www.platform.com">Platform Computing Corporation</a>. Interface to "LSF" was implemented in NCBI, however this was not included in this suite. Standalone server assumes that users have their own BLAST or RPS-BLAST database(s), that should be searched and want to have a simple WWW interface to such search. It is STRONLY recommended that user have experience in installation and running standalone NCBI BLAST programs. </P>
+<P>After files are uncompressed, server is ready to be used immediately. Any customizations to the program are welcomed. The source code for WWW BLAST is now part of the NCBI C toolkit, which can be downloaded from the NCBI FTP web site: <A HREF="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/README.htm">ftp://ftp.ncbi.nih.gov</A> <BR>The compilation of the NCBI C toolkit includes the WWW BLAST executables. The files in the C toolkit most relevant for the WWW BLAST executables are: wwwblast.c, wwwbutl.c, psiblast.c, wblast2.c.</P>
 <H3><A NAME="Whatsnew">What's new in this revision?</A></H3>
 
 <TABLE BORDER=1>
 <TR VALIGN=top>
+<TD> February 2, 2004
+<TD>
+<UL>
+<LI> All source code moved to the NCBI C toolkit.
+<LI> Mouseover feature fixed in graphical overview.
+<LI> All binaries synchronized with the latest NCBI C toolkit release. All future
+releases will be automatically synchronized with future toolkit releases.
+<LI> Recompilation procedure changed. WWW BLAST binaries are now compiled as part
+of the C toolkit.
+</UL>
+</TR>
+<TR VALIGN=top>
+<TD> November 21, 2003
+<TD>
+<UL>
+<LI> Fixed a bug with absent images on PSI-BLAST iterations.
+<LI> Removed header and progress messages from XML output. 
+<LI> All binaries recompiled with the newest version of the NCBI C toolkit libra
+ries.
+</UL>
+</TR>
+<TR VALIGN=top>
 <TD> May 9, 2003
 <TD>
 <UL>
diff --git a/network/wwwblast/readme.txt b/network/wwwblast/readme.txt
index a4d89b55..690f1dd8 100644
--- a/network/wwwblast/readme.txt
+++ b/network/wwwblast/readme.txt
@@ -41,25 +41,38 @@ Platform Computing Corporation <http://www.platform.com>. Interface to
 "LSF" was implemented in NCBI, however this was not included in this
 suite. Standalone server assumes that users have their own BLAST or
 RPS-BLAST database(s), that should be searched and want to have a simple
-WWW interface to such search. It is STRONLY recommended that user has
+WWW interface to such search. It is STRONLY recommended that user have
 experience in installation and running standalone NCBI BLAST programs.
 
 After files are uncompressed, server is ready to be used immediately.
-Any customizations to the program are welcomed and may be done by
-experienced programmers using source code, which is also provided.
-
-Recompilation of the server executables requires that programmer has
-compiled NCBI toolkit libraries. This toolkit can be downloaded from the
-NCBI FTP web site: ftp://ftp.ncbi.nih.gov
+Any customizations to the program are welcomed. The source code for WWW
+BLAST is now part of the NCBI C toolkit, which can be downloaded from
+the NCBI FTP web site: ftp://ftp.ncbi.nih.gov
 <ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/README.htm>
-After the NCBI toolkit is compiled, user needs to edit the Makefile in
-the blast/Src directory, and define the NCBI variable in the top line of
-the Makefile, so it points to the root directory where the NCBI toolkit
-is located.
+The compilation of the NCBI C toolkit includes the WWW BLAST
+executables. The files in the C toolkit most relevant for the WWW BLAST
+executables are: wwwblast.c, wwwbutl.c, psiblast.c, wblast2.c.
 
 
       What's new in this revision?
 
+February 2, 2004
+
+    * All source code moved to the NCBI C toolkit.
+    * Mouseover feature fixed in graphical overview.
+    * All binaries synchronized with the latest NCBI C toolkit release.
+      All future releases will be automatically synchronized with future
+      toolkit releases.
+    * Recompilation procedure changed. WWW BLAST binaries are now
+compiled as part of the C toolkit.
+
+November 21, 2003
+
+    * Fixed a bug with absent images on PSI-BLAST iterations.
+    * Removed header and progress messages from XML output.
+    * All binaries recompiled with the newest version of the NCBI C
+toolkit libra ries.
+
 May 9, 2003
 
     * Cleaned the Makefile for recompiling the sources.
@@ -487,10 +500,10 @@ the description of a configuration file.
       Server configuration file and logfile
 
 Default configuration file is "blast.rc" and logfile "wwwblast.log".
-Setting tag BLAST_TYPE to specific value may change these names.
-This is useful if few different search input pages use the same CGI
-search engine, but significantly different by content and priorities. A
-sample configuration file comes with this distribution:
+Setting tag BLAST_TYPE to specific value may change these names. This is
+useful if few different search input pages use the same CGI search
+engine, but significantly different by content and priorities. A sample
+configuration file comes with this distribution:
 
 This file will set how many CPUs will be used in the BLAST search and
 what databases may be used with what programs. Logfile currently stores
diff --git a/object/objfeat.c b/object/objfeat.c
index d96ffedf..b25f3944 100644
--- a/object/objfeat.c
+++ b/object/objfeat.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.20 $
+* $Revision: 6.21 $
 *
 * File Description:  Object manager for module NCBI-SeqFeat
 *
@@ -2923,9 +2923,10 @@ NLM_EXTERN OrgRefPtr LIBCALL OrgRefFree (OrgRefPtr orp)
     if (orp == NULL)
         return (OrgRefPtr)NULL;
 
-    MemFree(orp->taxname);
-    MemFree(orp->common);
+    orp->taxname = MemFree(orp->taxname);
+    orp->common = MemFree(orp->common);
     ValNodeFreeData(orp->mod);
+	orp->mod = NULL;
     anp = orp->db;
     while (anp != NULL)
     {
@@ -2934,8 +2935,11 @@ NLM_EXTERN OrgRefPtr LIBCALL OrgRefFree (OrgRefPtr orp)
         MemFree(anp);
         anp = next;
     }
+	orp->db = NULL;
     ValNodeFreeData(orp->syn);
+	orp->syn = NULL;
 	OrgNameFree(orp->orgname);
+	orp->orgname = NULL;
     return (OrgRefPtr)MemFree(orp);
 }
 
diff --git a/object/objtseq.c b/object/objtseq.c
index 93c7e3b2..d3be5e56 100644
--- a/object/objtseq.c
+++ b/object/objtseq.c
@@ -473,6 +473,10 @@ NLM_EXTERN TSeqPtr BioseqToTSeq (BioseqPtr bsp)
 			case SEQID_DDBJ:
 			case SEQID_EMBL:
 			case SEQID_SWISSPROT:
+		    case SEQID_OTHER:
+		    case SEQID_TPG:
+		    case SEQID_TPE:
+		    case SEQID_TPD:
 				SeqIdWrite(sip, buf, PRINTID_TEXTID_ACC_VER, 250);
 				tsp->accver = StringSave(buf);
 				break;
@@ -580,6 +584,10 @@ static TSeqPtr BioseqToMiniTSeq (BioseqPtr bsp)
 			case SEQID_DDBJ:
 			case SEQID_EMBL:
 			case SEQID_SWISSPROT:
+		    case SEQID_OTHER:
+		    case SEQID_TPG:
+		    case SEQID_TPE:
+		    case SEQID_TPD:
 				SeqIdWrite(sip, buf, PRINTID_TEXTID_ACC_VER, 250);
 				tsp->accver = StringSave(buf);
 				break;
diff --git a/platform/ibm_auto.ncbi.mk b/platform/ibm_auto.ncbi.mk
index b4e1dc53..cdb519e8 100644
--- a/platform/ibm_auto.ncbi.mk
+++ b/platform/ibm_auto.ncbi.mk
@@ -1,5 +1,5 @@
 #
-# $Id: ibm_auto.ncbi.mk,v 1.8 2003/05/22 18:22:14 beloslyu Exp $
+# $Id: ibm_auto.ncbi.mk,v 1.9 2004/01/09 19:01:51 beloslyu Exp $
 #
 # Initial version ddas@us.ibm.com 08/19/1999
 # Replace r6k with ibm_auto or ibm_pwr3:  cpsosa@us.ibm.com Jun-2001
@@ -13,7 +13,7 @@
 NCBI_DEFAULT_LCL = ibm
 NCBI_MAKE_SHELL = /bin/sh
 NCBI_AR = ar
-NCBI_CC = xlc_r
+NCBI_CC = xlc_r -qlanglvl=stdc99
 NCBI_CFLAGS1 = -c -qcpluscmt
 NCBI_LDFLAGS1 = -bmaxdata:0x40000000 -bmaxstack:0x10000000 -DPOSIX_THREADS_AVAIL -D_LARGE_FILES
 NCBI_OPTFLAG = -O3 -qmaxmem=-1 -qarch=auto -qcache=auto -DPOSIX_THREADS_AVAIL -D_LARGE_FILES
diff --git a/platform/ibm_auto64.ncbi.mk b/platform/ibm_auto64.ncbi.mk
index 7c1620af..bf265848 100644
--- a/platform/ibm_auto64.ncbi.mk
+++ b/platform/ibm_auto64.ncbi.mk
@@ -1,5 +1,5 @@
 #
-# $Id: ibm_auto64.ncbi.mk,v 1.2 2003/05/22 18:22:14 beloslyu Exp $
+# $Id: ibm_auto64.ncbi.mk,v 1.3 2004/01/09 19:01:51 beloslyu Exp $
 #
 # Initial version ddas@us.ibm.com 08/19/1999
 # Replace r6k with ibm_auto or ibm_pwr3:  cpsosa@us.ibm.com Jun-2001
@@ -13,7 +13,7 @@
 NCBI_DEFAULT_LCL = ibm
 NCBI_MAKE_SHELL = /bin/sh
 NCBI_AR = ar -X 64
-NCBI_CC = xlc_r -q64
+NCBI_CC = xlc_r -q64 -qlanglvl=stdc99
 NCBI_CFLAGS1 = -c -qcpluscmt
 NCBI_LDFLAGS1 = -D_LARGE_FILES
 NCBI_OPTFLAG = -O3 -qmaxmem=-1 -qarch=auto -qcache=auto -DPOSIX_THREADS_AVAIL -D_LARGE_FILES
diff --git a/platform/linux-x86.ncbi.mk b/platform/linux-x86.ncbi.mk
new file mode 100644
index 00000000..9225b73a
--- /dev/null
+++ b/platform/linux-x86.ncbi.mk
@@ -0,0 +1,51 @@
+#
+# $Id: linux-x86.ncbi.mk,v 1.31 2004/01/09 18:47:22 beloslyu Exp $
+#
+NCBI_DEFAULT_LCL = lnx
+NCBI_MAKE_SHELL = /bin/sh
+#warning, the flags -D__USE_FILE_OFFSET64 -D__USE_LARGEFILE64 will allow
+#you to work with large (>4Gb) files only if you have glibc version >= 2.1
+#NCBI_CC = gcc -pipe -D__USE_FILE_OFFSET64 -D__USE_LARGEFILE64
+#it appears the flags above do not work anymore with newer libc,
+#the new flags should work. Dima. 08/23/01
+NCBI_AR=ar
+NCBI_CC = gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
+NCBI_CFLAGS1 = -c
+NCBI_LDFLAGS1 = -O3 -mcpu=pentiumpro
+NCBI_OPTFLAG = -O3 -mcpu=pentiumpro
+NCBI_BIN_MASTER = /home/coremake/ncbi/bin
+NCBI_BIN_COPY = /home/coremake/ncbi/bin
+NCBI_INCDIR = /home/coremake/ncbi/include
+NCBI_LIBDIR = /home/coremake/ncbi/lib
+NCBI_ALTLIB = /home/coremake/ncbi/altlib
+#will work only when you have Motif installed!
+NCBI_VIBFLAG = -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF
+NCBI_VIBLIBS = -lXmu -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -ldl
+#warning! If you have only dynamic version of Motif or Lesstif
+#you should delete -Wl,-Bstatic sentence from the next line:
+NCBI_DISTVIBLIBS = -L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -ldl
+NCBI_OTHERLIBS = -lm
+NCBI_RANLIB = ranlib
+# Used by makedis.csh
+NCBI_MT_OTHERLIBS = -lpthread
+NCBI_OTHERLIBS_MT = $(NCBI_MT_OTHERLIBS) -lm
+NCBI_THREAD_OBJ = ncbithr.o
+NETENTREZVERSION = 2.02c2ASN1SPEC6 
+
+# uncomment OPENGL_TARGETS to build OpenGL apps; do not change
+# OPENGL_NCBI_LIBS! However, may need to set
+# OPENGL_INCLUDE and OPENGL_LIBS to suit local environment
+# OPENGL_TARGETS = Cn3D
+OPENGL_NCBI_LIBS = LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a
+OPENGL_INCLUDE = -I/usr/X11R6/include
+OPENGL_LIBS = -L/usr/X11R6/lib -lGL -lGLU
+NCBI_OGLLIBS = -L/usr/X11R6/lib -lGL -lGLU
+
+# uncomment (and change appropriately) these lines to build PNG
+# output support into Cn3D (OpenGL version only)
+#LIBPNG_DIR = /home/paul/Programs/libpng
+#ZLIB_DIR = /home/paul/Programs/zlib
+
+NCBI_LBSM_SRC = ncbi_lbsmd_stub.c
+NCBI_LBSM_OBJ = ncbi_lbsmd_stub.o
+
diff --git a/platform/linux.ncbi.mk b/platform/linux.ncbi.mk
index 1dd7e390..c93b99c8 100644
--- a/platform/linux.ncbi.mk
+++ b/platform/linux.ncbi.mk
@@ -1,20 +1,18 @@
 #
-# $Id: linux.ncbi.mk,v 1.29 2003/05/07 17:40:12 beloslyu Exp $
+# $Id: linux.ncbi.mk,v 1.32 2004/01/22 19:51:42 ucko Exp $
 #
 NCBI_DEFAULT_LCL = lnx
 NCBI_MAKE_SHELL = /bin/sh
 #warning, the flags -D__USE_FILE_OFFSET64 -D__USE_LARGEFILE64 will allow
 #you to work with large (>4Gb) files only if you have glibc version >= 2.1
 #NCBI_CC = gcc -pipe -D__USE_FILE_OFFSET64 -D__USE_LARGEFILE64
-#it appears the flags above do not working anymore with newer libc,
+#it appears the flags above do not work anymore with newer libc,
 #the new flags should work. Dima. 08/23/01
 NCBI_AR=ar
 NCBI_CC = gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
 NCBI_CFLAGS1 = -c
-NCBI_LDFLAGS1 = -O2
-NCBI_OPTFLAG = -O2
-#untested, try on your own risk on Linux/Intel
-#NCBI_OPTFLAG = -O3 -march=pentiumpro -funroll-loops
+NCBI_LDFLAGS1 = -O3
+NCBI_OPTFLAG = -O3
 NCBI_BIN_MASTER = /home/coremake/ncbi/bin
 NCBI_BIN_COPY = /home/coremake/ncbi/bin
 NCBI_INCDIR = /home/coremake/ncbi/include
diff --git a/platform/netbsd.ncbi.mk b/platform/netbsd.ncbi.mk
index 44feb899..64b976d2 100644
--- a/platform/netbsd.ncbi.mk
+++ b/platform/netbsd.ncbi.mk
@@ -1,5 +1,5 @@
 #
-# $Id: netbsd.ncbi.mk,v 1.8 2003/05/07 17:40:12 beloslyu Exp $
+# $Id: netbsd.ncbi.mk,v 1.9 2003/11/17 16:05:41 coulouri Exp $
 #
 # That platform is not supported and is contributed to NCBI by 
 #                     Brook Milligan <brook@trillium.NMSU.Edu>
@@ -9,8 +9,8 @@ NCBI_MAKE_SHELL = /bin/sh
 NCBI_AR=ar
 NCBI_CC = gcc -pipe
 NCBI_CFLAGS1 = -c
-NCBI_LDFLAGS1 = -O
-NCBI_OPTFLAG = -O
+NCBI_LDFLAGS1 = -O2
+NCBI_OPTFLAG = -O2
 NCBI_BIN_MASTER = /home/coremake/ncbi/bin
 NCBI_BIN_COPY = /home/coremake/ncbi/bin
 NCBI_INCDIR = /home/coremake/ncbi/include
diff --git a/sequin/sequin.h b/sequin/sequin.h
index 44ab2770..c3b73d01 100644
--- a/sequin/sequin.h
+++ b/sequin/sequin.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.99 $
+* $Revision: 6.118 $
 *
 * File Description: 
 *
@@ -165,6 +165,7 @@ extern void EditFeatureStrand (IteM i);
 extern void PrefixAuthorityWithOrganism (IteM i);
 extern void UpdateFastaSet (IteM i);
 extern void SeqLocAdjustByOffset (SeqLocPtr slp, Int4 offset);
+extern SeqLocPtr SeqLocWholeNew (BioseqPtr bsp);
 extern SeqFeatPtr SeqFeatCopy (SeqFeatPtr sfp);
 extern SeqLocPtr SeqLocReplaceLocalID (SeqLocPtr slp,
 				       SeqIdPtr  new_sip);
@@ -215,6 +216,21 @@ extern Boolean HasZeroLengthSequence (ForM newForm);
 extern Boolean SequencesFormHasProteins (ForM f);
 extern Boolean SequencesFormHasTooManyNucleotides (ForM f);
 
+extern void AppendOrReplaceString (
+  CharPtr PNTR string_loc,
+  CharPtr new_value,
+  Boolean PNTR asked_question,
+  Boolean PNTR do_replace,
+  Boolean PNTR use_semicolon
+);
+
+extern void ConsolidateOrganismNotes (IteM i);
+extern void ConsolidateLikeModifiersWithSemicolons (IteM i);
+extern void ConsolidateLikeModifiersWithoutSemicolons (IteM i);
+
+extern void ExtendPartialFeatures (IteM i);
+extern void TrimOrganismName (IteM i);
+
 extern void ConfirmSequencesFormParsing (ForM f, FormActnFunc putItAllTogether);
 
 extern ForM CreateHelpForm (Int2 left, Int2 top, CharPtr title,
@@ -282,6 +298,8 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp);
 extern void SetupNewFeaturesMenu (MenU m, BaseFormPtr bfp);
 extern void SetupNewDescriptorsMenu (MenU m, BaseFormPtr bfp);
 extern void SetupNewPublicationsMenu (MenU m, BaseFormPtr bfp);
+extern void SetupBatchApplyMenu (MenU s, BaseFormPtr bfp);
+extern void SetupBatchEditMenu (MenU s, BaseFormPtr bfp);
 extern MenU CreateAnalysisMenu (WindoW w, BaseFormPtr bfp, Boolean bspviewOK, Boolean docsumOK);
 extern void SetupSequinFilters (void);
 extern void SetupBioseqPageList (void);
@@ -294,6 +312,7 @@ extern void SequinCheckSocketsProc (void);
 
 extern Int4 MySeqEntryToAsn3 (SeqEntryPtr sep, Boolean strip, Boolean correct, Boolean force);
 extern void ValSeqEntryForm (ForM f);
+extern void ValSeqEntryFormEx (ForM f, Boolean doAligns);
 
 extern void InitSequinExtras (void);
 extern void FiniSequinExtras (void);
@@ -356,6 +375,7 @@ extern void VectorScreenProc (IteM i);
 extern void GenerateAutomaticDefLinesCommon (IteM i, Boolean addMods, Boolean smartMods, ButtoN b);
 extern void ForceTaxonFixupBtn (IteM i, ButtoN b);
 extern void CommonAddOrgOrModsToDefLines (IteM i, Int2 orgmod, Int2 subsource, ButtoN b);
+extern void PrefixDefLines (IteM i);
 extern void MRnaFromCdsProc (Uint2 entityID);
 extern void BioseqViewFormToolBar (GrouP h);
 extern Boolean DoBuildContig (void);
@@ -391,6 +411,7 @@ extern void SimplePowerBlastProc (IteM i);
 extern CharPtr MergeValNodeStrings (ValNodePtr list, Boolean useReturn);
 extern CharPtr JustSaveStringFromText (TexT t);
 
+extern void CommonApplyToAllProc (BaseFormPtr bfp, Int2 type);
 extern void ApplyTitle (IteM i);
 extern void ApplyCDS (IteM i);
 extern void ApplyRRNA (IteM i);
@@ -399,6 +420,7 @@ extern void LoadTPAAccessionNumbersFromFile (IteM i);
 extern void LoadSecondaryAccessionNumbersFromFile (IteM i);
 extern void LoadHistoryAccessionNumbersFromFile (IteM i);
 extern void LoadOrganismModifierTable (IteM i);
+extern void LoadFeatureQualifierTable (IteM i);
 
 extern void RemoveRNA (IteM i);
 extern void ConvertRNA (IteM i);
@@ -421,6 +443,7 @@ extern void AutoParseFeatureTableProc (IteM i);
 extern void RecomputeSuggest (IteM i);
 extern void RetranslateCdRegionsNoStop (IteM i);
 extern void RetranslateCdRegionsDoStop (IteM i);
+extern void RetranslateCdRegionsNoStopExceptEndCompleteCDS (IteM i);
 extern void AddGlobalCodeBreak (IteM i);
 extern void CorrectCDSGenCodes (IteM i);
 /* extern void CorrectCDSStartCodon (IteM i); */
@@ -432,7 +455,16 @@ extern void GenerateAutoDefLinesWithMods (IteM i);
 extern void GenerateAutoDefLinesSmartMods (IteM i);
 extern void testAutoDef (IteM i);
 extern void testAutoDefWithOptions (IteM i);
-extern void AutoDefBaseFormCommon (BaseFormPtr bfp, Boolean use_form);
+extern void AutoDefWithoutModifiers (IteM i);
+extern void AutoDefBaseFormCommon (BaseFormPtr bfp, Boolean use_form, Boolean use_modifiers);
+extern void AutoDefToolBtn (ButtoN b);
+extern void AutoDefOptionsToolBtn (ButtoN b);
+
+extern void RemoveDefLinesToolBtn (ButtoN b);
+extern void FindStringProcToolBtn (ButtoN b);
+extern void ParseLocalIDToSourceToolBtn (ButtoN b);
+extern void ResolveExistingLocalIDsToolBtn (ButtoN b);
+extern void GroupExplodeToolBtn (ButtoN b);
 
 extern void EditEvidenceFlag (IteM i);
 extern void EditExceptionFlag (IteM i);
@@ -454,9 +486,13 @@ extern void SelectBioseq (IteM i);
 
 extern void FuseFeature (IteM i);
 
+extern void MakeExonsFromCDSIntervals (IteM i);
+extern void MakeExonsFromMRNAIntervals (IteM i);
+
 extern Int2 LIBCALLBACK CreateDeleteByTextWindow (Pointer data);
 extern void ParseAsnOrFlatfileToAnywhere (IteM i);
 extern void ParseCommentToAnywhere (IteM i);
+extern void ParseLocalIDToAnywhere (IteM i);
 extern void RemoveTextInsideString (IteM i);
 extern void RemoveTextOutsideString (IteM i);
 
@@ -581,7 +617,30 @@ typedef struct sequencesform {
   Int2            currConfirmCount;
 } SequencesForm, PNTR SequencesFormPtr;
 
+typedef int (LIBCALLBACK *CompareFunc) (Nlm_VoidPtr, Nlm_VoidPtr);
+
+extern int LIBCALLBACK CompareImpFeatEnumFieldAssoc (VoidPtr ptr1, VoidPtr ptr2);
+extern int LIBCALLBACK CompareFeatureValNodeStrings (VoidPtr ptr1, VoidPtr ptr2);
+
+extern ValNodePtr InsertMostUsedFeatureValNodes (ValNodePtr old_list);
+
+extern void SortEnumFieldAssocPtrArray (EnumFieldAssocPtr alist, CompareFunc compar);
+
+extern ValNodePtr FindExactStringInStrings ( ValNodePtr strings, CharPtr value);
+
+extern EnumFieldAssocPtr InsertMostUsedFeatureEnumFieldAssoc (
+  EnumFieldAssocPtr alist
+);
+
+extern ValNodePtr BuildFeatureValNodeList (
+  Boolean prefer_most_used,
+  CharPtr wild_card_name,
+  Int4 wild_card_value,
+  Boolean skip_unusual,
+  Boolean skip_import
+);
 
+extern void SetTaxNameAndRemoveTaxRef (OrgRefPtr orp, CharPtr taxname);
 
 #ifdef __cplusplus
 }
diff --git a/sequin/sequin1.c b/sequin/sequin1.c
index 7d0b9236..693b038e 100644
--- a/sequin/sequin1.c
+++ b/sequin/sequin1.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.409 $
+* $Revision: 6.430 $
 *
 * File Description: 
 *
@@ -120,12 +120,10 @@ static char *time_of_compilation = "now";
 #include <taxutil.h>
 
 #ifdef USE_SPELL
-#ifdef WIN_MOTIF
 #include <spellapi.h>
 #endif
-#endif
 
-#define SEQ_APP_VER "5.00"
+#define SEQ_APP_VER "5.15"
 
 #ifndef CODECENTER
 static char* sequin_version_binary = "Sequin Indexer Services Version " SEQ_APP_VER " " __DATE__ " " __TIME__;
@@ -207,6 +205,7 @@ static IteM  findGeneItem = NULL;
 static IteM  findProtItem = NULL;
 static IteM  findPosItem = NULL;
 static IteM  validateItem = NULL;
+static MenU  validateMenu = NULL;
 static IteM  spellItem = NULL;
 static IteM  vectorScreenItem = NULL;
 static IteM  powerBlastItem = NULL;
@@ -274,6 +273,8 @@ static Boolean  dirsubMode = FALSE;
 static MenU     newDescMenu = NULL;
 static MenU     newFeatMenu = NULL;
 static MenU     newPubMenu = NULL;
+static MenU     batchApplyMenu = NULL;
+static MenU     batchEditMenu = NULL;
 static MenU     specialMenu = NULL;
 static MenU     analysisMenu = NULL;
 static Boolean  initialFormsActive = FALSE;
@@ -386,7 +387,7 @@ static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f)
 
 {
   Boolean         allRawOrSeg = TRUE;
-  MsgAnswer       ans;
+  MsgAnswer       ans = ANS_OK;
   Int2            errors;
   Int2            j;
   ErrSev          oldErrSev;
@@ -405,7 +406,7 @@ static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f)
     }
   }
   WatchCursor ();
- Update ();
+  Update ();
   vsp = ValidStructNew ();
   if (vsp != NULL) {
     /*SetChecklistValue (checklistForm, 6);*/
@@ -418,6 +419,11 @@ static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f)
     }
     oldErrSev = ErrSetMessageLevel (SEV_MAX);
     vsp->validateAlignments = TRUE;
+    vsp->alignFindRemoteBsp = TRUE;
+    vsp->doSeqHistAssembly = FALSE;
+    for (j = 0; j < 6; j++) {
+      vsp->errors [j] = 0;
+    }
     ValidateSeqEntry (sep, vsp);
     ErrSetMessageLevel (oldErrSev);
     ErrClear ();
@@ -432,13 +438,12 @@ static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f)
         errors += vsp->errors [j];
       }
     }
-    ValidStructFree (vsp);
     UseWindow ((WindoW) f);
     if (errors > 0) {
       ArrowCursor ();
       Update ();
       if (subtoolMode || smartnetMode) {
-        ans = Message (MSG_OKC, "%s\nFatal %d, Error %d, Warning %d, Info %d\n%s",
+        ans = Message (MSG_OKC, "%s\nReject %d, Error %d, Warning %d, Info %d\n%s",
                        "Submission failed validation test with:",
                        (int) vsp->errors [4], (int) vsp->errors [3],
                        (int) vsp->errors [2], (int) vsp->errors [1],
@@ -446,14 +451,15 @@ static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f)
       } else {
         ans = Message (MSG_OKC, validFailMsg);
       }
-      if (ans != ANS_OK) {
-        /*SetChecklistValue (checklistForm, 5);*/
-        return FALSE;
-      }
     }
+    ValidStructFree (vsp);
   }
   ArrowCursor ();
   Update ();
+  if (ans != ANS_OK) {
+    /*SetChecklistValue (checklistForm, 5);*/
+    return FALSE;
+  }
   return TRUE;
 }
 
@@ -1250,7 +1256,7 @@ static void SmartnetDoneFunc (BaseFormPtr bfp)
 
             /* reset update date in smart mode if GenBank or RefGene, and not HTGS */
 
-            SeqMgrExploreBioseqs (entityID, 0, (Pointer) resetUpdateDate, AllGenBankOrRefSeq, TRUE, TRUE, TRUE);
+            SeqMgrExploreBioseqs (bfp->input_entityID, 0, (Pointer) &resetUpdateDate, AllGenBankOrRefSeq, TRUE, TRUE, TRUE);
             if (/* ans == ANS_YES */ resetUpdateDate) {
                 SeqEntryExplore (sep, NULL, RemoveUpdateDates);
                 sdp = CreateNewDescriptor (sep, Seq_descr_update_date);
@@ -1433,6 +1439,11 @@ static void ProcessDoneButton (ForM f)
     }
     oldErrSev = ErrSetMessageLevel (SEV_MAX);
     vsp->validateAlignments = TRUE;
+    vsp->alignFindRemoteBsp = TRUE;
+    vsp->doSeqHistAssembly = FALSE;
+    for (j = 0; j < 6; j++) {
+      vsp->errors [j] = 0;
+    }
     ValidateSeqEntry (sep, vsp);
     ErrSetMessageLevel (oldErrSev);
     ErrClear ();
@@ -1463,7 +1474,12 @@ static void ProcessDoneButton (ForM f)
           vsp->suppressContext = ShouldSetSuppressContext ();
           oldErrHook = ErrSetHandler (ValidErrHook);
           oldErrSev = ErrSetMessageLevel (SEV_NONE);
-	  vsp->validateAlignments = TRUE;
+          vsp->validateAlignments = TRUE;
+          vsp->alignFindRemoteBsp = TRUE;
+          vsp->doSeqHistAssembly = FALSE;
+          for (j = 0; j < 6; j++) {
+            vsp->errors [j] = 0;
+          }
           ValidateSeqEntry (sep, vsp);
           ErrSetMessageLevel (oldErrSev);
           ErrSetHandler (oldErrHook);
@@ -1574,7 +1590,7 @@ static void Cn3DWinShowProc (IteM i)
 #endif
 */
 
-extern void ValSeqEntryForm (ForM f)
+extern void ValSeqEntryFormEx (ForM f, Boolean doAligns)
 
 {
   Boolean         allRawOrSeg = TRUE;
@@ -1613,15 +1629,22 @@ extern void ValSeqEntryForm (ForM f)
         }
         HideValidateDoc ();
         vsp->suppressContext = ShouldSetSuppressContext ();
-        vsp->validateAlignments = TRUE;
-        vsp->farIDsInAlignments = (Boolean) (subtoolMode || smartnetMode || dirsubMode);
-        if (GetSequinAppParam ("SETTINGS", "VALIDATEFARALIGNIDS", NULL, str, sizeof (str))) {
-          if (StringICmp (str, "TRUE") == 0) {
-            vsp->farIDsInAlignments = TRUE;
+        if (doAligns) {
+          vsp->validateAlignments = TRUE;
+          vsp->alignFindRemoteBsp = TRUE;
+          vsp->doSeqHistAssembly = TRUE;
+          vsp->farIDsInAlignments = (Boolean) (subtoolMode || smartnetMode || dirsubMode);
+          if (GetSequinAppParam ("SETTINGS", "VALIDATEFARALIGNIDS", NULL, str, sizeof (str))) {
+            if (StringICmp (str, "TRUE") == 0) {
+              vsp->farIDsInAlignments = TRUE;
+            }
           }
         }
         oldErrHook = ErrSetHandler (ValidErrHook);
         oldErrSev = ErrSetMessageLevel (SEV_NONE);
+        for (j = 0; j < 6; j++) {
+          vsp->errors [j] = 0;
+        }
         ValidateSeqEntry (sep, vsp);
         ErrSetMessageLevel (oldErrSev);
         ErrSetHandler (oldErrHook);
@@ -1647,6 +1670,12 @@ extern void ValSeqEntryForm (ForM f)
   }
 }
 
+extern void ValSeqEntryForm (ForM f)
+
+{
+  ValSeqEntryFormEx (f, TRUE);
+}
+
 static void ValSeqEntryProc (IteM i)
 
 {
@@ -1662,8 +1691,22 @@ static void ValSeqEntryProc (IteM i)
   }
 }
 
+static void ValSeqEntryProcNoAln (IteM i)
+
+{
+  BaseFormPtr  bfp;
+
+#ifdef WIN_MAC
+  bfp = (BaseFormPtr) currentFormDataPtr;
+#else
+  bfp = (BaseFormPtr) GetObjectExtra (i);
+#endif
+  if (bfp != NULL) {
+    ValSeqEntryFormEx (bfp->form, FALSE);
+  }
+}
+
 #ifdef USE_SPELL
-#ifdef WIN_MOTIF
 static void SpellCheckTheForm (ForM f)
 
 {
@@ -1715,6 +1758,9 @@ static void SpellCheckTheForm (ForM f)
         vsp->suppressContext = ShouldSetSuppressContext ();
         oldErrHook = ErrSetHandler (ValidErrHook);
         oldErrSev = ErrSetMessageLevel (SEV_NONE);
+        for (j = 0; j < 6; j++) {
+          vsp->errors [j] = 0;
+        }
         ValidateSeqEntry (sep, vsp);
         ErrSetMessageLevel (oldErrSev);
         ErrSetHandler (oldErrHook);
@@ -1759,7 +1805,6 @@ static void SpellCheckSeqEntryProc (IteM i)
   }
 }
 #endif
-#endif
 
 extern Int4 MySeqEntryToAsn3Ex (SeqEntryPtr sep, Boolean strip, Boolean correct, Boolean force, Boolean dotaxon);
 extern Int4 MySeqEntryToAsn3 (SeqEntryPtr sep, Boolean strip, Boolean correct, Boolean force)
@@ -3266,10 +3311,13 @@ static void BioseqViewFormActivated (WindoW w)
                    (HANDLE) newDescMenu,
                    (HANDLE) newFeatMenu,
                    (HANDLE) newPubMenu,
+                   (HANDLE) batchApplyMenu,
+                   (HANDLE) batchEditMenu,
                    (HANDLE) prepareItem,
-                   (HANDLE) validateItem,
                    (HANDLE) edithistoryitem,
                    NULL);
+  Enable (validateItem);
+  Enable (validateMenu);
   Enable (aluItem);
   Enable (submitItem);
   Enable (specialMenu);
@@ -3552,8 +3600,9 @@ static void MacDeactProc (WindoW w)
                    (HANDLE) newDescMenu,
                    (HANDLE) newFeatMenu,
                    (HANDLE) newPubMenu,
+                   (HANDLE) batchApplyMenu,
+                   (HANDLE) batchEditMenu,
                    (HANDLE) prepareItem,
-                   (HANDLE) validateItem,
                    (HANDLE) editsequenceitem,
                    (HANDLE) editseqalignitem,
                    (HANDLE) editseqsubitem,
@@ -3564,6 +3613,8 @@ static void MacDeactProc (WindoW w)
                    (HANDLE) featPropItem,
                    (HANDLE) updalignitem,
                    NULL);
+  Disable (validateItem);
+  Disable (validateMenu);
   Disable (aluItem);
   Disable (submitItem);
   Disable (vectorScreenItem);
@@ -4218,10 +4269,9 @@ static void AcceptChangeTargetProc (ButtoN b)
 
   cfp = (ChangeTargetFormPtr) GetObjectExtra (b);
   if (cfp == NULL) return;
-  Hide (cfp->form);
   GetTitle (cfp->seqid, str, sizeof (str));
   SetBioseqViewTarget (cfp->base, str);
-  Remove (cfp->form);
+  SetTitle (cfp->seqid, "");
 }
 
 static void ChangeTargetMessageProc (ForM f, Int2 mssg)
@@ -4415,7 +4465,7 @@ static void PreferencesProc (IteM i)
   SetGroupSpacing (g, 10, 10);
   pfp->prefs = CreateEntrezPrefsDialog (g, NULL);
   c = HiddenGroup (g, 2, 0, NULL);
-  b = PushButton (c, "Accept", AcceptPrefsProc);
+  b = DefaultButton (c, "Accept", AcceptPrefsProc);
   SetObjectExtra (b, pfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
   AlignObjects (ALIGN_CENTER, (HANDLE) pfp->prefs, (HANDLE) c, NULL);
@@ -5929,7 +5979,7 @@ static void CommonAddSeq (IteM i, Int2 type)
                 orp = OrgRefNew ();
                 biop->org = orp;
                 if (orp != NULL) {
-                  orp->taxname = StringSave (str);
+                  SetTaxNameAndRemoveTaxRef (orp, StringSave (str));
                 }
                 vnp = CreateNewDescriptor (sep, Seq_descr_source);
                 if (vnp != NULL) {
@@ -5944,7 +5994,7 @@ static void CommonAddSeq (IteM i, Int2 type)
               orp = OrgRefNew ();
               biop->org = orp;
               if (orp != NULL) {
-                orp->taxname = StringSave (tax);
+                SetTaxNameAndRemoveTaxRef (orp, tax);
               }
               vnp = CreateNewDescriptor (sep, Seq_descr_source);
               if (vnp != NULL) {
@@ -6093,7 +6143,6 @@ static void UpdateSeqWithAcc (IteM i)
   BaseFormPtr  bfp;
   BioseqPtr    bsp;
   SeqEntryPtr  sep;
-  SeqEntryPtr  source_sep = NULL;
 
 #ifdef WIN_MAC
   bfp = currentFormDataPtr;
@@ -6115,7 +6164,6 @@ static void ExtendSeqWithAcc (IteM i)
   BaseFormPtr  bfp;
   BioseqPtr    bsp;
   SeqEntryPtr  sep;
-  SeqEntryPtr  source_sep = NULL;
 
 #ifdef WIN_MAC
   bfp = currentFormDataPtr;
@@ -6394,15 +6442,21 @@ static void BioseqViewFormMenus (WindoW w)
     i = CommandItem (m, "Find by Position...", FindPosProc);
     SetObjectExtra (i, bfp, NULL);
     SeparatorItem (m);
-    i = CommandItem (m, "Validate.../ V", ValSeqEntryProc);
-    SetObjectExtra (i, bfp, NULL);
+    if (indexerVersion) {
+      sub = SubMenu (m, "Validate/ V");
+      i = CommandItem (sub, "Validate Record/ R", ValSeqEntryProc);
+      SetObjectExtra (i, bfp, NULL);
+      i = CommandItem (sub, "Validate no Alignments/ A", ValSeqEntryProcNoAln);
+      SetObjectExtra (i, bfp, NULL);
+    } else {
+      i = CommandItem (m, "Validate/ V", ValSeqEntryProc);
+      SetObjectExtra (i, bfp, NULL);
+    }
 #ifdef USE_SPELL
-#ifdef WIN_MOTIF
     SeparatorItem (m);
     i = CommandItem (m, "Spell Check...", SpellCheckSeqEntryProc);
     SetObjectExtra (i, bfp, NULL);
 #endif
-#endif
 /*#ifdef USE_BLAST*/
     if (useBlast) {
       /*
@@ -6447,8 +6501,10 @@ static void BioseqViewFormMenus (WindoW w)
       sub = SubMenu (m, "Font Selection");
       i = CommandItem (sub, "Display Font...", DisplayFontChangeProc);
       SetObjectExtra (i, bfp, NULL);
+      /*
       SeparatorItem (m);
       CreateLegendItem (m, bfp);
+      */
     }
 
 /*#ifdef EXTRA_SERVICES*/
@@ -6484,6 +6540,11 @@ static void BioseqViewFormMenus (WindoW w)
     m = PulldownMenu (w, "Annotate/ A");
     SetupNewFeaturesMenu (m, bfp);
     SeparatorItem (m);
+    sub = SubMenu (m, "Batch Feature Apply");
+    SetupBatchApplyMenu (sub, bfp);
+    sub = SubMenu (m, "Batch Feature Edit");
+    SetupBatchEditMenu (sub, bfp);
+    SeparatorItem (m);
     sub = SubMenu (m, "Publications");
     SetupNewPublicationsMenu (sub, bfp);
     SeparatorItem (m);
@@ -6498,8 +6559,10 @@ static void BioseqViewFormMenus (WindoW w)
       sub = SubMenu (m, "Font Selection");
       i = CommandItem (sub, "Display Font...", DisplayFontChangeProc);
       SetObjectExtra (i, bfp, NULL);
+      /*
       SeparatorItem (m);
       CreateLegendItem (m, bfp);
+      */
       SeparatorItem (m);
       sub = SubMenu (m, "Layout Override");
       CreateNewLayoutMenu (sub, bfp);
@@ -8186,15 +8249,11 @@ static void SetupDesktop (void)
   medviewprocs.createMenus = MedlineViewFormMenus;
 #endif
   medviewprocs.showAsnPage = TRUE;
-#ifdef WIN_MOTIF
   if (indexerVersion) {
     medviewprocs.useScrollText = TRUE;
   } else {
     medviewprocs.useScrollText = FALSE;
   }
-#else
-  medviewprocs.useScrollText = FALSE;
-#endif
   medviewprocs.handleMessages = SequinMedlineFormMessage;
   medviewprocs.makeControls = DoMakeMedViewerLinkControls;
   SetAppProperty ("MedlineDisplayForm", &medviewprocs);
@@ -8222,6 +8281,11 @@ static void SetupDesktop (void)
     seqviewprocs.createToolBar = BioseqViewFormToolBar; /* now in separate window */
   }
 #endif
+#ifdef WIN_MSWIN
+  if (indexerVersion) {
+    seqviewprocs.createToolBar = BioseqViewFormToolBar; /* now in separate window */
+  }
+#endif
 /*#ifdef INTERNAL_NCBI_SEQUIN*/
   if (indexerVersion) {
     seqviewprocs.allowScrollText = TRUE;
@@ -8289,15 +8353,11 @@ static void SetupDesktop (void)
 #ifdef WIN_MAC
   txtviewprocs.activateForm = TextViewProcFormActivated;
 #endif
-#ifdef WIN_MOTIF
   if (indexerVersion) {
     txtviewprocs.useScrollText = TRUE;
   } else {
     txtviewprocs.useScrollText = FALSE;
   }
-#else
-  txtviewprocs.useScrollText = FALSE;
-#endif
   SetAppProperty ("TextDisplayForm", &txtviewprocs);
 
   SetAppProperty ("HelpMessageProc", (Pointer) ProcessHelpMessage);
@@ -9095,13 +9155,17 @@ static void SetupMacMenus (void)
   findProtItem = CommandItem (m, "Find by Protein...", FindProtProc);
   findPosItem = CommandItem (m, "Find by Position...", FindPosProc);
   SeparatorItem (m);
-  validateItem = CommandItem (m, "Validate...", ValSeqEntryProc);
+  if (indexerVersion) {
+    validateMenu = SubMenu (m, "Validate");
+    CommandItem (validateMenu, "Validate Record/ V", ValSeqEntryProc);
+    CommandItem (validateMenu, "Validate no Alignments", ValSeqEntryProcNoAln);
+  } else {
+    validateItem = CommandItem (m, "Validate", ValSeqEntryProc);
+  }
 #ifdef USE_SPELL
-#ifdef WIN_MOTIF
   SeparatorItem (m);
   spellItem = CommandItem (m, "Spell Check...", SpellCheckSeqEntryProc);
 #endif
-#endif
 /*#ifdef USE_BLAST*/
   if (useBlast) {
     /*
@@ -9142,8 +9206,10 @@ static void SetupMacMenus (void)
     docsumfontItem = CommandItem (sub, "DocSum Font...", DocSumFontChangeProc);
   }
   displayfontItem = CommandItem (sub, "Display Font...", DisplayFontChangeProc);
+  /*
   SeparatorItem (m);
   legendItem = CreateLegendItem (m, NULL);
+  */
   SeparatorItem (m);
   sub = SubMenu (m, "Query Style");
   queryChoice = CreateQueryTypeChoice (sub, NULL);
@@ -9201,6 +9267,11 @@ static void SetupMacMenus (void)
   newFeatMenu = PulldownMenu (NULL, "Annotate");
   SetupNewFeaturesMenu (newFeatMenu, NULL);
   SeparatorItem (newFeatMenu);
+  batchApplyMenu = SubMenu (newFeatMenu, "Batch Feature Apply");
+  SetupBatchApplyMenu (batchApplyMenu, NULL);
+  batchEditMenu = SubMenu (newFeatMenu, "Batch Feature Edit");
+  SetupBatchEditMenu (batchEditMenu, NULL);
+  SeparatorItem (newFeatMenu);
   newPubMenu = SubMenu (newFeatMenu, "Publications");
   SetupNewPublicationsMenu (newPubMenu, NULL);
   SeparatorItem (newFeatMenu);
@@ -10261,7 +10332,6 @@ static VoidPtr LIBCALLBACK DumbUserDataFree (VoidPtr Pointer)
 static void SMCancelAllEdit(void)
 {
     ObjMgrPtr      omp;
-    ObjMgrDataPtr  tmp;
     OMUserDataPtr  omudp;
     Int2           num;
     SMUserDataPtr  sm_usr_data = NULL;
@@ -10307,7 +10377,7 @@ static Int4 SMReadBioseqObj(VoidPtr data, CharPtr buffer, Int4 length, Int4 fd)
     Int4           headlen;
     BioseqPtr      bsp;
     BioseqSetPtr   bssp = NULL, bssp2;
-    SeqEntryPtr    sep = NULL, sep1, sep2, oldsep;
+    SeqEntryPtr    sep = NULL, sep1, sep2;
     ObjMgrData     omdata;
     ObjMgrDataPtr  omdptop = NULL;
     Uint2          parenttype = 0;
@@ -10497,10 +10567,9 @@ static Int4 SMWriteBioseqObj(VoidPtr bio_data,
                              VoidPtr data)
 {
     ByteStorePtr    bsp;
-    Nlm_BSUnitPtr   bsup;
     AsnIoBSPtr      aibp;
     CharPtr buffer;
-    Int4 length, totlen, bytes =0;
+    Int4 length, totlen;
 
     bsp = BSNew(1024);
 
@@ -10583,7 +10652,6 @@ Int2 Main (void)
   */
   OMUserDataPtr  omudp;
   PaneL          p;
-  Int2           procval = OM_MSG_RET_NOPROC;
   CharPtr        ptr;
   SeqEntryPtr    sep;
   Int4           smartPort = 0; 
@@ -10732,6 +10800,16 @@ Int2 Main (void)
           entrezMode = TRUE;
         else if (StringCmp (argv[i], "-h") == 0)
           nohelpMode = TRUE;
+#ifdef USE_SMARTNET
+        else if (StringNCmp (argv[i], "-z", 2) == 0) {
+          smartnetMode = TRUE;
+          dirsubMode = TRUE;
+          if(*(argv[i]+2) != NULLB)
+            smartPort = atoi(argv[i]+2);
+          else
+            smartPort = SM_SERVER_PORT;
+        }
+#endif
       }
   }}
 #endif
@@ -11079,6 +11157,13 @@ Int2 Main (void)
           CleanupSequin ();
           return 0;
         } else {
+          if (! nohelpMode) {
+            SetTitle (w, "Creating help window");
+            if (helpForm == NULL) {
+              helpForm = CreateHelpForm (-95, -5, "Sequin Help", "sequin.hlp",
+                                         HideHelpForm, HelpActivateProc);
+            }
+          }
           SendHelpScrollMessage (helpForm, "Editing the Record", NULL);
         }
         ObjMgrSetOptions (OM_OPT_FREE_IF_NO_VIEW, subtoolEntityID);
@@ -11164,16 +11249,19 @@ Int2 Main (void)
   } else if (startupForm != NULL) {
     Show (startupForm);
     Select (startupForm);
-    if (! nohelpMode) {
-      Show (helpForm);
-      SendHelpScrollMessage (helpForm, "Introduction", NULL);
-    }
     Update ();
     initSubmitForm = CreateInitSubmitterForm (-5, -67, "Submitting Authors",
                                               GetFormat, BackToStartup,
                                               SubmitBlockActivateProc);
     formatForm = CreateFormatForm (-5, -67, "Sequence Format",
                                    GetOrgAndSeq, BackToSubmitter, FormatActivateProc);
+    if (! nohelpMode) {
+      Update ();
+      Show (helpForm);
+      Select (helpForm);
+      Update ();
+      SendHelpScrollMessage (helpForm, "Introduction", NULL);
+    }
   } else {
     Message (MSG_FATAL, "Unable to create window.");
     CleanupSequin ();
diff --git a/sequin/sequin10.c b/sequin/sequin10.c
index 4104e09c..580381de 100644
--- a/sequin/sequin10.c
+++ b/sequin/sequin10.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/3/2003
 *
-* $Revision: 1.154 $
+* $Revision: 1.197 $
 *
 * File Description: 
 *
@@ -48,7 +48,8 @@
 #include <explore.h>
 #include <edutil.h>
 #include <tofasta.h>
-
+#include <gbftdef.h>
+#include <gbfeat.h>
 
 /* The matchFunction functions are used to identify features that meet
  * specific requirements, usually that the feature is of a particular type.
@@ -154,7 +155,7 @@ static ValNodePtr FindStringInStrings (
 /* This function finds the first item in "strings" that is identical to
  * "value".
  */
-static ValNodePtr FindExactStringInStrings (
+extern ValNodePtr FindExactStringInStrings (
   ValNodePtr strings,
   CharPtr    value
 )
@@ -304,6 +305,7 @@ typedef struct organismdescriptionmodifiers {
   Boolean  keep_paren;
   Boolean  exclude_sp;
   Int4     clone_isolate_HIV_rule_num;
+  Boolean  use_modifiers;
 } OrganismDescriptionModifiers, PNTR OrganismDescriptionModifiersPtr;
 /* This is a list of the modifiers that are of interest */
 /* Note that if you modify the DefLineModifiers array, */ 
@@ -342,6 +344,7 @@ static ModifierItemGlobalData DefLineModifiers[] = {
   { "Isolation-source"     , FALSE, SUBSRC_isolation_source     , FALSE },
   { "Lab-host"             , FALSE, SUBSRC_lab_host             , FALSE },
   { "Map"                  , FALSE, SUBSRC_map                  , FALSE },
+  { "Old-lineage"          , TRUE , ORGMOD_old_lineage          , FALSE },
   { "Old-name"             , TRUE , ORGMOD_old_name             , FALSE },
   { "Pathovar"             , TRUE , ORGMOD_pathovar             , FALSE },
   { "Plasmid-name"         , FALSE, SUBSRC_plasmid_name         , TRUE  },
@@ -354,7 +357,7 @@ static ModifierItemGlobalData DefLineModifiers[] = {
   { "Serovar"              , TRUE , ORGMOD_serovar              , FALSE },
   { "Sex"                  , FALSE, SUBSRC_sex                  , FALSE },
   { "Specific-host"        , TRUE , ORGMOD_nat_host             , FALSE },
-  { "Specimen-voucher"     , TRUE , ORGMOD_specimen_voucher     , FALSE },
+  { "Specimen voucher"     , TRUE , ORGMOD_specimen_voucher     , FALSE },
   { "Strain"               , TRUE , ORGMOD_strain               , FALSE },
   { "Subclone"             , FALSE, SUBSRC_subclone             , FALSE },
   { "Subgroup"             , TRUE , ORGMOD_subgroup             , FALSE },
@@ -404,6 +407,7 @@ typedef enum {
   DEFLINE_POS_Isolation_source,
   DEFLINE_POS_Lab_host,
   DEFLINE_POS_Map,
+  DEFLINE_POS_Old_lineage,
   DEFLINE_POS_Old_name,
   DEFLINE_POS_Pathovar,
   DEFLINE_POS_Plasmid_name,
@@ -455,9 +459,7 @@ static void CountModifiersProc (
 )
 {
   ModifierItemLocalPtr ItemList;
-  OrgRefPtr     orp;
   OrgModPtr     mod;
-  OrgNamePtr    onp;
   SubSourcePtr  ssp;
   Int2 i;
   Boolean       found_this_modifier;
@@ -465,18 +467,13 @@ static void CountModifiersProc (
   if (biop == NULL) return;
   ItemList = (ModifierItemLocalPtr) userdata;
 
-  orp = biop->org;
-  if (orp == NULL) return;
-
-  onp = orp->orgname;
-  if (onp == NULL) return;
-
   for (i=0; i < NumDefLineModifiers; i++)
   {
     found_this_modifier = FALSE;
     if (DefLineModifiers[i].isOrgMod)
     {
-      mod = onp->mod;
+      if ( biop->org == NULL || biop->org->orgname == NULL) continue;
+      mod = biop->org->orgname->mod;
       while (mod != NULL
         && mod->subtype != DefLineModifiers[i].subtype)
       {
@@ -652,21 +649,16 @@ static void AddQualToBioSrcDescPtr (
   Int2 feature_index
 )
 {
-  OrgRefPtr          orp;
   OrgModPtr          mod;
-  OrgNamePtr         onp;
   SubSourcePtr       ssp;
 
   if (bsdp == NULL) return;
   if (bsdp->biop == NULL) return;
-  orp = bsdp->biop->org;
-  if (orp == NULL) return;
 
-  onp = orp->orgname;
-  if (onp == NULL) return;
   if (DefLineModifiers[feature_index].isOrgMod)
   {
-    mod = onp->mod;
+    if (bsdp->biop->org == NULL || bsdp->biop->org->orgname == NULL) return;
+    mod = bsdp->biop->org->orgname->mod;
     while (mod != NULL
         && mod->subtype != DefLineModifiers[feature_index].subtype)
     {
@@ -1116,8 +1108,11 @@ static void BuildTaxOrgGroupList (
         ogp->num_organisms ++;
       }
     }
-    prevOgp = ogp;
-    ogp = ogp->next;
+    if (cmpval < 0)
+    {
+      prevOgp = ogp;
+      ogp = ogp->next;
+    }
   }
   if (cmpval != 0)
   {
@@ -1140,18 +1135,55 @@ static void BuildTaxOrgGroupList (
   }
 }
 
+typedef struct bestsortdata {
+  Int4    feature_index;
+  Boolean all_unique;
+  Boolean all_present;
+  Boolean is_unique;
+} BestSortData, PNTR BestSortPtr;
+
+static Boolean Index1FoundBeforeIndex2 (
+  Int4 index1,
+  Int4 index2,
+  ValNodePtr list
+)
+{
+  ValNodePtr  vnp;
+  BestSortPtr bsp;
+  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  {
+    if ((bsp = vnp->data.ptrvalue) == NULL)
+    {
+      continue;
+    }
+    if (bsp->feature_index == index1) return TRUE;
+    if (bsp->feature_index == index2) return FALSE;
+  }
+  return FALSE;
+}
+
 /* This function determines whether or not we should try adding this modifier
  * to our combination.  If we've already tried it and not added it to the list,
  * there's no reason to try adding it again.
  */
-static Boolean okToTryAddingQual (
+static Boolean OkToTryAddingQual (
   ModifierCombinationPtr m,
   ModifierItemLocalPtr ItemList,
+  ValNodePtr           available_modifiers_list,
   Int2 feature_index
 )
 {
   ValNodePtr vnp;
 
+  /* if feature_index indicates a value we don't use for best combos, skip */
+  if (feature_index == DEFLINE_POS_Old_name
+    || feature_index == DEFLINE_POS_Old_lineage
+    || feature_index == DEFLINE_POS_Dosage
+    || feature_index == DEFLINE_POS_Map)
+  {
+    return FALSE;
+  }
+
   if (m == NULL) return TRUE;
 
   /* if feature_index is lower than anything else on list (other than */
@@ -1162,13 +1194,111 @@ static Boolean okToTryAddingQual (
     if (feature_index == m->modifier_indices->data.intvalue)
       return FALSE;
     if (! ItemList[m->modifier_indices->data.intvalue].required &&
-        feature_index < m->modifier_indices->data.intvalue)
+      Index1FoundBeforeIndex2 (feature_index,
+                               m->modifier_indices->data.intvalue, 
+                               available_modifiers_list))
+    {
       return FALSE;
+    }
     vnp = vnp->next;
   }
   return TRUE;
 }
 
+static ValNodePtr GetListOfAvailableModifiers ( ModifierItemLocalPtr ItemList)
+{
+  ValNodePtr  vnp, head;
+  Int2        feature_index;
+  BestSortPtr bsp;
+
+  head = NULL;
+  for (feature_index = 0; feature_index < NumDefLineModifiers; feature_index++)
+  {
+    if ( ItemList[feature_index].any_present)
+    {
+      bsp = (BestSortPtr) MemNew (sizeof (BestSortData));
+      if (bsp == NULL) return NULL;
+      bsp->feature_index = feature_index;
+      bsp->all_unique = ItemList[feature_index].all_unique;
+      bsp->all_present = ItemList[feature_index].all_present;
+      bsp->is_unique = ItemList[feature_index].is_unique;
+      vnp = ValNodeNew (head);
+      if (vnp == NULL) return NULL;
+      vnp->data.ptrvalue = bsp;
+      if (head == NULL) head = vnp;
+    }
+  }
+  return head;
+}
+
+static Int4 DefLineQualSortOrder [] = {
+  DEFLINE_POS_Transgenic,
+  DEFLINE_POS_Plasmid_name,
+  DEFLINE_POS_Endogenous_virus_name,
+  DEFLINE_POS_Strain,
+  DEFLINE_POS_Clone,
+  DEFLINE_POS_Isolate,
+  DEFLINE_POS_Haplotype,
+  DEFLINE_POS_Cultivar,
+  DEFLINE_POS_Specimen_voucher,
+  DEFLINE_POS_Ecotype,
+  DEFLINE_POS_Type,
+  DEFLINE_POS_Serotype,
+  DEFLINE_POS_Authority,
+  DEFLINE_POS_Breed
+};
+
+static int LIBCALLBACK SortByImportanceAndPresence (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+{
+  ValNodePtr  vnp1;
+  ValNodePtr  vnp2;
+  BestSortPtr bsp1, bsp2; 
+  Int4       num_defline_qual_sort_order, index;
+
+  if (ptr1 == NULL && ptr2 == NULL) return 0;
+  
+  if (ptr1 == NULL && ptr2 != NULL) return -1;
+  if (ptr1 != NULL && ptr2 == NULL) return 1;
+ 
+  vnp1 = *((ValNodePtr PNTR) ptr1);
+  vnp2 = *((ValNodePtr PNTR) ptr2);
+  if (vnp1 == NULL || vnp2 == NULL) return 0;
+  if (vnp1->data.ptrvalue == NULL || vnp2->data.ptrvalue == NULL) return 0;
+
+  bsp1 = vnp1->data.ptrvalue;
+  bsp2 = vnp2->data.ptrvalue;
+  if (bsp1->feature_index == bsp2->feature_index) return 0;
+
+  if (bsp1->all_present && bsp1->all_unique
+    && (! bsp2->all_present || ! bsp2->all_unique))
+  {
+    return -1;
+  }
+  if (bsp2->all_present && bsp2->all_unique
+    && (! bsp1->all_present || ! bsp1->all_unique))
+  {
+    return 1;
+  }
+
+  if ( ! bsp1->is_unique && bsp2->is_unique) return -1;
+  if ( ! bsp2->is_unique && bsp1->is_unique) return 1;
+
+  num_defline_qual_sort_order = sizeof (DefLineQualSortOrder) / sizeof (Int4);
+  for (index = 0; index < num_defline_qual_sort_order; index++)
+  {
+    if (bsp1->feature_index == DefLineQualSortOrder [ index ]) return -1;
+    if (bsp2->feature_index == DefLineQualSortOrder [ index ]) return 1;
+  }
+
+  if (bsp1->feature_index > bsp2->feature_index) return 1;
+  if (bsp1->feature_index < bsp2->feature_index) return -1;
+  return 0;
+}
+
+
 /* The function FindBestCombo tries to find the best combination of modifiers
  * to create unique organism descriptions.  This is accomplished by
  * creating a list of required modifiers, and then creating a list of
@@ -1202,7 +1332,9 @@ static ModifierCombinationPtr FindBestCombo(
   ModifierCombinationPtr mc_list, start_of_expand, best_found, end_of_list;
   ModifierCombinationPtr next_start_of_expand, m, newm;
   Int4 num_to_expand, next_num_to_expand;
-  Int2 i, feature_index;
+  Int2 i;
+  ValNodePtr available_modifier_list, vnp;
+  BestSortPtr bsp;
 
   best_found = NULL;
 
@@ -1214,12 +1346,17 @@ static ModifierCombinationPtr FindBestCombo(
   mc_list = NewModifierCombo (group_list);
   if (mc_list == NULL) return NULL;
 
+  available_modifier_list = GetListOfAvailableModifiers (ItemList);
+
   /* next, add in any required qualifiers */
-  for (feature_index = 0; feature_index < NumDefLineModifiers; feature_index++)
+  for (vnp = available_modifier_list; vnp != NULL; vnp = vnp->next)
   {
-    if (ItemList[feature_index].required)
+    bsp = vnp->data.ptrvalue;
+    if (bsp == NULL) return NULL;
+    if (ItemList[bsp->feature_index].required)
     {
-      AddQualToModifierCombo (mc_list, ItemList + feature_index, feature_index);
+      AddQualToModifierCombo (mc_list, ItemList + bsp->feature_index,
+                                       bsp->feature_index);
     }
   }
   if (mc_list->max_orgs_in_group == 1)
@@ -1229,6 +1366,8 @@ static ModifierCombinationPtr FindBestCombo(
     return best_found;
   }
 
+  available_modifier_list = SortValNode (available_modifier_list,
+                                         SortByImportanceAndPresence);
   start_of_expand = mc_list;
   end_of_list = mc_list;
   num_to_expand = 1;
@@ -1239,16 +1378,19 @@ static ModifierCombinationPtr FindBestCombo(
     for (i=0; i < num_to_expand && start_of_expand != NULL; i++)
     {
       /* try adding qualifiers */ 
-      for (feature_index = 0;
-           feature_index < NumDefLineModifiers && best_found == NULL;
-           feature_index++)
-      {
-        if ( ItemList[feature_index].any_present
-          && okToTryAddingQual (start_of_expand, ItemList, feature_index))
+      for (vnp = available_modifier_list;
+           vnp != NULL && best_found == NULL;
+           vnp = vnp->next)
+      {
+        bsp = vnp->data.ptrvalue;
+        if (bsp == NULL) return NULL;
+        if (OkToTryAddingQual (start_of_expand, ItemList,
+                               available_modifier_list,
+                               bsp->feature_index))
         {
           newm = CopyModifierCombo (start_of_expand);
-          AddQualToModifierCombo (newm, ItemList + feature_index,
-        feature_index);
+          AddQualToModifierCombo (newm, ItemList + bsp->feature_index,
+                                  bsp->feature_index);
           if (start_of_expand->num_groups >= newm->num_groups)
           {
             /* situation didn't get better, don't bother to add this one */
@@ -1297,7 +1439,13 @@ static ModifierCombinationPtr FindBestCombo(
       best_found = m;
     }
     else if (m->num_unique_orgs == best_found->num_unique_orgs
-           && m->num_groups < best_found->num_groups)
+           && m->num_groups > best_found->num_groups)
+    {
+      best_found = m;
+    }
+    else if (m->num_unique_orgs == best_found->num_unique_orgs
+           && m->num_groups == best_found->num_groups
+           && m->num_mods < best_found->num_groups)
     {
       best_found = m;
     }
@@ -1324,9 +1472,43 @@ static ModifierCombinationPtr FindBestCombo(
   return best_found;
 }
 
+/* create combo with the specified modifiers */
+static ModifierCombinationPtr CreateComboFromModList (
+  ModifierItemLocalPtr modList
+)
+{
+  ModifierCombinationPtr m;
+  Int4                   feature_index;
+
+  m = NewModifierCombo (NULL);
+  if (m == NULL) return NULL;
+  for (feature_index = 0; feature_index < NumDefLineModifiers; feature_index++)
+  {
+    if (modList[feature_index].any_present && modList [feature_index].required)
+    {
+      AddQualToModifierCombo (m, modList + feature_index, feature_index);
+    }
+  }
+  return m;
+}
+
+
 /* This is the callback function for sorting the modifier list.  It 
  * implements an order specified by the indexers.
  */
+static Int4 DefLineQualPresentationOrder [] = {
+  DEFLINE_POS_Transgenic,
+  DEFLINE_POS_Strain,
+  DEFLINE_POS_Isolate,
+  DEFLINE_POS_Cultivar,
+  DEFLINE_POS_Specimen_voucher,
+  DEFLINE_POS_Ecotype,
+  DEFLINE_POS_Type,
+  DEFLINE_POS_Serotype,
+  DEFLINE_POS_Authority,
+  DEFLINE_POS_Breed
+};
+
 static int LIBCALLBACK SortByImportance (
   VoidPtr ptr1,
   VoidPtr ptr2
@@ -1334,6 +1516,8 @@ static int LIBCALLBACK SortByImportance (
 {
   ValNodePtr vnp1;
   ValNodePtr vnp2;
+  Int4       num_defline_qual_sort_order, index;
+
   if (ptr1 == NULL && ptr2 == NULL) return 0;
   
   if (ptr1 == NULL && ptr2 != NULL) return -1;
@@ -1343,24 +1527,82 @@ static int LIBCALLBACK SortByImportance (
   vnp2 = *((ValNodePtr PNTR) ptr2);
   if (vnp1 == NULL || vnp2 == NULL) return 0;
   if (vnp1->data.intvalue == vnp2->data.intvalue) return 0;
-  /* transgenic is first, if present */
-  if (vnp1->data.intvalue == DEFLINE_POS_Transgenic) return -1;
-  if (vnp2->data.intvalue == DEFLINE_POS_Transgenic) return 1;
-  /* plasmid is first, if present, unless transgenic is present */
-  if (vnp1->data.intvalue == DEFLINE_POS_Plasmid_name) return -1;
-  if (vnp2->data.intvalue == DEFLINE_POS_Plasmid_name) return 1;
-  /* endogenous virus is first, if present, unless plasmid or transgenic is first */
-  if (vnp1->data.intvalue == DEFLINE_POS_Endogenous_virus_name) return -1;
-  if (vnp2->data.intvalue == DEFLINE_POS_Endogenous_virus_name) return 1;
-  /* strain is next most important */
-  if (vnp1->data.intvalue == DEFLINE_POS_Strain) return -1;
-  if (vnp2->data.intvalue == DEFLINE_POS_Strain) return 1;
-  /* clone is next most important */
-  if (vnp1->data.intvalue == DEFLINE_POS_Clone) return -1;
-  if (vnp2->data.intvalue == DEFLINE_POS_Clone) return 1;
-  /* isolate is next most important */
-  if (vnp1->data.intvalue == DEFLINE_POS_Isolate) return -1;
-  if (vnp2->data.intvalue == DEFLINE_POS_Isolate) return 1;
+
+  num_defline_qual_sort_order = sizeof (DefLineQualPresentationOrder) / sizeof (Int4);
+  for (index = 0; index < num_defline_qual_sort_order; index++)
+  {
+    if (vnp1->data.intvalue == DefLineQualPresentationOrder [ index ]) return -1;
+    if (vnp2->data.intvalue == DefLineQualPresentationOrder [ index ]) return 1;
+  }
+
+  if ((vnp1->data.intvalue < 0 || vnp1->data.intvalue > NumDefLineModifiers)
+    && (vnp2->data.intvalue < 0 || vnp2->data.intvalue > NumDefLineModifiers))
+  {
+    return 0;
+  }
+  if (vnp1->data.intvalue < 0 || vnp1->data.intvalue > NumDefLineModifiers)
+  {
+    return 1;
+  }
+  if (vnp2->data.intvalue < 0 || vnp2->data.intvalue > NumDefLineModifiers)
+  {
+    return -1;
+  }
+
+  if (DefLineModifiers [ vnp1->data.intvalue].isOrgMod
+    && (! DefLineModifiers [ vnp2->data.intvalue].isOrgMod
+      || vnp2->data.intvalue == DEFLINE_POS_Plasmid_name
+      || vnp2->data.intvalue == DEFLINE_POS_Endogenous_virus_name))
+  {
+    return -1;
+  }
+  if (DefLineModifiers [ vnp2->data.intvalue].isOrgMod
+    && (! DefLineModifiers [ vnp1->data.intvalue].isOrgMod
+      || vnp1->data.intvalue == DEFLINE_POS_Plasmid_name
+      || vnp1->data.intvalue == DEFLINE_POS_Endogenous_virus_name))
+  {
+    return 1;
+  }
+  
+  if (vnp1->data.intvalue == DEFLINE_POS_Plasmid_name)
+  {
+    return -1;
+  }
+  if (vnp2->data.intvalue == DEFLINE_POS_Plasmid_name)
+  {
+    return 1;
+  }
+    
+  if (vnp1->data.intvalue == DEFLINE_POS_Endogenous_virus_name)
+  {
+    return -1;
+  }
+  if (vnp2->data.intvalue == DEFLINE_POS_Endogenous_virus_name)
+  {
+    return 1;
+  }
+
+  if (! DefLineModifiers [ vnp1->data.intvalue].isOrgMod
+     && vnp2->data.intvalue == DEFLINE_POS_Clone)
+  {
+    return 1;
+  }
+  if (! DefLineModifiers [ vnp2->data.intvalue].isOrgMod
+     && vnp1->data.intvalue == DEFLINE_POS_Clone)
+  {
+    return -1;
+  }
+
+  if (! DefLineModifiers [ vnp1->data.intvalue].isOrgMod
+     && vnp2->data.intvalue == DEFLINE_POS_Haplotype)
+  {
+    return 1;
+  }
+  if (! DefLineModifiers [ vnp2->data.intvalue].isOrgMod
+     && vnp1->data.intvalue == DEFLINE_POS_Haplotype)
+  {
+    return -1;
+  }
 
   if (vnp1->data.intvalue > vnp2->data.intvalue) return 1;
   if (vnp1->data.intvalue < vnp2->data.intvalue) return -1;
@@ -1513,6 +1755,17 @@ static void AddModifierLabel (
   {
     StringCpy (modifier_text, "endogenous virus");
   }
+  else if (feature_index == DEFLINE_POS_Specimen_voucher)
+  {
+    if (use_labels)
+    {
+      StringCpy (modifier_text, "voucher");
+    } 
+    else
+    {
+      modifier_text [0] = 0;
+    }
+  }
   else if (use_labels || feature_index == DEFLINE_POS_Transgenic
     || feature_index == DEFLINE_POS_Plasmid_name)
   {
@@ -1721,8 +1974,6 @@ static CharPtr GetOrganismDescription (
   Char    modifier_text [256];
   ValNodePtr  strings;
   BioSourcePtr  biop;
-  OrgRefPtr  orp;
-  OrgNamePtr  onp;
   OrgModPtr  mod;
   SubSourcePtr  ssp;
   ValNodePtr  modifier_indices;
@@ -1730,6 +1981,8 @@ static CharPtr GetOrganismDescription (
   Int2    feature_index;
   CharPtr  org_desc;
   CharPtr  cp;
+  Int4    no_semicolon_len;
+  Int4    label_len;
 
   biop = NULL;
   strings = NULL;
@@ -1756,21 +2009,23 @@ static CharPtr GetOrganismDescription (
 
   ValNodeAddStr (&strings, 0, StringSave (taxName));
 
-  orp = biop->org;
-  if (orp == NULL) return NULL;
-  onp = orp->orgname;
-  if (onp == NULL) return NULL; 
   modifier_indices = CopyModifierIndices (m->modifier_indices);
   AddHIVModifierIndices (&modifier_indices, biop, modList, taxName,
                          odmp->clone_isolate_HIV_rule_num);
   modifier_indices = SortValNode (modifier_indices, SortByImportance);
-  vnp = modifier_indices;
-  while (vnp != NULL && (odmp->max_mods == -99 || odmp->max_mods > 0))
+  for (vnp = modifier_indices;
+       vnp != NULL && (odmp->max_mods == -99 || odmp->max_mods > 0);
+       vnp = vnp->next)
   {
     feature_index = vnp->data.intvalue;
-    if (DefLineModifiers[feature_index].isOrgMod)
+    if (! odmp->use_modifiers && !DefLineModifiers[feature_index].default_required)
+    {
+      /* do nothing */
+    }
+    else if (DefLineModifiers[feature_index].isOrgMod)
     {
-      mod = onp->mod;
+      if (biop->org == NULL || biop->org->orgname == NULL) continue;
+      mod = biop->org->orgname->mod;
       while (mod != NULL
         && mod->subtype != DefLineModifiers[feature_index].subtype)
       {
@@ -1778,20 +2033,32 @@ static CharPtr GetOrganismDescription (
       }
       if ( UseOrgModifier (mod, taxName))
       {
+        no_semicolon_len = StringCSpn (mod->subname, ";");
+
         if (mod->subtype == ORGMOD_nat_host)
         {
           sprintf (modifier_text, "from ");
+          if (no_semicolon_len > sizeof (modifier_text) - 6)
+          {
+            no_semicolon_len = sizeof (modifier_text) - 6;
+          }
           StringNCpy (modifier_text + 5, mod->subname,
-                      sizeof (modifier_text) - 6);
-          modifier_text[sizeof (modifier_text) - 1] = 0;
+                      no_semicolon_len);
+          modifier_text[no_semicolon_len + 5] = 0;
         }
         else
         {
           AddModifierLabel (odmp->use_labels, feature_index, modifier_text);
           if (modifier_text[0] != 0)
             StringCat (modifier_text, " ");
+          label_len = StringLen (modifier_text);
+          if (no_semicolon_len > sizeof (modifier_text) - label_len - 1)
+          {
+            no_semicolon_len = sizeof (modifier_text) - label_len - 1;
+          } 
           StringNCat (modifier_text, mod->subname,
-                      sizeof (modifier_text) - StringLen (modifier_text) - 1);
+                      no_semicolon_len);
+          modifier_text [ no_semicolon_len + label_len] = 0;
         }
         ValNodeCopyStr( &strings, 0, modifier_text);
         if (odmp->max_mods != -99)
@@ -1806,6 +2073,7 @@ static CharPtr GetOrganismDescription (
       }
       if (ssp != NULL)
       {
+        no_semicolon_len = StringCSpn (ssp->name, ";");
         AddModifierLabel (odmp->use_labels, feature_index, modifier_text);
         if (ssp->subtype == SUBSRC_transgenic)
         {
@@ -1814,8 +2082,12 @@ static CharPtr GetOrganismDescription (
         else if (ssp->subtype == SUBSRC_country)
         {
           sprintf (modifier_text, "from ");
-          StringNCpy (modifier_text + 5, ssp->name, sizeof (modifier_text) - 6);
-          modifier_text[sizeof (modifier_text) - 1] = 0;
+          if (no_semicolon_len > sizeof (modifier_text) - 6)
+          {
+            no_semicolon_len = sizeof (modifier_text) - 6;
+          }
+          StringNCpy (modifier_text + 5, ssp->name, no_semicolon_len);
+          modifier_text[5 + no_semicolon_len] = 0;
           cp = StringChr (modifier_text, ':');
           if (cp != NULL) *cp = 0;
         }
@@ -1825,15 +2097,19 @@ static CharPtr GetOrganismDescription (
         {
           if (modifier_text[0] != 0)
             StringCat (modifier_text, " ");
-          StringNCat (modifier_text, ssp->name,
-    sizeof (modifier_text) - StringLen (modifier_text) - 1);
+          label_len = StringLen (modifier_text);
+          if (no_semicolon_len > sizeof (modifier_text) - 1 - label_len)
+          {
+            no_semicolon_len = sizeof (modifier_text) - 1 - label_len;
+          }
+          StringNCat (modifier_text, ssp->name, no_semicolon_len);
+          modifier_text [ no_semicolon_len + label_len ] = 0;
         }
         ValNodeCopyStr( &strings, 0, modifier_text);
         if (odmp->max_mods != -99)
           odmp->max_mods --;
       }
     }
-    vnp = vnp->next;
   }
   org_desc = MergeValNodeStrings (strings, FALSE);
   ValNodeFreeData (strings);
@@ -2290,8 +2566,9 @@ static CharPtr GetInsertionSequenceDescription (
 {
   GBQualPtr gbqual;
 
-  if (sfp == NULL) return NULL;
+  if (sfp == NULL || sfp->qual == NULL) return NULL;
   
+  gbqual = sfp->qual;
   while (gbqual != NULL && StringCmp (gbqual->qual, "insertion_seq") != 0)
   {
     gbqual = gbqual->next;
@@ -2376,7 +2653,7 @@ static Boolean LIBCALLBACK IsControlRegion (
   if (sfp == NULL
     || sfp->idx.subtype != FEATDEF_misc_feature
     || sfp->comment == NULL
-    || StringCmp (sfp->comment, "control region") != 0)
+    || StringNCmp (sfp->comment, "control region", StringLen ("control region")) != 0)
   {
     return FALSE;
   }
@@ -2730,6 +3007,33 @@ static CharPtr GetNoncodingProductFeatProduct (
   return productname;
 }
 
+static Boolean LIBCALLBACK IsMiscFeat (
+  SeqFeatPtr sfp
+)
+{
+  if ( sfp == NULL
+    || sfp->idx.subtype != FEATDEF_misc_feature
+    || sfp->comment == NULL)
+  {
+    return FALSE;
+  }
+
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsOperon (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL 
+    || sfp->idx.subtype != FEATDEF_operon)
+  {
+    return FALSE;
+  }
+
+  return TRUE;
+}
+
 static Boolean IsRecognizedFeature (
   SeqFeatPtr sfp
 )
@@ -2756,7 +3060,9 @@ static Boolean IsRecognizedFeature (
     || IsIntergenicSpacer (sfp)
     || IsTransposon (sfp)
     || IsNoncodingProductFeat (sfp)
-    || IsPromoter (sfp))
+    || IsPromoter (sfp)
+    || IsMiscFeat (sfp)
+    || IsOperon (sfp))
   {
     return TRUE;
   }
@@ -3004,7 +3310,7 @@ static MatchRulePtr InitializeGroupingRules()
   if (grouping_rules == NULL) return NULL;
 
   grouping_rules[0].is_item = IsExon;
-  grouping_rules[0].num_match_rules = 6;
+  grouping_rules[0].num_match_rules = 7;
   grouping_rules[0].match_rules = MemNew (grouping_rules[0].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[0].match_rules == NULL) return NULL;
@@ -3014,9 +3320,10 @@ static MatchRulePtr InitializeGroupingRules()
   grouping_rules[0].match_rules[3] = IsmRNA;
   grouping_rules[0].match_rules[4] = IsGene;
   grouping_rules[0].match_rules[5] = IsEndogenousVirusSourceFeature;
+  grouping_rules[0].match_rules[6] = IsOperon;
 
   grouping_rules[1].is_item = IsIntron;
-  grouping_rules[1].num_match_rules = 6;
+  grouping_rules[1].num_match_rules = 7;
   grouping_rules[1].match_rules = MemNew (grouping_rules[1].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[1].match_rules == NULL) return NULL;
@@ -3026,9 +3333,10 @@ static MatchRulePtr InitializeGroupingRules()
   grouping_rules[1].match_rules[3] = IsDloop;
   grouping_rules[1].match_rules[4] = IsGene;
   grouping_rules[1].match_rules[5] = IsEndogenousVirusSourceFeature;
+  grouping_rules[1].match_rules[6] = IsOperon;
   
   grouping_rules[2].is_item = IsPromoter;
-  grouping_rules[2].num_match_rules = 4;
+  grouping_rules[2].num_match_rules = 5;
   grouping_rules[2].match_rules = MemNew (grouping_rules[2].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[2].match_rules == NULL) return NULL;
@@ -3036,9 +3344,10 @@ static MatchRulePtr InitializeGroupingRules()
   grouping_rules[2].match_rules[1] = IsmRNA;
   grouping_rules[2].match_rules[2] = IsGene;
   grouping_rules[2].match_rules[3] = IsEndogenousVirusSourceFeature;
+  grouping_rules[2].match_rules[4] = IsOperon;
  
   grouping_rules[3].is_item = IsCDS;
-  grouping_rules[3].num_match_rules = 4;
+  grouping_rules[3].num_match_rules = 5;
   grouping_rules[3].match_rules = MemNew (grouping_rules[3].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[3].match_rules == NULL) return NULL;
@@ -3046,18 +3355,20 @@ static MatchRulePtr InitializeGroupingRules()
   grouping_rules[3].match_rules[1] = IsInsertionSequence;
   grouping_rules[3].match_rules[2] = IsTransposon;
   grouping_rules[3].match_rules[3] = IsEndogenousVirusSourceFeature;
+  grouping_rules[3].match_rules[4] = IsOperon;
   
   grouping_rules[4].is_item = IsInsertionSequence;
-  grouping_rules[4].num_match_rules = 3;
+  grouping_rules[4].num_match_rules = 4;
   grouping_rules[4].match_rules = MemNew (grouping_rules[4].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[4].match_rules == NULL) return NULL;
   grouping_rules[4].match_rules[0] = IsTransposon;
   grouping_rules[4].match_rules[1] = IsInsertionSequence;
   grouping_rules[4].match_rules[2] = IsEndogenousVirusSourceFeature;
+  grouping_rules[4].match_rules[3] = IsOperon;
  
   grouping_rules[5].is_item = Is3UTR;
-  grouping_rules[5].num_match_rules = 4;
+  grouping_rules[5].num_match_rules = 5;
   grouping_rules[5].match_rules = MemNew (grouping_rules[5].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[5].match_rules == NULL) return NULL;
@@ -3065,9 +3376,10 @@ static MatchRulePtr InitializeGroupingRules()
   grouping_rules[5].match_rules[1] = IsmRNA;
   grouping_rules[5].match_rules[2] = IsGene;
   grouping_rules[5].match_rules[3] = IsEndogenousVirusSourceFeature;
+  grouping_rules[5].match_rules[4] = IsOperon;
  
   grouping_rules[6].is_item = Is5UTR;
-  grouping_rules[6].num_match_rules = 4;
+  grouping_rules[6].num_match_rules = 5;
   grouping_rules[6].match_rules = MemNew (grouping_rules[6].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[6].match_rules == NULL) return NULL;
@@ -3075,9 +3387,10 @@ static MatchRulePtr InitializeGroupingRules()
   grouping_rules[6].match_rules[1] = IsmRNA;
   grouping_rules[6].match_rules[2] = IsGene;
   grouping_rules[6].match_rules[3] = IsEndogenousVirusSourceFeature;
+  grouping_rules[6].match_rules[4] = IsOperon;
  
   grouping_rules[7].is_item = IsLTR;
-  grouping_rules[7].num_match_rules = 4;
+  grouping_rules[7].num_match_rules = 5;
   grouping_rules[7].match_rules = MemNew (grouping_rules[7].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[7].match_rules == NULL) return NULL;
@@ -3085,33 +3398,37 @@ static MatchRulePtr InitializeGroupingRules()
   grouping_rules[7].match_rules[1] = IsmRNA;
   grouping_rules[7].match_rules[2] = IsGene;
   grouping_rules[7].match_rules[3] = IsEndogenousVirusSourceFeature;
+  grouping_rules[7].match_rules[4] = IsOperon;
  
   grouping_rules[8].is_item = IsGene;
-  grouping_rules[8].num_match_rules = 3;
+  grouping_rules[8].num_match_rules = 4;
   grouping_rules[8].match_rules = MemNew (grouping_rules[8].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[8].match_rules == NULL) return NULL;
   grouping_rules[8].match_rules[0] = IsTransposon;
   grouping_rules[8].match_rules[1] = IsInsertionSequence;
   grouping_rules[8].match_rules[2] = IsEndogenousVirusSourceFeature;
+  grouping_rules[8].match_rules[3] = IsOperon;
 
   grouping_rules[9].is_item = IsTransposon;
-  grouping_rules[9].num_match_rules = 3;
+  grouping_rules[9].num_match_rules = 4;
   grouping_rules[9].match_rules = MemNew (grouping_rules[9].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[9].match_rules == NULL) return NULL;
   grouping_rules[9].match_rules[0] = IsTransposon;
   grouping_rules[9].match_rules[1] = IsInsertionSequence;
   grouping_rules[9].match_rules[2] = IsEndogenousVirusSourceFeature;
+  grouping_rules[9].match_rules[3] = IsOperon;
  
   grouping_rules[10].is_item = IsNoncodingProductFeat;
-  grouping_rules[10].num_match_rules = 3;
+  grouping_rules[10].num_match_rules = 4;
   grouping_rules[10].match_rules = MemNew (grouping_rules[10].num_match_rules
                                     * sizeof (matchFunction));
   if (grouping_rules[10].match_rules == NULL) return NULL;
   grouping_rules[10].match_rules[0] = IsTransposon;
   grouping_rules[10].match_rules[1] = IsInsertionSequence;
   grouping_rules[10].match_rules[2] = IsEndogenousVirusSourceFeature;
+  grouping_rules[10].match_rules[3] = IsOperon;
  
   return grouping_rules; 
 }
@@ -3748,6 +4065,10 @@ static CharPtr GetFeatureTypeWord (
   {
     return StringSave ("5' UTR");
   }
+  else if (IsOperon (sfp))
+  {
+    return StringSave ("operon");
+  }
   else if (biomol == MOLECULE_TYPE_GENOMIC)
   {
     if (IsPseudo (sfp))
@@ -3785,6 +4106,10 @@ static CharPtr GetFeatureTypeWord (
       return StringSave ("precursor RNA");
     }
   }
+  else if (biomol == MOLECULE_TYPE_OTHER_GENETIC_MATERIAL)
+  {
+    return StringSave ("gene");
+  }
   return StringSave ("");
 }
 
@@ -3865,7 +4190,7 @@ static CharPtr GetProductName (
     {
       if ( IstRNA (cds) )
       {
-        protein_name = MemNew ( StringLen (context.label) + 5);
+        protein_name = MemNew ( StringLen (context.label) + 6);
         if ( protein_name == NULL) return NULL;
         sprintf (protein_name, "tRNA-%s", context.label);
         return protein_name;
@@ -4038,6 +4363,7 @@ static void FindGeneProducts (
         }
         if (productfcp != NULL)
         {
+          fcp->is_alt_spliced = productfcp->is_alt_spliced;
           if (productfcp->feature_label_data.productname != NULL)
           {
             fcp->feature_label_data.productname =
@@ -4261,6 +4587,7 @@ static CharPtr GetGenericInterval (
     LabelClauses (featlist, biomol, bsp);
     ListClauses (featlist, &strings, FALSE, suppress_final_and);
     subfeatlist = MergeValNodeStrings (strings, FALSE);
+	ValNodeFreeData (strings);
     len += StringLen (subfeatlist) + 7;
   }
     
@@ -5050,6 +5377,123 @@ static void ReplaceRNAClauses (
   DeleteFeatureClauses (clause_list);
 }
 
+/* If we are applying a different rule for misc_feats, we need to recalculate
+ * their descriptions.
+ */
+static void RenameMiscFeats (ValNodePtr clause_list, Uint1 biomol)
+{
+  ValNodePtr       vnp, featlist;
+  FeatureClausePtr fcp, featlistclause;
+  SeqFeatPtr       sfp;
+  Int4             name_len;
+
+  for (vnp = clause_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice != DEFLINE_CLAUSEPLUS || vnp->data.ptrvalue == NULL)
+    {
+      continue;
+    }
+    fcp = vnp->data.ptrvalue;
+    for (featlist = fcp->featlist; featlist != NULL; featlist = featlist->next)
+    {
+      if ( featlist->data.ptrvalue == NULL)
+      {
+        continue;
+      }
+      if (featlist->choice == DEFLINE_CLAUSEPLUS)
+      {
+        featlistclause = featlist->data.ptrvalue;
+        RenameMiscFeats (featlistclause->featlist, biomol);
+        continue;
+      }
+      if (featlist->choice != DEFLINE_FEATLIST)
+      {
+        continue;
+      }
+      sfp = featlist->data.ptrvalue;
+      if (sfp->idx.subtype != FEATDEF_misc_feature
+        || sfp->comment == NULL
+        || IsIntergenicSpacer (sfp)
+        || IsControlRegion (sfp)) 
+      {
+        continue;
+      }
+      if (fcp->feature_label_data.description != NULL) 
+      {
+        fcp->feature_label_data.description
+                   = MemFree (fcp->feature_label_data.description);
+      }
+      name_len = StringCSpn (sfp->comment, ";");
+      fcp->feature_label_data.description = MemNew (name_len * sizeof (Char));
+      if (fcp->feature_label_data.description == NULL) return;
+      StringNCpy (fcp->feature_label_data.description, sfp->comment, name_len);
+      fcp->feature_label_data.description [ name_len ] = 0;
+      fcp->feature_label_data.typeword =
+            MemFree (fcp->feature_label_data.typeword);
+      if (biomol == MOLECULE_TYPE_GENOMIC)
+      {
+        fcp->feature_label_data.typeword = StringSave ("genomic sequence");
+      }
+      else if (biomol == MOLECULE_TYPE_MRNA)
+      {
+        fcp->feature_label_data.typeword = StringSave ("mRNA sequence");
+      }
+      else
+      {
+        fcp->feature_label_data.typeword = StringSave ("sequence");
+      }
+     
+      fcp->interval = MemFree (fcp->interval);
+      fcp->interval = "";
+    }
+  }
+}
+
+static void RemoveUnwantedMiscFeats (
+  ValNodePtr PNTR clause_list,
+  Boolean delete_now
+)
+{
+  ValNodePtr       vnp, featlist;
+  FeatureClausePtr fcp, featlistclause;
+  SeqFeatPtr       sfp;
+
+  for (vnp = *clause_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice != DEFLINE_CLAUSEPLUS || vnp->data.ptrvalue == NULL)
+    {
+      continue;
+    }
+    fcp = vnp->data.ptrvalue;
+    for (featlist = fcp->featlist; featlist != NULL; featlist = featlist->next)
+    {
+      if ( featlist->data.ptrvalue == NULL)
+      {
+        continue;
+      }
+      if (featlist->choice == DEFLINE_CLAUSEPLUS)
+      {
+        featlistclause = featlist->data.ptrvalue;
+        RemoveUnwantedMiscFeats (&(featlistclause->featlist), FALSE);
+        continue;
+      }
+      if (featlist->choice != DEFLINE_FEATLIST)
+      {
+        continue;
+      }
+      sfp = featlist->data.ptrvalue;
+      if ( sfp->idx.subtype == FEATDEF_misc_feature
+        && ! IsNoncodingProductFeat (sfp)
+        && ! IsControlRegion (sfp)
+        && ! IsIntergenicSpacer (sfp))
+      {
+        fcp->delete_me = TRUE;
+      }
+    }
+  }
+  DeleteFeatureClauses (clause_list);
+}
+
 /* When a feature is on the minus strand, the clauses are listed by 
  * sequence indexing in reverse biological order - we reverse the subclauses
  * for the feature in order to have them listed in the definition line
@@ -5460,15 +5904,21 @@ static void AutoDef_AddEnding (
   StringCat (str, ".");
 
   last_string = *strings;
-  while (last_string->next != NULL) last_string = last_string->next;
-  new_data_len = StringLen (last_string->data.ptrvalue) + StringLen (str) + 1;
-  new_data = (CharPtr) MemNew (new_data_len);
-  if (new_data == NULL) return;
-  StringCpy (new_data, last_string->data.ptrvalue);
-  StringCat (new_data, str);
-  MemFree (last_string->data.ptrvalue);
-  last_string->data.ptrvalue = new_data;
-
+  if (last_string == NULL)
+  {
+    ValNodeAddStr (strings, 0, StringSave ( str));
+  }
+  else
+  {
+    while (last_string->next != NULL) last_string = last_string->next;
+    new_data_len = StringLen (last_string->data.ptrvalue) + StringLen (str) + 1;
+    new_data = (CharPtr) MemNew (new_data_len);
+    if (new_data == NULL) return;
+    StringCpy (new_data, last_string->data.ptrvalue);
+    StringCat (new_data, str);
+    MemFree (last_string->data.ptrvalue);
+    last_string->data.ptrvalue = new_data;
+  }
 }
 
 static Boolean LastIntervalChangeBeforeEnd (
@@ -5812,7 +6262,7 @@ static void ListClauses (
       }
     }
 
-    clause_len = StringLen (thisclause->feature_label_data.description);
+    clause_len = StringLen (thisclause->feature_label_data.description) + 1;
 
     /* we need to place a comma between the description and the type word 
      * when the description ends with "precursor" and the type word
@@ -5864,7 +6314,8 @@ static void ListClauses (
     if (print_and)
       StringCat (clause_string, "and ");
     if (thisclause->feature_label_data.is_typeword_first && print_typeword
-      && thisclause->feature_label_data.typeword != NULL)
+      && thisclause->feature_label_data.typeword != NULL
+      && ! StringHasNoText (thisclause->feature_label_data.typeword))
     {
       StringCat (clause_string, thisclause->feature_label_data.typeword);
       if (typeword_is_plural)
@@ -5881,7 +6332,8 @@ static void ListClauses (
       }
     }
     if (! thisclause->feature_label_data.is_typeword_first && print_typeword
-      && thisclause->feature_label_data.typeword != NULL)
+      && thisclause->feature_label_data.typeword != NULL
+      && ! StringHasNoText (thisclause->feature_label_data.typeword))
     {
       if (thisclause->feature_label_data.description != NULL)
         StringCat (clause_string, " ");
@@ -5904,6 +6356,7 @@ static void ListClauses (
     {
       if (print_semicolon
         && (thisclause->interval == NULL
+          || StringHasNoText(thisclause->interval)
           || thisclause->interval[StringLen (thisclause->interval)] != ';'))
       {
         new_interval = MemNew (StringLen (thisclause->interval) + 2);
@@ -5920,7 +6373,8 @@ static void ListClauses (
         MemFree (thisclause->interval);
         thisclause->interval = new_interval;
       } 
-      if (thisclause->interval != NULL)
+      if (thisclause->interval != NULL
+        && !StringHasNoText (thisclause->interval))
       {
         ValNodeAddStr (strings, 0, StringSave (thisclause->interval));
       }
@@ -5932,22 +6386,16 @@ static void ListClauses (
   }
 }
 
-static Uint1 GetMoleculeType (
-  BioseqPtr bsp
-)
+static Uint1 GetMoleculeType 
+(BioseqPtr bsp,
+ Uint2     entityID)
 {
   SeqDescPtr         sdp;
   MolInfoPtr         mip;
+  SeqMgrDescContext  dcontext;
 
   if (bsp == NULL) return MOLECULE_TYPE_GENOMIC;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, NULL);
-  if (sdp == NULL)
-  {
-    for (sdp = bsp->descr;
-         sdp != NULL && sdp->choice != Seq_descr_molinfo;
-         sdp = sdp->next)
-    {}
-  }
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
   if (sdp == NULL) return MOLECULE_TYPE_GENOMIC;
   mip = (MolInfoPtr) sdp->data.ptrvalue;
   if (mip == NULL) return MOLECULE_TYPE_GENOMIC;
@@ -6201,6 +6649,7 @@ typedef struct deflinefeaturerequestlist {
   Boolean                suppress_alt_splice_phrase;
   Boolean                remove_subfeatures;
   DefLineType            feature_list_type;
+  Int4                   misc_feat_parse_rule;
 } DeflineFeatureRequestList, PNTR DeflineFeatureRequestListPtr;
 
 static void InitFeatureRequests (
@@ -6216,6 +6665,7 @@ static void InitFeatureRequests (
   feature_requests->suppress_alt_splice_phrase = FALSE;
   feature_requests->remove_subfeatures = FALSE;
   feature_requests->feature_list_type = DEFLINE_USE_FEATURES;
+  feature_requests->misc_feat_parse_rule = 2;
 }
 
 static Boolean RemoveCondition (
@@ -6443,6 +6893,48 @@ static void DeleteSubfeatures (
   }
 }
 
+static void DeleteOperonSubfeatures (
+  ValNodePtr PNTR feature_list,
+  Boolean         delete_now
+)
+{
+  ValNodePtr       clause, featlist;
+  FeatureClausePtr clause_fcp, fcp;
+
+  if (feature_list == NULL) return;
+  for (clause = *feature_list; clause != NULL; clause = clause->next)
+  {
+    if (clause->choice != DEFLINE_CLAUSEPLUS
+      || (clause_fcp = clause->data.ptrvalue) == NULL
+      || clause_fcp->featlist == NULL)
+    {
+      continue;
+    }
+    if (clause_fcp->featlist->choice == DEFLINE_FEATLIST
+      && IsOperon (clause_fcp->featlist->data.ptrvalue))
+    {
+      for (featlist = clause_fcp->featlist->next;
+           featlist != NULL;
+           featlist = featlist->next)
+      {
+        if (featlist->choice == DEFLINE_CLAUSEPLUS
+          && (fcp = featlist->data.ptrvalue) != NULL)
+        {
+          fcp->delete_me = TRUE;
+        }
+      }
+    }
+    else
+    {
+      DeleteSubfeatures ( &(clause_fcp->featlist), FALSE);
+    }
+  }
+  if (delete_now) 
+  {
+    DeleteFeatureClauses (feature_list);
+  }
+}
+
 static void RemoveFeats (
   ValNodePtr    list,
   matchFunction itemmatch
@@ -6957,6 +7449,7 @@ FeatureClausePtr NewFeatureClause (
 )
 {
   FeatureClausePtr fcp;
+  Boolean          partial5, partial3;
 
   fcp = (FeatureClausePtr) MemNew (sizeof (FeatureClauseData));
   if (fcp == NULL) return NULL;
@@ -6975,8 +7468,10 @@ FeatureClausePtr NewFeatureClause (
   fcp->is_unknown = FALSE;
   fcp->grp = NULL;
   if (sfp == NULL) return fcp;
+  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
   fcp->slp = SeqLocMerge (bsp, sfp->location, NULL,
                                  FALSE, TRUE, FALSE);
+  SetSeqLocPartial (fcp->slp, partial5, partial3);
   
   if (sfp->data.choice == SEQFEAT_GENE)
   {
@@ -7051,121 +7546,6 @@ static void ExtractSegmentClauses (
   ValNodePtr PNTR segment_clauses
 );
 
-static void CraftDefinitionLineForSeqEntryAndFeatureList (
-  BioseqPtr bsp,
-  Uint1      molecule_type,
-  SeqEntryPtr sep,
-  ValNodePtr  PNTR feature_list,
-  Boolean     isSegment,
-  ValNodePtr  PNTR seg_feature_list,
-  Int2 product_flag,
-  ModifierCombinationPtr m,
-  ModifierItemLocalPtr modList,
-  OrganismDescriptionModifiersPtr odmp,
-  DeflineFeatureRequestList PNTR feature_requests
-)
-{
-  ValNodePtr strings, clause;
-  CharPtr    str, tmp_str;
-  ValNodePtr tmp_feat_list;
- 
-  strings = NULL;
-  str = GetOrganismDescription (bsp, modList, m, odmp);
-  if (str == NULL) return;
-  str[0] = toupper (str [0]);
-
-  if (feature_requests->feature_list_type == DEFLINE_USE_FEATURES
-    && ( ! isSegment || (seg_feature_list != NULL && *seg_feature_list != NULL)))
-  {
-    ValNodeAddStr (&strings, 0, str);
-
-    GroupmRNAs (feature_list, bsp);
-
-    /* genes are added to other clauses */
-    GroupGenes (feature_list);
-
-    if (! feature_requests->suppress_alt_splice_phrase)
-    {
-      /* find alt-spliced CDSs */
-      FindAltSplices (*feature_list, bsp);
-    }
-
-    GroupAltSplicedExons (feature_list, bsp, TRUE);
-
-    /* now group clauses */
-    GroupAllClauses ( feature_list, bsp );
-
-    ExpandAltSplicedExons (*feature_list, bsp);
-
-    FindGeneProducts (*feature_list, bsp);
-
-    if (seg_feature_list != NULL && *seg_feature_list != NULL)
-    {
-      tmp_feat_list = NULL; 
-      ExtractSegmentClauses ( *seg_feature_list, *feature_list, &tmp_feat_list);
-      FreeListElement (*feature_list);
-      *feature_list = tmp_feat_list;
-    }
-   
-    /* remove exons and other unwanted features */
-    RemoveUnwantedFeatures (feature_list, bsp, isSegment, feature_requests);
-
-    RemoveGenesMentionedElsewhere (feature_list, *feature_list, TRUE);
-
-    if (feature_requests->remove_subfeatures)
-    {
-      DeleteSubfeatures (feature_list, TRUE);
-    }
-
-    CountUnknownGenes (feature_list, bsp);
-
-    ReplaceRNAClauses (feature_list, bsp);
-
-    /* take any exons on the minus strand */
-    /* and reverse their order within the clause */
-    ReverseClauses (feature_list, IsExon);
-
-    RenameExonSequences ( feature_list, bsp, TRUE);
-
-    LabelClauses (*feature_list, molecule_type, bsp);
-
-    ConsolidateClauses (feature_list, bsp, molecule_type, TRUE);
-
-    /* this allows genes to be listed together even if they are from */
-    /* separate sequences */
-/*    SmashTallClauses (feature_list, TRUE); */
-
-    clause = *feature_list;
-    ListClauses (clause, &strings, TRUE, FALSE);
-
-    AutoDef_AddEnding (clause, &strings, bsp, 
-                       product_flag);
-
-    str = MergeValNodeStrings (strings, FALSE);
-    ValNodeFreeData (strings);
-  }
-  else if ( feature_requests->feature_list_type == DEFLINE_COMPLETE_SEQUENCE)
-  {
-    tmp_str = MemNew (StringLen (str) + 30);
-    if (tmp_str == NULL) return;
-    StringCpy (tmp_str, str);
-    StringCat (tmp_str, ", complete sequence.");
-    MemFree (str);
-    str = tmp_str;
-  }
-  else if ( feature_requests->feature_list_type == DEFLINE_COMPLETE_GENOME)
-  {
-    tmp_str = MemNew (StringLen (str) + 30);
-    if (tmp_str == NULL) return;
-    StringCpy (tmp_str, str);
-    StringCat (tmp_str, ", complete genome.");
-    MemFree (str);
-    str = tmp_str;
-  }
-
-  ReplaceDefinitionLine (sep, str);
-}
-
 static Boolean FeatureIsOnSegment (
   SeqFeatPtr sfp, 
   ValNodePtr segment_features
@@ -7224,6 +7604,7 @@ static FeatureClausePtr CopyMatchingClauses (
   FeatureClausePtr new_fcp, copy_clause;
   ValNodePtr       featlist, new_feat;
   Boolean          found_feat_on_segment;
+  Boolean          partial5, partial3;
 
   new_fcp = (FeatureClausePtr) MemNew (sizeof (FeatureClauseData));
   if (new_fcp == NULL) return NULL;
@@ -7240,8 +7621,10 @@ static FeatureClausePtr CopyMatchingClauses (
   new_fcp->allelename = StringSave (fcp->allelename);
   new_fcp->interval = StringSave (fcp->interval);
   new_fcp->is_alt_spliced = fcp->is_alt_spliced;
+  CheckSeqLocForPartial (fcp->slp, &partial5, &partial3);
   new_fcp->slp = SeqLocMerge (BioseqFindFromSeqLoc (fcp->slp), fcp->slp, NULL,
                                  FALSE, TRUE, FALSE);
+  SetSeqLocPartial (new_fcp->slp, partial5, partial3);
   new_fcp->grp = fcp->grp;
   new_fcp->delete_me = FALSE;
   new_fcp->clause_info_only = fcp->clause_info_only;
@@ -7351,12 +7734,54 @@ typedef struct segmentdeflinedata {
   Int2 product_flag;
 } SegmentDefLineData, PNTR SegmentDefLinePtr;
 
-static Boolean LIBCALLBACK GetFeatsOnSeg (
+typedef struct segmentdeflinefeatureclausedata {
+  BioseqPtr  parent_bsp;
+  ValNodePtr parent_feature_list;
+  Uint1      molecule_type;
+  DeflineFeatureRequestList PNTR feature_requests;
+  Int2 product_flag;
+  ValNodePtr PNTR list;
+} SegmentDefLineFeatureClauseData, PNTR SegmentDefLineFeatureClausePtr;
+
+typedef struct deflinefeatclause {
+  SeqEntryPtr sep;
+  BioseqPtr   bsp;
+  CharPtr     clauselist;
+} DefLineFeatClauseData, PNTR DefLineFeatClausePtr;
+
+static void DefLineFeatClauseListFree (ValNodePtr vnp)
+{
+  DefLineFeatClausePtr deflist;
+
+  if (vnp == NULL) return;
+  DefLineFeatClauseListFree (vnp->next);
+  vnp->next = NULL;
+  deflist = vnp->data.ptrvalue;
+  if (deflist != NULL)
+  {
+    MemFree (deflist->clauselist);
+    MemFree (deflist);
+  }
+  ValNodeFree (vnp);
+}
+
+static CharPtr BuildFeatureClauses (
+  BioseqPtr bsp,
+  Uint1      molecule_type,
+  SeqEntryPtr sep,
+  ValNodePtr  PNTR feature_list,
+  Boolean     isSegment,
+  ValNodePtr  PNTR seg_feature_list,
+  Int2 product_flag,
+  DeflineFeatureRequestList PNTR feature_requests
+);
+
+static Boolean LIBCALLBACK GetFeatureClauseForSeg (
   SeqLocPtr slp,
   SeqMgrSegmentContextPtr context
 )
 {
-  SegmentDefLinePtr sdlp;
+  SegmentDefLineFeatureClausePtr sdlp;
   ValNodePtr        clause, tmp_parent_list;
   FeatureClausePtr  fcp, new_fcp;
   Int2              idx;
@@ -7366,9 +7791,10 @@ static Boolean LIBCALLBACK GetFeatsOnSeg (
   BioseqPtr         bsp;
   Uint2             entityID;
   SeqLocPtr         loc;
+  DefLineFeatClausePtr deflist;
 
   if (slp == NULL || context == NULL) return FALSE;
-  sdlp = (SegmentDefLinePtr) context->userdata;
+  sdlp = (SegmentDefLineFeatureClausePtr) context->userdata;
 
   sip = SeqLocId (slp);
   
@@ -7418,31 +7844,144 @@ static Boolean LIBCALLBACK GetFeatsOnSeg (
   tmp_parent_list = NULL;
   CopyFeatureList (NULL, sdlp->parent_feature_list, &tmp_parent_list);
 
-  CraftDefinitionLineForSeqEntryAndFeatureList (
-                            sdlp->parent_bsp,
+  deflist = (DefLineFeatClausePtr) MemNew (sizeof (DefLineFeatClauseData));
+  if (deflist == NULL) return TRUE;
+  deflist->sep = SeqMgrGetSeqEntryForData (bsp);
+  deflist->bsp = bsp;
+  deflist->clauselist = BuildFeatureClauses (sdlp->parent_bsp,
                             sdlp->molecule_type,
                             SeqMgrGetSeqEntryForData (bsp),
                             &tmp_parent_list,
                             TRUE,
                             &segment_feature_list,
                             sdlp->product_flag,
-                            sdlp->m, sdlp->modList, sdlp->odmp,
                             sdlp->feature_requests);
+  vnp = ValNodeNew (*(sdlp->list));
+  if (vnp == NULL) return TRUE;
+  if (*(sdlp->list) == NULL) *(sdlp->list) = vnp;
+  vnp->data.ptrvalue = deflist;
 
   FreeListElement (tmp_parent_list);
   FreeListElement (segment_feature_list);
   return TRUE;
 }
-  
 
-static void BuildDefinitionLine (
+static CharPtr BuildFeatureClauses (
+  BioseqPtr bsp,
+  Uint1      molecule_type,
+  SeqEntryPtr sep,
+  ValNodePtr  PNTR feature_list,
+  Boolean     isSegment,
+  ValNodePtr  PNTR seg_feature_list,
+  Int2 product_flag,
+  DeflineFeatureRequestList PNTR feature_requests
+)
+{
+  ValNodePtr strings = NULL;
+  ValNodePtr clause;
+  CharPtr    str = NULL;
+  ValNodePtr tmp_feat_list;
+
+  if (feature_requests->feature_list_type == DEFLINE_USE_FEATURES
+    && ( ! isSegment || (seg_feature_list != NULL && *seg_feature_list != NULL)))
+  {
+    GroupmRNAs (feature_list, bsp);
+
+    /* genes are added to other clauses */
+    GroupGenes (feature_list);
+
+    if (! feature_requests->suppress_alt_splice_phrase)
+    {
+      /* find alt-spliced CDSs */
+      FindAltSplices (*feature_list, bsp);
+    }
+
+    GroupAltSplicedExons (feature_list, bsp, TRUE);
+
+    /* now group clauses */
+    GroupAllClauses ( feature_list, bsp );
+
+    ExpandAltSplicedExons (*feature_list, bsp);
+
+    FindGeneProducts (*feature_list, bsp);
+
+    if (seg_feature_list != NULL && *seg_feature_list != NULL)
+    {
+      tmp_feat_list = NULL; 
+      ExtractSegmentClauses ( *seg_feature_list, *feature_list, &tmp_feat_list);
+      FreeListElement (*feature_list);
+      *feature_list = tmp_feat_list;
+    }
+   
+    /* remove exons and other unwanted features */
+    RemoveUnwantedFeatures (feature_list, bsp, isSegment, feature_requests);
+
+    RemoveGenesMentionedElsewhere (feature_list, *feature_list, TRUE);
+
+    if (feature_requests->remove_subfeatures)
+    {
+      DeleteSubfeatures (feature_list, TRUE);
+    }
+
+    DeleteOperonSubfeatures (feature_list, TRUE);
+
+    CountUnknownGenes (feature_list, bsp);
+
+    if (feature_requests->misc_feat_parse_rule == 1)
+    {
+      RenameMiscFeats (*feature_list, molecule_type);
+    }
+    else
+    {
+      RemoveUnwantedMiscFeats (feature_list, TRUE);
+    }
+
+    ReplaceRNAClauses (feature_list, bsp);
+
+    /* take any exons on the minus strand */
+    /* and reverse their order within the clause */
+    ReverseClauses (feature_list, IsExon);
+
+    RenameExonSequences ( feature_list, bsp, TRUE);
+
+    LabelClauses (*feature_list, molecule_type, bsp);
+
+    ConsolidateClauses (feature_list, bsp, molecule_type, TRUE);
+
+    /* this allows genes to be listed together even if they are from */
+    /* separate sequences */
+/*    SmashTallClauses (feature_list, TRUE); */
+
+    clause = *feature_list;
+    ListClauses (clause, &strings, TRUE, FALSE);
+
+    AutoDef_AddEnding (clause, &strings, bsp, 
+                       product_flag);
+
+    str = MergeValNodeStrings (strings, FALSE);
+	ValNodeFreeData (strings);
+  }
+  else if ( feature_requests->feature_list_type == DEFLINE_COMPLETE_SEQUENCE)
+  {
+    str = StringSave (", complete sequence.");
+  }
+  else if ( feature_requests->feature_list_type == DEFLINE_COMPLETE_GENOME)
+  {
+    str = StringSave (", complete genome.");
+  }
+  else
+  {
+    str = StringSave ("");
+  }
+  return str;
+}
+
+static void BuildDefLineFeatClauseList (
   SeqEntryPtr sep,
   Uint2 entityID,
   DeflineFeatureRequestList PNTR feature_requests,
-  ModifierCombinationPtr m,
-  ModifierItemLocalPtr modList,
-  OrganismDescriptionModifiersPtr odmp,
-  Int2 product_flag
+  Int2 product_flag,
+  ValNodePtr PNTR list
 )
 {
   BioseqSetPtr    bssp;
@@ -7450,9 +7989,12 @@ static void BuildDefinitionLine (
   ValNodePtr    head;
   Uint1      molecule_type;
   SeqEntryPtr   nsep;
-  SegmentDefLineData sdld;
+  SegmentDefLineFeatureClauseData sdld;
+  DefLineFeatClausePtr deflist;
+  ValNodePtr    vnp;
+
+  if (sep == NULL || list == NULL) return;
 
-  if (sep == NULL) return;
   if ( IS_Bioseq_set (sep))
   {
     bssp = (BioseqSetPtr) sep->data.ptrvalue;
@@ -7461,8 +8003,8 @@ static void BuildDefinitionLine (
     {
       for (sep = bssp->seq_set; sep != NULL; sep = sep->next)
       {
-        BuildDefinitionLine (sep, entityID, feature_requests, m, modList,
-                           odmp, product_flag);
+        BuildDefLineFeatClauseList (sep, entityID, feature_requests,
+                                    product_flag, list);
       }
       return;
     }
@@ -7477,24 +8019,29 @@ static void BuildDefinitionLine (
       bsp->seq_ext != NULL && bsp->seq_ext_type == 1) 
     {
       sdld.parent_bsp = bsp;
-      sdld.molecule_type = GetMoleculeType (bsp);
+      sdld.molecule_type = GetMoleculeType (bsp, entityID);
       sdld.parent_feature_list = GetFeatureList (bsp);
 
       sdld.feature_requests =  feature_requests;
-      sdld.m = m;
-      sdld.modList = modList;
-      sdld.odmp = odmp;
       sdld.product_flag = product_flag;
-      SeqMgrExploreSegments (bsp, (Pointer) &sdld, GetFeatsOnSeg);
-      CraftDefinitionLineForSeqEntryAndFeatureList (
-                            bsp,
+      sdld.list = list;
+      SeqMgrExploreSegments (bsp, (Pointer) &sdld, GetFeatureClauseForSeg);
+      deflist = (DefLineFeatClausePtr) MemNew (sizeof (DefLineFeatClauseData));
+      if (deflist == NULL) return;
+      deflist->sep = SeqMgrGetSeqEntryForData (bsp),
+      deflist->bsp = bsp;
+      deflist->clauselist = BuildFeatureClauses (bsp,
                             sdld.molecule_type,
                             SeqMgrGetSeqEntryForData (bsp),
                             &sdld.parent_feature_list,
                             FALSE,
                             NULL,
                             product_flag,
-                            m, modList, odmp, feature_requests);
+                            feature_requests);
+      vnp = ValNodeNew (*list);
+      if (vnp == NULL) return;
+      if (*list == NULL) *list = vnp;
+      vnp->data.ptrvalue = deflist;
       FreeListElement (sdld.parent_feature_list);
       return;
     }
@@ -7507,22 +8054,59 @@ static void BuildDefinitionLine (
   bsp = (BioseqPtr) sep->data.ptrvalue;
   if (bsp == NULL) return;
   if ( SpecialHandlingForSpecialTechniques (bsp)) return;
-  molecule_type = GetMoleculeType (bsp);
+  molecule_type = GetMoleculeType (bsp, entityID);
   head = GetFeatureList (bsp);
 
-  CraftDefinitionLineForSeqEntryAndFeatureList (
-                            bsp,
-                            molecule_type,
-                            SeqMgrGetSeqEntryForData (bsp),
-                            &head,
-                            FALSE,
-                            NULL,
-                            product_flag,
-                            m, modList, odmp, feature_requests);
+  deflist = (DefLineFeatClausePtr) MemNew (sizeof (DefLineFeatClauseData));
+  if (deflist == NULL) return;
+  deflist->sep = SeqMgrGetSeqEntryForData (bsp),
+  deflist->bsp = bsp;
+  deflist->clauselist = BuildFeatureClauses (bsp,
+                                             molecule_type,
+                                             SeqMgrGetSeqEntryForData (bsp),
+                                             &head,
+                                             FALSE,
+                                             NULL,
+                                             product_flag,
+                                             feature_requests);
+  vnp = ValNodeNew (*list);
+  if (vnp == NULL) return;
+  if (*list == NULL) *list = vnp;
+  vnp->data.ptrvalue = deflist;
   FreeListElement (head);
 
 }
 
+static Boolean AreFeatureClausesUnique (ValNodePtr list)
+{
+  ValNodePtr vnp1, vnp2;
+  DefLineFeatClausePtr deflist1, deflist2;
+
+  for (vnp1 = list; vnp1 != NULL && vnp1->next != NULL; vnp1 = vnp1->next)
+  {
+    deflist1 = vnp1->data.ptrvalue;
+    if (deflist1 == NULL || deflist1->clauselist == NULL) return FALSE;
+    
+    for (vnp2 = vnp1->next; vnp2 != NULL; vnp2 = vnp2->next)
+    {
+      deflist2 = vnp2->data.ptrvalue;
+      if (deflist2 == NULL || deflist2->clauselist == NULL
+        || StringCmp (deflist1->clauselist, deflist2->clauselist) == 0)
+      {
+        return FALSE;
+      }
+    }
+  }
+  return TRUE;
+}
+
+static void BuildDefinitionLinesFromFeatureClauseLists (
+  ValNodePtr list,
+  ModifierItemLocalPtr modList,
+  ModifierCombinationPtr m,
+  OrganismDescriptionModifiers odmp
+);
+
 typedef struct deflineformdata {
   FEATURE_FORM_BLOCK
 
@@ -7542,6 +8126,7 @@ typedef struct deflineformdata {
   ButtoN    remove_subfeatures;
   PopuP     featurePopup;
   GrouP     featureOptsGrp;
+  PopuP     misc_feat_parse_rule;
 } DefLineFormData, PNTR DefLineFormPtr;
 
 static void DefLineFormMessageProc (ForM f, Int2 mssg)
@@ -7619,6 +8204,7 @@ static void DoAutoDefLine (ButtoN b)
   OrganismDescriptionModifiers odmp;
   Int2 product_flag, feature_list_type;
   Int4 i;
+  ValNodePtr defline_clauses = NULL;
 
   dlfp = GetObjectExtra (b);
   if (b == NULL) return;
@@ -7629,6 +8215,7 @@ static void DoAutoDefLine (ButtoN b)
   odmp.use_labels = GetStatus (dlfp->use_labels);
   odmp.keep_paren = GetStatus (dlfp->keep_paren);
   odmp.exclude_sp = GetStatus (dlfp->exclude_sp);
+  odmp.use_modifiers = TRUE;
 
   if (dlfp->clone_isolate_HIV_rule_num == NULL)
   {
@@ -7694,6 +8281,9 @@ static void DoAutoDefLine (ButtoN b)
   dlfp->feature_requests.remove_subfeatures = 
                  GetStatus (dlfp->remove_subfeatures);
 
+  dlfp->feature_requests.misc_feat_parse_rule = 
+                 GetValue (dlfp->misc_feat_parse_rule);
+
   odmp.max_mods = GetValue (dlfp->modLimit);
   if (odmp.max_mods > 1)
   {
@@ -7718,8 +8308,14 @@ static void DoAutoDefLine (ButtoN b)
 
   SeqEntrySetScope (sep);
 
-  BuildDefinitionLine (sep, dlfp->input_entityID, &dlfp->feature_requests,
-       m, dlfp->modList, &odmp, product_flag);
+  BuildDefLineFeatClauseList (sep, dlfp->input_entityID,
+                              &dlfp->feature_requests,
+                              product_flag,
+                              &defline_clauses);
+
+  BuildDefinitionLinesFromFeatureClauseLists (defline_clauses, dlfp->modList,
+                                                m, odmp);
+  DefLineFeatClauseListFree (defline_clauses);
   ClearProteinTitlesInNucProts (dlfp->input_entityID, NULL);
   InstantiateProteinTitles (dlfp->input_entityID, NULL);
   ArrowCursor ();
@@ -8000,13 +8596,32 @@ static GrouP CreateDefLineFormFeatureListPopuP (
   
   return q;
 }
+
+static void SetMiscFeatRuleEnable (Handle a)
+{
+  DefLineFormPtr dlfp;
+
+  if (a == NULL || ( dlfp = (DefLineFormPtr) GetObjectExtra (a)) == NULL)
+  {
+    return;
+  }
+  if (dlfp->feature_requests.items != NULL
+    && GetStatus (dlfp->feature_requests.items[RemovableNoncodingProductFeat].keep_request))
+  {
+    Enable (dlfp->misc_feat_parse_rule);
+  }
+  else
+  {
+    Disable (dlfp->misc_feat_parse_rule);
+  }
+}
   
 static GrouP CreateDefLineFormFeatureOptionsGroup (
   GrouP          h,
   DefLineFormPtr dlfp
 )
 {
-  GrouP p, q, g;
+  GrouP p, q, g, r;
   Int4  i;
 
   p = HiddenGroup (h, -1, 0, NULL);
@@ -8032,10 +8647,19 @@ static GrouP CreateDefLineFormFeatureOptionsGroup (
     if (i != RemovableCDS)
     {
       dlfp->feature_requests.items[i].keep_request = 
-                     CheckBox (g, remove_items[i].group_name, NULL);
+                     CheckBox (g, remove_items[i].group_name, 
+                               (BtnActnProc) SetMiscFeatRuleEnable);
+      SetObjectExtra (dlfp->feature_requests.items[i].keep_request, dlfp, NULL);
       SetStatus (dlfp->feature_requests.items[i].keep_request, FALSE);
     }
   }
+  r = HiddenGroup (p, 2, 0, NULL);
+  StaticPrompt (r, "Misc Feat Parse Rule", 0, dialogTextHeight, programFont, 'l');
+  dlfp->misc_feat_parse_rule = PopupList (r, TRUE, NULL);
+  PopupItem (dlfp->misc_feat_parse_rule, "Product is comment before first semicolon");
+  PopupItem (dlfp->misc_feat_parse_rule, "Look for Noncoding Product Features");
+  SetValue (dlfp->misc_feat_parse_rule, 2);
+  Disable (dlfp->misc_feat_parse_rule);
 
   AlignObjects (ALIGN_CENTER, (HANDLE) q,
                  (HANDLE) dlfp->featureOptsGrp, NULL); 
@@ -8043,6 +8667,7 @@ static GrouP CreateDefLineFormFeatureOptionsGroup (
                  (HANDLE) dlfp->suppress_alt_splice_phrase,
                  (HANDLE) dlfp->remove_subfeatures,
                  (HANDLE) g,
+                 (HANDLE) r,
                  NULL);
 
   return p;
@@ -8118,7 +8743,7 @@ static void CreateDefLineForm (
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoAutoDefLine);
+  b = DefaultButton (c, "Accept", DoAutoDefLine);
   SetObjectExtra (b, dlfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -8148,15 +8773,57 @@ static void CreateDefLineForm (
   Update ();
 }
 
-extern void AutoDefBaseFormCommon (BaseFormPtr bfp, Boolean use_form)
+static void BuildDefinitionLinesFromFeatureClauseLists (
+  ValNodePtr list,
+  ModifierItemLocalPtr modList,
+  ModifierCombinationPtr m,
+  OrganismDescriptionModifiers odmp
+)
 {
-  SeqEntryPtr  sep;
+  ValNodePtr vnp;
+  DefLineFeatClausePtr defline_featclause;
+  CharPtr    org_desc, tmp_str;
+
+  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->data.ptrvalue != NULL)
+    {
+      defline_featclause = vnp->data.ptrvalue;
+      org_desc = GetOrganismDescription (defline_featclause->bsp,
+                                         modList, m, &odmp);
+      tmp_str = (CharPtr) MemNew ( StringLen (org_desc) + StringLen (defline_featclause->clauselist) + 2);
+      if (tmp_str == NULL) return;
+      StringCpy (tmp_str, org_desc);
+      if (defline_featclause->clauselist != NULL
+        && defline_featclause->clauselist [0] != ','
+        && defline_featclause->clauselist [0] != '.'
+        && defline_featclause->clauselist [0] != 0)
+      {
+        StringCat (tmp_str, " ");
+      }
+      StringCat (tmp_str, defline_featclause->clauselist);
+      tmp_str [0] = toupper (tmp_str [0]);
+      ReplaceDefinitionLine (defline_featclause->sep, tmp_str);
+      MemFree (org_desc);
+    }
+  }
+}
+
+extern void AutoDefBaseFormCommon (
+  BaseFormPtr bfp,
+  Boolean use_form,
+  Boolean use_modifiers
+)
+{
+  SeqEntryPtr sep;
   DeflineFeatureRequestList feature_requests;
   ModifierItemLocalPtr modList;
   ModifierCombinationPtr m;
   OrganismDescriptionModifiers odmp;
   Int4 index;
+  ValNodePtr defline_clauses = NULL;
 
+  if (bfp == NULL) return;
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
 
@@ -8166,9 +8833,9 @@ extern void AutoDefBaseFormCommon (BaseFormPtr bfp, Boolean use_form)
   if (modList == NULL) return;
   SetRequiredModifiers (modList);
   CountModifiers (modList, sep);
-  m = FindBestCombo (sep, modList);
   if (use_form)
   {
+    m = FindBestCombo (sep, modList);
     AddBestComboModifiersToModList ( m, modList);
     CreateDefLineForm (bfp, modList, &feature_requests);
   }
@@ -8182,9 +8849,22 @@ extern void AutoDefBaseFormCommon (BaseFormPtr bfp, Boolean use_form)
     odmp.keep_paren = TRUE;
     odmp.exclude_sp = TRUE;
     odmp.clone_isolate_HIV_rule_num = clone_isolate_HIV_rule_want_both;
+    odmp.use_modifiers = use_modifiers;
     ClearProteinTitlesInNucProts (bfp->input_entityID, NULL);
-    BuildDefinitionLine (sep, bfp->input_entityID, &feature_requests, m,
-       modList, &odmp, 0);
+    BuildDefLineFeatClauseList (sep, bfp->input_entityID, &feature_requests,
+                                0, &defline_clauses);
+    if ( AreFeatureClausesUnique (defline_clauses))
+    {
+      m = CreateComboFromModList (modList);
+    }
+    else
+    {
+      m = FindBestCombo (sep, modList);
+    }
+
+    BuildDefinitionLinesFromFeatureClauseLists (defline_clauses, modList,
+                                                m, odmp);
+    DefLineFeatClauseListFree (defline_clauses);
     if (modList != NULL)
     {
       for (index=0; index < NumDefLineModifiers; index++)
@@ -8202,7 +8882,7 @@ extern void AutoDefBaseFormCommon (BaseFormPtr bfp, Boolean use_form)
   FreeModifierCombo (m);
 }
 
-static void AutoDefCommon (IteM i, Boolean use_form)
+static void AutoDefCommon (IteM i, Boolean use_form, Boolean use_modifiers)
 {
   BaseFormPtr  bfp;
 
@@ -8212,34 +8892,57 @@ static void AutoDefCommon (IteM i, Boolean use_form)
   bfp = GetObjectExtra (i);
 #endif
   if (bfp == NULL || bfp->input_entityID == 0) return;
-  AutoDefBaseFormCommon (bfp, use_form);
+  AutoDefBaseFormCommon (bfp, use_form, use_modifiers);
 }
 
 extern void testAutoDef (IteM i)
 {
-  AutoDefCommon (i, FALSE);
+  AutoDefCommon (i, FALSE, TRUE);
 }
 
 extern void testAutoDefWithOptions (IteM i)
 {
-  AutoDefCommon (i, TRUE);
+  AutoDefCommon (i, TRUE, TRUE);
+}
+
+extern void AutoDefWithoutModifiers (IteM i)
+{
+  AutoDefCommon (i, FALSE, FALSE);
+}
+
+extern void AutoDefToolBtn (ButtoN b)
+{
+  BaseFormPtr  bfp;
+
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+  AutoDefBaseFormCommon (bfp, FALSE, TRUE);
+}
+
+extern void AutoDefOptionsToolBtn (ButtoN b)
+{
+  BaseFormPtr  bfp;
+
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+  AutoDefBaseFormCommon (bfp, TRUE, TRUE);
 }
 
-typedef struct orgmodlinedata {
+typedef struct tablelinedata {
   Int4 num_parts;
   ValNodePtr parts;
-} OrgModLineData, PNTR OrgModLinePtr;
+} TableLineData, PNTR TableLinePtr;
 
-static OrgModLinePtr MakeOrgModData (CharPtr line)
+static TableLinePtr MakeTableData (CharPtr line)
 {
-  OrgModLinePtr omlp;
+  TableLinePtr tlp;
   CharPtr p_start, p_end;
   Int4    plen;
   Boolean found_end;
 
   if (line == NULL) return NULL;
-  omlp = MemNew (sizeof (OrgModLineData));
-  if (omlp == NULL) return NULL;
+  tlp = MemNew (sizeof (TableLineData));
+  if (tlp == NULL) return NULL;
   p_start = line;
   found_end = FALSE;
   while (*p_start != 0 && !found_end)
@@ -8247,6 +8950,11 @@ static OrgModLinePtr MakeOrgModData (CharPtr line)
     plen = StringCSpn (p_start, "\t\n");
     if (plen == 0)
     {
+      if (tlp->num_parts > 0)
+      {
+        ValNodeAddStr (&tlp->parts, 0, StringSave (""));
+        tlp->num_parts ++;
+      }
       p_start++;
       continue;
     }
@@ -8260,55 +8968,36 @@ static OrgModLinePtr MakeOrgModData (CharPtr line)
       *p_end = 0;
     }
     TrimSpacesAroundString (p_start);
-    ValNodeAddStr (&omlp->parts, 0, StringSave (p_start));
-    omlp->num_parts ++;
+    ValNodeAddStr (&tlp->parts, 0, StringSave (p_start));
+    tlp->num_parts ++;
     if (!found_end)
     {
       p_start = p_end + 1;
     }
   }
-  if (omlp->num_parts == 0)
+  if (tlp->num_parts == 0)
   {
-    MemFree (omlp);
+    MemFree (tlp);
     return NULL;
   }
-  return omlp;  
+  return tlp;  
 }
 
-static void CleanUpOrgModData (ValNodePtr vnp)
+static void CleanUpTableData (ValNodePtr vnp)
 {
-  OrgModLinePtr omlp;
+  TableLinePtr tlp;
 
   if (vnp == NULL) return;
-  CleanUpOrgModData (vnp->next);
+  CleanUpTableData (vnp->next);
   vnp->next = NULL;
-  omlp = vnp->data.ptrvalue;
-  if (omlp != NULL)
+  tlp = vnp->data.ptrvalue;
+  if (tlp != NULL)
   {
-    ValNodeFreeData (omlp->parts);
+    ValNodeFreeData (tlp->parts);
   }
   ValNodeFree (vnp);
 }
 
-static void CombineOrganismModLines (OrgModLinePtr omlp1, OrgModLinePtr omlp2)
-{
-  ValNodePtr vnp;
-
-  if (omlp1->parts == NULL)
-  {
-    omlp1->parts = omlp2->parts;
-    omlp1->num_parts = omlp2->num_parts;
-    MemFree (omlp2);
-    return;
-  }
-  for (vnp = omlp1->parts; vnp->next != NULL; vnp = vnp->next)
-  {}
-  vnp->next = omlp2->parts;
-  omlp1->num_parts = omlp1->num_parts + omlp2->num_parts;
-  MemFree (omlp2);
-  return;
-}
-
 typedef struct orgmodlineformdata {
   Int4    column_number;
   CharPtr value_string;
@@ -8326,6 +9015,7 @@ typedef struct orgmodloadformdata {
   Int4              num_line_forms;
   Uint2             entityID;
   ButtoN            accept_button;
+  
 } OrgModLoadFormData, PNTR OrgModLoadFormPtr;
  
 static void SetFormModsAcceptButton (Handle a)
@@ -8359,7 +9049,7 @@ static void SetFormModsAcceptButton (Handle a)
     }
     else if (GetValue (form_data->line_forms [column_index].action_choice) == 1
       && GetValue (form_data->line_forms [column_index].match_choice) > 0
-      && GetValue (form_data->line_forms [column_index].match_choice) < 4)
+      && GetValue (form_data->line_forms [column_index].match_choice) < 5)
     {
       have_action = TRUE;
     }
@@ -8414,8 +9104,9 @@ static void BuildOrgModLineForm (
   PopupItem (omlfp->match_choice, "Accession");
   PopupItem (omlfp->match_choice, "Local ID");
   PopupItem (omlfp->match_choice, "Organism Taxonomy Name");
+  PopupItem (omlfp->match_choice, "TMSMART ID");
   PopupItem (omlfp->match_choice, "None");
-  SetValue (omlfp->match_choice, 4);
+  SetValue (omlfp->match_choice, 5);
 
   /* list of organism modifiers */
   omlfp->apply_choice = SingleList (g, 5, 8,
@@ -8439,7 +9130,7 @@ static void CleanupOrgModLoadForm (
   form_data = (OrgModLoadFormPtr)data;
   if (form_data == NULL) return;
   MemFree (form_data->line_forms);
-  CleanUpOrgModData (form_data->line_list);
+  CleanUpTableData (form_data->line_list);
   StdCleanupFormProc (g, data);
 } 
 
@@ -8554,7 +9245,7 @@ static void ApplyTableModsByTaxName (BioSourcePtr biop, Pointer userdata)
   OrgModLoadFormPtr form_data;
   Int4 column_index, part_index;
   ValNodePtr line, part;
-  OrgModLinePtr omlp;
+  TableLinePtr tlp;
   Boolean found_org;
   
   form_data = (OrgModLoadFormPtr) userdata;
@@ -8572,9 +9263,9 @@ static void ApplyTableModsByTaxName (BioSourcePtr biop, Pointer userdata)
     {
       for (line = form_data->line_list; line != NULL; line = line->next)
       {
-        omlp = line->data.ptrvalue;
-        if (omlp == NULL) continue;
-        part = omlp->parts;
+        tlp = line->data.ptrvalue;
+        if (tlp == NULL) continue;
+        part = tlp->parts;
         for (part_index = 0;
              part_index < column_index && part != NULL;
              part_index ++)
@@ -8584,7 +9275,7 @@ static void ApplyTableModsByTaxName (BioSourcePtr biop, Pointer userdata)
         if (part != NULL
           && StringCmp (part->data.ptrvalue, biop->org->taxname) == 0)
         {
-          ApplyQualsToOrg (biop, omlp->parts, form_data);
+          ApplyQualsToOrg (biop, tlp->parts, form_data);
           found_org = TRUE;
         }
       }
@@ -8592,18 +9283,69 @@ static void ApplyTableModsByTaxName (BioSourcePtr biop, Pointer userdata)
   }
 }
 
+static Boolean HasExtraAccession (
+  CharPtr acc_str,
+  GBBlockPtr gbp)
+{
+  ValNodePtr vnp;
+  if (acc_str == NULL || gbp == NULL) return FALSE;
+  for (vnp = gbp->extra_accessions;
+       vnp != NULL && StringCmp (acc_str, vnp->data.ptrvalue) != 0;
+       vnp = vnp->next)
+  {}
+  if (vnp != NULL)
+    return TRUE;
+  else
+    return FALSE;
+}
+
+static Boolean IDListHasValue (
+  CharPtr id,
+  SeqIdPtr list,
+  Boolean only_local,
+  Boolean look_for_tmsmart)
+{
+  SeqIdPtr sip;
+  Char     acc_str [256];
+  Int4     match_len;
+
+  for (sip = list; sip != NULL; sip = sip->next)
+  {
+    if ((! only_local && sip->choice != SEQID_LOCAL)
+      || (only_local && sip->choice == SEQID_LOCAL))
+    {
+      SeqIdWrite (sip, acc_str, PRINTID_REPORT, sizeof (acc_str));
+      if (look_for_tmsmart)
+      {
+        if (StringNCmp (acc_str, "TMSMART:", 8) == 0
+          && StringCmp (id, acc_str + 8) == 0)
+        {
+          return TRUE;
+        }
+      } else {
+        match_len = StringCSpn (acc_str, ".");
+        if (match_len > 0 && StringNCmp (id, acc_str, match_len) == 0)
+        {
+          return TRUE;
+        }
+      }
+    }
+  }
+  return FALSE;
+}
+
 static void ApplyTableModsByAccessionNumber (BioseqPtr bsp, Pointer userdata)
 {
   OrgModLoadFormPtr form_data;
   SeqDescrPtr       sdp;
   GBBlockPtr        gbp;
   Int4              column_index, part_index;
-  ValNodePtr        vnp;
   BioSourcePtr      biop;
   ValNodePtr        line, part;
-  OrgModLinePtr     omlp;
-  SeqIdPtr          sip;
-  Char              acc_str [256];
+  TableLinePtr      tlp;
+  Boolean           use_local_id;
+  Boolean           look_for_tmsmart;
+  Int4              match_choice;
   
   form_data = (OrgModLoadFormPtr) userdata;
   if (form_data == NULL || bsp == NULL) return;
@@ -8622,50 +9364,39 @@ static void ApplyTableModsByAccessionNumber (BioseqPtr bsp, Pointer userdata)
        column_index < form_data->num_line_forms;
        column_index ++)
   {
+    match_choice = GetValue (form_data->line_forms[column_index].match_choice);
     if (GetValue (form_data->line_forms[column_index].action_choice) == 1
-      && (GetValue (form_data->line_forms[column_index].match_choice) == 1
-        || GetValue (form_data->line_forms[column_index].match_choice) == 2))
+      && (match_choice == 1 || match_choice == 2 || match_choice == 4))
     {
+      if (match_choice == 1 || match_choice == 4) {
+        use_local_id = FALSE;
+      } else {
+        use_local_id = TRUE;
+      }
+      if (match_choice == 4) {
+        look_for_tmsmart = TRUE;
+      } else {
+        look_for_tmsmart = FALSE;
+      }
+
       for (line = form_data->line_list; line != NULL; line = line->next)
       {
-        omlp = line->data.ptrvalue;
-        if (omlp == NULL) continue;
-        part = omlp->parts;
+        tlp = line->data.ptrvalue;
+        if (tlp == NULL) continue;
+        part = tlp->parts;
         for (part_index = 0;
              part_index < column_index && part != NULL;
              part_index ++)
         {
           part = part->next;
         }
-        if (part != NULL)
+        if (part != NULL
+          && ( IDListHasValue ( part->data.ptrvalue,
+                                bsp->id, use_local_id, look_for_tmsmart)
+            || (! use_local_id && 
+                HasExtraAccession ( part->data.ptrvalue, gbp))))
         {
-          if (GetValue (form_data->line_forms[column_index].match_choice) == 1)
-          {
-            if (gbp != NULL)
-            {
-              for (vnp = gbp->extra_accessions;
-                   vnp != NULL
-                   && StringCmp (part->data.ptrvalue, vnp->data.ptrvalue) != 0;
-                   vnp = vnp->next)
-              {}
-              if (vnp != NULL)
-              {
-                ApplyQualsToOrg (biop, omlp->parts, form_data);
-              }
-            }
-          }
-          for (sip = bsp->id; sip != NULL; sip = sip->next)
-          {
-            if ((GetValue (form_data->line_forms[column_index].match_choice) == 1 && sip->choice != SEQID_LOCAL)
-              || (GetValue (form_data->line_forms[column_index].match_choice) == 2 && sip->choice == SEQID_LOCAL))
-            {
-              SeqIdWrite (sip, acc_str, PRINTID_REPORT, sizeof (acc_str));
-              if (StringCmp (part->data.ptrvalue, acc_str) == 0)
-              {
-                ApplyQualsToOrg (biop, omlp->parts, form_data);
-              }
-            }
-          }
+          ApplyQualsToOrg (biop, tlp->parts, form_data);
         }
       }
     }
@@ -8691,35 +9422,23 @@ static void DoAcceptFormMods (ButtoN b)
   Remove (form_data->form);
 }
 
-extern void LoadOrganismModifierTable (IteM i)
+static ValNodePtr ReadTableData (void)
 {
-  BaseFormPtr   bfp;
   Char          path [PATH_MAX];
   FILE          *fp;
   Char          str [8192];
   size_t        len = 8192;
-  ValNodePtr    line_list;
   Int4          max_columns;
   ValNodePtr    header_line;
+  ValNodePtr    line_list;
+  TableLinePtr  tlp;
   ValNodePtr    vnp;
-  OrgModLinePtr omlp;
-  WindoW        w;
-  GrouP         h, g, c;
-  OrgModLoadFormPtr form_data;
-  Int4          index;
-
-#ifdef WIN_MAC
-  bfp = currentFormDataPtr;
-#else
-  bfp = GetObjectExtra (i);
-#endif
-  if (bfp == NULL) return;
 
   path [0] = '\0';
-  if (! GetInputFileName (path, sizeof (path), NULL, "TEXT")) return;
+  if (! GetInputFileName (path, sizeof (path), NULL, "TEXT")) return NULL;
   
   fp = FileOpen (path, "r");
-  if (fp == NULL) return;
+  if (fp == NULL) return NULL;
 
   line_list = NULL;
   max_columns = 0;
@@ -8727,16 +9446,16 @@ extern void LoadOrganismModifierTable (IteM i)
   ReadLine (fp, str, len);
   while (Nlm_fileDone) 
   {
-    omlp = MakeOrgModData (str);
-    if (omlp != NULL)
+    tlp = MakeTableData (str);
+    if (tlp != NULL)
     {
       vnp = ValNodeNew (line_list);
-      if (vnp == NULL) return;
+      if (vnp == NULL) return NULL;
       if (line_list == NULL) line_list = vnp;
-      vnp->data.ptrvalue = omlp;
-      if (omlp->num_parts > max_columns)
+      vnp->data.ptrvalue = tlp;
+      if (tlp->num_parts > max_columns)
       {
-        max_columns = omlp->num_parts;
+        max_columns = tlp->num_parts;
         header_line = vnp;
       }
     }
@@ -8755,6 +9474,36 @@ extern void LoadOrganismModifierTable (IteM i)
     ValNodeFreeData (line_list);
     line_list = NULL;
   }
+  return header_line;
+}
+
+extern void LoadOrganismModifierTable (IteM i)
+{
+  BaseFormPtr   bfp;
+  ValNodePtr    header_line;
+  ValNodePtr    vnp;
+  TableLinePtr  tlp;
+  WindoW        w;
+  GrouP         h, g, c;
+  OrgModLoadFormPtr form_data;
+  Int4          index;
+  Int4          max_columns;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+
+  header_line = ReadTableData ();
+  if (header_line == NULL || header_line->data.ptrvalue == NULL) return;
+  tlp = header_line->data.ptrvalue;
+  max_columns = 0;
+  for (vnp = tlp->parts; vnp != NULL; vnp = vnp->next)
+  {
+    max_columns ++;
+  }
   
   form_data = MemNew (sizeof (OrgModLoadFormData));
   if (form_data == NULL) return;
@@ -8772,8 +9521,8 @@ extern void LoadOrganismModifierTable (IteM i)
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
   g = HiddenGroup (h, 3, 0, NULL);
-  omlp = header_line->data.ptrvalue;
-  vnp = omlp->parts;
+  tlp = header_line->data.ptrvalue;
+  vnp = tlp->parts;
   for (index = 0; index < max_columns; index++)
   {
     BuildOrgModLineForm (vnp->data.ptrvalue, index, g,
@@ -8782,7 +9531,7 @@ extern void LoadOrganismModifierTable (IteM i)
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  form_data->accept_button = PushButton (c, "Accept", DoAcceptFormMods);
+  form_data->accept_button = DefaultButton (c, "Accept", DoAcceptFormMods);
   SetObjectExtra (form_data->accept_button, form_data, NULL);
   Disable (form_data->accept_button);
   PushButton (c, "Cancel", StdCancelButtonProc);
@@ -8794,3 +9543,1430 @@ extern void LoadOrganismModifierTable (IteM i)
   Update ();
 }
 
+typedef struct qualifierselect {
+  LisT gene_quals;
+  LisT cds_quals;
+  LisT import_quals;
+} QualifierSelectData, PNTR QualifierSelectPtr;
+
+typedef struct featurequalloadformdata {
+  FEATURE_FORM_BLOCK
+
+  ValNodePtr             line_list;
+  ValNodePtr             featlist;
+  Int4                   num_feats;
+  Uint2                  entityID;
+  LisT                   feature_type;
+  QualifierSelectData    match_qual;
+  QualifierSelectData    apply_qual;
+  PopuP                  sequence_id_type;
+  PopuP                  sequence_column;
+  PopuP                  feature_column;
+  PopuP                  apply_column;
+  GrouP                  seq_group;
+  GrouP                  match_group;
+  GrouP                  apply_group;
+  Boolean                asked_about_replace;
+  Boolean                do_replace;
+  Boolean                use_semicolon;
+  ButtoN                 accept_button;
+} FeatureQualLoadFormData, PNTR FeatureQualLoadFormPtr;
+ 
+static void CleanupFeatureQualLoadForm (
+  GraphiC g,
+  VoidPtr data
+)
+{
+  FeatureQualLoadFormPtr form_data;
+
+  form_data = (FeatureQualLoadFormPtr)data;
+  if (form_data == NULL) return;
+  CleanUpTableData (form_data->line_list);
+  StdCleanupFormProc (g, data);
+} 
+
+typedef struct qualifierlistdata {
+  CharPtr item_name;
+} QualifierListData, PNTR QualifierListPtr;
+
+static Int4 GetSubtypeFromOffsetInFeatureList (Int4 list_offset,
+                                               ValNodePtr list)
+{
+  ValNodePtr vnp;
+
+  if (list == NULL || list_offset < 1) return -1;
+
+  vnp = list;
+  while (vnp != NULL && list_offset > 1)
+  {
+    list_offset --;
+    vnp = vnp->next;
+  }
+  if (list_offset > 1) return -1;
+  return vnp->choice;
+}
+
+static void ShowQualifierListBySubtype (QualifierSelectPtr qsp, Int4 feature_subtype)
+{
+  if (feature_subtype == -1) {
+    Hide (qsp->gene_quals);
+    Hide (qsp->cds_quals);
+    Hide (qsp->import_quals);
+  } else if (feature_subtype == FEATDEF_GENE) {
+    Show (qsp->gene_quals);
+    Hide (qsp->cds_quals);
+    Hide (qsp->import_quals);
+  } else if (feature_subtype == FEATDEF_CDS) {
+    Hide (qsp->gene_quals);
+    Show (qsp->cds_quals);
+    Hide (qsp->import_quals);
+  } else {
+    Hide (qsp->gene_quals);
+    Hide (qsp->cds_quals);
+    Show (qsp->import_quals);
+  }
+}
+
+static void ShowQualifierLists (FeatureQualLoadFormPtr form_data)
+{
+  Int4 feature_offset, feature_subtype;
+
+  if (form_data == NULL) return;
+
+  feature_offset = GetValue (form_data->feature_type);
+  feature_subtype = GetSubtypeFromOffsetInFeatureList (feature_offset,
+                                                       form_data->featlist);
+  ShowQualifierListBySubtype (&(form_data->match_qual), feature_subtype);
+  ShowQualifierListBySubtype (&(form_data->apply_qual), feature_subtype);
+}
+
+static QualifierListData GeneTableQualifiers [] = {
+  { "allele"},
+  { "locus" },
+  { "locus_tag"},
+  { "description"},
+  { "product"}
+};
+
+#define NUM_GENE_TABLE_QUALIFIERS 5
+
+static QualifierListData ProtTableQualifiers [] = {
+  { "product"},
+  { "description"},
+  { "comment"}
+};
+
+#define NUM_PROT_TABLE_QUALIFIERS 3
+
+/* check the appropriate list box for qualifier type,
+ * keeping in mind that the first item is always "none"
+ */
+static Int4 GetQualSelectBySubtype (QualifierSelectPtr qsp, Int4 feature_subtype)
+{
+  Int4 qual_choice = -1;
+
+  if (feature_subtype == -1) {
+    qual_choice = -1;
+  } else if (feature_subtype == FEATDEF_GENE) {
+    qual_choice = GetValue (qsp->gene_quals);
+    if (qual_choice < 2 
+      || qual_choice > NUM_GENE_TABLE_QUALIFIERS + 2) {
+      qual_choice = -1;
+    } else {
+      qual_choice = qual_choice - 1;
+    }
+  } else if (feature_subtype == FEATDEF_CDS) {
+    qual_choice = GetValue (qsp->cds_quals);
+    if (qual_choice < 2 
+      || qual_choice > NUM_PROT_TABLE_QUALIFIERS + 2) {
+      qual_choice = -1;
+    } else {
+      qual_choice = qual_choice - 1;
+    }
+  } else {
+    qual_choice = GetValue (qsp->import_quals);
+    if (qual_choice < 2
+      || qual_choice > ParFlat_TOTAL_GBQUAL + 2) {
+      qual_choice = -1;
+    } else {
+      qual_choice = qual_choice - 1;
+    }
+  }
+  return qual_choice;
+
+}
+
+static void SetFeatureQualAcceptButton (Handle a)
+{
+  FeatureQualLoadFormPtr form_data;
+  Boolean                have_feature_select_column;
+  Boolean                have_feature_qual_select_column;
+  Int4                   feature_select_choice;
+  Int4                   apply_qual_choice;
+  Int4                   match_qual_choice;
+  Int4                   feature_subtype;
+  Boolean                seqid_select_ok;
+  Int4                   seqid_select_type;
+  Int4                   seqid_select_column;
+
+  form_data = GetObjectExtra (a);
+  if (form_data == NULL) return;
+
+  ShowQualifierLists (form_data);
+  have_feature_qual_select_column = FALSE;
+  have_feature_select_column = FALSE;
+  seqid_select_ok = FALSE;
+
+  feature_select_choice = GetValue (form_data->feature_type);
+  if ( feature_select_choice > 0 && feature_select_choice < form_data->num_feats)
+  {
+    have_feature_select_column = TRUE;
+  }
+  
+  feature_subtype = GetSubtypeFromOffsetInFeatureList (feature_select_choice,
+                                                       form_data->featlist);
+  
+  apply_qual_choice = GetQualSelectBySubtype (&(form_data->apply_qual),
+                                              feature_subtype);
+  if (apply_qual_choice != -1)
+  {
+    have_feature_qual_select_column = TRUE;
+  }
+
+  /* if a column is selected for a sequence identifier, must select type */
+  /* if a column is not selected for a sequence identifier, must not select type */
+  seqid_select_type = GetValue (form_data->sequence_id_type);
+  seqid_select_column = GetValue (form_data->sequence_column);
+  if (seqid_select_type == 1 || seqid_select_type == 2) {
+    if (seqid_select_column > 0) {
+      seqid_select_ok = TRUE;
+    }
+  } else {
+    seqid_select_ok = TRUE;
+  }
+ 
+  /* if the feature column is not specified, must not have match qualifier */
+  /* and must have sequence ID */
+  /* if the feature column is specified, must have match qualifier */
+  match_qual_choice = GetQualSelectBySubtype (&(form_data->match_qual),
+                                              feature_subtype);
+  if (GetValue (form_data->feature_column) < 1)
+  {
+    if (match_qual_choice != -1)
+    {
+      have_feature_select_column = FALSE;
+    }
+    else if (seqid_select_column < 1)
+    {
+      have_feature_select_column = FALSE;
+    }
+  } else {
+    if (match_qual_choice == -1)
+    {
+      have_feature_select_column = FALSE;
+    }
+  }
+
+  if (GetValue (form_data->apply_column) < 1) {
+    have_feature_qual_select_column = FALSE;
+  }
+
+  if ( have_feature_select_column && have_feature_qual_select_column
+    && seqid_select_ok)
+  {
+    Enable (form_data->accept_button);
+  }
+  else
+  {
+    Disable (form_data->accept_button);
+  }
+}
+
+static Boolean ProductNameMatches (
+  SeqLocPtr slp,
+  BioseqPtr  bsp,
+  CharPtr   pString
+)
+{
+  SeqFeatPtr        sfp;
+  SeqMgrFeatContext fcontext;
+
+  if (slp == NULL || bsp == NULL || pString == NULL) return FALSE;
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &fcontext);
+  while (sfp != NULL)
+  {
+    if ( IsLocAInBonSameStrand (sfp->location, slp)
+      && StringStr ( fcontext.label, pString) != NULL)
+    {
+      return TRUE;
+    }
+    sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_CDREGION, 0, &fcontext);
+  }
+  return FALSE;
+}
+
+static Boolean GeneHasThisQualifier (
+  SeqFeatPtr sfp,
+  Uint2      entityID,
+  CharPtr    pString,
+  Int2       popup_offset
+)
+{
+  BioseqPtr  bsp;
+  GeneRefPtr grp;
+
+  if (sfp == NULL || pString == NULL) return FALSE;
+  if (popup_offset < 1 || popup_offset > NUM_GENE_TABLE_QUALIFIERS) return FALSE;
+
+  grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+  if (grp == NULL) return FALSE;
+
+  if ( StringCmp (GeneTableQualifiers [popup_offset - 1].item_name, "allele") == 0) {
+    if (StringCmp (pString, grp->allele) == 0) {
+      return TRUE;
+    } else {
+      return FALSE;
+    }
+  } else if ( StringCmp (GeneTableQualifiers [popup_offset - 1].item_name, "locus") == 0) {
+    if (StringCmp (pString, grp->locus) == 0) {
+      return TRUE;
+    } else {
+      return FALSE;
+    }
+  } else if ( StringCmp (GeneTableQualifiers [popup_offset - 1].item_name, "locus_tag") == 0) {
+    if (StringCmp (pString, grp->locus_tag) == 0) {
+      return TRUE;
+    } else {
+      return FALSE;
+    }
+  } else if ( StringCmp (GeneTableQualifiers [popup_offset - 1].item_name, "description") == 0) {
+    if (StringCmp (pString, grp->desc) == 0) {
+      return TRUE;
+    } else {
+      return FALSE;
+    }
+  } else if ( StringCmp (GeneTableQualifiers [popup_offset - 1].item_name, "product") == 0)
+  {
+    bsp = GetBioseqGivenSeqLoc (sfp->location, entityID);
+    return ProductNameMatches (sfp->location, bsp, pString);
+  }
+  return FALSE;
+}
+
+static Boolean ProteinHasThisQualifier (
+  SeqFeatPtr sfp,
+  CharPtr    pString,
+  Int2       popup_offset
+)
+{
+  ProtRefPtr prp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT || pString == NULL
+    || popup_offset < 1 || popup_offset > NUM_PROT_TABLE_QUALIFIERS)
+  {
+    return FALSE;
+  }
+
+  prp = sfp->data.value.ptrvalue;
+  if (prp == NULL) return FALSE;
+
+  if (StringCmp (ProtTableQualifiers [ popup_offset - 1].item_name, "product") == 0)
+  {
+    if (prp->name != NULL
+      && StringStr (prp->name->data.ptrvalue, pString) != NULL)
+    {
+      return TRUE;
+    }
+  } else if (StringCmp (ProtTableQualifiers [popup_offset - 1].item_name, "description") == 0) {
+    if (StringStr (prp->desc, pString) != NULL)
+    {
+      return TRUE;
+    }
+  } else if (StringCmp (ProtTableQualifiers [popup_offset - 1].item_name, "comment") == 0) {
+    if (StringStr (sfp->comment, pString) != NULL)
+    {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+static Boolean CDSHasThisQualifier (
+  SeqFeatPtr sfp,
+  Uint2      entityID,
+  CharPtr    pString,
+  Int2       popup_offset
+)
+{
+  SeqFeatPtr protein;
+
+  if (sfp == NULL || pString == NULL) return FALSE;
+
+  if (StringCmp (ProtTableQualifiers [popup_offset - 1].item_name, "comment") == 0) {
+    if (StringStr (sfp->comment, pString) != NULL)
+    {
+      return TRUE;
+    }
+  }
+  else
+  {
+    protein = FindBestProtein (entityID, sfp->product);
+    if (protein == NULL) return FALSE;
+    return ProteinHasThisQualifier (protein, pString, popup_offset);
+  }
+  return FALSE;
+}
+  
+static Boolean FeatureHasThisQualifier (
+  SeqFeatPtr sfp,
+  Uint2      entityID,
+  CharPtr    pString,
+  Int2       popup_offset
+)
+{
+  Int2      qualval;
+  GBQualPtr gbqual;
+
+  if (popup_offset < 1) return FALSE;
+  if (sfp == NULL || pString == NULL) return FALSE;
+
+  if (sfp->idx.subtype == FEATDEF_GENE)
+  {
+    return GeneHasThisQualifier (sfp, entityID, pString, popup_offset);
+  }
+  else if (sfp->idx.subtype == FEATDEF_CDS)
+  {
+    return CDSHasThisQualifier (sfp, entityID, pString, popup_offset);
+  }
+  else
+  {
+    for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
+    {
+      qualval = GBQualNameValid (gbqual->qual);
+      if (qualval > -1 && qualval == popup_offset -1)
+      {
+        return TRUE;
+      }
+    }
+  }
+  return FALSE; 
+}
+ 
+static CharPtr GetDataForColumnOffset (ValNodePtr column_data, Int4 offset)
+{
+  ValNodePtr vnp;
+
+  for (vnp = column_data; vnp != NULL && offset > 1; vnp = vnp->next)
+  {
+    offset --;
+  }
+  if (offset > 1 || vnp == NULL) {
+    return NULL;
+  } else {
+    return vnp->data.ptrvalue;
+  }
+}
+
+static Boolean ApplyQualToThisFeature (
+  SeqFeatPtr sfp,
+  ValNodePtr parts,
+  FeatureQualLoadFormPtr form_data
+)
+{
+  Int4       column_index;
+  CharPtr    val;
+  Int4       subtype;
+  Int4       popup_offset;
+
+  if (sfp == NULL || parts == NULL || form_data == NULL) return FALSE;
+
+  column_index = GetValue (form_data->feature_column);
+  subtype = GetSubtypeFromOffsetInFeatureList (
+                     GetValue (form_data->feature_type), form_data->featlist);
+  val = GetDataForColumnOffset (parts, column_index);
+
+  if (val != NULL && sfp->idx.subtype == subtype)
+  {
+    popup_offset = GetQualSelectBySubtype (&(form_data->match_qual),
+                                              subtype);
+    if (popup_offset < 1
+      || FeatureHasThisQualifier (sfp, form_data->entityID, val, popup_offset))
+    {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+typedef struct featurequaltabledata {
+  ValNodePtr parts;
+  FeatureQualLoadFormPtr form_data;
+} FeatureQualTableData, PNTR FeatureQualTablePtr;
+
+static void ApplyOneQualToProt (
+  SeqFeatPtr sfp,
+  Int2       popup_offset,
+  CharPtr    pString,
+  Boolean PNTR asked_about_replace,
+  Boolean PNTR do_replace,
+  Boolean PNTR use_semicolon)
+{
+  ProtRefPtr prp;
+  CharPtr    cp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT || pString == NULL
+    || popup_offset < 1 || popup_offset > NUM_PROT_TABLE_QUALIFIERS
+    || asked_about_replace == NULL
+    || do_replace == NULL
+    || use_semicolon == NULL)
+  {
+    return;
+  }
+
+  prp = sfp->data.value.ptrvalue;
+  if (prp == NULL) return;
+
+  if (StringCmp (ProtTableQualifiers [ popup_offset - 1].item_name, "product") == 0)
+  {
+    if (prp->name == NULL)
+    {
+      ValNodeAddStr (&prp->name, 0, StringSave (pString));
+    }
+    else
+    {
+      cp = prp->name->data.ptrvalue;
+      AppendOrReplaceString (&cp, pString,
+                            asked_about_replace, do_replace, use_semicolon);
+      prp->name->data.ptrvalue = cp;
+    }
+  } else if (StringCmp (ProtTableQualifiers [popup_offset - 1].item_name, "description") == 0) {
+    AppendOrReplaceString (&(prp->desc), pString,
+                            asked_about_replace, do_replace, use_semicolon);
+  } else if (StringCmp (ProtTableQualifiers [popup_offset - 1].item_name, "comment") == 0) {
+    AppendOrReplaceString (&(sfp->comment), pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+  }
+}
+
+static void ApplyOneQualToCDS (
+  SeqFeatPtr sfp,
+  Uint2      entityID,
+  Int2       feat_qual_choice,
+  CharPtr    pString,
+  Boolean PNTR asked_about_replace,
+  Boolean PNTR do_replace,
+  Boolean PNTR use_semicolon)
+{
+  SeqFeatPtr protein;
+
+  if (sfp == NULL || pString == NULL
+    || asked_about_replace == NULL
+    || do_replace == NULL
+    || use_semicolon == NULL)
+  {
+    return;
+  }
+
+  if (StringCmp (ProtTableQualifiers [feat_qual_choice - 1].item_name, "comment") == 0) {
+    AppendOrReplaceString (&(sfp->comment), pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+  }
+  else
+  {
+    protein = FindBestProtein (entityID, sfp->product);
+    if (protein == NULL) return;
+    ApplyOneQualToProt (protein, feat_qual_choice, pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+  }
+}
+
+static void ApplyGeneProductName (
+  SeqLocPtr slp,
+  Uint2     entityID,
+  CharPtr   pString,
+  Boolean PNTR asked_about_replace,
+  Boolean PNTR do_replace,
+  Boolean PNTR use_semicolon)
+{
+  SeqFeatPtr        sfp;
+  SeqMgrFeatContext fcontext;
+  Int4              prot_popup_offset;
+  BioseqPtr         bsp;
+
+  if (slp == NULL || pString == NULL
+    || asked_about_replace == NULL
+    || do_replace == NULL
+    || use_semicolon == NULL)
+  {
+    return;
+  }
+
+  bsp = GetBioseqGivenSeqLoc (slp, entityID);
+  if (bsp == NULL) return;
+
+  for (prot_popup_offset = 0;
+       prot_popup_offset < NUM_PROT_TABLE_QUALIFIERS
+         && StringCmp (ProtTableQualifiers [prot_popup_offset].item_name, "product") != 0;
+       prot_popup_offset ++)
+  {}
+  if (prot_popup_offset >= NUM_PROT_TABLE_QUALIFIERS) return;
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &fcontext);
+  while (sfp != NULL)
+  {
+    if ( IsLocAInBonSameStrand (sfp->location, slp))
+    {
+      ApplyOneQualToCDS (sfp, entityID, prot_popup_offset + 1, pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+    }
+    sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_CDREGION, 0, &fcontext);
+  }
+}
+
+static void ApplyOneQualToGene (
+  SeqFeatPtr sfp,
+  Uint2      entityID,
+  Int2       feat_qual_choice,
+  CharPtr    pString, 
+  Boolean PNTR asked_about_replace,
+  Boolean PNTR do_replace,
+  Boolean PNTR use_semicolon)
+{
+  GeneRefPtr grp;
+
+  if (sfp == NULL
+    || sfp->idx.subtype != FEATDEF_GENE
+    || feat_qual_choice < 1
+    || feat_qual_choice > NUM_GENE_TABLE_QUALIFIERS
+    || pString == NULL
+    || asked_about_replace == NULL
+    || do_replace == NULL
+    || use_semicolon == NULL)
+  {
+    return;
+  }
+
+  grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+  if (grp == NULL) return;
+
+  if (StringCmp ( GeneTableQualifiers [feat_qual_choice - 1].item_name,
+                 "allele") == 0) {
+    AppendOrReplaceString (&(grp->allele), pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+  } else if (StringCmp ( GeneTableQualifiers [feat_qual_choice - 1].item_name,
+                        "locus") == 0) {
+    AppendOrReplaceString (&(grp->locus), pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+  } else if (StringCmp ( GeneTableQualifiers [feat_qual_choice - 1].item_name,
+                        "locus_tag") == 0) {
+    AppendOrReplaceString (&(grp->locus_tag), pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+  } else if (StringCmp ( GeneTableQualifiers [feat_qual_choice - 1].item_name,
+                        "description") == 0) {
+    AppendOrReplaceString (&(grp->desc), pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+  } else if (StringCmp (GeneTableQualifiers [feat_qual_choice - 1].item_name,
+                        "product") == 0) {
+    ApplyGeneProductName (sfp->location, entityID, pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+  }
+}
+
+static void ApplyOneQualToImportFeature (
+  SeqFeatPtr sfp,
+  Int2 feat_qual_choice,
+  CharPtr pString,
+  Boolean PNTR asked_about_replace,
+  Boolean PNTR do_replace,
+  Boolean PNTR use_semicolon)
+{
+  GBQualPtr           gbqual;
+
+  if (sfp == NULL
+    || feat_qual_choice < 1
+    || feat_qual_choice > ParFlat_TOTAL_GBQUAL
+    || pString == NULL
+    || asked_about_replace == NULL
+    || do_replace == NULL
+    || use_semicolon == NULL)
+  {
+    return;
+  }
+
+  gbqual = sfp->qual;
+  while (gbqual != NULL
+    && StringCmp (gbqual->qual,
+                  ParFlat_GBQual_names [feat_qual_choice - 1].name) != 0)
+  {
+    gbqual = gbqual->next;
+  }
+  
+  if (gbqual == NULL)
+  {
+    gbqual = GBQualNew ();
+    if (gbqual == NULL) return;
+    gbqual->qual = StringSave ( ParFlat_GBQual_names [feat_qual_choice - 1].name);
+    gbqual->val = StringSave ( pString );
+    gbqual->next = sfp->qual;
+    sfp->qual = gbqual;
+  }
+  else
+  {
+    AppendOrReplaceString (&(gbqual->val), pString, 
+                            asked_about_replace, do_replace, use_semicolon);
+  }
+}
+
+static void ApplyOneQualToFeature (
+  SeqFeatPtr sfp,
+  Uint2      entityID,
+  Int2       feat_qual_choice,
+  CharPtr    pString,
+  Boolean PNTR asked_about_replace,
+  Boolean PNTR do_replace,
+  Boolean PNTR use_semicolon)
+{
+  if (sfp == NULL || pString == NULL 
+    || asked_about_replace == NULL
+    || do_replace == NULL
+    || use_semicolon == NULL)
+  {
+    return;
+  }
+
+  switch (sfp->idx.subtype)
+  {
+    case FEATDEF_GENE :
+      ApplyOneQualToGene (sfp, entityID, feat_qual_choice, pString,
+                            asked_about_replace, do_replace, use_semicolon);
+      break;
+    case FEATDEF_CDS :
+      ApplyOneQualToCDS (sfp, entityID, feat_qual_choice, pString,
+                            asked_about_replace, do_replace, use_semicolon);
+      break;
+    default :
+      ApplyOneQualToImportFeature (sfp, feat_qual_choice, pString,
+                            asked_about_replace, do_replace, use_semicolon);
+      break;
+  }
+}
+
+static CharPtr GetImpFeatKeyFromSubtype (Uint2 subtype)
+{
+  FeatDefPtr  curr;
+  Uint1       key;
+  CharPtr     label;
+
+  curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
+  while (curr != NULL) {
+    if (key == subtype)
+    {
+      return curr->typelabel;
+    }
+    curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
+  }
+  return NULL;
+}
+
+static void ApplyQualsToFeaturesOnBsp (BioseqPtr bsp,
+ FeatureQualLoadFormPtr form_data,
+ ValNodePtr             parts)
+{
+  SeqFeatPtr sfp;
+  SeqMgrFeatContext fcontext;
+  Boolean found_feature = FALSE;
+  Int4                subtype;
+  Int4                column_index;
+  Int2                qualval;
+  Int2                matchval;
+  CharPtr             val;
+  ImpFeatPtr          ifp;
+
+  subtype = GetSubtypeFromOffsetInFeatureList (
+                          GetValue (form_data->feature_type), 
+                          form_data->featlist);
+  column_index = GetValue (form_data->apply_column);
+  val = GetDataForColumnOffset (parts, column_index);
+  qualval = GetQualSelectBySubtype (&(form_data->apply_qual), subtype);
+  if (subtype == -1 || val == NULL || column_index < 1 || qualval < 1) {
+    /* do nothing */
+  }
+  else
+  {
+    sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
+    while (sfp != NULL)
+    {
+      if ( ApplyQualToThisFeature (sfp, parts, form_data))
+      {
+        found_feature = TRUE;
+        ApplyOneQualToFeature (sfp, form_data->entityID, qualval, val,
+                               &(form_data->asked_about_replace),
+                               &(form_data->do_replace),
+                               &(form_data->use_semicolon));
+      }
+      sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
+    }
+
+    /* only want to create new features if no feature matching qualifier
+     * was specified and no feature was found */
+    matchval = GetQualSelectBySubtype (&(form_data->match_qual), subtype);
+
+    if (! found_feature && matchval == -1)
+    {
+      if (subtype == FEATDEF_CDS)
+      {
+        sfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_CDREGION, NULL);
+        if (sfp == NULL) return;
+        sfp->data.value.ptrvalue = CdRegionNew ();
+      } else if (subtype == FEATDEF_GENE) {
+        sfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_GENE, NULL);
+        if (sfp == NULL) return;
+        sfp->data.value.ptrvalue = GeneRefNew ();
+      } else {
+        ifp = ImpFeatNew ();
+        if (ifp == NULL) return;
+        sfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_IMP, NULL);
+        if (sfp == NULL) return;
+        ifp->key = StringSave ( GetImpFeatKeyFromSubtype (subtype));
+        sfp->data.value.ptrvalue = ifp;
+      }
+      SeqMgrIndexFeatures (0, (Pointer) bsp);
+      ApplyOneQualToFeature (sfp, form_data->entityID, qualval, val,
+                               &(form_data->asked_about_replace),
+                               &(form_data->do_replace),
+                               &(form_data->use_semicolon));
+    }
+  }
+}
+
+static void ApplyTableQuals (BioseqPtr bsp, Pointer userdata)
+{
+  FeatureQualLoadFormPtr form_data;
+  SeqDescrPtr            sdp;
+  GBBlockPtr             gbp;
+  Int4                   column_index;
+  ValNodePtr             line;
+  TableLinePtr           tlp;
+  Boolean                use_local_id;
+  FeatureQualTableData   fqtd;
+  Int2                   seq_match_choice;
+  CharPtr                idval;
+  
+  form_data = (FeatureQualLoadFormPtr) userdata;
+  if (form_data == NULL || bsp == NULL) return;
+
+  gbp = NULL;
+  sdp = BioseqGetSeqDescr (bsp, Seq_descr_genbank, NULL);
+  if (sdp != NULL)
+  {
+    gbp = sdp->data.ptrvalue;
+  }
+
+  seq_match_choice = GetValue (form_data->sequence_id_type);
+  if (seq_match_choice == 1) {
+    use_local_id = FALSE;
+  }
+
+  fqtd.form_data = form_data;
+  if (seq_match_choice == 1 || seq_match_choice == 2)
+  {
+    column_index = GetValue (form_data->sequence_column);
+
+    for (line = form_data->line_list; line != NULL; line = line->next)
+    {
+      tlp = line->data.ptrvalue;
+      if (tlp == NULL) continue;
+      idval = GetDataForColumnOffset (tlp->parts, column_index);
+      if (idval != NULL
+        && ( IDListHasValue ( idval,
+                              bsp->id, use_local_id, FALSE)
+          || (! use_local_id && 
+              HasExtraAccession ( idval, gbp))))
+      {
+        fqtd.parts = tlp->parts;
+        ApplyQualsToFeaturesOnBsp (bsp, form_data, tlp->parts);
+      }
+    }
+  } else {
+    for (line = form_data->line_list; line != NULL; line = line->next)
+    {
+      tlp = line->data.ptrvalue;
+      if (tlp == NULL) continue;
+      fqtd.parts = tlp->parts;
+      ApplyQualsToFeaturesOnBsp (bsp, form_data, tlp->parts);
+    }
+  }
+}
+
+static void DoAcceptFeatureQuals (ButtoN b)
+{
+  FeatureQualLoadFormPtr form_data;
+  SeqEntryPtr   sep;
+
+  form_data = GetObjectExtra (b);
+  if (form_data == NULL) return;
+
+  sep = GetTopSeqEntryForEntityID (form_data->entityID);
+  if (sep == NULL) return;
+  
+  VisitBioseqsInSep (sep, form_data, ApplyTableQuals);
+  Update ();
+  ObjMgrSetDirtyFlag (form_data->entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, form_data->entityID, 0, 0);
+  Remove (form_data->form);
+}
+
+static PopuP BuildColumnSelector ( GrouP g,
+                                  FeatureQualLoadFormPtr parent_form,
+                                  ValNodePtr parts )
+{
+  PopuP      p;
+  ValNodePtr this_part;
+
+  if (g == NULL || parts == NULL) return NULL;
+
+  p = PopupList (g, TRUE, (PupActnProc) SetFeatureQualAcceptButton);
+  for (this_part = parts; this_part != NULL; this_part = this_part->next)
+  {
+    if (this_part->data.ptrvalue != NULL)
+    {
+      PopupItem (p, this_part->data.ptrvalue);
+    }
+  }
+  SetObjectExtra (p, parent_form, NULL);
+  return p;
+}
+
+static void BuildQualifierSelect ( GrouP parent, 
+                                  FeatureQualLoadFormPtr parent_form,
+                                  ValNodePtr parts,
+                                  QualifierSelectPtr qsp )
+{
+  GrouP g;
+  Int4  listheight = 4;
+  Int4  listwidth  = 13;
+  Int4  j;
+
+  if (parent_form == NULL || parts == NULL || qsp == NULL)
+  {
+    return;
+  }
+
+  g = HiddenGroup (parent, 0, 0, NULL);
+
+  qsp->gene_quals = SingleList (g, listwidth, listheight,
+                                   (LstActnProc) SetFeatureQualAcceptButton);
+  SetObjectExtra (qsp->gene_quals, parent_form, NULL);
+  ListItem (qsp->gene_quals, "None");
+  for (j=0; j < NUM_GENE_TABLE_QUALIFIERS; j++) {
+    ListItem (qsp->gene_quals, GeneTableQualifiers [j].item_name);
+  }
+  SetValue (qsp->gene_quals, 1);
+
+  qsp->cds_quals = SingleList (g, listwidth, listheight,
+                                   (LstActnProc) SetFeatureQualAcceptButton);
+  SetObjectExtra (qsp->cds_quals, parent_form, NULL);
+  ListItem (qsp->cds_quals, "None");
+  for (j=0; j < NUM_PROT_TABLE_QUALIFIERS; j++) {
+    ListItem (qsp->cds_quals, ProtTableQualifiers [j].item_name);
+  }
+  SetValue (qsp->cds_quals, 1);
+
+  qsp->import_quals = SingleList (g, listwidth, listheight,
+                                   (LstActnProc) SetFeatureQualAcceptButton);
+  SetObjectExtra (qsp->import_quals, parent_form, NULL);
+  ListItem (qsp->import_quals, "None");
+  for (j = 0; j < ParFlat_TOTAL_GBQUAL; j++) {
+    ListItem (qsp->import_quals, ParFlat_GBQual_names [j].name);
+  }
+  SetValue (qsp->import_quals, 1);
+}
+
+static void BuildSequenceSelect ( GrouP parent,
+                                  FeatureQualLoadFormPtr parent_form,
+                                  ValNodePtr parts )
+{
+  if (parent == NULL || parent_form == NULL || parts == NULL) return;
+
+  parent_form->seq_group = NormalGroup ( parent, 0, 2, "Sequence", programFont, NULL);
+  StaticPrompt (parent_form->seq_group, "Identifier Type", 0, popupMenuHeight, programFont, 'l');
+  parent_form->sequence_id_type = PopupList (parent_form->seq_group, TRUE, (PupActnProc) SetFeatureQualAcceptButton);
+  PopupItem (parent_form->sequence_id_type, "Accession");
+  PopupItem (parent_form->sequence_id_type, "Local ID");
+  PopupItem (parent_form->sequence_id_type, "None");
+  SetObjectExtra (parent_form->sequence_id_type, parent_form, NULL);
+  SetValue (parent_form->sequence_id_type, 3);
+
+  StaticPrompt (parent_form->seq_group, "Column", 0, popupMenuHeight, programFont, 'l');
+  parent_form->sequence_column = BuildColumnSelector ( parent_form->seq_group, parent_form, parts);
+}
+
+static void BuildFeatureSelect ( GrouP parent,
+                                 FeatureQualLoadFormPtr parent_form,
+                                 ValNodePtr parts )
+{
+  Int4  listheight = 4;
+  ValNodePtr vnp;
+
+  if (parent == NULL || parent_form == NULL || parts == NULL) return;
+
+  parent_form->match_group = NormalGroup ( parent, 0, 2,
+                                    "Feature to Edit", programFont, NULL);
+  StaticPrompt (parent_form->match_group, "Feature type", 0, 
+                                   popupMenuHeight, programFont, 'l');
+  parent_form->feature_type = SingleList (parent_form->match_group, 
+                                   9, listheight,
+                   (LstActnProc) SetFeatureQualAcceptButton);
+  SetObjectExtra (parent_form->feature_type, parent_form, NULL);
+  for (vnp = parent_form->featlist; vnp != NULL; vnp = vnp->next)
+  {
+    ListItem (parent_form->feature_type, (CharPtr) vnp->data.ptrvalue);
+  }
+
+  StaticPrompt (parent_form->match_group, "Qualifier to match", 0, popupMenuHeight, programFont, 'l');
+  BuildQualifierSelect ( parent_form->match_group, parent_form, parts, &(parent_form->match_qual));
+
+  StaticPrompt (parent_form->match_group, "Column", 0, popupMenuHeight, programFont, 'l');
+  parent_form->feature_column = BuildColumnSelector ( parent_form->match_group, parent_form, parts);
+  
+}
+
+static void BuildFeatureApply ( GrouP parent,
+                               FeatureQualLoadFormPtr parent_form,
+                               ValNodePtr parts )
+{
+  if (parent == NULL || parent_form == NULL || parts == NULL) return;
+
+  parent_form->apply_group = NormalGroup ( parent, 0, 2, "Qualifier to Edit", programFont, NULL);
+  
+  StaticPrompt (parent_form->apply_group, "Qualifier Name", 0, popupMenuHeight, programFont, 'l');
+  BuildQualifierSelect ( parent_form->apply_group, parent_form, parts, &(parent_form->apply_qual));
+
+  StaticPrompt (parent_form->apply_group, "Column", 0, popupMenuHeight, programFont, 'l');
+  parent_form->apply_column = BuildColumnSelector ( parent_form->apply_group, parent_form, parts);
+  
+}
+
+extern void LoadFeatureQualifierTable (IteM i)
+{
+  BaseFormPtr   bfp;
+  ValNodePtr    header_line;
+  ValNodePtr    vnp;
+  TableLinePtr  tlp;
+  WindoW        w;
+  GrouP         h, c;
+  FeatureQualLoadFormPtr form_data;
+  Int4          max_columns;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+
+  header_line = ReadTableData ();
+  if (header_line == NULL || header_line->data.ptrvalue == NULL) return;
+  tlp = header_line->data.ptrvalue;
+  max_columns = 0;
+  for (vnp = tlp->parts; vnp != NULL; vnp = vnp->next)
+  {
+    max_columns ++;
+  }
+  
+  form_data = MemNew (sizeof (FeatureQualLoadFormData));
+  if (form_data == NULL) return;
+  form_data->asked_about_replace = FALSE;
+  form_data->do_replace = FALSE;
+  form_data->use_semicolon = FALSE;
+  form_data->entityID = bfp->input_entityID;
+  form_data->line_list = header_line;
+  form_data->featlist = BuildFeatureValNodeList (TRUE, NULL, 0, TRUE, FALSE);
+  form_data->num_feats = 0;
+  for (vnp = form_data->featlist; vnp != NULL; vnp = vnp->next)
+  {
+    form_data->num_feats ++;
+  }
+
+  /* now create a dialog to display values */
+  w = FixedWindow (-50, -33, -10, -10, "Table Conversion", StdCloseWindowProc);
+  SetObjectExtra (w, form_data, CleanupFeatureQualLoadForm);
+  form_data->form = (ForM) w;
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  BuildSequenceSelect ( h, form_data, tlp->parts);
+  BuildFeatureSelect (h, form_data, tlp->parts);
+  BuildFeatureApply (h, form_data, tlp->parts);
+  ShowQualifierLists (form_data);
+
+  c = HiddenGroup (h, 4, 0, NULL);
+  form_data->accept_button = DefaultButton (c, "Accept", DoAcceptFeatureQuals);
+  SetObjectExtra (form_data->accept_button, form_data, NULL);
+  Disable (form_data->accept_button);
+  PushButton (c, "Cancel", StdCancelButtonProc);
+
+  AlignObjects (ALIGN_CENTER,
+                (HANDLE) form_data->seq_group, 
+                (HANDLE) form_data->match_group,
+                (HANDLE) form_data->apply_group,
+                (HANDLE) c, NULL);
+
+  RealizeWindow (w);
+  Show (w);
+  Update ();
+}
+
+typedef struct prefixformdata {
+  FEATURE_FORM_BLOCK
+
+  ModifierItemLocalPtr modList;
+  PopuP PNTR           popup_list;
+  ButtoN               add_org_name;
+  ButtoN               use_labels;
+} PrefixFormData, PNTR PrefixFormPtr;
+
+static void CleanupPrefixForm (
+  GraphiC g,
+  VoidPtr data
+)
+
+{
+  PrefixFormPtr  pfp;
+  Int4           i;
+
+  pfp = (PrefixFormPtr) data;
+  if (pfp != NULL) {
+    if (pfp->modList != NULL)
+    {
+      for (i=0; i < NumDefLineModifiers; i++)
+      {
+        ValNodeFree (pfp->modList[i].values_seen);
+      }
+      MemFree (pfp->modList);
+    }
+    if (pfp->popup_list != NULL)
+    {
+      MemFree (pfp->popup_list);
+    }
+  }
+  StdCleanupFormProc (g, data);
+}
+
+static Int4 GetDefLineModifierPopupIndex (
+  Int4 popup_index, 
+  ModifierItemLocalPtr modList
+)
+{
+  Int4 index;
+  Int4 want_index;
+  
+  want_index = 0;
+  for (index = 0;
+       index < NumDefLineModifiers && want_index < popup_index;
+       index++)
+  {
+    if (modList [index].any_present)
+    {
+      want_index ++;
+    }
+  }
+  if (index >= NumDefLineModifiers || index == 0
+    || want_index < popup_index)
+  {
+    return -1;
+  }
+  return index - 1;
+}
+
+static void AddPrefixesToOneDefLine (
+  PrefixFormPtr pfp,
+  BioseqPtr bsp,
+  SeqEntryPtr sep
+)
+{
+  BioSourcePtr biop;
+  SeqDescrPtr  sdp;
+  ValNodePtr   strings;
+  Int4         index;
+  Int4         qual_index;
+  Int4         popup_choice;
+  CharPtr      new_defline;
+  Char         taxName [196];
+  Char         modifier_text [256];
+  OrgRefPtr    orp;
+  OrgNamePtr   onp;
+  OrgModPtr    mod;
+  SubSourcePtr ssp;
+  CharPtr  org_desc;
+  CharPtr  cp;
+  SeqMgrDescContext  dcontext;
+  Boolean      use_labels;
+  Int4         no_semicolon_len;
+
+  if (bsp == NULL || pfp == NULL
+    || pfp->popup_list == NULL
+    || pfp->modList == NULL
+    || (biop = GetBiopForBsp (bsp)) == NULL)
+  {
+    return;
+  }
+
+  if (biop->org == NULL) return;
+  if (biop->org->taxname == NULL) return;
+  StringNCpy (taxName, biop->org->taxname, sizeof (taxName) - 1);
+  taxName [ sizeof (taxName) - 1] = 0;
+
+  strings = NULL;
+  CleanUpTaxName (taxName, TRUE);
+  if (GetStatus (pfp->add_org_name))
+  {
+    ValNodeCopyStr( &strings, 0, taxName);
+  }
+
+  use_labels = GetStatus (pfp->use_labels);
+
+  orp = biop->org;
+  if (orp == NULL) return;
+  onp = orp->orgname;
+  if (onp == NULL) return;
+  for (index = 0; index < NumDefLineModifiers; index ++)
+  {
+    if (pfp->popup_list [ index] != NULL
+      && (popup_choice = GetValue (pfp->popup_list [ index])) > 0)
+    {
+      qual_index = GetDefLineModifierPopupIndex (popup_choice, pfp->modList);
+      if (qual_index < 0 || qual_index >= NumDefLineModifiers) continue;
+      if (DefLineModifiers[qual_index].isOrgMod)
+      {
+        mod = onp->mod;
+        while (mod != NULL
+          && mod->subtype != DefLineModifiers[qual_index].subtype)
+        {
+          mod = mod->next;
+        }
+        if ( UseOrgModifier (mod, taxName))
+        {
+          no_semicolon_len = StringCSpn (mod->subname, ";");
+          if (mod->subtype == ORGMOD_nat_host)
+          {
+            sprintf (modifier_text, "from ");
+            if (no_semicolon_len > sizeof (modifier_text) - 6) {
+              no_semicolon_len = sizeof (modifier_text) - 6;
+            }
+            StringNCpy (modifier_text + 5, mod->subname, no_semicolon_len);
+            modifier_text[sizeof (modifier_text) - 1] = 0;
+          }
+          else
+          {
+            AddModifierLabel (use_labels, qual_index, modifier_text);
+            if (modifier_text[0] != 0)
+              StringCat (modifier_text, " ");
+            if (no_semicolon_len > sizeof (modifier_text) - StringLen (modifier_text) - 1) {
+              no_semicolon_len = sizeof (modifier_text) - StringLen (modifier_text) - 1;
+            }
+            StringNCat (modifier_text, mod->subname, no_semicolon_len);
+            modifier_text[sizeof (modifier_text) - 1] = 0;
+          }
+          ValNodeCopyStr( &strings, 0, modifier_text);
+        }
+      } else {
+        ssp = biop->subtype;
+        while (ssp != NULL
+            && ssp->subtype != DefLineModifiers[qual_index].subtype)
+        {
+          ssp = ssp->next;
+        }
+        if (ssp != NULL)
+        {
+          no_semicolon_len = StringCSpn (ssp->name, ";");
+          AddModifierLabel (use_labels, qual_index, modifier_text);
+          if (ssp->subtype == SUBSRC_country)
+          {
+            sprintf (modifier_text, "from ");
+            if (no_semicolon_len > sizeof (modifier_text) - 6) {
+              no_semicolon_len = sizeof (modifier_text) - 6;
+            }
+            StringNCpy (modifier_text + 5, ssp->name, no_semicolon_len);
+            modifier_text[sizeof (modifier_text) - 1] = 0;
+            cp = StringChr (modifier_text, ':');
+            if (cp != NULL) *cp = 0;
+          }
+          else if (ssp->name != NULL
+            && (ssp->subtype != SUBSRC_plasmid_name
+              || StringCmp (ssp->name, "unnamed") != 0))
+          {
+            if (modifier_text[0] != 0)
+              StringCat (modifier_text, " ");
+            if (no_semicolon_len > sizeof (modifier_text) - StringLen (modifier_text) - 1) {
+              no_semicolon_len = sizeof (modifier_text) - StringLen (modifier_text) - 1;
+            }
+ 
+            StringNCat (modifier_text, ssp->name, no_semicolon_len);
+            modifier_text[sizeof (modifier_text) - 1] = 0;
+          }
+          ValNodeCopyStr( &strings, 0, modifier_text);
+        }
+      }
+    }
+  }
+  org_desc = MergeValNodeStrings (strings, FALSE);
+  ValNodeFreeData (strings);
+
+  sdp = SeqEntryGetSeqDescr (sep, Seq_descr_title, NULL);
+  if (sdp == NULL) {
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_title, &dcontext);
+    if (sdp == NULL) return;
+    cp = (CharPtr) sdp->data.ptrvalue;
+    if (cp == NULL) return;
+    sdp = SeqDescrAdd (&(bsp->descr));
+    if (sdp == NULL) return;
+    sdp->choice = Seq_descr_title;
+    sdp->data.ptrvalue = StringSave (cp);
+  }
+  if (sdp == NULL) return;
+  if (StringHasNoText (sdp->data.ptrvalue)) return;
+  new_defline = MemNew ((StringLen (org_desc)
+                        + StringLen (sdp->data.ptrvalue) + 4) * sizeof (Char));
+  if (new_defline == NULL) return;
+  StringCpy (new_defline, org_desc);
+  StringCat (new_defline, " ");
+  StringCat (new_defline, sdp->data.ptrvalue);
+  MemFree (sdp->data.ptrvalue);
+  sdp->data.ptrvalue = new_defline;
+  ObjMgrSetDirtyFlag (pfp->input_entityID, TRUE);
+}
+
+static void AddPrefixesToDefLines (PrefixFormPtr pfp, SeqEntryPtr sep)
+{
+  BioseqSetPtr bssp;
+  if (pfp == NULL || sep == NULL) return;
+  if (IS_Bioseq_set (sep)) {
+    bssp = (BioseqSetPtr) sep->data.ptrvalue;
+    if (bssp != NULL && (bssp->_class == 7 ||
+                         (IsPopPhyEtcSet (bssp->_class)))) {
+      for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
+        AddPrefixesToDefLines (pfp, sep);
+      }
+      return;
+    }
+  }
+  if (! IS_Bioseq (sep)) return;
+  AddPrefixesToOneDefLine (pfp, sep->data.ptrvalue, sep);
+}
+
+static void DoPrefixDefLines (ButtoN b)
+{
+  PrefixFormPtr pfp;
+  SeqEntryPtr   sep;
+
+  pfp = GetObjectExtra (b);
+  if (pfp == NULL) return;
+
+  Hide (pfp->form);
+  WatchCursor ();
+  Update ();
+  sep = GetTopSeqEntryForEntityID (pfp->input_entityID);
+  if (sep == NULL) return;
+  AddPrefixesToDefLines (pfp, sep);
+
+  ArrowCursor ();
+  Update ();
+  ObjMgrSetDirtyFlag (pfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, pfp->input_entityID, 0, 0);
+}
+
+extern void PrefixDefLines (IteM i)
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+  ModifierItemLocalPtr modList;
+  Int4         index;
+  WindoW       w;
+  GrouP        h, g, k;
+  Int4         popup_index, item_index, listed_index;
+  GrouP        c;
+  ButtoN       b;
+  PrefixFormPtr pfp;
+  Char         label [256];
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL || bfp->input_entityID == 0) return;
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+
+  modList = MemNew (NumDefLineModifiers * sizeof (ModifierItemLocalData));
+  if (modList == NULL) return;
+  CountModifiers (modList, sep);
+
+  pfp = MemNew (sizeof (PrefixFormData));
+  if (pfp == NULL) return;
+  pfp->input_entityID = bfp->input_entityID;
+  pfp->modList = modList;
+  pfp->popup_list = MemNew (sizeof (PopuP) * NumDefLineModifiers);
+  if (pfp->popup_list == NULL) return;
+
+  w = FixedWindow (-50, -33, -10, -10, "Definition Line Prefixes",
+                   StdCloseWindowProc);
+  SetObjectExtra (w, pfp, CleanupPrefixForm);
+  pfp->form = (ForM) w;
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+  g = HiddenGroup (h, 4, 0, NULL);
+  for (index = 0; index < NumDefLineModifiers; index++)
+  {
+    pfp->popup_list [index] = NULL;
+  }
+  popup_index = 0;
+  for (index = 0; index < NumDefLineModifiers; index++)
+  {
+    if (modList [ index].any_present)
+    {
+      k = HiddenGroup (g, 2, 0, NULL);
+      sprintf (label, "%d", popup_index + 1);
+      StaticPrompt (k, label, 0, popupMenuHeight, programFont, 'l');
+      pfp->popup_list[popup_index] = PopupList (k, TRUE, NULL);
+      listed_index = 0;
+      for (item_index = 0; item_index < NumDefLineModifiers; item_index ++)
+      {
+        if (modList [item_index].any_present)
+        {
+          PopupItem (pfp->popup_list[popup_index], 
+                   DefLineModifiers[item_index].name);
+          listed_index ++;
+        }
+      }
+      PopupItem (pfp->popup_list[popup_index], "Ignore");
+      listed_index++;
+      SetValue (pfp->popup_list[popup_index], listed_index);
+      popup_index ++;
+    }
+  }
+
+  pfp->add_org_name = CheckBox (h, "Prefix with taxonomy name", NULL);
+  SetStatus (pfp->add_org_name, TRUE);
+  pfp->use_labels = CheckBox (h, "Use modifier labels", NULL);
+  SetStatus (pfp->use_labels, TRUE);
+
+  c = HiddenGroup (h, 4, 0, NULL);
+  b = DefaultButton (c, "Accept", DoPrefixDefLines);
+  SetObjectExtra (b, pfp, NULL);
+  PushButton (c, "Cancel", StdCancelButtonProc);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) pfp->add_org_name,
+                (HANDLE) pfp->use_labels,
+                (HANDLE) c, NULL);
+  RealizeWindow (w);
+  Show (w);
+  Update ();
+
+}
+
diff --git a/sequin/sequin2.c b/sequin/sequin2.c
index 1447b8da..76e76662 100644
--- a/sequin/sequin2.c
+++ b/sequin/sequin2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.146 $
+* $Revision: 6.155 $
 *
 * File Description: 
 *
@@ -1942,7 +1942,7 @@ static void LetUserFixNucleotideInfo (SequencesFormPtr sqfp)
     MultiLinePrompt (fnfp->pptGrp, sourceModMsg, 25 * stdCharWidth, programFont);
 
     c = HiddenGroup (h, 2, 0, NULL);
-    b = PushButton (c, "OK", AcceptNucleotideFixup);
+    b = DefaultButton (c, "OK", AcceptNucleotideFixup);
     SetObjectExtra (b, fnfp, NULL);
 
     AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) fnfp->modGrp,
@@ -2367,7 +2367,7 @@ static void LetUserFixProteinInfo (SequencesFormPtr sqfp)
     }
 
     c = HiddenGroup (w, 2, 0, NULL);
-    acceptBtn = PushButton (c, "OK", AcceptThisFixup);
+    acceptBtn = DefaultButton (c, "OK", AcceptThisFixup);
     SetObjectExtra (acceptBtn, fpfp, NULL);
 
     AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, (HANDLE) fpfp->orf, NULL);
@@ -2699,7 +2699,7 @@ extern Boolean ProcessOneNucleotideTitle (Int2 seqPackage, DialoG genbio, PopuP
               biop->org = orp;
               if (orp != NULL) {
                 TrimSpacesAroundString (str);
-                orp->taxname = StringSave (str);
+                SetTaxNameAndRemoveTaxRef (orp, StringSave (str));
                 if (masterbiop != NULL) {
                   masterorp = masterbiop->org;
                   if (masterorp != NULL) {
@@ -2729,7 +2729,7 @@ extern Boolean ProcessOneNucleotideTitle (Int2 seqPackage, DialoG genbio, PopuP
               orp = OrgRefNew ();
               biop->org = orp;
               if (orp != NULL) {
-                orp->taxname = StringSave (masterorp->taxname);
+                SetTaxNameAndRemoveTaxRef (orp, StringSave (masterorp->taxname));
                 orp->common = StringSave (masterorp->common);
                 masteronp = masterorp->orgname;
                 if (masteronp != NULL) {
@@ -2952,7 +2952,7 @@ extern Boolean ProcessOneNucleotideTitle (Int2 seqPackage, DialoG genbio, PopuP
             orp = OrgRefNew ();
             biop->org = orp;
             if (orp != NULL) {
-              orp->taxname = StringSave (masterorp->taxname);
+              SetTaxNameAndRemoveTaxRef (orp, StringSave (masterorp->taxname));
               orp->common = StringSave (masterorp->common);
               onp = orp->orgname;
               if (onp == NULL) {
@@ -6969,7 +6969,7 @@ extern void LoadTPAAccessionNumbersFromFile (
     }
     if (need_seqid)
     {
-      seqid_len = StringCSpn (str, " ");
+      seqid_len = StringCSpn (str, " \t");
       if (seqid_len > 0)
       {
         StringNCpy (seqid, str, seqid_len);
@@ -6991,7 +6991,7 @@ extern void LoadTPAAccessionNumbersFromFile (
     found_end = FALSE;
     while (*cp != 0)
     {
-      if (*cp == ' ' || *cp == ',')
+      if (*cp == ' ' || *cp == ',' || *cp == '\t')
       {
         cp++;
       }
@@ -7108,6 +7108,38 @@ static void AddHistory (
   }
 }
 
+static Boolean DoIDsMatch (CharPtr seqid, BioseqPtr bsp, Boolean AllowLocal)
+{
+  Char         str [128];
+  Int4         seqid_len;
+  SeqIdPtr     sip;
+
+  if (bsp == NULL) return FALSE;
+
+  SeqIdWrite (bsp->id, str, PRINTID_REPORT, sizeof (str));
+  seqid_len = StringCSpn (str, ".");
+  if (seqid_len > 0)
+  {
+    str [ seqid_len ] = 0;
+  }
+  if (StringCmp (str, seqid) == 0) return TRUE;
+
+  for (sip = bsp->id; sip != NULL; sip = sip->next)
+  {
+    if (sip->choice == SEQID_LOCAL && AllowLocal)
+    {
+      SeqIdWrite (bsp->id, str, PRINTID_REPORT, sizeof (str));
+      seqid_len = StringCSpn (str, ".");
+      if (seqid_len > 0)
+      {
+        str [ seqid_len ] = 0;
+      }
+      if (StringCmp (str, seqid) == 0) return TRUE;
+    }
+  }
+  return FALSE;
+}
+
 static Boolean AddAccessionToGenbankBlock (
   CharPtr     seqid,
   ValNodePtr  acc_list,
@@ -7117,10 +7149,8 @@ static Boolean AddAccessionToGenbankBlock (
 {
   BioseqPtr    bsp;
   BioseqSetPtr bssp;
-  Int4         seqid_len;
   GBBlockPtr   gbp;
   ValNodePtr   last_one;
-  Char         str [128];
   SeqDescrPtr       sdp;
 
   if (seqid == NULL || acc_list == NULL
@@ -7145,13 +7175,7 @@ static Boolean AddAccessionToGenbankBlock (
 
   bsp = (BioseqPtr) sep->data.ptrvalue;
   if (bsp == NULL) return FALSE;
-  SeqIdWrite (bsp->id, str, PRINTID_REPORT, sizeof (str));
-  seqid_len = StringCSpn (str, ".");
-  if (seqid_len > 0)
-  {
-    str [ seqid_len ] = 0;
-  }
-  if (StringCmp (str, seqid) != 0) return FALSE;
+  if (! DoIDsMatch (seqid, bsp, TRUE)) return FALSE;
 
   sdp = BioseqGetSeqDescr (bsp, Seq_descr_genbank, NULL);
 
@@ -7321,3 +7345,393 @@ extern void LoadHistoryAccessionNumbersFromFile (
   LoadSecondaryAccessionNumbersPlusHistFromFile (i, TRUE);
 }
 
+/* This section of code is used for managing lists of features.
+ * Sometimes the features will be displayed alphabetically, sometimes
+ * they will be displayed alphabetically with a list of the most used features
+ * also appearing at the top of the list.
+ */
+
+/* This is used to compare feature names with the special alphabetical order */
+static int CompareFeatureNames (CharPtr cp1, CharPtr cp2)
+{
+  /* NULL name goes at the end */
+  if (cp1 == NULL && cp2 == NULL) return 0;
+  if (cp1 == NULL) return 1;
+  if (cp2 == NULL) return -1;
+
+  /* starts with a space goes at the beginning */
+  if (cp1 [0] == ' ' && cp2 [0] == ' ') return 0;
+  if (cp1 [0] == ' ') return -1;
+  if (cp2 [0] == ' ') return 1;
+
+  /* Is "All" or [ALL FEATURES] goes at the beginning */
+  if ((StringCmp (cp1, "All") == 0
+    || StringCmp (cp1, "[ALL FEATURES]") == 0)
+    && (StringCmp (cp2, "All") == 0
+    || StringCmp (cp2, "[ALL FEATURES]") == 0))
+  {
+    return 0;
+  }
+  if (StringCmp (cp1, "All") == 0
+    || StringCmp (cp1, "[ALL FEATURES]") == 0)
+  {
+    return -1;
+  }
+  if (StringCmp (cp2, "All") == 0
+    || StringCmp (cp2, "[ALL FEATURES]") == 0)
+  {
+    return 1;
+  }
+
+  /* starts with a number -> goes at the end */
+  if (cp1 [0] >= '0' && cp1 [0] <= '9'
+   && cp2 [0] >= '0' && cp2 [0] <= '9')
+  {
+    return StringICmp (cp1, cp2);
+  }
+  if (cp1 [0] >= '0' && cp1 [0] <= '9')
+  {
+    return 1;
+  }
+  if (cp2 [0] >= '0' && cp2 [0] <= '9')
+  {
+    return -1;
+  }
+
+  /* starts with a tilde or dash - sort with other tildes, put before numbers after alphas */
+  if (cp1 [0] == '~' && cp2 [0] == '~') 
+  {
+    return StringICmp (cp1 + 1, cp2 + 1);
+  }
+  if (cp1 [0] == '~') return 1;
+  if (cp2 [0] == '~') return -1;
+
+  if (cp1 [0] == '-' && cp2 [0] == '-') 
+  {
+    return StringICmp (cp1 + 1, cp2 + 1);
+  }
+  if (cp1 [0] == '-') return 1;
+  if (cp2 [0] == '-') return -1;
+
+  return StringICmp (cp1, cp2);
+}
+
+extern int LIBCALLBACK CompareFeatureValNodeStrings (VoidPtr ptr1, VoidPtr ptr2)
+{
+  ValNodePtr vnp1, vnp2;
+
+  if (ptr1 == NULL || ptr2 == NULL) return 0;
+
+  vnp1 = *((ValNodePtr PNTR) ptr1);
+  vnp2 = *((ValNodePtr PNTR) ptr2);
+
+  if (vnp1 == NULL || vnp2 == NULL) return 0;
+
+  return CompareFeatureNames (vnp1->data.ptrvalue, vnp2->data.ptrvalue);
+}
+
+extern int LIBCALLBACK CompareImpFeatEnumFieldAssoc (VoidPtr ptr1, VoidPtr ptr2)
+{
+  ValNodePtr        vnp1, vnp2;
+  EnumFieldAssocPtr ap1, ap2;
+
+  if (ptr1 == NULL || ptr2 == NULL) return 0;
+
+  vnp1 = *((ValNodePtr PNTR) ptr1);
+  vnp2 = *((ValNodePtr PNTR) ptr2);
+  if (vnp1 == NULL || vnp2 == NULL) return 0;
+
+  ap1 = (EnumFieldAssocPtr) vnp1->data.ptrvalue;
+  ap2 = (EnumFieldAssocPtr) vnp2->data.ptrvalue;
+  if (ap1 == NULL || ap2 == NULL) return 0;
+
+  return CompareFeatureNames (ap1->name, ap2->name);
+}
+
+CharPtr MostUsedFeatureList[] = { 
+  "CDS",
+  "exon",
+  "Gene",
+  "intron",
+  "mRNA",
+  "rRNA",
+  "RNA"
+};
+
+extern ValNodePtr InsertMostUsedFeatureValNodes (ValNodePtr old_list)
+{
+  ValNodePtr new_list, new_item, old_item;
+  Int4       index;
+
+  new_list = NULL;
+  for (index = 0;
+       index < sizeof (MostUsedFeatureList) / sizeof (CharPtr);
+       index ++)
+  {
+    old_item = FindExactStringInStrings ( old_list, MostUsedFeatureList [index])
+;
+    if (old_item == NULL) continue;
+    new_item = ValNodeNew ( new_list);
+    if (new_item == NULL) return old_list;
+    new_item->choice = old_item->choice;
+    new_item->data.ptrvalue = StringSave (MostUsedFeatureList [index]);
+    if (new_list == NULL) new_list = new_item;
+  }
+  if (new_item != NULL)
+  {
+    if (old_list != NULL &&
+      ( StringCmp (old_list->data.ptrvalue, "All") == 0
+       || StringCmp (old_list->data.ptrvalue, "[ALL FEATURES]") == 0))
+    {
+      new_item->next = old_list->next;
+      old_list->next = new_list;
+      new_list = old_list;
+    }
+    else
+    {
+      new_item->next = old_list;
+    }
+  }
+  else
+  {
+    new_list = old_list;
+  }
+  return new_list;
+}
+
+static EnumFieldAssocPtr FindEnumFieldAssoc (
+  EnumFieldAssocPtr alist,
+  CharPtr findStr
+)
+{
+  EnumFieldAssocPtr ap;
+  
+  for (ap = alist; ap != NULL && ap->name != NULL; ap++)
+  {
+    if (StringCmp (ap->name, findStr) == 0) return ap;
+  }
+  return NULL;
+}
+
+static void CopyEnumFieldAssoc (EnumFieldAssocPtr ap1, EnumFieldAssocPtr ap2)
+{
+  if (ap1 == NULL || ap2 == NULL) return;
+
+  ap1->name = StringSave (ap2->name);
+  ap1->value = ap2->value;
+}
+
+extern EnumFieldAssocPtr InsertMostUsedFeatureEnumFieldAssoc (
+  EnumFieldAssocPtr alist
+)
+{
+  Int4              num_total_fields, index, new_index;
+  EnumFieldAssocPtr ap, new_alist, old_ap;
+
+  num_total_fields = sizeof (MostUsedFeatureList) / sizeof (CharPtr);
+
+  for (ap = alist; ap != NULL && ap->name != NULL; ap++)
+  {
+    num_total_fields ++;
+  }
+  /* need the last null field */
+  num_total_fields ++;
+
+  new_alist = MemNew (num_total_fields * sizeof (EnumFieldAssoc));
+  if (new_alist == NULL) return alist;
+
+  /* copy the first item if wildcard */
+  if (StringCmp (alist->name, "[ALL FEATURES]") == 0)
+  {
+    CopyEnumFieldAssoc (new_alist, alist);
+    new_index = 1;
+  }
+  else
+  {
+    new_index = 0;
+  }
+
+  for (index = 0;
+       index < sizeof (MostUsedFeatureList) / sizeof (CharPtr);
+       index ++)
+  {
+    old_ap = FindEnumFieldAssoc (alist, MostUsedFeatureList [index]);
+    if (old_ap == NULL) continue;
+    CopyEnumFieldAssoc (new_alist + new_index++, old_ap);
+  }
+
+  for (ap = alist; ap != NULL && ap->name != NULL; ap++)
+  {
+    CopyEnumFieldAssoc (new_alist + new_index ++, ap);
+  }
+  /* copy over the last null field */
+  if (ap != NULL)
+  {
+    CopyEnumFieldAssoc (new_alist + new_index ++, ap);
+  }
+  return new_alist;
+  
+}
+
+extern void SortEnumFieldAssocPtrArray (EnumFieldAssocPtr alist, CompareFunc compar)
+{
+  ValNodePtr        head, vnp;
+  EnumFieldAssocPtr ap;
+  Int4              index;
+
+  /* first, create ValNode list so we can sort the data */
+  head = NULL;
+  for (ap = alist; ap != NULL && ap->name != NULL; ap++)
+  {
+    vnp = ValNodeNew (head);
+    if (vnp == NULL) return;
+    vnp->data.ptrvalue = MemNew (sizeof (EnumFieldAssoc));
+    if (vnp->data.ptrvalue == NULL) return;
+    MemCpy (vnp->data.ptrvalue, ap, sizeof (EnumFieldAssoc));
+    if (head == NULL) head = vnp;
+  }
+
+  /* Now sort the ValNode list */
+  head = SortValNode (head, compar);
+
+  /* Now repopulate the EnumFieldAssoc list */
+  index = 0;
+  for (vnp = head; vnp != NULL; vnp = vnp->next)
+  {
+    MemCpy (alist + index++, vnp->data.ptrvalue, sizeof (EnumFieldAssoc));
+  }
+
+  /* And free the ValNode list */
+  ValNodeFreeData (head);
+}
+
+static Uint2 UnusualFeatureTypes [] = {
+  FEATDEF_ORG,
+  FEATDEF_mutation,
+  FEATDEF_site_ref,
+  FEATDEF_gap,
+  FEATDEF_NON_STD_RESIDUE,
+  FEATDEF_NUM
+};
+ 
+extern ValNodePtr BuildFeatureValNodeList (
+  Boolean prefer_most_used,
+  CharPtr wild_card_name,
+  Int4    wild_card_value,
+  Boolean skip_unusual,
+  Boolean skip_import
+)
+{
+  FeatDefPtr  curr;
+  ValNodePtr  head, vnp;
+  Uint1       key;
+  CharPtr     label = NULL;
+  Uint2       subtype;
+  Int4        index;
+  Boolean     skip;
+  Char        str [256];
+
+  head = NULL;
+  curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
+  while (curr != NULL) {
+    skip = FALSE;
+    if (skip_unusual)
+    {
+      for (index = 0;
+           ! skip && index < sizeof ( UnusualFeatureTypes ) / sizeof (Uint2);
+           index ++)
+      {
+        if (curr->featdef_key == UnusualFeatureTypes [ index ]) skip = TRUE;
+      }
+    }
+    if (key != FEATDEF_BAD && ! skip) {
+      
+      subtype = curr->featdef_key;
+      if (subtype != FEATDEF_misc_RNA &&
+          subtype != FEATDEF_precursor_RNA &&
+          subtype != FEATDEF_mat_peptide &&
+          subtype != FEATDEF_sig_peptide &&
+          subtype != FEATDEF_transit_peptide &&
+          subtype != FEATDEF_Imp_CDS)
+      {
+        StringNCpy_0 (str, curr->typelabel, sizeof (str) - 1);
+      }
+      else if (! skip_import)
+      {
+        StringNCpy_0 (str, curr->typelabel, sizeof (str) - 10);
+        StringCat (str, "_imp");
+      }
+      else
+      {
+        skip = TRUE;
+      }
+      if (! skip)
+      {
+        vnp = ValNodeNew (head);
+        if (head == NULL) {
+          head = vnp;
+        }
+        if (vnp != NULL) {
+          vnp->choice = subtype;
+          vnp->data.ptrvalue = StringSave (str);
+        }
+      }
+    }
+    curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
+  }
+  if (head != NULL) {
+    head = SortValNode (head, CompareFeatureValNodeStrings);
+    head = InsertMostUsedFeatureValNodes (head);
+    if (wild_card_name != NULL)
+    {
+      vnp = ValNodeNew (NULL);
+      if (vnp != NULL) {
+        vnp->choice = wild_card_value;
+        vnp->data.ptrvalue = StringSave (wild_card_name);
+        vnp->next = head;
+        head = vnp;
+      }
+    }
+  }
+  return head;
+}
+
+extern void SetTaxNameAndRemoveTaxRef (OrgRefPtr orp, CharPtr taxname)
+{
+  ValNodePtr      vnp, next;
+  ValNodePtr PNTR prev;
+  DbtagPtr        dbt;
+  Boolean         remove_taxrefs;
+
+  if (orp == NULL) return;
+
+  if ( taxname == NULL || orp->taxname == NULL
+    || StringCmp (taxname, orp->taxname) != 0)
+  {
+    remove_taxrefs = TRUE;
+  }
+  MemFree (orp->taxname);
+  orp->taxname = taxname;
+
+  if (! remove_taxrefs) return;
+
+  orp->common = MemFree (orp->common);
+
+  vnp = orp->db;
+  if (vnp == NULL) return;
+  prev = (ValNodePtr PNTR) &(orp->db);
+  while (vnp != NULL) {
+    next = vnp->next;
+    dbt = (DbtagPtr) vnp->data.ptrvalue;
+    if (dbt != NULL && StringICmp ((CharPtr) dbt->db, "taxon") == 0) {
+      *prev = vnp->next;
+      vnp->next = NULL;
+      DbtagFree (dbt);
+      ValNodeFree (vnp);
+    } else {
+      prev = (ValNodePtr PNTR) &(vnp->next);
+    }
+    vnp = next;
+  }
+}
+
diff --git a/sequin/sequin3.c b/sequin/sequin3.c
index b8d5ef57..bc951a19 100644
--- a/sequin/sequin3.c
+++ b/sequin/sequin3.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.302 $
+* $Revision: 6.347 $
 *
 * File Description: 
 *
@@ -49,6 +49,7 @@
 #include <import.h>
 #include <gather.h>
 #include <asn2gnbk.h>
+#include <asn2gnbp.h>
 #include <edutil.h>
 #include <gbfeat.h>
 #include <gbftdef.h>
@@ -1087,19 +1088,30 @@ static ValNodePtr RemoveDbxrefList (ValNodePtr vnp)
   return NULL;
 }
 
-static void DoRemoveGeneDbxrefs (SeqFeatPtr sfp, Pointer userdata)
+static void DoRemoveDbxrefs (SeqFeatPtr sfp, Pointer userdata)
 
 {
   GeneRefPtr  grp;
+  Uint1       feattype;
 
-  if (sfp->data.choice != SEQFEAT_GENE) return;
+  if (sfp == NULL) return;
+
+  if (userdata != NULL && (feattype = *(Uint1 PNTR)userdata) != sfp->data.choice) return;
   sfp->dbxref = RemoveDbxrefList (sfp->dbxref);
+  if (sfp->data.choice != SEQFEAT_GENE) return;
   grp = (GeneRefPtr) sfp->data.value.ptrvalue;
   if (grp == NULL) return;
   grp->db = RemoveDbxrefList (grp->db);
 }
 
-static void RemoveGeneDbxrefs (IteM i)
+static void DoRemoveBioSourceDbxrefs (BioSourcePtr biop, Pointer userdata)
+{
+  if (biop == NULL || biop->org == NULL) return;
+  
+  biop->org->db = RemoveDbxrefList (biop->org->db);
+}
+
+static void RemoveDbxrefsCommon (IteM i, Uint1 PNTR subtype)
 
 {
   BaseFormPtr  bfp;
@@ -1113,11 +1125,42 @@ static void RemoveGeneDbxrefs (IteM i)
   if (bfp == NULL) return;
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
-  VisitFeaturesInSep (sep, NULL, DoRemoveGeneDbxrefs);
+  VisitFeaturesInSep (sep, subtype, DoRemoveDbxrefs);
+  if (subtype == NULL)
+  {
+    VisitBioSourcesInSep (sep, NULL, DoRemoveBioSourceDbxrefs);
+  }
   ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
+static void RemoveGeneDbxrefs (IteM i)
+{
+  Uint1        subtype = SEQFEAT_GENE;
+  RemoveDbxrefsCommon (i, &subtype);
+}
+
+static void RemoveRNADbxrefs (IteM i)
+
+{
+  Uint1        subtype = SEQFEAT_RNA;
+
+  RemoveDbxrefsCommon (i, &subtype);
+}
+
+static void RemoveCDSDbxrefs (IteM i)
+
+{
+  Uint1        subtype = FEATDEF_CDS;
+  RemoveDbxrefsCommon (i, &subtype);
+}
+
+static void RemoveAllDbxrefs (IteM i)
+
+{
+  RemoveDbxrefsCommon (i, NULL);
+}
+
 static void RemoveCDDRegions (IteM i)
 
 {
@@ -1234,9 +1277,10 @@ static void LastDitchLookup (BioSourcePtr biop)
   if (ssp != NULL) {
     ssp->subtype = 255;
     ssp->name = orp->taxname;
+	orp->taxname = NULL;
     ssp->next = biop->subtype;
     biop->subtype = ssp;
-    orp->taxname = StringSave (orgname);
+    SetTaxNameAndRemoveTaxRef (orp, StringSave (orgname));
   }
 }
 
@@ -1958,7 +2002,7 @@ static Boolean AlistMessage (EnumFieldAssocPtr al, UIEnumPtr val, UIEnum dflt, C
     InitEnumPopup (alistBoxPopup, al, NULL);
     SetEnumPopup (alistBoxPopup, al, dflt);
     c = HiddenGroup (g, 2, 0, NULL);
-    PushButton (c, "Accept", AcceptAlistMessage);
+    DefaultButton (c, "Accept", AcceptAlistMessage);
     PushButton (c, "Cancel", CancelAlistMessage);
     AlignObjects (ALIGN_CENTER, (HANDLE) ppt, (HANDLE) alistBoxPopup, (HANDLE) c, NULL);
     RealizeWindow (w);
@@ -2229,7 +2273,7 @@ static void MultiTransformProc (IteM i, Uint2 targettype)
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoMultiTransform);
+  b = DefaultButton (c, "Accept", DoMultiTransform);
   SetObjectExtra (b, mfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -3603,7 +3647,7 @@ static void ZapRBSGene (SeqFeatPtr sfp, Pointer userdata)
 
   if (sfp->idx.subtype != FEATDEF_RBS) return;
   grp = SeqMgrGetGeneXref (sfp);
-  if (grp != NULL) return;
+  if (grp != NULL && (! SeqMgrGeneIsSuppressed (grp))) return;
   gene = SeqMgrGetOverlappingGene (sfp->location, &gcontext);
   if (gene == NULL) return;
   diff = SeqLocAinB (sfp->location, gene->location);
@@ -3945,6 +3989,7 @@ static void CopyBankitComments (IteM i)
 }
 
 static ENUM_ALIST(molinfo_biomol_alist)
+  {"Any",                  254},
   {" ",                      0},
   {"Genomic DNA or RNA",     1},
   {"Precursor RNA",          2},
@@ -3963,6 +4008,7 @@ static ENUM_ALIST(molinfo_biomol_alist)
 END_ENUM_ALIST
 
 static ENUM_ALIST(molinfo_tech_alist)
+  {"Any",              254},
   {" ",                  0},
   {"Standard",           1},
   {"EST",                2},
@@ -3988,6 +4034,7 @@ static ENUM_ALIST(molinfo_tech_alist)
 END_ENUM_ALIST
 
 static ENUM_ALIST(molinfo_complete_alist)
+  {"Any",     254},
   {" ",         0},
   {"Complete",  1},
   {"Partial",   2},
@@ -3998,6 +4045,7 @@ static ENUM_ALIST(molinfo_complete_alist)
 END_ENUM_ALIST
 
 static ENUM_ALIST(mol_alist)
+{"Any",             Seq_mol_other - 1},
 {" ",               0},
 {"DNA",             Seq_mol_dna},
 {"RNA",             Seq_mol_rna},
@@ -4007,6 +4055,7 @@ static ENUM_ALIST(mol_alist)
 END_ENUM_ALIST
 
 static ENUM_ALIST(topology_alist)
+{"Any",             254},
 {" ",               0},
 {"Linear",          TOPOLOGY_LINEAR},
 {"Circular",        TOPOLOGY_CIRCULAR},
@@ -4015,6 +4064,7 @@ static ENUM_ALIST(topology_alist)
 END_ENUM_ALIST
 
 static ENUM_ALIST(strand_alist)
+{"Any",             254},
 {" ",               Seq_strand_unknown},
 {"Single",          Seq_strand_plus},
 {"Double",          Seq_strand_minus},
@@ -4023,15 +4073,122 @@ static ENUM_ALIST(strand_alist)
 {"Other",           Seq_strand_other},
 END_ENUM_ALIST
 
+static ValNodePtr MakeValNodeListFromEnum ( EnumFieldAssocPtr al)
+{
+  EnumFieldAssocPtr efap;
+  ValNodePtr        list;
+
+  efap = al;
+  list = NULL;
+  while (efap->name != NULL)
+  {
+    ValNodeAddStr (&list, efap->value, StringSave (efap->name));
+    efap ++;
+  }
+  return list;
+}
+
+static void ReplaceValNodeString (ValNodePtr list, CharPtr find, CharPtr repl)
+{
+  ValNodePtr vnp;
+
+  if (list == NULL || find == NULL || repl == NULL) return;
+
+  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  {
+    if (StringCmp (vnp->data.ptrvalue, find) == 0)
+    {
+      MemFree (vnp->data.ptrvalue);
+      vnp->data.ptrvalue = StringSave (repl);
+    }
+  }
+}
+
+static void InitValNodePopup (ValNodePtr list, PopuP p)
+{
+  ValNodePtr vnp;
+
+  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->data.ptrvalue != NULL)
+    {
+      PopupItem (p, vnp->data.ptrvalue);
+    }
+  }
+}
+
+static Int2 GetValNodePopup (PopuP p, ValNodePtr list)
+{
+  ValNodePtr vnp;
+  Int2       popupval;
+
+  popupval = GetValue (p);
+  if (popupval == 0)
+  {
+    return -1;
+  }
+  for (vnp = list; vnp != NULL && popupval > 1; vnp = vnp->next)
+  {
+    if (vnp->data.ptrvalue != NULL)
+    {
+      popupval --;
+    }
+  }
+  if (popupval > 1 || vnp == NULL) return -1;
+  return vnp->choice;
+}
+
+static void SetValNodePopupValue (ValNodePtr list, PopuP p, CharPtr val)
+{
+  ValNodePtr vnp;
+  Int2       popupval;
+
+  popupval = 1;
+  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->data.ptrvalue != NULL)
+    {
+      if (StringCmp (vnp->data.ptrvalue, val) == 0)
+      {
+        SetValue (p, popupval);
+      }
+      popupval ++;
+    }
+  }
+}
+
 typedef struct molinfoblock {
   PopuP           moltype;
+  ValNodePtr      moltype_values;
   PopuP           technique;
+  ValNodePtr      technique_values;
   PopuP           complete;
+  ValNodePtr      complete_values;
   PopuP           molPopup;
+  ValNodePtr      mol_values;
   PopuP           topologyPopup;
+  ValNodePtr      topology_values;
   PopuP           strandPopup;
+  ValNodePtr      strand_values;
 } MolInfoBlock, PNTR MolInfoBlockPtr;
 
+static void FreeMolInfoBlockData (MolInfoBlockPtr mibp)
+{
+  if (mibp == NULL) return;
+  ValNodeFreeData (mibp->moltype_values);
+  mibp->moltype_values = NULL;
+  ValNodeFreeData (mibp->technique_values);
+  mibp->technique_values = NULL;
+  ValNodeFreeData (mibp->complete_values);
+  mibp->complete_values = NULL;
+  ValNodeFreeData (mibp->mol_values);
+  mibp->mol_values = NULL;
+  ValNodeFreeData (mibp->topology_values);
+  mibp->topology_values = NULL;
+  ValNodeFreeData (mibp->strand_values);
+  mibp->strand_values = NULL;
+}
+
 typedef struct molinfoedit {
   DESCRIPTOR_FORM_BLOCK
   SeqEntryPtr     sep;
@@ -4047,7 +4204,20 @@ static CharPtr  labels [] = {
   "Class", "Topology", "Strand", NULL
 };
 
-static void CreateMolInfoBlock (MolInfoBlockPtr mibp, GrouP h)
+static void SetupMolInfoBlockPopup (GrouP g, PopuP PNTR p, ValNodePtr PNTR v,
+                                    EnumFieldAssocPtr al, Boolean IsTo)
+{
+  *p = PopupList (g, TRUE, NULL);
+  *v = MakeValNodeListFromEnum ( al );
+  if (IsTo)
+  {
+    ReplaceValNodeString (*v, "Any", "No change");
+  }
+  InitValNodePopup (*v, *p);
+  SetValue (*p, 1);
+}
+
+static void CreateMolInfoBlock (MolInfoBlockPtr mibp, GrouP h, Boolean IsTo)
 
 {
   GrouP  g;
@@ -4061,31 +4231,50 @@ static void CreateMolInfoBlock (MolInfoBlockPtr mibp, GrouP h)
   g = HiddenGroup (h, -2, 0, NULL);
 
   StaticPrompt (g, "Molecule", wid, popupMenuHeight, programFont, 'l');
-  mibp->moltype = PopupList (g, TRUE, NULL);
-  InitEnumPopup (mibp->moltype, molinfo_biomol_alist, NULL);
-  SetEnumPopup (mibp->moltype, molinfo_biomol_alist, 0);
+  SetupMolInfoBlockPopup (g, &(mibp->moltype), &(mibp->moltype_values),
+                          molinfo_biomol_alist, IsTo);
 
   StaticPrompt (g, "Technique", wid, popupMenuHeight, programFont, 'l');
-  mibp->technique = PopupList (g, TRUE, NULL);
-  InitEnumPopup (mibp->technique, molinfo_tech_alist, NULL);
-  SetEnumPopup (mibp->technique, molinfo_tech_alist, 0);
+  SetupMolInfoBlockPopup (g, &(mibp->technique), &(mibp->technique_values),
+                          molinfo_tech_alist, IsTo);
 
   StaticPrompt (g, "Completedness", wid, popupMenuHeight, programFont, 'l');
-  mibp->complete = PopupList (g, TRUE, NULL);
-  InitEnumPopup (mibp->complete, molinfo_complete_alist, NULL);
-  SetEnumPopup (mibp->complete, molinfo_complete_alist, 0);
+  SetupMolInfoBlockPopup (g, &(mibp->complete), &(mibp->complete_values),
+                          molinfo_complete_alist, IsTo);
 
   StaticPrompt (g, "Class", wid, popupMenuHeight, programFont, 'l');
-  mibp->molPopup = PopupList (g, TRUE, NULL);
-  InitEnumPopup (mibp->molPopup, mol_alist, NULL);
+  SetupMolInfoBlockPopup (g, &(mibp->molPopup), &(mibp->mol_values),
+                          mol_alist, IsTo);
 
   StaticPrompt (g, "Topology", wid, popupMenuHeight, programFont, 'l');
-  mibp->topologyPopup = PopupList (g, TRUE, NULL);
-  InitEnumPopup (mibp->topologyPopup, topology_alist, NULL);
+  SetupMolInfoBlockPopup (g, &(mibp->topologyPopup), &(mibp->topology_values),
+                          topology_alist, IsTo);
 
   StaticPrompt (g, "Strand", wid, popupMenuHeight, programFont, 'l');
-  mibp->strandPopup = PopupList (g, TRUE, NULL);
-  InitEnumPopup (mibp->strandPopup, strand_alist, NULL);
+  SetupMolInfoBlockPopup (g, &(mibp->strandPopup), &(mibp->strand_values),
+                          strand_alist, IsTo);
+}
+
+static void SetMolInfoBlockWildCard ( MolInfoBlockPtr mibp )
+{
+  if (mibp == NULL) return;
+  SetValue (mibp->moltype, 1);
+  SetEnumPopup (mibp->technique, molinfo_tech_alist, 0);
+  SetEnumPopup (mibp->complete, molinfo_complete_alist, 0);
+  SetValue (mibp->molPopup, 1);
+  SetValue (mibp->topologyPopup, 1);
+  SetValue (mibp->strandPopup, 1);
+}
+
+static void SetMolInfoBlockDefault ( MolInfoBlockPtr mibp )
+{
+  if (mibp == NULL) return;
+  SetEnumPopup (mibp->moltype, molinfo_biomol_alist, 0);
+  SetEnumPopup (mibp->technique, molinfo_tech_alist, 0);
+  SetEnumPopup (mibp->complete, molinfo_complete_alist, 0);
+  SetEnumPopup (mibp->molPopup, mol_alist, 0);
+  SetEnumPopup (mibp->topologyPopup, topology_alist, 0);
+  SetEnumPopup (mibp->strandPopup, strand_alist, 0);
 }
 
 static void EditMolInfoCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent)
@@ -4095,7 +4284,6 @@ static void EditMolInfoCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, In
   MolInfoEditPtr  miep;
   MolInfoPtr      mip;
   ValNodePtr      sdp;
-  UIEnum          val;
 
   if (mydata == NULL) return;
   if (sep == NULL || sep->data.ptrvalue == NULL) return;
@@ -4110,22 +4298,34 @@ static void EditMolInfoCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, In
     bsp = (BioseqPtr) sep->data.ptrvalue;
     if ((ISA_na (bsp->mol) && miep->nucsOK) ||
         (ISA_aa (bsp->mol) && miep->protsOK)) {
-      if (GetEnumPopup (miep->from.molPopup, mol_alist, &val) &&
-          bsp->mol == (Uint1) val) {
-        if (GetEnumPopup (miep->to.molPopup, mol_alist, &val)) {
-          bsp->mol = (Uint1) val;
+      if ((Uint1)GetValNodePopup (miep->from.molPopup,
+                                  miep->from.mol_values) == bsp->mol
+        || GetValue (miep->from.molPopup) == 1)
+      {
+        if (GetValue (miep->to.molPopup) != 1)
+        {
+          bsp->mol = (Uint1) GetValNodePopup (miep->to.molPopup,
+                                              miep->to.mol_values);
         }
       }
-      if (GetEnumPopup (miep->from.strandPopup, strand_alist, &val) &&
-          bsp->strand == (Uint1) val) {
-        if (GetEnumPopup (miep->to.strandPopup, strand_alist, &val)) {
-          bsp->strand = (Uint1) val;
+      if ((Uint1)GetValNodePopup (miep->from.strandPopup,
+                                  miep->to.strand_values) == bsp->strand
+        || GetValue (miep->from.strandPopup) == 1)
+      {
+        if (GetValue (miep->to.strandPopup) != 1)
+        {
+          bsp->strand = (Uint1) GetValNodePopup (miep->to.strandPopup,
+                                                 miep->to.strand_values);
         }
       }
-      if (GetEnumPopup (miep->from.topologyPopup, topology_alist, &val) &&
-          bsp->topology == (Uint1) val) {
-        if (GetEnumPopup (miep->to.topologyPopup, topology_alist, &val)) {
-          bsp->topology = (Uint1) val;
+      if ((Uint1) GetValNodePopup (miep->from.topologyPopup,
+                                   miep->from.topology_values) == bsp->topology
+        || GetValue (miep->from.topologyPopup) == 1)
+      {
+        if (GetValue (miep->to.topologyPopup) != 1)
+        {
+          bsp->topology = (Uint1) GetValNodePopup (miep->to.topologyPopup,
+                                                   miep->to.topology_values);
         }
       }
       sdp = bsp->descr;
@@ -4137,28 +4337,40 @@ static void EditMolInfoCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, In
     }
     sdp = bssp->descr;
   } else {
-          return;
+    return;
   }
 
   while (sdp != NULL) {
     if (sdp->choice == Seq_descr_molinfo && sdp->data.ptrvalue != NULL) {
       mip = (MolInfoPtr) sdp->data.ptrvalue;
-      if (GetEnumPopup (miep->from.moltype, molinfo_biomol_alist, &val) &&
-          mip->biomol == (Uint1) val) {
-        if (GetEnumPopup (miep->to.moltype, molinfo_biomol_alist, &val)) {
-          mip->biomol = (Uint1) val;
+      if ((Uint2) GetValNodePopup (miep->from.moltype,
+                                   miep->from.moltype_values) == mip->biomol
+        || GetValue (miep->from.moltype) == 1)
+      {
+        if ( GetValue (miep->to.moltype) != 1)
+        {
+          mip->biomol = (Uint1) GetValNodePopup (miep->to.moltype,
+                                                 miep->to.moltype_values);
         }
       }
-      if (GetEnumPopup (miep->from.technique, molinfo_tech_alist, &val) &&
-          mip->tech == (Uint1) val) {
-        if (GetEnumPopup (miep->to.technique, molinfo_tech_alist, &val)) {
-          mip->tech = (Uint1) val;
+      if ((Uint1) GetValNodePopup (miep->from.technique,
+                                   miep->from.technique_values) == mip->tech
+        || GetValue (miep->from.technique) == 1)
+      {
+        if ( GetValue (miep->to.technique) != 1)
+        {
+          mip->tech = (Uint1) GetValNodePopup (miep->to.technique,
+                                     miep->to.technique_values);
         }
       }
-      if (GetEnumPopup (miep->from.complete, molinfo_complete_alist, &val) &&
-          mip->completeness == (Uint1) val) {
-        if (GetEnumPopup (miep->to.complete, molinfo_complete_alist, &val)) {
-          mip->completeness = (Uint1) val;
+      if ((Uint1) GetValNodePopup (miep->from.complete,
+                              miep->from.complete_values) == mip->completeness
+        || GetValue (miep->from.complete) == 1)
+      {
+        if ( GetValue (miep->to.complete) != 1)
+        {
+          mip->completeness = (Uint1) GetValNodePopup (miep->to.complete,
+                                                   miep->to.complete_values);
         }
       }
     }
@@ -4181,6 +4393,8 @@ static void DoProcessEditMolInfo (ButtoN b)
   miep->nucsOK = (Boolean) (val == 1 || val == 2);
   miep->protsOK = (Boolean) (val == 1 || val == 3);
   SeqEntryExplore (miep->sep, (Pointer) miep, EditMolInfoCallback);
+  FreeMolInfoBlockData (&(miep->from));
+  FreeMolInfoBlockData (&(miep->to));
   ArrowCursor ();
   Update ();
   ObjMgrSetDirtyFlag (miep->input_entityID, TRUE);
@@ -4225,18 +4439,18 @@ static void EditMolInfoFields (IteM i)
   RadioButton (miep->constraint, "All Sequences");
   RadioButton (miep->constraint, "Nucleotides");
   RadioButton (miep->constraint, "Proteins");
-  SetValue (miep->constraint, 1);
+  SetValue (miep->constraint, 2);
 
   g = HiddenGroup (w, 2, 0, NULL);
   h = HiddenGroup (g, 0, 2, NULL);
   StaticPrompt (h, "From", 0, 0, programFont, 'c');
-  CreateMolInfoBlock (&miep->from, h);
+  CreateMolInfoBlock (&miep->from, h, FALSE);
   h = HiddenGroup (g, 0, 2, NULL);
   StaticPrompt (h, "To", 0, 0, programFont, 'c');
-  CreateMolInfoBlock (&miep->to, h);
+  CreateMolInfoBlock (&miep->to, h, TRUE);
 
   c = HiddenGroup (w, 2, 0, NULL);
-  b = PushButton (c, "Accept", DoProcessEditMolInfo);
+  b = DefaultButton (c, "Accept", DoProcessEditMolInfo);
   SetObjectExtra (b, miep, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
   AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) g, (HANDLE) c, NULL);
@@ -4245,13 +4459,78 @@ static void EditMolInfoFields (IteM i)
   Update ();
 }
 
+static void RibosomalRNAToGenomicDNAVisitFunc (
+  BioseqPtr bsp,
+  Pointer userdata
+)
+{
+  SeqDescrPtr sdp;
+  MolInfoPtr mip;
+  SeqMgrDescContext  dcontext;
+
+  if (bsp == NULL) return;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp == NULL 
+    || sdp->choice != Seq_descr_molinfo
+    || sdp->data.ptrvalue == NULL)
+  {
+    return;
+  }
+  mip = (MolInfoPtr) sdp->data.ptrvalue;
+  if (mip->biomol == MOLECULE_TYPE_RRNA)
+  {
+    mip->biomol = MOLECULE_TYPE_GENOMIC;
+    bsp->mol = MOLECULE_CLASS_DNA;
+    bsp->strand = 0;
+    bsp->topology = 0;
+  }
+}
+
+static void RibosomalRNAToGenomicDNA (BaseFormPtr bfp)
+{
+  SeqEntryPtr     sep;
+
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+
+  VisitBioseqsInSep (sep, NULL, RibosomalRNAToGenomicDNAVisitFunc);
+
+  Update ();
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+static void RibosomalRNAToGenomicDNAMenuItem (IteM i)
+{
+  BaseFormPtr     bfp;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+
+  RibosomalRNAToGenomicDNA (bfp);
+}
+
+static void RibosomalRNAToGenomicDNAToolBtn (ButtoN b)
+{
+  BaseFormPtr  bfp;
+
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+  
+  RibosomalRNAToGenomicDNA (bfp);
+}
+
 static void DoApplyMolInfo (SeqEntryPtr sep, MolInfoEditPtr miep)
 
 {
   BioseqPtr     bsp;
   BioseqSetPtr  bssp;
   MolInfoPtr    mip;
-  UIEnum        val;
   ValNodePtr    vnp;
 
   if (sep == NULL || sep->data.ptrvalue == NULL || miep == NULL) return;
@@ -4274,14 +4553,20 @@ static void DoApplyMolInfo (SeqEntryPtr sep, MolInfoEditPtr miep)
     bsp = (BioseqPtr) sep->data.ptrvalue;
     if ((ISA_na (bsp->mol) && miep->nucsOK) ||
         (ISA_aa (bsp->mol) && miep->protsOK)) {
-      if (GetEnumPopup (miep->to.molPopup, mol_alist, &val) && val > 0) {
-        bsp->mol = (Uint1) val;
+      if ( GetValue (miep->to.molPopup) != 1)
+      {
+        bsp->mol = (Uint1) GetValNodePopup (miep->to.molPopup,
+                                            miep->to.mol_values);
       }
-      if (GetEnumPopup (miep->to.strandPopup, strand_alist, &val) && val > 0) {
-        bsp->strand = (Uint1) val;
+      if ( GetValue (miep->to.strandPopup) != 1)
+      {
+        bsp->strand = (Uint1) GetValNodePopup (miep->to.strandPopup,
+                                               miep->to.strand_values);
       }
-      if (GetEnumPopup (miep->to.topologyPopup, topology_alist, &val) && val > 0) {
-        bsp->topology = (Uint1) val;
+      if (GetValue (miep->to.topologyPopup) != 1)
+      {
+        bsp->topology = (Uint1) GetValNodePopup (miep->to.topologyPopup,
+                                                 miep->to.topology_values);
       }
     } else return;
   } else if (IS_Bioseq_set (sep)) {
@@ -4295,14 +4580,20 @@ static void DoApplyMolInfo (SeqEntryPtr sep, MolInfoEditPtr miep)
   vnp = CreateNewDescriptor (sep, Seq_descr_molinfo);
   if (vnp != NULL) {
     vnp->data.ptrvalue = (Pointer) mip;
-    if (GetEnumPopup (miep->to.moltype, molinfo_biomol_alist, &val)) {
-      mip->biomol = (Uint1) val;
+    if ( GetValue (miep->to.moltype) != 1)
+    {
+      mip->biomol = (Uint1) GetValNodePopup (miep->to.moltype,
+                                             miep->to.moltype_values);
     }
-    if (GetEnumPopup (miep->to.technique, molinfo_tech_alist, &val)) {
-      mip->tech = (Uint1) val;
+    if ( GetValue (miep->to.technique) != 1)
+    {
+      mip->tech = (Uint1) GetValNodePopup (miep->to.technique,
+                                           miep->to.technique_values);
     }
-    if (GetEnumPopup (miep->to.complete, molinfo_complete_alist, &val)) {
-      mip->completeness = (Uint1) val;
+    if ( GetValue (miep->to.complete) != 1)
+    {
+      mip->completeness = (Uint1) GetValNodePopup (miep->to.complete,
+                                                   miep->to.complete_values);
     }
   }
 }
@@ -4322,6 +4613,7 @@ static void DoProcessApplyMolInfo (ButtoN b)
   miep->nucsOK = (Boolean) (val == 1);
   miep->protsOK = (Boolean) (val == 2);
   DoApplyMolInfo (miep->sep, miep);
+  FreeMolInfoBlockData (&miep->to);
   ArrowCursor ();
   Update ();
   ObjMgrSetDirtyFlag (miep->input_entityID, TRUE);
@@ -4369,10 +4661,10 @@ static void ApplyMolInfo (IteM i)
 
   g = HiddenGroup (w, 2, 0, NULL);
   h = HiddenGroup (g, 0, 2, NULL);
-  CreateMolInfoBlock (&miep->to, h);
+  CreateMolInfoBlock (&miep->to, h, TRUE);
 
   c = HiddenGroup (w, 2, 0, NULL);
-  b = PushButton (c, "Accept", DoProcessApplyMolInfo);
+  b = DefaultButton (c, "Accept", DoProcessApplyMolInfo);
   SetObjectExtra (b, miep, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
   AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) g, (HANDLE) c, NULL);
@@ -4634,7 +4926,7 @@ static ForM CreateBioseqSetEditForm (BioseqSetPtr bssp, Uint2 entityID)
     }
 
     c = HiddenGroup (w, 2, 0, NULL);
-    b = PushButton (c, "Accept", AcceptBioseqSetEditProc);
+    b = DefaultButton (c, "Accept", AcceptBioseqSetEditProc);
     SetObjectExtra (b, bsfp, NULL);
     PushButton (c, "Cancel", StdCancelButtonProc);
     AlignObjects (ALIGN_CENTER, (HANDLE) h, (HANDLE) c, NULL);
@@ -4671,6 +4963,273 @@ extern Int2 LIBCALLBACK BioseqSetEditFunc (Pointer data)
 }
 
 /*#ifdef EXTRA_SERVICES*/
+static CharPtr ReadALine (CharPtr str, size_t size, FILE *fp)
+
+{
+  Char     ch;
+  CharPtr  ptr;
+  CharPtr  rsult;
+
+  if (str == NULL || size < 1 || fp == NULL) return NULL;
+  *str = '\0';
+  rsult = FileGets (str, size, fp);
+  if (rsult != NULL) {
+    ptr = str;
+    ch = *ptr;
+    while (ch != '\0' && ch != '\n' && ch != '\r') {
+      ptr++;
+      ch = *ptr;
+    }
+    *ptr = '\0';
+  }
+  return rsult;
+}
+
+static ValNodePtr UniqueAndCountValNodeCS (ValNodePtr list)
+
+{
+  Int4          count;
+  ValNodePtr    curr;
+  CharPtr       last;
+  size_t        len;
+  ValNodePtr    next;
+  Pointer PNTR  prev;
+  CharPtr       str;
+  CharPtr       tmp;
+  ValNodePtr    vnp;
+
+  if (list == NULL) return NULL;
+  last = (CharPtr) list->data.ptrvalue;
+  vnp = list->next;
+  if (vnp == NULL) return list;
+  prev = (Pointer PNTR) &(list->next);
+  count = 1;
+  curr = list;
+  while (vnp != NULL) {
+    next = vnp->next;
+    str = (CharPtr) vnp->data.ptrvalue;
+    if (StringCmp (last, str) == 0) {
+      vnp->next = NULL;
+      *prev = next;
+      ValNodeFreeData (vnp);
+      count++;
+    } else {
+      len = StringLen (last) + 20;
+      tmp = (CharPtr) MemNew (len);
+      if (tmp != NULL) {
+        sprintf (tmp, "%6ld   %s", (long) count, last);
+        curr->data.ptrvalue = MemFree (curr->data.ptrvalue);
+        curr->data.ptrvalue = tmp;
+      }
+      last = (CharPtr) vnp->data.ptrvalue;
+      prev = (Pointer PNTR) &(vnp->next);
+      count = 1;
+      curr = vnp;
+    }
+    vnp = next;
+  }
+  len = StringLen (last) + 20;
+  tmp = (CharPtr) MemNew (len);
+  if (tmp != NULL) {
+    sprintf (tmp, "%6ld   %s", (long) count, last);
+    curr->data.ptrvalue = MemFree (curr->data.ptrvalue);
+    curr->data.ptrvalue = tmp;
+  }
+
+  return list;
+}
+
+static int LIBCALLBACK SortVnpByStringCS (VoidPtr ptr1, VoidPtr ptr2)
+
+{
+  CharPtr     str1;
+  CharPtr     str2;
+  ValNodePtr  vnp1;
+  ValNodePtr  vnp2;
+
+  if (ptr1 != NULL && ptr2 != NULL) {
+    vnp1 = *((ValNodePtr PNTR) ptr1);
+    vnp2 = *((ValNodePtr PNTR) ptr2);
+    if (vnp1 != NULL && vnp2 != NULL) {
+      str1 = (CharPtr) vnp1->data.ptrvalue;
+      str2 = (CharPtr) vnp2->data.ptrvalue;
+      if (str1 != NULL && str2 != NULL) {
+        return StringCmp (str1, str2);
+      }
+    }
+  }
+  return 0;
+}
+
+static int LIBCALLBACK SortVnpByChoiceAndStringCS (VoidPtr ptr1, VoidPtr ptr2)
+
+{
+  CharPtr     str1;
+  CharPtr     str2;
+  ValNodePtr  vnp1;
+  ValNodePtr  vnp2;
+
+  if (ptr1 != NULL && ptr2 != NULL) {
+    vnp1 = *((ValNodePtr PNTR) ptr1);
+    vnp2 = *((ValNodePtr PNTR) ptr2);
+    if (vnp1 != NULL && vnp2 != NULL) {
+      str1 = (CharPtr) vnp1->data.ptrvalue;
+      str2 = (CharPtr) vnp2->data.ptrvalue;
+      if (str1 != NULL && str2 != NULL) {
+        if (vnp1->choice > vnp2->choice) {
+          return 1;
+        } else if (vnp1->choice < vnp2->choice) {
+          return -1;
+        }
+        return StringCmp (str1, str2);
+      }
+    }
+  }
+  return 0;
+}
+
+static ValNodePtr SortFlatFile (ValNodePtr head, Boolean reverse, Boolean byblock)
+
+{
+  ValNodePtr  next;
+  ValNodePtr  tail = NULL;
+  ValNodePtr  vnp;
+
+  if (head == NULL) return NULL;
+
+  if (byblock) {
+    head = ValNodeSort (head, SortVnpByChoiceAndStringCS);
+  } else {
+    head = ValNodeSort (head, SortVnpByStringCS);
+  }
+  if (reverse) {
+    for (vnp = head; vnp != NULL; vnp = next) {
+      next = vnp->next;
+      vnp->next = tail;
+      tail = vnp;
+    }
+    head = tail;
+  } else {
+    head = UniqueAndCountValNodeCS (head);
+  }
+
+  return head;
+}
+
+static void CaptureFFLine (CharPtr str, Pointer userdata, BlockType blocktype)
+
+{
+  Char             ch;
+  CharPtr          copy;
+  ValNodePtr PNTR  head;
+  CharPtr          ptr;
+  CharPtr          tmp;
+  ValNodePtr       vnp;
+
+  head = (ValNodePtr PNTR) userdata;
+  copy = StringSaveNoNull (str);
+  if (copy == NULL) return;
+
+  ptr = copy;
+  tmp = StringChr (ptr, '\n');
+  while (tmp != NULL) {
+    ch = *tmp;
+    *tmp = '\0';
+    vnp = ValNodeCopyStr (NULL, (Uint1) blocktype, ptr);
+    if (*head == NULL) {
+      *head = vnp;
+    } else {
+      vnp->next = *head;
+      *head = vnp;
+    }
+    *tmp = ch;
+    tmp++;
+    ptr = tmp;
+    tmp = StringChr (ptr, '\n');
+  }
+
+  MemFree (copy);
+}
+
+static void SUCCommonProc (IteM i, Boolean reverse, Boolean byblock, ButtoN b)
+
+{
+  BaseFormPtr  bfp;
+  FILE         *fp;
+  ValNodePtr   head = NULL;
+  ErrSev       level;
+  Boolean      okay;
+  SeqEntryPtr  oldscope;
+  Char         path [PATH_MAX];
+  SeqEntryPtr  sep;
+  CharPtr      str;
+  ValNodePtr   vnp;
+  XtraBlock    xtra;
+
+  if (b != NULL) {
+    bfp = GetObjectExtra (b);
+  } else {
+#ifdef WIN_MAC
+    bfp = currentFormDataPtr;
+#else
+    bfp = GetObjectExtra (i);
+#endif
+  }
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  WatchCursor ();
+  Update ();
+  MemSet ((Pointer) &xtra, 0, sizeof (XtraBlock));
+  xtra.ffwrite = CaptureFFLine;
+  xtra.userdata = (Pointer) &head;
+  level = ErrSetMessageLevel (SEV_MAX);
+  oldscope = SeqEntrySetScope (sep);
+  okay = SeqEntryToGnbk (sep, NULL, GENBANK_FMT, SEQUIN_MODE, NORMAL_STYLE, 0, 0, 0, &xtra, NULL);
+  SeqEntrySetScope (oldscope);
+  ErrSetMessageLevel (level);
+  if (okay) {
+    head = SortFlatFile (head, FALSE, byblock);
+    if (reverse) {
+      head = SortFlatFile (head, TRUE, FALSE);
+    }
+    TmpNam (path);
+    fp = FileOpen (path, "w");
+    if (fp != NULL) {
+      for (vnp = head; vnp != NULL; vnp = vnp->next) {
+        str = (CharPtr) vnp->data.ptrvalue;
+        fprintf (fp, "%s\n", str);
+      }
+      FileClose (fp);
+    }
+    LaunchGeneralTextViewer (path, "Sort Unique Count");
+    FileRemove (path);
+    ValNodeFreeData (head);
+  }
+  ArrowCursor ();
+  Update ();
+}
+
+static void SUCProc (IteM i)
+
+{
+  SUCCommonProc (i, FALSE, FALSE, NULL);
+}
+
+static void SUCRProc (IteM i)
+
+{
+  SUCCommonProc (i, TRUE, FALSE, NULL);
+}
+
+static void SUCBProc (IteM i)
+
+{
+  SUCCommonProc (i, FALSE, TRUE, NULL);
+}
+/*#endif*/
+
+#if 0
 #ifdef OS_UNIX
 extern void SUCCommonProc (IteM i, Boolean reverse, ButtoN b);
 extern void SUCCommonProc (IteM i, Boolean reverse, ButtoN b)
@@ -4737,7 +5296,7 @@ static void SUCRProc (IteM i)
   SUCCommonProc (i, TRUE, NULL);
 }
 #endif
-/*#endif*/
+#endif
 
 /*#ifdef INTERNAL_NCBI_SEQUIN*/
 /*#ifdef NEW_TAXON_SERVICE*/
@@ -4755,37 +5314,28 @@ static void SUCRProc (IteM i)
 *  Then add version number to top of each file
 */
 
-static void WriteTaxNode (CharPtr sci, CharPtr com, CharPtr syn,
-                          Int4 gc, Int4 mgc, CharPtr div,
-                          Int4 taxID, FILE *fout)
+static Boolean WriteTaxNode (CharPtr sci, CharPtr com, CharPtr syn,
+                             Int4 gc, Int4 mgc, CharPtr div,
+                             Int4 taxID, FILE *fout)
 
 {
   Char  str [256];
 
-  if (fout == NULL) return;
+  if (fout == NULL) return FALSE;
   if (sci != NULL && sci [0] != '\0') {
     if (div == NULL || div [0] == '\0') div = "???";
     if (com != NULL && com [0] != '\0') {
       sprintf (str, "%s\t%s\t%ld\t%ld\t%s\t%ld\n", sci, com,
                (long) gc, (long) mgc, div, (long) taxID);
       fprintf (fout, "%s", str);
-      /*
-      sprintf (str, "%s\tC\t%s\t%ld\t%ld\t%s\t%ld\n", com, sci,
-               (long) gc, (long) mgc, div, (long) taxID);
-      fprintf (fout, "%s", str);
-      */
-    /*
-    } else if (syn != NULL && syn [0] != '\0') {
-      sprintf (str, "%s\tC\t%s\t%ld\t%ld\t%s\t%ld\n", syn, sci,
-               (long) gc, (long) mgc, div, (long) taxID);
-      fprintf (fout, "%s", str);
-    */
     } else {
       sprintf (str, "%s\t\t%ld\t%ld\t%s\t%ld\n", sci,
                (long) gc, (long) mgc, div, (long) taxID);
       fprintf (fout, "%s", str);
     }
+    return TRUE;
   }
+  return FALSE;
 }
 
 static void WriteLineage (Int4 taxID, CharPtr lineage, FILE *fout)
@@ -4800,6 +5350,7 @@ static void ProcessTaxNode (CharPtr orgname, FILE *fout1, FILE *fout2)
 {
   Int4           gc;
   Int4           mgc;
+  OrgModPtr      omp;
   OrgNamePtr     onp;
   OrgRefPtr      orp;
   Int4           taxID;
@@ -4822,10 +5373,18 @@ static void ProcessTaxNode (CharPtr orgname, FILE *fout1, FILE *fout2)
     if (onp != NULL) {
       gc = onp->gcode;
       mgc = onp->mgcode;
-      WriteLineage (taxID, onp->lineage, fout2);
     }
-    WriteTaxNode (orp->taxname, orp->common, NULL, gc,
-                  mgc, tdp->div, taxID, fout1);
+    if (WriteTaxNode (orp->taxname, orp->common, NULL, gc, mgc, tdp->div, taxID, fout1)) {
+      if (onp != NULL) {
+        WriteLineage (taxID, onp->lineage, fout2);
+        for (omp = onp->mod; omp != NULL; omp = omp->next) {
+          if (omp->subtype == ORGMOD_gb_anamorph ||
+              omp->subtype == ORGMOD_gb_synonym) {
+            WriteTaxNode (omp->subname, orp->common, NULL, gc, mgc, tdp->div, taxID, fout1);
+          }
+        }
+      }
+    }
     /*
     vnp = orp->syn;
     while (vnp != NULL) {
@@ -5251,7 +5810,7 @@ static void ProcessPub (IteM i, Int2 type)
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoProcessPub);
+  b = DefaultButton (c, "Accept", DoProcessPub);
   SetObjectExtra (b, pfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -5422,6 +5981,242 @@ static void RemoveSeqHistAssembly (IteM i)
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
+static void LeaveFirstAssemblyProc (BioseqPtr bsp, Pointer userdata)
+
+{
+  SeqHistPtr   hist;
+  SeqAlignPtr  next;
+  SeqAlignPtr  sap;
+
+  hist = bsp->hist;
+  if (hist == NULL) return;
+  sap = hist->assembly;
+  if (sap == NULL) return;
+  next = sap->next;
+  if (next == NULL) return;
+  sap->next = NULL;
+  SeqAlignFree (next);
+}
+
+static void LeaveFirstSeqHistAssembly (IteM i)
+
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  VisitBioseqsInSep (sep, NULL, LeaveFirstAssemblyProc);
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+static void FindTPAAccns (SeqDescrPtr sdp, Pointer userdata)
+
+{
+  UserFieldPtr     curr;
+  ValNodePtr PNTR  head;
+  ObjectIdPtr      oip;
+  CharPtr          str;
+  UserFieldPtr     ufp;
+  UserObjectPtr    uop;
+  ValNodePtr       vnp;
+
+  if (sdp == NULL || sdp->choice != Seq_descr_user) return;
+  uop = (UserObjectPtr) sdp->data.ptrvalue;
+  if (uop == NULL) return;
+  oip = uop->type;
+  if (oip == NULL) return;
+  if (StringCmp (oip->str, "TpaAssembly") != 0) return;
+  head = (ValNodePtr PNTR) userdata;
+  if (head == NULL) return;
+  for (curr = uop->data; curr != NULL; curr = curr->next) {
+    if (curr->choice != 11) continue;
+    for (ufp = curr->data.ptrvalue; ufp != NULL; ufp = ufp->next) {
+      if (ufp->choice != 1) continue;
+      oip = ufp->label;
+      if (oip == NULL || StringICmp (oip->str, "accession") != 0) continue;
+      str = (CharPtr) ufp->data.ptrvalue;
+      if (StringHasNoText (str)) continue;
+      vnp = ValNodeCopyStr (NULL, 0, str);
+      vnp->next = *head;
+      *head = vnp;
+    }
+  }
+}
+
+typedef struct streamfsa {
+  FILE  *fp;
+  Char  buf [128];
+  Int2  idx;
+  Int2  maxlen;
+} StreamFsa, PNTR StreamFsaPtr;
+
+static void LIBCALLBACK FsaStreamProc (
+  CharPtr sequence,
+  Pointer userdata
+)
+
+{
+  Char          ch;
+  StreamFsaPtr  sfp;
+
+  if (StringHasNoText (sequence) || userdata == NULL) return;
+  sfp = (StreamFsaPtr) userdata;
+
+  ch = *sequence;
+  while (ch != '\0') {
+    sfp->buf [sfp->idx] = ch;
+    (sfp->idx)++;
+
+    if (sfp->idx >= sfp->maxlen) {
+      sfp->buf [sfp->idx] = '\0';
+      fprintf (sfp->fp, "%s\n", sfp->buf);
+      sfp->idx = 0;
+    }
+
+    sequence++;
+    ch = *sequence;
+  }
+}
+
+static void StreamFastaForBsp (BioseqPtr bsp, FILE *fp)
+
+{
+  Char       id [41];
+  StreamFsa  sf;
+
+  if (bsp == NULL || fp == NULL) return;
+
+  id [0] = '\0';
+  SeqIdWrite (bsp->id, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
+  fprintf (fp, ">%s\n", id);
+
+  MemSet ((Pointer) &sf, 0, sizeof (StreamFsa));
+  sf.fp = fp;
+  sf.idx = 0;
+  sf.maxlen = 60;
+  SeqPortStream (bsp, TRUE, (Pointer) &sf, FsaStreamProc);
+
+  if (sf.idx > 0) {
+    sf.buf [sf.idx] = '\0';
+    fprintf (fp, "%s\n", sf.buf);
+  }
+}
+
+static void CreateTPABlastDB (IteM i)
+
+{
+  BaseFormPtr  bfp;
+  BioseqPtr    bsp;
+  FILE         *fp;
+  ValNodePtr   head = NULL;
+  Char         path [PATH_MAX];
+  SeqEntryPtr  sep;
+  SeqIdPtr     sip;
+  CharPtr      str;
+  ValNodePtr   vnp;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  VisitDescriptorsInSep (sep, (Pointer) &head, FindTPAAccns);
+  if (head == NULL) return;
+  head = ValNodeSort (head, SortVnpByString);
+  head = UniqueValNode (head);
+  if (! GetOutputFileName (path, sizeof (path), NULL)) return;
+  fp = FileOpen (path, "w");
+  if (fp == NULL) return;
+  for (vnp = head; vnp != NULL; vnp = vnp->next) {
+    str = (CharPtr) vnp->data.ptrvalue;
+    if (StringHasNoText (str)) continue;
+    Message (MSG_POST, "Making DB for %s", str);
+    sip = SeqIdFromAccessionDotVersion (str);
+    bsp = BioseqLockById (sip);
+    StreamFastaForBsp (bsp, fp);
+    BioseqUnlock (bsp);
+  }
+  FileClose (fp);
+  ValNodeFreeData (head);
+}
+
+static void FindBioseqForHist (SeqIdPtr sip, Pointer userdata)
+
+{
+  BioseqPtr       bsp;
+  BioseqPtr PNTR  bspp;
+
+  bsp = BioseqFindCore (sip);
+  if (bsp == NULL) return;
+  bspp = (BioseqPtr PNTR) userdata;
+  *bspp = bsp;
+}
+
+static void AttachSapToHistory (SeqAlignPtr sap)
+
+{
+  BioseqPtr   bsp = NULL;
+  SeqHistPtr  shp;
+
+  VisitSeqIdsInSeqAlign (sap, (Pointer) &bsp, FindBioseqForHist);
+  if (bsp == NULL) return;
+  shp = SeqHistNew ();
+  shp->assembly = sap;
+  bsp->hist = shp;
+}
+
+static void ReadSeqHistAssembly (IteM i)
+
+{
+  BaseFormPtr  bfp;
+  Pointer      dataptr;
+  Uint2        datatype;
+  FILE         *fp;
+  Char         path [PATH_MAX];
+  SeqAlignPtr  salp;
+  SeqAnnotPtr  sap;
+  SeqEntryPtr  sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  if (! GetInputFileName (path, sizeof (path), "", "TEXT")) return;
+  fp = FileOpen (path, "r");
+  if (fp == NULL) return;
+
+  while ((dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE)) != NULL) {
+    if (datatype == OBJ_SEQANNOT) {
+      sap = (SeqAnnotPtr) dataptr;
+      if (sap != NULL && sap->type == 2) {
+        salp = (SeqAlignPtr) sap->data;
+        sap->data = NULL;
+        AttachSapToHistory (salp);
+        SeqAnnotFree (sap);
+      }
+    }
+  }
+
+  FileClose (fp);
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
 typedef struct recondata {
   BioseqPtr   prod;
   SeqFeatPtr  cds;
@@ -5931,6 +6726,179 @@ static void LogLocation (SeqMgrFeatContextPtr context, FILE *fp)
   }
 }
 
+typedef struct correctgeneformdata {
+  FEATURE_FORM_BLOCK
+
+  ButtoN      setIntervalBtn;
+  ButtoN      setStrandBtn;
+  Boolean     setInterval;
+  Boolean     setStrand;
+  SeqEntryPtr sep;
+} CorrectGeneFormData, PNTR CorrectGeneFormPtr;
+
+typedef struct genesforcdsdata {
+  SeqFeatPtr cds;
+  ValNodePtr gene_list;
+} GenesForCDSData, PNTR GenesForCDSPtr;
+
+static void FindGenesForCDS (SeqFeatPtr sfp, Pointer userdata)
+{
+  GenesForCDSPtr gfc;
+  ValNodePtr     vnp;
+
+  gfc = (GenesForCDSPtr) userdata;
+
+  if (gfc == NULL || sfp == NULL || sfp->idx.subtype != FEATDEF_GENE) return;
+
+  if (SeqLocAinB (gfc->cds->location, sfp->location) > -1
+    || SeqLocAinB (sfp->location, gfc->cds->location) > -1)
+  {
+    vnp = ValNodeNew (gfc->gene_list);
+    if (vnp == NULL) return;
+    vnp->data.ptrvalue = sfp;
+    if (gfc->gene_list == NULL)
+    {
+      gfc->gene_list = vnp;
+    }
+  }
+}
+
+static void SetSeqLocStrand (SeqLocPtr location, Uint2 strand)
+{
+  SeqLocPtr slp;
+  SeqIntPtr sip;
+  SeqPntPtr spp;
+
+  slp = SeqLocFindNext (location, NULL);
+  while (slp != NULL)
+  {
+    if (slp == NULL || slp->data.ptrvalue == NULL) 
+    {
+      slp = SeqLocFindNext (location, slp);
+      continue;
+    }
+    if (slp->choice == SEQLOC_INT)
+    {
+      sip = (SeqIntPtr)slp->data.ptrvalue;
+      sip->strand = strand;
+    }
+    else if (slp->choice == SEQLOC_PNT)
+    {
+      spp = (SeqPntPtr)slp->data.ptrvalue;
+      spp->strand = strand;
+    }
+    slp = SeqLocFindNext (location, slp);
+  }
+}
+  
+static void CorrectOneCDSGene (SeqFeatPtr sfp, Pointer userdata)
+{
+  CorrectGeneFormPtr cgp;
+  GenesForCDSData    gfc;
+  SeqFeatPtr         gene;
+  SeqLocPtr          slp;
+  BioseqPtr          bsp;
+
+  if (sfp == NULL || (cgp = (CorrectGeneFormPtr)userdata) == NULL) return;
+
+  gfc.cds = sfp;
+  gfc.gene_list = NULL;
+  VisitFeaturesInSep (cgp->sep, &gfc, FindGenesForCDS);
+
+  if (gfc.gene_list == NULL) return;
+  if (gfc.gene_list->next != NULL
+    || gfc.gene_list->data.ptrvalue == NULL)
+  {
+    ValNodeFree (gfc.gene_list);
+    return;
+  }
+
+  gene = gfc.gene_list->data.ptrvalue;
+  if (cgp->setInterval)
+  {
+    bsp = BioseqFindFromSeqLoc (sfp->location);
+    slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, TRUE, FALSE);
+    SeqLocFree (gene->location);
+    gene->location = slp;
+  }
+  if (cgp->setStrand)
+  {
+    SetSeqLocStrand (gene->location, SeqLocStrand (sfp->location));
+  }
+
+  ValNodeFree (gfc.gene_list);
+}
+
+static void CorrectGenesForCDSs (ButtoN b)
+{
+  CorrectGeneFormPtr cgp;
+  
+  cgp = GetObjectExtra (b);
+  if (cgp == NULL) return;
+
+  Hide (cgp->form);
+  WatchCursor ();
+  Update ();
+
+  cgp->setStrand = GetStatus (cgp->setStrandBtn);
+  cgp->setInterval = GetStatus (cgp->setIntervalBtn);
+  cgp->sep = GetTopSeqEntryForEntityID (cgp->input_entityID);
+  VisitFeaturesInSep (cgp->sep, cgp, CorrectOneCDSGene);
+  ObjMgrSetDirtyFlag (cgp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, cgp->input_entityID, 0, 0);
+  ArrowCursor ();
+  Update ();
+
+}
+
+static void CorrectGenes (IteM i)
+{
+  BaseFormPtr        bfp;
+  CorrectGeneFormPtr cgp;
+  WindoW             w;
+  GrouP              g, c;
+  ButtoN             b;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+
+  cgp = MemNew (sizeof (CorrectGeneFormData));
+  if (cgp == NULL) return;
+  
+  w = FixedWindow (-50, -33, -20, -10, "Correct Genes for CDSs",
+                   StdCloseWindowProc);
+  SetObjectExtra (w, cgp, StdCleanupFormProc);
+  cgp->form = (ForM) w;
+
+  cgp->input_entityID = bfp->input_entityID;
+  cgp->input_itemID = bfp->input_itemID;
+  cgp->input_itemtype = bfp->input_itemtype;
+
+  g = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (g, 10, 10);
+  cgp->setIntervalBtn = CheckBox (g, "Set gene interval to match CDS", NULL);
+  SetStatus (cgp->setIntervalBtn, TRUE);
+  cgp->setStrandBtn = CheckBox (g, "Set gene strand to match CDS", NULL);
+  SetStatus (cgp->setStrandBtn, TRUE);
+
+  c = HiddenGroup (g, 2, 0, NULL);
+  b = DefaultButton(c, "Accept", CorrectGenesForCDSs);
+  SetObjectExtra(b, cgp, NULL);
+  PushButton (c, "Cancel", StdCancelButtonProc);
+
+  AlignObjects (ALIGN_CENTER,
+                (HANDLE) cgp->setIntervalBtn,
+                (HANDLE) cgp->setStrandBtn,
+	        (HANDLE) c, NULL);
+  RealizeWindow(w);
+  Show(w);
+  Update();
+}
+
 static void ResetAllGenes (SeqEntryPtr sep,
 			Boolean doMinus, Boolean doPlus, FILE *fp)
 {
@@ -5944,6 +6912,8 @@ static void ResetAllGenes (SeqEntryPtr sep,
   BioseqPtr		bsp;
   SeqLocPtr		slp;
   SeqLocPtr		tmpslp;
+  Boolean               cds_partial5, cds_partial3;
+  Boolean               partial5, partial3;
 
   if (sep == NULL) return;
   if ( IS_Bioseq_set (sep))
@@ -5968,6 +6938,8 @@ static void ResetAllGenes (SeqEntryPtr sep,
       if (fcontext.strand != Seq_strand_minus && !doPlus)
         continue;
       slp = NULL;
+      partial3 = FALSE;
+      partial5 = FALSE;
       /* look for next feature, starting right after the gene */
       /* an overlapping CDS won't occur before the gene in the indexing */
       cds = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &cdscontext);
@@ -5979,6 +6951,9 @@ static void ResetAllGenes (SeqEntryPtr sep,
              && cdscontext.strand != Seq_strand_minus))
             && SeqLocAinB (cds->location, gene->location) > -1)
         {
+          CheckSeqLocForPartial (cds->location, &cds_partial5, &cds_partial3);
+          partial5 |= cds_partial5;
+          partial3 |= cds_partial3;
           tmpslp = SeqLocMerge (bsp, cds->location, slp, TRUE, TRUE, FALSE);
           if (tmpslp == NULL) return;
           SeqLocFree (slp);
@@ -5990,6 +6965,7 @@ static void ResetAllGenes (SeqEntryPtr sep,
 
       if (slp != NULL)
       {
+        SetSeqLocPartial (slp, partial5, partial3);
         if (fp != NULL
           && (SeqLocStart (gene->location) != SeqLocStart (slp)
             || SeqLocStop (gene->location) != SeqLocStop (slp)))
@@ -6598,7 +7574,7 @@ static void ExtendGeneReg (IteM i)
   Disable (egfp->LogUnextendedEvents);
 
   c = HiddenGroup (g, 2, 0, NULL);
-  b = PushButton(c, "Accept", DoExtendGene);
+  b = DefaultButton(c, "Accept", DoExtendGene);
   SetObjectExtra(b, egfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -6678,6 +7654,31 @@ static void ResynchronizePeptidePartials (IteM i)
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
+static void UnsetPartialForTruncatedProteins (SeqFeatPtr sfp, Pointer userdata)
+{
+  Boolean partial5, partial3;
+
+  if (sfp == NULL) return;
+  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+  SetSeqLocPartial (sfp->location, partial5, FALSE);
+}
+
+static void UnsetCDSPartialForTruncatedProteins (SeqFeatPtr sfp, Pointer userdata) 
+{
+  Boolean partial5, partial3;
+  BioseqPtr product_bsp, prot_bsp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION
+      || sfp->location == NULL) return;
+  if ((prot_bsp = (BioseqPtr)userdata) == NULL) return;
+
+  product_bsp = BioseqFindFromSeqLoc (sfp->product);
+  if (product_bsp == prot_bsp) {
+    CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+    SetSeqLocPartial (sfp->location, partial5, FALSE);
+  }
+}
+
 static void TruncProtsCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent)
 
 {
@@ -6686,6 +7687,8 @@ static void TruncProtsCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int
   Int4          i;
   Int2          residue;
   SeqPortPtr    spp;
+  Boolean       found_stop;
+  SeqEntryPtr   topsep;
 
   if (! IS_Bioseq (sep)) return;
   bsp = (BioseqPtr) sep->data.ptrvalue;
@@ -6693,6 +7696,8 @@ static void TruncProtsCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int
   if (! ISA_aa (bsp->mol)) return;
   if (bsp->repr != Seq_repr_raw && bsp->repr != Seq_repr_const) return;
 
+  topsep = (SeqEntryPtr) mydata;
+
   bs = BSNew (1000);
   if (bs == NULL) return;
   spp = SeqPortNew (bsp, 0, -1, 0, Seq_code_ncbieaa);
@@ -6705,12 +7710,21 @@ static void TruncProtsCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int
     i++;
     residue = SeqPortGetResidue (spp);
   }
+  if (residue == '*') {
+    found_stop = TRUE;
+  } else {
+    found_stop = FALSE;
+  }
 
   SeqPortFree (spp);
   bsp->seq_data = BSFree (bsp->seq_data);
   bsp->seq_data = bs;
   bsp->length = BSLen (bs);
   bsp->seq_data_type = Seq_code_ncbieaa;
+  if (found_stop) {
+    VisitFeaturesOnBsp (bsp, NULL, UnsetPartialForTruncatedProteins);
+    VisitFeaturesInSep (topsep, bsp,  UnsetCDSPartialForTruncatedProteins);
+  }
 }
 
 static void TruncProtsAtStops (IteM i)
@@ -6727,7 +7741,7 @@ static void TruncProtsAtStops (IteM i)
   if (bfp == NULL) return;
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
-  SeqEntryExplore (sep, NULL, TruncProtsCallback);
+  SeqEntryExplore (sep, sep, TruncProtsCallback);
   ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
@@ -6794,6 +7808,27 @@ static void TrimProtFeatLengths (IteM i)
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
+static void FixProtsAndCDSsBasedOnStopCodons (IteM i, Boolean fix_genes)
+{
+  TruncProtsAtStops (i);
+  TrimProtFeatLengths (i);
+  RecomputeSuggest (i);
+  RetranslateCdRegionsNoStop (i);
+  if (fix_genes) {
+    DoGeneReset (i);
+  }
+}
+
+static void FixProtsAndCDSsBasedOnStopCodonsFixGenes (IteM i)
+{
+  FixProtsAndCDSsBasedOnStopCodons (i, TRUE);
+}
+
+static void FixProtsAndCDSsBasedOnStopCodonsNoFixGenes (IteM i)
+{
+  FixProtsAndCDSsBasedOnStopCodons (i, FALSE);
+}
+
 static void TrimNucsCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent)
 
 {
@@ -6829,6 +7864,21 @@ static void TrimNsFromNucs (IteM i)
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
+static void TrimNsFromNucsToolBtn (ButtoN b)
+
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+
+  if (b == NULL) return;
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  SeqEntryExplore (sep, (Pointer) sep, TrimNucsCallback);
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
 static Boolean s_NextQualifies (SeqFeatPtr sfp,
 				BioseqPtr  bsp,
 				Int2       level,
@@ -7181,7 +8231,7 @@ static void ToolBtn2 (ButtoN b)
   bfp = (BaseFormPtr) GetObjectExtra (b);
   if (bfp == NULL) return;
 
-  AutoDefBaseFormCommon (bfp, FALSE);
+  AutoDefBaseFormCommon (bfp, FALSE, TRUE);
 }
 
 /*
@@ -7288,15 +8338,11 @@ static void ToolBtn9 (ButtoN b)
   WatchCursor ();
   Update ();
   GatherProcLaunch (OMPROC_EDIT, FALSE, bfp->input_entityID, bfp->input_itemID,
-                    bfp->input_itemtype, OBJ_SEQFEAT, FEATDEF_COMMENT, 0, 0);
+                    bfp->input_itemtype, OBJ_SEQFEAT, FEATDEF_misc_feature, 0, 0);
   ArrowCursor ();
   Update ();
 }
 
-#ifdef WIN_MOTIF
-extern void SUCCommonProc (IteM i, Boolean reverse, ButtoN b);
-#endif
-
 static void ToolBtn10 (ButtoN b)
 
 {
@@ -7305,9 +8351,7 @@ static void ToolBtn10 (ButtoN b)
   bfp = (BaseFormPtr) GetObjectExtra (b);
   if (bfp == NULL) return;
 
-#ifdef WIN_MOTIF
-  SUCCommonProc (NULL, FALSE, b);
-#endif
+  SUCCommonProc (NULL, FALSE, TRUE, b);
 }
 
 static void ToolBtn11 (ButtoN b)
@@ -7536,6 +8580,8 @@ static ButtoN SqnPushButton (GrouP prnt, CharPtr title, BtnActnProc actn, BaseFo
   return b;
 }
 
+static void FixCapitalizationToolBtn (ButtoN b);
+
 extern void BioseqViewFormToolBar (GrouP h)
 
 {
@@ -7545,28 +8591,56 @@ extern void BioseqViewFormToolBar (GrouP h)
   bfp = (BaseFormPtr) GetObjectExtra (h);
   if (bfp == NULL) return;
   g = HiddenGroup (h, 1, 0, NULL);
-  SqnPushButton (g, "Save", ToolBtn1, bfp);
-  SqnPushButton (g, "Auto_Def", ToolBtn2, bfp);
-  if (useTaxon) {
-    /* SqnPushButton (g, "Tax_Fix", ToolBtn3, bfp); */
-    SqnPushButton (g, "Tax_Fix/Clean_Up", ToolBtn3, bfp);
-  }
-  SqnPushButton (g, "Def_Org", ToolBtn4, bfp);
-  SqnPushButton (g, "CDS", ToolBtn5, bfp);
-  SqnPushButton (g, "rRNA", ToolBtn6, bfp);
-  SqnPushButton (g, "mRna_CDS", ToolBtn7, bfp);
-  SqnPushButton (g, "ORF_Find", ToolBtn8, bfp);
-  SqnPushButton (g, "misc_feat", ToolBtn9, bfp);
-#ifdef WIN_MOTIF
-  SqnPushButton (g, "SUC", ToolBtn10, bfp);
-#endif
-  SqnPushButton (g, "sub_affil", ToolBtn11, bfp);
-  SqnPushButton (g, "sub_add", ToolBtn12, bfp);
-  SqnPushButton (g, "cit-sub-upd", ToolBtn16, bfp);
-  SqnPushButton (g, "del_GBbck", ToolBtn13, bfp);
-  SqnPushButton (g, "rem_prot_titles", ToolBtn17, bfp);
-  SqnPushButton (g, "Validate", ToolBtn14, bfp);
-  SqnPushButton (g, "Desktop", ToolBtn15, bfp);
+  if (indexerVersion)
+  {
+    SqnPushButton (g, "Auto_Def", AutoDefToolBtn, bfp);
+    SqnPushButton (g, "Auto_Def Options", AutoDefOptionsToolBtn, bfp);
+    if (useTaxon) {
+      SqnPushButton (g, "Tax_Fix/Clean_Up", ToolBtn3, bfp);
+    }
+    SqnPushButton (g, "CDS", ToolBtn5, bfp);
+    SqnPushButton (g, "rRNA", ToolBtn6, bfp);
+    SqnPushButton (g, "misc_feat", ToolBtn9, bfp);
+    SqnPushButton (g, "mRna_CDS", ToolBtn7, bfp);
+    SqnPushButton (g, "ORF_Find", ToolBtn8, bfp);
+    SqnPushButton (g, "SUC", ToolBtn10, bfp);
+    SqnPushButton (g, "rRNA->DNA", RibosomalRNAToGenomicDNAToolBtn, bfp);
+    SqnPushButton (g, "Fix Caps", FixCapitalizationToolBtn, bfp);
+    SqnPushButton (g, "Remove DefLines", RemoveDefLinesToolBtn, bfp);
+    SqnPushButton (g, "Trim Ns", TrimNsFromNucsToolBtn, bfp);
+    SqnPushButton (g, "Find ASN.1", FindStringProcToolBtn, bfp);
+    SqnPushButton (g, "Local ID->Src", ParseLocalIDToSourceToolBtn, bfp);
+    SqnPushButton (g, "Fix Local IDs", ResolveExistingLocalIDsToolBtn, bfp);
+    SqnPushButton (g, "Group Explode", GroupExplodeToolBtn, bfp);
+    SqnPushButton (g, "cit-sub-upd", ToolBtn16, bfp);
+    SqnPushButton (g, "del_GBbck", ToolBtn13, bfp);
+    SqnPushButton (g, "rem_prot_titles", ToolBtn17, bfp);
+    SqnPushButton (g, "Validate", ToolBtn14, bfp);
+    SqnPushButton (g, "Desktop", ToolBtn15, bfp);
+  }
+  else
+  {
+    SqnPushButton (g, "Save", ToolBtn1, bfp);
+    SqnPushButton (g, "Auto_Def", ToolBtn2, bfp);
+    if (useTaxon) {
+      /* SqnPushButton (g, "Tax_Fix", ToolBtn3, bfp); */
+      SqnPushButton (g, "Tax_Fix/Clean_Up", ToolBtn3, bfp);
+    }
+    SqnPushButton (g, "Def_Org", ToolBtn4, bfp);
+    SqnPushButton (g, "CDS", ToolBtn5, bfp);
+    SqnPushButton (g, "rRNA", ToolBtn6, bfp);
+    SqnPushButton (g, "mRna_CDS", ToolBtn7, bfp);
+    SqnPushButton (g, "ORF_Find", ToolBtn8, bfp);
+    SqnPushButton (g, "misc_feat", ToolBtn9, bfp);
+    SqnPushButton (g, "SUC", ToolBtn10, bfp);
+    SqnPushButton (g, "sub_affil", ToolBtn11, bfp);
+    SqnPushButton (g, "sub_add", ToolBtn12, bfp);
+    SqnPushButton (g, "cit-sub-upd", ToolBtn16, bfp);
+    SqnPushButton (g, "del_GBbck", ToolBtn13, bfp);
+    SqnPushButton (g, "rem_prot_titles", ToolBtn17, bfp);
+    SqnPushButton (g, "Validate", ToolBtn14, bfp);
+    SqnPushButton (g, "Desktop", ToolBtn15, bfp);
+  }
 }
 
 static void MakeToolBarWindow (IteM i)
@@ -7959,7 +9033,7 @@ static ForM CreateGetNWindow (CdsDelFormPtr cdfp)
   
   c = HiddenGroup (w, 4, 0, NULL);
   SetGroupSpacing (c, 10, 2);
-  b = PushButton (c, "Accept", RemoveNthCDS_AcceptCallback);
+  b = DefaultButton (c, "Accept", RemoveNthCDS_AcceptCallback);
   SetObjectExtra (b, cdfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
   AlignObjects (ALIGN_CENTER, (HANDLE) j, (HANDLE) c, NULL);
@@ -8349,6 +9423,7 @@ static void FixCapitalizationInTitle (CharPtr PNTR pTitle)
 static void FixCapitalizationInAuthor (AuthorPtr pAuthor)
 {
   NameStdPtr pNameStandard;
+  CharPtr    cp;
   
   if (pAuthor == NULL)
     return;
@@ -8359,6 +9434,11 @@ static void FixCapitalizationInAuthor (AuthorPtr pAuthor)
   {
     FixCapitalizationInElement (&(pNameStandard->names[0]), FALSE, FALSE);
     FixCapitalizationInElement (&(pNameStandard->names[1]), FALSE, FALSE);
+    /* Set initials to all caps */
+    for (cp = pNameStandard->names[4]; cp != NULL && *cp != 0; cp++)
+    {
+      *cp = toupper (*cp);
+    }
   }
 }
 
@@ -8367,6 +9447,7 @@ static void FixCapitalizationInAuthor (AuthorPtr pAuthor)
 #define FIX_PUB_TITLE_CAPITALIZATION	4
 #define FIX_PUB_AFFIL_CAPITALIZATION	8
 #define FIX_SELECTED			16
+#define FIX_ALL                         32
 
 static void FixPubdesc (PubdescPtr pdp, Pointer userdata)
 {
@@ -8396,7 +9477,7 @@ static void FixPubdesc (PubdescPtr pdp, Pointer userdata)
     case PUB_Gen :
       cgp = (CitGenPtr) vnp->data.ptrvalue;   
       if( !(cgp->cit != NULL && StringCmp(cgp->cit, "unpublished") != 0)
-	&& !(iType & FIX_SELECTED) ) return;
+	&& !((iType & FIX_SELECTED) || (iType & FIX_ALL)) ) return;
       alp = cgp->authors;
       title = &(cgp->title);
       break;
@@ -8406,7 +9487,7 @@ static void FixPubdesc (PubdescPtr pdp, Pointer userdata)
       title = NULL;
       break;
     case PUB_Article :
-      if( ! (iType & FIX_SELECTED)) return;
+      if ( !((iType & FIX_SELECTED) || (iType & FIX_ALL)) ) return;
       cap = (CitArtPtr) vnp->data.ptrvalue;
       alp = cap->authors;
       if(cap->title != NULL)
@@ -8416,7 +9497,7 @@ static void FixPubdesc (PubdescPtr pdp, Pointer userdata)
       break;
     case PUB_Book :
     case PUB_Man :
-      if( ! (iType & FIX_SELECTED)) return;
+      if ( !((iType & FIX_SELECTED) || (iType & FIX_ALL)) ) return;
       cbp = (CitBookPtr) vnp->data.ptrvalue;
       alp = cbp->authors;
       if(cbp->title != NULL)
@@ -8425,7 +9506,7 @@ static void FixPubdesc (PubdescPtr pdp, Pointer userdata)
       }
       break;
     case PUB_Patent :
-      if( ! (iType & FIX_SELECTED)) return;
+      if ( !((iType & FIX_SELECTED) || (iType & FIX_ALL)) ) return;
       cpp = (CitPatPtr) vnp->data.ptrvalue;
       alp = cpp->authors;
       title = &(cpp->title);
@@ -8483,9 +9564,8 @@ static void FixPubdesc (PubdescPtr pdp, Pointer userdata)
 }
 
 /* This function is used to apply fixes to citations */
-static void FixPubs (IteM i, Int4 iType)
+static void FixPubs (BaseFormPtr bfp, Int4 iType)
 {
-  BaseFormPtr  bfp;
   SeqEntryPtr  sep;
   SelStructPtr	sel;
   SeqFeatPtr	sfp;
@@ -8494,14 +9574,16 @@ static void FixPubs (IteM i, Int4 iType)
   SeqMgrDescContext dcontext;
   PubdescPtr	pdp;
 
-#ifdef WIN_MAC
-  bfp = currentFormDataPtr;
-#else
-  bfp = GetObjectExtra (i);
-#endif
   if (bfp == NULL) return;
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
-  sel = ObjMgrGetSelected ();
+  if (iType & FIX_ALL)
+  {
+    sel = NULL;
+  }
+  else
+  {
+    sel = ObjMgrGetSelected ();
+  }
   if(sel == NULL)
   {
     VisitPubdescsInSep (sep, (Pointer)iType, FixPubdesc);
@@ -8540,24 +9622,50 @@ static void FixPubs (IteM i, Int4 iType)
   Update ();
 }
 
+static void FixPubsMenuItem (IteM i, Int4 iType)
+{
+  BaseFormPtr bfp;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+
+  if (bfp == NULL) return;
+  FixPubs (bfp, iType);
+}
+
+static void FixCapitalizationToolBtn (ButtoN b)
+{
+  BaseFormPtr  bfp;
+
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+  FixPubs (bfp, FIX_PUB_AUTHOR_CAPITALIZATION
+              | FIX_PUB_TITLE_CAPITALIZATION
+              | FIX_PUB_AFFIL_CAPITALIZATION
+              | FIX_ALL);
+}
+
 static void FixNameOrder (IteM i)
 {
-  FixPubs (i, FIX_AUTHOR_NAME_ORDER);
+  FixPubsMenuItem (i, FIX_AUTHOR_NAME_ORDER);
 }
 
 static void FixAuthorCapitalization (IteM i)
 {
-  FixPubs (i, FIX_PUB_AUTHOR_CAPITALIZATION);
+  FixPubsMenuItem (i, FIX_PUB_AUTHOR_CAPITALIZATION);
 }
 
 static void FixTitleCapitalization (IteM i)
 {
-  FixPubs (i, FIX_PUB_TITLE_CAPITALIZATION);
+  FixPubsMenuItem (i, FIX_PUB_TITLE_CAPITALIZATION);
 }
 
 static void FixAffiliationCapitalization (IteM i)
 {
-  FixPubs (i, FIX_PUB_AFFIL_CAPITALIZATION);
+  FixPubsMenuItem (i, FIX_PUB_AFFIL_CAPITALIZATION);
 }
 
 extern void LookupAllPubs (IteM i);
@@ -8610,6 +9718,8 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
 #endif
   i = CommandItem (x, "Default Options", testAutoDef);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "No Modifiers", AutoDefWithoutModifiers);
+  SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Select Options...", testAutoDefWithOptions);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
@@ -8628,6 +9738,8 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Cultivar", AddCultivarToDefLines);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "List", PrefixDefLines);
+  SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
   i = CommandItem (s, "Parse Def Line to Source", ParseDefToSource);
   SetObjectExtra (i, bfp, NULL);
@@ -8657,6 +9769,9 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   i = CommandItem (s, "Append Modifier to Organism", AddModToOrg);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
+  i = CommandItem (s, "Trim Organism Name", TrimOrganismName);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
   i = CommandItem (s, "Prefix Authority with Organism", PrefixAuthorityWithOrganism);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Parse Trinomial into Subspecies", ParseTrinomial);
@@ -8669,6 +9784,18 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Clear Source Focus", ClearSourceFocus);
   SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+  i = CommandItem (s, "Consolidate Organism Notes", ConsolidateOrganismNotes);
+  SetObjectExtra (i, bfp, NULL);
+  x = SubMenu (s, "Consolidate Like Modifiers");
+  i = CommandItem (x, "With semicolons", ConsolidateLikeModifiersWithSemicolons);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "Without semicolons", ConsolidateLikeModifiersWithoutSemicolons);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+  i = CommandItem (s, "Load Organism Modifiers from File",
+                   LoadOrganismModifierTable);
+  SetObjectExtra (i, bfp, NULL);
 
   s = SubMenu (m, "Apply/ A");
   i = CommandItem (s, "Add CDS", ApplyCDS);
@@ -8742,9 +9869,6 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   i = CommandItem (s, "Remove ALL Gene Xrefs", RemoveAllGeneXrefs);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
-  i = CommandItem (s, "Remove Gene Db_xrefs", RemoveGeneDbxrefs);
-  SetObjectExtra (i, bfp, NULL);
-  SeparatorItem (s);
   i = CommandItem (s, "Remove CDD Regions", RemoveCDDRegions);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Remove CDD Alignments", RemoveCDDAligns);
@@ -8777,6 +9901,15 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Clear Gene Pseudo", ClearGenePseudo);
   SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+  i = CommandItem (s, "Remove Gene Db_xrefs", RemoveGeneDbxrefs);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Remove RNA Db_xrefs", RemoveRNADbxrefs);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Remove CDS Db_xrefs", RemoveCDSDbxrefs);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Remove ALL Db_xrefs", RemoveAllDbxrefs);
+  SetObjectExtra (i, bfp, NULL);
   if (indexerVersion) {
     SeparatorItem (s);
     i = CommandItem (s, "Remove Local IDs from Bioseqs", RemoveLocalIDs);
@@ -8802,6 +9935,7 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   SeparatorItem (s);
   i = CommandItem (s, "Convert Source Qual", ConvertSource);
   SetObjectExtra (i, bfp, NULL);
+
   i = CommandItem (s, "Convert CDS-Gene-Prot", ConvertCDSet);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Convert RNA Qual", ConvertRNA);
@@ -8829,6 +9963,18 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
 
+  i = CommandItem (s, "Parse Text from Local ID", ParseLocalIDToAnywhere);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+
+  i = CommandItem (s, "Load Secondary Accession Numbers From File",
+                   LoadSecondaryAccessionNumbersFromFile);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Load History Accession Numbers From File",
+                   LoadHistoryAccessionNumbersFromFile);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+
   i = CommandItem (s, "BankIt Comment to Comment Descriptor", CopyBankitComments);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
@@ -8845,6 +9991,9 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   i = CommandItem (s, "Protein Description to Second Name", ProtDescToSecondName);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
+  i = CommandItem (s, "Change Ribosomal RNA to Genomic DNA", RibosomalRNAToGenomicDNAMenuItem);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
   i = CommandItem (s, "Transform to Bond", TransformToBond);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Transform to Site", TransformToSite);
@@ -8879,10 +10028,24 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   i = CommandItem (s, "Edit Feature Strand", EditFeatureStrand);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
+  i = CommandItem (s, "Extend Partial Features", ExtendPartialFeatures);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
   i = CommandItem (s, "Extend Gene", ExtendGeneReg);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Reset Genes to CDSs", DoGeneReset);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Correct Genes for CDSs", CorrectGenes);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+  i = CommandItem (s, "Make Exons from CDS Intervals", MakeExonsFromCDSIntervals);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Make Exons from mRNA Intervals", MakeExonsFromMRNAIntervals);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+  i = CommandItem (s, "Load Feature Qualifiers from File",
+                   LoadFeatureQualifierTable);
+  SetObjectExtra (i, bfp, NULL);
   if (indexerVersion) {
     SeparatorItem (s);
     i = CommandItem (s, "Edit Locus", EditLocusProc);
@@ -8975,14 +10138,18 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   i = CommandItem (s, "Process Oligonucleotide PCR Primers", ParseInOligoPrimers);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
-  i = CommandItem (s, "Parse Table of Features", AutoParseFeatureTableProc);
+  x = SubMenu (s, "Adjust Proteins and CDSs for Stop Codons");
+  i = CommandItem (x, "With Gene Reset", FixProtsAndCDSsBasedOnStopCodonsFixGenes);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "Without Gene Reset", FixProtsAndCDSsBasedOnStopCodonsNoFixGenes);
   SetObjectExtra (i, bfp, NULL);
-  SeparatorItem (s);
   x = SubMenu (s, "Retranslate Coding Regions");
   i = CommandItem (x, "Obey Stop Codon", RetranslateCdRegionsNoStop);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Ignore Stop Codon", RetranslateCdRegionsDoStop);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "Ignore Stop Codon Except at End of Complete CDS", RetranslateCdRegionsNoStopExceptEndCompleteCDS);
+  SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Retranscribe mRNA Products", ReprocessmRNAProducts);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Regenerate Peptide Products", ReprocessPeptideProducts);
@@ -9033,8 +10200,15 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
     i = CommandItem (s, "Infer Seq-Hist from Delta", CreateSeqHistDelta);
     SetObjectExtra (i, bfp, NULL);
     SeparatorItem (s);
+    i = CommandItem (s, "Read Seq-Hist Assembly BLASTs", ReadSeqHistAssembly);
+    SetObjectExtra (i, bfp, NULL);
+    i = CommandItem (s, "Create TPA BLAST Database", CreateTPABlastDB);
+    SetObjectExtra (i, bfp, NULL);
+    SeparatorItem (s);
     i = CommandItem (s, "Remove Seq-Hist Assembly", RemoveSeqHistAssembly);
     SetObjectExtra (i, bfp, NULL);
+    i = CommandItem (s, "Leave First TPA Assembly", LeaveFirstSeqHistAssembly);
+    SetObjectExtra (i, bfp, NULL);
     SeparatorItem (s);
     i = CommandItem (s, "Add Gaps of 100 to HTGS Deltas", AddDelta100Gaps);
     SetObjectExtra (i, bfp, NULL);
@@ -9051,16 +10225,6 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
     i = CommandItem (s, "Load TPA Accession Numbers From File",
                      LoadTPAAccessionNumbersFromFile);
     SetObjectExtra (i, bfp, NULL);
-    i = CommandItem (s, "Load Secondary Accession Numbers From File",
-                     LoadSecondaryAccessionNumbersFromFile);
-    SetObjectExtra (i, bfp, NULL);
-    i = CommandItem (s, "Load History Accession Numbers From File",
-                     LoadHistoryAccessionNumbersFromFile);
-    SetObjectExtra (i, bfp, NULL);
-    SeparatorItem (s);
-    i = CommandItem (s, "Load Organism Modifiers from File",
-                     LoadOrganismModifierTable);
-    SetObjectExtra (i, bfp, NULL);
     SeparatorItem (s);
   }
   i = CommandItem (s, "Raw Sequence with Ns to Delta Sequence", RawSeqToDeltaSeq);
@@ -9116,23 +10280,60 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   }
   if (extraServices) {
     SeparatorItem (s);
-    i = CommandItem (s, "Make ToolBar Window", MakeToolBarWindow);
+    i = CommandItem (s, "Make ToolBar Window/ T", MakeToolBarWindow);
     SetObjectExtra (i, bfp, NULL);
   }
-#ifdef OS_UNIX
   SeparatorItem (m);
   i = CommandItem (m, "Sort Unique Count/ U", SUCProc);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (m, "Sort Unique Count Resorted/ N", SUCRProc);
   SetObjectExtra (i, bfp, NULL);
-#endif
+  i = CommandItem (m, "Sort Unique Count By Group", SUCBProc);
+  SetObjectExtra (i, bfp, NULL);
 /*#ifdef INTERNAL_NCBI_SEQUIN*/
 /*#ifdef NEW_TAXON_SERVICE*/
-  /*
+/*
   SeparatorItem (m);
   i = CommandItem (m, "Prepare TaxList", PrepareTaxListProc);
-  */
+*/
 /*#endif*/
 /*#endif*/
 }
 
+extern void SetupBatchApplyMenu (MenU s, BaseFormPtr bfp)
+
+{
+  IteM  i;
+
+  i = CommandItem (s, "Add CDS", ApplyCDS);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Add RNA", ApplyRRNA);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Add other Feature", ApplyImpFeat);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Add Qualifier", AddQualifier);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+  i = CommandItem (s, "Add Source Qual", AddSource);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Add CDS-Gene-Prot", AddCDSet);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Add RNA Qual", AddRNA);
+  SetObjectExtra (i, bfp, NULL);
+}
+
+extern void SetupBatchEditMenu (MenU s, BaseFormPtr bfp)
+
+{
+  IteM  i;
+
+  i = CommandItem (s, "Edit Qualifiers", EditQualifier);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Edit Source Qual", EditSource);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Edit CDS-Gene-Prot", EditCDSet);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Edit RNA Qual", EditRNA);
+  SetObjectExtra (i, bfp, NULL);
+}
+
diff --git a/sequin/sequin4.c b/sequin/sequin4.c
index 0e73b5b8..5af827b9 100644
--- a/sequin/sequin4.c
+++ b/sequin/sequin4.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/28/96
 *
-* $Revision: 6.185 $
+* $Revision: 6.200 $
 *
 * File Description: 
 *
@@ -1069,56 +1069,79 @@ static void SqnCleanUpSegGap (SeqAlignPtr sap)
    return;
 }
 
+static void NoMoreSegGapForOneAlignment (SeqAlignPtr sap, Pointer userdata)
+{
+  SeqAlignPtr       salp;
+
+  salp = sap;
+  while (salp != NULL)
+  {
+    if (salp->saip != NULL)
+    {
+       SeqAlignIndexFree(salp->saip);
+       salp->saip = NULL;
+    } else {
+       AlnMgr2IndexSingleChildSeqAlign(salp); /* make sure it's dense-seg */
+       SeqAlignIndexFree(salp->saip);
+       salp->saip = NULL;
+    }
+    SqnCleanUpSegGap(salp);
+    AlnMgr2IndexSingleChildSeqAlign(salp);
+    salp = salp->next;
+  }
+}
+
+
 static Int2 LIBCALLBACK NoMoreSegGap (Pointer data)
 {
   OMProcControlPtr  ompcp;
-  SeqAlignPtr       salp, sap;
+  SeqAlignPtr       sap;
   SeqAnnotPtr       sanp;
 
   ompcp = (OMProcControlPtr) data;
   if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR;
   switch (ompcp->input_itemtype) {
     case OBJ_SEQALIGN :
+      sap = (SeqAlignPtr) ompcp->input_data;
+      if (sap == NULL)
+      {
+        return OM_MSG_RET_ERROR;
+      }
+      else
+      {
+        NoMoreSegGapForOneAlignment (sap, NULL);
+      }
       break;
     case OBJ_SEQANNOT :
+      sanp = (SeqAnnotPtr) ompcp->input_data;
+      if (sanp->type != 2)
+      {
+        return OM_MSG_RET_ERROR;
+      }
+      else if ((sap = (SeqAlignPtr)(sanp->data)) == NULL)
+      {
+        return OM_MSG_RET_ERROR;
+      }
+      else
+      {
+        NoMoreSegGapForOneAlignment (sap, NULL);
+      }
+      break;
+    case OBJ_BIOSEQ :
+      VisitAlignmentsOnBsp (ompcp->input_data, NULL, NoMoreSegGapForOneAlignment);
+      break;
+    case OBJ_BIOSEQSET :
+      VisitAlignmentsInSet (ompcp->input_data, NULL, NoMoreSegGapForOneAlignment);
       break;
     case 0 :
       return OM_MSG_RET_ERROR;
+      break;
     default :
       return OM_MSG_RET_ERROR;
+      break;
   }
-  if (ompcp->input_data == NULL) return OM_MSG_RET_ERROR;
-  sap = NULL;
-  if (ompcp->input_itemtype == OBJ_SEQALIGN)
-     sap = (SeqAlignPtr) ompcp->input_data;
-  else
-  {
-     sanp = (SeqAnnotPtr) ompcp->input_data;
-     if (sanp->type == 2)
-        sap = (SeqAlignPtr)(sanp->data);
-  }
-  if (sap == NULL) return OM_MSG_RET_ERROR;
-  salp = sap;
-  while (salp != NULL)
-  {
-     if (salp->saip != NULL)
-     {
-        SeqAlignIndexFree(salp->saip);
-        salp->saip = NULL;
-     } else
-     {
-        AlnMgr2IndexSingleChildSeqAlign(salp); /* make sure it's dense-seg */
-        SeqAlignIndexFree(salp->saip);
-        salp->saip = NULL;
-     }
-     SqnCleanUpSegGap(salp);
-     AlnMgr2IndexSingleChildSeqAlign(salp);
-     salp = salp->next;
-  }
-
   ObjMgrSetDirtyFlag (ompcp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, ompcp->input_entityID, 0, 0);
-
   return OM_MSG_RET_DONE;
 }
 
@@ -2051,8 +2074,49 @@ static Int2 LIBCALLBACK GroupExplodeFunc (Pointer data)
     return OM_MSG_RET_ERROR;
 }
 
+extern void GroupExplodeToolBtn (ButtoN b)
+{
+  BaseFormPtr       bfp;
+  SelStructPtr      ssp;
+  Boolean           isDirty = FALSE;
+  SeqEntryPtr       sep;
+  SeqFeatPtr        sfp;
+  SeqMgrFeatContext context;
+
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+
+  ssp  = ObjMgrGetSelected();
+  while (NULL != ssp) {
+    if (ssp->itemtype == OBJ_SEQFEAT)
+    {
+      sep = GetTopSeqEntryForEntityID (ssp->entityID);
+    
+      sfp = SeqMgrGetDesiredFeature (ssp->entityID, NULL, ssp->itemID, 0, NULL, &context);
+      if (sfp != NULL && ExplodeGroup (sep, sfp))
+      {
+        isDirty = TRUE;
+      }
+    }
+    ssp = ssp->next;
+  }
+
+  /* If any actual exploding was done then */
+  /* force an update to be done.           */
+
+  if (isDirty)
+  {
+    ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+    ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID,
+		     bfp->input_itemID, bfp->input_itemtype);
+  }
+}
+
 static Boolean MakeExonsAndIntronsFromFeature (SeqEntryPtr sep, BioseqPtr bsp,
-                                               SeqLocPtr location, SeqFeatPtr putafterhere)
+                                               SeqLocPtr location,
+                                               SeqFeatPtr putafterhere,
+                                               Boolean MakeIntrons,
+                                               Int4 first_exon_number)
 
 {
   SeqFeatPtr  curr;
@@ -2070,6 +2134,9 @@ static Boolean MakeExonsAndIntronsFromFeature (SeqEntryPtr sep, BioseqPtr bsp,
   Uint1       strand;
   Int4        tmp;
   Boolean     partial5, partial3;
+  GBQualPtr   gbqual;
+  Int4        part_number;
+  Char        number_text [256];
 
   if (sep == NULL || bsp == NULL || location == NULL || putafterhere == NULL) return FALSE;
   putbeforehere = putafterhere->next;
@@ -2078,6 +2145,7 @@ static Boolean MakeExonsAndIntronsFromFeature (SeqEntryPtr sep, BioseqPtr bsp,
   if (slp == NULL) return FALSE;
   first = TRUE;
   last = 0;
+  part_number = first_exon_number;
   while (slp != NULL) {
     CheckSeqLocForPartial (slp, &partial5, &partial3);
     next = SeqLocFindNext (location, slp);
@@ -2095,7 +2163,7 @@ static Boolean MakeExonsAndIntronsFromFeature (SeqEntryPtr sep, BioseqPtr bsp,
         start = stop;
         stop = tmp;
       }
-      if (! first) {
+      if (! first && MakeIntrons) {
         sfp = SeqFeatNew ();
         if (sfp != NULL) {
           sfp->data.choice = SEQFEAT_IMP;
@@ -2111,6 +2179,15 @@ static Boolean MakeExonsAndIntronsFromFeature (SeqEntryPtr sep, BioseqPtr bsp,
             sfp->data.value.ptrvalue = (Pointer) ifp;
             ifp->key = StringSave ("intron");
           }
+          gbqual = GBQualNew ();
+          if (gbqual != NULL)
+          {
+            sprintf (number_text, "%d", part_number - 1);
+            gbqual->qual = StringSave ("number");
+            gbqual->val = StringSave (number_text);
+            gbqual->next = sfp->qual;
+            sfp->qual = gbqual;
+          }
           curr->next = sfp;
           curr = sfp;
         }
@@ -2132,6 +2209,16 @@ static Boolean MakeExonsAndIntronsFromFeature (SeqEntryPtr sep, BioseqPtr bsp,
           ifp->key = StringSave ("exon");
         }
         SetSeqLocPartial (sfp->location, partial5, partial3);
+        gbqual = GBQualNew ();
+        if (gbqual != NULL)
+        {
+          sprintf (number_text, "%d", part_number);
+          gbqual->qual = StringSave ("number");
+          gbqual->val = StringSave (number_text);
+          gbqual->next = sfp->qual;
+          sfp->qual = gbqual;
+        }
+        part_number ++;
         curr->next = sfp;
         curr = sfp;
       }
@@ -2142,6 +2229,163 @@ static Boolean MakeExonsAndIntronsFromFeature (SeqEntryPtr sep, BioseqPtr bsp,
   return TRUE;
 }
 
+typedef struct makeexondata {
+  FEATURE_FORM_BLOCK
+
+  ButtoN      make_introns_button;
+  TexT        exon_number_field;
+  ButtoN      accept;
+
+  SeqEntryPtr sep;
+  Boolean     make_introns;
+  Int4        first_exon_number;
+  Uint1       feature_type;
+} MakeExonData, PNTR MakeExonPtr;
+
+static void MakeExonsFromFeatureIntervalsVisitFunc (SeqFeatPtr sfp, Pointer userdata)
+{
+  MakeExonPtr mep;
+  BioseqPtr   bsp;
+
+  if (sfp == NULL || (mep = (MakeExonPtr) userdata) == NULL || sfp->idx.subtype != mep->feature_type)
+  {
+    return;
+  }
+
+  mep = (MakeExonPtr) userdata;
+  bsp = BioseqFindFromSeqLoc (sfp->location);
+
+  MakeExonsAndIntronsFromFeature (mep->sep, bsp, sfp->location, sfp,
+      mep->make_introns, mep->first_exon_number);
+  
+}
+
+static void DoMakeExonsFromFeatureIntervals (ButtoN b)
+{
+  MakeExonPtr mep;
+  Char        exon_number_str [256];
+
+  if (b == NULL || (mep = (MakeExonPtr) GetObjectExtra (b)) == NULL) return;
+
+  Hide (mep->form);
+
+  WatchCursor ();
+  Update ();
+
+  mep->sep = GetTopSeqEntryForEntityID (mep->input_entityID);
+  mep->make_introns = GetStatus (mep->make_introns_button);
+  GetTitle (mep->exon_number_field,
+            exon_number_str,
+            sizeof (exon_number_str) - 1 );
+  mep->first_exon_number = atoi (exon_number_str);
+  VisitFeaturesInSep (mep->sep, mep, 
+                      MakeExonsFromFeatureIntervalsVisitFunc);
+  ObjMgrSetDirtyFlag (mep->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, mep->input_entityID, 0, 0);
+  ArrowCursor ();
+  Update ();
+}
+
+static void CheckExonNumberText (TexT number_field)
+{
+  MakeExonPtr mep;
+  Char        exon_number_str [256];
+  CharPtr     cp;
+
+  if (number_field == NULL || (mep = (MakeExonPtr)GetObjectExtra (number_field)) == NULL) return;
+
+  GetTitle (mep->exon_number_field,
+            exon_number_str,
+            sizeof (exon_number_str) - 1 );
+  if (exon_number_str [0] == 0) 
+  {
+    Disable (mep->accept);
+    return;
+  }
+
+  for (cp = exon_number_str; cp != NULL && *cp != 0; cp++)
+  {
+    if (*cp != '0' && *cp != '1' && *cp != '2' && *cp != '3'
+      && *cp != '4' && *cp != '5' && *cp != '6' && *cp != '7'
+      && *cp != '8' && *cp != '9')
+    {
+      Disable (mep->accept);
+      return;
+    }
+  }
+  Enable (mep->accept);
+  return;
+}
+ 
+static void CommonMakeExonsFromFeatureIntervals (
+  IteM i,
+  Boolean make_introns,
+  Uint1 feature_type
+)
+{
+  BaseFormPtr  bfp;
+  MakeExonPtr  mep;
+  WindoW       w;
+  GrouP        h, p, c;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+
+  if (bfp == NULL) return;
+
+  mep = MemNew (sizeof (MakeExonData));
+  if (mep == NULL) return;
+  mep->input_entityID = bfp->input_entityID;
+  mep->feature_type = feature_type;
+
+  if (feature_type == FEATDEF_CDS)
+  {
+    w = FixedWindow (-50, -33, -10, -10, "Make Exons from CDS", NULL);
+  }
+  else if (feature_type == FEATDEF_mRNA)
+  {
+    w = FixedWindow (-50, -33, -10, -10, "Make Exons from mRNA", NULL);
+  }
+  else
+  {
+    w = FixedWindow (-50, -33, -10, -10, "Make Exons from Feature", NULL);
+  }
+
+  SetObjectExtra (w, mep, StdCleanupFormProc);
+  mep->form = (ForM) w;
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  p = HiddenGroup (h, 2, 0, NULL);
+  StaticPrompt (p, "First Exon Number", 0, 0, programFont, 'c');
+  mep->exon_number_field = DialogText (p, "1", 3, CheckExonNumberText);
+  SetObjectExtra (mep->exon_number_field, mep, NULL);
+  mep->make_introns_button = CheckBox (p, "Make Introns", NULL);
+
+  c = HiddenGroup (h, 4, 0, NULL);
+  mep->accept = DefaultButton (c, "Accept", DoMakeExonsFromFeatureIntervals);
+  SetObjectExtra (mep->accept, mep, NULL);
+  PushButton (c, "Cancel", StdCancelButtonProc);
+  AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, NULL);
+  RealizeWindow (w);
+  Show (w);
+  Update ();
+}
+
+extern void MakeExonsFromCDSIntervals (IteM i)
+{
+  CommonMakeExonsFromFeatureIntervals (i, FALSE, FEATDEF_CDS);
+}
+
+extern void MakeExonsFromMRNAIntervals (IteM i)
+{
+  CommonMakeExonsFromFeatureIntervals (i, TRUE, FEATDEF_mRNA);
+}
+
 static Int2 LIBCALLBACK MakeExonIntron (Pointer data)
 
 {
@@ -2175,7 +2419,7 @@ static Int2 LIBCALLBACK MakeExonIntron (Pointer data)
   nbsp = (BioseqPtr) nsep->data.ptrvalue;
   if (nbsp == NULL) return OM_MSG_RET_ERROR;
 
-  if (MakeExonsAndIntronsFromFeature (sep, nbsp, sfp->location, sfp))
+  if (MakeExonsAndIntronsFromFeature (sep, nbsp, sfp->location, sfp, TRUE, 1))
   {
     ObjMgrSetDirtyFlag (ompcp->input_entityID, TRUE);
     ObjMgrSendMsg (OM_MSG_UPDATE, ompcp->input_entityID, ompcp->input_itemID,
@@ -3905,6 +4149,21 @@ static ProtRefPtr FindBestProtRef (Uint2 entityID, SeqFeatPtr cds)
   return pfl.prp;
 }
 
+/* if gene location matches mRNA exactly, make it partial on both ends */
+static void MakeMRNAGenesPartial (SeqFeatPtr sfp, Pointer userdata)
+{
+  SeqFeatPtr mrna;
+
+  if (sfp == NULL || userdata == NULL) return;
+  if (sfp->data.choice != SEQFEAT_GENE) return;
+
+  mrna = (SeqFeatPtr) userdata;
+
+  if (SeqLocAinB (mrna->location, sfp->location) != 0) return;
+
+  SetSeqLocPartial (sfp->location, TRUE, TRUE);
+}
+
 extern void MRnaFromCdsProc (Uint2 entityID)
 
 {
@@ -3971,6 +4230,7 @@ extern void MRnaFromCdsProc (Uint2 entityID)
               rna->next = cds->next;
               cds->next = rna;
             }
+            VisitFeaturesOnBsp (bsp, (Pointer) rna, MakeMRNAGenesPartial);
           } else {
             rna->next = cds->next;
             cds->next = rna;
@@ -4143,12 +4403,15 @@ static void RevCompFeats (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 inde
 {
   BioseqPtr     bsp;
   BioseqSetPtr  bssp;
+  CodeBreakPtr  cbp;
+  CdRegionPtr   crp;
+  RnaRefPtr     rrp;
   SeqAnnotPtr   sap;
   SeqFeatPtr    sfp;
   SeqIdPtr      sip;
   SeqLocPtr     slp;
   Boolean       split;
-
+  tRNAPtr       trp;
 
   if (mydata == NULL) return;
   if (sep == NULL || sep->data.ptrvalue == NULL) return;
@@ -4173,6 +4436,35 @@ static void RevCompFeats (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 inde
                                     bsp->length - 1, Seq_strand_minus, &split);
             sfp->location = SeqLocFree (sfp->location);
             sfp->location = slp;
+            switch (sfp->data.choice) {
+              case SEQFEAT_CDREGION :
+                crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+                if (crp != NULL) {
+                  for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
+                    sip = SeqLocId (cbp->loc);
+                    slp = SeqLocCopyRegion (sip, cbp->loc, bsp, 0,
+                                            bsp->length - 1, Seq_strand_minus, &split);
+                    cbp->loc = SeqLocFree (cbp->loc);
+                    cbp->loc = slp;
+                  }
+                }
+                break;
+              case SEQFEAT_RNA :
+                rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+                if (rrp != NULL && rrp->ext.choice == 2) {
+                  trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+                  if (trp != NULL && trp->anticodon != NULL) {
+                    sip = SeqLocId (trp->anticodon);
+                    slp = SeqLocCopyRegion (sip, trp->anticodon, bsp, 0,
+                                            bsp->length - 1, Seq_strand_minus, &split);
+                    trp->anticodon = SeqLocFree (trp->anticodon);
+                    trp->anticodon = slp;
+                  }
+                }
+                break;
+              default :
+                break;
+            }
           }
         }
         sfp = sfp->next;
@@ -6559,6 +6851,7 @@ static void CheckFeatForNuclID_callback (SeqFeatPtr sfp, Pointer userdata)
     /* Get the location Seq ID for this CDS feature */
     
     featSip = SeqLocId (sfp->location);
+    if (featSip == NULL) return;
     oip     = (ObjectIdPtr) featSip->data.ptrvalue;
     
     /* If the location Seq ID matches the old Seq Id */
@@ -6799,21 +7092,14 @@ static void ResolveExistingIDsCallback (SeqEntryPtr sep, Pointer mydata, Int4 in
 
 extern Int2 DoOneSegFixup (SeqEntryPtr sep, Boolean ask);
 
-extern void ResolveExistingLocalIDs (IteM i);
-extern void ResolveExistingLocalIDs (IteM i)
+static void ResolveExistingLocalIDsBaseForm (BaseFormPtr bfp)
 
 {
   MsgAnswer     ans;
-  BaseFormPtr   bfp;
   Boolean       doParts = FALSE;
   LclIdListPtr  head = NULL;
   SeqEntryPtr   sep;
 
-#ifdef WIN_MAC
-  bfp = currentFormDataPtr;
-#else
-  bfp = GetObjectExtra (i);
-#endif
   if (bfp == NULL) return;
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
@@ -6828,6 +7114,30 @@ extern void ResolveExistingLocalIDs (IteM i)
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
+extern void ResolveExistingLocalIDs (IteM i);
+extern void ResolveExistingLocalIDs (IteM i)
+{
+  BaseFormPtr   bfp;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+
+  if (bfp == NULL) return;
+  ResolveExistingLocalIDsBaseForm (bfp);
+}
+
+extern void ResolveExistingLocalIDsToolBtn (ButtoN b)
+{
+  BaseFormPtr   bfp;
+
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+  ResolveExistingLocalIDsBaseForm (bfp);
+}
+
 extern void SetSourceFocus (IteM i);
 extern void ClearSourceFocus (IteM i);
 
@@ -7048,7 +7358,7 @@ extern void ExtraAccToHistByPos (IteM i)
   ahp->which = DialogText (g, "", 5, NULL);
 
   c = HiddenGroup (h, 2, 0, NULL);
-  b = PushButton (c, "Accept", DoProcessExtraAccToHis);
+  b = DefaultButton (c, "Accept", DoProcessExtraAccToHis);
   SetObjectExtra (b, ahp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
   AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
@@ -7255,16 +7565,12 @@ extern void EditFeatureStrand (IteM i)
   ButtoN         b;
   BaseFormPtr    bfp;
   GrouP          c;
-  FeatDefPtr     curr;
   EditStrandPtr  esp;
   GrouP          g;
   GrouP          h;
   ValNodePtr     head;
   GrouP          k;
-  Uint1          key;
-  CharPtr        label = NULL;
   Int2           listHeight;
-  Uint2          subtype;
   ValNodePtr     vnp;
   WindoW         w;
 
@@ -7307,41 +7613,11 @@ extern void EditFeatureStrand (IteM i)
 
   /* Create a val node list of all feature types */
 
-  head = ValNodeNew (NULL);
-  curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
-  while (curr != NULL) {
-    if (key != FEATDEF_BAD) {
-      subtype = curr->featdef_key;
-      if (subtype != FEATDEF_misc_RNA &&
-          subtype != FEATDEF_precursor_RNA &&
-          subtype != FEATDEF_mat_peptide &&
-          subtype != FEATDEF_sig_peptide &&
-          subtype != FEATDEF_transit_peptide &&
-          subtype != FEATDEF_Imp_CDS) {
-        vnp = ValNodeNew (head);
-        if (head == NULL) {
-          head = vnp;
-        }
-        if (vnp != NULL) {
-          vnp->choice = subtype;
-          vnp->data.ptrvalue = StringSave (curr->typelabel);
-        }
-      }
-    }
-    curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
-  }
+  head = BuildFeatureValNodeList (TRUE, "[ALL FEATURES]", 0, FALSE, TRUE);
 
   /* Use the val node list to populate the feature list box */
 
   if (head != NULL) {
-    head = SortValNode (head, SortVnpByString);
-    vnp = ValNodeNew (NULL);
-    if (vnp != NULL) {
-      vnp->choice = 0;
-      vnp->data.ptrvalue = StringSave ("[ALL FEATURES]");
-    }
-    vnp->next = head;
-    head = vnp;
     for (vnp = head; vnp != NULL; vnp = vnp->next)
       ListItem (esp->feature, (CharPtr) vnp->data.ptrvalue);
   }
@@ -7372,7 +7648,7 @@ extern void EditFeatureStrand (IteM i)
   /* Create accept and cancel buttons */
 
   c = HiddenGroup (h, 2, 0, NULL);
-  b = PushButton (c, "Accept", DoEditFeatureStrand);
+  b = DefaultButton (c, "Accept", DoEditFeatureStrand);
   SetObjectExtra (b, esp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -7430,3 +7706,214 @@ extern void ClearMrnaProducts (IteM i)
   ClearFeatProducts (i, FEATDEF_mRNA);
 }
 
+static void ConsolidateOneLikeSubSourceModifier (
+  SubSourcePtr match_to,
+  Boolean use_semicolon
+)
+{
+  SubSourcePtr prev, index;
+  Int4         len, num_matches;
+  CharPtr      new_value;
+
+  if (match_to == NULL) return;
+  len = StringLen (match_to->name) + 1;
+  num_matches = 0;
+  prev = match_to;
+  index = match_to->next;
+  while (index != NULL)
+  {
+    if (index->subtype == match_to->subtype && index->name != NULL)
+    {
+      len += StringLen (index->name) + 2;
+      num_matches++;
+    }
+    index = index->next;
+  }
+  if (num_matches == 0) return;
+
+  new_value = MemNew (len * sizeof (char));
+  if (new_value == NULL) return;
+
+  StringCpy (new_value, match_to->name);
+  index = match_to->next;
+  while (index != NULL)
+  {
+    if (index->subtype == match_to->subtype && index->name != NULL)
+    {
+      if (use_semicolon)
+      {
+        StringCat (new_value, "; ");
+      }
+      else
+      {
+        StringCat (new_value, " ");
+      }
+      StringCat (new_value, index->name);
+      prev->next = index->next;
+      index->next = NULL;
+      SubSourceFree (index);
+      index = prev;
+    }
+    prev = index;
+    index = index->next;
+  }
+  MemFree (match_to->name);
+  match_to->name = new_value; 
+}
+  
+static void ConsolidateOneLikeOrganismModifier (
+  OrgModPtr match_to,
+  Boolean use_semicolon
+)
+{
+  OrgModPtr prev, index;
+  Int4      len, num_matches;
+  CharPtr   new_value;
+
+  if (match_to == NULL) return;
+  len = StringLen (match_to->subname) + 1;
+  num_matches = 0;
+  prev = match_to;
+  index = match_to->next;
+  while (index != NULL)
+  {
+    if (index->subtype == match_to->subtype && index->subname != NULL)
+    {
+      len += StringLen (index->subname) + 2;
+      num_matches++;
+    }
+    index = index->next;
+  }
+  if (num_matches == 0) return;
+
+  new_value = MemNew (len * sizeof (char));
+  if (new_value == NULL) return;
+
+  StringCpy (new_value, match_to->subname);
+  index = match_to->next;
+  while (index != NULL)
+  {
+    if (index->subtype == match_to->subtype && index->subname != NULL)
+    {
+      if (use_semicolon)
+      {
+        StringCat (new_value, "; ");
+      }
+      else
+      {
+        StringCat (new_value, " ");
+      }
+      StringCat (new_value, index->subname);
+      prev->next = index->next;
+      index->next = NULL;
+      OrgModFree (index);
+      index = prev;
+    }
+    prev = index;
+    index = index->next;
+  }
+  MemFree (match_to->subname);
+  match_to->subname = new_value; 
+}
+  
+static void ConsolidateLikeModifiersProc (BioSourcePtr biop, Pointer userdata)
+{
+  SubSourcePtr ssp;
+  OrgModPtr    mod;
+  Boolean      use_semicolon;
+
+  if (biop == NULL || userdata == NULL) return;
+
+  use_semicolon = *((Boolean PNTR) userdata);
+
+  for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next)
+  {
+    if (ssp->name != NULL)
+    {
+      ConsolidateOneLikeSubSourceModifier (ssp, use_semicolon);
+    }
+  }
+    
+  if (biop->org == NULL || biop->org->orgname == NULL) return;
+  for (mod = biop->org->orgname->mod; mod != NULL; mod = mod->next)
+  {
+    if (mod->subname != NULL)
+    {
+      ConsolidateOneLikeOrganismModifier (mod, use_semicolon);
+    }
+  }
+}
+
+static void ConsolidateLikeModifiers (IteM i, Boolean use_semicolon)
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  VisitBioSourcesInSep (sep, &use_semicolon, ConsolidateLikeModifiersProc);
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+extern void ConsolidateLikeModifiersWithSemicolons (IteM i)
+{
+  ConsolidateLikeModifiers (i, TRUE);
+}
+
+extern void ConsolidateLikeModifiersWithoutSemicolons (IteM i)
+{
+  ConsolidateLikeModifiers (i, FALSE);
+}
+
+static void ConsolidateOrganismNotesProc (BioSourcePtr biop, Pointer userdata)
+{
+  SubSourcePtr ssp, note_ssp;
+  OrgModPtr    mod, note_mod;
+
+  if (biop == NULL) return;
+
+  for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next)
+  {
+    if (ssp->subtype == 255 && ssp->name != NULL)
+    {
+      ConsolidateOneLikeSubSourceModifier (ssp, TRUE);
+      note_ssp = ssp;
+    }
+  }
+    
+  if (biop->org == NULL || biop->org->orgname == NULL) return;
+  for (mod = biop->org->orgname->mod; mod != NULL; mod = mod->next)
+  {
+    if (mod->subtype == 255 && mod->subname != NULL)
+    {
+      ConsolidateOneLikeOrganismModifier (mod, TRUE);
+      note_mod = mod;
+    }
+  }
+}
+
+extern void ConsolidateOrganismNotes (IteM i)
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  VisitBioSourcesInSep (sep, NULL, ConsolidateOrganismNotesProc);
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
diff --git a/sequin/sequin5.c b/sequin/sequin5.c
index 449b7dc4..4f4baf9a 100644
--- a/sequin/sequin5.c
+++ b/sequin/sequin5.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   8/26/97
 *
-* $Revision: 6.153 $
+* $Revision: 6.165 $
 *
 * File Description:
 *
@@ -76,6 +76,7 @@
 #include <subutil.h>
 #include <explore.h>
 #include <import.h>
+#include <salutil.h>
 
 static void CommonLaunchBioseqViewer (SeqEntryPtr sep, CharPtr path, Boolean directToEditor)
 
@@ -819,7 +820,7 @@ void EditLocusProc (IteM i)
   StaticPrompt (g, "Accession: ", 0, stdLineHeight, systemFont, 'l');
   elp->accnnumber = StaticPrompt (g, "", 20 * stdCharWidth, stdLineHeight, systemFont, 'l');
   c = HiddenGroup (w, 2, 0, NULL);
-  b = PushButton (c, "Accept", StdAcceptFormButtonProc);
+  b = DefaultButton (c, "Accept", StdAcceptFormButtonProc);
   SetObjectExtra (b, elp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
   AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
@@ -3197,7 +3198,7 @@ static ForM CreatePowBlastForm (Uint2 entityID, SeqEntryPtr sep)
     AlignObjects (ALIGN_MIDDLE, (HANDLE) ppt4, (HANDLE) pfp->stringency, NULL);
 
     c = HiddenGroup (w, 4, 0, NULL);
-    pfp->accept = PushButton (c, "Accept", PowBlastFormAcceptProc);
+    pfp->accept = DefaultButton (c, "Accept", PowBlastFormAcceptProc);
     SetObjectExtra (pfp->accept, pfp, NULL);
     Disable (pfp->accept);
     PushButton (c, "Cancel", StdCancelButtonProc);
@@ -5546,7 +5547,7 @@ static ForM CreateAutoParseForm (Uint2 entityID, SeqEntryPtr sep, BioseqPtr targ
     }
 
     c = HiddenGroup (w, 4, 0, NULL);
-    b = PushButton (c, "Accept", AutoParseAcceptProc);
+    b = DefaultButton (c, "Accept", AutoParseAcceptProc);
     SetObjectExtra (b, afp, NULL);
     PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -5857,7 +5858,7 @@ void AutoParseFeatureTableProc (IteM i)
     SetValue (ppp->tabDelimited, 1);
 
     c = HiddenGroup (w, 4, 0, NULL);
-    b = PushButton (c, "Accept", PreParseAcceptProc);
+    b = DefaultButton (c, "Accept", PreParseAcceptProc);
     SetObjectExtra (b, ppp, NULL);
     PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -6011,6 +6012,7 @@ typedef struct qualformdata {
   EnumFieldAssoc PNTR realalist;
   EnumFieldAssoc PNTR alist;
   ValNodePtr     bsplist;
+  ButtoN         leaveDlgUp;
 } QualFormData, PNTR QualFormPtr;
 
 static void LIBCALLBACK AsnWriteQualifierForDCallBack (AsnExpOptStructPtr pAEOS)
@@ -6174,83 +6176,6 @@ extern void SeqLocAdjustByOffset (SeqLocPtr slp,
 
 /*=========================================================================*/
 /*                                                                         */
-/* SeqLocAddToEnd ()                                                       */
-/*                                                                         */
-/*=========================================================================*/
-
-static Boolean SeqLocAddToEnd (SeqLocPtr slp, Int4 length)
-{
-  SeqIntPtr sinp;
-
-  switch (slp->choice) {
-  case SEQLOC_INT :
-    sinp = (SeqIntPtr) slp->data.ptrvalue;
-    if (NULL == sinp)
-      return FALSE;
-    sinp->to += length;
-    break;
-  case SEQLOC_EMPTY :
-  case SEQLOC_NULL :
-  case SEQLOC_WHOLE :
-  case SEQLOC_PNT :
-  case SEQLOC_PACKED_PNT :
-  case SEQLOC_PACKED_INT :
-  case SEQLOC_MIX :
-  case SEQLOC_EQUIV :
-  case SEQLOC_BOND :
-  case SEQLOC_FEAT :
-  default :
-    break;
-  }
-
-  return TRUE;
-}
-
-/*=========================================================================*/
-/*                                                                         */
-/* SeqLocGetLength ()                                                      */
-/*                                                                         */
-/*=========================================================================*/
-
-static Int4 SeqLocGetLength (SeqLocPtr slp)
-{
-  SeqIntPtr sinp;
-  Int4      length;
-
-  switch (slp->choice) {
-  case SEQLOC_INT :
-
-    sinp = (SeqIntPtr) slp->data.ptrvalue;
-    if (NULL == sinp)
-      return 0;
-
-    if (sinp->from < sinp->to)
-      length = sinp->to - sinp->from + 1;
-    else
-      length = sinp->from - sinp->to + 1;
-
-    break;
-
-  case SEQLOC_EMPTY :
-  case SEQLOC_NULL :
-  case SEQLOC_WHOLE :
-  case SEQLOC_PNT :
-  case SEQLOC_PACKED_PNT :
-  case SEQLOC_PACKED_INT :
-  case SEQLOC_MIX :
-  case SEQLOC_EQUIV :
-  case SEQLOC_BOND :
-  case SEQLOC_FEAT :
-  default :
-    length = 0;
-    break;
-  }
-
-  return length;
-}
-
-/*=========================================================================*/
-/*                                                                         */
 /* MoveProteinFeatures ()                                                  */
 /*                                                                         */
 /*=========================================================================*/
@@ -6437,6 +6362,41 @@ static void ConvertProtsToMatPeptides (BioseqPtr bsp)
   return;
 }
 
+static void ConvertFirstMatProteinToPolyProtein (
+  BioseqPtr nucBsp,
+  SeqFeatPtr firstMatCDS
+)
+{
+
+  SeqLocPtr firstMatLoc;
+  BioseqPtr firstMatBsp;
+  Uint1     strand;
+
+  if (nucBsp == NULL
+    || firstMatCDS == NULL)
+  {
+    return;
+  }
+
+  firstMatBsp = BioseqFindFromSeqLoc (firstMatCDS->product);
+  if (firstMatBsp == NULL) return;
+
+  strand = SeqLocStrand (firstMatCDS->location);
+  firstMatLoc = firstMatCDS->location;
+  firstMatCDS->location = SeqLocMerge (nucBsp, firstMatLoc, NULL, FALSE, TRUE, FALSE);
+  expand_seq_loc (0, nucBsp->length - 1, strand, firstMatCDS->location);
+
+  SetSeqLocPartial (firstMatCDS->location, TRUE, TRUE);
+  firstMatCDS->partial = TRUE;
+  SeqLocFree (firstMatLoc);
+
+  firstMatBsp->seq_data = BSFree (firstMatBsp->seq_data);
+  firstMatBsp->seq_data = ProteinFromCdRegion (firstMatCDS, FALSE);
+  firstMatBsp->length = BSLen (firstMatBsp->seq_data);
+  SetSeqFeatProduct (firstMatCDS, firstMatBsp);
+
+}
+
 /*=========================================================================*/
 /*                                                                         */
 /* MergeProteinBioseqs ()                                                  */
@@ -6450,12 +6410,7 @@ static Boolean MergeProteinBioseqs (BioseqSetPtr bssp)
   BioseqPtr          protBsp;
   SeqEntryPtr        sep;
   Int4               offset;
-  Uint1              seqtype;
-  SeqPortPtr         spp;
-  Int2               residue;
   SeqFeatPtr         cdsSfp;
-  SeqFeatPtr         firstProtCDS;
-  Int4               cdsLen;
   Boolean            found;
   SeqMgrFeatContext  fcontext;
 
@@ -6489,8 +6444,9 @@ static Boolean MergeProteinBioseqs (BioseqSetPtr bssp)
       /* offset for the next Bioseq.   */
       
       if (NULL == firstProtBsp)	{
+        ConvertFirstMatProteinToPolyProtein (bsp, cdsSfp);
+        protBsp = BioseqFindFromSeqLoc (cdsSfp->product);
 	firstProtBsp = protBsp;
-	firstProtCDS = SeqMgrGetCDSgivenProduct (firstProtBsp, NULL);
 	offset = firstProtBsp->length;
       }
       
@@ -6500,41 +6456,16 @@ static Boolean MergeProteinBioseqs (BioseqSetPtr bssp)
       else {
 
 	/* Move all features to 1st protein Bioseq */
-	
-	MoveProteinAnnots (firstProtBsp, protBsp, &offset);
-	
-	/* Merge the actual sequences */
-	
-	seqtype = Seq_code_ncbieaa;
-	spp = SeqPortNew(protBsp, 0, protBsp->length-1, protBsp->strand,
-			 seqtype);
-	
-	while ((residue = SeqPortGetResidue(spp)) != SEQPORT_EOF) {
-	  if (! IS_residue(residue))
-	    ErrPost(CTX_NCBIOBJ, 1, "Non-residue in MergeProteinBioseqs [%d]",
-		    (int)residue);
-	  else 
-	    BSPutByte(firstProtBsp->seq_data, residue);
-	}
-	
-	SeqPortFree(spp);
-	firstProtBsp->length += protBsp->length;
-	
-	/* Mark for deletion the original Bioseq */
-	
-	offset += protBsp->length;
-	protBsp->idx.deleteme = TRUE;
+	offset = fcontext.left / 3;
 
-	/* Mark for deletion any CDS */
-	/* pointing to this Bioseq.  */
+	MoveProteinAnnots (firstProtBsp, protBsp, &offset);
 
-	cdsSfp = SeqMgrGetCDSgivenProduct (protBsp, NULL);
+        /* Mark for deletion the original Bioseq */
+	protBsp->idx.deleteme = TRUE;
+        /* Mark for deletion the CDS */
+        /* pointing to this Bioseq.  */
 	cdsSfp->idx.deleteme = TRUE;
 
-	/* Adjust the length of the merged Bioseq's CDS */
-
-	cdsLen = SeqLocGetLength (cdsSfp->location);
-	SeqLocAddToEnd (firstProtCDS->location, cdsLen);
       }
 
     cdsSfp = SeqMgrGetNextFeature (protBsp, cdsSfp, SEQFEAT_CDREGION,
@@ -8112,7 +8043,11 @@ static void DoProcessQualifier (ButtoN b)
           qfp->findStr = JustSaveStringFromText (qfp->findthis);
           PrepareToConvertToCDS (sep, qfp->input_entityID,
 				 qfp->subtype, qfp->findStr);
-          Remove (qfp->form);
+          if (GetStatus (qfp->leaveDlgUp)) {
+            Show (qfp->form);
+          } else {
+            Remove (qfp->form);
+          }
           return;
 	}
       }
@@ -8151,7 +8086,11 @@ static void DoProcessQualifier (ButtoN b)
   DeleteMarkedObjects (qfp->input_entityID, 0, NULL);
   ObjMgrSetDirtyFlag (qfp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, qfp->input_entityID, 0, 0);
-  Remove (qfp->form);
+  if (GetStatus (qfp->leaveDlgUp)) {
+    Show (qfp->form);
+  } else {
+    Remove (qfp->form);
+  }
 }
 
 static void QualMessageProc (ForM f, Int2 mssg)
@@ -8177,6 +8116,15 @@ static void CleanupQualForm (GraphiC g, VoidPtr data)
   if (qfp != NULL) {
     MemFree (qfp->findStr);
     MemFree (qfp->replaceStr);
+    if (qfp->alist != NULL
+      && qfp->alist != qfp->realalist
+      && qfp->alist != qfp->realalist + 1)
+    {
+      for (j = 0; qfp->alist [j].name != NULL; j++) {
+        MemFree (qfp->alist [j].name);
+      }
+      MemFree (qfp->alist);
+    }
     if (qfp->realalist != NULL) {
       for (j = 0; qfp->realalist [j].name != NULL; j++) {
         MemFree (qfp->realalist [j].name);
@@ -8258,6 +8206,7 @@ static void ProcessQualifier (IteM i, Int2 type)
   } else {
     ap = import_featdef_alist (FALSE, FALSE, FALSE);
   }
+  SortEnumFieldAssocPtrArray (ap, CompareImpFeatEnumFieldAssoc);
   qfp->realalist = ap;
   if (type == CONVERT_FEAT) {
     ap++;
@@ -8265,7 +8214,15 @@ static void ProcessQualifier (IteM i, Int2 type)
     ap->name = MemFree (ap->name);
     ap->name = StringSave ("[ALL FEATURES]");
   }
-  qfp->alist = ap;
+ 
+  if (type == CONVERT_FEAT)
+  { 
+    qfp->alist = InsertMostUsedFeatureEnumFieldAssoc (ap);
+  }
+  else
+  {
+    qfp->alist = ap;
+  }
 
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
@@ -8365,9 +8322,10 @@ static void ProcessQualifier (IteM i, Int2 type)
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoProcessQualifier);
+  b = DefaultButton (c, "Accept", DoProcessQualifier);
   SetObjectExtra (b, qfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
+  qfp->leaveDlgUp = CheckBox (c, "Leave Dialog Up", NULL);
 
   AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) k, (HANDLE) c, NULL);
   RealizeWindow (w);
@@ -8617,13 +8575,79 @@ typedef struct sourceformdata {
 
   Boolean        replaceOldAsked;
   Boolean        doReplaceAll;
+  Boolean        use_semicolon;
+  ButtoN         leaveDlgUp;
 } SourceFormData, PNTR SourceFormPtr;
 
+extern void AppendOrReplaceString (
+  CharPtr PNTR string_loc,
+  CharPtr new_value,
+  Boolean PNTR asked_question,
+  Boolean PNTR do_replace,
+  Boolean PNTR use_semicolon
+)
+{
+  MsgAnswer ans;
+  CharPtr   tmp_value, tmp_new_value;
+
+  if (string_loc == NULL
+    || new_value == NULL
+    || asked_question == NULL
+    || do_replace == NULL
+    || use_semicolon == NULL)
+  {
+    return;
+  }
+
+  if (! *asked_question && !StringHasNoText (*string_loc))
+  {
+    *asked_question = TRUE;
+    ArrowCursor ();
+    ans = Message (MSG_YN, "Do you wish to overwrite existing content?");
+    *do_replace = (Boolean) (ans == ANS_YES);
+    if (! *use_semicolon)
+    {
+      if (! *do_replace)
+      {
+        ans = Message (MSG_YN, "Separate items with semicolon?");
+        *use_semicolon = (Boolean) (ans == ANS_YES);
+      }
+    }
+    WatchCursor ();
+    Update ();
+  }
+  if (*do_replace || StringHasNoText (*string_loc))
+  {
+    MemFree (*string_loc);
+    *string_loc = StringSave (new_value);
+  }
+  else
+  {
+    tmp_value = MemNew (StringLen (*string_loc) + StringLen ( new_value) + 3);
+    if (tmp_value == NULL) return;
+    StringCpy (tmp_value, *string_loc);
+    TrimSpacesAroundString (tmp_value);
+    if (*use_semicolon)
+    {
+      StringCat (tmp_value, "; ");
+    }
+    else
+    {
+      StringCat (tmp_value, " ");
+    }
+    tmp_new_value = StringSave (new_value);
+    TrimSpacesAroundString (tmp_new_value);
+    StringCat (tmp_value, tmp_new_value);
+    MemFree (tmp_new_value);
+    MemFree (*string_loc);
+    *string_loc = tmp_value;
+  }
+}
+
 static SubSourcePtr FindSubSource (BioSourcePtr biop, Uint1 subtype, SourceFormPtr sfp,
                                    Boolean forceRemove, Boolean convertNote, Boolean is_feat)
 
 {
-  MsgAnswer     ans;
   SubSourcePtr  PNTR  prev;
   SubSourcePtr  ssp;
   SubSourcePtr  tmp;
@@ -8641,18 +8665,6 @@ static SubSourcePtr FindSubSource (BioSourcePtr biop, Uint1 subtype, SourceFormP
           SubSourceFree (ssp);
           return NULL;
         }
-      } else if (sfp->type == ADD_SOURCE) {
-        if (! sfp->replaceOldAsked) {
-          sfp->replaceOldAsked = TRUE;
-          ArrowCursor ();
-          ans = Message (MSG_YN, "Do you wish to overwrite existing modifiers?");
-          WatchCursor ();
-          Update ();
-          sfp->doReplaceAll = (Boolean) (ans == ANS_YES);
-        }
-        if (sfp->doReplaceAll) {
-          return ssp;
-        }
       } else {
         return ssp;
       }
@@ -8681,7 +8693,6 @@ static SubSourcePtr FindSubSource (BioSourcePtr biop, Uint1 subtype, SourceFormP
 static OrgModPtr FindOrgMod (BioSourcePtr biop, Uint1 subtype, SourceFormPtr sfp, Boolean forceRemove, Boolean convertNote)
 
 {
-  MsgAnswer   ans;
   OrgModPtr   mod;
   OrgNamePtr  onp;
   OrgRefPtr   orp;
@@ -8722,18 +8733,6 @@ static OrgModPtr FindOrgMod (BioSourcePtr biop, Uint1 subtype, SourceFormPtr sfp
           OrgModFree (mod);
           return NULL;
         }
-      } else if (sfp->type == ADD_SOURCE) {
-        if (! sfp->replaceOldAsked) {
-          sfp->replaceOldAsked = TRUE;
-          ArrowCursor ();
-          ans = Message (MSG_YN, "Do you wish to overwrite existing modifiers?");
-          WatchCursor ();
-          Update ();
-          sfp->doReplaceAll = (Boolean) (ans == ANS_YES);
-        }
-        if (sfp->doReplaceAll) {
-          return mod;
-        }
       } else {
         return mod;
       }
@@ -8771,7 +8770,7 @@ static void ConvertSourceString (OrgRefPtr orp, Int2 fromval, Int2 toval)
   switch (fromval) {
     case 1 :
       tmp = orp->taxname;
-      orp->taxname = NULL;
+      SetTaxNameAndRemoveTaxRef (orp, NULL);
       break;
     case 2 :
       tmp = orp->common; 
@@ -8797,7 +8796,7 @@ static void ConvertSourceString (OrgRefPtr orp, Int2 fromval, Int2 toval)
 
   switch (toval) {
     case 1 :
-      orp->taxname = tmp;
+      SetTaxNameAndRemoveTaxRef (orp, tmp);
       break;
     case 2 :
       orp->common = tmp;
@@ -8873,6 +8872,241 @@ static Uint1 AssignSubtype (Uint1 subtype)
   return subtype;
 }
 
+static void RemoveSubSourceByPtr (BioSourcePtr biop, SubSourcePtr to_remove)
+{
+  SubSourcePtr ssp, prev;
+
+  if (biop == NULL || to_remove == NULL) return;
+  
+  prev = NULL;
+  ssp = biop->subtype;
+  while (ssp != NULL)
+  {
+    if (ssp == to_remove)
+    {
+      if (prev == NULL)
+      {
+        biop->subtype = ssp->next;
+        ssp->next = NULL;
+        SubSourceFree (ssp);
+        ssp = biop->subtype;
+      }
+      else
+      {
+        prev->next = ssp->next;
+        ssp->next = NULL;
+        SubSourceFree (ssp);
+        ssp = prev->next;
+      }
+    }
+    else
+    {
+      prev = ssp;
+      ssp = ssp->next;
+    }
+  }
+}
+
+static void ConvertSubSourceModifier (
+  BioSourcePtr  biop,
+  SourceFormPtr sfp,
+  Boolean       is_feat,
+  SubSourcePtr  ssp_from
+)
+{
+  SubSourcePtr ssp_to;
+
+  if (biop == NULL || sfp == NULL || ssp_from == NULL) return;
+  ssp_to = FindSubSource (biop, sfp->toval - 100, sfp, TRUE, FALSE, is_feat);
+  if (ssp_to != NULL)
+  {
+    AppendOrReplaceString (&(ssp_to->name), ssp_from->name,
+                           &(sfp->replaceOldAsked),
+                           &(sfp->doReplaceAll),
+                           &(sfp->use_semicolon));
+    RemoveSubSourceByPtr (biop, ssp_from);
+  }
+  else
+  {
+    ssp_from->subtype = AssignSubtype (sfp->toval);
+  }
+}
+ 
+static void RemoveOrgModByPtr (BioSourcePtr biop, OrgModPtr to_remove)
+{
+  OrgModPtr mod, prev;
+  
+  if (biop == NULL
+    || biop->org == NULL
+    || biop->org->orgname == NULL
+    || biop->org->orgname->mod == NULL
+    || to_remove == NULL)
+  {
+    return;
+  }
+
+  prev = NULL;
+  mod = biop->org->orgname->mod;
+  while (mod != NULL)
+  {
+    if (mod == to_remove)
+    {
+      if (prev == NULL)
+      {
+        biop->org->orgname->mod = mod->next;
+        mod->next = NULL;
+        OrgModFree (mod);
+        mod = biop->org->orgname->mod;
+      }
+      else
+      {
+        prev->next = mod->next;
+        mod->next = NULL;
+        OrgModFree (mod);
+        mod = prev->next;
+      }
+    }
+    else
+    {
+      prev = mod;
+      mod = mod->next;
+    }
+  }
+}
+
+static void ConvertOrganismModifier (
+  BioSourcePtr  biop,
+  SourceFormPtr sfp,
+  Boolean       is_feat,
+  OrgModPtr     mod_from
+)
+{
+  OrgModPtr mod_to;
+
+  if (biop == NULL || sfp == NULL || mod_from == NULL) return;
+  mod_to = FindOrgMod (biop, sfp->toval, sfp, FALSE, FALSE);
+  if (mod_to != NULL)
+  {
+    AppendOrReplaceString (&(mod_to->subname), mod_from->subname,
+                           &(sfp->replaceOldAsked),
+                           &(sfp->doReplaceAll),
+                           &(sfp->use_semicolon));
+    RemoveOrgModByPtr (biop, mod_from);
+  }
+  else
+  {
+    mod_from->subtype = AssignSubtype (sfp->toval);
+  }
+}
+
+static void ConvertSubSourceToOrgMod (
+  BioSourcePtr biop,
+  SourceFormPtr sfp,
+  Boolean is_feat,
+  SubSourcePtr ssp
+)
+{
+  OrgModPtr mod;
+
+  if (biop == NULL
+    || sfp == NULL
+    || ssp == NULL)
+  {
+    return;
+  }
+
+  if (sfp->toval == 55)
+  {
+    mod = FindOrgMod (biop, 255, sfp, FALSE, FALSE);
+  }
+  else
+  {
+    mod = FindOrgMod (biop, sfp->toval, sfp, FALSE, FALSE);
+  }
+  if (mod == NULL)
+  {
+    if (biop->org == NULL) 
+    {
+      biop->org = OrgRefNew ();
+      if (biop->org == NULL) return;
+    } 
+    if (biop->org->orgname == NULL)
+    {
+      biop->org->orgname = OrgNameNew ();
+      if (biop->org->orgname == NULL) return;
+    }
+    mod = OrgModNew ();
+    if (sfp->toval == 55)
+    {
+      mod->subtype = 255;
+    }
+    else
+    {
+      mod->subtype = sfp->toval;
+    }
+    mod->subname = StringSave (ssp->name);
+    mod->next = biop->org->orgname->mod;
+    biop->org->orgname->mod = mod;
+  }
+  else
+  {
+    AppendOrReplaceString (&(mod->subname), ssp->name,
+                           &(sfp->replaceOldAsked),
+                           &(sfp->doReplaceAll),
+                           &(sfp->use_semicolon));
+  }
+  RemoveSubSourceByPtr (biop, ssp);
+}
+ 
+static void ConvertOrgModToSubSource (
+  BioSourcePtr biop,
+  SourceFormPtr sfp,
+  Boolean is_feat,
+  OrgModPtr mod
+)
+{
+  SubSourcePtr ssp;
+
+  if (biop == NULL
+    || sfp == NULL
+    || mod == NULL)
+  {
+    return;
+  }
+
+  if (sfp->toval == 155)
+  {
+    ssp = FindSubSource (biop, 255, sfp, FALSE, FALSE, is_feat);
+  }
+  else
+  {
+    ssp = FindSubSource (biop, sfp->toval - 100, sfp, FALSE, FALSE, is_feat);
+  }
+  if (ssp == NULL)
+  {
+    ssp = SubSourceNew ();
+    if (sfp->toval == 155)
+    {
+      ssp->subtype = 255;
+    }
+    else
+    {
+      ssp->subtype = sfp->toval - 100;
+    }
+    ssp->name = StringSave (mod->subname);
+    ssp->next = biop->subtype;
+    biop->subtype = ssp;
+  }
+  else
+  {
+    AppendOrReplaceString (&(ssp->name), mod->subname,
+                           &(sfp->replaceOldAsked),
+                           &(sfp->doReplaceAll),
+                           &(sfp->use_semicolon));
+  }
+  RemoveOrgModByPtr (biop, mod);
+}
+ 
 static void ProcessBioSourceFunc (BioSourcePtr biop, SourceFormPtr sfp, Boolean is_feat)
 
 {
@@ -8884,6 +9118,7 @@ static void ProcessBioSourceFunc (BioSourcePtr biop, SourceFormPtr sfp, Boolean
   CharPtr       str = NULL;
   CharPtr       str1 = NULL;
   CharPtr       str2 = NULL;
+  CharPtr       tmp_str;
 
   if (biop == NULL || sfp == NULL) return;
   if (sfp->choice == 1) {
@@ -8913,19 +9148,13 @@ static void ProcessBioSourceFunc (BioSourcePtr biop, SourceFormPtr sfp, Boolean
         if (sfp->toval < 1) return;
         if (StringHasNoText (sfp->findStr) || StringISearch (str, sfp->findStr) != NULL) {
           if (sfp->toval >= 100 && ssp != NULL) {
-            ssp->subtype = AssignSubtype (sfp->toval);
+            ConvertSubSourceModifier (biop, sfp, is_feat, ssp);
           } else if (sfp->toval < 100 && mod != NULL) {
-            mod->subtype = AssignSubtype (sfp->toval);
+            ConvertOrganismModifier (biop, sfp, is_feat, mod);
           } else if (sfp->toval < 100 && ssp != NULL) {
-            mod = FindOrgMod (biop, sfp->toval, sfp, FALSE, TRUE);
-            if (mod == NULL) return;
-            mod->subname = StringSave (str);
-            ssp = FindSubSource (biop, sfp->fromval - 100, sfp, TRUE, FALSE, is_feat);
+            ConvertSubSourceToOrgMod (biop, sfp, is_feat, ssp);
           } else if (sfp->toval >= 100 && mod != NULL) {
-            ssp = FindSubSource (biop, sfp->toval - 100, sfp, FALSE, TRUE, is_feat);
-            if (ssp == NULL) return;
-            ssp->name = StringSave (str);
-            mod = FindOrgMod (biop, sfp->fromval, sfp, TRUE, FALSE);
+            ConvertOrgModToSubSource (biop, sfp, is_feat, mod);
           }
         }
         break;
@@ -8944,19 +9173,23 @@ static void ProcessBioSourceFunc (BioSourcePtr biop, SourceFormPtr sfp, Boolean
         break;
       case ADD_SOURCE :
         if (ssp != NULL) {
-          ssp->name = MemFree (ssp->name);
-          ssp->name = StringSave (sfp->findStr);
+          AppendOrReplaceString (&(ssp->name), sfp->findStr,
+                           &(sfp->replaceOldAsked),
+                           &(sfp->doReplaceAll),
+                           &(sfp->use_semicolon));
           if (ssp->name == NULL &&
               (ssp->subtype == SUBSRC_germline ||
                ssp->subtype == SUBSRC_rearranged ||
                ssp->subtype == SUBSRC_environmental_sample)) {
-            ssp->name = StringSave ("");
+              ssp->name = StringSave ("");
           } else if (ssp->subtype == SUBSRC_transgenic && (! is_feat)) {
             ssp->name = StringSave ("");
           }
         } else if (mod != NULL) {
-          mod->subname = MemFree (mod->subname);
-          mod->subname = StringSave (sfp->findStr);
+          AppendOrReplaceString (&(mod->subname), sfp->findStr,
+                           &(sfp->replaceOldAsked),
+                           &(sfp->doReplaceAll),
+                           &(sfp->use_semicolon));
         }
         break;
       default :
@@ -8975,7 +9208,6 @@ static void ProcessBioSourceFunc (BioSourcePtr biop, SourceFormPtr sfp, Boolean
         }
         break;
       case EDIT_SOURCE :
-        break;
       case ADD_SOURCE :
         biop->genome = sfp->fromval;
         break;
@@ -9012,7 +9244,7 @@ static void ProcessBioSourceFunc (BioSourcePtr biop, SourceFormPtr sfp, Boolean
         switch (sfp->fromval) {
           case 1 :
             if (orp != NULL) {
-              orp->taxname = MemFree (orp->taxname);
+              SetTaxNameAndRemoveTaxRef (orp, MemFree (orp->taxname));
             }
             break;
           case 2 :
@@ -9043,7 +9275,10 @@ static void ProcessBioSourceFunc (BioSourcePtr biop, SourceFormPtr sfp, Boolean
             if (orp != NULL) {
               foundit = StringISearch (orp->taxname, sfp->findStr);
               if (foundit != NULL) {
-                EditSourceString (&(orp->taxname), sfp, foundit);
+                tmp_str = StringSave (orp->taxname);
+                foundit = StringISearch (tmp_str, sfp->findStr);
+                EditSourceString (&(tmp_str), sfp, foundit);
+                SetTaxNameAndRemoveTaxRef (orp, tmp_str);
               }
             }
             break;
@@ -9247,6 +9482,7 @@ static void DoProcessSource (ButtoN b)
     }
     if (sfp->type != EDIT_SOURCE
       || (! StringHasNoText (sfp->findStr))
+      || sfp->choice == 2
       || sfp->choice == 3) {
       sfp->replaceOldAsked = FALSE;
       sfp->doReplaceAll = FALSE;
@@ -9283,7 +9519,11 @@ static void DoProcessSource (ButtoN b)
   }
   ObjMgrSetDirtyFlag (sfp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, sfp->input_entityID, 0, 0);
-  Remove (sfp->form);
+  if (GetStatus (sfp->leaveDlgUp)) {
+    Show (sfp->form);
+  } else {
+    Remove (sfp->form);
+  }
 }
 
 
@@ -9395,6 +9635,61 @@ static void SourceApplyToPartsProc (ButtoN b)
   }
 }
 
+static void ClearProcessSourceDlg (ButtoN b)
+{
+  SourceFormPtr  sfp;
+
+  sfp = (SourceFormPtr) GetObjectExtra (b);
+  if (sfp == NULL) return;
+
+  if ( sfp->onlyThisPart != NULL) {
+    Disable (sfp->onlyThisPart);
+  }
+  SetValue (sfp->sourceGroup, 1);
+  Hide (sfp->modGrp);
+  switch (sfp->type) {
+    case REMOVE_SOURCE :
+      SetEnumPopup (sfp->fromgen, biosource_genome_alistX, 0);
+      SetEnumPopup (sfp->fromref, orgref_textfield_alist, 0);
+      SetTitle (sfp->findthis, "");
+      SetValue (sfp->frommod, 1);
+      SetValue (sfp->fromorigin, 1);
+      break;
+    case CONVERT_SOURCE :
+      SetEnumPopup (sfp->fromgen, biosource_genome_alistX, 0);
+      SetEnumPopup (sfp->togen, biosource_genome_alistX, 0);
+      SetEnumPopup (sfp->fromref, orgref_textfield_alist, 0);
+      SetEnumPopup (sfp->toref, orgref_textfield_alist, 0);
+      SetTitle (sfp->findthis, "");
+      SetValue (sfp->frommod, 1);
+      SetValue (sfp->tomod, 1);
+      SetValue (sfp->fromorigin, 1);
+      SetValue (sfp->toorigin, 1);
+      break;
+    case EDIT_SOURCE :
+      SetEnumPopup (sfp->fromgen, biosource_genome_alistX, 0);
+      SetEnumPopup (sfp->fromref, orgref_textfield_alist, 0);
+      SetTitle (sfp->findthis, "");
+      SetTitle (sfp->replacewith, "");
+      SetValue (sfp->frommod, 1);
+      SetValue (sfp->fromorigin, 1);
+      break;
+    case ADD_SOURCE :
+      SetEnumPopup (sfp->fromgen, biosource_genome_alistX, 0);
+      SetTitle (sfp->findthis, "");
+      SetValue (sfp->frommod, 1);
+      SetValue (sfp->fromorigin, 1);
+      break;
+    default :
+      break;
+  }
+  Hide (sfp->genGrp);
+  Hide (sfp->refGrp);
+  Show (sfp->modGrp);
+  SafeHide (sfp->originGrp);
+  Select (sfp->findthis);
+}
+
 static void ProcessSource (IteM i, Int2 type)
 
 {
@@ -9465,6 +9760,8 @@ static void ProcessSource (IteM i, Int2 type)
     StaticPrompt (x, "Apply only to particular numbered segment", 0, dialogTextHeight, programFont, 'l');
     sfp->onlyThisPart = DialogText (x, "", 4, NULL);
     Disable (sfp->onlyThisPart);
+  } else {
+    sfp->onlyThisPart = NULL;
   }
 
   sfp->sourceGroup = HiddenGroup (h, 4, 0, ChangeSourceGroup);
@@ -9625,9 +9922,12 @@ static void ProcessSource (IteM i, Int2 type)
   SafeHide (sfp->originGrp);
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoProcessSource);
+  b = DefaultButton (c, "Accept", DoProcessSource);
   SetObjectExtra (b, sfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
+  b = PushButton (c, "Clear", ClearProcessSourceDlg);
+  SetObjectExtra (b, sfp, NULL);
+  sfp->leaveDlgUp = CheckBox (c, "Leave Dialog Up", NULL);
 
   AlignObjects (ALIGN_CENTER, (HANDLE) c, (HANDLE) sfp->sourceGroup,
                 (HANDLE) sfp->modGrp, (HANDLE) sfp->genGrp,
diff --git a/sequin/sequin6.c b/sequin/sequin6.c
index 1c936a0a..3d1c1727 100644
--- a/sequin/sequin6.c
+++ b/sequin/sequin6.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   11/12/97
 *
-* $Revision: 6.116 $
+* $Revision: 6.143 $
 *
 * File Description: 
 *
@@ -50,6 +50,7 @@
 #include <import.h>
 #include <objsub.h>
 #include <explore.h>
+#include <subutil.h>
 
 #define NUMBER_OF_SUFFIXES    7
 
@@ -289,6 +290,7 @@ typedef struct convertformdata {
   Boolean            includeright;
   Boolean            replaceOldAsked;
   Boolean            doReplaceAll;
+  Boolean            use_semicolon;
   Boolean            isDirty;
   ButtoN             removeBefore;
   ButtoN             removeAfter;
@@ -297,9 +299,14 @@ typedef struct convertformdata {
   GrouP              ifNotFoundGroup;
   Int2               ifNotFound;
   Int2               index;
-  Boolean            isCommentConvert;
+  Int4               parsetype;
 } ConvertFormData, PNTR ConvertFormPtr;
 
+/* values for parse type */
+#define PARSETYPE_FILE    0
+#define PARSETYPE_COMMENT 1
+#define PARSETYPE_LOCALID 2
+
 /* Values for ifNotFound field */
 
 #define DO_NOTHING       2
@@ -407,7 +414,8 @@ static void SetConvertAcceptButton (Handle a)
       {
         if ((! TextHasNoText (cfp->atleft)) ||
           (! TextHasNoText (cfp->atright)) ||
-          cfp->isCommentConvert)
+          cfp->parsetype == PARSETYPE_COMMENT ||
+          cfp->parsetype == PARSETYPE_LOCALID)
         {
           SafeEnable (cfp->accept);
           return;
@@ -1225,7 +1233,7 @@ extern Int2 LIBCALLBACK CreateDeleteByTextWindow (Pointer data)
   cfp = (ConvertFormPtr) MemNew (sizeof (ConvertFormData));
   if (cfp == NULL)
     return OM_MSG_RET_ERROR;
-  cfp->isCommentConvert = FALSE;
+  cfp->parsetype = PARSETYPE_FILE;
 
   w = FixedWindow (-50, -33, -10, -10, "Delete By Text String",
 		   StdCloseWindowProc);
@@ -1309,7 +1317,7 @@ extern Int2 LIBCALLBACK CreateDeleteByTextWindow (Pointer data)
   /* Add Accept and Cancel buttons */
 
   c = HiddenGroup (h, 4, 0, NULL);
-  cfp->accept = PushButton (c, "Accept", DeleteByText_Callback);
+  cfp->accept = DefaultButton (c, "Accept", DeleteByText_Callback);
   SetObjectExtra (cfp->accept, cfp, NULL);
   Disable (cfp->accept);
   PushButton (c, "Cancel", StdCancelButtonProc);
@@ -1329,49 +1337,14 @@ extern Int2 LIBCALLBACK CreateDeleteByTextWindow (Pointer data)
   return OM_MSG_RET_OK;
 }
 
-static Boolean ShouldReplaceParsedString (ConvertFormPtr cfp)
-
-{
-  MsgAnswer  ans;
-
-  if (cfp == NULL) return FALSE;
-  if (! cfp->replaceOldAsked) {
-    cfp->replaceOldAsked = TRUE;
-    ArrowCursor ();
-    Update ();
-    ans = Message (MSG_YN, "Do you wish to overwrite existing contents?");
-    WatchCursor ();
-    Update ();
-    cfp->doReplaceAll = (Boolean) (ans == ANS_YES);
-  }
-  return cfp->doReplaceAll;
-}
-
 static CharPtr SaveOrReplaceStringCopy (ConvertFormPtr cfp, CharPtr str, CharPtr current)
 
 {
-  size_t   len;
-  CharPtr  tmp;
-
   if (cfp == NULL) return NULL;
   if (StringHasNoText (str)) return current;
-  if (current != NULL) {
-    if (ShouldReplaceParsedString (cfp)) {
-      MemFree (current);
-    } else {
-      len = StringLen (str) + StringLen (current) + 4;
-      tmp = MemNew (len);
-      if (tmp != NULL) {
-        StringCpy (tmp, current);
-        StringCat (tmp, "; ");
-        StringCat (tmp, str);
-        /* str is within asn2ff string, so must not MemFree (str); */
-        MemFree (current);
-        return tmp;
-      }
-    }
-  }
-  return StringSave (str);
+  AppendOrReplaceString (&current, str, &(cfp->replaceOldAsked),
+                         &(cfp->doReplaceAll), &(cfp->use_semicolon));
+  return current;
 }
 
 static void ConvertAFeatureField (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent)
@@ -1388,6 +1361,7 @@ static void ConvertAFeatureField (SeqEntryPtr sep, Pointer mydata, Int4 index, I
   SeqFeatPtr      sfp;
   ValNodePtr      vnp;
   SeqFeatXrefPtr  xref;
+  CharPtr         cp;
 
   if (sep == NULL || sep->data.ptrvalue == NULL) return;
   cfp = (ConvertFormPtr) mydata;
@@ -1424,10 +1398,15 @@ static void ConvertAFeatureField (SeqEntryPtr sep, Pointer mydata, Int4 index, I
                 break;
               case 6 :
                 if (! StringHasNoText (cfp->foundstr)) {
-                  if (grp->syn != NULL && ShouldReplaceParsedString (cfp)) {
+                  if (grp->syn != NULL) {
                     vnp = grp->syn;
-                    vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
-                    vnp->data.ptrvalue = StringSave (cfp->foundstr);
+                    cp = vnp->data.ptrvalue;
+                    AppendOrReplaceString (&cp,
+                                           cfp->foundstr,
+                                           &(cfp->replaceOldAsked),
+                                           &(cfp->doReplaceAll),
+                                           &(cfp->use_semicolon));
+                    vnp->data.ptrvalue = cp;
                   } else {
                     vnp = ValNodeNew (NULL);
                     if (vnp != NULL) {
@@ -1485,10 +1464,15 @@ static void ConvertAFeatureField (SeqEntryPtr sep, Pointer mydata, Int4 index, I
             switch (cfp->subtype) {
               case 1 :
                 if (! StringHasNoText (cfp->foundstr)) {
-                  if (prp->name != NULL && ShouldReplaceParsedString (cfp)) {
+                  if (prp->name != NULL) {
                     vnp = prp->name;
-                    vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
-                    vnp->data.ptrvalue = StringSave (cfp->foundstr);
+                    cp = vnp->data.ptrvalue;
+                    AppendOrReplaceString (&cp,
+                                           cfp->foundstr,
+                                           &(cfp->replaceOldAsked),
+                                           &(cfp->doReplaceAll),
+                                           &(cfp->use_semicolon));
+                    vnp->data.ptrvalue = cp;
                   } else {
                     vnp = ValNodeNew (NULL);
                     if (vnp != NULL) {
@@ -1504,10 +1488,15 @@ static void ConvertAFeatureField (SeqEntryPtr sep, Pointer mydata, Int4 index, I
                 break;
               case 3 :
                 if (! StringHasNoText (cfp->foundstr)) {
-                  if (prp->ec != NULL && ShouldReplaceParsedString (cfp)) {
+                  if (prp->ec != NULL) {
                     vnp = prp->ec;
-                    vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
-                    vnp->data.ptrvalue = StringSave (cfp->foundstr);
+                    cp = vnp->data.ptrvalue;
+                    AppendOrReplaceString (&cp,
+                                           cfp->foundstr,
+                                           &(cfp->replaceOldAsked),
+                                           &(cfp->doReplaceAll),
+                                           &(cfp->use_semicolon));
+                    vnp->data.ptrvalue = cp;
                   } else {
                     vnp = ValNodeNew (NULL);
                     if (vnp != NULL) {
@@ -1520,10 +1509,15 @@ static void ConvertAFeatureField (SeqEntryPtr sep, Pointer mydata, Int4 index, I
                 break;
               case 4 :
                 if (! StringHasNoText (cfp->foundstr)) {
-                  if (prp->activity != NULL && ShouldReplaceParsedString (cfp)) {
+                  if (prp->activity != NULL) {
                     vnp = prp->activity;
-                    vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
-                    vnp->data.ptrvalue = StringSave (cfp->foundstr);
+                    cp = vnp->data.ptrvalue;
+                    AppendOrReplaceString (&cp,
+                                           cfp->foundstr,
+                                           &(cfp->replaceOldAsked),
+                                           &(cfp->doReplaceAll),
+                                           &(cfp->use_semicolon));
+                    vnp->data.ptrvalue = cp;
                   } else {
                     vnp = ValNodeNew (NULL);
                     if (vnp != NULL) {
@@ -1602,7 +1596,7 @@ static void ConvertASourceField (BioSourcePtr biop, ConvertFormPtr cfp)
       if (orp == NULL) return;
       switch (cfp->subtype) {
         case ORGREF_SCI_NAME_FIELD :
-          orp->taxname = SaveOrReplaceStringCopy (cfp, cfp->foundstr, orp->taxname);
+          SetTaxNameAndRemoveTaxRef (orp, SaveOrReplaceStringCopy (cfp, cfp->foundstr, orp->taxname));
           break;
         case ORGREF_COMMON_NAME_FIELD :
           orp->common = SaveOrReplaceStringCopy (cfp, cfp->foundstr, orp->common);
@@ -1729,6 +1723,13 @@ static void FoundStringForConversion (Uint2 entityID, SeqEntryPtr sep, ConvertFo
       break;
     case ORGMOD_SUBSOURCE_TYPE :
       SeqEntryToBioSource (sep, NULL, NULL, 0, &biop);
+      if (biop == NULL && cfp->parsetype == PARSETYPE_LOCALID
+        && IS_Bioseq (sep))
+      {
+        sep = GetBestTopParentForData (cfp->input_entityID,
+                                       sep->data.ptrvalue);
+        SeqEntryToBioSource (sep, NULL, NULL, 0, &biop);
+      }
       ConvertASourceField (biop, cfp);
       break;
     case IMPORT_FEAT_TYPE :
@@ -1803,34 +1804,116 @@ static CharPtr FindStringForConversion (CharPtr string, ConvertFormPtr cfp)
   return NULL;
 }
 
-static void ConvertOneComment (SeqDescrPtr sdp, Pointer userdata)
+static void ConvertBioseqComments (BioseqPtr bsp, Pointer userdata)
 {
   CharPtr           string;
   CommentConvertPtr ccp;
   ConvertFormPtr    cfp;
   CharPtr           result;
-
-  if (sdp == NULL
-    || sdp->choice != Seq_descr_comment
-    || sdp->data.ptrvalue == NULL
+  SeqDescrPtr       sdp;
+  SeqFeatPtr        sfp;
+  SeqEntryPtr       sep, psep;
+  SeqMgrDescContext dcontext;
+  SeqMgrFeatContext fcontext;
+  UserObjectPtr     uop;
+  ObjectIdPtr       oip;
+  UserFieldPtr      ufp;
+
+  if (bsp == NULL
     || (ccp = (CommentConvertPtr) userdata) == NULL
     || (cfp = ccp->cfp) == NULL)
   {
     return;
   }
-  string = StringSave (sdp->data.ptrvalue);
 
-  if (string == NULL || *string == '\0') 
+  sep = SeqMgrGetSeqEntryForData (bsp);
+  if (sep == NULL) return;
+ 
+  psep = GetBestTopParentForDataEx (ccp->entityID, bsp, TRUE);
+  if (psep != NULL) sep = psep;
+ 
+  /* Get descriptor comments */   
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_comment, &dcontext);
+  while (sdp != NULL)
   {
-    MemFree (string);
-    return;
+    if (sdp->data.ptrvalue != NULL)
+    {
+      string = StringSave (sdp->data.ptrvalue);
+
+      if (string == NULL || *string == '\0') 
+      {
+        MemFree (string);
+        return;
+      }
+
+      if ((result = FindStringForConversion (string, cfp)) != NULL)
+      {
+        FoundStringForConversion (ccp->entityID, sep, cfp, result);
+      }
+      MemFree (string);
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_comment, &dcontext);
+  }
+
+  /* get BankIt comments */
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL)
+  {
+    if (sdp->data.ptrvalue != NULL && sdp->extended != 0)
+    {
+      uop = (UserObjectPtr) sdp->data.ptrvalue;
+      oip = uop->type;
+      if (oip != NULL && StringCmp (oip->str, "Submission") == 0)
+      {
+        for (ufp = uop->data; ufp != NULL; ufp = ufp->next)
+        {
+          oip = ufp->label;
+          if (oip != NULL && StringCmp (oip->str, "AdditionalComment") == 0)
+          {
+            string = StringSave (ufp->data.ptrvalue);
+
+            if (string == NULL || *string == '\0') 
+            {
+              MemFree (string);
+              return;
+            }
+
+            if ((result = FindStringForConversion (string, cfp)) != NULL)
+            {
+              FoundStringForConversion (ccp->entityID, sep, cfp, result);
+            }
+            MemFree (string);
+          }
+        }
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
   }
+  
 
-  if ((result = FindStringForConversion (string, cfp)) != NULL)
+  /* get feature comments */
+  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_COMMENT, 0, &fcontext);
+  while (sfp != NULL)
   {
-    FoundStringForConversion (ccp->entityID, ccp->sep, cfp, result);
+    if (sfp->comment != NULL)
+    {
+      string = StringSave (sfp->comment);
+
+      if (string == NULL || *string == '\0') 
+      {
+        MemFree (string);
+        return;
+      }
+
+      if ((result = FindStringForConversion (string, cfp)) != NULL)
+      {
+        FoundStringForConversion (ccp->entityID, sep, cfp, result);
+      }
+      MemFree (string);
+    }
+    sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_COMMENT, 0, &fcontext);
   }
-  MemFree (string);
+
 }
 
 static void ConvertFromComment (
@@ -1847,7 +1930,51 @@ static void ConvertFromComment (
   ccd.entityID = entityID;
   ccd.sep = sep;
   ccd.cfp = cfp;
-  VisitDescriptorsOnSep (sep, &ccd, ConvertOneComment);
+  VisitBioseqsInSep (sep, &ccd, ConvertBioseqComments);
+  ErrSetMessageLevel (level);
+}
+
+static void ConvertOneLocalID (BioseqPtr bsp, Pointer userdata)
+{
+  SeqEntryPtr sep;
+  SeqIdPtr    sip;
+  Char        str [256];
+  CharPtr           result;
+  ConvertFormPtr    cfp;
+
+  if (bsp == NULL || userdata == NULL) return;
+
+  cfp = (ConvertFormPtr) userdata;
+  sep = SeqMgrGetSeqEntryForData (bsp);
+  if (sep == NULL) return;
+
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_LOCAL) {
+      SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str));
+      if (StringNICmp (str, "tmpseq_", 7) != 0 &&
+          StringNICmp (str, "segseq_", 7) != 0 &&
+          StringNICmp (str, "SEG_dna", 7) != 0 &&
+          str [0] != 0)
+      {
+        if ((result = FindStringForConversion (str, cfp)) != NULL)
+        {
+          FoundStringForConversion (cfp->input_entityID, sep, cfp, result);
+        }
+      }
+    }
+  }
+}
+
+static void ConvertFromLocalIDs (
+  SeqEntryPtr sep,
+  ConvertFormPtr cfp
+)
+{
+  ErrSev           level;
+
+  level = ErrSetMessageLevel (SEV_MAX);
+
+  VisitBioseqsInSep (sep, cfp, ConvertOneLocalID);
   ErrSetMessageLevel (level);
 }
 
@@ -1943,11 +2070,18 @@ static void DoOneConvert (Uint2 entityID, SeqEntryPtr sep, ConvertFormPtr cfp, M
   Char          str [64];
 
   if (sep == NULL || cfp == NULL) return;
+  if (cfp->parsetype == PARSETYPE_COMMENT)
+  {
+    ConvertFromComment (entityID, sep, cfp);
+    return;
+  }
+  else if (cfp->parsetype == PARSETYPE_LOCALID)
+  {
+    ConvertFromLocalIDs (sep, cfp);
+    return;
+  }
+
   if (IS_Bioseq_set (sep)) {
-    if (cfp->report == 3)
-    {
-      ConvertFromComment (entityID, sep, cfp);
-    }
     bssp = (BioseqSetPtr) sep->data.ptrvalue;
     if (bssp != NULL && (bssp->_class == 7 ||
                          (IsPopPhyEtcSet (bssp->_class)))) {
@@ -1962,18 +2096,26 @@ static void DoOneConvert (Uint2 entityID, SeqEntryPtr sep, ConvertFormPtr cfp, M
     sprintf (str, "Parsing component %d", (int) cfp->index);
     MonitorStrValue (mon, str);
   }
-  switch (cfp->report) {
-    case 1 :
-      ConvertFromFlatFile (entityID, sep, cfp, GENBANK_FMT);
-      break;
-    case 2 :
-      ConvertFromFlatFile (entityID, sep, cfp, EMBL_FMT);
-      break;
-    case 3 :
-      ConvertFromComment (entityID, sep, cfp);
-      break;
-    default :
-      break;
+  if (cfp->parsetype == PARSETYPE_FILE)
+  {
+    switch (cfp->report) {
+      case 1 :
+        ConvertFromFlatFile (entityID, sep, cfp, GENBANK_FMT);
+        break;
+      case 2 :
+        ConvertFromFlatFile (entityID, sep, cfp, EMBL_FMT);
+        break;
+      default :
+        break;
+    }
+  }
+  else if (cfp->parsetype == PARSETYPE_COMMENT)
+  {
+    ConvertFromComment (entityID, sep, cfp);
+  }
+  else if (cfp->parsetype == PARSETYPE_LOCALID)
+  {
+    ConvertFromLocalIDs (sep, cfp);
   }
 }
 
@@ -2187,6 +2329,7 @@ static void RemoveASourceText (BioSourcePtr biop, ConvertFormPtr cfp)
   OrgNamePtr    onp;
   OrgRefPtr     orp;
   SubSourcePtr  ssp;
+  CharPtr       tmp_str;
 
   if (biop == NULL || cfp == NULL) return;
   switch (cfp->type) {
@@ -2195,7 +2338,9 @@ static void RemoveASourceText (BioSourcePtr biop, ConvertFormPtr cfp)
       if (orp == NULL) return;
       switch (cfp->subtype) {
         case ORGREF_SCI_NAME_FIELD :
-          SearchAndExciseText (&orp->taxname, cfp);
+          tmp_str = StringSave (orp->taxname);
+          SearchAndExciseText (&tmp_str, cfp);
+          SetTaxNameAndRemoveTaxRef (orp, tmp_str);
           break;
         case ORGREF_COMMON_NAME_FIELD :
           SearchAndExciseText (&orp->common, cfp);
@@ -2374,10 +2519,14 @@ static void DoConvertProc (ButtoN b)
 	  cfp->endQuotesFlag = FALSE;
         cfp->includeleft = (Boolean) (GetValue (cfp->leftbehav) == 2);
         cfp->includeright = (Boolean) (GetValue (cfp->rightbehav) == 2);
-        if (cfp->report == 3)
+        if (cfp->parsetype == PARSETYPE_COMMENT)
         {
           mon = MonitorStrNewEx ("Parsing Text From Comments", 20, FALSE);
         }
+        else if (cfp->parsetype == PARSETYPE_LOCALID)
+        {
+          mon = MonitorStrNewEx ("Parsing Text From Local IDs", 20, FALSE);
+        }
         else
         {
           mon = MonitorStrNewEx ("Parsing Text From FlatFile", 20, FALSE);
@@ -2506,7 +2655,7 @@ static void CleanupParseForm (GraphiC g, VoidPtr data)
   StdCleanupFormProc (g, data);
 }
 
-static void BuildParseToAnywhereDialog (IteM i, Boolean use_files)
+static void BuildParseToAnywhereDialog (IteM i, Int4 parsetype)
 
 {
   EnumFieldAssocPtr  ap;
@@ -2534,14 +2683,8 @@ static void BuildParseToAnywhereDialog (IteM i, Boolean use_files)
   cfp = (ConvertFormPtr) MemNew (sizeof (ConvertFormData));
   if (cfp == NULL) return;
 
-  if (use_files)
-  {
-    cfp->isCommentConvert = FALSE;
-  }
-  else
-  {
-    cfp->isCommentConvert = TRUE;
-  }
+  cfp->parsetype = parsetype;
+
   w = FixedWindow (-50, -33, -10, -10, "General Field Conversion", StdCloseWindowProc);
   SetObjectExtra (w, cfp, CleanupParseForm);
   cfp->form = (ForM) w;
@@ -2560,7 +2703,7 @@ static void BuildParseToAnywhereDialog (IteM i, Boolean use_files)
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
 
-  if (use_files)
+  if (cfp->parsetype == PARSETYPE_FILE)
   {
     q = HiddenGroup (h, 4, 0, NULL);
     StaticPrompt (q, "File format to parse", 0, stdLineHeight, programFont, 'l');
@@ -2632,7 +2775,7 @@ static void BuildParseToAnywhereDialog (IteM i, Boolean use_files)
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  cfp->accept = PushButton (c, "Accept", DoConvertProc);
+  cfp->accept = DefaultButton (c, "Accept", DoConvertProc);
   SetObjectExtra (cfp->accept, cfp, NULL);
   Disable (cfp->accept);
   PushButton (c, "Cancel", StdCancelButtonProc);
@@ -2648,13 +2791,18 @@ static void BuildParseToAnywhereDialog (IteM i, Boolean use_files)
 extern void ParseAsnOrFlatfileToAnywhere (IteM i)
 
 {
-  BuildParseToAnywhereDialog (i, TRUE);
+  BuildParseToAnywhereDialog (i, PARSETYPE_FILE);
 }
 
 extern void ParseCommentToAnywhere (IteM i)
 
 {
-  BuildParseToAnywhereDialog (i, FALSE);
+  BuildParseToAnywhereDialog (i, PARSETYPE_COMMENT);
+}
+
+extern void ParseLocalIDToAnywhere (IteM i)
+{
+  BuildParseToAnywhereDialog (i, PARSETYPE_LOCALID);
 }
 
 /*---------------------------------------------------------------------*/
@@ -3635,7 +3783,7 @@ extern void RemoveTextOutsideString (IteM i)
   if (cfp == NULL)
     return;
 
-  cfp->isCommentConvert = FALSE;
+  cfp->parsetype = PARSETYPE_FILE;
 
   /* Create a window for getting user input */
 
@@ -3768,7 +3916,7 @@ extern void RemoveTextOutsideString (IteM i)
   /* Accept and Cancel buttons */
 
   buttonGroup = HiddenGroup (mainGroup, 4, 0, NULL);
-  cfp->accept = PushButton (buttonGroup, "Accept",
+  cfp->accept = DefaultButton (buttonGroup, "Accept",
 			    RemOutTxt_AcceptCallback);
   SetObjectExtra (cfp->accept, cfp, NULL);
   Disable (cfp->accept);
@@ -3814,7 +3962,7 @@ extern void RemoveTextInsideString (IteM i)
   cfp = (ConvertFormPtr) MemNew (sizeof (ConvertFormData));
   if (cfp == NULL) return;
 
-  cfp->isCommentConvert = FALSE;
+  cfp->parsetype = PARSETYPE_FILE;
 
   w = FixedWindow (-50, -33, -10, -10, "General Text Excision", StdCloseWindowProc);
   SetObjectExtra (w, cfp, StdCleanupFormProc);
@@ -3892,7 +4040,7 @@ extern void RemoveTextInsideString (IteM i)
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  cfp->accept = PushButton (c, "Accept", DoRemoveTextProc);
+  cfp->accept = DefaultButton (c, "Accept", DoRemoveTextProc);
   SetObjectExtra (cfp->accept, cfp, NULL);
   Disable (cfp->accept);
   PushButton (c, "Cancel", StdCancelButtonProc);
@@ -4114,7 +4262,7 @@ static ENUM_ALIST(rnax_subtype_alist)
   {"snRNA",        5},
   {"scRNA",        6},
   {"snoRNA",       7},
-  {"Other RNA",  255},
+  {"misc_RNA",   255},
 END_ENUM_ALIST
 
 typedef struct applyformdata {
@@ -4140,6 +4288,8 @@ typedef struct applyformdata {
   EnumFieldAssoc PNTR realalist;
   EnumFieldAssoc PNTR alist;
   GrouP          strand_group;
+  PopuP          reading_frame;
+  ButtoN         leaveDlgUp;
 } ApplyFormData, PNTR ApplyFormPtr;
 
 typedef struct alreadyhas {
@@ -4318,34 +4468,42 @@ static void Apply_AddCDS (Uint2        entityID,
   if (! TextHasNoText (afp->featcomment)) {
     sfp->comment = SaveStringFromTextAndStripNewlines (afp->featcomment);
   }
-  max = 0;
-  frame = 0;
-  for (i = 1; i <= 3; i++) {
-    crp->frame = (Uint1) i;
-    bs = ProteinFromCdRegionEx (sfp, FALSE, FALSE);
-    len = BSLen (bs);
-    BSFree (bs);
-    lens [i] = len;
-    if (len > max) {
-      max = len;
-      frame = (Uint1) i;
-    }
-  }
-  str [0] = '\0';
-  if (IS_Bioseq (nsep)) {
-    bsp = (BioseqPtr) nsep->data.ptrvalue;
-    if (bsp != NULL) {
-      sip = SeqIdFindBest (bsp->id, 0);
-      SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str) - 1);
+
+  if (GetValue (afp->reading_frame) < 1 || GetValue (afp->reading_frame) > 3)
+  {
+    max = 0;
+    frame = 0;
+    for (i = 1; i <= 3; i++) {
+      crp->frame = (Uint1) i;
+      bs = ProteinFromCdRegionEx (sfp, FALSE, FALSE);
+      len = BSLen (bs);
+      BSFree (bs);
+      lens [i] = len;
+      if (len > max) {
+        max = len;
+        frame = (Uint1) i;
+      }
     }
-  }
-  for (i = 1; i <= 3; i++) {
-    if (lens [i] == max && i != frame) {
-      (afp->errcount)++;
-      ValNodeCopyStr (&(afp->ambigList), 0, str);
+    str [0] = '\0';
+    if (IS_Bioseq (nsep)) {
+      bsp = (BioseqPtr) nsep->data.ptrvalue;
+      if (bsp != NULL) {
+        sip = SeqIdFindBest (bsp->id, 0);
+        SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str) - 1);
+      }
     }
+    for (i = 1; i <= 3; i++) {
+      if (lens [i] == max && i != frame) {
+        (afp->errcount)++;
+        ValNodeCopyStr (&(afp->ambigList), 0, str);
+      }
+    }
+    crp->frame = frame;
+  }
+  else
+  {
+    crp->frame = GetValue (afp->reading_frame);
   }
-  crp->frame = frame;
 
   /* Create corresponding protein sequence data for the CDS */
 
@@ -4591,7 +4749,7 @@ static void RealApplyBioFeatToAll (Uint2        entityID,
     if (val > 0) {
       ifp = ImpFeatNew ();
       if (ifp != NULL) {
-        if (val > 1) {
+        if (val > 0) {
           for (i = 1, ap = afp->alist; ap->name != NULL; i++, ap++) {
             if (i == val) {
               ifp->key = StringSave (ap->name);
@@ -4790,6 +4948,11 @@ Int2 ApplyAnnotationToAll (Int2 type, SeqEntryPtr sep,
   return 0;
 }
 
+static void CommonApplyToAllProcBfpInfo (Uint2 entityID,
+                                         Uint4 itemID,
+                                         Uint2 itemtype,
+                                         Int2 type);
+
 static void NowReadyToApplyToAll (ApplyFormPtr afp, DialoG gbquals)
 
 {
@@ -4868,6 +5031,13 @@ static void NowReadyToApplyToAll (ApplyFormPtr afp, DialoG gbquals)
   ObjMgrSetDirtyFlag (afp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, afp->input_entityID, 0, 0);
   Remove (afp->form);
+  if (afp->type == ADD_IMP && GetStatus (afp->leaveDlgUp))
+  {
+    CommonApplyToAllProcBfpInfo (afp->input_entityID,
+                                 afp->input_itemID,
+                                 afp->input_itemtype,
+                                 ADD_IMP);
+  }
 }
 
 typedef struct qualsform {
@@ -5014,31 +5184,27 @@ static void CleanupApplyToAllForm (GraphiC g, VoidPtr data)
   StdCleanupFormProc (g, data);
 }
 
-static void CommonApplyToAllProc (IteM i, Int2 type)
-
+static void CommonApplyToAllProcBfpInfo (Uint2 entityID,
+                                         Uint4 itemID,
+                                         Uint2 itemtype,
+                                         Int2 type)
 {
   ApplyFormPtr       afp;
   EnumFieldAssocPtr  ap;
-  BaseFormPtr        bfp;
   ButtoN             b;
   GrouP              c;
   GrouP              g = NULL;
   GrouP              h;
   GrouP              p;
   GrouP              q;
+  GrouP              r;
   SeqEntryPtr        sep;
   StdEditorProcsPtr  sepp;
   WindoW             w;
   GrouP              x;
   GrouP              z;
 
-#ifdef WIN_MAC
-  bfp = currentFormDataPtr;
-#else
-  bfp = GetObjectExtra (i);
-#endif
-  if (bfp == NULL) return;
-  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  sep = GetTopSeqEntryForEntityID (entityID);
   if (sep == NULL) return;
   afp = (ApplyFormPtr) MemNew (sizeof (ApplyFormData));
   if (afp == NULL) return;
@@ -5053,9 +5219,9 @@ static void CommonApplyToAllProc (IteM i, Int2 type)
     afp->appmessage = sepp->handleMessages;
   }
 
-  afp->input_entityID = bfp->input_entityID;
-  afp->input_itemID = bfp->input_itemID;
-  afp->input_itemtype = bfp->input_itemtype;
+  afp->input_entityID = entityID;
+  afp->input_itemID = itemID;
+  afp->input_itemtype = itemtype;
 
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
@@ -5086,6 +5252,17 @@ static void CommonApplyToAllProc (IteM i, Int2 type)
     SetValue (afp->strand_group, 1);
   }
 
+  if (type == ADD_CDS) {
+    r = HiddenGroup (h, 2, 0, NULL);
+    StaticPrompt (r, "Codon Start", 0, dialogTextHeight, programFont, 'l');
+    afp->reading_frame = PopupList (r, TRUE, NULL);
+    PopupItem (afp->reading_frame, "1");
+    PopupItem (afp->reading_frame, "2");
+    PopupItem (afp->reading_frame, "3");
+    PopupItem (afp->reading_frame, "Best");
+    SetValue (afp->reading_frame, 4);
+  }
+
   if (type == ADD_TITLE) {
     p = HiddenGroup (h, 0, 2, NULL);
     StaticPrompt (p, "Title", 0, 0, programFont, 'c');
@@ -5104,6 +5281,7 @@ static void CommonApplyToAllProc (IteM i, Int2 type)
       afp->geneName = DialogText (p, "", 20, NULL);
     } else if (type == ADD_IMP) {
       ap = import_featdef_alist (FALSE, FALSE, FALSE);
+      SortEnumFieldAssocPtrArray (ap, CompareImpFeatEnumFieldAssoc);
       afp->realalist = ap;
       ap++;
       afp->alist = ap;
@@ -5131,12 +5309,23 @@ static void CommonApplyToAllProc (IteM i, Int2 type)
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoTheApplyToAllProc);
+  b = DefaultButton (c, "Accept", DoTheApplyToAllProc);
   SetObjectExtra (b, afp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
+  if (afp->type == ADD_IMP) {
+    afp->leaveDlgUp = CheckBox (c, "Leave Dialog Up", NULL);
+  } else {
+    afp->leaveDlgUp = NULL;
+  }
 
-  AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, (HANDLE) z,
-                (HANDLE) g, (HANDLE) afp->strand_group, (HANDLE) q, NULL);
+  if (type == ADD_CDS)
+  {
+    AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, (HANDLE) z,
+                  (HANDLE) g, (HANDLE) afp->strand_group, (HANDLE) r, (HANDLE) q, NULL);
+  } else {
+    AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, (HANDLE) z,
+                  (HANDLE) g, (HANDLE) afp->strand_group, (HANDLE) q, NULL);
+  }
   RealizeWindow (w);
   Show (w);
   if (type == ADD_TITLE) {
@@ -5149,28 +5338,50 @@ static void CommonApplyToAllProc (IteM i, Int2 type)
   Update ();
 }
 
+extern void CommonApplyToAllProc (BaseFormPtr bfp, Int2 type)
+{
+  if (bfp == NULL) return;
+  CommonApplyToAllProcBfpInfo (bfp->input_entityID,
+                               bfp->input_itemID,
+                               bfp->input_itemtype, type);
+}
+
+static void CommonApplyToAllProcMenuItem (IteM i, Int2 type)
+{
+  BaseFormPtr bfp;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+
+  CommonApplyToAllProc (bfp, type);
+}
+
 extern void ApplyTitle (IteM i)
 
 {
-  CommonApplyToAllProc (i, ADD_TITLE);
+  CommonApplyToAllProcMenuItem (i, ADD_TITLE);
 }
 
 extern void ApplyCDS (IteM i)
 
 {
-  CommonApplyToAllProc (i, ADD_CDS);
+  CommonApplyToAllProcMenuItem (i, ADD_CDS);
 }
 
 extern void ApplyRRNA (IteM i)
 
 {
-  CommonApplyToAllProc (i, ADD_RRNA);
+  CommonApplyToAllProcMenuItem (i, ADD_RRNA);
 }
 
 extern void ApplyImpFeat (IteM i)
 
 {
-  CommonApplyToAllProc (i, ADD_IMP);
+  CommonApplyToAllProcMenuItem (i, ADD_IMP);
 }
 
 #define SUBMISSION_PAGE   0
@@ -6597,6 +6808,15 @@ static ENUM_ALIST(rna_field_alist)
   {"Product GBQUAL",       3},
 END_ENUM_ALIST
 
+static ENUM_ALIST(rna_removal_field_alist)
+  {" ",                    0},
+  {"Name",                 1},
+  {"Comment",              2},
+  {"Product GBQUAL",       3},
+  {"Anticodon",            4},
+  {"Codons Recognized",    5},
+END_ENUM_ALIST
+
 static ENUM_ALIST(rna_subtype_alist)
   {" ",           99},
   {"unknown",      0},
@@ -6607,7 +6827,7 @@ static ENUM_ALIST(rna_subtype_alist)
   {"snRNA",        5},
   {"scRNA",        6},
   {"snoRNA",       7},
-  {"Other RNA",  255},
+  {"misc_RNA",   255},
 END_ENUM_ALIST
 
 typedef struct rnaformdata {
@@ -6874,6 +7094,7 @@ static Boolean CleanupEachRNAFunc (GatherContextPtr gcp)
   RnaRefPtr       rrp;
   SeqFeatPtr      sfp;
   UIEnum          val;
+  tRNAPtr         trp;
 
   if (gcp == NULL) return TRUE;
   rfp = (RnaFormPtr) gcp->userdata;
@@ -6939,6 +7160,27 @@ static Boolean CleanupEachRNAFunc (GatherContextPtr gcp)
             gbqual = nextqual;
           }
           break;
+        case 4 :
+          if (rrp->ext.choice == 2) {
+            trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+            if (trp != NULL && trp->anticodon != NULL) {
+              trp->anticodon = SeqLocFree (trp->anticodon);
+            }
+          }
+          break;
+        case 5 :
+          if (rrp->ext.choice == 2) {
+            trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+            if (trp != NULL) {
+              trp->codon [0] = 255;
+              trp->codon [1] = 255;
+              trp->codon [2] = 255;
+              trp->codon [3] = 255;
+              trp->codon [4] = 255;
+              trp->codon [5] = 255;
+            }
+          }
+          break;
         default :
           break;
       }
@@ -6968,8 +7210,15 @@ static void DoProcessRnaProc (ButtoN b)
   Update ();
   rfp->fromval = 0;
   rfp->toval = 0;
-  if (GetEnumPopup (rfp->fromfield, rna_field_alist, &val)) {
-    rfp->fromval = (Int2) val;
+
+  if (rfp->type == REMOVE_RNA) {
+    if (GetEnumPopup (rfp->fromfield, rna_removal_field_alist, &val)) {
+      rfp->fromval = (Int2) val;
+    }
+  } else {
+    if (GetEnumPopup (rfp->fromfield, rna_field_alist, &val)) {
+      rfp->fromval = (Int2) val;
+    }
   }
   if (GetEnumPopup (rfp->tofield, rna_field_alist, &val)) {
     rfp->toval = (Int2) val;
@@ -7084,8 +7333,8 @@ static void ProcessRNA (IteM i, Int2 type)
       StaticPrompt (g, "Remove", 0, popupMenuHeight, programFont, 'l');
       rfp->fromfield = PopupList (g, TRUE, NULL);
       SetObjectExtra (rfp->fromfield, rfp, NULL);
-      InitEnumPopup (rfp->fromfield, rna_field_alist, NULL);
-      SetEnumPopup (rfp->fromfield, rna_field_alist, 0);
+      InitEnumPopup (rfp->fromfield, rna_removal_field_alist, NULL);
+      SetEnumPopup (rfp->fromfield, rna_removal_field_alist, 0);
       break;
     case CONVERT_RNA :
       StaticPrompt (g, "From", 0, popupMenuHeight, programFont, 'l');
@@ -7158,7 +7407,7 @@ static void ProcessRNA (IteM i, Int2 type)
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoProcessRnaProc);
+  b = DefaultButton (c, "Accept", DoProcessRnaProc);
   SetObjectExtra (b, rfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -7192,6 +7441,74 @@ extern void EditRNA (IteM i)
   ProcessRNA (i, EDIT_RNA);
 }
 
+typedef struct orgnamechangedata {
+  CharPtr oldname;
+  CharPtr newname;
+} OrgNameChangeData, PNTR OrgNameChangePtr;
+
+static void ReplaceOldOrgNameInTitle (SeqDescrPtr sdp, OrgNameChangePtr oncp)
+{
+  CharPtr oldtitle, newtitle, orgnamestart;
+  Int4    oldorglen;
+
+  if (sdp == NULL || oncp == NULL
+    || oncp->oldname == NULL || oncp->newname == NULL)
+  {
+    return;
+  }
+
+  oldtitle = sdp->data.ptrvalue;
+
+  if (oldtitle == NULL) return;
+
+  orgnamestart = StringRChr (oldtitle, '[');
+  if (orgnamestart == NULL) return;
+  oldorglen = StringLen (oncp->oldname);
+  if (StringNCmp (orgnamestart + 1, oncp->oldname, oldorglen) == 0
+    && orgnamestart [ oldorglen + 1] == ']')
+  {
+    newtitle = MemNew (StringLen (oldtitle) - StringLen (oncp->oldname) + StringLen (oncp->newname) + 2);   
+    if (newtitle == NULL) return;
+    StringNCpy (newtitle, oldtitle, orgnamestart - oldtitle + 1);
+    StringCat (newtitle, oncp->newname);
+    StringCat (newtitle, "]");
+    MemFree (sdp->data.ptrvalue);
+    sdp->data.ptrvalue = newtitle;
+  }
+}
+
+static void FixProteinTitleAfterOrganismNameChange (BioseqPtr bsp, Pointer userdata)
+{
+  OrgNameChangePtr oncp;
+  SeqDescrPtr sdp;
+  BioSourcePtr biop;
+
+  if (bsp == NULL
+    || ! ISA_aa (bsp->mol)
+    || (oncp = (OrgNameChangePtr)userdata) == NULL
+    || oncp->oldname == NULL
+    || oncp->newname == NULL)
+  {
+    return;
+  }
+
+  for (sdp = bsp->descr; sdp != NULL; sdp = sdp->next) {
+    if (sdp->choice == Seq_descr_title)
+    {
+      ReplaceOldOrgNameInTitle (sdp, oncp);
+    }
+    else if (sdp->choice == Seq_descr_source)
+    {
+      biop = sdp->data.ptrvalue;
+      if (biop != NULL && biop->org != NULL 
+        && StringCmp (biop->org->taxname, oncp->oldname) == 0)
+      {
+        SetTaxNameAndRemoveTaxRef (biop->org, StringSave (oncp->newname));
+      }   
+    }   
+  }
+}
+
 typedef struct parseformdata {
   FEATURE_FORM_BLOCK
 
@@ -7203,115 +7520,135 @@ typedef struct parseformdata {
   Boolean        parsedef;
   Char           path [PATH_MAX];
   FILE           *fp;
+  Boolean        replaceOldAsked;
+  Boolean        doReplaceAll;
+  Boolean        use_semicolon;
+  ButtoN         leaveDlgUp;
 } ParseFormData, PNTR ParseFormPtr;
 
-static void DoOneParseItem (Uint2 entityID, SeqEntryPtr sep, ParseFormPtr pfp, BioSourcePtr topbiop, CharPtr useme, SeqEntryPtr nps)
-
+typedef struct localidfinddata {
+  CharPtr str;
+  Int4    str_size;
+} LocalIDFindData, PNTR LocalIDFindPtr;
+  
+static void LookForLocalID (BioseqPtr bsp, Pointer userdata)
 {
-  BioSourcePtr  biop;
-  BioseqPtr     bsp;
-  BioseqSetPtr  bssp;
-  OrgModPtr     mod;
-  SeqEntryPtr   nsep;
-  OrgNamePtr    onp;
-  Uint1         orgmodtype;
-  OrgRefPtr     orp;
-  CharPtr       ptr;
+  LocalIDFindPtr lidfp;
   SeqIdPtr      sip;
-  SubSourcePtr  ssp;
-  Char          str [256];
-  Uint1         subsourcetype;
-  Uint1         subtype;
-  Int2          taxnameval;
-  SeqEntryPtr   tmp;
-  OrgModPtr     tmpmod;
-  SubSourcePtr  tmpssp;
-  ValNodePtr    ttl;
-  Char          txt [128];
-  UIEnum        val;
-  ValNodePtr    vnp;
 
-  if (sep == NULL || pfp == NULL) return;
-  if (IS_Bioseq_set (sep)) {
-    bssp = (BioseqSetPtr) sep->data.ptrvalue;
-    if (bssp != NULL) {
-      /* if nucprot set, look for biosource here */
-      biop = NULL;
-      SeqEntryToBioSource (sep, NULL, NULL, 0, &biop);
-      if (biop != NULL && topbiop != NULL) {
-        topbiop = biop;
-      }
-      for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) {
-        DoOneParseItem (entityID, tmp, pfp, topbiop, useme, sep);
+  if (bsp == NULL || (lidfp = (LocalIDFindPtr) userdata) == NULL) {
+    return;
+  }
+  if (lidfp->str [0] != 0) return;
+
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_LOCAL) {
+      SeqIdWrite (sip, lidfp->str, PRINTID_REPORT, lidfp->str_size);
+      if (StringNICmp (lidfp->str, "tmpseq_", 7) == 0 ||
+          StringNICmp (lidfp->str, "segseq_", 7) == 0 ||
+          StringNICmp (lidfp->str, "SEG_dna", 7) == 0)
+      {
+        /* don't want to use this one */
+        lidfp->str [0] = 0;
+      } else {
+        return;
       }
-      return;
     }
   }
+}
+
+static void FindLocalIDForOrganism (
+  SeqEntryPtr  sep,
+  CharPtr      str,
+  Int4         str_size
+)
+{
+  LocalIDFindData lidfd;
+
+  if (sep == NULL || sep->data.ptrvalue == NULL) return;
+  lidfd.str = str;
+  lidfd.str_size = str_size;
+  VisitBioseqsInSep (sep, (Pointer) &lidfd, LookForLocalID);
+}
+
+static void GetDataForOrganism (
+  SeqEntryPtr  sep,
+  CharPtr      str,
+  Int4         str_size,
+  CharPtr      useme,
+  ParseFormPtr pfp
+)
+{
+  SeqEntryPtr nsep;
+  ValNodePtr    ttl;
+  Char          txt [128];
+  CharPtr       ptr;
+
+  str [0] = 0;
+  if (sep == NULL || pfp == NULL) return;
   nsep = FindNucSeqEntry (sep);
-  if (nsep != NULL && nsep->data.ptrvalue != NULL) {
-    str [0] = '\0';
-    if (useme != NULL) {
-      StringNCpy_0 (str, useme, sizeof (str));
-    } else if (pfp->parsedef) {
-      ttl = SeqEntryGetSeqDescr (nsep, Seq_descr_title, NULL);
-      if (ttl == NULL && nps != NULL) {
-        ttl = SeqEntryGetSeqDescr (nps, Seq_descr_title, NULL);
-      }
-      if (ttl == NULL || ttl->data.ptrvalue == NULL) return;
-      StringNCpy_0 (str, (CharPtr) ttl->data.ptrvalue, sizeof (str));
-      GetTitle (pfp->atleft, txt, sizeof (txt));
-      if (! StringHasNoText (txt)) {
-        ptr = StringISearch (str, txt);
-        if (ptr != NULL) {
-          StringNCpy_0 (str, ptr + StringLen (txt), sizeof (str));
-        }
-      }
-      GetTitle (pfp->atright, txt, sizeof (txt));
-      if (txt [0] != '\0' /* ! StringHasNoText (txt) */) {
-        ptr = StringISearch (str, txt);
-        if (ptr != NULL) {
-          *ptr = '\0';
-        }
-      }
-    } else {
-      bsp = (BioseqPtr) nsep->data.ptrvalue;
-      for (sip = bsp->id; sip != NULL; sip = sip->next) {
-        if (sip->choice == SEQID_LOCAL) {
-          SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str));
-          if (StringNICmp (str, "tmpseq_", 7) == 0 ||
-              StringNICmp (str, "segseq_", 7) == 0 ||
-              StringNICmp (str, "SEG_dna", 7) == 0) return;
-        }
+  if (nsep == NULL || nsep->data.ptrvalue == NULL) return;
+
+  if (useme != NULL) {
+    StringNCpy_0 (str, useme, str_size);
+  } else if (pfp->parsedef) {
+    ttl = SeqEntryGetSeqDescr (nsep, Seq_descr_title, NULL);
+    if (ttl == NULL && sep != nsep) {
+      ttl = SeqEntryGetSeqDescr (sep, Seq_descr_title, NULL);
+    }
+    if (ttl == NULL || ttl->data.ptrvalue == NULL) return;
+    StringNCpy_0 (str, (CharPtr) ttl->data.ptrvalue, str_size);
+    GetTitle (pfp->atleft, txt, sizeof (txt));
+    if (! StringHasNoText (txt)) {
+      ptr = StringISearch (str, txt);
+      if (ptr != NULL) {
+        StringNCpy_0 (str, ptr + StringLen (txt), str_size);
       }
     }
-    if (StringHasNoText (str)) return;
-    biop = NULL;
-    SeqEntryToBioSource (sep, NULL, NULL, 0, &biop);
-    taxnameval = GetValue (pfp->taxname);
-    if (taxnameval == 2) {
-      if (biop == NULL) {
-        biop = BioSourceNew ();
-        if (biop != NULL) {
-          orp = OrgRefNew ();
-          biop->org = orp;
-          vnp = CreateNewDescriptor (sep, Seq_descr_source);
-          if (vnp != NULL) {
-            vnp->data.ptrvalue = (Pointer) biop;
-          }
-        }
+    GetTitle (pfp->atright, txt, sizeof (txt));
+    if (txt [0] != '\0' /* ! StringHasNoText (txt) */) {
+      ptr = StringISearch (str, txt);
+      if (ptr != NULL) {
+        *ptr = '\0';
       }
-      if (biop == NULL) return;
-      orp = biop->org;
-      if (orp == NULL) return;
-      orp->taxname = MemFree (orp->taxname);
-      orp->taxname = StringSave (str);
-      return;
     }
-    if (biop == NULL && topbiop != NULL) {
-      biop = (BioSourcePtr) AsnIoMemCopy ((Pointer) topbiop,
-                                          (AsnReadFunc) BioSourceAsnRead,
-                                          (AsnWriteFunc) BioSourceAsnWrite);
+  } else {
+    FindLocalIDForOrganism (nsep, str, str_size);
+    if (str [0] == 0) {
+      FindLocalIDForOrganism (sep, str, str_size);
+    }
+  }
+  return;
+}
+
+static void ApplyDataToBioSourcePtr (
+  ParseFormPtr pfp,
+  BioSourcePtr biop,
+  BioSourcePtr topbiop,
+  SeqEntryPtr  sep,
+  CharPtr      data
+)
+{
+  Int2          taxnameval;
+  ValNodePtr    vnp;
+  OrgRefPtr     orp;
+  OrgModPtr     mod;
+  Uint1         orgmodtype;
+  Uint1         subsourcetype;
+  UIEnum        val;
+  Uint1         subtype;
+  OrgNamePtr    onp;
+  OrgModPtr     tmpmod;
+  SubSourcePtr  ssp;
+  SubSourcePtr  tmpssp;
+
+  taxnameval = GetValue (pfp->taxname);
+  if (taxnameval == 2) {
+    if (biop == NULL) {
+      biop = BioSourceNew ();
       if (biop != NULL) {
+        orp = OrgRefNew ();
+        biop->org = orp;
         vnp = CreateNewDescriptor (sep, Seq_descr_source);
         if (vnp != NULL) {
           vnp->data.ptrvalue = (Pointer) biop;
@@ -7319,81 +7656,144 @@ static void DoOneParseItem (Uint2 entityID, SeqEntryPtr sep, ParseFormPtr pfp, B
       }
     }
     if (biop == NULL) return;
-    orgmodtype = 0;
-    subsourcetype = 0;
-    if (taxnameval == 3) {
-      orgmodtype = 255;
-    } else if (taxnameval == 4) {
-      subsourcetype = 255;
-    } else if (GetEnumPopup (pfp->orgmod, orgmod_subtype_alist, &val) && val > 0) {
-      orgmodtype = val;
-    } else if (GetEnumPopup (pfp->subsource, subsource_subtype_alist, &val) && val > 0) {
-      subsourcetype = val;
+    orp = biop->org;
+    if (orp == NULL) return;
+    SetTaxNameAndRemoveTaxRef (orp, StringSave (data));
+  }
+  if (biop == NULL && topbiop != NULL) {
+    biop = (BioSourcePtr) AsnIoMemCopy ((Pointer) topbiop,
+                                        (AsnReadFunc) BioSourceAsnRead,
+                                        (AsnWriteFunc) BioSourceAsnWrite);
+    if (biop != NULL) {
+      vnp = CreateNewDescriptor (sep, Seq_descr_source);
+      if (vnp != NULL) {
+        vnp->data.ptrvalue = (Pointer) biop;
+      }
     }
-    if (! StringHasNoText (str)) {
-      if (orgmodtype > 0) {
-        subtype = orgmodtype;
-        orp = biop->org;
-        if (orp == NULL) {
-          orp = OrgRefNew ();
-          biop->org = orp;
+  }
+  if (biop == NULL) return;
+  orgmodtype = 0;
+  subsourcetype = 0;
+  if (taxnameval == 3) {
+    orgmodtype = 255;
+  } else if (taxnameval == 4) {
+    subsourcetype = 255;
+  } else if (GetEnumPopup (pfp->orgmod, orgmod_subtype_alist, &val) && val > 0) {
+    orgmodtype = val;
+  } else if (GetEnumPopup (pfp->subsource, subsource_subtype_alist, &val) && val > 0) {
+    subsourcetype = val;
+  }
+  if (! StringHasNoText (data)) {
+    if (orgmodtype > 0) {
+      subtype = orgmodtype;
+      orp = biop->org;
+      if (orp == NULL) {
+        orp = OrgRefNew ();
+        biop->org = orp;
+      }
+      if (orp != NULL) {
+        onp = orp->orgname;
+        if (onp == NULL) {
+          onp = OrgNameNew ();
+          orp->orgname = onp;
         }
-        if (orp != NULL) {
-          onp = orp->orgname;
-          if (onp == NULL) {
-            onp = OrgNameNew ();
-            orp->orgname = onp;
+        if (onp != NULL) {
+          mod = onp->mod;
+          while (mod != NULL && mod->subtype != subtype) {
+            mod = mod->next;
           }
-          if (onp != NULL) {
-            mod = onp->mod;
-            while (mod != NULL && mod->subtype != subtype) {
-              mod = mod->next;
-            }
-            if (mod == NULL) {
-              mod = OrgModNew ();
-              if (onp->mod == NULL) {
-                onp->mod = mod;
-              } else {
-                tmpmod = onp->mod;
-                while (tmpmod->next != NULL) {
-                  tmpmod = tmpmod->next;
-                }
-                tmpmod->next = mod;
+          if (mod == NULL) {
+            mod = OrgModNew ();
+            if (onp->mod == NULL) {
+              onp->mod = mod;
+            } else {
+              tmpmod = onp->mod;
+              while (tmpmod->next != NULL) {
+                tmpmod = tmpmod->next;
               }
-            }
-            if (mod != NULL) {
-              mod->subtype = subtype;
-              mod->subname = MemFree (mod->subname);
-              mod->subname = StringSave (str);
+              tmpmod->next = mod;
             }
           }
+          if (mod != NULL) {
+            mod->subtype = subtype;
+            AppendOrReplaceString (&(mod->subname), data,
+                                   &(pfp->replaceOldAsked),
+                                   &(pfp->doReplaceAll),
+                                   &(pfp->use_semicolon));
+          }
         }
-      } else if (subsourcetype > 0) {
-        subtype = subsourcetype;
-        ssp = biop->subtype;
-        while (ssp != NULL && ssp->subtype != subtype) {
-          ssp = ssp->next;
-        }
-        if (ssp == NULL) {
-          ssp = SubSourceNew ();
-          if (biop->subtype == NULL) {
-            biop->subtype = ssp;
-          } else {
-            tmpssp = biop->subtype;
-            while (tmpssp->next != NULL) {
-              tmpssp = tmpssp->next;
-            }
-            tmpssp->next = ssp;
+      }
+    } else if (subsourcetype > 0) {
+      subtype = subsourcetype;
+      ssp = biop->subtype;
+      while (ssp != NULL && ssp->subtype != subtype) {
+        ssp = ssp->next;
+      }
+      if (ssp == NULL) {
+        ssp = SubSourceNew ();
+        if (biop->subtype == NULL) {
+          biop->subtype = ssp;
+        } else {
+          tmpssp = biop->subtype;
+          while (tmpssp->next != NULL) {
+            tmpssp = tmpssp->next;
           }
+          tmpssp->next = ssp;
         }
-        if (ssp != NULL) {
-          ssp->subtype = subtype;
-          ssp->name = MemFree (ssp->name);
-          ssp->name = StringSave (str);
+      }
+      if (ssp != NULL) {
+        ssp->subtype = subtype;
+        AppendOrReplaceString (&(ssp->name), data,
+                               &(pfp->replaceOldAsked),
+                               &(pfp->doReplaceAll),
+                               &(pfp->use_semicolon));
+      }
+    }
+  }
+}
+
+static void DoOneParseItem (Uint2 entityID, SeqEntryPtr sep, ParseFormPtr pfp, BioSourcePtr topbiop, CharPtr useme, SeqEntryPtr nps)
+
+{
+  BioSourcePtr  biop;
+  BioseqSetPtr  bssp;
+  Char          str [256];
+  SeqEntryPtr   tmp;
+  OrgNameChangeData oncd;
+
+  if (sep == NULL || pfp == NULL) return;
+  if (IS_Bioseq_set (sep)) {
+    bssp = (BioseqSetPtr) sep->data.ptrvalue;
+    if (bssp != NULL) {
+      /* if nucprot set, look for biosource here */
+      biop = NULL;
+      SeqEntryToBioSource (sep, NULL, NULL, 0, &biop);
+      if (biop != NULL && topbiop != NULL) {
+        topbiop = biop;
+        if (bssp->_class == BioseqseqSet_class_nuc_prot)
+        {
+          GetDataForOrganism ( sep, str, sizeof (str), useme, pfp);
+          if (topbiop->org != NULL && topbiop->org->taxname != NULL)
+          {
+            oncd.oldname = topbiop->org->taxname;
+            oncd.newname = str;
+            VisitBioseqsInSep (sep, &oncd, FixProteinTitleAfterOrganismNameChange);
+          }
+          ApplyDataToBioSourcePtr (pfp, topbiop, NULL, sep, str);
+          return;
         }
       }
+      for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) {
+        DoOneParseItem (entityID, tmp, pfp, topbiop, useme, sep);
+      }
+      return;
     }
   }
+  GetDataForOrganism ( sep, str, sizeof (str), useme, pfp);
+  if (StringHasNoText (str)) return;
+  biop = NULL;
+  SeqEntryToBioSource (sep, NULL, NULL, 0, &biop);
+  ApplyDataToBioSourcePtr (pfp, biop, topbiop, sep, str);
 }
 
 static void DoOneParse (Uint2 entityID, SeqEntryPtr sep, ParseFormPtr pfp, BioSourcePtr topbiop)
@@ -7410,7 +7810,7 @@ static void DoOneParse (Uint2 entityID, SeqEntryPtr sep, ParseFormPtr pfp, BioSo
   if (sep == NULL || pfp == NULL) return;
   if (pfp->fp != NULL) {
     ReadLine (pfp->fp, str, sizeof (str)); /* FileGets on Mac sometimes sees '\r' instead of '\n' */
-    while (Nlm_fileDone) {
+    while (Nlm_fileDone || str [0] != 0) {
       if (! StringHasNoText (str)) {
         ptr = StringChr (str, '\t');
         if (ptr != NULL) {
@@ -7433,6 +7833,7 @@ static void DoOneParse (Uint2 entityID, SeqEntryPtr sep, ParseFormPtr pfp, BioSo
           }
         }
       }
+      str [0] = 0;
       ReadLine (pfp->fp, str, sizeof (str));
     }
     return;
@@ -7475,7 +7876,11 @@ static void DoParseDeflineProc (ButtoN b)
   Update ();
   ObjMgrSetDirtyFlag (pfp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, pfp->input_entityID, 0, 0);
-  Remove (pfp->form);
+  if (GetStatus (pfp->leaveDlgUp)) {
+    Show (pfp->form);
+  } else {
+    Remove (pfp->form);
+  }
 }
 
 static void ParseDeflineMessageProc (ForM f, Int2 mssg)
@@ -7491,11 +7896,10 @@ static void ParseDeflineMessageProc (ForM f, Int2 mssg)
   }
 }
 
-static void ParseDefOrLocalIDToSource (IteM i, Boolean parsedef, CharPtr path)
+static void ParseDefOrLocalIDToSource (BaseFormPtr bfp, Boolean parsedef, CharPtr path)
 
 {
   ButtoN             b;
-  BaseFormPtr        bfp;
   GrouP              c;
   GrouP              g;
   GrouP              h;
@@ -7505,11 +7909,6 @@ static void ParseDefOrLocalIDToSource (IteM i, Boolean parsedef, CharPtr path)
   StdEditorProcsPtr  sepp;
   WindoW             w;
 
-#ifdef WIN_MAC
-  bfp = currentFormDataPtr;
-#else
-  bfp = GetObjectExtra (i);
-#endif
   if (bfp == NULL) return;
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
@@ -7571,9 +7970,10 @@ static void ParseDefOrLocalIDToSource (IteM i, Boolean parsedef, CharPtr path)
   SetEnumPopup (pfp->subsource, subsource_subtype_alist, 0);
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoParseDeflineProc);
+  b = DefaultButton (c, "Accept", DoParseDeflineProc);
   SetObjectExtra (b, pfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
+  pfp->leaveDlgUp = CheckBox (c, "Leave Dialog Up", NULL);
 
   AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, (HANDLE) g, NULL);
   RealizeWindow (w);
@@ -7583,16 +7983,46 @@ static void ParseDefOrLocalIDToSource (IteM i, Boolean parsedef, CharPtr path)
   Update ();
 }
 
+static void ParseDefOrLocalIDToSourceMenuItem (IteM i, Boolean parsedef, CharPtr path)
+{
+  BaseFormPtr bfp;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+
+  if (bfp == NULL) return;
+
+  ParseDefOrLocalIDToSource (bfp, parsedef, path);
+}
+
+static void ParseDefOrLocalIDToSourceToolBtn (ButtoN b, Boolean parsedef, CharPtr path)
+{
+  BaseFormPtr bfp;
+
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+
+  ParseDefOrLocalIDToSource (bfp, parsedef, path);
+}
+
 extern void ParseDefToSource (IteM i)
 
 {
-  ParseDefOrLocalIDToSource (i, TRUE, NULL);
+  ParseDefOrLocalIDToSourceMenuItem (i, TRUE, NULL);
 }
 
 extern void ParseLocalIDToSource (IteM i)
 
 {
-  ParseDefOrLocalIDToSource (i, FALSE, NULL);
+  ParseDefOrLocalIDToSourceMenuItem (i, FALSE, NULL);
+}
+
+extern void ParseLocalIDToSourceToolBtn (ButtoN b)
+{
+  ParseDefOrLocalIDToSourceToolBtn (b, FALSE, NULL);
 }
 
 extern void ParseFileToSource (IteM i)
@@ -7601,31 +8031,84 @@ extern void ParseFileToSource (IteM i)
   Char  path [PATH_MAX];
 
   if (GetInputFileName (path, sizeof (path), "", "TEXT")) {
-    ParseDefOrLocalIDToSource (i, FALSE, path);
+    ParseDefOrLocalIDToSourceMenuItem (i, FALSE, path);
+  }
+}
+
+static void TrimOrgNameCallback (BioSourcePtr biop, Pointer userdata)
+{
+  OrgRefPtr     orp;
+  CharPtr       tmp;
+  CharPtr       word_break;
+
+  if (biop == NULL) return;
+
+  orp = biop->org;
+  if (orp == NULL || StringHasNoText (orp->taxname)) return;
+
+  tmp = StringSave (orp->taxname);
+
+  word_break = StringStr (tmp, " ");
+  if (word_break == NULL) return;
+
+  if (StringNCmp (word_break + 1, "sp.", 3) == 0)
+  {
+    word_break = StringStr (word_break + 1, " ");
+    if (word_break == NULL) return;
   }
+
+  word_break = StringStr (word_break + 1, " ");
+  if (word_break == NULL) return;
+  *word_break = 0;
+  
+  SetTaxNameAndRemoveTaxRef (orp, tmp);
+}
+
+extern void TrimOrganismName (IteM i)
+{
+  BaseFormPtr bfp;
+  SeqEntryPtr sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+
+  VisitBioSourcesInSep (sep, NULL, TrimOrgNameCallback);
+  Update ();
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
 typedef struct addmodinfo {
   Boolean isOrgMod;
   Uint1 subtype;
+  Boolean only_sp;
+  CharPtr abbreviation;
+  Boolean use_abbreviation;
 } AddModInfo, PNTR AddModInfoPtr;
 
 typedef struct addmodlistitem {
   Boolean isOrgMod;
   Uint1 subtype;
   CharPtr name;
+  CharPtr abbreviation;
 } AddModListItem, PNTR AddModListItemPtr;
 
 static AddModListItem mods_list[] = {
-{ TRUE, 24, "Authority" },
-{ FALSE, 3, "Clone" },
-{ FALSE, 6, "Genotype" },
-{ FALSE, 5, "Haplotype" },
-{ TRUE, 17, "Isolate" },
-{ TRUE, 23, "Specimen-voucher" },
-{ TRUE, 2, "Strain" },
-{ TRUE, 22, "Sub-species" },
-{ TRUE, 6, "Variety" }
+{ TRUE, ORGMOD_authority, "Authority", NULL },
+{ FALSE, SUBSRC_clone, "Clone", NULL },
+{ FALSE, SUBSRC_genotype, "Genotype", NULL },
+{ FALSE, SUBSRC_haplotype, "Haplotype", NULL },
+{ TRUE, ORGMOD_isolate, "Isolate", NULL },
+{ TRUE, ORGMOD_specimen_voucher, "Specimen voucher", NULL },
+{ TRUE, ORGMOD_strain, "Strain", NULL },
+{ TRUE, ORGMOD_sub_species, "Sub-species", "subsp." },
+{ TRUE, ORGMOD_variety, "Variety", "var." }
 };
 
 static void AddModToOrgProc (BioSourcePtr biop, Pointer userdata)
@@ -7648,6 +8131,8 @@ static void AddModToOrgProc (BioSourcePtr biop, Pointer userdata)
   orp = biop->org;
   if (orp == NULL) return;
 
+  if (ami->only_sp && StringStr (orp->taxname, " sp.") == NULL) return;
+  
   onp = orp->orgname;
   if (onp == NULL) return;
 
@@ -7694,10 +8179,19 @@ static void AddModToOrgProc (BioSourcePtr biop, Pointer userdata)
     if (influenza) {
       len += 2;
     }
+    if (ami->abbreviation != NULL && ami->use_abbreviation)
+    {
+      len += StringLen (ami->abbreviation) + 1;
+    }
     str = MemNew (len);
     if (str != NULL) {
       StringCpy (str, orp->taxname);
       StringCat (str, " ");
+      if (ami->abbreviation != NULL && ami->use_abbreviation)
+      {
+        StringCat (str, ami->abbreviation);
+        StringCat (str, " ");
+      }
       if (influenza) {
         StringCat (str, "(");
       }
@@ -7705,8 +8199,7 @@ static void AddModToOrgProc (BioSourcePtr biop, Pointer userdata)
       if (influenza) {
         StringCat (str, ")");
       }
-      orp->taxname = MemFree (orp->taxname);
-      orp->taxname = str;
+      SetTaxNameAndRemoveTaxRef (biop->org, str);
     }
   }
 }
@@ -7715,6 +8208,8 @@ typedef struct addmodformptr {
   FEATURE_FORM_BLOCK
 
   PopuP modifier_to_add;
+  ButtoN only_sp;
+  ButtoN use_abbreviation;
 
 } AddModFormData, PNTR AddModFormPtr;
 
@@ -7740,6 +8235,9 @@ static void DoAddModToOrg (ButtoN b)
 
   ami->isOrgMod = mods_list[mod_index].isOrgMod;
   ami->subtype = mods_list[mod_index].subtype;
+  ami->abbreviation = mods_list[mod_index].abbreviation;
+  ami->only_sp = GetStatus (amfp->only_sp);
+  ami->use_abbreviation = GetStatus (amfp->use_abbreviation);
   VisitBioSourcesInSep (sep, ami, AddModToOrgProc);
   Update ();
   ObjMgrSetDirtyFlag (amfp->input_entityID, TRUE);
@@ -7747,6 +8245,29 @@ static void DoAddModToOrg (ButtoN b)
   Remove (amfp->form);
 }
 
+static void ChangeModPopup (PopuP p)
+{
+  AddModFormPtr amfp;
+  Int4          mod_index;
+  
+  amfp = (AddModFormPtr) GetObjectExtra (p);
+  if (amfp == NULL) return;
+
+  mod_index = GetValue (amfp->modifier_to_add);
+  if (mod_index < 1
+    || mod_index > sizeof (mods_list) / sizeof (AddModListItem))
+    return;
+  mod_index = mod_index - 1;
+  if ( mods_list [mod_index].abbreviation != NULL)
+  {
+    Enable (amfp->use_abbreviation);
+  }
+  else
+  {
+    Disable (amfp->use_abbreviation);
+  }
+}
+
 extern void AddModToOrg (IteM i)
 {
   BaseFormPtr  bfp;
@@ -7778,20 +8299,26 @@ extern void AddModToOrg (IteM i)
   g = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (g, 10, 10);
 
-  h = HiddenGroup (g, 0, 1, NULL);
-  amfp->modifier_to_add = PopupList (h, TRUE, NULL);
+  h = HiddenGroup (g, 1, 0, NULL);
+  amfp->modifier_to_add = PopupList (h, TRUE, ChangeModPopup);
   for (index=0; index< sizeof (mods_list) / sizeof (AddModListItem); index++)
   {
     PopupItem (amfp->modifier_to_add, mods_list[index].name);
   }
+  SetObjectExtra (amfp->modifier_to_add, amfp, NULL);
   SetValue (amfp->modifier_to_add, 1);
 
+  amfp->only_sp = CheckBox (g, "Only append to sp. organisms", NULL);
+  amfp->use_abbreviation = CheckBox (g, "Use abbreviation (subsp. or var.)", NULL);
+  SetStatus (amfp->use_abbreviation, TRUE);
+  Disable (amfp->use_abbreviation);
+
   c = HiddenGroup (g, 2, 0, NULL);
-  b = PushButton(c, "Accept", DoAddModToOrg);
+  b = DefaultButton(c, "Accept", DoAddModToOrg);
   SetObjectExtra(b, amfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
-  AlignObjects (ALIGN_CENTER, (HANDLE) h, (HANDLE) c, NULL);
+  AlignObjects (ALIGN_CENTER, (HANDLE) h, (HANDLE) amfp->only_sp, (HANDLE) c, NULL);
   RealizeWindow(w);
   Show(w);
   Update();
@@ -8821,7 +9348,7 @@ extern void EditGenbankElements (Handle i)
   gfp->clearTaxonomy = CheckBox (g, "Clear Lineage", NULL);
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoEditGenbank);
+  b = DefaultButton (c, "Accept", DoEditGenbank);
   SetObjectExtra (b, gfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
diff --git a/sequin/sequin7.c b/sequin/sequin7.c
index 68c4d6be..2bdfabb9 100644
--- a/sequin/sequin7.c
+++ b/sequin/sequin7.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/3/98
 *
-* $Revision: 6.122 $
+* $Revision: 6.133 $
 *
 * File Description: 
 *
@@ -1119,7 +1119,7 @@ static SeqLocPtr AskForInterval (SeqEntryPtr sep, BioseqPtr nuc, BioseqPtr prot)
   d = CreateIntervalEditorDialog (g, NULL, 4, 2, sep, TRUE, FALSE);
   c = HiddenGroup (g, 2, 0, NULL);
   SetGroupSpacing (c, 10, 2);
-  PushButton (c, "Accept", AcceptAskProc);
+  DefaultButton (c, "Accept", AcceptAskProc);
   PushButton (c, "Cancel", CancelAskProc);
   AlignObjects (ALIGN_CENTER, (HANDLE) d, (HANDLE) c, (HANDLE) m, NULL);
   Show (w);
@@ -2624,7 +2624,7 @@ extern ForM CreateGenomeCenterForm (Int2 left, Int2 top, CharPtr title,
   Hide (ffp->controlblock);
 
   c = HiddenGroup (h, 2, 0, NULL);
-  ffp->okBtn = PushButton (c, "Accept", AcceptFa2htgs);
+  ffp->okBtn = DefaultButton (c, "Accept", AcceptFa2htgs);
   SetObjectExtra (ffp->okBtn, ffp, NULL);
   Disable (ffp->okBtn);
   b = PushButton (c, "Cancel", CancelFa2htgs);
@@ -3115,7 +3115,7 @@ extern void PrepareToConvertToCDS (SeqEntryPtr sep, Uint2 entityID,
   ccp->retain = CheckBox (h, "Retain original features", NULL);
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoConvertToCDS);
+  b = DefaultButton (c, "Accept", DoConvertToCDS);
   SetObjectExtra (b, ccp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -3548,6 +3548,7 @@ typedef struct cdsetformdata {
 
   PopuP          protSubType;
   GrouP          protSubGrp;
+  ButtoN         leaveDlgUp;
 } CdsetFormData, PNTR CdsetFormPtr;
 
 typedef struct geneprotfind {
@@ -4101,6 +4102,7 @@ static Boolean CleanupEachCDSFunc (GatherContextPtr gcp)
   ProtRefPtr    prp;
   SeqFeatPtr    sfp;
   CharPtr       str;
+  UIEnum        val;
 
   if (gcp == NULL) return TRUE;
   cfp = (CdsetFormPtr) gcp->userdata;
@@ -4123,6 +4125,15 @@ static Boolean CleanupEachCDSFunc (GatherContextPtr gcp)
     cds = sfp;
   } else return TRUE;
 
+  /* if a protein subtype is selected, delete only that subtype */
+  if (cfp->protSubType != NULL && prot != NULL && prp != NULL) {
+    if (GetEnumPopup (cfp->protSubType, prot_subtype_alist, &val)) {
+      if (val < 5 && (Uint1) val != prp->processed) {
+        return TRUE;
+      }
+    }
+  }
+
   /* If there is a string constraint, only delete if */
   /* the field contains that string.                 */
   
@@ -4359,7 +4370,11 @@ static void DoProcessCDSet (ButtoN b)
   sep = GetTopSeqEntryForEntityID (cfp->input_entityID);
   SeqEntryExplore (sep, NULL, CleanupEmptyFeatCallback);
   ObjMgrSendMsg (OM_MSG_UPDATE, cfp->input_entityID, 0, 0);
-  Remove (cfp->form);
+  if (GetStatus (cfp->leaveDlgUp)) {
+    Show (cfp->form);
+  } else {
+    Remove (cfp->form);
+  }
 }
 
 static Boolean SetCDSExample (GatherContextPtr gcp)
@@ -4591,7 +4606,22 @@ static void CleanupCdsetForm (GraphiC g, VoidPtr data)
   StdCleanupFormProc (g, data);
 }
 
+static void ClearProcessCDSetDlg (ButtoN b)
 
+{
+  CdsetFormPtr  cfp;
+
+  cfp = (CdsetFormPtr) GetObjectExtra (b);
+  if (cfp == NULL) return;
+
+  SetValue ( cfp->fromfield, 0);
+  SetValue ( cfp->tofield, 0);
+  SetValue ( cfp->protSubType, 0);
+  SafeHide (cfp->protSubGrp);
+  SetTitle ( cfp->findthis, "");
+  SetTitle ( cfp->replacewith, "");
+  SafeSetTitle (cfp->example, "");
+}
 
 static void ProcessCDSet (IteM i, Int2 type)
 
@@ -4725,7 +4755,14 @@ static void ProcessCDSet (IteM i, Int2 type)
   cfp->example = StaticPrompt (x, "", 14 * stdCharWidth, 0, programFont, 'l');
 
   y = NULL;
-  cfp->protSubGrp = NULL;
+
+  cfp->protSubGrp = HiddenGroup (h, 2, 0, NULL);
+  StaticPrompt (cfp->protSubGrp, "Protein subtype", 0, dialogTextHeight, programFont, 'l');
+  cfp->protSubType = PopupList (cfp->protSubGrp, TRUE, NULL);
+  InitEnumPopup (cfp->protSubType, prot_subtype_alist, NULL);
+  SetEnumPopup (cfp->protSubType, prot_subtype_alist, (UIEnum) 5);
+  SafeHide (cfp->protSubGrp);
+
   switch (type) {
     case REMOVE_CDSET :
       y = HiddenGroup (h, 2, 0, NULL);
@@ -4746,13 +4783,6 @@ static void ProcessCDSet (IteM i, Int2 type)
       cfp->findthis = DialogText (y, "", 14, NULL);
       break;
     case EDIT_CDSET :
-      cfp->protSubGrp = HiddenGroup (h, 2, 0, NULL);
-      StaticPrompt (cfp->protSubGrp, "Protein subtype", 0, dialogTextHeight, programFont, 'l');
-      cfp->protSubType = PopupList (cfp->protSubGrp, TRUE, NULL);
-      InitEnumPopup (cfp->protSubType, prot_subtype_alist, NULL);
-      SetEnumPopup (cfp->protSubType, prot_subtype_alist, (UIEnum) 5);
-      Hide (cfp->protSubGrp);
-
       y = HiddenGroup (h, 2, 0, NULL);
       StaticPrompt (y, "Find", 0, dialogTextHeight, programFont, 'c');
       cfp->findthis = DialogText (y, "", 14, NULL);
@@ -4766,9 +4796,12 @@ static void ProcessCDSet (IteM i, Int2 type)
   b1 = PushButton (h, "Legend", CDSetLegend);
 
   c = HiddenGroup (w, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoProcessCDSet);
+  b = DefaultButton (c, "Accept", DoProcessCDSet);
   SetObjectExtra (b, cfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
+  b = PushButton (c, "Clear", ClearProcessCDSetDlg);
+  SetObjectExtra (b, cfp, NULL);
+  cfp->leaveDlgUp = CheckBox (c, "Leave Dialog Up", NULL);
 
   AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) b1, (HANDLE) y,
                 (HANDLE) cfp->protSubGrp, NULL);
@@ -5085,7 +5118,7 @@ extern void SwapQualifiers (IteM i)
   /* Create Accept and Cancel buttons */
 
   c = HiddenGroup (w, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoSwapQualifiers);
+  b = DefaultButton (c, "Accept", DoSwapQualifiers);
   SetObjectExtra (b, cfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -5332,15 +5365,15 @@ static void CommonFindReplaceProc (ButtoN b, Boolean replace, Boolean replaceAll
 
   ffp = (FindFormPtr) GetObjectExtra (b);
   if (ffp != NULL) {
-    findme = SaveStringFromText (ffp->findTxt);
+    findme = JustSaveStringFromText (ffp->findTxt);
     ObjMgrDeSelect (0, 0, 0, 0, NULL);
     caseCounts = GetStatus (ffp->caseCounts);
     wholeWord = GetStatus (ffp->wholeWord);
     doSeqIdLocal = GetStatus (ffp->doSeqIdLocal);
     if (replace) {
-      changeme = SaveStringFromText (ffp->replaceTxt);
+      changeme = JustSaveStringFromText (ffp->replaceTxt);
       FindReplaceInEntity (ffp->input_entityID, findme, changeme, caseCounts, wholeWord, replaceAll,
-                           TRUE, UPDATE_ONCE, NULL, NULL, NULL, doSeqIdLocal);
+                           FALSE, UPDATE_ONCE, NULL, NULL, NULL, doSeqIdLocal);
       GetRidOfEmptyFeatsDescStrings (ffp->input_entityID, NULL);
       ObjMgrSetDirtyFlag (ffp->input_entityID, TRUE);
       ObjMgrSendMsg (OM_MSG_UPDATE, ffp->input_entityID, 0, 0);
@@ -5437,7 +5470,6 @@ static void FindByLabelOrPosProc (ButtoN b)
     ObjMgrAlsoSelect (context.entityID, context.itemID, OBJ_SEQFEAT, 0, NULL);
   }
 
-  Remove (ffp->form);
 }
 
 static void ClearFindTextProc (ButtoN b)
@@ -5599,6 +5631,22 @@ extern void FindStringProc (IteM i)
   }
 }
 
+extern void FindStringProcToolBtn (ButtoN b)
+
+{
+  BaseFormPtr  bfp;
+  ForM         w;
+
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+
+  w = CreateFindForm (-90, -66, "Find", bfp->input_entityID,
+                      bfp->input_itemID, bfp->input_itemtype, FIND_ASN);
+  Show (w);
+  Select (w);
+
+}
+
 extern void FindFlatfileProc (IteM i)
 
 {
@@ -6937,27 +6985,22 @@ static void DoEditPartials (ButtoN b)
   pfp->orderjoinpolicy = GetValue (pfp->orderJoinState);
   pfp->findThisStr = JustSaveStringFromText (pfp->findThis);
 
-  val = GetValue (pfp->feature);
-  vnp = NULL;
-  if (val > 0) {
-    vnp = pfp->featlist;
-    while (vnp != NULL && val > 1) {
-      val--;
-      vnp = vnp->next;
-    }
-  }
-
-  if (vnp != NULL)
-    pfp->subtype = vnp->choice;
-  else
-    pfp->subtype = 0;
-
   pfp->omp = ObjMgrGet ();
   pfp->omtp = NULL;
   if (pfp->omp != NULL)
     pfp->omtp = ObjMgrTypeFind (pfp->omp, OBJ_SEQFEAT, NULL, NULL);
 
-  SeqEntryExplore (sep, (Pointer) pfp, PartialCallback);
+  val = 1;
+  for (vnp = pfp->featlist; vnp != NULL; vnp = vnp->next)
+  {
+    if (GetItemStatus ( pfp->feature, val))
+    {
+      pfp->subtype = vnp->choice;
+
+      SeqEntryExplore (sep, (Pointer) pfp, PartialCallback);
+    }
+    val++;
+  }
 
   ArrowCursor ();
   Update ();
@@ -6997,18 +7040,14 @@ extern void EditFeaturePartials (IteM i)
   BaseFormPtr        bfp;
   ButtoN             b;
   GrouP              c;
-  FeatDefPtr         curr;
   GrouP              g;
   GrouP              h;
   ValNodePtr         head;
   GrouP              k;
-  Uint1              key;
-  CharPtr            label = NULL;
   Int2               listHeight;
   PartialFormPtr     pfp;
   SeqEntryPtr        sep;
   StdEditorProcsPtr  sepp;
-  Uint2              subtype;
   ValNodePtr         vnp;
   WindoW             w;
   GrouP              x;
@@ -7049,42 +7088,16 @@ extern void EditFeaturePartials (IteM i)
   } else {
     listHeight = 8;
   }
-  pfp->feature = SingleList (g, 16, listHeight, NULL);
-
-  head = ValNodeNew (NULL);
-  curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
-  while (curr != NULL) {
-    if (key != FEATDEF_BAD) {
-      subtype = curr->featdef_key;
-      if (subtype != FEATDEF_misc_RNA &&
-          subtype != FEATDEF_precursor_RNA &&
-          subtype != FEATDEF_mat_peptide &&
-          subtype != FEATDEF_sig_peptide &&
-          subtype != FEATDEF_transit_peptide &&
-          subtype != FEATDEF_Imp_CDS) {
-        vnp = ValNodeNew (head);
-        if (head == NULL) {
-          head = vnp;
-        }
-        if (vnp != NULL) {
-          vnp->choice = subtype;
-          vnp->data.ptrvalue = StringSave (curr->typelabel);
-        }
+  pfp->feature = MultiList (g, 16, listHeight, NULL);
+
+  head = BuildFeatureValNodeList (TRUE, "[ALL FEATURES]", 0, FALSE, TRUE);
+  if (head != NULL)
+  {
+    for (vnp = head; vnp != NULL; vnp = vnp->next) {
+      if ( vnp->data.ptrvalue != NULL ) {
+        ListItem (pfp->feature, (CharPtr) vnp->data.ptrvalue);
       }
     }
-    curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
-  }
-  if (head != NULL) {
-    head = SortValNode (head, SortVnpByString);
-    vnp = ValNodeNew (NULL);
-    if (vnp != NULL) {
-      vnp->choice = 0;
-      vnp->data.ptrvalue = StringSave ("[ALL FEATURES]");
-    }
-    vnp->next = head;
-    head = vnp;
-    for (vnp = head; vnp != NULL; vnp = vnp->next)
-      ListItem (pfp->feature, (CharPtr) vnp->data.ptrvalue);
   }
   pfp->featlist = head;
 
@@ -7133,7 +7146,7 @@ extern void EditFeaturePartials (IteM i)
   pfp->findThis = DialogText (y, "", 14, NULL);
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoEditPartials);
+  b = DefaultButton (c, "Accept", DoEditPartials);
   SetObjectExtra (b, pfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -8321,7 +8334,7 @@ extern void EditSeqEndsProc (IteM i)
   SafeDisable (esp->trimCountText);
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoEditSeqEndsProc);
+  b = DefaultButton (c, "Accept", DoEditSeqEndsProc);
   SetObjectExtra (b, esp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
diff --git a/sequin/sequin8.c b/sequin/sequin8.c
index bfd7f5ab..e9a5dc1a 100644
--- a/sequin/sequin8.c
+++ b/sequin/sequin8.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   2/3/98
 *
-* $Revision: 6.234 $
+* $Revision: 6.250 $
 *
 * File Description: 
 *
@@ -266,19 +266,15 @@ extern void EditEvidenceFlag (IteM i)
   BaseFormPtr        bfp;
   ButtoN             b;
   GrouP              c;
-  FeatDefPtr         curr;
   EvidenceFormPtr    efp;
   GrouP              g;
   GrouP              h;
   ValNodePtr         head;
   GrouP              k;
-  Uint1              key;
-  CharPtr            label = NULL;
   Int2               listHeight;
   GrouP              q;
   SeqEntryPtr        sep;
   StdEditorProcsPtr  sepp;
-  Uint2              subtype;
   ValNodePtr         vnp;
   WindoW             w;
 
@@ -318,35 +314,8 @@ extern void EditEvidenceFlag (IteM i)
     listHeight = 8;
   }
   efp->objlist = SingleList (g, 16, listHeight, NULL);
-  head = ValNodeNew (NULL);
+  head = BuildFeatureValNodeList (TRUE, "[ALL FEATURES]", 0, FALSE, TRUE);
   if (head != NULL) {
-    head->choice = 0;
-    head->data.ptrvalue = StringSave ("[ALL FEATURES]");
-  }
-  curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
-  while (curr != NULL) {
-    if (key != FEATDEF_BAD) {
-      subtype = curr->featdef_key;
-      if (subtype != FEATDEF_misc_RNA &&
-          subtype != FEATDEF_precursor_RNA &&
-          subtype != FEATDEF_mat_peptide &&
-          subtype != FEATDEF_sig_peptide &&
-          subtype != FEATDEF_transit_peptide &&
-          subtype != FEATDEF_Imp_CDS) {
-        vnp = ValNodeNew (head);
-        /* if (head == NULL) {
-          head = vnp;
-        } */
-        if (vnp != NULL) {
-          vnp->choice = subtype;
-          vnp->data.ptrvalue = StringSave (curr->typelabel);
-        }
-      }
-    }
-    curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
-  }
-  if (head != NULL) {
-    head = SortValNode (head, SortByVnpChoice);
     for (vnp = head; vnp != NULL; vnp = vnp->next) {
       ListItem (efp->objlist, (CharPtr) vnp->data.ptrvalue);
     }
@@ -366,7 +335,7 @@ extern void EditEvidenceFlag (IteM i)
   efp->findthis = DialogText (k, "", 14, NULL);
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoEvidence);
+  b = DefaultButton (c, "Accept", DoEvidence);
   SetObjectExtra (b, efp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -670,21 +639,17 @@ extern void EditExceptionFlag (IteM i)
   BaseFormPtr        bfp;
   ButtoN             b;
   GrouP              c;
-  FeatDefPtr         curr;
   ExceptionFormPtr   efp;
   GrouP              g;
   GrouP              h;
   ValNodePtr         head;
   GrouP              j;
   GrouP              k;
-  Uint1              key;
-  CharPtr            label = NULL;
   Int2               listHeight;
   PrompT             ppt;
   GrouP              q, r;
   SeqEntryPtr        sep;
   StdEditorProcsPtr  sepp;
-  Uint2              subtype;
   ValNodePtr         vnp;
   WindoW             w;
 
@@ -724,35 +689,8 @@ extern void EditExceptionFlag (IteM i)
     listHeight = 8;
   }
   efp->objlist = SingleList (g, 16, listHeight, NULL);
-  head = ValNodeNew (NULL);
+  head = BuildFeatureValNodeList (TRUE, "[ALL FEATURES]", 0, FALSE, TRUE);
   if (head != NULL) {
-    head->choice = 0;
-    head->data.ptrvalue = StringSave ("[ALL FEATURES]");
-  }
-  curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
-  while (curr != NULL) {
-    if (key != FEATDEF_BAD) {
-      subtype = curr->featdef_key;
-      if (subtype != FEATDEF_misc_RNA &&
-          subtype != FEATDEF_precursor_RNA &&
-          subtype != FEATDEF_mat_peptide &&
-          subtype != FEATDEF_sig_peptide &&
-          subtype != FEATDEF_transit_peptide &&
-          subtype != FEATDEF_Imp_CDS) {
-        vnp = ValNodeNew (head);
-        /* if (head == NULL) {
-          head = vnp;
-        } */
-        if (vnp != NULL) {
-          vnp->choice = subtype;
-          vnp->data.ptrvalue = StringSave (curr->typelabel);
-        }
-      }
-    }
-    curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
-  }
-  if (head != NULL) {
-    head = SortValNode (head, SortByVnpChoice);
     for (vnp = head; vnp != NULL; vnp = vnp->next) {
       ListItem (efp->objlist, (CharPtr) vnp->data.ptrvalue);
     }
@@ -786,7 +724,7 @@ extern void EditExceptionFlag (IteM i)
   SetValue (efp->prodgrp, 3);
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoException);
+  b = DefaultButton (c, "Accept", DoException);
   SetObjectExtra (b, efp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -991,6 +929,7 @@ typedef struct recompdata {
   MonitorPtr  mon;
   BioseqPtr   batchbsp;
   Boolean     include_stop;
+  Boolean     no_stop_at_end_of_complete_cds;
 } RecompData, PNTR RecompDataPtr;
 
 static Int2 GeneticCodeFromCrp (CdRegionPtr crp)
@@ -1038,33 +977,205 @@ static Int2 GeneticCodeFromCrp (CdRegionPtr crp)
   return code;
 }
 
-static Boolean RecomputeSuggCallback (GatherContextPtr gcp)
+static void ExtendSeqLocToEnd (SeqLocPtr slp, BioseqPtr bsp, Boolean end5)
+{
+  Uint1          strand;
+  SeqLocPtr      slp_to_change, slp_index;
+  Int4           extent_to_change;
+  Int4           start, stop;
+  SeqIdPtr       sip;
+  
+  if (slp == NULL || bsp == NULL) return;
+
+  slp_to_change = NULL;
+  strand = SeqLocStrand (slp);
+  switch (slp->choice)
+  {
+    case SEQLOC_INT:
+      slp_to_change = slp;
+      break;
+    case SEQLOC_MIX:
+      sip = SeqLocId (slp);
+      if (sip == NULL) return; /* can only process if all on one bioseq */
+      slp_to_change = NULL;
+      if ((strand == Seq_strand_minus && end5)
+        || (strand != Seq_strand_minus && !end5))
+      {
+        extent_to_change = 0;
+        for (slp_index = (SeqLocPtr)slp->data.ptrvalue; slp_index != NULL; slp_index = slp_index->next)
+        {
+          stop = GetOffsetInBioseq (slp_index, bsp, SEQLOC_STOP);
+          if (stop > extent_to_change)
+          {
+            slp_to_change = slp_index;
+            extent_to_change = stop;
+          }
+        }
+      }
+      else
+      {
+        extent_to_change = bsp->length;
+        for (slp_index = (SeqLocPtr)slp->data.ptrvalue; slp_index != NULL; slp_index = slp_index->next)
+        {
+          start = GetOffsetInBioseq (slp_index, bsp, SEQLOC_START);
+          if (start < extent_to_change)
+          {
+            slp_to_change = slp_index;
+            extent_to_change = start;
+          }
+        }
+      }
+      break;
+  }
+
+  if (slp_to_change != NULL)
+  {
+    if ((strand == Seq_strand_minus && end5)
+      || (strand != Seq_strand_minus && !end5))
+    {
+      start = GetOffsetInBioseq (slp_to_change, bsp, SEQLOC_START);
+      stop = bsp->length - 1;
+    }
+    else
+    {
+      start = 0;
+      stop = GetOffsetInBioseq (slp_to_change, bsp, SEQLOC_STOP);
+    }
+    expand_seq_loc (start, stop, strand, slp_to_change);
+  }
+}
+
+static void ExtendOnePartialFeature (SeqFeatPtr sfp, Pointer userdata)
+{
+  BioseqPtr bsp;
+  Boolean   partial3, partial5;
+
+  if (sfp == NULL) return;
+  bsp = BioseqFindFromSeqLoc (sfp->location);
+  if (bsp == NULL) return;
+  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+  if (partial5)
+  {
+    ExtendSeqLocToEnd (sfp->location, bsp, TRUE);
+  }
+  if (partial3)
+  {
+    ExtendSeqLocToEnd (sfp->location, bsp, FALSE);
+  }
+}
+
+extern void ExtendPartialFeatures (IteM i)
+{
+  BaseFormPtr       bfp;
+  SeqEntryPtr       sep;
+  SelStructPtr      sel;
+  SeqFeatPtr        sfp;
+  SeqMgrFeatContext fcontext;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  sel = ObjMgrGetSelected ();
+  WatchCursor ();
+  Update ();
+  if (sel == NULL)
+  {
+    VisitFeaturesInSep (sep, NULL, ExtendOnePartialFeature);
+  }
+  else
+  {
+    while (sel != NULL)
+    {
+      if (sel->entityID == bfp->input_entityID
+        && sel->itemtype == OBJ_SEQFEAT)
+      {
+        sfp = SeqMgrGetDesiredFeature (bfp->input_entityID, NULL, sel->itemID, 0, NULL, &fcontext);
+        if (sfp != NULL)
+        {
+          ExtendOnePartialFeature (sfp, NULL);
+        }
+      }
+      sel = sel->next;
+    }
+  }
+  ArrowCursor ();
+  Update ();
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+static Boolean HasValidStartCodon (SeqFeatPtr cds)
+{
+  ByteStorePtr  bs;
+  CharPtr       prot;
+
+  if (cds == NULL) return FALSE;
+
+  bs = ProteinFromCdRegionEx (cds, TRUE, FALSE);
+
+  if (bs == NULL) return FALSE;
+  prot = BSMerge (bs, NULL);
+  bs = BSFree (bs);
+  if (prot == NULL) return FALSE;
+  if (prot [0] != 'M') return FALSE;
+  return TRUE;
+}
+
+static void FixReadingFrame (
+  CdRegionPtr crp,
+  SeqLocPtr slp,
+  BioseqPtr bsp,
+  Int4 start
+)
+{
+  Int4 offset;
+
+  if (crp == NULL || slp == NULL) return;
+
+  if (SeqLocStrand (slp) == Seq_strand_minus)
+  {
+    offset = bsp->length - start;
+  }
+  else
+  {
+    offset = start;
+  }
+  start = start % 3;
+  start = start + 1;
+  crp->frame = start;
+}
+
+static void RecomputeSuggestedIntervalsForCDS (
+  RecompDataPtr rdp,
+  SeqFeatPtr    sfp,
+  Uint2         entityID
+)
 
 {
   Int2           code;
   CdRegionPtr    crp;
   BioseqPtr      nucbsp;
   BioseqPtr      protbsp;
-  RecompDataPtr  rdp;
-  SeqFeatPtr     sfp;
   SeqIdPtr       sip;
   SeqLocPtr      slp;
   Char           str [256];
   Char           tmp [256];
+  Boolean        partial3, partial5;
+  Int4           start;
 
-  if (gcp == NULL) return TRUE;
-  if (gcp->thistype != OBJ_SEQFEAT) return TRUE;
-  rdp = (RecompDataPtr) gcp->userdata;
-  if (rdp == NULL) return TRUE;
-  sfp = (SeqFeatPtr) gcp->thisitem;
-  if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return TRUE;
+  if (rdp == NULL) return;
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return;
   crp = (CdRegionPtr) sfp->data.value.ptrvalue;
-  if (crp == NULL) return TRUE;
-  /* if (CdsTranslatesProperly (sfp, gcp)) return TRUE; */
+  if (crp == NULL) return;
 
   code = GeneticCodeFromCrp (crp);
 
-  nucbsp = GetBioseqGivenSeqLoc (sfp->location, gcp->entityID);
+  nucbsp = GetBioseqGivenSeqLoc (sfp->location, entityID);
   if (nucbsp != NULL && rdp->batchbsp != NULL && nucbsp != rdp->batchbsp) {
     ClearBatchSuggestNucleotide ();
     rdp->batchbsp = NULL;
@@ -1087,24 +1198,68 @@ static Boolean RecomputeSuggCallback (GatherContextPtr gcp)
         Update ();
       }
       slp = PredictCodingRegion (nucbsp, protbsp, code);
-      if (slp == NULL) return TRUE;
+      if (slp == NULL) return;
+
+      /* correct for partial conditions */
+      CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+
       sfp->location = SeqLocFree (sfp->location);
       sfp->location = slp;
+
+      /* if no valid start codon, cds is 5' partial */
+      if (! HasValidStartCodon (sfp))
+      {
+        partial5 = TRUE;
+      }
+
+      if (partial5 || partial3)
+      {
+        if (partial5)
+        {
+          start = GetOffsetInBioseq (sfp->location, nucbsp, SEQLOC_START);
+          ExtendSeqLocToEnd (sfp->location, nucbsp, TRUE);
+          FixReadingFrame (crp, sfp->location, nucbsp, start);
+        }
+        if (partial3)
+        {
+          ExtendSeqLocToEnd (sfp->location, nucbsp, FALSE);
+        }
+        SetSeqLocPartial (sfp->location, partial5, partial3);
+      }
       sfp->partial = LocationHasNullsBetween (sfp->location);
+      sfp->partial |= partial5 || partial3;
     }
   }
+}
+
+static Boolean RecomputeSuggCallback (GatherContextPtr gcp)
+{
+  RecompDataPtr  rdp;
+  SeqFeatPtr     sfp;
+
+  if (gcp == NULL) return TRUE;
+  if (gcp->thistype != OBJ_SEQFEAT) return TRUE;
+  rdp = (RecompDataPtr) gcp->userdata;
+  if (rdp == NULL) return TRUE;
+  sfp = (SeqFeatPtr) gcp->thisitem;
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return TRUE;
+
+  RecomputeSuggestedIntervalsForCDS (rdp, sfp, gcp->entityID);
   return TRUE;
 }
 
 extern void RecomputeSuggest (IteM i)
 
 {
-  BaseFormPtr  bfp;
-  Int2         code;
-  GatherScope  gs;
-  SeqEntryPtr  nucsep;
-  RecompData   rd;
-  SeqEntryPtr  sep;
+  BaseFormPtr       bfp;
+  Int2              code;
+  GatherScope       gs;
+  SeqEntryPtr       nucsep;
+  RecompData        rd;
+  SeqEntryPtr       sep;
+  SelStructPtr      sel;
+  SeqFeatPtr        sfp;
+  SeqMgrFeatContext fcontext;
 
 #ifdef WIN_MAC
   bfp = currentFormDataPtr;
@@ -1114,11 +1269,13 @@ extern void RecomputeSuggest (IteM i)
   if (bfp == NULL) return;
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
+  sel = ObjMgrGetSelected ();
   WatchCursor ();
   Update ();
   rd.count = 0;
   rd.mon = MonitorStrNewEx ("Correcting Coding Regions", 20, FALSE);
   rd.batchbsp = NULL;
+  rd.no_stop_at_end_of_complete_cds = FALSE;
   nucsep = FindNucSeqEntry (sep);
   if (nucsep != NULL && IS_Bioseq (nucsep)) {
     rd.batchbsp = (BioseqPtr) nucsep->data.ptrvalue;
@@ -1127,15 +1284,34 @@ extern void RecomputeSuggest (IteM i)
     code = SeqEntryToGeneticCode (sep, NULL, NULL, 0);
     SetBatchSuggestNucleotide (rd.batchbsp, code);
   }
-  MemSet ((Pointer) (&gs), 0, sizeof (GatherScope));
-  gs.seglevels = 1;
-  gs.get_feats_location = FALSE;
-  MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean)));
-  gs.ignore[OBJ_BIOSEQ] = FALSE;
-  gs.ignore[OBJ_BIOSEQ_SEG] = FALSE;
-  gs.ignore[OBJ_SEQFEAT] = FALSE;
-  gs.ignore[OBJ_SEQANNOT] = FALSE;
-  GatherEntity (bfp->input_entityID, (Pointer) (&rd), RecomputeSuggCallback, &gs);
+  if (sel == NULL)
+  {
+    MemSet ((Pointer) (&gs), 0, sizeof (GatherScope));
+    gs.seglevels = 1;
+    gs.get_feats_location = FALSE;
+    MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean)));
+    gs.ignore[OBJ_BIOSEQ] = FALSE;
+    gs.ignore[OBJ_BIOSEQ_SEG] = FALSE;
+    gs.ignore[OBJ_SEQFEAT] = FALSE;
+    gs.ignore[OBJ_SEQANNOT] = FALSE;
+    GatherEntity (bfp->input_entityID, (Pointer) (&rd), RecomputeSuggCallback, &gs);
+  }
+  else
+  {
+    while (sel != NULL)
+    {
+      if (sel->entityID == bfp->input_entityID
+        && sel->itemtype == OBJ_SEQFEAT)
+      {
+        sfp = SeqMgrGetDesiredFeature (bfp->input_entityID, NULL, sel->itemID, 0, NULL, &fcontext);
+        if (sfp != NULL && sfp->idx.subtype == FEATDEF_CDS)
+        {
+          RecomputeSuggestedIntervalsForCDS (&rd, sfp, bfp->input_entityID);
+        }
+      }
+      sel = sel->next;
+    }
+  }
   MonitorFree (rd.mon);
   if (rd.batchbsp != NULL) {
     ClearBatchSuggestNucleotide ();
@@ -1146,7 +1322,12 @@ extern void RecomputeSuggest (IteM i)
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
-static Boolean RetranslateOneCDS (SeqFeatPtr sfp, Uint2 entityID, Boolean include_stop)
+static Boolean RetranslateOneCDS (
+  SeqFeatPtr sfp,
+  Uint2 entityID,
+  Boolean include_stop,
+  Boolean no_stop_at_end_of_complete_cds
+)
 
 {
   SeqFeatPtr    bestprot;
@@ -1229,7 +1410,10 @@ static Boolean RetranslateOneCDS (SeqFeatPtr sfp, Uint2 entityID, Boolean includ
     bsp = BioseqFind (sip);
     if (bsp != NULL && ISA_aa (bsp->mol) && bsp->repr == Seq_repr_raw) {
       bestprot = FindBestProtein (entityID, sfp->product);
-      bs = ProteinFromCdRegionEx (sfp, include_stop, FALSE);
+      bs = ProteinFromCdRegionExWithTrailingCodonHandling (sfp,
+                                              include_stop,
+                                              FALSE,
+                                              no_stop_at_end_of_complete_cds );
       if (bs == NULL) return TRUE;
       prot = BSMerge (bs, NULL);
       bs = BSFree (bs);
@@ -1311,10 +1495,14 @@ static Boolean RetranslateCDSCallback (GatherContextPtr gcp)
   rdp = (RecompDataPtr) gcp->userdata;
   if (rdp == NULL) return TRUE;
   sfp = (SeqFeatPtr) gcp->thisitem;
-  return RetranslateOneCDS (sfp, gcp->entityID, rdp->include_stop);
+  return RetranslateOneCDS (sfp, gcp->entityID, rdp->include_stop,
+                            rdp->no_stop_at_end_of_complete_cds);
 }
 
-static void RetranslateCdRegions (IteM i, Boolean include_stop)
+static void RetranslateCdRegions (
+  IteM i,
+  Boolean include_stop,
+  Boolean no_stop_at_end_of_complete_cds )
 
 {
   BaseFormPtr  bfp;
@@ -1335,6 +1523,7 @@ static void RetranslateCdRegions (IteM i, Boolean include_stop)
   rd.count = 0;
   rd.mon = MonitorStrNewEx ("Correcting Coding Regions", 20, FALSE);
   rd.include_stop = include_stop;
+  rd.no_stop_at_end_of_complete_cds = no_stop_at_end_of_complete_cds;
   MemSet ((Pointer) (&gs), 0, sizeof (GatherScope));
   gs.seglevels = 1;
   gs.get_feats_location = FALSE;
@@ -1354,15 +1543,21 @@ static void RetranslateCdRegions (IteM i, Boolean include_stop)
 extern void RetranslateCdRegionsNoStop (IteM i)
 
 {
-  RetranslateCdRegions (i, FALSE);
+  RetranslateCdRegions (i, FALSE, FALSE);
 }
 
 extern void RetranslateCdRegionsDoStop (IteM i)
 
 {
-  RetranslateCdRegions (i, TRUE);
+  RetranslateCdRegions (i, TRUE, FALSE);
 }
 
+extern void RetranslateCdRegionsNoStopExceptEndCompleteCDS (IteM i)
+{
+  RetranslateCdRegions (i, TRUE, TRUE);
+}
+
+
 static void DoReprocessPeptides (SeqFeatPtr sfp, Pointer userdata)
 
 {
@@ -1677,7 +1872,7 @@ static Boolean LIBCALLBACK ApplyCodeBreak_FeatureCallback (SeqFeatPtr sfp,
 
       /* Retranslate the CDS */
 
-      RetranslateOneCDS (sfp, fcontext->entityID, TRUE);
+      RetranslateOneCDS (sfp, fcontext->entityID, TRUE, FALSE);
 
     }
     basePtr += 3;
@@ -1999,7 +2194,7 @@ extern void AddGlobalCodeBreak (IteM i)
   /* Add Accept and Cancel buttons */
 
   buttGroup = HiddenGroup (breakWin, 2, 0, NULL);
-  cbfp->acceptButton = PushButton (buttGroup, "Accept",
+  cbfp->acceptButton = DefaultButton (buttGroup, "Accept",
 				   DoAddCodeBreak_Callback);
   SetObjectExtra (cbfp->acceptButton, cbfp, NULL);
   SafeDisable (cbfp->acceptButton);
@@ -2864,6 +3059,7 @@ static void DoRemoveAsnObject (ButtoN b)
   ValNodePtr     tmp;
   Int2           val;
   ValNodePtr     vnp;
+  Boolean        removed_some_features;
 
   rfp = GetObjectExtra (b);
   if (rfp == NULL) return;
@@ -2877,65 +3073,72 @@ static void DoRemoveAsnObject (ButtoN b)
   } else {
     rfp->itemtype = OBJ_SEQDESC;
   }
-  vnp = NULL;
-  val = GetValue (rfp->objlist);
-  if (val > 0) {
-    vnp = rfp->head;
-    while (vnp != NULL && val > 1) {
-      val--;
-      vnp = vnp->next;
-    }
+
+  rfp->omp = ObjMgrGet ();
+  rfp->omtp = NULL;
+  if (rfp->omp != NULL) {
+    rfp->omtp = ObjMgrTypeFind (rfp->omp, rfp->itemtype, NULL, NULL);
   }
-  if (vnp != NULL) {
-    rfp->omp = ObjMgrGet ();
-    rfp->omtp = NULL;
-    if (rfp->omp != NULL) {
-      rfp->omtp = ObjMgrTypeFind (rfp->omp, rfp->itemtype, NULL, NULL);
-    }
-    rfp->subtype = vnp->choice;
-    if (rfp->itemtype != 0 && rfp->subtype != 0 && rfp->omtp != NULL) {
-      if (rfp->is_feature) {
-        SeqEntryExplore (sep, (Pointer) rfp, RemoveFeatureCallback);
-        if (rfp->bsplist != NULL) {
-          ans = Message (MSG_YN, "Remove protein products?");
-          if (ans == ANS_YES) {
-            for (tmp = rfp->bsplist; tmp != NULL; tmp = tmp->next) {
-              bsp = (BioseqPtr) tmp->data.ptrvalue;
-              itemID = GetItemIDGivenPointer (rfp->input_entityID, OBJ_BIOSEQ, (Pointer) bsp);
-              if (itemID > 0) {
-                MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl));
-                ompc.do_not_reload_from_cache = TRUE;
-                ompc.input_entityID = rfp->input_entityID;
-                ompc.input_itemID = itemID;
-                ompc.input_itemtype = OBJ_BIOSEQ;
-                if (! DetachDataForProc (&ompc, FALSE)) {
-                  Message (MSG_POSTERR, "DetachDataForProc failed");
-                }
-              }
+
+ if (rfp->itemtype == 0 || rfp->omtp == NULL) return;
+
+  removed_some_features = FALSE;
+
+  val = 1;
+  for (vnp = rfp->head; vnp != NULL; vnp = vnp->next)
+  {
+    if (GetItemStatus (rfp->objlist, val))
+    {
+      rfp->subtype = vnp->choice;
+      if (rfp->subtype != 0) {
+        if (rfp->is_feature) {
+          SeqEntryExplore (sep, (Pointer) rfp, RemoveFeatureCallback);
+          removed_some_features = TRUE;
+        } else {
+          SeqEntryExplore (sep, (Pointer) rfp, RemoveDescriptorCallback);
+        }
+      }
+    }
+    val ++;
+  }
+
+  if (removed_some_features) {
+    if (rfp->bsplist != NULL) {
+      ans = Message (MSG_YN, "Remove protein products?");
+      if (ans == ANS_YES) {
+        for (tmp = rfp->bsplist; tmp != NULL; tmp = tmp->next) {
+          bsp = (BioseqPtr) tmp->data.ptrvalue;
+          itemID = GetItemIDGivenPointer (rfp->input_entityID, OBJ_BIOSEQ, (Pointer) bsp);
+          if (itemID > 0) {
+            MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl));
+            ompc.do_not_reload_from_cache = TRUE;
+            ompc.input_entityID = rfp->input_entityID;
+            ompc.input_itemID = itemID;
+            ompc.input_itemtype = OBJ_BIOSEQ;
+            if (! DetachDataForProc (&ompc, FALSE)) {
+              Message (MSG_POSTERR, "DetachDataForProc failed");
             }
           }
         }
-        if (rfp->bssplist != NULL) {
-          ans = Message (MSG_YN, "Remove cDNA nuc-prot products?");
-          if (ans == ANS_YES) {
-            for (tmp = rfp->bssplist; tmp != NULL; tmp = tmp->next) {
-              bssp = (BioseqSetPtr) tmp->data.ptrvalue;
-              itemID = GetItemIDGivenPointer (rfp->input_entityID, OBJ_BIOSEQSET, (Pointer) bssp);
-              if (itemID > 0) {
-                MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl));
-                ompc.do_not_reload_from_cache = TRUE;
-                ompc.input_entityID = rfp->input_entityID;
-                ompc.input_itemID = itemID;
-                ompc.input_itemtype = OBJ_BIOSEQSET;
-                if (! DetachDataForProc (&ompc, FALSE)) {
-                  Message (MSG_POSTERR, "DetachDataForProc failed");
-                }
-              }
+      }
+    }
+    if (rfp->bssplist != NULL) {
+      ans = Message (MSG_YN, "Remove cDNA nuc-prot products?");
+      if (ans == ANS_YES) {
+        for (tmp = rfp->bssplist; tmp != NULL; tmp = tmp->next) {
+          bssp = (BioseqSetPtr) tmp->data.ptrvalue;
+          itemID = GetItemIDGivenPointer (rfp->input_entityID, OBJ_BIOSEQSET, (Pointer) bssp);
+          if (itemID > 0) {
+            MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl));
+            ompc.do_not_reload_from_cache = TRUE;
+            ompc.input_entityID = rfp->input_entityID;
+            ompc.input_itemID = itemID;
+            ompc.input_itemtype = OBJ_BIOSEQSET;
+            if (! DetachDataForProc (&ompc, FALSE)) {
+              Message (MSG_POSTERR, "DetachDataForProc failed");
             }
           }
         }
-      } else {
-        SeqEntryExplore (sep, (Pointer) rfp, RemoveDescriptorCallback);
       }
     }
   }
@@ -2947,6 +3150,64 @@ static void DoRemoveAsnObject (ButtoN b)
   Remove (rfp->form);
 }
 
+static void RemoveDefLinesCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent)
+
+{
+  BioseqPtr      bsp;
+  BioseqSetPtr   bssp;
+  ValNodePtr     nextsdp;
+  Pointer PNTR   prevsdp;
+  ValNodePtr     sdp;
+
+  if (sep == NULL || sep->data.ptrvalue == NULL) return;
+  if (IS_Bioseq (sep)) {
+    bsp = (BioseqPtr) sep->data.ptrvalue;
+    sdp = bsp->descr;
+    prevsdp = (Pointer PNTR) &(bsp->descr);
+  } else if (IS_Bioseq_set (sep)) {
+    bssp = (BioseqSetPtr) sep->data.ptrvalue;
+    sdp = bssp->descr;
+    prevsdp = (Pointer PNTR) &(bssp->descr);
+  } else return;
+
+  while (sdp != NULL) {
+    nextsdp = sdp->next;
+    if (sdp->choice == Seq_descr_title)
+    {
+      *(prevsdp) = sdp->next;
+      sdp->next = NULL;
+      SeqDescFree (sdp);
+    } else {
+      prevsdp = (Pointer PNTR) &(sdp->next);
+    }
+    sdp = nextsdp;
+  }
+}
+
+extern void RemoveDefLinesToolBtn (ButtoN b)
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+
+  bfp = (BaseFormPtr) GetObjectExtra (b);
+  if (bfp == NULL) return;
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  
+  WatchCursor ();
+  Update ();
+
+  SeqEntryExplore (sep, NULL, RemoveDefLinesCallback);
+
+  ArrowCursor ();
+  Update ();
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+  ObjMgrDeSelect (0, 0, 0, 0, NULL);
+  CommonApplyToAllProc (bfp, ADD_TITLE);
+}
+
 int LIBCALLBACK SortByVnpChoice (VoidPtr ptr1, VoidPtr ptr2)
 
 {
@@ -3016,65 +3277,6 @@ static CharPtr descNames [] = {
 #endif
 */
 
-CharPtr MostUsedFeatureList[] = { "All", "CDS", "Gene", "mRNA", "rRNA", "RNA" };
-
-static Boolean isMostUsedFeature (CharPtr featname)
-{
-  Int2 i;
-
-  if (featname == NULL) return FALSE;
-
-  for (i=0; i < sizeof (MostUsedFeatureList) / sizeof (CharPtr); i++)
-  {
-    if (StringCmp (featname, MostUsedFeatureList[i]) == 0)
-      return TRUE;
-  }
-  return FALSE;
-}
-
-static int LIBCALLBACK SortMostUsedFeaturesFirst (VoidPtr ptr1, VoidPtr ptr2)
-
-{
-  ValNodePtr   vnp1;
-  ValNodePtr   vnp2;
-  CharPtr      str1;
-  CharPtr      str2;
-  Boolean      str1_is_most_used;
-  Boolean      str2_is_most_used;
-
-  /* Check parameters */
-
-  if ((NULL == ptr1) || (NULL == ptr2))
-    return 0;
-
-  vnp1 = *((ValNodePtr PNTR) ptr1);
-  vnp2 = *((ValNodePtr PNTR) ptr2);
-  if ((NULL == vnp1) || (NULL == vnp2))
-    return 0;
-
-  str1 = (CharPtr) vnp1->data.ptrvalue;
-  str2 = (CharPtr) vnp2->data.ptrvalue;
-  if ((NULL == str1) || (NULL == str2))
-    return 0;
-
-  str1_is_most_used = isMostUsedFeature (str1);
-  str2_is_most_used = isMostUsedFeature (str2);
-
-  if ((str1_is_most_used && str2_is_most_used)
-    || (!str1_is_most_used && !str2_is_most_used))
-  {
-    return SortVnpByString (ptr1, ptr2);
-  }
-  else if (str1_is_most_used)
-  {
-    return -1;
-  }
-  else
-  {
-    return 1;
-  }
-}
-
 CharPtr MostUsedDescriptorList[] = { "Title" };
 
 static Boolean isMostUsedDescriptor (CharPtr descname)
@@ -3140,21 +3342,16 @@ static void RemoveAsnObject (IteM i, Boolean feature)
   BaseFormPtr        bfp;
   ButtoN             b;
   GrouP              c;
-  FeatDefPtr         curr;
   GrouP              g;
   GrouP              h;
   ValNodePtr         head;
   Int2               j;
   GrouP              k;
-  Uint1              key;
-  CharPtr            label = NULL;
   Int2               listHeight;
   GrouP              m;
   RemoveFormPtr      rfp;
   SeqEntryPtr        sep;
   StdEditorProcsPtr  sepp;
-  Char               str [256];
-  Uint2              subtype;
   CharPtr            title;
   ValNodePtr         vnp;
   WindoW             w;
@@ -3204,51 +3401,10 @@ static void RemoveAsnObject (IteM i, Boolean feature)
   } else {
     listHeight = 8;
   }
-  rfp->objlist = SingleList (g, 16, listHeight, NULL);
+  rfp->objlist = MultiList (g, 16, listHeight, NULL);
   head = NULL;
   if (feature) {
-    curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
-    while (curr != NULL) {
-      if (key != FEATDEF_BAD) {
-        subtype = curr->featdef_key;
-        if (subtype == FEATDEF_ORG || 
-		subtype == FEATDEF_mutation ||
-		subtype == FEATDEF_site_ref ||
-		subtype == FEATDEF_gap ||
-		subtype == FEATDEF_NON_STD_RESIDUE ||
-		subtype == FEATDEF_NUM)
-        {
-          /* indexers requested that these features not appear in the list */
-        }
-        else
-        {
-          vnp = ValNodeNew (head);
-	  if (head == NULL)
-	    head = vnp;
-          if (vnp != NULL) {
-            vnp->choice = subtype;
-            if (subtype != FEATDEF_misc_RNA &&
-                subtype != FEATDEF_precursor_RNA &&
-                subtype != FEATDEF_mat_peptide &&
-                subtype != FEATDEF_sig_peptide &&
-                subtype != FEATDEF_transit_peptide &&
-                subtype != FEATDEF_Imp_CDS) {
-              vnp->data.ptrvalue = StringSave (curr->typelabel);
-            } else {
-              StringNCpy_0 (str, curr->typelabel, sizeof (str) - 10);
-              StringCat (str, "_imp");
-              vnp->data.ptrvalue = StringSave (str);
-            }
-          }
-        }
-      }
-      curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
-    }
-    vnp = ValNodeNew (head);
-    if (vnp != NULL) {
-      vnp->choice = ALL_FEATURES;
-      vnp->data.ptrvalue = StringSave ("All");
-    }
+    head = BuildFeatureValNodeList (TRUE, "All", ALL_FEATURES, TRUE, FALSE);
   } else {
     for (j = 1; descNames [j] != NULL; j++) {
       if (StringHasNoText (descNames [j])) continue;
@@ -3261,19 +3417,9 @@ static void RemoveAsnObject (IteM i, Boolean feature)
         vnp->data.ptrvalue = StringSave (descNames [j]);
       }
     }
+    head = SortValNode (head, SortMostUsedDescriptorsFirst);
   }
   if (head != NULL) {
-    /*
-    head = SortValNode (head, SortByVnpChoice);
-    */
-    if (feature)
-    {
-      head = SortValNode (head, SortMostUsedFeaturesFirst);
-    }
-    else
-    {
-      head = SortValNode (head, SortMostUsedDescriptorsFirst);
-    }
 
     for (vnp = head; vnp != NULL; vnp = vnp->next) {
       ListItem (rfp->objlist, (CharPtr) vnp->data.ptrvalue);
@@ -3297,7 +3443,7 @@ static void RemoveAsnObject (IteM i, Boolean feature)
   }
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoRemoveAsnObject);
+  b = DefaultButton (c, "Accept", DoRemoveAsnObject);
   SetObjectExtra (b, rfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -3338,6 +3484,172 @@ typedef struct selectformdata {
   Char           findStr [128];
 } SelectFormData, PNTR SelectFormPtr;
 
+static Boolean StringListMatchesString (ValNodePtr string_list, CharPtr findStr)
+{
+  ValNodePtr vnp;
+
+  if (StringHasNoText (findStr)) return TRUE;
+  for (vnp = string_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (StringStr (vnp->data.ptrvalue, findStr) != NULL) return TRUE;
+  }
+  return FALSE;
+}
+
+static Boolean PubJournalMatchesString (CitJourPtr cjp, CharPtr findStr)
+{
+  if (cjp == NULL || cjp->title == NULL) return FALSE;
+  if (StringListMatchesString (cjp->title, findStr)) return TRUE;
+  return FALSE;
+}
+
+static Boolean PubBookMatchesString (CitBookPtr cbp, CharPtr findStr)
+{
+  if (cbp == NULL || cbp->title == NULL) return FALSE;
+  if (StringListMatchesString (cbp->title, findStr)) return TRUE;
+  return FALSE;
+}
+
+static Boolean PubArticleMatchesString (CitArtPtr cap, CharPtr findStr)
+{
+  if (cap == NULL || cap->fromptr == NULL) return FALSE;
+  switch (cap->from)
+  {
+    case 1:
+      if (PubJournalMatchesString (cap->fromptr, findStr)) return TRUE;
+    case 2:
+    case 3:
+      if (PubBookMatchesString (cap->fromptr, findStr)) return TRUE;
+  }
+  return FALSE;
+}
+
+static Boolean PubdescMatchesString ( ValNodePtr vnp, CharPtr findStr)
+{
+  CitGenPtr       cgp;
+  CitPatPtr       cpp;
+  MedlineEntryPtr mep;
+  ValNodePtr      pub;
+
+ 
+  if (vnp == NULL) return FALSE;
+  switch (vnp->choice)
+  {
+    case PUB_Gen :
+      cgp = (CitGenPtr) vnp->data.ptrvalue;
+      if (cgp == NULL) return FALSE;
+      if (StringStr (cgp->title, findStr) != NULL) return TRUE;
+      if (StringListMatchesString (cgp->journal, findStr)) return TRUE;
+      break;
+    case PUB_Medline :
+      mep = (MedlineEntryPtr) vnp->data.ptrvalue;
+      if (mep == NULL) return FALSE;
+      if ( PubArticleMatchesString (mep->cit, findStr)) return TRUE;
+      break;
+    case PUB_Article :
+      if ( PubArticleMatchesString (vnp->data.ptrvalue, findStr)) return TRUE;
+      break;
+    case PUB_Journal :
+      if (PubJournalMatchesString (vnp->data.ptrvalue, findStr)) return TRUE;
+      break;
+    case PUB_Patent :
+      cpp = (CitPatPtr) vnp->data.ptrvalue;
+      if (cpp == NULL || cpp->title == NULL) return FALSE;
+      if (StringStr (cpp->title, findStr) != NULL) return TRUE;
+      break;
+    case PUB_Book :
+    case PUB_Man :
+      if (PubBookMatchesString (vnp->data.ptrvalue, findStr)) return TRUE;
+      break;
+    case PUB_Equiv :
+      for (pub = vnp->data.ptrvalue; pub != NULL; pub = pub->next)
+      {
+        if (PubdescMatchesString (pub, findStr)) return TRUE;
+      }
+      break;
+  }
+  return FALSE;
+}
+    
+static Boolean FeatureMatchesString (SeqFeatPtr sfp, CharPtr findStr)
+{
+  SeqMgrFeatContext context;
+  SeqFeatPtr        new_sfp;
+  PubdescPtr        pdp;
+  ValNodePtr        vnp;
+
+  if (sfp == NULL) return FALSE;
+  if (StringHasNoText (findStr)) return TRUE;
+  if (sfp->data.choice == SEQFEAT_PUB)
+  {
+    if( (pdp = (PubdescPtr) sfp->data.value.ptrvalue) == NULL) return FALSE;
+    for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next)
+    {
+      if (PubdescMatchesString (sfp->data.value.ptrvalue, findStr))
+      {
+        return TRUE;
+      }
+    }
+    return FALSE;
+  }
+
+  new_sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, 0, 0, sfp,
+                                     &context);
+  if (new_sfp != sfp || StringStr (context.label, findStr) == NULL)
+    return FALSE;
+
+  return TRUE;
+}
+  
+static Boolean DescriptorMatchesString ( SeqDescPtr sdp, CharPtr findStr)
+{
+  CharPtr      cp;
+  OrgRefPtr    orp;
+  BioSourcePtr biop;
+  PubdescPtr   pdp;
+  ValNodePtr   vnp;
+
+  if (sdp == NULL) return FALSE;
+  if (StringHasNoText (findStr)) return TRUE;
+
+  switch (sdp->choice)
+  {
+    case Seq_descr_name:
+    case Seq_descr_title:
+    case Seq_descr_comment:
+    case Seq_descr_region:
+      cp = sdp->data.ptrvalue;
+      if (StringStr (cp, findStr) == NULL) return FALSE;
+      break;
+    case Seq_descr_org:
+      orp = sdp->data.ptrvalue;
+      if (orp == NULL || orp->taxname == NULL) return FALSE;
+      if (StringStr (orp->taxname, findStr) == NULL) return FALSE;
+      break;
+    case Seq_descr_source:
+      biop = sdp->data.ptrvalue;
+      if (biop == NULL || biop->org == NULL || biop->org->taxname == NULL) return FALSE;
+      if (StringStr (biop->org->taxname, findStr) == NULL) return FALSE;
+      break;
+    case Seq_descr_pub:
+      if( (pdp = (PubdescPtr) sdp->data.ptrvalue) == NULL) return FALSE;
+      for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next)
+      {
+        if (PubdescMatchesString (vnp, findStr))
+        {
+          return TRUE;
+        }
+      }
+      return FALSE;
+      break;
+    default:
+      return FALSE;
+      break;
+  }
+    
+  return TRUE;
+}
+
 static Boolean SelectObjCallback (GatherContextPtr gcp)
 
 {
@@ -3353,6 +3665,17 @@ static Boolean SelectObjCallback (GatherContextPtr gcp)
   if (omtp == NULL) return TRUE;
   subtype = (*(omtp->subtypefunc)) ((Pointer) gcp->thisitem);
   if (subtype != selfp->subtype) return TRUE;
+
+  if (gcp->thistype == OBJ_SEQFEAT
+    && ! FeatureMatchesString (gcp->thisitem, selfp->findStr))
+  {
+    return TRUE;
+  }
+  if (gcp->thistype == OBJ_SEQDESC
+    && ! DescriptorMatchesString (gcp->thisitem, selfp->findStr))
+  {
+    return TRUE;
+  }
   ObjMgrAlsoSelect (gcp->entityID, gcp->itemID, gcp->thistype, 0, NULL);
   return TRUE;
 }
@@ -3397,6 +3720,10 @@ static void DoSelectAsnObject (ButtoN b)
       vnp = vnp->next;
     }
   }
+  if (selfp->type == SLCT_FEAT || selfp->type == SLCT_DESC)
+  {
+    GetTitle (selfp->findthis, selfp->findStr, sizeof (selfp->findStr) - 1);
+  }
   if (selfp->type == SLCT_BIOSEQ || vnp != NULL) {
     selfp->omp = ObjMgrGet ();
     selfp->omtp = NULL;
@@ -3457,18 +3784,15 @@ static void SelectAsnObject (IteM i, Int2 type)
   BaseFormPtr        bfp;
   ButtoN             b;
   GrouP              c;
-  FeatDefPtr         curr;
   GrouP              g;
   GrouP              h;
+  GrouP              k;
   ValNodePtr         head;
   Int2               j;
-  Uint1              key;
-  CharPtr            label = NULL;
   Int2               listHeight;
   SelectFormPtr      selfp;
   SeqEntryPtr        sep;
   StdEditorProcsPtr  sepp;
-  Uint2              subtype;
   CharPtr            title;
   ValNodePtr         vnp;
   WindoW             w;
@@ -3538,23 +3862,10 @@ static void SelectAsnObject (IteM i, Int2 type)
   selfp->objlist = SingleList (g, 16, listHeight, NULL);
   head = NULL;
   if (type == SLCT_FEAT) {
-    curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
-    while (curr != NULL) {
-      if (key != FEATDEF_BAD) {
-        subtype = curr->featdef_key;
-        vnp = ValNodeNew (head);
-        if (head == NULL) {
-          head = vnp;
-        }
-        if (vnp != NULL) {
-          vnp->choice = subtype;
-          vnp->data.ptrvalue = StringSave (curr->typelabel);
-        }
-      }
-      curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
-    }
+    head = BuildFeatureValNodeList (TRUE, NULL, ALL_FEATURES, TRUE, FALSE);
   } else if (type == SLCT_DESC) {
     for (j = 1; descNames [j] != NULL; j++) {
+      if (StringHasNoText (descNames [j])) continue;
       vnp = ValNodeNew (head);
       if (head == NULL) {
         head = vnp;
@@ -3566,19 +3877,35 @@ static void SelectAsnObject (IteM i, Int2 type)
     }
   }
   if (head != NULL) {
-    head = SortValNode (head, SortByVnpChoice);
+    if (type != SLCT_FEAT) {
+      head = SortValNode (head, SortByVnpChoice);
+    }
     for (vnp = head; vnp != NULL; vnp = vnp->next) {
       ListItem (selfp->objlist, (CharPtr) vnp->data.ptrvalue);
     }
   }
   selfp->head = head;
 
+  if (selfp->type == SLCT_FEAT || selfp->type == SLCT_DESC)
+  {
+    k = HiddenGroup (h, 0, 2, NULL);
+    StaticPrompt (k, "Optional string constraint", 0, dialogTextHeight, programFont, 'c');
+    selfp->findthis = DialogText (k, "", 14, NULL);
+  }
+
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoSelectAsnObject);
+  b = DefaultButton (c, "Accept", DoSelectAsnObject);
   SetObjectExtra (b, selfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
-  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
+  if (selfp->type == SLCT_FEAT || selfp->type == SLCT_DESC)
+  {
+    AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) k, (HANDLE) c, NULL);
+  }
+  else
+  {
+    AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
+  }
   RealizeWindow (w);
   if (type == SLCT_BIOSEQ) {
     DoSelectAsnObject (b);
@@ -3833,7 +4160,7 @@ extern void FuseFeature (IteM i)
   ffp->head = head;
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoFuseFeature);
+  b = DefaultButton (c, "Accept", DoFuseFeature);
   SetObjectExtra (b, ffp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -4397,7 +4724,7 @@ static ForM CreateRefGeneDescForm (Int2 left, Int2 top, Int2 width,
     rfp->data = CreateRefGeneDialog (g);
 
     c = HiddenGroup (w, 2, 0, NULL);
-    b = PushButton (c, "Accept", StdAcceptFormButtonProc);
+    b = DefaultButton (c, "Accept", StdAcceptFormButtonProc);
     SetObjectExtra (b, rfp, NULL);
     PushButton (c, "Cancel", StdCancelButtonProc);
     AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
@@ -4532,8 +4859,10 @@ typedef struct cka_acc {
 
 static Int4     CKA_blast_wordsize;
 static FloatHi  CKA_blast_expect_value;
+static Boolean  CKA_blast_allow_repeats;
 static Int4     CKA_blast_detailed_wordsize;
 static FloatHi  CKA_blast_detailed_expect_value;
+static Boolean  CKA_blast_detailed_allow_repeats;
 
 static SeqAlignPtr CKA_MakeAlign(BioseqPtr bsp, CKA_AccPtr acc_head);
 
@@ -5515,7 +5844,9 @@ static SeqAlignPtr CKA_MakeAlign(BioseqPtr bsp, CKA_AccPtr acc_head)
       if (acc->sap != NULL && acc->sap->next != NULL)
       {
          AlnMgr2IndexLite(acc->sap);
-         CKA_RemoveInconsistentAlnsFromSet(acc->sap, -1);
+         if (!CKA_blast_allow_repeats) {
+           CKA_RemoveInconsistentAlnsFromSet(acc->sap, -1);
+         }
          sap_tmp = acc->sap;
          acc->sap = (SeqAlignPtr)(acc->sap->segs);
          sap_tmp->segs = NULL;
@@ -5638,6 +5969,7 @@ extern void CreateSeqHistTPA (IteM i)
 {
   CKA_blast_wordsize = 28;
   CKA_blast_expect_value = 0.000001;
+  CKA_blast_allow_repeats = FALSE;
   DoCreateSeqHistTPA(i);
 }
 
@@ -5751,6 +6083,7 @@ extern void CreateSeqHistDelta (IteM i)
 
 static TexT blast_wordsize_text = NULL;
 static TexT blast_expect_value_text = NULL;
+static ButtoN blast_allow_repeats_button = NULL;
 static IteM blast_i;
 
 static void DoAcceptBlastOptions (ButtoN b)
@@ -5768,6 +6101,8 @@ static void DoAcceptBlastOptions (ButtoN b)
    if (sscanf (buf, "%lf", &val2) == 1) {
      CKA_blast_expect_value = CKA_blast_detailed_expect_value = (FloatHi) val2;
    }
+   CKA_blast_allow_repeats = CKA_blast_detailed_allow_repeats =
+     (Boolean) GetStatus (blast_allow_repeats_button);
    Remove (ParentWindow (b));
    DoCreateSeqHistTPA(blast_i);
 }
@@ -5804,6 +6139,11 @@ extern void CreateSeqHistTPADetailed (IteM i)
    sprintf(buf, "%f", CKA_blast_expect_value);
    blast_expect_value_text = DialogText (g, buf, 10, NULL);
 
+   blast_allow_repeats_button = CheckBox (g, "Allow Repeats", NULL);
+   if (CKA_blast_detailed_allow_repeats) {
+     SetStatus(blast_allow_repeats_button, TRUE);
+   }
+
    c = HiddenGroup (w, 2, 0, NULL);
    SetGroupSpacing (c, 5, 5);
    DefaultButton (c, "Accept", DoAcceptBlastOptions);
@@ -6166,7 +6506,7 @@ static ForM CreateAssemblyDescForm (Int2 left, Int2 top, Int2 width,
     afp->data = CreateAssemblyDialog (g);
 
     c = HiddenGroup (w, 2, 0, NULL);
-    b = PushButton (c, "Accept", StdAcceptFormButtonProc);
+    b = DefaultButton (c, "Accept", StdAcceptFormButtonProc);
     SetObjectExtra (b, afp, NULL);
     PushButton (c, "Cancel", StdCancelButtonProc);
     AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
@@ -6644,7 +6984,7 @@ extern void EditSequenceHistory (IteM i)
   AlignObjects (ALIGN_CENTER, (HANDLE) hfp->deleted, (HANDLE) hfp->deleted_date, NULL);
 
   c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton (c, "Accept", DoChangeHistory);
+  b = DefaultButton (c, "Accept", DoChangeHistory);
   SetObjectExtra (b, hfp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -9351,7 +9691,7 @@ static ForM CreateDefLineModForm (Uint2 entityID, SeqEntryPtr sep, BioseqPtr tar
     }
 
     c = HiddenGroup (w, 4, 0, NULL);
-    b = PushButton (c, "Accept", DefLineModFormAcceptProc);
+    b = DefaultButton (c, "Accept", DefLineModFormAcceptProc);
     SetObjectExtra (b, dfp, NULL);
     PushButton (c, "Cancel", StdCancelButtonProc);
 
diff --git a/sequin/sequin9.c b/sequin/sequin9.c
index d439ea7f..32704a8e 100644
--- a/sequin/sequin9.c
+++ b/sequin/sequin9.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   4/20/99
 *
-* $Revision: 6.187 $
+* $Revision: 6.195 $
 *
 * File Description: 
 *
@@ -129,6 +129,7 @@ typedef struct upsdata {
   Boolean             useGUI;
   Boolean             do_update;
   ButtoN              add_cit_subs;
+  ButtoN              update_proteins;
 } UpsData, PNTR UpsDataPtr;
 
 /*---------------------*/
@@ -430,6 +431,8 @@ static void SimpleRsiteProc (IteM i)
 
 static VQUEUE  vsquerylist = NULL;
 
+static Int2 vsquerynum = 0;
+
 static void LIBCALLBACK AnnounceCallback (CharPtr requestID, CharPtr seqID, Int2 estimatedSeconds)
 
 {
@@ -441,6 +444,8 @@ static void LIBCALLBACK AnnounceCallback (CharPtr requestID, CharPtr seqID, Int2
   }
   Message (MSG_POST, "Queued rID %s, seqID %s, estimated seconds = %d",
            requestID, seqID, (int) estimatedSeconds);
+
+  vsquerynum++;
 }
 
 static Boolean LIBCALLBACK VecScreenCallback (
@@ -671,6 +676,8 @@ extern void SubmitToNCBI (IteM i)
 
 static QUEUE  cddquerylist = NULL;
 
+static Int2  cddquerynum = 0;
+
 #include <cddapi.h>
 
 #define CDD_EXPECT_VALUE 0.01
@@ -721,6 +728,8 @@ static void SearchCDD (BioseqPtr bsp, Pointer userdata)
   dofeats = (BoolPtr) userdata;
   if (! CddAsynchronousQuery (bsp, CDD_EXPECT_VALUE, TRUE, TRUE, *dofeats, "cdd", &cddquerylist, CddProc, (Pointer) bsp)) {
     ErrPostEx (SEV_ERROR, 0, 0, "Unable to run CDD search");
+  } else {
+    cddquerynum++;
   }
 }
 
@@ -813,8 +822,16 @@ extern void SequinCheckSocketsProc (void)
     pendingqueries--;
   }
   remaining = VecScreenCheckQueue (&vsquerylist);
+  if (remaining < vsquerynum) {
+    vsquerynum = remaining;
+    Message (MSG_POST, "There are %d vector screens remaining", (int) vsquerynum);
+  }
   remaining = QBlastCheckQueue (&qbquerylist);
   remaining = CddCheckQueue (&cddquerylist);
+  if (remaining < cddquerynum) {
+    cddquerynum = remaining;
+    Message (MSG_POST, "There are %d cdd searches remaining", (int) cddquerynum);
+  }
 }
 
 static Boolean LIBCALLBACK DemoModeResultProc (CONN conn, VoidPtr userdata, EIO_Status status)
@@ -1607,7 +1624,7 @@ static void BuildArgumentForm (NewObjectPtr nop, BaseFormPtr bfp, Int2 which)
 
   c = HiddenGroup (w, 2, 0, NULL);
   SetGroupSpacing (c, 10, 3);
-  b = PushButton (c, "Accept", AcceptArgumentFormProc);
+  b = DefaultButton (c, "Accept", AcceptArgumentFormProc);
   SetObjectExtra (b, ufp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
@@ -4096,150 +4113,319 @@ static void AcceptExtend (ButtoN b)
 }
 
 static void PrepareToUpdateSequences (UpsDataPtr udp);
-
-static void UpdateOneProtein (SeqFeatPtr sfp, Pointer userdata)
+static Boolean PrepareUpdatePtr (UpsDataPtr    udp);
+static ForM UpdateSequenceForm (UpsDataPtr udp);
+static void UpdateOneSequence (
+  UpsDataPtr   udp,
+  Int2         rmcval,
+  Int2         sfbval,
+  Boolean      add_cit_subs,
+  Boolean      update_proteins);
+
+static UpsDataPtr PrepareUpdatePtrForProtein (
+  SeqFeatPtr sfp,
+  Uint2 input_entityID,
+  Uint4 input_itemID,
+  Uint4 input_itemtype
+)
 {
-  BaseFormPtr   bfp;
-  BioseqPtr     protBsp;  /* This will point to the old version of the
-                           * protein bioseq
-                           */
   ByteStorePtr  bs;
-  BioseqPtr     newBsp;
   CharPtr       newprot, ptr;
   Char          ch;
-  UpsDataPtr    udp_copy;
   Boolean       star_at_end;
   SeqEntryPtr   nwsep;
-  
-  bfp = (BaseFormPtr) userdata;
-  if ( bfp == NULL
-    || sfp == NULL
+  BioseqPtr     newBsp, protBsp;
+  UpsDataPtr    udp_copy;
+ 
+  if (sfp == NULL
     || sfp->idx.subtype != FEATDEF_CDS
     || sfp->product == NULL
     || (protBsp = BioseqFindFromSeqLoc (sfp->product)) == NULL)
   {
-    return;
+    return NULL;
   }
- 
-  newprot = NULL;
   bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
+  if (bs == NULL) return NULL;
+  
+  newprot = BSMerge (bs, NULL);
+  bs = BSFree (bs);
+  if (newprot == NULL) return NULL;
+  
+  ptr = newprot;
+  ch = *ptr;
+  while (ch != '\0')
+  {
+    *ptr = TO_UPPER (ch);
+    if (ch == '*') {
+      star_at_end = 1;
+    } else {
+      star_at_end = 0;
+    }
+    ptr++;
+    ch = *ptr;
+  }
+  if (star_at_end) 
+  {
+    ptr [ StringLen (ptr) - 1] = 0;
+  }
+  bs = BSNew (1000);
   if (bs != NULL)
   {
-    newprot = BSMerge (bs, NULL);
-    bs = BSFree (bs);
-    if (newprot != NULL)
+    ptr = newprot;
+    BSWrite (bs, (VoidPtr) ptr, (Int4) StringLen (ptr));
+  } 
+  MemFree (newprot);
+  
+  newBsp = BioseqNew ();
+  if (newBsp == NULL) return NULL;
+
+  newBsp->id = SeqIdParse ("lcl|CdRgnTransl");
+  newBsp->repr = Seq_repr_raw;
+  newBsp->mol = Seq_mol_aa;
+  newBsp->seq_data_type = Seq_code_ncbieaa;
+  newBsp->seq_data = bs;
+  newBsp->length = BSLen (bs);
+
+  /* create SeqEntry for temporary protein bioseq to live in */
+  nwsep = SeqEntryNew ();
+  nwsep->choice = 1;
+  nwsep->data.ptrvalue = newBsp;
+  SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) newBsp, nwsep);
+
+  udp_copy = MemNew (sizeof (UpsData));
+  if (udp_copy == NULL) return NULL;
+  udp_copy->input_entityID = input_entityID;
+  udp_copy->input_itemID   = input_itemID;
+  udp_copy->input_itemtype = input_itemtype;
+  udp_copy->fp             = NULL;
+  udp_copy->isSet          = FALSE;
+  udp_copy->useGUI         = TRUE;
+  udp_copy->convertPubs    = CONVERTPUBS_NO; /* was CONVERTPUBS_NOT_SET */
+  udp_copy->do_update      = TRUE;
+  udp_copy->newbsp = newBsp;
+  udp_copy->oldbsp = protBsp;
+  udp_copy->seq1 = GetSequenceByBsp (protBsp);
+  udp_copy->seq2 = GetSequenceByBsp (newBsp);
+  if (StringCmp (udp_copy->seq1, udp_copy->seq2) == 0
+    || (star_at_end == 1
+      && StringNCmp (udp_copy->seq1,
+                     udp_copy->seq2,
+                     StringLen (udp_copy->seq1)) == 0))
+  {
+    SeqEntryFree (nwsep);
+    MemFree (udp_copy->seq1);
+    MemFree (udp_copy->seq2);
+    MemFree (udp_copy);
+    return NULL;
+  }
+  return udp_copy;
+}
+
+static void FixProtRefPtr (SeqFeatPtr sfp, Pointer userdata)
+{
+  ProtRefPtr prp;
+  BioseqPtr  bsp;
+  Int4       offset;
+  Int4       start;
+  Int4       stop;
+  Uint1      strand;
+
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_PROT) return;
+  prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+  bsp = BioseqFindFromSeqLoc (sfp->location);
+  offset = GetOffsetInBioseq (sfp->location, bsp, SEQLOC_RIGHT_END);
+  if (bsp->length - 1 > offset)
+  {
+    start = GetOffsetInBioseq (sfp->location, bsp, SEQLOC_START);
+    stop = GetOffsetInBioseq (sfp->location, bsp, SEQLOC_STOP);
+    strand = SeqLocStrand (sfp->location);
+    if (strand == Seq_strand_minus)
     {
-      ptr = newprot;
-      ch = *ptr;
-      while (ch != '\0')
-      {
-        *ptr = TO_UPPER (ch);
-        if (ch == '*') {
-          star_at_end = 1;
-        } else {
-          star_at_end = 0;
-        }
-        ptr++;
-        ch = *ptr;
-      }
-      if (star_at_end) 
-      {
-        ptr [ StringLen (ptr) - 1] = 0;
-      }
-      bs = BSNew (1000);
-      if (bs != NULL)
-      {
-        ptr = newprot;
-        BSWrite (bs, (VoidPtr) ptr, (Int4) StringLen (ptr));
-      } 
-      MemFree (newprot);
+      expand_seq_loc (bsp->length - 1, stop, strand, sfp->location);
     }
-    newBsp = BioseqNew ();
-    if (newBsp != NULL)
+    else
     {
-      newBsp->id = SeqIdParse ("lcl|CdRgnTransl");
-      newBsp->repr = Seq_repr_raw;
-      newBsp->mol = Seq_mol_aa;
-      newBsp->seq_data_type = Seq_code_ncbieaa;
-      newBsp->seq_data = bs;
-      newBsp->length = BSLen (bs);
-
-      /* create SeqEntry for temporary protein bioseq to live in */
-      nwsep = SeqEntryNew ();
-      nwsep->choice = 1;
-      nwsep->data.ptrvalue = newBsp;
-      SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) newBsp, nwsep);
-
-      udp_copy = MemNew (sizeof (UpsData));
-      if (udp_copy == NULL) return;
-      udp_copy->input_entityID = bfp->input_entityID;
-      udp_copy->input_itemID   = bfp->input_itemID;
-      udp_copy->input_itemtype = bfp->input_itemtype;
-      udp_copy->fp             = NULL;
-      udp_copy->isSet          = FALSE;
-      udp_copy->useGUI         = TRUE;
-      udp_copy->convertPubs    = CONVERTPUBS_NO; /* was CONVERTPUBS_NOT_SET */
-      udp_copy->do_update      = TRUE;
-      udp_copy->newbsp = newBsp;
-      udp_copy->oldbsp = protBsp;
-      udp_copy->seq1 = GetSequenceByBsp (protBsp);
-      udp_copy->seq2 = GetSequenceByBsp (newBsp);
-      if (StringCmp (udp_copy->seq1, udp_copy->seq2) == 0
-        || (star_at_end == 1
-          && StringNCmp (udp_copy->seq1,
-                         udp_copy->seq2,
-                         StringLen (udp_copy->seq1)) == 0))
-      {
-        SeqEntryFree (nwsep);
-        MemFree (udp_copy->seq1);
-        MemFree (udp_copy->seq2);
-        MemFree (udp_copy);
-      }
-      else
-      {
-        PrepareToUpdateSequences (udp_copy);
-      }
+      expand_seq_loc (start, bsp->length - 1, strand, sfp->location);
     }
   }
 }
-
-extern void UpdateProteinsFromCDS ( IteM i)
+  
+extern SeqLocPtr SeqLocWholeNew (BioseqPtr bsp)
 {
-  BaseFormPtr bfp;
-  SeqEntryPtr sep;
+  ValNodePtr vnp;
 
-#ifdef WIN_MAC
-  bfp = currentFormDataPtr;
-#else
-  bfp = GetObjectExtra (i);
-#endif
+  if (bsp == NULL) return NULL;
 
-  if (bfp == NULL)
+  vnp = ValNodeNew (NULL);
+
+  if (vnp == NULL) return NULL;
+
+  vnp->choice = SEQLOC_WHOLE;
+  vnp->data.ptrvalue = (Pointer) SeqIdFindBest (bsp->id, 0);
+  return (SeqLocPtr)vnp;
+}
+
+static void UpdateOneProtein (SeqFeatPtr sfp, Pointer userdata)
+{
+  BaseFormPtr   bfp;
+  UpsDataPtr    udp_copy;
+  SeqLocPtr     new_product;
+  
+  bfp = (BaseFormPtr) userdata;
+  if ( bfp == NULL
+    || sfp == NULL
+    || sfp->idx.subtype != FEATDEF_CDS
+    || sfp->product == NULL)
+  {
     return;
-  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
-  if (sep == NULL) return;
+  }
+ 
+  udp_copy = PrepareUpdatePtrForProtein (sfp,
+                                         bfp->input_entityID,
+                                         bfp->input_itemID,
+                                         bfp->input_itemtype);
+  if (udp_copy == NULL) return;
 
-  VisitFeaturesInSep (sep, (Pointer) bfp, UpdateOneProtein);
+  if ( ! PrepareUpdatePtr (udp_copy)) return;
 
-  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
-  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+  UpdateOneSequence (udp_copy, 1, 1, FALSE, FALSE);
+  if (sfp->product->choice != SEQLOC_WHOLE)
+  {
+    new_product = SeqLocWholeNew (udp_copy->oldbsp);
+    if (new_product == NULL) return;
+    SeqLocFree (sfp->product);
+    sfp->product = new_product;
+  }
+  VisitFeaturesOnBsp (udp_copy->oldbsp, NULL, FixProtRefPtr);
 }
 
-static void AcceptRMC (ButtoN b)
+static Boolean CheckForIDCollision (
+  BioseqPtr oldbsp,
+  BioseqPtr newbsp,
+  BoolPtr islocal
+)
+
+{
+  SeqIdPtr  sip;
+
+  if (oldbsp == NULL || newbsp == NULL) return FALSE;
+  for (sip = newbsp->id; sip != NULL; sip = sip->next) {
+    if (SeqIdIn (sip, oldbsp->id)) {
+      if (sip->choice == SEQID_LOCAL) {
+        *islocal = TRUE;
+      }
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+static CharPtr convPubDescMssg =
+"Do you wish to convert publications to apply only to the appropriate ranges?";
+
+static Boolean PrepareUpdatePtr (UpsDataPtr    udp)
 {
-  UpsDataPtr   udp;
   Uint2        entityID;
-  Int2         rmcval, sfbval;
+  SeqEntryPtr  oldsep, newsep;
+  SeqIdPtr     tempid = NULL;
+  SeqIdPtr     sip;
+  MsgAnswer    ans;
+  Boolean      islocal = FALSE;
+  SeqIdPtr     lclid = NULL;
+  Char         buf [64];
+  Boolean      descfilt [SEQDESCR_MAX];
+  Boolean      featfilt [SEQFEAT_MAX];
+  SeqAlignPtr  salp = NULL;
+  Boolean      revcomp = FALSE;
+
+  if (udp->oldbsp == NULL || udp->newbsp == NULL) return FALSE;
+  if (ISA_na (udp->oldbsp->mol) != ISA_na (udp->newbsp->mol)) {
+    Message (MSG_OK, "Both sequences must be either nucleotides or proteins");
+    return FALSE;
+  }
+
+  entityID = ObjMgrGetEntityIDForPointer (udp->oldbsp);
+  oldsep = GetBestTopParentForData (entityID, udp->oldbsp);
+  entityID = ObjMgrGetEntityIDForPointer (udp->newbsp);
+  newsep = GetBestTopParentForData (entityID, udp->newbsp);
+  if (oldsep == NULL || newsep == NULL)
+    return FALSE;
+
+  if (CONVERTPUBS_NOT_SET == udp->convertPubs) 
+  {
+    if (Message (MSG_YN, convPubDescMssg) == ANS_YES) {
+      ConvertPubSrcComDescsToFeats (oldsep, TRUE, FALSE, FALSE, FALSE);
+      ConvertPubSrcComDescsToFeats (newsep, TRUE, FALSE, FALSE, FALSE);
+      udp->convertPubs = CONVERTPUBS_YES;
+    }
+    else
+      udp->convertPubs = CONVERTPUBS_NO;
+  }
+
+  tempid = NULL;
+  if (CheckForIDCollision (udp->oldbsp, udp->newbsp, &islocal)) {
+    sip = SeqIdParse ("lcl|SequinUpdateSequence");
+    if (sip != NULL) {
+      if (islocal) {
+        entityID = ObjMgrGetEntityIDForPointer (udp->newbsp);
+        for (lclid = udp->newbsp->id;
+             lclid != NULL && lclid->choice != SEQID_LOCAL;
+             lclid = lclid->next) continue;
+        if (lclid != NULL) {
+          SeqIdWrite (lclid, buf, PRINTID_REPORT, sizeof (buf) - 1);
+          FindReplaceInEntity (entityID, buf, "SequinUpdateSequence", TRUE, FALSE, TRUE,
+                               FALSE, UPDATE_NEVER, descfilt, featfilt, NULL, TRUE);
+          SeqMgrReplaceInBioseqIndex (udp->newbsp);
+        } else {
+          Message (MSG_OK, "Unable to find colliding local id");
+          return FALSE;
+        }
+      } else {
+        /* unlink colliding id, temporarily replace */
+        tempid = udp->newbsp->id;
+        udp->newbsp->id = sip;
+        SeqMgrReplaceInBioseqIndex (udp->newbsp);
+      }
+    }
+  }
+  salp = Sqn_GlobalAlign2Seq (udp->oldbsp, udp->newbsp, &revcomp);
+  if (tempid != NULL) {
+    /* add back colliding id now that blast is done */
+    sip->next = tempid;
+    SeqMgrReplaceInBioseqIndex (udp->newbsp);
+  }
+
+  if (salp == NULL) {
+    ans = Message (MSG_YN, "There is no alignment between the sequences. "
+		   "Do you wish to continue anyway?");
+    if (ans == ANS_NO)
+      return FALSE;
+  }
+
+  udp->salp     = salp;
+  udp->revcomp  = revcomp;
+  udp->diffOrgs = FALSE;
+  udp->recomb1  = -1;
+  udp->recomb2  = -1;
+
+  return TRUE;
+}
+
+static void UpdateProteinsOnNewBsp (SeqFeatPtr sfp, Pointer userdata);
+
+static void UpdateOneSequence (
+  UpsDataPtr   udp,
+  Int2         rmcval,
+  Int2         sfbval,
+  Boolean      add_cit_subs,
+  Boolean      update_proteins
+)
+{
   SeqAnnotPtr  sap = NULL;
+  Uint2        entityID;
   SeqEntryPtr  sep;
   Boolean      update = FALSE;
-
-  udp = (UpsDataPtr) GetObjectExtra (b);
-  if (udp == NULL) return;
-  SafeHide (udp->form);
-
-  sfbval = GetValue (udp->sfb);
-  rmcval = GetValue (udp->rmc);
+  Boolean      feature_update = FALSE;
 
   if (sfbval == 1 || sfbval == 3) {
     switch (rmcval) {
@@ -4281,21 +4467,25 @@ static void AcceptRMC (ButtoN b)
         case 1 :
           if (DoFeaturePropWithOffset (udp, 0, &sap, FALSE)) {
             update = TRUE;
+            feature_update = TRUE;
           }
           break;
         case 2 :
           if (DoFeaturePropWithOffset (udp, 0, &sap, FALSE)) {
             update = TRUE;
+            feature_update = TRUE;
           }
           break;
         case 3 :
           if (DoFeaturePropWithOffset (udp, udp->old5 - udp->new5, &sap, FALSE)) {
             update = TRUE;
+            feature_update = TRUE;
           }
           break;
         case 4 :
           if (DoFeaturePropWithOffset (udp, udp->old5 - udp->new5, &sap, TRUE)) {
             update = TRUE;
+            feature_update = TRUE;
           }
           break;
         default :
@@ -4307,21 +4497,25 @@ static void AcceptRMC (ButtoN b)
       case 1 :
         if (DoFeaturePropThruAlign (udp, &sap)) {
           update = TRUE;
+          feature_update = TRUE;
         }
         break;
       case 2 :
         if (DoFeaturePropThruAlign (udp, &sap)) {
           update = TRUE;
+          feature_update = TRUE;
         }
         break;
       case 3 :
         if (DoFeaturePropThruAlign (udp, &sap)) {
           update = TRUE;
+          feature_update = TRUE;
         }
         break;
       case 4 :
         if (DoFeaturePropThruAlign (udp, &sap)) {
           update = TRUE;
+          feature_update = TRUE;
         }
         break;
       default :
@@ -4341,13 +4535,99 @@ static void AcceptRMC (ButtoN b)
   }
   if (update) {
     entityID = ObjMgrGetEntityIDForPointer (udp->oldbsp);
-    if (GetStatus (udp->add_cit_subs))
+    if (add_cit_subs
+      && (feature_update || StringCmp (udp->seq1, udp->seq2) != 0))
     {
       AddCitSubToUpdatedSequence ( udp->oldbsp, entityID);
     }
+    if (update_proteins)
+    {
+      sep = GetBestTopParentForData (entityID, udp->oldbsp);
+      VisitFeaturesInSep (sep, udp, UpdateProteinsOnNewBsp);
+    }
     ObjMgrSetDirtyFlag (entityID, TRUE);
     ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
   }
+}
+
+static void UpdateProteinsOnNewBsp (SeqFeatPtr sfp, Pointer userdata)
+{
+  UpsDataPtr    udp_orig, udp_copy;
+  Int2          sfbval, rmcval;
+  SeqLocPtr     new_product;
+
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_CDS || userdata == NULL)
+  {
+    return;
+  }
+  udp_orig = (UpsDataPtr) userdata;
+
+  udp_copy = PrepareUpdatePtrForProtein (sfp,
+                                         udp_orig->input_entityID,
+                                         udp_orig->input_itemID,
+                                         udp_orig->input_itemtype);
+
+  if (udp_copy == NULL) return;
+
+  if (! PrepareUpdatePtr (udp_copy)) return;
+  
+  if (udp_copy != NULL)
+  {
+    sfbval = GetValue (udp_orig->sfb);
+    rmcval = GetValue (udp_orig->rmc);
+
+    UpdateOneSequence (udp_copy, rmcval, sfbval,
+                     GetStatus (udp_orig->add_cit_subs),
+                     FALSE);
+    if (sfp->product->choice != SEQLOC_WHOLE)
+    {
+      new_product = SeqLocWholeNew (udp_copy->oldbsp);
+      if (new_product == NULL) return;
+      SeqLocFree (sfp->product);
+      sfp->product = new_product;
+    }
+    VisitFeaturesOnBsp (udp_copy->oldbsp, NULL, FixProtRefPtr);
+  }
+}
+
+extern void UpdateProteinsFromCDS ( IteM i)
+{
+  BaseFormPtr bfp;
+  SeqEntryPtr sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+
+  if (bfp == NULL)
+    return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+
+  WatchCursor ();
+  VisitFeaturesInSep (sep, (Pointer) bfp, UpdateOneProtein);
+  ArrowCursor ();
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+static void AcceptRMC (ButtoN b)
+{
+  UpsDataPtr   udp;
+  Int2         rmcval, sfbval;
+
+  udp = (UpsDataPtr) GetObjectExtra (b);
+  if (udp == NULL) return;
+  SafeHide (udp->form);
+
+  sfbval = GetValue (udp->sfb);
+  rmcval = GetValue (udp->rmc);
+
+  UpdateOneSequence (udp, rmcval, sfbval,
+                     GetStatus (udp->add_cit_subs),
+                     GetStatus (udp->update_proteins));
 
   Remove (udp->form);
 }
@@ -4411,152 +4691,15 @@ static void AcceptRMCAll (ButtoN b)
 
 static void DoAcceptRMCSet (UpsDataPtr udp)
 {
-  Uint2        entityID;
   Int2         rmcval;
-  SeqAnnotPtr  sap = NULL;
-  SeqEntryPtr  sep;
   Int2         sfbval;
-  Boolean      update = FALSE;
-  Boolean      feature_update = FALSE;
 
   SafeHide (udp->form);
 
   sfbval = GetValue (udp->sfb);
   rmcval = GetValue (udp->rmc);
-  if (sfbval == 1 || sfbval == 3) {
-    switch (rmcval) {
-      case 1 :
-        if (ReplaceSequence (udp))
-          update = TRUE;
-        break;
-      case 2 :
-	if (NULL == udp->salp) {
-	  if (Merge5PrimeNoOverlap (udp))
-          {
-	    update = TRUE;
-          }
-	}
-	else {
-	  if (Merge5Prime (udp))
-          {
-	    update = TRUE;
-          }
-        }
-        break;
-      case 3 :
-	if (NULL == udp->salp) {
-	  if (Merge3PrimeNoOverlap (udp))
-          {
-	    update = TRUE;
-          }
-	}
-	else {
-	  if (Merge3Prime (udp))
-          {
-	    update = TRUE;
-          }
-        }
-        break;
-      case 4 :
-        if (PatchSequence (udp))
-        {
-          update = TRUE;
-        }
-        break;
-      default :
-        break;
-    }
-    if ( sfbval == 3) {
-      switch (rmcval) {
-        case 1 :
-          if (DoFeaturePropWithOffset (udp, 0, &sap, FALSE))
-          {
-            update = TRUE;
-            feature_update = TRUE;
-          }
-          break;
-        case 2 :
-          if (DoFeaturePropWithOffset (udp, 0, &sap, FALSE))
-          {
-            update = TRUE;
-            feature_update = TRUE;
-          }
-          break;
-        case 3 :
-          if (DoFeaturePropWithOffset (udp, udp->old5 - udp->new5, &sap, FALSE))
-          {
-            update = TRUE;
-            feature_update = TRUE;
-          }
-          break;
-        case 4 :
-          if (DoFeaturePropWithOffset (udp, udp->old5 - udp->new5, &sap, TRUE))
-          {
-            update = TRUE;
-            feature_update = TRUE;
-          }
-          break;
-        default :
-          break;
-      }
-    }
-  } else if (sfbval == 2) {
-    switch (rmcval) {
-      case 1 :
-        if (DoFeaturePropThruAlign (udp, &sap))
-        {
-          update = TRUE;
-          feature_update = TRUE;
-        }
-        break;
-      case 2 :
-        if (DoFeaturePropThruAlign (udp, &sap))
-        {
-          update = TRUE;
-          feature_update = TRUE;
-        }
-        break;
-      case 3 :
-        if (DoFeaturePropThruAlign (udp, &sap))
-        {
-          update = TRUE;
-          feature_update = TRUE;
-        }
-        break;
-      case 4 :
-        if (DoFeaturePropThruAlign (udp, &sap))
-        {
-          update = TRUE;
-          feature_update = TRUE;
-        }
-        break;
-      default :
-        break;
-    }
-  }
-
-  if (sfbval == 2 || sfbval == 3) {
-    if (update) {
-      entityID = ObjMgrGetEntityIDForPointer (udp->oldbsp);
-      sep = GetTopSeqEntryForEntityID (entityID);
-      /* need to set scope to be sure we mark the right bioseq for deletion */
-      SeqEntrySetScope (sep);
-      ResolveDuplicateFeats (udp, udp->oldbsp, sap);
-      SeqEntrySetScope (NULL);
-      DeleteMarkedObjects (entityID, 0, NULL);
-    }
-  }
-
-  if (update) {
-    entityID = ObjMgrGetEntityIDForPointer (udp->oldbsp);
-    if (GetStatus (udp->add_cit_subs) 
-      && (feature_update || StringCmp (udp->seq1, udp->seq2) != 0))
-    {
-      AddCitSubToUpdatedSequence ( udp->oldbsp, entityID);
-    }
-    ObjMgrSetDirtyFlag (entityID, TRUE);
-    ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
-  }
+  UpdateOneSequence (udp, rmcval, sfbval, GetStatus (udp->add_cit_subs),
+                     GetStatus (udp->update_proteins));
 
   Remove (udp->form);
   FreeUdpFields (udp);
@@ -5911,21 +6054,26 @@ static ForM UpdateSequenceForm (UpsDataPtr udp)
                   (HANDLE) gp3, (HANDLE) udp->keepProteinIDs, NULL);
   }
   udp->add_cit_subs = CheckBox (g, "Add Cit-subs for Updated Sequences", NULL);
+  if (! ISA_aa (udp->oldbsp->mol))
+  {
+    udp->update_proteins = CheckBox (g, "Update proteins for Updated Sequences", NULL);
+    SetStatus (udp->update_proteins, TRUE);
+  }
 
   if (! udp->do_update) {
     c = HiddenGroup (w, 4, 0, NULL);
-    udp->accept = PushButton (c, "Accept", AcceptExtend);
+    udp->accept = DefaultButton (c, "Accept", AcceptExtend);
     SetObjectExtra (udp->accept, (Pointer) udp, NULL);
   } else if (TRUE == udp->isSet) {
     c = HiddenGroup (w, 5, 0, NULL);
-    udp->accept = PushButton (c, "Accept", AcceptRMCSet);
+    udp->accept = DefaultButton (c, "Accept", AcceptRMCSet);
     SetObjectExtra (udp->accept, (Pointer) udp, NULL);
-    udp->acceptAll = PushButton (c, "Accept All", AcceptRMCAll);
+    udp->acceptAll = DefaultButton (c, "Accept All", AcceptRMCAll);
     SetObjectExtra (udp->acceptAll, (Pointer) udp, NULL);
   }
   else {
     c = HiddenGroup (w, 4, 0, NULL);
-    udp->accept = PushButton (c, "Accept", AcceptRMC);
+    udp->accept = DefaultButton (c, "Accept", AcceptRMC);
     SetObjectExtra (udp->accept, (Pointer) udp, NULL);
   }
   
@@ -6022,133 +6170,17 @@ static Boolean LIBCALL SeqEntryHasPubs (SeqEntryPtr sep)
   return rsult;
 }
 
-static Boolean CheckForIDCollision (
-  BioseqPtr oldbsp,
-  BioseqPtr newbsp,
-  BoolPtr islocal
-)
-
-{
-  SeqIdPtr  sip;
-
-  if (oldbsp == NULL || newbsp == NULL) return FALSE;
-  for (sip = newbsp->id; sip != NULL; sip = sip->next) {
-    if (SeqIdIn (sip, oldbsp->id)) {
-      if (sip->choice == SEQID_LOCAL) {
-        *islocal = TRUE;
-      }
-      return TRUE;
-    }
-  }
-  return FALSE;
-}
-
 /*=====================================================================*/
 /*                                                                     */
 /* PrepareToUpdateSequences ()                                         */
 /*                                                                     */
 /*=====================================================================*/
 
-static CharPtr convPubDescMssg =
-"Do you wish to convert publications to apply only to the appropriate ranges?";
-
 static void PrepareToUpdateSequences (UpsDataPtr udp)
 {
-  Char         buf [64];
-  Boolean      descfilt [SEQDESCR_MAX];
-  Boolean      featfilt [SEQFEAT_MAX];
-  Uint2        entityID;
   ForM         f;
-  Boolean      islocal = FALSE;
-  SeqIdPtr     lclid = NULL;
-  SeqEntryPtr  oldsep;
-  SeqEntryPtr  newsep;
-  Boolean      revcomp = FALSE;
-  SeqAlignPtr  salp = NULL;
-  SeqIdPtr     tempid = NULL;
-  SeqIdPtr     sip;
-  MsgAnswer    ans;
-
-  if (udp->oldbsp == NULL || udp->newbsp == NULL) return;
-  if (ISA_na (udp->oldbsp->mol) != ISA_na (udp->newbsp->mol)) {
-    Message (MSG_OK, "Both sequences must be either nucleotides or proteins");
-    return;
-  }
-
-  entityID = ObjMgrGetEntityIDForPointer (udp->oldbsp);
-  oldsep = GetBestTopParentForData (entityID, udp->oldbsp);
-  entityID = ObjMgrGetEntityIDForPointer (udp->newbsp);
-  newsep = GetBestTopParentForData (entityID, udp->newbsp);
-  if (oldsep == NULL || newsep == NULL)
-    return;
-
-  /*
-  if (SeqEntryHasPubs (oldsep) || SeqEntryHasPubs (newsep)) {
-    if ((FALSE == udp->isSet) || (TRUE == udp->useGUI)) {
-      if (Message (MSG_YN, convPubDescMssg) == ANS_YES) {
-	ConvertPubSrcComDescsToFeats (oldsep, TRUE, FALSE, FALSE, FALSE);
-	ConvertPubSrcComDescsToFeats (newsep, TRUE, FALSE, FALSE, FALSE);
-      }
-    }
-    else 
-  */
-  if (CONVERTPUBS_NOT_SET == udp->convertPubs) 
-    if (Message (MSG_YN, convPubDescMssg) == ANS_YES) {
-      ConvertPubSrcComDescsToFeats (oldsep, TRUE, FALSE, FALSE, FALSE);
-      ConvertPubSrcComDescsToFeats (newsep, TRUE, FALSE, FALSE, FALSE);
-      udp->convertPubs = CONVERTPUBS_YES;
-    }
-    else
-      udp->convertPubs = CONVERTPUBS_NO;
-  /*
-  }
-  */
-
-  tempid = NULL;
-  if (CheckForIDCollision (udp->oldbsp, udp->newbsp, &islocal)) {
-    sip = SeqIdParse ("lcl|SequinUpdateSequence");
-    if (sip != NULL) {
-      if (islocal) {
-        entityID = ObjMgrGetEntityIDForPointer (udp->newbsp);
-        for (lclid = udp->newbsp->id;
-             lclid != NULL && lclid->choice != SEQID_LOCAL;
-             lclid = lclid->next) continue;
-        if (lclid != NULL) {
-          SeqIdWrite (lclid, buf, PRINTID_REPORT, sizeof (buf) - 1);
-          FindReplaceInEntity (entityID, buf, "SequinUpdateSequence", TRUE, FALSE, TRUE,
-                               FALSE, UPDATE_NEVER, descfilt, featfilt, NULL, TRUE);
-          SeqMgrReplaceInBioseqIndex (udp->newbsp);
-        } else {
-          Message (MSG_OK, "Unable to find colliding local id");
-          return;
-        }
-      } else {
-        /* unlink colliding id, temporarily replace */
-        tempid = udp->newbsp->id;
-        udp->newbsp->id = sip;
-        SeqMgrReplaceInBioseqIndex (udp->newbsp);
-      }
-    }
-  }
-  salp = Sqn_GlobalAlign2Seq (udp->oldbsp, udp->newbsp, &revcomp);
-  if (tempid != NULL) {
-    /* add back colliding id now that blast is done */
-    sip->next = tempid;
-    SeqMgrReplaceInBioseqIndex (udp->newbsp);
-  }
 
-  if (salp == NULL) {
-    ans = Message (MSG_YN, "There is no alignment between the sequences. "
-		   "Do you wish to continue anyway?");
-    if (ans == ANS_NO)
-      return;
-  }
-
-  udp->salp     = salp;
-  udp->revcomp  = revcomp;
-  udp->diffOrgs = FALSE;
-  udp->recomb1  = -1;
-  udp->recomb2  = -1;
+  if ( ! PrepareUpdatePtr (udp)) return;
 
   if (TRUE == udp->useGUI) {
     f = UpdateSequenceForm (udp);
@@ -6530,8 +6562,38 @@ extern void UpdateSeqAfterDownload (
 )
 
 {
+  MsgAnswer   ans;
   UpsDataPtr  udp;
 
+  /* convert delta lit to raw so sequence can be updated */
+
+  if (oldbsp->repr == Seq_repr_delta && DeltaLitOnly (oldbsp)) {
+    if (indexerVersion) {
+      SegOrDeltaBioseqToRaw (oldbsp);
+      ObjMgrSetDirtyFlag (oldbsp->idx.entityID, TRUE);
+    } else {
+      ans = Message (MSG_YN, "Only raw sequences can be updated."
+		     " Do you wish to convert this delta sequence to raw?");
+      if (ans == ANS_YES) {
+        SegOrDeltaBioseqToRaw (oldbsp);
+        ObjMgrSetDirtyFlag (oldbsp->idx.entityID, TRUE);
+      }
+    }
+  }
+
+  if (newbsp->repr == Seq_repr_delta && DeltaLitOnly (newbsp)) {
+    if (indexerVersion) {
+      SegOrDeltaBioseqToRaw (newbsp);
+      ObjMgrSetDirtyFlag (newbsp->idx.entityID, TRUE);
+    } else {
+      ans = Message (MSG_YN, "Only raw sequences can be updated."
+		     " Do you wish to convert this delta sequence to raw?");
+      if (ans == ANS_YES) {
+        SegOrDeltaBioseqToRaw (newbsp);
+        ObjMgrSetDirtyFlag (newbsp->idx.entityID, TRUE);
+      }
+    }
+  }
   /* Create data ptr */
 
   udp = (UpsDataPtr) MemNew (sizeof (UpsData));
@@ -6561,8 +6623,38 @@ extern void ExtendSeqAfterDownload (
 )
 
 {
+  MsgAnswer   ans;
   UpsDataPtr  udp;
 
+  /* convert delta lit to raw so sequence can be updated */
+
+  if (oldbsp->repr == Seq_repr_delta && DeltaLitOnly (oldbsp)) {
+    if (indexerVersion) {
+      SegOrDeltaBioseqToRaw (oldbsp);
+      ObjMgrSetDirtyFlag (oldbsp->idx.entityID, TRUE);
+    } else {
+      ans = Message (MSG_YN, "Only raw sequences can be extended."
+		     " Do you wish to convert this delta sequence to raw?");
+      if (ans == ANS_YES) {
+        SegOrDeltaBioseqToRaw (oldbsp);
+        ObjMgrSetDirtyFlag (oldbsp->idx.entityID, TRUE);
+      }
+    }
+  }
+
+  if (newbsp->repr == Seq_repr_delta && DeltaLitOnly (newbsp)) {
+    if (indexerVersion) {
+      SegOrDeltaBioseqToRaw (newbsp);
+      ObjMgrSetDirtyFlag (newbsp->idx.entityID, TRUE);
+    } else {
+      ans = Message (MSG_YN, "Only raw sequences can be extended."
+		     " Do you wish to convert this delta sequence to raw?");
+      if (ans == ANS_YES) {
+        SegOrDeltaBioseqToRaw (newbsp);
+        ObjMgrSetDirtyFlag (newbsp->idx.entityID, TRUE);
+      }
+    }
+  }
   /* Create data ptr */
 
   udp = (UpsDataPtr) MemNew (sizeof (UpsData));
@@ -7502,7 +7594,7 @@ static ForM FeaturePropagateForm (
   fdp->fixCDS = CheckBox (g, "Cleanup CDS partials after propagation", NULL);
 
   c = HiddenGroup (w, 4, 0, NULL);
-  fdp->accept = PushButton (c, "Accept", AcceptFeatProp);
+  fdp->accept = DefaultButton (c, "Accept", AcceptFeatProp);
   SetObjectExtra (fdp->accept, (Pointer) fdp, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
 
diff --git a/tools/actutils.c b/tools/actutils.c
index 50528c15..3167c282 100644
--- a/tools/actutils.c
+++ b/tools/actutils.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: actutils.c,v 6.34 2003/06/30 15:01:29 whlavina Exp $";
+static char const rcsid[] = "$Id: actutils.c,v 6.35 2004/01/02 18:11:28 kans Exp $";
 
 /* ===========================================================================
 *
@@ -30,13 +30,16 @@ static char const rcsid[] = "$Id: actutils.c,v 6.34 2003/06/30 15:01:29 whlavina
 *
 * Version Creation Date:   2/00
 *
-* $Revision: 6.34 $
+* $Revision: 6.35 $
 *
 * File Description: utility functions for alignments
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: actutils.c,v $
+* Revision 6.35  2004/01/02 18:11:28  kans
+* Sqn_GlobalAlign2Seq flips code break, anticodon when reverse complementing sequence
+*
 * Revision 6.34  2003/06/30 15:01:29  whlavina
 * Correct minus strand handling in CreaeContinuousAln functions; previous
 * code could corrupt alignments (stop2-start1>1 would imply len<-2 if
@@ -2519,7 +2522,9 @@ static void SPI_flip_sa_list (SeqAlignPtr sap)
 
 NLM_EXTERN SeqAlignPtr Sqn_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp)
 {
-   AMAlignIndex2Ptr      amaip;
+   AMAlignIndex2Ptr     amaip;
+   CodeBreakPtr         cbp;
+   CdRegionPtr          crp;
    Int4                 i;
    BLAST_OptionsBlkPtr  options;
    CharPtr              program = "blastn";
@@ -2536,9 +2541,11 @@ NLM_EXTERN SeqAlignPtr Sqn_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, Bool
    Int4                 extnd = 20;
    SeqMgrFeatContext    context;
    Uint2                entityID;
+   RnaRefPtr            rrp;
    SeqFeatPtr           sfp;
    SeqIdPtr             sip;
    SeqLocPtr            slp;
+   tRNAPtr              trp;
 
    if (bsp1 == NULL || bsp2 == NULL)
       return NULL;
@@ -2588,6 +2595,33 @@ NLM_EXTERN SeqAlignPtr Sqn_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, Bool
        slp = SeqLocCopyRegion (sip, sfp->location, bsp2, 0, bsp2->length - 1, Seq_strand_minus, FALSE);
        sfp->location = SeqLocFree (sfp->location);
        sfp->location = slp;
+       switch (sfp->data.choice) {
+         case SEQFEAT_CDREGION :
+           crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+           if (crp != NULL) {
+             for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
+               sip = SeqLocId (cbp->loc);
+               slp = SeqLocCopyRegion (sip, cbp->loc, bsp2, 0, bsp2->length - 1, Seq_strand_minus, FALSE);
+               cbp->loc = SeqLocFree (cbp->loc);
+               cbp->loc = slp;
+             }
+           }
+           break;
+         case SEQFEAT_RNA :
+           rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+           if (rrp != NULL && rrp->ext.choice == 2) {
+             trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+             if (trp != NULL && trp->anticodon != NULL) {
+               sip = SeqLocId (trp->anticodon);
+               slp = SeqLocCopyRegion (sip, trp->anticodon, bsp2, 0, bsp2->length - 1, Seq_strand_minus, FALSE);
+               trp->anticodon = SeqLocFree (trp->anticodon);
+               trp->anticodon = slp;
+             }
+           }
+           break;
+         default :
+           break;
+       }
        sfp = SeqMgrGetNextFeature (bsp2, sfp, 0, 0, &context);
      }
      SeqMgrClearFeatureIndexes (entityID, NULL);
diff --git a/tools/blast.c b/tools/blast.c
index f6249f32..7fc601c9 100644
--- a/tools/blast.c
+++ b/tools/blast.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: blast.c,v 6.391 2003/10/23 17:46:17 dondosha Exp $";
+static char const rcsid[] = "$Id: blast.c,v 6.397 2004/01/06 22:37:10 dondosha Exp $";
 
-/* $Id: blast.c,v 6.391 2003/10/23 17:46:17 dondosha Exp $
+/* $Id: blast.c,v 6.397 2004/01/06 22:37:10 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -49,9 +49,27 @@ Detailed Contents:
 	further manipulation.
 
 ******************************************************************************
- * $Revision: 6.391 $
+ * $Revision: 6.397 $
  *
  * $Log: blast.c,v $
+ * Revision 6.397  2004/01/06 22:37:10  dondosha
+ * Use BLAST_HSPfree function
+ *
+ * Revision 6.396  2003/12/29 15:42:46  coulouri
+ * tblastn query concatenation fixes from morgulis
+ *
+ * Revision 6.395  2003/12/12 16:01:23  madden
+ * Change to signature of BlastCutoffs, remove BlastCutoffs_simple
+ *
+ * Revision 6.394  2003/12/10 17:05:27  dondosha
+ * Added function ReevaluateScoreWithAmbiguities to reevaluate score for one HSP; use it after greedy traceback
+ *
+ * Revision 6.393  2003/11/19 18:09:13  dondosha
+ * Use consistent rounding in length adjustment calculation
+ *
+ * Revision 6.392  2003/11/10 20:15:29  dondosha
+ * Bug fix in BLASTMergeHsps
+ *
  * Revision 6.391  2003/10/23 17:46:17  dondosha
  * Fix in BlastGetDbChunk for looking up ordinal ids within a range
  *
@@ -3256,7 +3274,7 @@ do_blast_search(VoidPtr ptr)
                    if (!search->handle_results)
                       status = BlastReevaluateWithAmbiguities(search, index1);
                 } else {
-                   MegaBlastReevaluateWithAmbiguities(search, index1);
+                   MegaBlastReevaluateWithAmbiguities(search);
                 }
 		
                 if (search->handle_results)
@@ -3289,7 +3307,7 @@ do_blast_search(VoidPtr ptr)
                    if (!search->handle_results)
                       status = BlastReevaluateWithAmbiguities(search, index);
                 } else {
-                   MegaBlastReevaluateWithAmbiguities(search, index);
+                   MegaBlastReevaluateWithAmbiguities(search);
                 }
                 if (search->handle_results)
                    search->handle_results((VoidPtr) search);
@@ -4004,7 +4022,7 @@ Boolean BlastCalculateEffectiveLengths(BLAST_OptionsBlkPtr options,
 		}
 		else
 		{
-			*length_adjustment = (Int4) ((kbp->logK)+log((Nlm_FloatHi)(length-last_length_adjustment)*(Nlm_FloatHi)(MAX(1, (dblen)-(dbseq_num*last_length_adjustment)))))/(kbp->H);
+			*length_adjustment = Nlm_Nint(((kbp->logK)+log((Nlm_FloatHi)(length-last_length_adjustment)*(Nlm_FloatHi)(MAX(1, (dblen)-(dbseq_num*last_length_adjustment)))))/(kbp->H));
 		}
 		if (*length_adjustment >= length-min_query_length)
 		{
@@ -5918,8 +5936,7 @@ BLASTMergeHsps(BlastSearchBlkPtr search, BLAST_HSPPtr hsp1, BLAST_HSPPtr hsp2,
       if (new_segment1->s_end <= new_segment2->s_end) {
          new_segment1 = new_segment1->next;
          num1++;
-      }
-      if (new_segment1->s_end >= new_segment2->s_end) {
+      } else {
          new_segment2 = new_segment2->next;
          num2++;
       }
@@ -6054,9 +6071,7 @@ BLASTMergeHitLists(BlastSearchBlkPtr search, BLAST_HitListPtr hitlist1,
              OVERLAP_DIAG_CLOSE) {
             if (merge_hsps) {
                if (BLASTMergeHsps(search, hspp1[index], hspp2[index1], start)) {
-                  hspp2[index1]->gap_info = 
-                     GapXEditBlockDelete(hspp2[index1]->gap_info);
-                  hspp2[index1] = MemFree(hspp2[index1]);
+                  hspp2[index1] = BLAST_HSPFree(hspp2[index1]);
                   break;
                }
             } else { /* No gap information available */
@@ -6161,8 +6176,7 @@ BlastReapPartialHitlistByEvalue(BlastSearchBlkPtr search, Int4 start)
                                                  searchsp_eff);
 
             if (hsp->evalue > 10*search->pbp->cutoff_e) {
-               hsp->gap_info = GapXEditBlockDelete(hsp->gap_info);
-               hsp = MemFree(hsp);
+               hsp = BLAST_HSPFree(hsp);
                search->current_hitlist->hsp_array[index] = NULL;
             }
          }
@@ -7824,8 +7838,8 @@ BlastWordExtend_prelim(BlastSearchBlkPtr search, Int4 q_off, Int4 s_off, Int4 wo
         /* AM: Support for query multiplexing. */
 	if( search->prog_number == blast_type_tblastn && search->mult_queries )
 	{
-	  query_num = GetQueryNum( search->mult_queries, q_off, 
-	                           q_off + word_width + 1, 0 );
+	  query_num = GetQueryNum( search->mult_queries, q_off - word_width + 1, 
+	                           q_off + 1, 0 );
           X = search->mult_queries->dropoff_2nd_pass_array[query_num];
 	}
 	else X=pbp->X;
@@ -9459,6 +9473,7 @@ BlastSaveCurrentHitlist(BlastSearchBlkPtr search)
 	/* AM: Support for query concatenation. */
 	if( search->mult_queries && !retval ) return 0;
 
+
 	if (search->pbp->gapped_calculation &&
 		search->prog_number != blast_type_blastn)
 		kbp = search->sbp->kbp_gap[search->first_context];
@@ -9745,10 +9760,8 @@ BlastSaveCurrentHitlist(BlastSearchBlkPtr search)
 		        mq_worst_result 
 			  = result_info->results[result_info->NumResults - 1];
                         --tmp_num_results;
-                        del_index = ResultIndex( mq_worst_result->best_evalue,
-			                         mq_worst_result->high_score,
-						 mq_worst_result->subject_id,
-						 results, hitlist_count );
+			del_index = ResultIndex1( mq_worst_result,
+			                          results, hitlist_count );
                         BlastFreeHeap( search, results[del_index] );
 
 			if( results[del_index]->seqalign )
@@ -9881,27 +9894,26 @@ blast_set_parameters(BlastSearchBlkPtr search,
 
 	meff = (Nlm_FloatHi) search->context[search->first_context].query->length;
 	if (pbp->mb_params)
-	   BlastCutoffs_simple(&s, &e, kbp, searchsp, TRUE);
+	   BlastCutoffs(&s, &e, kbp, searchsp, TRUE, search->pbp->gap_decay_rate );
 	else
 	{
 	   if (pbp->gapped_calculation && search->prog_number != blast_type_blastn)
-	   { /* AM: Changed to support query concatenation. */
-	     if( !search->mult_queries )
-	   	BlastCutoffs_simple(&s, &e, kbp_gap, searchsp, FALSE);
-             else
-	        BlastCutoffs_simple( &s, &e, kbp_gap, 
-		                     search->mult_queries->MinSearchSpEff, 
-				     FALSE );
-           }
+     { /* AM: Changed to support query concatenation. */
+       if( !search->mult_queries )
+         BlastCutoffs(&s, &e, kbp_gap, searchsp, FALSE, 0.0 );
+       else
+         BlastCutoffs( &s, &e, kbp_gap,
+                       search->mult_queries->MinSearchSpEff, 
+                       FALSE, 0.0 );
+     }
 	   else
-	   { /* AM: Changed to support query concatenation. */
-	     if( !search->mult_queries )
-	   	BlastCutoffs_simple(&s, &e, kbp, searchsp, FALSE);
-             else
-	        BlastCutoffs_simple( &s, &e, kbp, 
-		                     search->mult_queries->MinSearchSpEff, 
-				     FALSE ); 
-           }
+     { /* AM: Changed to support query concatenation. */
+       if( !search->mult_queries )
+         BlastCutoffs(&s, &e, kbp, searchsp, FALSE, 0.0 );
+       else
+         BlastCutoffs( &s, &e, kbp, search->mult_queries->MinSearchSpEff, 
+                        FALSE, 0.0 ); 
+     }
 	}
 	/* Determine the secondary cutoff score, S2, to use */
 	if (e2 == 0. && !pbp->cutoff_s2_set)
@@ -9920,24 +9932,26 @@ blast_set_parameters(BlastSearchBlkPtr search,
 /*
 		BlastCutoffs(&s2, &e2, kbp, meff, avglen, TRUE);
 */
-		if (pbp->gapped_calculation && search->prog_number != blast_type_blastn)
-		{
-		  if( !search->mult_queries )
-			BlastCutoffs(&s2, &e2, kbp_gap, MIN(avglen,meff), avglen, TRUE);
-                  else
-		    BlastCutoffs( &s2, &e2, kbp_gap, 
-		                  MIN( avglen,search->mult_queries->MinLen ), 
-				  avglen, TRUE ); 
-                }
-		else
-		{ /* AM: Changed to support query concatenation. */
-		  if( !search->mult_queries )
-			BlastCutoffs(&s2, &e2, kbp, MIN(avglen,meff), avglen, TRUE);
-                  else
-		    BlastCutoffs( &s2, &e2, kbp, 
-		                  MIN(avglen,2*(search->mult_queries->MinLen)), 
-				  avglen, TRUE ); 
-                }
+    if (pbp->gapped_calculation && search->prog_number != blast_type_blastn)
+    {
+      if( !search->mult_queries )
+        BlastCutoffs(&s2, &e2, kbp_gap, MIN(avglen,meff) * avglen,
+                     TRUE, search->pbp->gap_decay_rate );
+      else
+        BlastCutoffs( &s2, &e2, kbp_gap, 
+                      MIN( avglen,search->mult_queries->MinLen ) * avglen,
+                      TRUE, search->pbp->gap_decay_rate ); 
+    }
+    else
+    { /* AM: Changed to support query concatenation. */
+      if( !search->mult_queries )
+        BlastCutoffs(&s2, &e2, kbp, MIN(avglen,meff) * avglen,
+                     TRUE, search->pbp->gap_decay_rate );
+      else
+        BlastCutoffs( &s2, &e2, kbp, 
+                      MIN(avglen,2*(search->mult_queries->MinLen)) * avglen,
+                      TRUE, search->pbp->gap_decay_rate ); 
+    }
 		/* Adjust s2 to be in line with s, as necessary */
 		s2 = MAX(s2, 1);
 		if (s2 > s)
@@ -11351,9 +11365,7 @@ BlastReapHitlistByEvalue (BlastSearchBlkPtr search)
 			if (hsp->evalue > cutoff &&
 				(search->pbp->no_check_score || search->pbp->cutoff_s > hsp->score))
 			{
-                            hsp_array[index]->gap_info = 
-                               GapXEditBlockDelete(hsp_array[index]->gap_info);
-                            hsp_array[index] = MemFree(hsp_array[index]);
+                            hsp_array[index] = BLAST_HSPFree(hsp_array[index]);
                             hsp_deleted = TRUE;
 			}
 			else
diff --git a/tools/blastconcat.c b/tools/blastconcat.c
index 8deaf72d..ab8a1fae 100644
--- a/tools/blastconcat.c
+++ b/tools/blastconcat.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: blastconcat.c,v 1.4 2003/05/30 17:25:36 coulouri Exp $";
+static char const rcsid[] = "$Id: blastconcat.c,v 1.5 2003/12/29 15:42:46 coulouri Exp $";
 
 /* ===========================================================================
 *
@@ -33,8 +33,11 @@ Contents: implementation of functions needed for query multiplexing
           functionality.
 
 ******************************************************************************/
-/* $Revision: 1.4 $ 
+/* $Revision: 1.5 $ 
 *  $Log: blastconcat.c,v $
+*  Revision 1.5  2003/12/29 15:42:46  coulouri
+*  tblastn query concatenation fixes from morgulis
+*
 *  Revision 1.4  2003/05/30 17:25:36  coulouri
 *  add rcsid
 *
@@ -877,6 +880,56 @@ void LIBCALL InitHitLists PROTO(( BlastSearchBlkPtr search ))
     }
   }
 }
+/* TEMPORARY FUNCTION - FOR DEBUGGING ONLY */
+void LIBCALL MQ_CheckLists PROTO(( BLASTResultHitlistPtr PNTR local, Int4 lsize,
+                                   BLASTResultHitlistPtr PNTR res, Int4 rsize ))
+{
+  Int4 i, j;
+
+  for( i = 0; i < lsize; ++i )
+  {
+    int found = 0;
+
+    for( j = 0; j < rsize; ++j )
+      if( local[i] == res[j] )
+      {
+        found = 1;
+        break;
+      }
+
+    if( !found )
+    {
+      fprintf( stderr, "ERROR: %d is not in res\n", i );
+      return;
+    }
+  }
+}
+
+/* ResultIndex1():
+
+   This function first calls the binary search via ResultIndex(). Then tries
+   to locate the exact object in the array by pointer.
+
+*/
+Int4 LIBCALL ResultIndex1 PROTO(( BLASTResultHitlistPtr ptr,
+                                 BLASTResultHitlistPtr PNTR results,
+				 Int4 num_elements ))
+{
+  Int4 del_index = ResultIndex( ptr->best_evalue, ptr->high_score,
+                                ptr->subject_id, results, num_elements );
+  ASSERT( del_index < num_elements );
+  
+  if( results[del_index] == ptr ) return del_index;
+
+  while( del_index >= 0 && results[del_index]->subject_id == ptr->subject_id )
+    --del_index;
+
+  while( ++del_index < num_elements && results[del_index] != ptr );
+
+  ASSERT( del_index < num_elements );
+
+  return del_index;
+}
 
 /* ResultIndex():
 
diff --git a/tools/blastconcatdef.h b/tools/blastconcatdef.h
index aa519e85..7a4bf7e7 100644
--- a/tools/blastconcatdef.h
+++ b/tools/blastconcatdef.h
@@ -31,8 +31,11 @@ Contents: type definitions and function prototypes for query
           multiplexing code.
 
 ******************************************************************************/
-/* $Revision: 1.1 $ 
+/* $Revision: 1.2 $ 
 *  $Log: blastconcatdef.h,v $
+*  Revision 1.2  2003/12/29 15:42:46  coulouri
+*  tblastn query concatenation fixes from morgulis
+*
 *  Revision 1.1  2003/03/24 20:47:28  madden
 *  Utilities for concatenation of blastn/tblastn queries
 *
@@ -143,6 +146,9 @@ Uint4 LIBCALL GetNumSpacers PROTO(( BLAST_OptionsBlkPtr options,
                                     Boolean believe_query,
 				    BspArray fake_bsp_arr ));
 void LIBCALL InitHitLists PROTO(( BlastSearchBlkPtr search ));
+Int4 LIBCALL ResultIndex1 PROTO(( BLASTResultHitlistPtr ptr,
+                                  BLASTResultHitlistPtr PNTR results,
+				  Int4 num_elements ));
 Int4 LIBCALL ResultIndex PROTO(( Nlm_FloatHi target_e, Int4 target_score, Int4 subject_id,
                                  BLASTResultHitlistPtr PNTR results,
 				 Int4 num_elements ));
diff --git a/tools/blastdef.h b/tools/blastdef.h
index 7e5fcd8f..1dcb0458 100644
--- a/tools/blastdef.h
+++ b/tools/blastdef.h
@@ -30,8 +30,23 @@ Author: Tom Madden
 Contents: #defines and definitions for structures used by BLAST.
 
 ******************************************************************************/
-/* $Revision: 6.149 $ 
+/* $Revision: 6.154 $ 
 * $Log: blastdef.h,v $
+* Revision 6.154  2004/01/27 20:46:06  dondosha
+* Allow values 0, 1, 2 for no_traceback megablast option
+*
+* Revision 6.153  2004/01/05 22:09:26  madden
+* Put back dashes in date
+*
+* Revision 6.152  2004/01/02 13:44:32  coulouri
+* Revert to hardcoded BLAST_RELEASE_DATE
+*
+* Revision 6.151  2003/12/29 15:51:18  coulouri
+* Bump version, use __DATE__ instead of hardcoded date
+*
+* Revision 6.150  2003/11/06 19:52:13  dondosha
+* Added error MBTemplateType, so it can be returned when wordsize/template length combination is wrong
+*
 * Revision 6.149  2003/10/02 19:30:11  madden
 * add field seAlign to SWResults for use in kappa.c
 *
@@ -856,8 +871,8 @@ extern "C" {
 #endif
 
 /* the version of BLAST. */
-#define BLAST_ENGINE_VERSION "2.2.6"
-#define BLAST_RELEASE_DATE "Apr-09-2003"
+#define BLAST_ENGINE_VERSION "2.2.7"
+#define BLAST_RELEASE_DATE "Jan-02-2004"
 
 /* Defines for program numbers. (Translated in BlastGetProgramNumber). */
 #define blast_type_undefined 0
@@ -1104,7 +1119,7 @@ typedef struct _blast_optionsblk {
         Int4            max_num_patterns; /* Maximum number of patterns to be used in PHI-Blast search */
 	Boolean         no_check_score;
         Boolean         is_megablast_search; /* Is this a MegaBlast search? */
-        Boolean         no_traceback;    /* No traceback in MegaBLAST extension */
+        Uint1         no_traceback;    /* No traceback in MegaBLAST extension */
         Boolean         is_rps_blast;     /* If this RPS Blast ? */
         SeqLocPtr       query_lcase_mask; /* Masking of input DNA regions */
         Boolean         sort_gi_list;     /* Should the gi list be sorted? */
@@ -1170,7 +1185,7 @@ struct _blast_wizardoptionsblk {
     CharPtr         matrix;
     MBDiscWordType  mb_disc_type;
     Int2            mb_template_length;
-    Boolean         no_traceback;
+    Uint1           no_traceback;
     Int2            penalty;
     FloatLo         perc_identity;
     Boolean         perform_culling;
@@ -1254,11 +1269,12 @@ typedef enum {
    TEMPL_11_18_OPT = 8,
    TEMPL_12_18_OPT = 9,
    TEMPL_11_21_OPT = 10,
-   TEMPL_12_21_OPT = 11
+   TEMPL_12_21_OPT = 11,
+   TEMPL_ERROR = -1
 } MBTemplateType;
 
 typedef struct _mb_parameter_blk_ {
-   Boolean no_traceback;    /* No traceback in greedy extension */
+   Uint1 no_traceback;    /* No traceback in greedy extension */
    Boolean is_neighboring;  /* Is this a neighboring task? */ 
    Boolean full_seqids;     /* Print full seqids in tabular output? */
    FloatLo perc_identity;   /* Identity percentage cut-off */
diff --git a/tools/blastkar.c b/tools/blastkar.c
index 831bc3c2..7e6e6e35 100644
--- a/tools/blastkar.c
+++ b/tools/blastkar.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: blastkar.c,v 6.90 2003/06/30 20:01:32 dondosha Exp $";
+static char const rcsid[] = "$Id: blastkar.c,v 6.95 2003/12/12 16:00:34 madden Exp $";
 
 /* ===========================================================================
 *
@@ -49,8 +49,24 @@ Detailed Contents:
 	- calculate pseuod-scores from p-values.
 
 ****************************************************************************** 
- * $Revision: 6.90 $
+ * $Revision: 6.95 $
  * $Log: blastkar.c,v $
+ * Revision 6.95  2003/12/12 16:00:34  madden
+ * Add gap_decay_rate to BlastCutoffs, remove BlastCutoffs_simple, protection against overflow, removal of defunct _real variables (all from Mike Gertz)
+ *
+ * Revision 6.94  2003/11/30 03:36:38  camacho
+ * Fix compilation error
+ *
+ * Revision 6.93  2003/11/28 22:39:40  camacho
+ * +static keyword to BlastKarlinLtoH
+ *
+ * Revision 6.92  2003/11/28 15:16:38  camacho
+ * Combine newkar.c's contents with blastkar.c
+ *
+ * Revision 6.91  2003/11/26 19:08:10  madden
+ * simplified BlastKarlinLtoH and BlastKarlinLHtoK and provided better protection against overflow, new function NlmKarlinLambdaNR (all from Mike Gertz)
+ *
+ *
  * Revision 6.90  2003/06/30 20:01:32  dondosha
  * Correction in logic of finding matrices by BLASTMAT environment variable
  *
@@ -2975,10 +2991,10 @@ BlastKarlinkGapBlkFill(BLAST_KarlinBlkPtr kbp, Int4 gap_open, Int4 gap_extend, I
 			{
 				if (kbp)
 				{
-					kbp->Lambda_real = kbp->Lambda = values[index][3];
-					kbp->K_real = kbp->K = values[index][4];
-					kbp->logK_real = kbp->logK = log(kbp->K);
-					kbp->H_real = kbp->H = values[index][5];
+					kbp->Lambda = values[index][3];
+					kbp->K = values[index][4];
+					kbp->logK = log(kbp->K);
+					kbp->H = values[index][5];
 				}
 				found_values = TRUE;
 				break;
@@ -3127,6 +3143,40 @@ BlastKarlinReportAllowedValues(const Char *matrix_name, ValNodePtr PNTR error_re
 	return 0;
 }
 
+/*
+	BlastKarlinLtoH
+
+	Calculate H, the relative entropy of the p's and q's
+*/
+static Nlm_FloatHi LIBCALL
+BlastKarlinLtoH(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi	lambda)
+{
+	BLAST_Score	score;
+	Nlm_FloatHi	H, etonlam, sum, scale;
+
+	Nlm_FloatHi PNTR probs = sfp->sprob;
+	BLAST_Score low   = sfp->obs_min,  high  = sfp->obs_max;
+
+	if (lambda < 0.) {
+		return -1.;
+	}
+	if (BlastScoreChk(low, high) != 0) return -1.;
+
+	etonlam = exp( - lambda );
+  sum = low * probs[low];
+  for( score = low + 1; score <= high; score++ ) {
+    sum = score * probs[score] + etonlam * sum;
+  }
+
+  scale = Nlm_Powi( etonlam, high );
+  if( scale > 0 ) {
+    H = lambda * sum/scale;
+  } else { /* Underflow of exp( -lambda * high ) */
+    H = lambda * exp( lambda * high + log(sum) );
+  }
+	return H;
+}
+
 /* 
         Everything below here was (more or less) copied from the old 
         karlin.c and could work separately from the stuff above. 
@@ -3206,41 +3256,41 @@ BlastKarlinBlkCalc(BLAST_KarlinBlkPtr kbp, BLAST_ScoreFreqPtr sfp)
 
 	/* Calculate the parameter Lambda */
 
-	kbp->Lambda_real = kbp->Lambda = BlastKarlinLambdaNR(sfp);
+	kbp->Lambda = BlastKarlinLambdaNR(sfp);
 	if (kbp->Lambda < 0.)
 		goto ErrExit;
 
 
 	/* Calculate H */
 
-	kbp->H_real = kbp->H = BlastKarlinLtoH(sfp, kbp->Lambda);
+	kbp->H = BlastKarlinLtoH(sfp, kbp->Lambda);
 	if (kbp->H < 0.)
 		goto ErrExit;
 
 
 	/* Calculate K and log(K) */
 
-	kbp->K_real = kbp->K = BlastKarlinLHtoK(sfp, kbp->Lambda, kbp->H);
+	kbp->K = BlastKarlinLHtoK(sfp, kbp->Lambda, kbp->H);
 	if (kbp->K < 0.)
 		goto ErrExit;
-	kbp->logK_real = kbp->logK = log(kbp->K);
+	kbp->logK = log(kbp->K);
 
 	/* Normal return */
 	return 0;
 
 ErrExit:
-	kbp->Lambda = kbp->H = kbp->K
-		= kbp->Lambda_real = kbp->H_real = kbp->K_real = -1.;
+	kbp->Lambda = kbp->H = kbp->K = -1.;
 #ifdef BLASTKAR_HUGE_VAL
-	kbp->logK_real = kbp->logK = BLASTKAR_HUGE_VAL;
+	kbp->logK = BLASTKAR_HUGE_VAL;
 #else
-	kbp->logK_real = kbp->logK = 1.e30;
+	kbp->logK = 1.e30;
 #endif
 	return 1;
 }
 #define DIMOFP0	(iter*range + 1)
 #define DIMOFP0_MAX (BLAST_KARLIN_K_ITER_MAX*BLAST_SCORE_RANGE_MAX+1)
 
+
 Nlm_FloatHi
 BlastKarlinLHtoK(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi	lambda, Nlm_FloatHi H)
 {
@@ -3260,7 +3310,7 @@ BlastKarlinLHtoK(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi	lambda, Nlm_FloatHi H)
 	int		iter;
 	Nlm_FloatHi	sumlimit;
 	Nlm_FloatHi	PNTR p, PNTR ptrP, PNTR ptr1, PNTR ptr2, PNTR ptr1e;
-	Nlm_FloatHi	etolami, etolam;
+	Nlm_FloatHi	x;
         Boolean         bi_modal_score = FALSE;
 
 	if (lambda <= 0. || H <= 0.) {
@@ -3289,7 +3339,7 @@ BlastKarlinLHtoK(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi	lambda, Nlm_FloatHi H)
 	range = high - low;
 
 	av = H/lambda;
-	etolam = exp((Nlm_FloatHi)lambda);
+	x = exp((Nlm_FloatHi) -lambda);
 
 	if (low == -1 || high == 1) {
            if (high == 1)
@@ -3298,7 +3348,7 @@ BlastKarlinLHtoK(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi	lambda, Nlm_FloatHi H)
               score_avg = sfp->score_avg / d;
               K = (score_avg * score_avg) / av;
            }
-           return K * (1.0 - 1./etolam);
+           return K * (1.0 - x);
 	}
 
 	sumlimit = BLAST_KARLIN_K_SUMLIMIT_DEFAULT;
@@ -3341,11 +3391,13 @@ BlastKarlinLHtoK(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi	lambda, Nlm_FloatHi H)
               if (ptrP - P0 <= range)
                  --last;
            }
-           etolami = Nlm_Powi((Nlm_FloatHi)etolam, lo - 1);
-           for (sum = 0., i = lo; i != 0; ++i) {
-              etolami *= etolam;
-              sum += *++ptrP * etolami;
-           }
+					 /* Horner's rule */
+					 sum = *++ptrP;
+					 for( i = lo + 1; i < 0; i++ ) {
+						 sum = *++ptrP + sum * x;
+					 }
+					 sum *= x;
+
            for (; i <= hi; ++i)
               sum += *++ptrP;
            oldsum2 = oldsum;
@@ -3366,92 +3418,21 @@ BlastKarlinLHtoK(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi	lambda, Nlm_FloatHi H)
            }
         }
 
-	if (etolam > 0.05) 
-	{
-           etolami = 1 / etolam;
-           K = exp((Nlm_FloatHi)-2.0*Sum) / (av*(1.0 - etolami));
+	if (x <  1.0 / 0.05 ) {
+		K = exp((double)-2.0*Sum) / (av*(1.0 - x));
+	} else {
+		K = -exp((double)-2.0*Sum) / (av*Expm1(-(double)lambda));
 	}
-	else
-           K = -exp((Nlm_FloatHi)-2.0*Sum) / (av*Nlm_Expm1(-(Nlm_FloatHi)lambda));
 
 CleanUp:
 #ifndef BLAST_KARLIN_K_STACKP
 	if (P0 != NULL)
 		MemFree(P0);
 #endif
+
 	return K;
 }
 
-/*
-	BlastKarlinLambdaBis
-
-	Calculate Lambda using the bisection method (slow).
-*/
-Nlm_FloatHi
-BlastKarlinLambdaBis(BLAST_ScoreFreqPtr sfp)
-{
-	register Nlm_FloatHi	PNTR sprob;
-	Nlm_FloatHi	lambda, up, newval;
-	BLAST_Score	i, low, high, d;
-	int		j;
-	register Nlm_FloatHi	sum, x0, x1;
-
-	if (sfp->score_avg >= 0.) {
-		return -1.;
-	}
-	low = sfp->obs_min;
-	high = sfp->obs_max;
-	if (BlastScoreChk(low, high) != 0)
-		return -1.;
-
-	sprob = sfp->sprob;
-
-        /* Find greatest common divisor of all scores */
-    	for (i = 1, d = -low; i <= high-low && d > 1; ++i) {
-           if (sprob[i+low] != 0)
-              d = Nlm_Gcd(d, i);
-        }
-
-        high = high / d;
-        low = low / d;
-
-	up = BLAST_KARLIN_LAMBDA0_DEFAULT;
-	for (lambda=0.; ; ) {
-		up *= 2;
-		x0 = exp((Nlm_FloatHi)up);
-		x1 = Nlm_Powi((Nlm_FloatHi)x0, low - 1);
-		if (x1 > 0.) {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i*d] * (x1 *= x0);
-		}
-		else {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i*d] * exp(up * i);
-		}
-		if (sum >= 1.0)
-			break;
-		lambda = up;
-	}
-
-	for (j=0; j<BLAST_KARLIN_LAMBDA_ITER_DEFAULT; ++j) {
-		newval = (lambda + up) / 2.;
-		x0 = exp((Nlm_FloatHi)newval);
-		x1 = Nlm_Powi((Nlm_FloatHi)x0, low - 1);
-		if (x1 > 0.) {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i*d] * (x1 *= x0);
-		}
-		else {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i*d] * exp(newval * i);
-		}
-		if (sum > 1.0)
-			up = newval;
-		else
-			lambda = newval;
-	}
-	return (lambda + up) / (2. * d);
-}
 
 /******************* Fast Lambda Calculation Subroutine ************************
 	Version 1.0	May 16, 1991
@@ -3461,100 +3442,189 @@ BlastKarlinLambdaBis(BLAST_ScoreFreqPtr sfp)
 	guess (lambda0) obtained perhaps by the bisection method.
 *******************************************************************************/
 
+/**
+ * Find positive solution to sum_{i=low}^{high} exp(i lambda) = 1.
+ * 
+ * @param probs probabilities of a score occuring 
+ * @param d the gcd of the possible scores. This equals 1 if the scores
+ * are not a lattice
+ * @param low the lowest possible score
+ * @param high the highest possible score
+ * @param lambda0 an initial value for lambda
+ * @param tolx the tolerance to which lambda must be computed
+ * @param itmax the maximum number of times the function may be
+ * evaluated
+ * @param maxNewton the maximum permissible number of Newton
+ * iteration. After that the computation will proceed by bisection.
+ * @param itn a pointer to an integer that will receive the actually
+ * number of iterations performed.
+ *
+ * Let phi(lambda) =  sum_{i=low}^{high} exp(i lambda) - 1. Then phi(lambda)
+ * may be written
+ *
+ *     phi(lamdba) = exp(u lambda) p( exp(-lambda) )
+ *
+ * where p(x) is a polynomial that has exactly two zeros, one at x = 1
+ * and one at y = exp(-lamdba). It is simpler, more numerically
+ * efficient and stable to apply Newton's method to p(x) than to
+ * phi(lambda).
+ *
+ * We define a safeguarded Newton iteration as follows. Let the
+ * initial interval of uncertainty be [0,1]. If p'(x) >= 0, we bisect
+ * the interval. Otherwise we try a Newton step. If the Newton iterate
+ * lies in the current interval of uncertainty and it reduces the
+ * value of | p(x) | by at least 10%, we accept the new
+ * point. Otherwise, we bisect the current interval of uncertainty.
+ * It is clear that this method converges to a zero of p(x).  Since
+ * p'(x) > 0 in an interval containing x = 1, the method cannot
+ * converge to x = 1 and therefore converges to the only other zero,
+ * y.
+ */
+
+static Nlm_FloatHi 
+NlmKarlinLambdaNR( Nlm_FloatHi PNTR probs, BLAST_Score d,
+									 BLAST_Score low, BLAST_Score high, 
+									 Nlm_FloatHi lambda0, Nlm_FloatHi tolx,
+									 int itmax, int maxNewton, int * itn ) 
+{
+  int k;
+  Nlm_FloatHi x0, x, a = 0, b = 1;
+  Nlm_FloatHi f = 4;  /* Larger than any possible value of the poly in [0,1] */
+  int isNewton = 0; /* we haven't yet taken a Newton step. */
+
+  assert( d > 0 );
+
+	x0 = exp( -lambda0 );
+  x = ( 0 < x0 && x0 < 1 ) ? x0 : .5;
+  
+  for( k = 0; k < itmax; k++ ) { /* all iteration indices k */
+    int i;
+    Nlm_FloatHi g, fold = f;
+    int wasNewton = isNewton; /* If true, then the previous step was a */
+                              /* Newton step */
+    isNewton  = 0;            /* Assume that this step is not */
+    
+    /* Horner's rule for evaluating a polynomial and its derivative */
+    g = 0;
+    f = probs[low];
+    for( i = low + d; i < 0; i += d ) {
+      g = x * g + f;
+      f = f * x + probs[i];
+    }
+    g = x * g + f;
+    f = f * x + probs[0] - 1;
+    for( i = d; i <= high; i += d ) {
+      g = x * g + f;
+      f = f * x + probs[i];
+    }
+    /* End Horner's rule */
+
+    if( f > 0 ) {
+      a = x; /* move the left endpoint */
+    } else if( f < 0 ) { 
+      b = x; /* move the right endpoint */
+    } else { /* f == 0 */
+      break; /* x is an exact solution */
+    }
+    if( b - a < 2 * a * ( 1 - b ) * tolx ) {
+      /* The midpoint of the interval converged */
+      x = (a + b) / 2; break;
+    }
+
+    if( k >= maxNewton ||
+        /* If convergence of Newton's method appears to be failing; or */
+				( wasNewton && fabs( f ) > .9 * fabs(fold) ) ||  
+        /* if the previous iteration was a Newton step but didn't decrease 
+         * f sufficiently; or */
+        g >= 0 
+        /* if a Newton step will move us away from the desired solution */
+        ) { /* then */
+      /* bisect */
+      x = (a + b)/2;
+    } else {
+      /* try a Newton step */
+      double p = - f/g;
+      double y = x + p;
+      if( y <= a || y >= b ) { /* The proposed iterate is not in (a,b) */
+        x = (a + b)/2;
+      } else { /* The proposed iterate is in (a,b). Accept it. */
+        isNewton = 1;
+        x = y;
+        if( fabs( p ) < tolx * x * (1-x) ) break; /* Converged */
+      } /* else the proposed iterate is in (a,b) */
+    } /* else try a Newton step. */ 
+  } /* end for all iteration indices k */
+	*itn = k; 
+  return -log(x)/d;
+}
+
+
 Nlm_FloatHi
 BlastKarlinLambdaNR(BLAST_ScoreFreqPtr sfp)
 {
 	BLAST_Score	low;			/* Lowest score (must be negative)  */
 	BLAST_Score	high;			/* Highest score (must be positive) */
-	int		j;
+	int		itn;
 	BLAST_Score	i, d;
 	Nlm_FloatHi PNTR	sprob;
-	Nlm_FloatHi	lambda0, sum, slope, temp, x0, x1, amt;
+	Nlm_FloatHi	returnValue;
 
 	low = sfp->obs_min;
 	high = sfp->obs_max;
 	if (sfp->score_avg >= 0.) {	/* Expected score must be negative */
 		return -1.0;
 	}
-	if (BlastScoreChk(low, high) != 0)
-		return -1.;
-
-	lambda0 = BLAST_KARLIN_LAMBDA0_DEFAULT;
-
+	if (BlastScoreChk(low, high) != 0) return -1.;
+	
 	sprob = sfp->sprob;
-        /* Find greatest common divisor of all scores */
-    	for (i = 1, d = -low; i <= high-low && d > 1; ++i) {
-           if (sprob[i+low] != 0)
-              d = Nlm_Gcd(d, i);
-        }
-
-        high = high / d;
-        low = low / d;
-	/* Calculate lambda */
-
-	for (j=0; j<20; ++j) { /* limit of 20 should never be close-approached */
-		sum = -1.0;
-		slope = 0.0;
-		if (lambda0 < 0.01)
-			break;
-		x0 = exp((Nlm_FloatHi)lambda0);
-		x1 = Nlm_Powi((Nlm_FloatHi)x0, low - 1);
-		if (x1 == 0.)
-			break;
-		for (i=low; i<=high; i++) {
-			sum += (temp = sprob[i*d] * (x1 *= x0));
-			slope += temp * i;
-		}
-		lambda0 -= (amt = sum/slope);
-		if (ABS(amt/lambda0) < BLAST_KARLIN_LAMBDA_ACCURACY_DEFAULT) {
-			/*
-			Does it appear that we may be on the verge of converging
-			to the ever-present, zero-valued solution?
-			*/
-			if (lambda0 > BLAST_KARLIN_LAMBDA_ACCURACY_DEFAULT)
-				return lambda0 / d;
-			break;
+	/* Find greatest common divisor of all scores */
+	for (i = 1, d = -low; i <= high-low && d > 1; ++i) {
+		if (sprob[i+low] != 0) {
+			d = Nlm_Gcd(d, i);
 		}
 	}
-	return BlastKarlinLambdaBis(sfp);
-}
+	returnValue =
+		NlmKarlinLambdaNR( sprob, d, low, high,
+											 BLAST_KARLIN_LAMBDA0_DEFAULT,
+											 BLAST_KARLIN_LAMBDA_ACCURACY_DEFAULT,
+											 20, 20 + BLAST_KARLIN_LAMBDA_ITER_DEFAULT, &itn );
 
-/*
-	BlastKarlinLtoH
 
-	Calculate H, the relative entropy of the p's and q's
-*/
+	return returnValue;
+}
+
 Nlm_FloatHi LIBCALL
-BlastKarlinLtoH(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi	lambda)
+impalaKarlinLambdaNR(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi initialLambda)
 {
-	BLAST_Score	score;
-	Nlm_FloatHi	av, etolam, etolami;
+	Nlm_FloatHi returnValue;
+	int itn;
+	Nlm_FloatHi PNTR	sprob = sfp->sprob;
 
-	if (lambda < 0.) {
-		return -1.;
-	}
-	if (BlastScoreChk(sfp->obs_min, sfp->obs_max) != 0)
-		return -1.;
-
-	etolam = exp((Nlm_FloatHi)lambda);
-	etolami = Nlm_Powi((Nlm_FloatHi)etolam, sfp->obs_min - 1);
-	if (etolami > 0.) 
-	{
-	    av = 0.0;
-	    for (score=sfp->obs_min; score<=sfp->obs_max; score++)
-   			av += sfp->sprob[score] * score * (etolami *= etolam);
+	if (sfp->score_avg >= 0.) {	/* Expected score must be negative */
+		return -1.0;
 	}
-	else 
 	{
-	    av = 0.0;
-	    for (score=sfp->obs_min; score<=sfp->obs_max; score++)
-   			av += sfp->sprob[score] * score * exp(lambda * score);
+		Boolean foundPositive = FALSE;
+		BLAST_Score	j;
+		for(j = 1; j <=sfp->obs_max; j++) {
+			if (sprob[j] > 0.0) {
+				foundPositive = TRUE;
+				break;
+			}
+		}
+		if (!foundPositive) return(-1);
 	}
 
-    	return lambda * av;
+	returnValue =
+		NlmKarlinLambdaNR( sprob, 1, sfp->obs_min, sfp->obs_max,
+			                 initialLambda, BLAST_KARLIN_LAMBDA_ACCURACY_DEFAULT,
+											 20, 20 + BLAST_KARLIN_LAMBDA_ITER_DEFAULT, &itn );
+
+	return returnValue;
 }
 
 
+
 static Nlm_FloatHi
 BlastGapDecayInverse(Nlm_FloatHi pvalue, unsigned nsegs, Nlm_FloatHi decayrate)
 {
@@ -3584,19 +3654,9 @@ Int2 LIBCALL
 BlastCutoffs(BLAST_ScorePtr S, /* cutoff score */
 	Nlm_FloatHi PNTR E, /* expected no. of HSPs scoring at or above S */
 	BLAST_KarlinBlkPtr kbp,
-	Nlm_FloatHi qlen, /* length of query sequence */
-	Nlm_FloatHi dblen, /* length of database or database sequence */
-	Nlm_Boolean dodecay) /* TRUE ==> use gapdecay feature */
-{
-	return BlastCutoffs_simple(S, E, kbp, qlen*dblen, dodecay);
-}
-
-Int2 LIBCALL
-BlastCutoffs_simple(BLAST_ScorePtr S, /* cutoff score */
-	Nlm_FloatHi PNTR E, /* expected no. of HSPs scoring at or above S */
-	BLAST_KarlinBlkPtr kbp,
 	Nlm_FloatHi searchsp, /* size of search space. */
-	Nlm_Boolean dodecay) /* TRUE ==> use gapdecay feature */
+	Nlm_Boolean dodecay,  /* TRUE ==> use gapdecay feature */
+  Nlm_FloatHi gap_decay_rate )
 {
 	BLAST_Score	s = *S, es;
 	Nlm_FloatHi	e = *E, esave;
@@ -3614,7 +3674,7 @@ BlastCutoffs_simple(BLAST_ScorePtr S, /* cutoff score */
 	if (e > 0.) 
 	{
 		if (dodecay)
-			e = BlastGapDecayInverse(e, 1, 0.5);
+			e = BlastGapDecayInverse(e, 1, gap_decay_rate);
 		es = BlastKarlinEtoS_simple(e, kbp, searchsp);
 	}
 	/*
@@ -3633,7 +3693,7 @@ BlastCutoffs_simple(BLAST_ScorePtr S, /* cutoff score */
 	{
 		e = BlastKarlinStoE_simple(s, kbp, searchsp);
 		if (dodecay)
-			e = BlastGapDecay(e, 1, 0.5);
+			e = BlastGapDecay(e, 1, gap_decay_rate);
 		*E = e;
 	}
 
@@ -4022,7 +4082,7 @@ BlastSmallGapSumE(BLAST_KarlinBlkPtr kbp, Int4 gap, Nlm_FloatHi gap_prob, Nlm_Fl
 			sum_e = sum_e/gap_prob;
 	}
 
-	return sum_e;
+	return (sum_e <= INT4_MAX) ?  sum_e : INT4_MAX;
 }
 
 /*
@@ -4057,7 +4117,7 @@ BlastUnevenGapSumE(BLAST_KarlinBlkPtr kbp, Int4 p_gap, Int4 n_gap, Nlm_FloatHi g
 			sum_e = sum_e/gap_prob;
 	}
 
-	return sum_e;
+	return (sum_e <= INT4_MAX) ?  sum_e : INT4_MAX; 
 }
 
 /*
@@ -4094,7 +4154,7 @@ BlastLargeGapSumE(BLAST_KarlinBlkPtr kbp, Nlm_FloatHi gap_prob, Nlm_FloatHi gap_
 			sum_e = sum_e/(1.0 - gap_prob);
 	}
 
-	return sum_e;
+	return (sum_e <= INT4_MAX) ?  sum_e : INT4_MAX; 
 }
 
 /********************************************************************
diff --git a/tools/blastkar.h b/tools/blastkar.h
index 7d289851..41d56aa3 100644
--- a/tools/blastkar.h
+++ b/tools/blastkar.h
@@ -32,8 +32,17 @@ Contents: definitions and prototypes used by blastkar.c to calculate BLAST
 
 ******************************************************************************/
 
-/* $Revision: 6.31 $ 
+/* $Revision: 6.34 $ 
 * $Log: blastkar.h,v $
+* Revision 6.34  2003/12/12 16:00:46  madden
+* Add gap_decay_rate to BlastCutoffs, remove BlastCutoffs_simple, removal of defunct _real variables (all from Mike Gertz)
+*
+* Revision 6.33  2003/11/28 22:39:41  camacho
+* +static keyword to BlastKarlinLtoH
+*
+* Revision 6.32  2003/11/26 19:09:09  madden
+* Remove ref to BlastKarlinLambdaBis (no longer needed per Mike Gertz)
+*
 * Revision 6.31  2003/02/27 19:07:56  madden
 * Add functions PrintMatrixMessage and PrintAllowedValuesMessage
 *
@@ -308,9 +317,6 @@ typedef struct {
 		Nlm_FloatHi	Lambda; /* Lambda value used in statistics */
 		Nlm_FloatHi	K, logK; /* K value used in statistics */
 		Nlm_FloatHi	H; /* H value used in statistics */
-		/* "real" values are ones actually found, may be replaced by above */
-		Nlm_FloatHi	Lambda_real, K_real, logK_real, H_real;
-		Int4 q_frame, s_frame; /* reading frame for query and subject.*/
 		Nlm_FloatHi	paramC;	/* for use in seed. */
 	} BLAST_KarlinBlk, PNTR BLAST_KarlinBlkPtr;
 
@@ -499,12 +505,8 @@ Int2 LIBCALL BlastKarlinReportAllowedValues(const Char *matrix_name, ValNodePtr
 
 Nlm_FloatHi BlastKarlinLHtoK PROTO((BLAST_ScoreFreqPtr sfp, Nlm_FloatHi lambda, Nlm_FloatHi H));
 
-Nlm_FloatHi BlastKarlinLambdaBis PROTO((BLAST_ScoreFreqPtr sfp));
-
 Nlm_FloatHi BlastKarlinLambdaNR PROTO((BLAST_ScoreFreqPtr sfp));
 
-Nlm_FloatHi LIBCALL BlastKarlinLtoH PROTO((BLAST_ScoreFreqPtr sfp, Nlm_FloatHi  lambda));
-
 BLAST_Score LIBCALL BlastKarlinEtoS PROTO((Nlm_FloatHi  E, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi  qlen, Nlm_FloatHi  dblen));
 
 BLAST_Score LIBCALL BlastKarlinEtoS_simple PROTO((Nlm_FloatHi  E, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi searchsp)); 
@@ -521,10 +523,9 @@ Nlm_FloatHi LIBCALL BlastKarlinStoE PROTO((BLAST_Score S, BLAST_KarlinBlkPtr kbp
 
 Nlm_FloatHi LIBCALL BlastKarlinStoE_simple PROTO((BLAST_Score S, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi  searchsp));
 
-Int2 LIBCALL BlastCutoffs PROTO((BLAST_ScorePtr S, Nlm_FloatHi PNTR E, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi qlen, Nlm_FloatHi dblen, Nlm_Boolean dodecay));
-
+Int2 LIBCALL BlastCutoffs PROTO((BLAST_ScorePtr S, Nlm_FloatHi PNTR E, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi search_sp, Nlm_Boolean dodecay,
+  Nlm_FloatHi gap_decay_rate));
 
-Int2 LIBCALL BlastCutoffs_simple PROTO((BLAST_ScorePtr S, Nlm_FloatHi PNTR E, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi search_sp, Nlm_Boolean dodecay));
 Nlm_FloatHi LIBCALL BlastKarlinStoLen PROTO((BLAST_KarlinBlkPtr kbp, BLAST_Score S));
 
 /* SumP function. Called by BlastSmallGapSumE and BlastLargeGapSumE. */
diff --git a/tools/blastool.c b/tools/blastool.c
index e1ad48da..3dc73492 100644
--- a/tools/blastool.c
+++ b/tools/blastool.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: blastool.c,v 6.253 2003/09/12 16:02:06 dondosha Exp $";
+static char const rcsid[] = "$Id: blastool.c,v 6.258 2003/12/30 15:14:40 camacho Exp $";
 
 /* ===========================================================================
 *
@@ -34,8 +34,25 @@ Contents: Utilities for BLAST
 
 ******************************************************************************/
 /*
-* $Revision: 6.253 $
+* $Revision: 6.258 $
 * $Log: blastool.c,v $
+* Revision 6.258  2003/12/30 15:14:40  camacho
+* Fix to MergeDbGiListsWithOIDLists:
+* When searching gi lists for matches in rdfp linked list, isolate each
+* element of the linked list first.
+*
+* Revision 6.257  2003/12/23 23:28:27  dondosha
+* Use number of identities from the seqalign to calculate percent identity in tabular output
+*
+* Revision 6.256  2003/12/12 16:01:23  madden
+* Change to signature of BlastCutoffs, remove BlastCutoffs_simple
+*
+* Revision 6.255  2003/11/10 16:59:42  dondosha
+* Print the seqid in AcknowledgeBlastQuery for any non-local id
+*
+* Revision 6.254  2003/10/29 17:46:59  dondosha
+* Allow 2-stage greedy extension in megablast
+*
 * Revision 6.253  2003/09/12 16:02:06  dondosha
 * If gap open is non-zero for megablast, require gap extension option to be non-zero too
 *
@@ -1076,30 +1093,50 @@ FormatBlastParameters(BlastSearchBlkPtr search)
            cutoff = 0;
         }
         if (search->last_context <= 1) {
-           evalue = pbp->cutoff_e;
-           if (StringCmp(search->prog_name, "blastn") == 0 ||
-               search->pbp->gapped_calculation == FALSE) {
-	     /* AM: Changed to support query concatenation. */
-             if( !search->mult_queries )
-               BlastCutoffs(&cutoff, &evalue, search->sbp->kbp[search->first_context], (Nlm_FloatHi) search->context[search->first_context].query->effective_length, (Nlm_FloatHi) search->dblen_eff, FALSE);
-             else
-               { BlastCutoffs(&cutoff, &evalue, search->sbp->kbp[search->first_context], (Nlm_FloatHi) search->mult_queries->MinLenEff, (Nlm_FloatHi) search->dblen_eff, FALSE); }
-
-              sprintf(buffer, "S2: %ld (%4.1f bits)", (long) cutoff, (((cutoff)*(search->sbp->kbp[search->first_context]->Lambda))-(search->sbp->kbp[search->first_context]->logK))/NCBIMATH_LN2);
-           } else {
-	     if( !search->mult_queries )
-               BlastCutoffs(&cutoff, &evalue, search->sbp->kbp_gap[search->first_context], (Nlm_FloatHi) search->context[search->first_context].query->effective_length, (Nlm_FloatHi) search->dblen_eff, FALSE);
-             else
-               BlastCutoffs( &cutoff, &evalue, 
-	                     search->sbp->kbp_gap[search->first_context],
-			     (Nlm_FloatHi)search->mult_queries->MinLenEff, 
-			     (Nlm_FloatHi)search->dblen_eff, FALSE );
-
-              sprintf(buffer, "S2: %ld (%4.1f bits)", (long) cutoff, (((cutoff)*(search->sbp->kbp_gap[search->first_context]->Lambda))-(search->sbp->kbp_gap[search->first_context]->logK))/NCBIMATH_LN2);
-           }
-           add_string_to_buffer(buffer, &ret_buffer, &ret_buffer_length);
+          evalue = pbp->cutoff_e;
+          if (StringCmp(search->prog_name, "blastn") == 0 ||
+              search->pbp->gapped_calculation == FALSE) {
+            /* AM: Changed to support query concatenation. */
+            if( !search->mult_queries ) {
+              Nlm_FloatHi search_sp =
+                search->context[search->first_context]
+                .query->effective_length *
+                (Nlm_FloatHi) search->dblen_eff;
+              BlastCutoffs(&cutoff, &evalue,
+                           search->sbp->kbp[search->first_context],
+                           search_sp, FALSE, 0.0 );
+            } else {
+              Nlm_FloatHi search_sp =
+                search->mult_queries->MinLenEff *
+                (Nlm_FloatHi) search->dblen_eff;
+              BlastCutoffs(&cutoff, &evalue,
+                           search->sbp->kbp[search->first_context],
+                           search_sp, FALSE, 0.0 );
+            }
+            
+            sprintf(buffer, "S2: %ld (%4.1f bits)", (long) cutoff, (((cutoff)*(search->sbp->kbp[search->first_context]->Lambda))-(search->sbp->kbp[search->first_context]->logK))/NCBIMATH_LN2);
+          } else {
+            if( !search->mult_queries ) {
+              Nlm_FloatHi search_sp =
+                search->context[search->first_context]
+                .query->effective_length *
+                (Nlm_FloatHi) search->dblen_eff;
+              BlastCutoffs(&cutoff, &evalue,
+                           search->sbp->kbp_gap[search->first_context],
+                           search_sp, FALSE, 0.0  );
+            } else {
+              Nlm_FloatHi search_sp =
+                search->mult_queries->MinLenEff *
+                (Nlm_FloatHi)search->dblen_eff;
+              BlastCutoffs( &cutoff, &evalue, 
+                            search->sbp->kbp_gap[search->first_context],
+                            search_sp, FALSE, 0.0 );
+            }
+            sprintf(buffer, "S2: %ld (%4.1f bits)", (long) cutoff, (((cutoff)*(search->sbp->kbp_gap[search->first_context]->Lambda))-(search->sbp->kbp_gap[search->first_context]->logK))/NCBIMATH_LN2);
+          }
+          add_string_to_buffer(buffer, &ret_buffer, &ret_buffer_length);
         }
-	return ret_buffer;
+        return ret_buffer;
 }
 
 /*
@@ -1430,7 +1467,7 @@ AcknowledgeBlastQuery(BioseqPtr bsp, Int4 line_length, FILE *outfp, Boolean beli
 		ff_AddString("<b>Query=</b> ");
 	else
 		ff_AddString("Query= ");
-	if (bsp->id && believe_query)
+	if (bsp->id && (bsp->id->choice != SEQID_LOCAL || believe_query))
 	{
 		SeqIdWrite(bsp->id, buffer, PRINTID_FASTA_LONG, BUFFER_LENGTH);
 		if (StringNCmp(buffer, "lcl|", 4) == 0)
@@ -2622,7 +2659,11 @@ static
 void MergeDbGiListsWithOIDLists(ReadDBFILEPtr rdfp_chain, ValNodePtr *err_ret,
         BlastGiListPtr *bglpp) 
 {
-    ReadDBFILEPtr  rdfp = NULL, rdfp_tmp = NULL;
+    ReadDBFILEPtr rdfp = NULL;  /* holds an individual element of the
+                                   rdfp_chain linked list */
+    ReadDBFILEPtr rdfp_tmp = NULL; /* holds the rest of the rdfp linked list
+                                      when searching for gis in a rdfp element
+                                      */
     BlastDoubleInt4Ptr	list=NULL, global_list = NULL;
     BlastGiListPtr tmp_list = NULL;
     Int4	i, index, ngis = 0, total_num_gis = 0, start;
@@ -2646,6 +2687,10 @@ void MergeDbGiListsWithOIDLists(ReadDBFILEPtr rdfp_chain, ValNodePtr *err_ret,
             ErrPostEx(SEV_FATAL, 1, 0, "Out of memory");
             return;
         }
+
+        /* Isolate the current rdfp element */
+        rdfp_tmp = rdfp->next;
+        rdfp->next = NULL;
            
         /* See which gis in rdfp->gilist belong to this rdfp */
         for (index=0, i=0; i < ngis; i++) {
@@ -2658,6 +2703,9 @@ void MergeDbGiListsWithOIDLists(ReadDBFILEPtr rdfp_chain, ValNodePtr *err_ret,
             }
         }
 
+        /* Restore the rdfp_chain linked list */
+        rdfp->next = rdfp_tmp;
+
         /* After this point we don't really need the rdfp->gilist */
         rdfp->gilist = Int4ListFree(rdfp->gilist);
 
@@ -4917,6 +4965,17 @@ void BlastPrintTabulatedResultsEx(SeqAlignPtr seqalign, BioseqPtr query_bsp,
       q_shift, s_shift, fp, num_formatted, print_query_info);
 }
 
+static Int4 FindNumIdentInScore(ScorePtr score)
+{
+   Int4 num_ident = 0;
+   for ( ; score; score = score->next) {
+      if (!strcmp(score->id->str, "num_ident")) {
+         num_ident = score->value.intvalue;
+      }
+   }
+   return num_ident;
+}
+
 void BlastPrintTabularResults(SeqAlignPtr seqalign, BioseqPtr query_bsp,
         SeqLocPtr query_slp, Int4 num_alignments, CharPtr blast_program, 
         Boolean is_ungapped, Boolean is_ooframe, Boolean believe_query, 
@@ -5056,6 +5115,8 @@ void BlastPrintTabularResults(SeqAlignPtr seqalign, BioseqPtr query_bsp,
                } else
                   num_gap_opens++;
             }
+            if ((num_ident = FindNumIdentInScore(sap->score)) > 0)
+               perc_ident = num_ident;
             perc_ident = perc_ident / align_length * 100;
             
             if (dsp->strands[0] != dsp->strands[1]) {
@@ -6433,7 +6494,7 @@ BLASTPostSearchLogic(BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options,
                   seqalign = SumBlastGetGappedAlignmentTraceback(
                                 search, index, FALSE, FALSE, 
                                 sequence+1, length);
-               } else if (!search->pbp->mb_params->no_traceback) {
+               } else {
                   /* Mega BLAST with non-greedy extension */
                   SumBlastGetGappedAlignmentEx(search, index, FALSE, FALSE, 
                                                sequence+1, length, TRUE,
diff --git a/tools/blastpri.h b/tools/blastpri.h
index db75abc8..421a5d0f 100644
--- a/tools/blastpri.h
+++ b/tools/blastpri.h
@@ -32,8 +32,14 @@ Contents: prototypes for "private" BLAST functions, these should not be called
 
 ******************************************************************************/
 
-/* $Revision: 6.109 $ 
+/* $Revision: 6.111 $ 
 * $Log: blastpri.h,v $
+* Revision 6.111  2004/01/16 23:43:43  dondosha
+* No more need for special argument for partial search: it is set in options
+*
+* Revision 6.110  2004/01/06 22:36:24  dondosha
+* Added BLAST_HSPFree function that frees the edit block and the HSP
+*
 * Revision 6.109  2003/08/20 22:12:56  dondosha
 * Added BlastPrintTabularResults with an extra boolean parameter for OOF alignments
 *
@@ -832,7 +838,6 @@ CharPtr FormatBlastParameters PROTO((BlastSearchBlkPtr search));
 
 
 SeqAlignPtr LIBCALL BioseqBlastEngineCore PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options, Int4Ptr *pos_matrix));
-SeqAlignPtr LIBCALL BioseqBlastEngineCoreEx PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options, Int4Ptr *pos_matrix, Boolean partial));
 
 Uint1Ptr GetSequenceWithDenseSeg PROTO((DenseSegPtr dsp, Boolean query, Int4Ptr start, Int4Ptr length));
 
@@ -1045,6 +1050,7 @@ SeqAlignPtr BlastClusterHitsFromSeqAlign PROTO((SeqAlignPtr seqalign, CharPtr pr
 SeqAlignPtr RedoAlignmentCore PROTO((BlastSearchBlkPtr search,   
   BLAST_OptionsBlkPtr options, Int4 hitlist_count, Boolean adjustParameters,
   Boolean SmithWaterman));
+BLAST_HSPPtr BLAST_HSPFree PROTO((BLAST_HSPPtr hsp));
 void BLASTResultFreeHsp PROTO((BLASTResultHitlistPtr result));
 void BLASTPostSearchLogic PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr
                                  options, SeqAlignPtr PNTR seqalignp,
diff --git a/tools/blastutl.c b/tools/blastutl.c
index 12a77967..1efd5cef 100644
--- a/tools/blastutl.c
+++ b/tools/blastutl.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: blastutl.c,v 6.417 2003/08/20 22:14:08 dondosha Exp $";
+static char const rcsid[] = "$Id: blastutl.c,v 6.429 2004/01/30 16:54:45 dondosha Exp $";
 
 /* ===========================================================================
 *
@@ -32,12 +32,48 @@ Author: Tom Madden
 
 Contents: Utilities for BLAST
 
-$Revision: 6.417 $
+$Revision: 6.429 $
 
 ******************************************************************************/
 /*
  *
 * $Log: blastutl.c,v $
+* Revision 6.429  2004/01/30 16:54:45  dondosha
+* Check if HSP needs to be deleted after reevaluation with ambiguities, after greedy traceback
+*
+* Revision 6.428  2004/01/28 16:54:03  dondosha
+* Restored the code that shifts subject coordinates for blastn traceback with long subject sequences
+*
+* Revision 6.427  2004/01/25 05:06:21  dondosha
+* Translate only relevant parts of long subject sequences for tblastn traceback
+*
+* Revision 6.426  2004/01/16 23:43:44  dondosha
+* No more need for special argument for partial search: it is set in options
+*
+* Revision 6.425  2004/01/14 17:01:06  dondosha
+* Gapped alignment is position based only if posMatrix exists
+*
+* Revision 6.424  2004/01/09 18:13:24  dondosha
+* In [Get,Check]StartForGappedAlignment: if posMatrix not available, use square matrix for calculations
+*
+* Revision 6.423  2004/01/06 22:37:40  dondosha
+* Use BLAST_HSPfree function; in particular fixes a bug with wrong memory being freed
+*
+* Revision 6.422  2003/12/11 23:46:28  dondosha
+* Correction in setting hit ranges after repeats filtering
+*
+* Revision 6.421  2003/12/10 17:05:28  dondosha
+* Added function ReevaluateScoreWithAmbiguities to reevaluate score for one HSP; use it after greedy traceback
+*
+* Revision 6.420  2003/11/24 22:06:41  madden
+* Tblastn optimization, only fetch part of sequence needed
+*
+* Revision 6.419  2003/10/30 18:37:19  dondosha
+* Fix for megablast with non-greedy traceback
+*
+* Revision 6.418  2003/10/29 17:46:59  dondosha
+* Allow 2-stage greedy extension in megablast
+*
 * Revision 6.417  2003/08/20 22:14:08  dondosha
 * Little correction in call to OOFBlastHSPGetNumIdentical
 *
@@ -2490,7 +2526,7 @@ BlastTwoSequencesCoreEx (BlastSearchBlkPtr search, BioseqPtr subject_bsp, Uint1P
 	}
         if (search->pbp->mb_params) {
            search->subject->sequence = subject_seq;
-           MegaBlastReevaluateWithAmbiguities(search, 0);
+           MegaBlastReevaluateWithAmbiguities(search);
         }
         status = BlastReapHitlistByEvalue(search);
 
@@ -4210,7 +4246,7 @@ BlastGetSubjectIdEx(BlastSearchBlkPtr search, Int4 hit_number, Boolean ordinal_n
     Uint4	header;
     BLASTResultsStructPtr result_struct;
     
-    if (search->pbp->mb_params && search->pbp->mb_params->use_dyn_prog)
+    if (search->pbp->mb_params)
        result_struct = search->mb_result_struct[query_number];
     else
        result_struct = search->result_struct;
@@ -4353,13 +4389,6 @@ SeqAlignPtr LIBCALL
 BioseqBlastEngineCore(BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options,
                         Int4Ptr *pos_matrix)
 {
-   return BioseqBlastEngineCoreEx(search, options, pos_matrix, FALSE);
-}
-
-SeqAlignPtr LIBCALL
-BioseqBlastEngineCoreEx(BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options,
-                        Int4Ptr *pos_matrix, Boolean partial)
-{
 	BLASTResultHspPtr hsp, hsp1;
 	BlastResultHspWithIdPtr PNTR hspp;
 	BLASTResultsStructPtr result_struct;
@@ -4565,7 +4594,7 @@ BioseqBlastEngineCoreEx(BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options,
 	}
 #endif  /* Clustering hits */
 
-    if (partial) {
+    if (options->no_traceback) {
        BlastStopAwakeThread(search->thr_info);
        return NULL;
     }
@@ -6388,8 +6417,8 @@ GetTranslation(Uint1Ptr query_seq, Int4 nt_length, Int2 frame, Int4Ptr length, C
 		if (IS_residue(new_residue))
 		{
 			prot_seq[index_prot] = new_residue;
-			index_prot++;
 		}
+		index_prot++;
 	}
 	prot_seq[index_prot] = NULLB;
 	*length = index_prot-1;
@@ -7544,6 +7573,13 @@ FilterWithSeg (Uint1Ptr sequence, Int4 length, Uint1 alphabet)
 #endif
 }
 
+
+BLAST_HSPPtr BLAST_HSPFree(BLAST_HSPPtr hsp)
+{
+   hsp->gap_info = GapXEditBlockDelete(hsp->gap_info);
+   return (BLAST_HSPPtr) MemFree(hsp);
+}
+
 /* 
 	Frees memory used for HSP's on the ResultHitlist.
 	Should be called as the SeqAlignPtr for a hitlist
@@ -7784,6 +7820,7 @@ Int4 GetStartForGappedAlignment (BlastSearchBlkPtr search, BLAST_HSPPtr hsp, Uin
 {
     Int4 index1, max_offset, score, max_score, hsp_end;
     Uint1Ptr query_var, subject_var;
+    Boolean positionBased = (search->positionBased && search->sbp->posMatrix);
     
     if (hsp->query.length <= HSP_MAX_WINDOW) {
         max_offset = hsp->query.offset + hsp->query.length/2;
@@ -7794,19 +7831,23 @@ Int4 GetStartForGappedAlignment (BlastSearchBlkPtr search, BLAST_HSPPtr hsp, Uin
     query_var = query + hsp->query.offset;
     subject_var = subject + hsp->subject.offset;
     score=0;
-    for (index1=hsp->query.offset; index1<hsp_end; index1++) {
-        if (!(search->positionBased))
-            score += matrix[*query_var][*subject_var];
-        else
-            score += search->sbp->posMatrix[index1][*subject_var];
-        query_var++; subject_var++;
+    if (!positionBased) {
+       for (index1=hsp->query.offset; index1<hsp_end; index1++) {
+          score += matrix[*query_var][*subject_var];
+          query_var++; subject_var++;
+       }
+    } else {
+       for (index1=hsp->query.offset; index1<hsp_end; index1++) {
+          score += search->sbp->posMatrix[index1][*subject_var];
+          query_var++; subject_var++;
+       }
     }
     max_score = score;
     max_offset = hsp_end - 1;
     hsp_end = hsp->query.end - 
         MAX(0, hsp->query.length - hsp->subject.length);
     for (index1=hsp->query.offset + HSP_MAX_WINDOW; index1<hsp_end; index1++) {
-        if (!(search->positionBased)) {
+        if (!positionBased) {
             score -= matrix[*(query_var-HSP_MAX_WINDOW)][*(subject_var-HSP_MAX_WINDOW)];
             score += matrix[*query_var][*subject_var];
         } else {
@@ -7838,7 +7879,8 @@ CheckStartForGappedAlignment (BlastSearchBlkPtr search, BLAST_HSPPtr hsp, Uint1P
 {
 	Int4 index1, score, start, end, width;
 	Uint1Ptr query_var, subject_var;
-
+        Boolean positionBased = 
+           (search->positionBased && search->sbp->posMatrix);
 
 	width = MIN((hsp->query.gapped_start-hsp->query.offset), HSP_MAX_WINDOW/2);
 	start = hsp->query.gapped_start - width;
@@ -7851,7 +7893,7 @@ CheckStartForGappedAlignment (BlastSearchBlkPtr search, BLAST_HSPPtr hsp, Uint1P
 	score=0;
 	for (index1=start; index1<end; index1++)
 	{
-	  if (!(search->positionBased))
+	  if (!positionBased)
 	    score += matrix[*query_var][*subject_var];
 	  else
 	    score += search->sbp->posMatrix[index1][*subject_var];
@@ -7883,6 +7925,9 @@ GetDbSubjRatio(BlastSearchBlkPtr search, Int4 subject_length)
 	return db_subj_ratio;
 }
 
+/* The following value should be divisible by 3, to make sure that frames stay
+   the same when translations are restricted to partial sequence. */
+#define SUBJECT_ADJUSTMENT 2100
 SeqAlignPtr LIBCALL 
 BlastGetGapAlgnTbckWithReaddb (BlastSearchBlkPtr search, Int4 hit_number, Boolean ordinal_number)
 
@@ -7891,6 +7936,9 @@ BlastGetGapAlgnTbckWithReaddb (BlastSearchBlkPtr search, Int4 hit_number, Boolea
 	BioseqPtr subject_bsp;
 	Boolean subject_allocated = FALSE;
 	Int4 index1, subject_length, rev_subject_length;
+	Int4 subject_start, subject_end;
+	Int4 hsp_count;
+	BLASTResultHspPtr hsp_array;
 	SeqAlignPtr seqalign;
 	SeqPortPtr spp;
 	Uint1Ptr subject, rev_subject;
@@ -7904,9 +7952,29 @@ BlastGetGapAlgnTbckWithReaddb (BlastSearchBlkPtr search, Int4 hit_number, Boolea
     		spp = SeqPortNew(subject_bsp, 0, -1, Seq_strand_plus, Seq_code_ncbi4na);
 		/* make one longer to "protect" ALIGN. */
 		subject = MemNew((1+subject_bsp->length)*sizeof(Uint1));
-		for (index1=0; index1<subject_bsp->length; index1++)
+		hsp_array = result_hitlist->hsp_array;
+		hsp_count = result_hitlist->hspcnt;
+		for (index1=0; index1<hsp_count; index1++)
 		{
-			subject[index1] = SeqPortGetResidue(spp);
+			if (hsp_array[index1].subject_frame > 0)
+			{ /* Get subsequence corresponding to this hsp. */
+				Int4 offset;
+
+				subject_start = 3*hsp_array[index1].subject_offset;
+				subject_end = subject_start + 3*hsp_array[index1].subject_length;
+
+				/* add SUBJECT_ADJUSTMENT bases to either end. */
+				subject_start = MAX(subject_start - SUBJECT_ADJUSTMENT, 0);
+				subject_end = MIN(subject_end + SUBJECT_ADJUSTMENT, subject_bsp->length);
+
+				SeqPortSeek(spp, subject_start, SEEK_SET);
+
+				for (offset=subject_start; offset<subject_end; offset++)
+					subject[offset] = SeqPortGetResidue(spp);
+
+				if (subject_start == 0 && subject_end == subject_bsp->length)
+					break;    /* entire sequence has been fetched. */
+			}
 		}
 		/* Gap character in last space. */
 		subject[subject_bsp->length] = NULLB;
@@ -7916,9 +7984,29 @@ BlastGetGapAlgnTbckWithReaddb (BlastSearchBlkPtr search, Int4 hit_number, Boolea
     		spp = SeqPortNew(subject_bsp, 0, -1, Seq_strand_minus, Seq_code_ncbi4na);
 		/* make one longer to "protect" ALIGN. */
 		rev_subject = MemNew((1+subject_bsp->length)*sizeof(Uint1));
-		for (index1=0; index1<subject_bsp->length; index1++)
+		hsp_array = result_hitlist->hsp_array;
+		hsp_count = result_hitlist->hspcnt;
+		for (index1=0; index1<hsp_count; index1++)
 		{
-			rev_subject[index1] = SeqPortGetResidue(spp);
+			if (hsp_array[index1].subject_frame < 0)
+			{ /* Get subsequence corresponding to this hsp. */
+				Int4 offset;
+
+				subject_start = 3*hsp_array[index1].subject_offset;
+				subject_end = subject_start + 3*hsp_array[index1].subject_length;
+
+				/* add SUBJECT_ADJUSTMENT bases to either end. */
+				subject_start = MAX(subject_start - SUBJECT_ADJUSTMENT, 0);
+				subject_end = MIN(subject_end + SUBJECT_ADJUSTMENT, subject_bsp->length);
+
+				SeqPortSeek(spp, subject_start, SEEK_SET);
+
+				for (offset=subject_start; offset<subject_end; offset++)
+					rev_subject[offset] = SeqPortGetResidue(spp);
+
+				if (subject_start == 0 && subject_end == subject_bsp->length)
+					break;    /* entire sequence has been fetched. */
+			}
 		}
 		/* Gap character in last space. */
 		rev_subject[subject_bsp->length] = NULLB;
@@ -8598,11 +8686,11 @@ BlastHitRangeLoad (BlastSearchBlkPtr search, BLAST_HSPPtr *hsp_array, Int4 hspcn
 		if (hsp->query.frame >= 0)
 		{
 			tmp->gi = hsp->query.offset;
-			tmp->ordinal_id = hsp->query.end;
+			tmp->ordinal_id = hsp->query.end - 1;
 		}
 		else
 		{
-			tmp->gi = query_length - hsp->query.end - 1;
+			tmp->gi = query_length - hsp->query.end;
 			tmp->ordinal_id = query_length - hsp->query.offset - 1;
 		}
 		tmp++;
@@ -8677,9 +8765,8 @@ static void BLASTCheckHSPInclusion(BLAST_HSPPtr *hsp_array, Int4 hspcnt,
                            mean, that current HSP should be removed. */
 
                         if(hsp_array[index] != NULL) {
-                            hsp_array[index]->gap_info = GapXEditBlockDelete(hsp_array[index]->gap_info);
-                            hsp_array[index] = MemFree(hsp_array[index]);
-			    break;
+                           hsp_array[index] = BLAST_HSPFree(hsp_array[index]);
+                           break;
                         }
                     }
                 }
@@ -8689,6 +8776,7 @@ static void BLASTCheckHSPInclusion(BLAST_HSPPtr *hsp_array, Int4 hspcnt,
     return;
 }
 
+
 /*
 	Take a BLAST_HSPPtr (array of HSP's) and get a traceback for them.
 */
@@ -8717,7 +8805,9 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
     Int4 max_start = MAX_DBSEQ_LEN / 2, start_shift;
     Int4 align_length;
     Int4 query_num; /* AM: Added to support query concatenation. */
-    
+    Boolean partial_translation;
+    Int4 translation_length;
+
     pbp = search->pbp;
     MemSet(&result_hsp, 0, sizeof(BLASTResultHsp));
     
@@ -8744,13 +8834,16 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
     gap_align->shift_pen = pbp->shift_pen; 
     
     gap_align->discontinuous = pbp->discontinuous;
-    gap_align->positionBased = search->positionBased;
+    gap_align->positionBased = 
+       (search->positionBased && search->sbp->posMatrix);
     gap_align->gap_open = pbp->gap_open;
     gap_align->gap_extend = pbp->gap_extend;
     gap_align->decline_align = pbp->decline_align;
     gap_align->x_parameter = pbp->gap_x_dropoff_final;
     gap_align->matrix = search->sbp->matrix;
     gap_align->posMatrix = search->sbp->posMatrix;
+    partial_translation = (subject_length > SUBJECT_ADJUSTMENT);
+
     for (index=0; index<hspcnt; index++) {
         hsp_start_is_contained = FALSE;
         hsp_end_is_contained = FALSE;
@@ -8842,6 +8935,8 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
                 gap_align->translate2 = FALSE;
             }
 
+            start_shift = 0;
+
             if (StringCmp(search->prog_name, "tblastn") == 0 ||
                 StringCmp(search->prog_name, "psitblastn") == 0) {
                 gap_align->translate1 = FALSE;
@@ -8851,7 +8946,32 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
                     translated_subject = translated_subject_orig + 3;
                     translated_subject_length_orig = MemNew(8*sizeof(Int4));
                     translated_subject_length = translated_subject_length_orig + 3;
-                } if (translated_subject[hsp->subject.frame] == NULL) {
+                } 
+                if (partial_translation) {
+                   translated_subject[hsp->subject.frame] = 
+                      MemFree(translated_subject[hsp->subject.frame]);
+                   /* NB: since SUBJECT_ADJUSTMENT is divisible by 3, the frame
+                      will remain the same.
+                   */
+                   start_shift = 
+                      MAX(0, 3*hsp->subject.offset - SUBJECT_ADJUSTMENT);
+                   translation_length =
+                      MIN(3*hsp->subject.end + SUBJECT_ADJUSTMENT, subject_length)
+                      - start_shift;
+                   if (hsp->subject.frame > 0) {
+                      translated_subject[hsp->subject.frame] =
+                         GetTranslation(subject+start_shift, translation_length, hsp->subject.frame, &translated_subject_length[hsp->subject.frame], search->db_genetic_code);
+                   } else {
+                      translated_subject[hsp->subject.frame] =
+                         GetTranslation(rev_subject+start_shift, translation_length, hsp->subject.frame, &translated_subject_length[hsp->subject.frame], search->db_genetic_code);
+                   }
+                   /* Below, the start_shift will be used for the protein
+                      coordinates, so need to divide it by 3 */
+                   start_shift /= CODON_LENGTH;
+                   hsp->subject.offset -= start_shift;
+                   hsp->subject.gapped_start -= start_shift;
+
+                } else if (translated_subject[hsp->subject.frame] == NULL) {
                     if (hsp->subject.frame > 0) {
                         translated_subject[hsp->subject.frame] =
                             GetTranslation(subject, subject_length, hsp->subject.frame, &translated_subject_length[hsp->subject.frame], search->db_genetic_code);
@@ -8891,28 +9011,39 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
                     gap_align->s_start = hsp->subject.gapped_start;
                 }
             }
-            
-            if (gap_align->s_start > max_start) {
-               start_shift = (gap_align->s_start / max_start) * max_start;
-               gap_align->subject = gap_align->subject + start_shift;
-               
-               gap_align->s_start %= max_start;
-            } else
-               start_shift = 0;
-
-            gap_align->subject_length =
-               MIN(gap_align->subject_length - start_shift, 
-                   gap_align->s_start + hsp->subject.length + max_start);
-
 
+            if (search->prog_number == blast_type_blastn) {
+               /* For blastn, use only part of a long subject sequence, 
+                  because the placeholders for the gapped alignment 
+                  information have only been allocated for at most a 
+                  certain length */
+               if (gap_align->s_start > max_start) {
+                  start_shift = (gap_align->s_start / max_start) * max_start;
+                  gap_align->subject = gap_align->subject + start_shift;
+                  
+                  gap_align->s_start %= max_start;
+               } else
+                  start_shift = 0;
+               
+               gap_align->subject_length =
+                  MIN(gap_align->subject_length - start_shift, 
+                      gap_align->s_start + hsp->subject.length + max_start);
+            }
 
-            if (do_traceback)
-                PerformGappedAlignmentWithTraceback(gap_align);
-            else
+            if (do_traceback) {
+               if (!search->pbp->mb_params || 
+                   search->pbp->mb_params->use_dyn_prog) {
+                  PerformGappedAlignmentWithTraceback(gap_align);
+               } else {
+                  PerformGreedyAlignmentWithTraceback(gap_align, search->abmp,
+                                                      search->sbp);
+               }
+            } else {
                 PerformGappedAlignment(gap_align);
-           
+            }
+
             if (gap_align->score >= min_score_to_keep) {
-                
+               
                 if(search->pbp->is_ooframe) {
                     hsp->query.offset = gap_align->subject_start + start_shift;
                     hsp->subject.offset = gap_align->query_start;
@@ -8940,7 +9071,16 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
                 }
 
 		keep = TRUE;
-                if (search->prog_number == blast_type_blastp ||
+                /* If greedy alignment was used for traceback, we still need
+                   to reevaluate the score with ambiguity information */
+                if (search->pbp->mb_params &&
+                    !search->pbp->mb_params->use_dyn_prog &&
+                    ReevaluateScoreWithAmbiguities(search, subject, hsp)) {
+                   /* HSP became below the cutoff after reevaluation */
+                   keep = FALSE;
+                }
+
+                if (keep && search->prog_number == blast_type_blastp ||
                     search->prog_number == blast_type_blastn) {
                    if (search->pbp->mb_params) {
                       FloatHi searchsp_eff = (FloatHi) search->dblen_eff *
@@ -8985,37 +9125,39 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
 #endif
                 }
 
-                if (search->pbp->is_ooframe) {
-                   OOFBlastHSPGetNumIdentical(gap_align->query, 
-                      gap_align->subject-start_shift, hsp, NULL, 
-                      &hsp->num_ident, &align_length);
-                } else {
-                   search->subject->sequence_start = 
-                      gap_align->subject - start_shift - 1;
-                   BlastHSPGetNumIdentical(search, hsp, NULL, &hsp->num_ident,
-                                           &align_length);
-                }
-                if (search->pbp->mb_params &&
-                    search->pbp->mb_params->use_dyn_prog) {
-                   if (hsp->num_ident * 100 < 
-                       align_length * search->pbp->mb_params->perc_identity) {
-                      keep = FALSE;
+                if (keep) {
+                   if (search->pbp->is_ooframe) {
+                      OOFBlastHSPGetNumIdentical(gap_align->query, 
+                                                 gap_align->subject-start_shift, hsp, NULL, 
+                                                 &hsp->num_ident, &align_length);
+                   } else {
+                      search->subject->sequence_start = 
+                         gap_align->subject - start_shift - 1;
+                      BlastHSPGetNumIdentical(search, hsp, NULL, &hsp->num_ident,
+                                              &align_length);
                    }
-                }
-                search->subject->sequence_start = NULL;
-
-		if (search->pbp->scalingFactor != 0.0 && search->pbp->scalingFactor != 1.0)
-		{	/* Scale down score for blastp and tblastn. */
-                	hsp->score = (hsp->score+(0.5*search->pbp->scalingFactor))/search->pbp->scalingFactor;
-		}
+                   if (search->pbp->mb_params &&
+                       search->pbp->mb_params->use_dyn_prog) {
+                      if (hsp->num_ident * 100 < 
+                          align_length * search->pbp->mb_params->perc_identity) {
+                         keep = FALSE;
+                      }
+                   }
+                   search->subject->sequence_start = NULL;
 
+                   if (search->pbp->scalingFactor != 0.0 && search->pbp->scalingFactor != 1.0)
+                      /* Scale down score for blastp and tblastn. */
+                      hsp->score = (hsp->score+(0.5*search->pbp->scalingFactor))/search->pbp->scalingFactor;
+                   
 				/* only one alignment considered for blast[np]. */
 				/* This may be changed by LinkHsps for blastx or tblastn. */
-                hsp->num = 1;
-		if ((search->prog_number == blast_type_tblastn ||
-		     search->prog_number == blast_type_psitblastn) && 
-                    search->pbp->longest_intron > 0) 
-                   hsp->evalue = BlastKarlinStoE_simple(hsp->score, search->sbp->kbp_gap[search->first_context], search->searchsp_eff);
+                   hsp->num = 1;
+                   if ((search->prog_number == blast_type_tblastn ||
+                        search->prog_number == blast_type_psitblastn) && 
+                       search->pbp->longest_intron > 0) 
+                      hsp->evalue = BlastKarlinStoE_simple(hsp->score, 
+                                       search->sbp->kbp_gap[search->first_context], search->searchsp_eff);
+                }
 
                 for (index2=0; index2<index && keep == TRUE; index2++) {
                     hsp2 = hsp_array[index2];
@@ -9035,10 +9177,11 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
                         } else {
                             new_hspcnt--;
                             if (do_traceback) {
-                                seqalign_array[index2] = SeqAlignFree(seqalign_array[index2]);
-                                hsp_array[index2]->gap_info = GapXEditBlockDelete(hsp_array[index2]->gap_info);
+                                seqalign_array[index2] = 
+                                   SeqAlignFree(seqalign_array[index2]);
                             }
-                            hsp_array[index2] = MemFree(hsp_array[index2]);
+                            hsp_array[index2] = 
+                               BLAST_HSPFree(hsp_array[index2]);
                         }
                     }
                 }
@@ -9046,18 +9189,13 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
                 if (keep) {
                     new_hspcnt++;
                 } else {
-                    hsp_array[index] = MemFree(hsp_array[index]);
-                    if (do_traceback)
-                        gap_align->edit_block = GapXEditBlockDelete(gap_align->edit_block);
+                   hsp_array[index] = BLAST_HSPFree(hsp_array[index]);
                 }
             } else {	/* Should be kept? */
-                hsp_array[index] = MemFree(hsp_array[index]);
-                if (do_traceback)
-                    gap_align->edit_block = GapXEditBlockDelete(gap_align->edit_block);
+                hsp_array[index] = BLAST_HSPFree(hsp_array[index]);
             }
         } else { /* Contained within another HSP, delete. */
-            hsp_array[index]->gap_info = GapXEditBlockDelete(hsp_array[index]->gap_info);
-            hsp_array[index] = MemFree(hsp_array[index]);
+            hsp_array[index] = BLAST_HSPFree(hsp_array[index]);
         }
     }
     if (search->pbp->scalingFactor != 0.0 && search->pbp->scalingFactor != 1.0)
@@ -9122,9 +9260,7 @@ RealBlastGetGappedAlignmentTraceback(BlastSearchBlkPtr search, Uint1Ptr subject,
        of HSPs per database sequence */
     if (search->pbp->hsp_num_max > new_hspcnt) {
        for (index=new_hspcnt; index<search->pbp->hsp_num_max; ++index) {
-          hsp_array[index]->gap_info = 
-             GapXEditBlockDelete(hsp_array[index]->gap_info);
-          hsp_array[index] = MemFree(hsp_array[index]);
+          hsp_array[index] = BLAST_HSPFree(hsp_array[index]);
        }
        new_hspcnt = MIN(new_hspcnt, search->pbp->hsp_num_max);
     }
@@ -9242,8 +9378,8 @@ SumBlastGetGappedAlignmentEx (BlastSearchBlkPtr search, Int4 hit_number, Boolean
 	SeqIdPtr subject_id=NULL, sip, subject_id_var;
 	Nlm_FloatHi current_evalue=DBL_MAX;
 	ValNodePtr vnp, vnp_start;
-        BLASTResultsStructPtr result_struct;
-        Boolean is_megablast = (search->pbp->mb_params && search->pbp->mb_params->use_dyn_prog);
+   BLASTResultsStructPtr result_struct;
+   Boolean is_megablast = (search->pbp->mb_params != NULL);
 
 	if (search == NULL)
 		return FALSE;
@@ -9555,7 +9691,8 @@ BlastPreliminaryGappedScore (BlastSearchBlkPtr search, Uint1Ptr subject, Int4 su
                 gap_align->is_ooframe = pbp->is_ooframe;
                 gap_align->shift_pen = pbp->shift_pen; 
                 gap_align->discontinuous = pbp->discontinuous;
-		gap_align->positionBased = search->positionBased;
+		gap_align->positionBased = 
+                   (search->positionBased && search->sbp->posMatrix);
 		gap_align->include_query = 0;
 		gap_align->gap_open = pbp->gap_open;
 		gap_align->gap_extend = pbp->gap_extend;
@@ -9874,7 +10011,8 @@ BlastGetGappedScore (BlastSearchBlkPtr search, Int4 subject_length, Uint1Ptr sub
                 gap_align->is_ooframe = pbp->is_ooframe;
                 gap_align->shift_pen = pbp->shift_pen; 
                 gap_align->discontinuous = pbp->discontinuous;
-		gap_align->positionBased = search->positionBased;
+		gap_align->positionBased = 
+                   (search->positionBased && search->sbp->posMatrix);
 		gap_align->include_query = 0;
 		gap_align->gap_open = pbp->gap_open;
 		gap_align->gap_extend = pbp->gap_extend;
@@ -10497,16 +10635,13 @@ bove.*/
 	{
 		if (new_index >= hspcnt)
 		{ /* this HSP is less significant than others on a full list.*/
-                   new_hsp->gap_info = GapXEditBlockDelete(new_hsp->gap_info);
-                   new_hsp = MemFree(new_hsp);
+                   new_hsp = BLAST_HSPFree(new_hsp);
                    return;
 		}
 		else
 		{ /* Delete the last HSP on the list. */
                    hspcnt = --current_hitlist->hspcnt;
-                   hsp_array[hspcnt]->gap_info = 
-                      GapXEditBlockDelete(hsp_array[hspcnt]->gap_info);
-                   hsp_array[hspcnt] = MemFree(hsp_array[hspcnt]);
+                   hsp_array[hspcnt] = BLAST_HSPFree(hsp_array[hspcnt]);
 		}
 	}
 	current_hitlist->hspcnt++;
diff --git a/tools/gapxdrop.c b/tools/gapxdrop.c
index a1856943..8e1f4572 100644
--- a/tools/gapxdrop.c
+++ b/tools/gapxdrop.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: gapxdrop.c,v 6.75 2003/08/20 22:11:49 dondosha Exp $";
+static char const rcsid[] = "$Id: gapxdrop.c,v 6.76 2003/11/07 21:52:52 dondosha Exp $";
 
 /* ===========================================================================
 *
@@ -34,8 +34,11 @@ Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden
 Contents: Functions to perform a gapped alignment on two sequences.
 
 ****************************************************************************/
-/* $Revision: 6.75 $
+/* $Revision: 6.76 $
 * $Log: gapxdrop.c,v $
+* Revision 6.76  2003/11/07 21:52:52  dondosha
+* Fixed SEMI_G_ALIGN_EX so it produces correct scores, by making code exactly correspond to ALIGN_EX
+*
 * Revision 6.75  2003/08/20 22:11:49  dondosha
 * Removed some garbage code
 *
@@ -807,7 +810,7 @@ ALIGN_EX(Uint1Ptr A, Uint1Ptr B, Int4 M, Int4 N, Int4Ptr S, Int4Ptr pei,
 	}
 	if (best_score - c > X){
 	  if (tt == i) tt++;
-	  else { dp->CC =  MININT; }
+	  else { dp->CC = MININT; }
 	} else {
 	  cb = i;
 	  if (c > best_score) {
@@ -924,6 +927,7 @@ static Int4 SEMI_G_ALIGN_EX(Uint1Ptr A, Uint1Ptr B, Int4 M, Int4 N,
   register GapXDPPtr dp;
   Uint1Ptr Bptr;
   Int4 B_increment=1;
+  Int4 next_c, next_f;
   
   if(!score_only) {
     return ALIGN_EX(A, B, M, N, S, pei, pej, sapp, gap_align, query_offset, reversed, reverse_sequence);
@@ -946,12 +950,12 @@ static Int4 SEMI_G_ALIGN_EX(Uint1Ptr A, Uint1Ptr B, Int4 M, Int4 N,
   dyn_prog = (GapXDPPtr)Nlm_Malloc(j);
 
   dyn_prog[0].CC = 0; c = dyn_prog[0].DD = -m;
-  dyn_prog[0].FF = -m;
+  dyn_prog[0].FF = -m - decline_penalty;
   for(i = 1; i <= N; i++) {
     if(c < -X) break;
     dyn_prog[i].CC = c;
     dyn_prog[i].DD = c - m; 
-    dyn_prog[i].FF = c-m;
+    dyn_prog[i].FF = c-m - decline_penalty;
     c -= h;
   }
 
@@ -985,64 +989,50 @@ static Int4 SEMI_G_ALIGN_EX(Uint1Ptr A, Uint1Ptr B, Int4 M, Int4 N,
       e = c =f = MININT;
       Bptr = &B[tt];
       if(reverse_sequence)
-	Bptr = &B[N-tt];
+         Bptr = &B[N-tt];
       for (cb = i = tt, dp = &dyn_prog[i]; i < j; i++) {
+         d = dp->DD;
 	 Bptr += B_increment;
-	  d = dp->DD;
-	  if (e < f) e = f;
-	  if (d < f) d = f;
-	  if (c < d || c < e) {
-	      if (d < e) {
-		  c = e;
-	      } else {
-		  c = d; 
-	      }
-	      if (best_score - c > X) {
-		  c = dp->CC+wa[*Bptr]; f = dp->FF;
-		  if (tt == i) tt++;
-		  else { dp->CC =dp->FF= MININT;}
-	      } else {
-		  cb = i;
-                  if ((c-=m) > (d-=h)) {
-                      dp->DD = c;
-                  } else {
-                      dp->DD = d;
-                  }
-                  if (c > (e-=h)) {
-                      e = c;
-                  }
-                  c+=m;
-		  d = dp->CC+wa[*Bptr]; dp->CC = c; c=d;
-		  d = dp->FF; dp->FF = f-decline_penalty; f = d;
-	      }
-	  } else {
-	      if (best_score - c > X){
-		  c = dp->CC+wa[*Bptr]; f= dp->FF;
-		  if (tt == i) tt++;
-		  else { dp->CC =dp->FF= MININT;}
-	      } else {
-		  cb = i; 
-		  if (c > best_score) {
-		      best_score = c;
-		      *pei = j_r; *pej = i;
-		  } 
-		  if ((c-=m) > (d-=h)) {
-		      dp->DD = c; 
-		  } else {
-		      dp->DD = d;
-		  } 
-		  if (c > (e-=h)) {
-		      e = c;
-		  } 
-		  c+=m;
-		  d = dp->FF;
-		  if (c-g>f) dp->FF = c-g-decline_penalty; else dp->FF = f-decline_penalty;
-		  f = d;
-		  d = dp->CC+wa[*Bptr]; dp->CC = c; c = d;
-	      }
-	  }
-	  dp++;
+         next_c = dp->CC+wa[*Bptr];   /* Bptr is & B[i+1]; */
+         next_f = dp->FF;
+
+         if (c < f) c = f;
+         if (f > d) d = f;
+         else if (c < d) c= d;
+         
+         if (f > e) e = f;
+         else if (c < e) c = e;
+         
+         if (best_score - c > X){
+            if (tt == i) tt++;
+            else { dp->CC = MININT; }
+         } else {
+            cb = i;
+            if (c > best_score) {
+               best_score = c;
+               *pei = j_r; *pej = i;
+            }
+            if ((c-=m) > (d-=h)) {
+               dp->DD = c; 
+            } else {
+               dp->DD = d;
+            } 
+            if (c > (e-=h)) {
+               e = c; 
+            }
+            c+=m; 
+            if (f < c-g) { 
+               dp->FF = c-g-decline_penalty; 
+            } else {
+               dp->FF = f-decline_penalty;
+            }
+            dp->CC = c;
+         }
+         c = next_c;
+         f = next_f;
+         dp++;
       }
+
       if (tt == j) break;
       if (cb < j-1) { j = cb+1;}
       else while (e >= best_score-X && j <= N) {
@@ -1054,7 +1044,6 @@ static Int4 SEMI_G_ALIGN_EX(Uint1Ptr A, Uint1Ptr B, Int4 M, Int4 N,
       }
   }
   
-
   MemFree(dyn_prog);
 
   return best_score;
diff --git a/tools/kappa.c b/tools/kappa.c
index e16bd0c7..e5ae43b8 100644
--- a/tools/kappa.c
+++ b/tools/kappa.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: kappa.c,v 6.34 2003/10/22 20:37:19 madden Exp $";
+static char const rcsid[] = "$Id: kappa.c,v 6.37 2004/01/27 20:31:52 madden Exp $";
 
-/* $Id: kappa.c,v 6.34 2003/10/22 20:37:19 madden Exp $ 
+/* $Id: kappa.c,v 6.37 2004/01/27 20:31:52 madden Exp $ 
 *   ==========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -34,9 +34,18 @@ Author: Alejandro Schaffer
 Contents: Utilities for doing Smith-Waterman alignments and adjusting
     the scoring system for each match in blastpgp
 
- $Revision: 6.34 $
+ $Revision: 6.37 $
 
  $Log: kappa.c,v $
+ Revision 6.37  2004/01/27 20:31:52  madden
+ remove extra setting of kbp_gap
+
+ Revision 6.36  2004/01/06 17:48:44  dondosha
+ Do not free Karlin block in RedoAlignmentCore, because its pointer is passed outside
+
+ Revision 6.35  2003/12/01 19:15:27  madden
+ Add one byte to filteredMatchingSequence to prevent ABR/ABW
+
  Revision 6.34  2003/10/22 20:37:19  madden
  Set kbp to rescaled values, use upper-case for SCALING_FACTOR define
 
@@ -1584,6 +1593,7 @@ SeqAlignPtr RedoAlignmentCore(BlastSearchBlkPtr search,
    Int4 queryLength; /*the length of the query sequence*/
    Uint1Ptr matchingSequence; /*one sequence that matches the query*/
    Uint1Ptr  filteredMatchingSequence; /*other representations of matchingSequence*/
+   Uint1Ptr  filteredMatchingSequenceStart; /* other representations of matchingSequence with one more byte on beginning*/
    Int4 matchingSequenceLength; /*length of matching sequence*/
    Int4 matchStart, queryStart; /*starting positions for local alignment*/
    Int4 queryEnd, matchEnd, finalQueryEnd, finalMatchEnd; /*end positions of optimal local alignment*/
@@ -1740,12 +1750,10 @@ SeqAlignPtr RedoAlignmentCore(BlastSearchBlkPtr search,
      if (search->positionBased) 
      {
        search->sbp->kbp_gap_psi[0] = kbp;
-       search->sbp->kbp_gap[0] = kbp;
      }
      else 
      {
        search->sbp->kbp_gap_std[0] = kbp;
-       search->sbp->kbp_gap[0] = kbp;
      }
 
      resProb = (Nlm_FloatHi *) MemNew (PROTEIN_ALPHABET * sizeof(Nlm_FloatHi));
@@ -1812,7 +1820,8 @@ SeqAlignPtr RedoAlignmentCore(BlastSearchBlkPtr search,
      /*filteredMatchingSequence = matchingSequence;*/
 
      /* switch to this if we want to filter the match*/
-     filteredMatchingSequence = MemNew((matchingSequenceLength+1) * sizeof(Uint1));
+     filteredMatchingSequenceStart = MemNew((matchingSequenceLength+2) * sizeof(Uint1));
+     filteredMatchingSequence = filteredMatchingSequenceStart+1;
      segResult(bsp_db, matchingSequence, filteredMatchingSequence, matchingSequenceLength); 
      foundFirstAlignment = FALSE;
      if (adjustParameters) {
@@ -2076,7 +2085,7 @@ SeqAlignPtr RedoAlignmentCore(BlastSearchBlkPtr search,
      }
      index++;
      if (matchingSequence != filteredMatchingSequence)
-       MemFree(filteredMatchingSequence);
+       MemFree(filteredMatchingSequenceStart);
      if (bsp_db) {
        if (bioseq_unlock) {
          BioseqUnlock(bsp_db); bsp_db = NULL; 
@@ -2126,7 +2135,6 @@ SeqAlignPtr RedoAlignmentCore(BlastSearchBlkPtr search,
        freeStartFreqs(startFreqRatios,PROTEIN_ALPHABET);
        MemFree(queryProb);
      }
-     MemFree(kbp);
      MemFree(resProb);
      MemFree(scoreArray);
      MemFree(return_sfp);
diff --git a/tools/mbalign.c b/tools/mbalign.c
index 609dc6e9..bf9a3d43 100644
--- a/tools/mbalign.c
+++ b/tools/mbalign.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: mbalign.c,v 6.40 2003/05/30 17:25:36 coulouri Exp $";
+static char const rcsid[] = "$Id: mbalign.c,v 6.41 2003/10/29 17:46:59 dondosha Exp $";
 
-/* $Id: mbalign.c,v 6.40 2003/05/30 17:25:36 coulouri Exp $
+/* $Id: mbalign.c,v 6.41 2003/10/29 17:46:59 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,12 +32,15 @@ static char const rcsid[] = "$Id: mbalign.c,v 6.40 2003/05/30 17:25:36 coulouri
 *
 * Initial Creation Date: 10/27/1999
 *
-* $Revision: 6.40 $
+* $Revision: 6.41 $
 *
 * File Description:
 *        Alignment functions for Mega Blast program
 *
 * $Log: mbalign.c,v $
+* Revision 6.41  2003/10/29 17:46:59  dondosha
+* Allow 2-stage greedy extension in megablast
+*
 * Revision 6.40  2003/05/30 17:25:36  coulouri
 * add rcsid
 *
@@ -691,6 +694,8 @@ Int4 MegaBlastGreedyAlign(const UcharPtr s1, Int4 len1,
     }
     if (S==NULL) 
        space = 0;
+    else if (!space)
+       abmp->space = space = new_mb_space();
     else 
        refresh_mb_space(space);
     
@@ -935,7 +940,9 @@ Int4 MegaBlastAffineGreedyAlign (const UcharPtr s1, Int4 len1,
     flast_d = abmp->flast_d_affine;
     if (S==NULL) {
         space = 0;
-    } else { 
+    } else if (!space) {
+       abmp->space = space = new_mb_space();
+    } else {
         refresh_mb_space(space);
     }
     max_row = max_row_free + D_diff;
diff --git a/tools/mblast.c b/tools/mblast.c
index 5e0fd082..9e83593e 100644
--- a/tools/mblast.c
+++ b/tools/mblast.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: mblast.c,v 6.190 2003/05/30 17:25:36 coulouri Exp $";
+static char const rcsid[] = "$Id: mblast.c,v 6.199 2004/01/27 20:46:06 dondosha Exp $";
 
 /* ===========================================================================
 *
@@ -40,9 +40,36 @@ Detailed Contents:
 	- Functions specific to Mega BLAST
 
 ******************************************************************************
- * $Revision: 6.190 $
+ * $Revision: 6.199 $
  *
  * $Log: mblast.c,v $
+ * Revision 6.199  2004/01/27 20:46:06  dondosha
+ * Allow values 0, 1, 2 for no_traceback megablast option
+ *
+ * Revision 6.198  2004/01/23 22:29:11  dondosha
+ * Increase hitlist size for preliminary alignment if traceback is delayed
+ *
+ * Revision 6.197  2004/01/16 23:43:45  dondosha
+ * No more need for special argument for partial search: it is set in options
+ *
+ * Revision 6.196  2004/01/13 15:46:54  dondosha
+ * Changed cast to nearest integer in length adjustment calculation
+ *
+ * Revision 6.195  2004/01/06 22:37:10  dondosha
+ * Use BLAST_HSPfree function
+ *
+ * Revision 6.194  2003/12/10 17:05:28  dondosha
+ * Added function ReevaluateScoreWithAmbiguities to reevaluate score for one HSP; use it after greedy traceback
+ *
+ * Revision 6.193  2003/11/06 19:53:07  dondosha
+ * Fix in MegaBlastSetupSearchInternalByLoc when query submitted as Bioseq instead of SeqLoc; removed unused variables
+ *
+ * Revision 6.192  2003/11/05 21:11:09  dondosha
+ * Fix for traceback with greedy algorithm
+ *
+ * Revision 6.191  2003/10/29 17:46:59  dondosha
+ * Allow 2-stage greedy extension in megablast
+ *
  * Revision 6.190  2003/05/30 17:25:36  coulouri
  * add rcsid
  *
@@ -861,13 +888,6 @@ static Int2 mb_two_hit_min_step;
 SeqAlignPtr PNTR
 BioseqMegaBlastEngineCore(BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options)
 {
-   return BioseqMegaBlastEngineCoreEx(search, options, FALSE);
-}
-
-SeqAlignPtr PNTR
-BioseqMegaBlastEngineCoreEx(BlastSearchBlkPtr search, BLAST_OptionsBlkPtr
-                            options, Boolean partial)
-{
 	SeqAlignPtr seqalign, PNTR seqalignp;
         Int2 num_queries;
         CharPtr tmpstr;
@@ -890,26 +910,20 @@ start_timer;
 	stop_timer("BioseqBlastEngineCore: before do_the_blast_run()");
 	do_the_blast_run(search);
 
-       if (!search->pbp->mb_params->no_traceback) {
-          search->sbp->kbp_gap[search->first_context] = search->sbp->kbp[search->first_context];
-         
-          search->pbp->gap_open = options->gap_open;
-          search->pbp->gap_extend = options->gap_extend;
-         
-          search->sbp->kbp_gap[search->first_context] = NULL;
-          if (search->pbp->mb_params->use_dyn_prog) {
-             search->context[search->first_context].query->length =
-                search->query_context_offsets[search->first_context+1] - 1;
-          }
-         
-          /* If this is a partial search, do not compute the seqaligns,
-             but only if traceback has not been done yet */
-          if (partial && search->pbp->mb_params->use_dyn_prog) {
-             BlastStopAwakeThread(search->thr_info);
-             return NULL;
-          }
-       }
-
+   /* If this is a partial search, we do not do traceback, so can return
+      immediately */
+   if (options->no_traceback == 1 || search->handle_results) {
+      BlastStopAwakeThread(search->thr_info);
+      return NULL;
+   }
+   
+   /* So far the length of the first query was set to the total 
+      concatenated length. It can be reset to the real length of the 
+      first query sequence here. */
+   search->context[search->first_context].query->length =
+      search->query_context_offsets[search->first_context+1] - 1;
+   
+   
 start_timer;
         num_queries = search->last_context / 2 + 1;
         seqalignp = (SeqAlignPtr PNTR) 
@@ -939,11 +953,11 @@ MegaBlastSetUpSearchWithReadDbInternal (SeqLocPtr query_slp, BioseqPtr
 	BlastSearchBlkPtr search;
 	Boolean options_alloc=FALSE;
 	Int2 status, first_context, last_context;
-        Int8	dblen, real_dblen;
-	Int4	query_length, real_dbseq_num;
-        Int4		i;
+        Int8	dblen;
+	Int4	query_length;
 	Nlm_FloatHi	searchsp_eff=0;
-        
+        Int4 hitlist_size;
+
 	/* Allocate default options if none are allocated yet. */
 	if (options == NULL)
 	{
@@ -951,6 +965,14 @@ MegaBlastSetUpSearchWithReadDbInternal (SeqLocPtr query_slp, BioseqPtr
 		options_alloc = TRUE;
 	}
 
+        /* Increase the hitlist size for the preliminary gapped alignment,
+           if traceback is delayed */
+        if (options->no_traceback) {
+           hitlist_size = 
+              MIN(2*options->hitlist_size, options->hitlist_size + 50);
+        } else {
+           hitlist_size = options->hitlist_size;
+        }
      
 	/* last context is the total number of contexts in concatenated 
 	   queries */
@@ -959,7 +981,7 @@ MegaBlastSetUpSearchWithReadDbInternal (SeqLocPtr query_slp, BioseqPtr
 	   query_length = SeqLocTotalLen(prog_name, query_slp);
            MegaBlastGetFirstAndLastContext(prog_name, query_slp, &first_context, &last_context, options->strand_option);
 	} else {
-	   query_length = query_bsp->length;
+	   query_length = 2*query_bsp->length + 3;
            BlastGetFirstAndLastContext(prog_name, query_slp, &first_context, &last_context, options->strand_option);
         }
 		
@@ -974,7 +996,7 @@ MegaBlastSetUpSearchWithReadDbInternal (SeqLocPtr query_slp, BioseqPtr
 	search = BlastSearchBlkNewExtra(options->wordsize, qlen,
 					dbname, FALSE, 0,
 					options->threshold_second,
-					options->hitlist_size, prog_name, NULL,
+					hitlist_size, prog_name, NULL,
 					first_context, last_context, rdfp,
 					options->window_size);
 
@@ -1074,12 +1096,6 @@ FindGiInGiList(Uint4 query_gi, BlastDoubleInt4Ptr gi_list,
    return FALSE;
 }
 
-#define DROPOFF_NUMBER_OF_BITS 10.0
-#define TOP_HALFBYTE 0xf0
-#define BOTTOM_HALFBYTE 0x0f
-static Uint1 inverse_halfbyte[16] = 
-{ 0, 8, 4, 12, 2, 10, 6, 14, 1, 9, 5, 13, 3, 11, 7, 15 };
-
 #define MIN_LIMIT_HSP_NUM 1e20
 #define BLASTNA_N_RESIDUE 14
 
@@ -1093,22 +1109,20 @@ MegaBlastSetUpSearchInternalByLoc (BlastSearchBlkPtr search, SeqLocPtr
 								  positives)))
 
 {
-   BioseqPtr bsp;
    Boolean mask_at_hash=FALSE, private_slp_delete;
-   Boolean query_is_na, db_is_na;
    Char buffer[128];
-   Int2 retval, status, rem;
+   Int2 retval, status;
    Int4 effective_query_length, query_length,
-      index, index1, length, length_adjustment=0, last_length_adjustment,
+      index, length, length_adjustment=0, last_length_adjustment,
       min_query_length, full_query_length=0;
-   Int4 context, last_context, num_queries;
+   Int4 context, num_queries;
    Nlm_FloatHi avglen;
-   SeqIdPtr query_id, qid;
+   SeqIdPtr qid;
    SeqLocPtr filter_slp=NULL, private_slp=NULL, private_slp_rev=NULL, slp,
       tmp_slp;
-   Uint1 residue, strand, seq_data_type;
+   Uint1 residue;
    Uint1Ptr query_seq, query_seq_start, query_seq_rev, query_seq_start_rev;
-   Uint1Ptr query_seq_combined, sequence;
+   Uint1Ptr query_seq_combined;
    CharPtr filter_string;
    Uint4 query_gi;
    Int4 homo_gilist_size, mouse_gilist_size, rat_gilist_size;
@@ -1143,6 +1157,9 @@ MegaBlastSetUpSearchInternalByLoc (BlastSearchBlkPtr search, SeqLocPtr
       private_slp_delete = FALSE;
       search->query_slp = private_slp;
       search->allocated += BLAST_SEARCH_ALLOC_QUERY_SLP;
+      /* Now let query_length be the total length of 2 strands together with
+         sentinel bytes */
+      query_length = 2*query_length + 3;
    } else {
       search->query_slp = query_slp;
       query_length = SeqLocTotalLen(search->prog_name, query_slp);
@@ -1499,11 +1516,12 @@ MegaBlastSetUpSearchInternalByLoc (BlastSearchBlkPtr search, SeqLocPtr
       completely masked */
    while (!search->sbp->kbp[context])
       context++;
+
    min_query_length = (Int4) 1/(search->sbp->kbp[context]->K);
    
    last_length_adjustment = 0;
    for (index=0; index<5; index++) {
-      length_adjustment = (Int4) ((search->sbp->kbp[context]->logK)+log((Nlm_FloatHi)(length-last_length_adjustment)*(Nlm_FloatHi)(MAX(1, (search->dblen)-(search->dbseq_num*last_length_adjustment)))))/(search->sbp->kbp[context]->H);
+      length_adjustment = Nlm_Nint(((search->sbp->kbp[context]->logK)+log((Nlm_FloatHi)(length-last_length_adjustment)*(Nlm_FloatHi)(MAX(1, (search->dblen)-(search->dbseq_num*last_length_adjustment)))))/(search->sbp->kbp[context]->H));
       if (length_adjustment >= length-min_query_length) {
          length_adjustment = length-min_query_length;
          break;
@@ -1686,7 +1704,6 @@ BlastFillQueryOffsets(BlastSearchBlkPtr search, SeqLocPtr query_slp,
    Int2 num_contexts;
    Int2 i = 0;
    Int4 length;
-   Uint1 strand;
 
    if (slp == NULL) return search;
    /* Note: the last offset will be equal to the combined query length + 1, for
@@ -1726,7 +1743,6 @@ static int LIBCALLBACK
 evalue_compare_seqaligns(VoidPtr v1, VoidPtr v2)
 {
    SeqAlignPtr sap1, sap2, PNTR sapp1, PNTR sapp2;
-   SeqIdPtr id1, id2;
 
    sapp1 = (SeqAlignPtr PNTR) v1;
    sapp2 = (SeqAlignPtr PNTR) v2;
@@ -1952,17 +1968,16 @@ MegaBlastWordFinder_disc(BlastSearchBlkPtr search, LookupTablePtr lookup)
    register Uint1Ptr subject;
    register Int4 s_off, ecode, mask, q_off, extra_code;
    Int4 ecode1, ecode2;
-   Int4 index, index1;
    Int4 subj_length = search->subject->length;
-   Int4 query_length = search->context[search->first_context].query->length;
-   MbStackPtr estack;
    Int4 min_hit_size;
    PV_ARRAY_TYPE *pv_array = lookup->pv_array;
    Int4 pv_array_bts;
    Int4 bit0, no_bit0;
    Int2 word_length;
+#ifdef USE_HASH_TABLE
    Uint1Ptr hash_buf;
    Int4 hash_shift, hash_mask, crc, size;
+#endif
    MegaBlastParameterBlkPtr mb_params = search->pbp->mb_params;
    Int2 template_length = mb_params->template_length;
    MBTemplateType template_type = mb_params->template_type;
@@ -2302,18 +2317,17 @@ MegaBlastWordFinder_disc_1b(BlastSearchBlkPtr search, LookupTablePtr lookup)
    register Uint1Ptr subject;
    register Int4 s_off, ecode, mask, q_off, extra_code;
    Int4 ecode1, ecode2;
-   Int4 index, index1;
    Int4 subj_length = search->subject->length;
-   Int4 query_length = search->context[search->first_context].query->length;
-   MbStackPtr estack;
    Int4 min_hit_size;
    PV_ARRAY_TYPE *pv_array = lookup->pv_array;
    Int4 pv_array_bts;
    Uint1 bit;
    Int4 no_bit0, bit0;
    Int2 word_length;
+#ifdef USE_HASH_TABLE
    Uint1Ptr hash_buf;
    Int4 hash_shift, hash_mask, crc, size;
+#endif
    MegaBlastParameterBlkPtr mb_params = search->pbp->mb_params;
    Int2 template_length = mb_params->template_length;
    MBTemplateType template_type = mb_params->template_type;
@@ -2671,10 +2685,7 @@ MegaBlastWordFinder(BlastSearchBlkPtr search, LookupTablePtr lookup)
 {
    register Uint1Ptr subject;
    register Int4 s_off, ecode, mask, q_off;
-   Int4 index, index1;
    Int4 subj_length = search->subject->length;
-   Int4 query_length = search->context[search->first_context].query->length;
-   MbStackPtr estack;
    Int4 min_hit_size;
    PV_ARRAY_TYPE *pv_array = lookup->pv_array;
    Int4 pv_array_bts;
@@ -2759,11 +2770,10 @@ diag_compare_match(VoidPtr v1, VoidPtr v2)
 #define MB_MAX_LENGTH_TO_UNPACK 400
 Int2 MegaBlastGappedAlign(BlastSearchBlkPtr search)
 {
-   BLAST_HSPPtr hsp, PNTR hsp_array;
    MegaBlastExactMatchPtr PNTR e_hsp_array;
    MegaBlastExactMatchPtr e_hsp;
-   Int4 index, i, hspcnt, new_hspcnt=0, buf_len=0;
-   Uint1Ptr subject0 = NULL, seq_4na, seq_2na;
+   Int4 index, i, hspcnt, buf_len=0;
+   Uint1Ptr subject0 = NULL;
    Boolean delete_hsp;
    GapAlignBlkPtr gap_align;
    Boolean use_dyn_prog = search->pbp->mb_params->use_dyn_prog;
@@ -2875,13 +2885,12 @@ Int4
 MegaBlastExtendHit(BlastSearchBlkPtr search, LookupTablePtr lookup, 
 		   Int4 s_off, Int4 q_off) {
    Int4 index, len = 4*lookup->mb_lt->width; 
-   Int4 query_offset, subject_offset, index1, step;
-   Int2 skip, min_hit_length;
+   Int4 index1, step;
+   Int2 min_hit_length;
    MbStackPtr estack;
-   Int4 diag, level, stack_top;
+   Int4 diag, stack_top;
    BLAST_ExtendWordParamsPtr ewp_params = search->ewp_params;
    register Int4 window;
-   CharPtr str;
    Int4 step_unit;
    Boolean one_word, hit_ready, two_hits;
 
@@ -3038,7 +3047,7 @@ MegaBlastNtWordExtend(BlastSearchBlkPtr search, Uint1Ptr subject0,
         BLAST_ScoreBlkPtr       sbp;
 	Int4 q_avail, s_avail;
 	/* Variables for the call to MegaBlastGreedyAlign */
-	Int4 ndiff, q_ext_l, q_ext_r, s_ext_l, s_ext_r;
+	Int4 q_ext_l, q_ext_r, s_ext_l, s_ext_r;
 	edit_script_t *ed_script_fwd=NULL, *ed_script_rev=NULL;
 	Boolean good_hit;
         Uint1 rem;
@@ -3126,6 +3135,74 @@ MegaBlastNtWordExtend(BlastSearchBlkPtr search, Uint1Ptr subject0,
 	return 0;
 }
 
+#define NO_UNPACK_MBALIGN_ARG 4
+void PerformGreedyAlignmentWithTraceback(GapAlignBlkPtr gap_align,
+        GreedyAlignMemPtr gamp, BLAST_ScoreBlkPtr sbp)
+{
+    Int4 score, s_ext_r, q_ext_r, s_ext_l, q_ext_l;
+    Uint1Ptr query0, subject0, query, subject;
+    Int4 X = gap_align->x_parameter;
+    Int4 reward = sbp->reward;
+    Int4 penalty = -sbp->penalty;
+    Int4 q_off, s_off, q_avail, s_avail;
+    edit_script_t *ed_script_fwd=NULL, *ed_script_rev=NULL;
+    GapXEditScriptPtr esp = NULL;
+
+    query0 = gap_align->query;
+    subject0 = gap_align->subject;
+    q_off = gap_align->q_start;
+    s_off = gap_align->s_start;
+    query = query0 + q_off;
+    subject = subject0 + s_off;
+    q_avail = gap_align->query_length - q_off;
+    s_avail = gap_align->subject_length - s_off;
+    ed_script_fwd = edit_script_new();
+    ed_script_rev = edit_script_new();
+
+    /* extend to the right */
+    score = MegaBlastAffineGreedyAlign(subject, s_avail, query, q_avail, 
+               FALSE, X, reward, penalty, gap_align->gap_open, 
+               gap_align->gap_extend, &s_ext_r, &q_ext_r, gamp, 
+               ed_script_fwd, NO_UNPACK_MBALIGN_ARG);
+    /* extend to the left */
+    score += MegaBlastAffineGreedyAlign(subject0, s_off, query0, q_off, 
+                TRUE, X, reward, penalty, gap_align->gap_open, 
+                gap_align->gap_extend, &s_ext_l, &q_ext_l, gamp, 
+                ed_script_rev, NO_UNPACK_MBALIGN_ARG);
+
+    /* In basic case the greedy algorithm returns number of 
+       differences, hence we need to convert it to score */
+    if (gap_align->gap_open==0 && gap_align->gap_extend==0) 
+       score = 
+          (q_ext_r + s_ext_r + q_ext_l + s_ext_l)*sbp->reward/2 - 
+          score*(sbp->reward - sbp->penalty);
+    else if (sbp->reward % 2 == 1)
+       score /= 2;
+    
+    edit_script_append(ed_script_rev, ed_script_fwd);
+    esp = MBToGapXEditScript(ed_script_rev);
+
+    edit_script_free(ed_script_fwd);
+    edit_script_free(ed_script_rev);
+
+    gap_align->score = score;
+    gap_align->query_start = q_off - q_ext_l;
+    gap_align->subject_start = s_off - s_ext_l;
+    gap_align->query_stop = q_off + q_ext_r;
+    gap_align->subject_stop = s_off + s_ext_r;
+    gap_align->edit_block = GapXEditBlockNew(gap_align->query_start, gap_align->subject_start);
+
+    gap_align->edit_block->start1 = gap_align->query_start;
+    gap_align->edit_block->start2 = gap_align->subject_start;
+    gap_align->edit_block->length1 = gap_align->query_length;
+    gap_align->edit_block->length2 = gap_align->subject_length;
+    gap_align->edit_block->frame1 = gap_align->query_frame;
+    gap_align->edit_block->frame2 = gap_align->subject_frame;
+    gap_align->edit_block->reverse = 0;
+    
+    gap_align->edit_block->esp = esp;
+}
+
 /* A routine to mask the residues from a mask SeqLoc by changing to a given 
  * value (mask_residue).
  * The buffer should contain an already decoded sequence. 
@@ -3227,16 +3304,14 @@ diag_compare_hsps(VoidPtr v1, VoidPtr v2)
 	    h1->subject.offset >= h2->subject.offset && 
 	    h1->subject.end <= h2->subject.end && 
             h1->evalue >= h2->evalue) { 
-	   h1->gap_info = GapXEditBlockDelete(h1->gap_info); 
-	   *hp1 = MemFree(*hp1);
+	   *hp1 = BLAST_HSPFree(h1);
 	   return 1; 
 	} else if (h1->query.offset <= h2->query.offset &&  
 		   h1->query.end >= h2->query.end &&  
 		   h1->subject.offset <= h2->subject.offset && 
 		   h1->subject.end >= h2->subject.end && 
                    h1->evalue <= h2->evalue) { 
-	   h2->gap_info = GapXEditBlockDelete(h2->gap_info); 
-	   *hp2 = MemFree(*hp2);
+	   *hp2 = BLAST_HSPFree(h2);
 	   return -1; 
 	}
 
@@ -3275,18 +3350,14 @@ BlastSortUniqHspArray(BLAST_HitListPtr hitlist)
              q_end <= hsp_array[index1]->query.end && 
              s_end <= hsp_array[index1]->subject.end &&
              evalue >= hsp_array[index1]->evalue) {
-            hsp_array[index]->gap_info = 
-               GapXEditBlockDelete(hsp_array[index]->gap_info);
-            hsp_array[index] = MemFree(hsp_array[index]);
+            hsp_array[index] = BLAST_HSPFree(hsp_array[index]);
             break;
          } else if (q_off <= hsp_array[index1]->query.offset && 
              s_off <= hsp_array[index1]->subject.offset && 
              q_end >= hsp_array[index1]->query.end && 
              s_end >= hsp_array[index1]->subject.end &&
              evalue <= hsp_array[index1]->evalue) {
-            hsp_array[index1]->gap_info = 
-               GapXEditBlockDelete(hsp_array[index1]->gap_info);
-            hsp_array[index1] = MemFree(hsp_array[index1]);
+            hsp_array[index1] = BLAST_HSPFree(hsp_array[index1]);
             shift_needed = TRUE;
          }
       }
@@ -3362,7 +3433,7 @@ MegaBlastGapInfoToSeqAlign(BlastSearchBlkPtr search, Int4 subject_index,
    BLASTResultHitlistPtr result_hitlist;
    SeqIdPtr subject_id;
    BLASTResultHspPtr hsp_array;
-   Int4 index, i;
+   Int4 index;
    SeqIdPtr query_id, new_subject_seqid;
    StdSegPtr ssp;
    ValNodePtr gi_list=NULL;
@@ -3459,27 +3530,171 @@ MegaBlastGetNumIdentical(Uint1Ptr query, Uint1Ptr subject, Int4 q_start,
    return ident;
 }
 
+/* Reevaluate score of one HSP, using ambiguity information */
+Boolean ReevaluateScoreWithAmbiguities(BlastSearchBlkPtr search,
+           Uint1Ptr subject_start, BLAST_HSPPtr hsp)
+{
+   BLAST_Score	sum, score, gap_open, gap_extend;
+   BLAST_ScorePtr PNTR    matrix;
+   Uint1Ptr query_start, query, subject;
+   Uint1Ptr new_q_start, new_s_start, new_q_end, new_s_end;
+   Int4 index, i, context, last_esp_num;
+   Int2 factor;
+   Uint1 mask = 0x0f;
+   Boolean delete_hsp;
+   GapXEditBlockPtr gap_info = hsp->gap_info;
+   GapXEditScriptPtr esp, last_esp, prev_esp, first_esp;
+   FloatHi searchsp_eff;
+   Int4 align_length;
+
+   if (search->sbp->reward % 2 == 1) 
+      factor = 2;
+   else 
+      factor = 1;
+
+   if (search->pbp->gap_open == 0 && search->pbp->gap_extend == 0) {
+      gap_open = 0;
+      gap_extend = 
+         (search->sbp->reward - 2*search->sbp->penalty) * factor / 2;
+   } else {
+      gap_open = factor*search->pbp->gap_open;
+      gap_extend = factor*search->pbp->gap_extend;
+   }
+
+   matrix = search->sbp->matrix;
+
+   context = hsp->context;
+
+   searchsp_eff = (FloatHi) search->dblen_eff *
+      ((FloatHi) search->context[context].query->effective_length);
+      
+   query_start = search->context[context].query->sequence;
+   query = query_start + hsp->query.offset; 
+   subject = subject_start + hsp->subject.offset;
+   score = 0;
+   sum = 0;
+   new_q_start = new_q_end = query;
+   new_s_start = new_s_end = subject;
+   i = 0;
+   
+   esp = gap_info->esp;
+   prev_esp = NULL;
+   last_esp = first_esp = esp;
+   last_esp_num = 0;
+   
+   while (esp) {
+      if (esp->op_type == GAPALIGN_SUB) {
+         sum += factor*matrix[*query & mask][*subject];
+         query++;
+         subject++;
+         i++;
+      } else if (esp->op_type == GAPALIGN_DEL) {
+         sum -= gap_open + gap_extend * esp->num;
+         subject += esp->num;
+         i += esp->num;
+      } else if (esp->op_type == GAPALIGN_INS) {
+         sum -= gap_open + gap_extend * esp->num;
+         query += esp->num;
+         i += esp->num;
+      }
+      
+      if (sum < 0) {
+         if (score < search->pbp->cutoff_s2 ||
+             BlastKarlinStoE_simple(score, search->sbp->kbp[context],
+                                    searchsp_eff) > search->pbp->cutoff_e) {
+            /* Start from new offset */
+            new_q_start = query;
+            new_s_start = subject;
+            score = sum = 0;
+            if (i < esp->num) {
+               esp->num -= i;
+               first_esp = esp;
+               i = 0;
+            } else {
+               first_esp = esp->next;
+            }
+            /* Unlink the bad part of the esp chain 
+               so it can be freed later */
+            if (prev_esp)
+               prev_esp->next = NULL;
+            last_esp = NULL;
+         } else {
+            /* Stop here */
+            break;
+         }
+      } else if (sum > score) {
+         /* Remember this point as the best scoring end point */
+         score = sum;
+         last_esp = esp;
+         last_esp_num = i;
+         new_q_end = query;
+         new_s_end = subject;
+      }
+      if (i >= esp->num) {
+         i = 0;
+         prev_esp = esp;
+         esp = esp->next;
+      }
+   }
+   
+   score /= factor;
+   
+   delete_hsp = FALSE;
+
+   if (score >= search->pbp->cutoff_s2) {
+      hsp->score = score;
+      searchsp_eff = (FloatHi) search->dblen_eff *
+         (FloatHi) search->context[context].query->effective_length;
+      hsp->evalue = BlastKarlinStoE_simple(score,
+                       search->sbp->kbp[context], searchsp_eff);
+      if (hsp->evalue > search->pbp->cutoff_e) {
+         delete_hsp = TRUE;
+      } else {
+         hsp->query.length = new_q_end - new_q_start;
+         hsp->subject.length = new_s_end - new_s_start;
+         hsp->query.offset = new_q_start - query_start;
+         hsp->query.end = hsp->query.offset + hsp->query.length;
+         hsp->subject.offset = new_s_start - subject_start;
+         hsp->subject.end = hsp->subject.offset + hsp->subject.length;
+         /* Make corrections in edit block and free any parts that
+            are no longer needed */
+         if (first_esp != hsp->gap_info->esp) {
+            GapXEditScriptDelete(hsp->gap_info->esp);
+            hsp->gap_info->esp = first_esp;
+         }
+         if (last_esp->next != NULL) {
+            GapXEditScriptDelete(last_esp->next);
+            last_esp->next = NULL;
+         }
+         last_esp->num = last_esp_num;
+         BlastHSPGetNumIdentical(search, hsp, NULL, &hsp->num_ident, 
+                                 &align_length);
+      }
+   } else {
+      delete_hsp = TRUE;
+   }
+
+   if (delete_hsp) { /* This HSP is now below the cutoff */
+      if (first_esp != NULL && first_esp != hsp->gap_info->esp)
+         GapXEditScriptDelete(first_esp);
+      hsp->gap_info = GapXEditBlockDelete(hsp->gap_info);
+   }
+
+   return delete_hsp;
+}
+
 /* In the following function the forward strand is assumed */
 
 Int2
-MegaBlastReevaluateWithAmbiguities(BlastSearchBlkPtr search, Int4 sequence_number)
+MegaBlastReevaluateWithAmbiguities(BlastSearchBlkPtr search)
 {
-   register BLAST_Score	sum, score, gap_open, gap_extend;
-   register BLAST_ScorePtr PNTR    matrix;
    BLAST_HitListPtr current_hitlist;
    BLAST_HSPPtr PNTR hsp_array, hsp;
-   Uint1Ptr query, subject, query_start, subject_start = NULL;
-   Uint1Ptr new_q_start, new_s_start, new_q_end, new_s_end;
-   Int4 index, context, hspcnt, buf_len=0, i;
-   Int2 factor;
-   Uint1 mask = 0x0f;
-   GapXEditScriptPtr esp, last_esp, prev_esp, first_esp;
+   Uint1Ptr subject_start = NULL;
+   Int4 index, context, hspcnt, buf_len=0;
    Boolean purge, delete_hsp;
-   FloatHi searchsp_eff;
-   Int4 last_esp_num;
    Int4 query_length;
    Int2 status;
-   Int4 align_length;
 
    if (!search->pbp->mb_params)
       return 1;
@@ -3497,8 +3712,10 @@ MegaBlastReevaluateWithAmbiguities(BlastSearchBlkPtr search, Int4 sequence_numbe
    hspcnt = current_hitlist->hspcnt;
    
    hsp_array = current_hitlist->hsp_array;
-   /* In case of no traceback, only adjust the offsets */
-   if (search->pbp->mb_params->no_traceback) {
+   /* In case of greedy extension without traceback, 
+      only adjust the offsets */
+   if (!search->pbp->mb_params->use_dyn_prog && 
+       search->pbp->mb_params->no_traceback) {
       for (index=0; index<hspcnt; index++) {
          if (hsp_array[index] != NULL) {
             /* Adjust the query offsets here */
@@ -3520,22 +3737,6 @@ MegaBlastReevaluateWithAmbiguities(BlastSearchBlkPtr search, Int4 sequence_numbe
       /* All HSPs have been deleted */
       return 0;
    
-   if (search->sbp->reward % 2 == 1) 
-      factor = 2;
-   else 
-      factor = 1;
-
-   if (search->pbp->gap_open == 0 && search->pbp->gap_extend == 0) {
-      gap_open = 0;
-      gap_extend = 
-         (search->sbp->reward - 2*search->sbp->penalty) * factor / 2;
-   } else {
-      gap_open = factor*search->pbp->gap_open;
-      gap_extend = factor*search->pbp->gap_extend;
-   }
-
-   matrix = search->sbp->matrix;
-
    /* Can happen only when subject was being unpacked on the fly 
       during gapped extensions */
    if (!search->subject->sequence_start)
@@ -3561,8 +3762,8 @@ MegaBlastReevaluateWithAmbiguities(BlastSearchBlkPtr search, Int4 sequence_numbe
 
       if (search->pbp->mb_params->use_dyn_prog) {
          /* Check if the extension jumped through the border between
-            sequences or sequence strands. If this happens, leave the part which 
-            contains the original offset pair, saved in gapped_start's
+            sequences or sequence strands. If this happens, leave the part 
+            which contains the original offset pair, saved in gapped_start's
          */
          Int4 extra_length;
          query_length = search->query_context_offsets[context+1] - 
@@ -3595,118 +3796,10 @@ MegaBlastReevaluateWithAmbiguities(BlastSearchBlkPtr search, Int4 sequence_numbe
          continue;
       }
 
-      query_start = (Uint1Ptr) search->context[context].query->sequence;
-      searchsp_eff = (FloatHi) search->dblen_eff *
-            (FloatHi) search->context[context].query->effective_length;
-      
-      query = query_start + hsp->query.offset; 
-      subject = subject_start + hsp->subject.offset;
-      score = 0;
-      sum = 0;
-      new_q_start = new_q_end = query;
-      new_s_start = new_s_end = subject;
-      i = 0;
-
-      esp = hsp->gap_info->esp;
-      prev_esp = NULL;
-      last_esp = first_esp = esp;
-      last_esp_num = 0;
-
-      while (esp) {
-         if (esp->op_type == GAPALIGN_SUB) {
-            sum += factor*matrix[*query & mask][*subject];
-            query++;
-            subject++;
-            i++;
-         } else if (esp->op_type == GAPALIGN_DEL) {
-            sum -= gap_open + gap_extend * esp->num;
-            subject += esp->num;
-            i += esp->num;
-         } else if (esp->op_type == GAPALIGN_INS) {
-            sum -= gap_open + gap_extend * esp->num;
-            query += esp->num;
-            i += esp->num;
-         }
-         
-         if (sum < 0) {
-            if (score < search->pbp->cutoff_s2 ||
-                   BlastKarlinStoE_simple(score, search->sbp->kbp[context],
-                   searchsp_eff) > search->pbp->cutoff_e) {
-               /* Start from new offset */
-               new_q_start = query;
-               new_s_start = subject;
-               score = sum = 0;
-               if (i < esp->num) {
-                  esp->num -= i;
-                  first_esp = esp;
-                  i = 0;
-               } else {
-                  first_esp = esp->next;
-               }
-               /* Unlink the bad part of the esp chain 
-                  so it can be freed later */
-               if (prev_esp)
-                  prev_esp->next = NULL;
-               last_esp = NULL;
-            } else {
-               /* Stop here */
-               break;
-            }
-         } else if (sum > score) {
-            /* Remember this point as the best scoring end point */
-            score = sum;
-            last_esp = esp;
-            last_esp_num = i;
-            new_q_end = query;
-            new_s_end = subject;
-         }
-         if (i >= esp->num) {
-            i = 0;
-            prev_esp = esp;
-            esp = esp->next;
-         }
-      }
-      
-      score /= factor;
-
-      delete_hsp = FALSE;
-      if (score >= search->pbp->cutoff_s2) {
-         hsp->score = score;
-         searchsp_eff = (FloatHi) search->dblen_eff *
-            (FloatHi) search->context[context].query->effective_length;
-         hsp->evalue = BlastKarlinStoE_simple(score,
-                          search->sbp->kbp[context], searchsp_eff);
-         if (hsp->evalue > search->pbp->cutoff_e) {
-            delete_hsp = TRUE;
-         } else {
-            hsp->query.length = new_q_end - new_q_start;
-            hsp->subject.length = new_s_end - new_s_start;
-            hsp->query.offset = new_q_start - query_start;
-            hsp->query.end = hsp->query.offset + hsp->query.length;
-            hsp->subject.offset = new_s_start - subject_start;
-            hsp->subject.end = hsp->subject.offset + hsp->subject.length;
-            /* Make corrections in edit block and free any parts that
-               are no longer needed */
-            if (first_esp != hsp->gap_info->esp) {
-               GapXEditScriptDelete(hsp->gap_info->esp);
-               hsp->gap_info->esp = first_esp;
-            }
-            if (last_esp->next != NULL) {
-               GapXEditScriptDelete(last_esp->next);
-               last_esp->next = NULL;
-            }
-            last_esp->num = last_esp_num;
-            BlastHSPGetNumIdentical(search, hsp, NULL, &hsp->num_ident, 
-                                    &align_length);
-         }
-      } else {
-         delete_hsp = TRUE;
-      }
+      delete_hsp =
+         ReevaluateScoreWithAmbiguities(search, subject_start, hsp);
 
       if (delete_hsp) { /* This HSP is now below the cutoff */
-         if (first_esp != NULL && first_esp != hsp->gap_info->esp)
-            GapXEditScriptDelete(first_esp);
-         hsp->gap_info = GapXEditBlockDelete(hsp->gap_info);
          hsp_array[index] = MemFree(hsp_array[index]);
          purge = TRUE;
       }
@@ -3734,10 +3827,8 @@ MegaBlastReevaluateWithAmbiguities(BlastSearchBlkPtr search, Int4 sequence_numbe
       */
       for (index=search->pbp->hsp_num_max; 
            index < search->current_hitlist->hspcnt; ++index) {
-         current_hitlist->hsp_array[index]->gap_info = 
-            GapXEditBlockDelete(current_hitlist->hsp_array[index]->gap_info);
          current_hitlist->hsp_array[index] = 
-            MemFree(current_hitlist->hsp_array[index]);
+            BLAST_HSPFree(current_hitlist->hsp_array[index]);
       }
       search->current_hitlist->hspcnt = search->pbp->hsp_num_max;
    }
@@ -3799,8 +3890,6 @@ void PrintMaskedSequence(BioseqPtr query_bsp, SeqLocPtr mask_slp,
    SeqLocPtr query_slp = NULL;
    SeqPortPtr spp;
    Uint1Ptr query_seq, seq_line;
-   BioseqPtr masked_bsp;
-   ByteStorePtr byte_sp;
    Int4 index, id_length = 0, defline_len;
    Uint1 residue;
    CharPtr buffer = NULL;
@@ -3863,13 +3952,11 @@ MegaBlastSaveCurrentHitlist(BlastSearchBlkPtr search)
 	BLAST_KarlinBlkPtr kbp;
 	BLASTResultHspPtr hsp_array;
 	Int4 hspcnt, index, index1, new_index, old_index, low_index, high_index;
-	Int4 hitlist_count, hitlist_max, hspmax, hspset_cnt, high_score=0, retval;
+	Int4 hitlist_count, hitlist_max, hspmax, high_score=0, retval;
 	Nlm_FloatHi current_evalue=DBL_MAX;
-	Int2 deleted;
-	Int4 query_length, i, hsp_index, new_size;
+	Int4 query_length, hsp_index, new_size;
         Int4Ptr hsp_array_sizes;
-	Int2 context, num_queries, query_index;
-	SeqIdPtr subject_id=NULL;
+	Int2 num_queries, query_index;
         Boolean PNTR do_not_reallocate;
         Boolean use_dyn_prog = search->pbp->mb_params->use_dyn_prog;
 
@@ -3994,7 +4081,7 @@ MegaBlastSaveCurrentHitlist(BlastSearchBlkPtr search)
            query_length = 
               search->query_context_offsets[hsp->context+1] -
               search->query_context_offsets[hsp->context] - 1;
-           if (!use_dyn_prog) {
+           if (!use_dyn_prog && !search->pbp->mb_params->no_traceback) {
               hsp->gap_info->start1 = hsp->query.offset;
               hsp->gap_info->start2 = hsp->subject.offset;
               hsp->gap_info->frame1 = hsp_array[hsp_index].query_frame;
@@ -4244,4 +4331,5 @@ MBTemplateType GetMBTemplateType(Int2 weight, Int2 length, MBDiscWordType type)
             return TEMPL_12_21_OPT;
       }
    }
+   return TEMPL_ERROR;
 }
diff --git a/tools/mblast.h b/tools/mblast.h
index a8109ade..dd84413a 100644
--- a/tools/mblast.h
+++ b/tools/mblast.h
@@ -32,8 +32,17 @@ Contents: prototypes for "public" Mega BLAST functions (ones that other utilitil
 
 ******************************************************************************/
 
-/* $Revision: 6.46 $ 
+/* $Revision: 6.49 $ 
 * $Log: mblast.h,v $
+* Revision 6.49  2004/01/16 23:43:44  dondosha
+* No more need for special argument for partial search: it is set in options
+*
+* Revision 6.48  2003/12/10 17:05:28  dondosha
+* Added function ReevaluateScoreWithAmbiguities to reevaluate score for one HSP; use it after greedy traceback
+*
+* Revision 6.47  2003/10/29 17:47:00  dondosha
+* Allow 2-stage greedy extension in megablast
+*
 * Revision 6.46  2002/09/03 13:52:45  kans
 * added prototypes for MegaBlastWordFinder and MegaBlastGappedAlign for Mac compiler
 *
@@ -232,9 +241,6 @@ BioseqMegaBlastEngineByLoc PROTO((SeqLocPtr slp, CharPtr progname, CharPtr datab
 SeqAlignPtr PNTR
 BioseqMegaBlastEngineCore PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options));
 
-SeqAlignPtr PNTR
-BioseqMegaBlastEngineCoreEx PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options, Boolean partial));
-
 BlastSearchBlkPtr BlastFillQueryOffsets PROTO((BlastSearchBlkPtr search, SeqLocPtr query_slp, Int4 wordsize));
 
 BlastSearchBlkPtr 
@@ -258,8 +264,11 @@ MegaBlastGetNumIdentical PROTO((Uint1Ptr query, Uint1Ptr subject,
                                 Int4 q_start, Int4 s_start, Int4 length, 
                                 Boolean reverse));
 
+Boolean ReevaluateScoreWithAmbiguities(BlastSearchBlkPtr search,
+           Uint1Ptr subject_start, BLAST_HSPPtr hsp);
+
 Int2
-MegaBlastReevaluateWithAmbiguities PROTO((BlastSearchBlkPtr search, Int4 sequence_number));
+MegaBlastReevaluateWithAmbiguities PROTO((BlastSearchBlkPtr search));
 
 Int4 BinarySearchInt4 PROTO((Int4 n, Int4Ptr A, Int4 size));
 
@@ -277,9 +286,10 @@ MegaBlastParameterBlkPtr
 MegaBlastParameterBlkNew PROTO((BLAST_OptionsBlkPtr options));
 
 Int4 
-MegaBlastWordFinder(BlastSearchBlkPtr search, LookupTablePtr lookup);
-Int2 MegaBlastGappedAlign(BlastSearchBlkPtr search);
+MegaBlastWordFinder PROTO((BlastSearchBlkPtr search, LookupTablePtr lookup));
 
+void PerformGreedyAlignmentWithTraceback(GapAlignBlkPtr gap_align,
+        GreedyAlignMemPtr gamp, BLAST_ScoreBlkPtr sbp);
 
 #ifdef __cplusplus
 }
diff --git a/tools/ncbisrti.h b/tools/ncbisrti.h
index dd1fef61..e4c8c1ed 100644
--- a/tools/ncbisrti.h
+++ b/tools/ncbisrti.h
@@ -1,4 +1,4 @@
-/* $Id: ncbisrti.h,v 6.2 1998/06/01 14:52:38 madden Exp $
+/* $Id: ncbisrti.h,v 6.3 2003/12/03 02:10:52 kans Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,12 +29,15 @@
 *
 * Initial Version Creation Date: 03/24/1997
 *
-* $Revision: 6.2 $
+* $Revision: 6.3 $
 *
 * File Description:
 *         Internal include file for SORTing library
 *
 * $Log: ncbisrti.h,v $
+* Revision 6.3  2003/12/03 02:10:52  kans
+* added defines missing from Mac OS 10.3 headers
+*
 * Revision 6.2  1998/06/01 14:52:38  madden
 * Change to using TmpNam
 *
@@ -77,6 +80,16 @@
 
 #endif /* OS_UNIX */
 
+/* Missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+#ifdef __MWERKS__
+#ifdef OS_UNIX_DARWIN
+#ifndef __SCHAR_MAX__
+#define __SCHAR_MAX__ 127
+#endif
+#endif
+#endif
+/* End missing from /usr/include/gcc/darwin/3.3/machine/limits.h */
+
 #define MERGEALLOC 16384
 
 #define UCHAR_LIM (UCHAR_MAX + 1)
diff --git a/tools/newkar.c b/tools/newkar.c
deleted file mode 100644
index 7248fc1d..00000000
--- a/tools/newkar.c
+++ /dev/null
@@ -1,142 +0,0 @@
-static char const rcsid[] = "$Id: newkar.c,v 6.3 2003/05/30 17:25:37 coulouri Exp $";
-
-#include <ncbi.h>
-#include <ncbimath.h>
-#include <objcode.h>
-#include <objseq.h>
-#include <sequtil.h>
-#include <blastkar.h>
-#include <blastpri.h>
-
-/*
-	impalaKarlinLambdaBis
-
-	Calculate Lambda using the bisection method (slow).
-*/
-static Nlm_FloatHi
-impalaKarlinLambdaBis(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi initialLambda)
-{
-	Nlm_FloatHi	PNTR sprob;
-	Nlm_FloatHi	lambda, up, newval;
-	BLAST_Score	i, low, high;
-	int		j;
-	Nlm_FloatHi	sum, x0, x1;
-        Nlm_FloatHi     returnValue;
-
-	if (sfp->score_avg >= 0.) {
-		return -1.;
-	}
-	low = sfp->obs_min;
-	high = sfp->obs_max;
-	/* if (BlastScoreChk(low, high) != 0)
-		return -1.; */
-
-	sprob = sfp->sprob;
-	up = initialLambda;
-	for (lambda=0.; ; ) {
-		up *= 2;
-		x0 = exp((Nlm_FloatHi)up);
-		x1 = Nlm_Powi((Nlm_FloatHi)x0, low - 1);
-		if (x1 > 0.) {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i] * (x1 *= x0);
-		}
-		else {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i] * exp(up * i);
-		}
-		if (sum >= 1.0)
-			break;
-		lambda = up;
-	}
-
-	for (j=0; j<BLAST_KARLIN_LAMBDA_ITER_DEFAULT; ++j) {
-		newval = (lambda + up) / 2.;
-		x0 = exp((Nlm_FloatHi)newval);
-		x1 = Nlm_Powi((Nlm_FloatHi)x0, low - 1);
-		if (x1 > 0.) {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i] * (x1 *= x0);
-		}
-		else {
-			for (sum=0., i=low; i<=high; ++i)
-				sum += sprob[i] * exp(newval * i);
-		}
-		if (sum > 1.0)
-			up = newval;
-		else
-			lambda = newval;
-	}
-        returnValue = (lambda + up) /2;
-	return (returnValue);
-}
-
-/******************* Fast Lambda Calculation Subroutine ************************
-	Version 1.0	May 16, 1991
-	Program by:	Stephen Altschul
-
-	Uses Newton-Raphson method (fast) to solve for Lambda, given an initial
-	guess (lambda0) obtained perhaps by the bisection method.
-*******************************************************************************/
-
-Nlm_FloatHi LIBCALL
-impalaKarlinLambdaNR(BLAST_ScoreFreqPtr sfp, Nlm_FloatHi initialLambda)
-{
-	BLAST_Score	low;			/* Lowest score (must be negative)  */
-	BLAST_Score	high;			/* Highest score (must be positive) */
-	int		j;
-	BLAST_Score	i;
-	Nlm_FloatHi PNTR	sprob;
-	Nlm_FloatHi	lambda0, sum, slope, temp, x0, x1, amt;
-        Nlm_FloatHi returnValue;
-	Boolean foundPositive;
-
-	low = sfp->obs_min;
-	high = sfp->obs_max;
-	if (sfp->score_avg >= 0.) {	/* Expected score must be negative */
-		return -1.0;
-	}
-	/* if (BlastScoreChk(low, high) != 0)
-		return -1.; */
-
-	lambda0 = initialLambda;
-
-	/* Calculate lambda */
-
-	sprob = sfp->sprob;
-	foundPositive = FALSE;
-	for(j = 1; j <=high; j++)
-	  if (sprob[j] > 0.0) {
-            foundPositive = TRUE;
-            break;
-	  }
-        if (!foundPositive)
-	  return(-1);
-	for (j=0; j<40; ++j) { /* limit of 20 should never be close-approached */
-		sum = -1.0;
-		slope = 0.0;
-		if (lambda0 < 0.01)
-			break;
-		x0 = exp((Nlm_FloatHi)lambda0);
-		x1 = Nlm_Powi((Nlm_FloatHi)x0, low - 1);
-		if (x1 == 0.)
-			break;
-		for (i=low; i<=high; ++i) {
-			sum += (temp = sprob[i] * (x1 *= x0));
-			slope += temp * i;
-		}
-		lambda0 -= (amt = sum/slope);
-		if (ABS(amt/lambda0) < BLAST_KARLIN_LAMBDA_ACCURACY_DEFAULT) {
-			/*
-			Does it appear that we may be on the verge of converging
-			to the ever-present, zero-valued solution?
-			*/
-			if (lambda0 > BLAST_KARLIN_LAMBDA_ACCURACY_DEFAULT)
-				return lambda0;
-			break;
-		}
-	}
-	returnValue= impalaKarlinLambdaBis(sfp, initialLambda);
-        return(returnValue);
-}
-
diff --git a/tools/readdb.c b/tools/readdb.c
index fd0440b9..96e10722 100644
--- a/tools/readdb.c
+++ b/tools/readdb.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: readdb.c,v 6.424 2003/10/01 19:03:50 camacho Exp $";
+static char const rcsid[] = "$Id: readdb.c,v 6.429 2004/01/29 20:48:07 coulouri Exp $";
 
-/* $Id: readdb.c,v 6.424 2003/10/01 19:03:50 camacho Exp $ */
+/* $Id: readdb.c,v 6.429 2004/01/29 20:48:07 coulouri Exp $ */
 /*
 * ===========================================================================
 *
@@ -50,7 +50,7 @@ Detailed Contents:
 *
 * Version Creation Date:   3/22/95
 *
-* $Revision: 6.424 $
+* $Revision: 6.429 $
 *
 * File Description: 
 *       Functions to rapidly read databases from files produced by formatdb.
@@ -65,6 +65,22 @@ Detailed Contents:
 *
 * RCS Modification History:
 * $Log: readdb.c,v $
+* Revision 6.429  2004/01/29 20:48:07  coulouri
+* Only limit volume sizes on 32-bit platforms
+*
+* Revision 6.428  2004/01/28 19:34:51  camacho
+* Added sanity check for alias files
+*
+* Revision 6.427  2004/01/26 13:52:31  camacho
+* Do not use snprintf
+*
+* Revision 6.426  2004/01/23 21:13:54  camacho
+* 1. Refactored code to create multiple volumes.
+* 2. Set the maximum sequence file size to 1GB.
+*
+* Revision 6.425  2004/01/12 23:06:36  camacho
+* Sort link bit gi lists
+*
 * Revision 6.424  2003/10/01 19:03:50  camacho
 * Fix in readdb_get_totals_ex2 to use the alias file length/number of entries when
 * gilist is populated.
@@ -1755,6 +1771,7 @@ static ValNodePtr IntValNodeCopy(ValNodePtr vnp);
 static int LIBCALLBACK ID_Compare(VoidPtr i, VoidPtr j);
 static void FDBBlastDefLineSetBit(Int2 bit_no, ValNodePtr PNTR retval);
 static ReadDBFILEPtr readdb_merge_gifiles (ReadDBFILEPtr rdfp_chain);
+static Boolean s_IsTextFile(const char* filename);
 
 #if defined(OS_UNIX_SOL) || defined(OS_UNIX_LINUX)
 #ifdef  HAVE_MADVISE
@@ -2448,6 +2465,11 @@ readdb_read_alias_file(CharPtr filename)
     if (fp == NULL)
         return NULL;
 
+    if (!s_IsTextFile(filename)) {
+        ErrPostEx(SEV_ERROR, 0, 1, "%s is not a valid alias file\n", filename);
+        return NULL;
+    }
+
     file_path = Nlm_FilePathFind(filename);
     
     buffer = MemNew(buflen + 1);
@@ -5396,6 +5418,7 @@ readdb_get_sequence_length (ReadDBFILEPtr rdfp, Int4 sequence_number)
             Nlm_SwapUint4(rdfp->sequence_index[sequence_number]) - 1;
     }
 
+#if 0
     /* For nucl. return "unpacked" length and get the remainder out
     of the last byte. */
     if (is_prot == FALSE)
@@ -5420,6 +5443,7 @@ and the last two bits of the byte holds the size of the remainder (0-3). */
         length *= 4;
         length += remainder;
     }
+#endif
 
     return length;
 }
@@ -7482,6 +7506,7 @@ ValNodePtr FDBLoadLinksTable(void)
             ErrPostEx(SEV_ERROR,0,0,"Could not read %s", filename);
             continue;
         }
+        HeapSort(gis->i, gis->count, sizeof(Int4), ID_Compare);
         lk_info = (LinkInfoPtr) MemNew(sizeof(LinkInfo));
         lk_info->bit_number = bit;
         lk_info->gi_list = gis;
@@ -8370,6 +8395,146 @@ static Boolean FDBDumpDefline(FormatDBPtr fdbp, CharPtr title, CharPtr seq_id)
   return TRUE;
 }
 
+/* Maximum size of sequence file: 1GB */
+#if LONG_BIT!=64
+#define SEQFILE_SIZE_MAX 1000000000UL
+#endif
+
+/* Creates a new volume of the blast database being created if the sequence
+ * being added causes it to exceed the volume limitations (number of
+ * letters/sequences) */
+static Int4 FDBCreateNewVolume(FormatDBPtr fdbp, 
+                               const ByteStorePtr seq,
+                               Int4 seq_length,
+                               const Uint4Ptr ambiguities)
+{
+  FDB_optionsPtr options = fdbp->options;
+  Int4 amb_size = 0; /* size of ambiguities for this sequence */
+  Int4 seq_size = 0; /* length of sequence file with new sequence being added */
+  Int4 hdr_size = 0; /* size of the header file without new sequence */
+  Char extension_prefix = options->is_protein ? 'p' : 'n';
+
+  if (ambiguities) {
+      amb_size = sizeof(*ambiguities) * ((*ambiguities)&0x7fffffffUL);
+  }
+  seq_size = (ftell(fdbp->fd_seq) + BSLen(seq) + 1 + amb_size);
+  hdr_size = ftell(fdbp->aip_def ? fdbp->aip_def->fp : fdbp->fd_def);
+
+  if ( /* if bases_in_volume was specified, don't exceed that */
+       (options->bases_in_volume && 
+        (fdbp->TotalLen + seq_length > options->bases_in_volume)) ||
+       /* if sequences_in_volume was specified, don't exceed that (will be
+        * deprecated) */
+       (options->sequences_in_volume && 
+        (fdbp->num_of_seqs+1) > options->sequences_in_volume)  ||
+       /* if sequence file is about to grow larger than SEQFILE_SIZE_MAX */
+#if defined(SEQFILE_SIZE_MAX)
+       ( seq_size > SEQFILE_SIZE_MAX) ||
+#endif
+       /* if header file is about to grow too large (assuming header can not 
+        * exceed 2G - 2000000000b) */
+       ( hdr_size > 2000000000UL)
+      )
+    {
+      Char dbnamebuf[PATH_MAX];
+      FormatDBPtr tmp_fdbp = NULL;
+#if 0
+      ErrLogPrintf("New volume : tell:%d  seq:%d  amd:%d  total: %d  (%d)\n",
+                   ftell(fdbp->fd_seq),BSLen(*seq_data),amb_size,
+                   seq_size, seq_size > 0x7fffffff );
+#endif
+      if (options->volume == 1) {
+          sprintf(dbnamebuf, "%s.00", options->base_name);
+      } else {
+          sprintf(dbnamebuf, "%s", options->base_name);
+      }
+      ErrLogPrintf("Closing volume %s with %ld sequences, %s letters"
+                   "(.%csq file = %ld bytes; .%chr file = %ld bytes)\n", 
+                   dbnamebuf, fdbp->num_of_seqs, 
+                   Nlm_Int8tostr(fdbp->TotalLen, 1),
+                   extension_prefix, (long)seq_size, 
+                   extension_prefix, (long)hdr_size);
+      tmp_fdbp = (FormatDBPtr) MemNew(sizeof(FormatDB));
+      MemCpy(tmp_fdbp, fdbp, sizeof(FormatDB));
+
+      if(FormatDBClose(tmp_fdbp))
+         return 9;
+      options->volume++;
+      
+      /* When second volume is created, add suffix .00 to all 
+         first volume files */
+      if (options->volume == 1)
+        {
+          Char  oldnamebuf[FILENAME_MAX], newnamebuf[FILENAME_MAX];
+          int len = StringLen(options->base_name) + 2;
+          sprintf(oldnamebuf, "%s.%cin", options->base_name, extension_prefix);
+          sprintf(newnamebuf, "%s.00.%cin", options->base_name,
+                  extension_prefix);
+          if (FileLength(oldnamebuf) > 0)
+            FileRename(oldnamebuf, newnamebuf);
+          StringCpy(oldnamebuf + len, "hr");
+          StringCpy(newnamebuf + len + 3, "hr");
+          if (FileLength(oldnamebuf) > 0)
+            FileRename(oldnamebuf, newnamebuf);
+          StringCpy(oldnamebuf + len, "sq");
+          StringCpy(newnamebuf + len + 3, "sq");
+          if (FileLength(oldnamebuf) > 0)
+            FileRename(oldnamebuf, newnamebuf);
+          StringCpy(oldnamebuf + len, "nd");
+          StringCpy(newnamebuf + len + 3, "nd");
+          if (FileLength(oldnamebuf) > 0)
+            FileRename(oldnamebuf, newnamebuf);
+          StringCpy(oldnamebuf + len, "ni");
+          StringCpy(newnamebuf + len + 3, "ni");
+          if (FileLength(oldnamebuf) > 0)
+            FileRename(oldnamebuf, newnamebuf);
+          StringCpy(oldnamebuf + len, "sd");
+          StringCpy(newnamebuf + len + 3, "sd");
+          if (FileLength(oldnamebuf) > 0)
+            FileRename(oldnamebuf, newnamebuf);
+          StringCpy(oldnamebuf + len, "si");
+          StringCpy(newnamebuf + len + 3, "si");
+          if (FileLength(oldnamebuf) > 0)
+            FileRename(oldnamebuf, newnamebuf);
+         if (options->dump_info) {
+             StringCpy(oldnamebuf + len, "di");
+             StringCpy(newnamebuf + len + 3, "di");
+             if (FileLength(oldnamebuf) > 0)
+                 FileRename(oldnamebuf, newnamebuf);
+         }
+         if (options->is_protein) {
+             /* PIG ISAM files */
+             StringCpy(oldnamebuf + len, "pd");
+             StringCpy(newnamebuf + len + 3, "pd");
+             if (FileLength(oldnamebuf) > 0)
+                 FileRename(oldnamebuf, newnamebuf);
+             StringCpy(oldnamebuf + len, "pi");
+             StringCpy(newnamebuf + len + 3, "pi");
+             if (FileLength(oldnamebuf) > 0)
+                 FileRename(oldnamebuf, newnamebuf);
+         }
+
+          MemFree(options->base_name);
+          newnamebuf[len+1] = NULLB;
+          options->base_name = StringSave(newnamebuf);
+        }
+
+      {
+        CharPtr ptr;
+      ptr = options->base_name + StringLen(options->base_name) - 2;
+      sprintf(ptr, "%02ld", (long) options->volume);
+      }
+      
+      if ((tmp_fdbp = FormatDBInit(options)) == NULL)
+        return 2;
+      
+      MemCpy(fdbp, tmp_fdbp, sizeof(FormatDB));
+      MemFree(tmp_fdbp);
+    }
+
+  return 0;
+}
+
 Int2 FDBAddSequence (FormatDBPtr fdbp, BlastDefLinePtr bdp, 
                      Uint1 seq_data_type, ByteStorePtr *seq_data, 
                      Int4 SequenceLen, 
@@ -8493,8 +8658,8 @@ Int2 FDBAddSequence2 (FormatDBPtr fdbp, BlastDefLinePtr bdp,
 {
   Uint4               hash;
   Boolean             bdp_was_allocated = FALSE;
-  FormatDBPtr         tmp_fdbp;
   DI_Record direc;
+  Int4 retval = 0;
   
 #if 0
   /* testing heap overuse */
@@ -8508,101 +8673,9 @@ Int2 FDBAddSequence2 (FormatDBPtr fdbp, BlastDefLinePtr bdp,
   }
 
   /* If too many bases in thise file, start a new volume */
-  if (fdbp->options->bases_in_volume > 0 || fdbp->options->sequences_in_volume > 0 || 1)
-    {
-      FDB_optionsPtr options = fdbp->options;
-      int amb_size= sizeof(*AmbCharPtr)*(AmbCharPtr==NULL?0:(*AmbCharPtr)&0x7fffffffUL);
-      int nl = (ftell(fdbp->fd_seq) + BSLen(*seq_data) + 1 + amb_size);
-      int hdrsize = ftell(fdbp->aip_def?fdbp->aip_def->fp:fdbp->fd_def) ;
-
-      if ((options->bases_in_volume && (fdbp->TotalLen + SequenceLen > options->bases_in_volume)) ||
-          (options->sequences_in_volume && (fdbp->num_of_seqs+1) > options->sequences_in_volume)  ||
-          ( nl > 0x7fffffffUL) ||
-          ( hdrsize > 2000000000UL /* assuming header can not exceed 2G - 2000000000b */ )
-          )
-        {
-          ErrLogPrintf("New volume : tell:%d  seq:%d  amd:%d  total: %d  (%d)\n",
-                       ftell(fdbp->fd_seq),BSLen(*seq_data),amb_size,
-                       nl, nl > 0x7fffffff );
-          tmp_fdbp = (FormatDBPtr) MemNew(sizeof(FormatDB));
-          MemCpy(tmp_fdbp, fdbp, sizeof(FormatDB));
-
-          if(FormatDBClose(tmp_fdbp))
-             return 9;
-          options->volume++;
-          
-          /* When second volume is created, add suffix .00 to all 
-             first volume files */
-          if (options->volume == 1)
-            {
-              Char  oldnamebuf[FILENAME_MAX], newnamebuf[FILENAME_MAX];
-              int len = StringLen(options->base_name) + 2;
-              sprintf(oldnamebuf, "%s.%cin", options->base_name,
-                      fdbp->options->is_protein ? 'p' : 'n');
-              sprintf(newnamebuf, "%s.00.%cin", options->base_name, 
-                      fdbp->options->is_protein ? 'p' : 'n');
-              if (FileLength(oldnamebuf) > 0)
-                FileRename(oldnamebuf, newnamebuf);
-              StringCpy(oldnamebuf + len, "hr");
-              StringCpy(newnamebuf + len + 3, "hr");
-              if (FileLength(oldnamebuf) > 0)
-                FileRename(oldnamebuf, newnamebuf);
-              StringCpy(oldnamebuf + len, "sq");
-              StringCpy(newnamebuf + len + 3, "sq");
-              if (FileLength(oldnamebuf) > 0)
-                FileRename(oldnamebuf, newnamebuf);
-              StringCpy(oldnamebuf + len, "nd");
-              StringCpy(newnamebuf + len + 3, "nd");
-              if (FileLength(oldnamebuf) > 0)
-                FileRename(oldnamebuf, newnamebuf);
-              StringCpy(oldnamebuf + len, "ni");
-              StringCpy(newnamebuf + len + 3, "ni");
-              if (FileLength(oldnamebuf) > 0)
-                FileRename(oldnamebuf, newnamebuf);
-              StringCpy(oldnamebuf + len, "sd");
-              StringCpy(newnamebuf + len + 3, "sd");
-              if (FileLength(oldnamebuf) > 0)
-                FileRename(oldnamebuf, newnamebuf);
-              StringCpy(oldnamebuf + len, "si");
-              StringCpy(newnamebuf + len + 3, "si");
-              if (FileLength(oldnamebuf) > 0)
-                FileRename(oldnamebuf, newnamebuf);
-             if (options->dump_info) {
-                 StringCpy(oldnamebuf + len, "di");
-                 StringCpy(newnamebuf + len + 3, "di");
-                 if (FileLength(oldnamebuf) > 0)
-                     FileRename(oldnamebuf, newnamebuf);
-             }
-             if (options->is_protein) {
-                 /* PIG ISAM files */
-                 StringCpy(oldnamebuf + len, "pd");
-                 StringCpy(newnamebuf + len + 3, "pd");
-                 if (FileLength(oldnamebuf) > 0)
-                     FileRename(oldnamebuf, newnamebuf);
-                 StringCpy(oldnamebuf + len, "pi");
-                 StringCpy(newnamebuf + len + 3, "pi");
-                 if (FileLength(oldnamebuf) > 0)
-                     FileRename(oldnamebuf, newnamebuf);
-             }
+  if ( (retval = FDBCreateNewVolume(fdbp, *seq_data, SequenceLen, AmbCharPtr)))
+      return retval;
 
-              MemFree(options->base_name);
-              newnamebuf[len+1] = NULLB;
-              options->base_name = StringSave(newnamebuf);
-            }
-
-          {
-            CharPtr ptr;
-          ptr = options->base_name + StringLen(options->base_name) - 2;
-          sprintf(ptr, "%02ld", (long) options->volume);
-          }
-          
-          if ((tmp_fdbp = FormatDBInit(options)) == NULL)
-            return 2;
-          
-          MemCpy(fdbp, tmp_fdbp, sizeof(FormatDB));
-          MemFree(tmp_fdbp);
-        }
-    } /* bases in volume > 0 */
   assert(ftell(fdbp->fd_seq)+BSLen(*seq_data) + 1 + (AmbCharPtr==NULL?0:(*AmbCharPtr)&0x7fffffffUL) < 0x7fffffffUL );
   fdbp->TotalLen += SequenceLen;
     
@@ -12105,3 +12178,24 @@ readdb_pig2oid(ReadDBFILEPtr rdfp, Int4 pig, Int4Ptr start)
 
     return retval;
 }
+
+static Boolean s_IsTextFile(const char* filename)
+{
+    FILE* fp = NULL;
+    Boolean retval = TRUE;
+    Int4 i = 0;
+
+    if ( !(fp = FileOpen(filename, "r"))) {
+        return FALSE;
+    }
+
+    for (i = 0; i < 10 && !feof(fp); i++) {
+        int c = getc(fp);
+        if ( ! (isprint(c) || isspace(c)) ) {
+            retval = FALSE;
+            break;
+        }
+    }
+    FileClose(fp);
+    return retval;
+}
diff --git a/tools/salign.c b/tools/salign.c
index c9c88051..662adc5d 100644
--- a/tools/salign.c
+++ b/tools/salign.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: salign.c,v 6.6 2003/05/30 17:25:37 coulouri Exp $";
+static char const rcsid[] = "$Id: salign.c,v 6.7 2003/12/29 21:45:37 coulouri Exp $";
 
 /*   salign.c
 * ===========================================================================
@@ -395,7 +395,7 @@ static SeqAlignPtr SortBlastHits (SeqAlignPtr salp, Int4 threshold, Uint1 choice
   Boolean     goOn = TRUE;
   Boolean     ok;
 
-  if (salp == NULL || choice < 0)
+  if (salp == NULL)
      return salp;
   sap = SeqAnnotForSeqAlign (salp);
   sap2 = (SeqAnnotPtr) AsnIoMemCopy ((Pointer) sap, (AsnReadFunc) SeqAnnotAsnRead, (AsnWriteFunc) SeqAnnotAsnWrite);
diff --git a/tools/spidey.c b/tools/spidey.c
index 595796a3..ea80eb6a 100644
--- a/tools/spidey.c
+++ b/tools/spidey.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: spidey.c,v 6.64 2003/10/21 15:26:17 kans Exp $";
+static char const rcsid[] = "$Id: spidey.c,v 6.67 2003/12/12 21:25:26 kskatz Exp $";
 
 /* ===========================================================================
 *
@@ -30,13 +30,22 @@ static char const rcsid[] = "$Id: spidey.c,v 6.64 2003/10/21 15:26:17 kans Exp $
 *
 * Version Creation Date:   5/01
 *
-* $Revision: 6.64 $
+* $Revision: 6.67 $
 *
 * File Description: mrna-to-genomic alignment algorithms and functions
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: spidey.c,v $
+* Revision 6.67  2003/12/12 21:25:26  kskatz
+* Fixed bug in SPI_CheckForPolyAExon() where multiple SeqAlignPtr's to the same object were not handled carefully: one of the ptr's was being accessed when the object was freed via the other ptr.
+*
+* Revision 6.66  2003/12/12 17:57:04  kskatz
+* Fixed a potential array bounds read error in SPI_CheckMrnaOrder()
+*
+* Revision 6.65  2003/12/10 16:53:22  kskatz
+* Ensured that 'ovl' when used is never negative once set in SPI_AdjustOverlaps() [see revision 6.57]
+*
 * Revision 6.64  2003/10/21 15:26:17  kans
 * fixed typo of SPI_IvalPt to SPI_IvalPtr
 *
@@ -4325,18 +4334,22 @@ static void SPI_CheckForPolyAExon(SeqAlignPtr sap)
       sap_target = amaip->saps[amaip->numsaps-1];
    salp = (SeqAlignPtr)(sap->segs);
    salp_prev = NULL;
-   while (salp != NULL)
-   {
-      if (salp == sap_target)
-      {
-         if (salp_prev == NULL)
-            sap->segs = (Pointer)(sap_target->next);
-         else
-            salp_prev->next = sap_target->next;
-         SeqAlignFree(sap_target);
-      }
-      salp_prev = salp;
-      salp = salp->next;
+   while (salp != NULL){
+       if (salp == sap_target){
+           if (salp_prev == NULL){
+               sap->segs = (Pointer)(sap_target->next);
+           }
+           else {
+               salp_prev->next = sap_target->next;
+           }
+           SeqAlignFree(sap_target);
+           sap_target = 0;
+           salp = 0;
+       }
+       else {
+           salp_prev = salp;
+           salp = salp->next;
+       }
    }
    AMAlignIndexFreeEitherIndex(sap);
    AlnMgr2IndexLite(sap);
@@ -5812,7 +5825,7 @@ static void SPI_AdjustOverlaps(SeqAlignPtr sap1, SeqAlignPtr sap2, Int4 n, SPI_m
       }
       ovl = -ovl;
    }
-   ovl = MIN(abs(ovl), start2-stop1);
+   ovl = MIN(abs(ovl), abs(start2-stop1));
    if (spot->interspecies == TRUE)
       fluff = SPI_FLUFF;
    else
@@ -5841,7 +5854,7 @@ static void SPI_AdjustOverlaps(SeqAlignPtr sap1, SeqAlignPtr sap2, Int4 n, SPI_m
       }
       i = 0;
       buf = (Uint1Ptr)MemNew((2*fluff+ovl+spllen+2)*sizeof(Uint1));
-      buf2 = (Uint1Ptr)MemNew((2*fluff+(abs(ovl))+spllen+2)*sizeof(Uint1));
+      buf2 = (Uint1Ptr)MemNew((2*fluff+ovl+spllen+2)*sizeof(Uint1));
       SeqPortRead(spp, buf2, 2*fluff+ovl+spllen+2);
       for (f=0; f<SPI_NUMSITES; f++)
       {
@@ -10691,7 +10704,8 @@ static void SPI_CheckMrnaOrder(SPI_IvalPtr PNTR spi_pp, const int num)
   
     for (x = 0, ival = spi_pp[x], ival2 = spi_pp[x + 1]; 
          x < num && ival != 0 && ival2 != 0; 
-         ++x, ival = spi_pp[x], ival2 = spi_pp[x + 1]){
+         ++x, ival = spi_pp[x], 
+             ival2 = (x + 1 < num ? spi_pp[x + 1] : 0)){
         if (x < num - 2){ /* three to window */
             ival3 = spi_pp[x + 2];
             if ((ival->strand == Seq_strand_plus == ival2->strand
diff --git a/util/tables/raw_scoremat.c b/util/tables/raw_scoremat.c
index d0c4e47d..67cecf3c 100644
--- a/util/tables/raw_scoremat.c
+++ b/util/tables/raw_scoremat.c
@@ -1,4 +1,4 @@
-/*  $Id: raw_scoremat.c,v 1.2 2003/10/02 15:37:34 ivanov Exp $
+/*  $Id: raw_scoremat.c,v 1.3 2003/12/29 21:25:50 ucko Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -40,6 +40,7 @@
 #include "sm_blosum80.c"
 #include "sm_pam30.c"
 #include "sm_pam70.c"
+#include "sm_pam250.c"
 
 static const char kNCBIstdaa[] = "-ABCDEFGHIKLMNPQRSTVWXYZU*";
 
@@ -112,6 +113,9 @@ void NCBISM_Unpack(const SNCBIPackedScoreMatrix* psm,
 /*
  * ===========================================================================
  * $Log: raw_scoremat.c,v $
+ * Revision 1.3  2003/12/29 21:25:50  ucko
+ * +PAM250
+ *
  * Revision 1.2  2003/10/02 15:37:34  ivanov
  * Get rid of compilation warnings
  *
diff --git a/util/tables/raw_scoremat.h b/util/tables/raw_scoremat.h
index 434e4a0a..b2289436 100644
--- a/util/tables/raw_scoremat.h
+++ b/util/tables/raw_scoremat.h
@@ -1,7 +1,7 @@
 #ifndef UTIL_TABLES___SCOREMAT__H
 #define UTIL_TABLES___SCOREMAT__H
 
-/*  $Id: raw_scoremat.h,v 1.1 2003/08/21 19:48:19 ucko Exp $
+/*  $Id: raw_scoremat.h,v 1.2 2003/12/29 21:25:50 ucko Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -76,6 +76,7 @@ extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Blosum62;
 extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Blosum80;
 extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Pam30;
 extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Pam70;
+extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Pam250;
 
 #ifdef __cplusplus
 }
@@ -85,6 +86,9 @@ extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Pam70;
 * ===========================================================================
 *
 * $Log: raw_scoremat.h,v $
+* Revision 1.2  2003/12/29 21:25:50  ucko
+* +PAM250
+*
 * Revision 1.1  2003/08/21 19:48:19  ucko
 * Add tables library (shared with C) for raw score matrices, etc.
 *
diff --git a/util/tables/sm_pam250.c b/util/tables/sm_pam250.c
new file mode 100644
index 00000000..4044224a
--- /dev/null
+++ b/util/tables/sm_pam250.c
@@ -0,0 +1,98 @@
+/*  $Id: sm_pam250.c,v 1.1 2003/12/29 21:25:51 ucko Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author:  Aaron Ucko (via ./convert_scoremat.pl)
+*
+* File Description:
+*   Protein alignment score matrices; shared between the two toolkits.
+*
+* ===========================================================================
+*/
+
+#include <util/tables/raw_scoremat.h>
+
+/* This matrix was produced by "pam" Version 1.0.7 [01-Feb-98] */
+/* using Dayhoff et al. (1978) mutability data. */
+/* PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049 */
+/* Expected score = -0.844, Entropy = 0.354 bits */
+/* Lowest score = -8, Highest score = 17 */
+
+static const TNCBIScore s_Pam250PSM[24][24] = {
+    /*       A,  R,  N,  D,  C,  Q,  E,  G,  H,  I,  L,  K,
+             M,  F,  P,  S,  T,  W,  Y,  V,  B,  Z,  X,  * */
+    /*A*/ {  2, -2,  0,  0, -2,  0,  0,  1, -1, -1, -2, -1,
+            -1, -3,  1,  1,  1, -6, -3,  0,  0,  0,  0, -8 },
+    /*R*/ { -2,  6,  0, -1, -4,  1, -1, -3,  2, -2, -3,  3,
+             0, -4,  0,  0, -1,  2, -4, -2, -1,  0, -1, -8 },
+    /*N*/ {  0,  0,  2,  2, -4,  1,  1,  0,  2, -2, -3,  1,
+            -2, -3,  0,  1,  0, -4, -2, -2,  2,  1,  0, -8 },
+    /*D*/ {  0, -1,  2,  4, -5,  2,  3,  1,  1, -2, -4,  0,
+            -3, -6, -1,  0,  0, -7, -4, -2,  3,  3, -1, -8 },
+    /*C*/ { -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5,
+            -5, -4, -3,  0, -2, -8,  0, -2, -4, -5, -3, -8 },
+    /*Q*/ {  0,  1,  1,  2, -5,  4,  2, -1,  3, -2, -2,  1,
+            -1, -5,  0, -1, -1, -5, -4, -2,  1,  3, -1, -8 },
+    /*E*/ {  0, -1,  1,  3, -5,  2,  4,  0,  1, -2, -3,  0,
+            -2, -5, -1,  0,  0, -7, -4, -2,  3,  3, -1, -8 },
+    /*G*/ {  1, -3,  0,  1, -3, -1,  0,  5, -2, -3, -4, -2,
+            -3, -5,  0,  1,  0, -7, -5, -1,  0,  0, -1, -8 },
+    /*H*/ { -1,  2,  2,  1, -3,  3,  1, -2,  6, -2, -2,  0,
+            -2, -2,  0, -1, -1, -3,  0, -2,  1,  2, -1, -8 },
+    /*I*/ { -1, -2, -2, -2, -2, -2, -2, -3, -2,  5,  2, -2,
+             2,  1, -2, -1,  0, -5, -1,  4, -2, -2, -1, -8 },
+    /*L*/ { -2, -3, -3, -4, -6, -2, -3, -4, -2,  2,  6, -3,
+             4,  2, -3, -3, -2, -2, -1,  2, -3, -3, -1, -8 },
+    /*K*/ { -1,  3,  1,  0, -5,  1,  0, -2,  0, -2, -3,  5,
+             0, -5, -1,  0,  0, -3, -4, -2,  1,  0, -1, -8 },
+    /*M*/ { -1,  0, -2, -3, -5, -1, -2, -3, -2,  2,  4,  0,
+             6,  0, -2, -2, -1, -4, -2,  2, -2, -2, -1, -8 },
+    /*F*/ { -3, -4, -3, -6, -4, -5, -5, -5, -2,  1,  2, -5,
+             0,  9, -5, -3, -3,  0,  7, -1, -4, -5, -2, -8 },
+    /*P*/ {  1,  0,  0, -1, -3,  0, -1,  0,  0, -2, -3, -1,
+            -2, -5,  6,  1,  0, -6, -5, -1, -1,  0, -1, -8 },
+    /*S*/ {  1,  0,  1,  0,  0, -1,  0,  1, -1, -1, -3,  0,
+            -2, -3,  1,  2,  1, -2, -3, -1,  0,  0,  0, -8 },
+    /*T*/ {  1, -1,  0,  0, -2, -1,  0,  0, -1,  0, -2,  0,
+            -1, -3,  0,  1,  3, -5, -3,  0,  0, -1,  0, -8 },
+    /*W*/ { -6,  2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3,
+            -4,  0, -6, -2, -5, 17,  0, -6, -5, -6, -4, -8 },
+    /*Y*/ { -3, -4, -2, -4,  0, -4, -4, -5,  0, -1, -1, -4,
+            -2,  7, -5, -3, -3,  0, 10, -2, -3, -4, -2, -8 },
+    /*V*/ {  0, -2, -2, -2, -2, -2, -2, -1, -2,  4,  2, -2,
+             2, -1, -1, -1,  0, -6, -2,  4, -2, -2, -1, -8 },
+    /*B*/ {  0, -1,  2,  3, -4,  1,  3,  0,  1, -2, -3,  1,
+            -2, -4, -1,  0,  0, -5, -3, -2,  3,  2, -1, -8 },
+    /*Z*/ {  0,  0,  1,  3, -5,  3,  3,  0,  2, -2, -3,  0,
+            -2, -5,  0,  0, -1, -6, -4, -2,  2,  3, -1, -8 },
+    /*X*/ {  0, -1,  0, -1, -3, -1, -1, -1, -1, -1, -1, -1,
+            -1, -2, -1,  0,  0, -4, -2, -1, -1, -1, -1, -8 },
+    /***/ { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
+            -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,  1 }
+};
+const SNCBIPackedScoreMatrix NCBISM_Pam250 = {
+    "ARNDCQEGHILKMFPSTWYVBZX*",
+    s_Pam250PSM[0],
+    -8
+};
diff --git a/vibrant/image.c b/vibrant/image.c
index 12689d06..45d2537d 100644
--- a/vibrant/image.c
+++ b/vibrant/image.c
@@ -27,7 +27,7 @@
 *
 * Author:  Alex Smirnov,  Denis Vakatov
 *
-* $Revision: 6.6 $
+* $Revision: 6.7 $
 *
 * File Description:
 *       Image(pixmap) processing.
@@ -37,6 +37,9 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: image.c,v $
+* Revision 6.7  2003/11/17 17:03:29  kans
+* changed C++ style comments to C comments
+*
 * Revision 6.6  2002/03/28 13:35:48  kans
 * only include MoreCarbonAccessors.h if not OS_UNIX_DARWIN
 *
@@ -365,8 +368,8 @@ Nlm_Boolean Nlm_AllocateImage ( Nlm_Image image, Nlm_Uint2Ptr width,
   im->pixelMap->bounds.left = 0;
   im->pixelMap->bounds.top = 0;
   im->pixelMap->cmpSize = 8;
-// 2001-03-22:  Joshua Juran
-// Evidently these two members don't exist in Carbon.  So don't set them.
+  /* 2001-03-22:  Joshua Juran */
+  /* Evidently these two members don't exist in Carbon.  So don't set them. */
 #if !TARGET_API_MAC_CARBON
   im->pixelMap->planeBytes = 0;
   im->pixelMap->pmReserved = 0;
diff --git a/vibrant/ncbidraw.c b/vibrant/ncbidraw.c
index 36ef9889..ec3f4209 100644
--- a/vibrant/ncbidraw.c
+++ b/vibrant/ncbidraw.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.35 $
+* $Revision: 6.36 $
 *
 * File Description: 
 *       Vibrant drawing functions.
@@ -37,6 +37,9 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: ncbidraw.c,v $
+* Revision 6.36  2003/11/17 17:03:30  kans
+* changed C++ style comments to C comments
+*
 * Revision 6.35  2003/03/19 21:13:22  kans
 * protect UNIX version of ScrollRect
 *
@@ -6311,8 +6314,8 @@ extern void Nlm_CopyPixmap ( Nlm_RectPtr r, Nlm_Int1Ptr source,
   pixelMap->bounds.left = 0;
   pixelMap->bounds.top = 0;
   pixelMap->cmpSize = 8;
-// 2001-03-22:  Joshua Juran
-// Evidently these two members don't exist in Carbon.  So don't set them.
+  /* 2001-03-22:  Joshua Juran */
+  /* Evidently these two members don't exist in Carbon.  So don't set them. */
 #if !TARGET_API_MAC_CARBON
   pixelMap->planeBytes = 0;
   pixelMap->pmReserved = 0;
@@ -6415,10 +6418,10 @@ extern void Nlm_SetUpDrawingTools (void)
 
   Nlm_updateRgn = (Nlm_RegioN) (NewRgn ());
   SetRectRgn ((Nlm_RgnTool) Nlm_updateRgn, -32768, -32768, 32767, 32767);
-  //HLock ((Handle) Nlm_updateRgn);
+  /* HLock ((Handle) Nlm_updateRgn); */
   GetRegionBounds(Nlm_updateRgn, &bounds);
   Local__RectToolToRecT (&bounds, &Nlm_updateRect);
-  //HUnlock ((Handle) Nlm_updateRgn);
+  /* HUnlock ((Handle) Nlm_updateRgn); */
 
   Nlm_fontList = NULL;
   Nlm_fontInUse = NULL;
diff --git a/vibrant/palette.c b/vibrant/palette.c
index c9638a03..68d4cd25 100644
--- a/vibrant/palette.c
+++ b/vibrant/palette.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.0 $
+* $Revision: 6.1 $
 *
 * File Description:   Active graphics objects
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: palette.c,v $
+* Revision 6.1  2003/11/07 16:02:30  rsmith
+* Renamed static function NewPalette to Nlm_NewPalette to avoid a name conflict on Mac.
+*
 * Revision 6.0  1997/08/25 18:56:11  madden
 * Revision changed to 6.0
 *
@@ -314,7 +317,7 @@ static void PaletteClick (PaneL p, PoinT pt)
   }
 }
 
-static void NewPalette (PalettE p, Int2 minwid, PaletteProc actn)
+static void Nlm_NewPalette (PalettE p, Int2 minwid, PaletteProc actn)
 
 {
   PoinT        npt;
@@ -348,7 +351,7 @@ static void ResetPalette (PaneL p)
   if (pdata.drawHandles != NULL) {
     HandFree (pdata.drawHandles);
   }
-  NewPalette ((PalettE) p, pdata.width, pdata.action);
+  Nlm_NewPalette ((PalettE) p, pdata.width, pdata.action);
 }
 
 extern PalettE PalettePanel (SlatE s, Int2 pixwidth, PaletteProc actn)
@@ -363,7 +366,7 @@ extern PalettE PalettePanel (SlatE s, Int2 pixwidth, PaletteProc actn)
     p = (PalettE) CustomPanel (s,  DrawPalette, sizeof (PaletteData), ResetPalette);
     if (p != NULL) {
       SetPanelClick ((PaneL) p, PaletteClick, NULL, NULL, NULL);
-      NewPalette (p, pixwidth, actn);
+      Nlm_NewPalette (p, pixwidth, actn);
     }
     RestorePort (tempPort);
   }
diff --git a/vibrant/vibbutns.c b/vibrant/vibbutns.c
index 47795182..4dde5b31 100644
--- a/vibrant/vibbutns.c
+++ b/vibrant/vibbutns.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.7 $
+* $Revision: 6.8 $
 *
 * File Description: 
 *       Vibrant button functions
@@ -41,6 +41,9 @@
 *
 *
 * $Log: vibbutns.c,v $
+* Revision 6.8  2004/01/20 23:34:38  sinyakov
+* [WIN_MSWIN]: fixed to display '&' character in button text
+*
 * Revision 6.7  2002/03/07 19:18:21  kans
 * check box wid += 4 for Aqua
 *
@@ -970,6 +973,35 @@ LRESULT CALLBACK EXPORT ButtonProc (HWND hwnd, UINT message,
   Nlm_currentWindowTool = tempHWnd;
   return rsult;
 }
+
+
+static void Nlm_PrepareTitleMsWin(Nlm_CharPtr temp, Nlm_CharPtr title,
+				  size_t siztemp)
+{
+    /* duplicate existing '&' */
+    Nlm_Uint4 src_pos = 0;
+    Nlm_Uint4 dest_pos = 0;
+
+    for(src_pos = 0, dest_pos = 0;
+	title[src_pos] != '\0' && dest_pos+1 < siztemp;
+	++src_pos)
+    {
+	if(title[src_pos] == '&')
+	{
+	    if(dest_pos + 2 < siztemp)
+	    {
+		temp[dest_pos++] = '&';
+		temp[dest_pos++] = title[src_pos];
+	    }
+	    else
+		break;
+	}
+	else
+	    temp[dest_pos++] = title[src_pos];
+    }
+
+    temp[dest_pos] = '\0';
+}
 #endif
 
 #ifdef WIN_MOTIF
@@ -1057,7 +1089,11 @@ static void Nlm_NewButton (Nlm_ButtoN b, Nlm_CharPtr title,
 
   Nlm_GetRect ((Nlm_GraphiC) b, &r);
   wptr = Nlm_ParentWindowPtr ((Nlm_GraphiC) b);
+#ifdef WIN_MSWIN
+  Nlm_PrepareTitleMsWin (temp, title, sizeof (temp));
+#else
   Nlm_StringNCpy_0 (temp, title, sizeof (temp));
+#endif
   c = (Nlm_ControlTool) 0;
   border = 0;
   offset = 0;
diff --git a/vibrant/vibdefns.h b/vibrant/vibdefns.h
index 48d29fd3..3d83a0d5 100644
--- a/vibrant/vibdefns.h
+++ b/vibrant/vibdefns.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.9 $
+* $Revision: 6.12 $
 *
 * File Description: 
 *       Vibrant alias definitions
@@ -37,6 +37,16 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: vibdefns.h,v $
+* Revision 6.12  2004/01/05 17:11:20  kans
+* added defines for functions to control dual monitor usage
+*
+* Revision 6.11  2003/10/30 17:32:16  kans
+* removed define for SetTextColor, which was conflicting with Win32 symbol
+*
+* Revision 6.10  2003/10/29 19:10:00  bazhin
+* Added function Nlm_SetTextColor(Nlm_TexT t, Nlm_Uint4 r, Nlm_Uint4 g,
+*                                 Nlm_Uint4 b).
+*
 * Revision 6.9  2002/01/09 15:23:54  kans
 * added HasAquaMenuLayout
 *
@@ -252,6 +262,11 @@ extern "C" {
 #define SetWindowExtra Nlm_SetWindowExtra
 #define GetWindowExtra Nlm_GetWindowExtra
 
+#define HasDualScreen Nlm_HasDualScreen
+#define UseFullScreen Nlm_UseFullScreen
+#define UseLeftScreen Nlm_UseLeftScreen
+#define UseRightScreen Nlm_UseRightScreen
+
 #define NormalGroup Nlm_NormalGroup
 #define HiddenGroup Nlm_HiddenGroup
 #define SetGroupMargins Nlm_SetGroupMargins
diff --git a/vibrant/vibforms.c b/vibrant/vibforms.c
index ab716df0..fe2afc30 100644
--- a/vibrant/vibforms.c
+++ b/vibrant/vibforms.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.12 $
+* $Revision: 6.13 $
 *
 * File Description: 
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: vibforms.c,v $
+* Revision 6.13  2004/01/16 22:35:37  kans
+* added WidestString and WidestAlist
+*
 * Revision 6.12  2002/01/09 15:11:23  kans
 * SetEnumPopupEx and SetEnumPopupByNameEx to suppress error if 0 or NULL initial value, called by dialog creators
 *
@@ -1218,6 +1221,30 @@ extern Int2 MaxStringWidths (CharPtr PNTR strs)
   return (max + 2);
 }
 
+extern CharPtr WidestString (CharPtr PNTR strs)
+
+{
+  Int2     i;
+  Int2     len;
+  Int2     max;
+  CharPtr  str;
+
+  str = NULL;
+  max = 0;
+  if (strs != NULL) {
+    i = 0;
+    while (strs [i] != NULL) {
+      len = StringWidth (strs [i]);
+      if (len > max) {
+        max = len;
+        str = strs [i];
+      }
+      i++;
+    }
+  }
+  return str;
+}
+
 extern Int2 MaxAlistWidths (EnumFieldAssocPtr al)
 
 {
@@ -1246,6 +1273,28 @@ extern Int2 MaxAlistWidths (EnumFieldAssocPtr al)
   return max;
 }
 
+extern CharPtr WidestAlist (EnumFieldAssocPtr al)
+
+{
+  Int2     i;
+  Int2     len;
+  Int2     max;
+  CharPtr  str;
+
+  str = NULL;
+  max = 0;
+  if (al != NULL) {
+    for (i = 1; al->name != NULL; i++, al++) {
+      len = StringWidth (al->name);
+      if (len > max) {
+        max = len;
+        str = al->name;
+      }
+    }
+  }
+  return str;
+}
+
 extern GrouP MultiLinePromptEx (GrouP prnt, CharPtr text, Int2 maxWidth, FonT font, Boolean stripSpaces)
 
 {
diff --git a/vibrant/vibforms.h b/vibrant/vibforms.h
index cd5451d2..657031bc 100644
--- a/vibrant/vibforms.h
+++ b/vibrant/vibforms.h
@@ -29,13 +29,16 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.8 $
+* $Revision: 6.9 $
 *
 * File Description: 
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: vibforms.h,v $
+* Revision 6.9  2004/01/16 22:35:38  kans
+* added WidestString and WidestAlist
+*
 * Revision 6.8  2002/08/07 18:13:42  kans
 * G/SetPrimitiveIDs, itemID is Uint4
 *
@@ -204,7 +207,9 @@ extern Nlm_CharPtr Nlm_SaveStringFromText (Nlm_TexT t);
 extern ValNodePtr Nlm_SetTextFromVnp (Nlm_TexT t, ValNodePtr vnp);
 extern ValNodePtr Nlm_GetVnpFromText (Nlm_TexT t, ValNodePtr vnp, Nlm_Boolean last);
 extern Nlm_Int2 Nlm_MaxStringWidths (Nlm_CharPtr PNTR strs);
+extern Nlm_CharPtr Nlm_WidestString (Nlm_CharPtr PNTR strs);
 extern Nlm_Int2 Nlm_MaxAlistWidths (Nlm_EnumFieldAssocPtr al);
+extern Nlm_CharPtr Nlm_WidestAlist (Nlm_EnumFieldAssocPtr al);
 extern Nlm_GrouP Nlm_MultiLinePrompt (Nlm_GrouP prnt, Nlm_CharPtr text, Nlm_Int2 maxWidth, Nlm_FonT font);
 extern Nlm_GrouP Nlm_MultiLinePromptEx (Nlm_GrouP prnt, Nlm_CharPtr text, Nlm_Int2 maxWidth, Nlm_FonT font, Nlm_Boolean stripSpaces);
 
@@ -513,7 +518,9 @@ extern Nlm_CharPtr Nlm_ExtractTagListColumn (Nlm_CharPtr source, Nlm_Int2 col);
 #define SetTextFromVnp Nlm_SetTextFromVnp
 #define GetVnpFromText Nlm_GetVnpFromText
 #define MaxStringWidths Nlm_MaxStringWidths
+#define WidestString Nlm_WidestString
 #define MaxAlistWidths Nlm_MaxAlistWidths
+#define WidestAlist Nlm_WidestAlist
 #define MultiLinePrompt Nlm_MultiLinePrompt
 #define MultiLinePromptEx Nlm_MultiLinePromptEx
 #define JustInvalObject Nlm_JustInvalObject
diff --git a/vibrant/vibmenus.c b/vibrant/vibmenus.c
index f0e66410..b83ebb1a 100644
--- a/vibrant/vibmenus.c
+++ b/vibrant/vibmenus.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.16 $
+* $Revision: 6.18 $
 *
 * File Description: 
 *       Vibrant menu functions
@@ -37,6 +37,12 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: vibmenus.c,v $
+* Revision 6.18  2004/01/20 23:35:38  sinyakov
+* [WIN_MSWIN] implemented menu accelerators
+*
+* Revision 6.17  2003/11/17 17:03:30  kans
+* changed C++ style comments to C comments
+*
 * Revision 6.16  2003/03/27 19:35:43  kans
 * Nlm_PrepareTitle removes non-Mac accelerator from Mac menu item
 *
@@ -822,7 +828,7 @@ static void Nlm_DeskAccProc (Nlm_ChoicE c)
 
 {
 #if TARGET_API_MAC_CARBON >= 1
-    // Carbon will create, fill, and handle everything in the Apple menu
+    /* Carbon will create, fill, and handle everything in the Apple menu */
     return;
 #else
   Nlm_MenuTool  h;
@@ -3920,6 +3926,172 @@ static void Nlm_AddTitleAccel(Widget w, Nlm_CharPtr title, Nlm_Int4 flags)
 }
 #endif /* WIN_MOTIF */
 
+#ifdef WIN_MSWIN
+
+extern Nlm_Handle Nlm_GetWindowHAccel (Nlm_WindoW w);
+extern void Nlm_SetWindowHAccel (Nlm_WindoW w, Nlm_Handle h);
+
+static void Nlm_AddAccel(Nlm_MenU m, Nlm_Int2 id, Nlm_Char key)
+{
+    HACCEL haccel = NULL;   /* handle to accelerator table */
+
+    int i;                  /* loop counter */
+    LPACCEL lpaccelNew;     /* pointer to new accelerator table */
+    HACCEL haccelOld;       /* handle to old accelerator table  */
+    int nAccelerators;      /* number of accelerators in table  */
+
+    BYTE fAccelFlags;       /* accelerator flags */
+
+    Nlm_WindoW w;	    /* top-level window that contains the menu */
+
+    if(key == 0)
+	/* no accelerator key specified */
+	return;
+
+    if(IS_ALPHA(key))
+    {
+        fAccelFlags = FCONTROL;
+	key = TO_UPPER(key) - 'A' + 1;
+    }
+    else
+    if(IS_DIGIT(key))
+    {
+        fAccelFlags = FCONTROL | FVIRTKEY;
+    }
+    else
+	/* key is not supported */
+	return;
+
+    /* Get top-level window */
+    w = Nlm_GetParentWindow((Nlm_GraphiC)m);
+    if(w == NULL)
+	/* failure */
+	return;
+
+    haccel = Nlm_GetWindowHAccel(w);
+
+    /* Save the current accelerator table. */
+
+    haccelOld = haccel; 
+ 
+    /* Count the number of entries in the current 
+       table, allocate a buffer for the table, and 
+       then copy the table into the buffer,
+       reserving space for a new accelerator */
+ 
+    if(haccelOld)
+	nAccelerators = CopyAcceleratorTable(haccelOld, NULL, 0); 
+    else
+	nAccelerators = 0;
+
+    lpaccelNew = (LPACCEL) Nlm_MemNew((nAccelerators + 1) * sizeof(ACCEL));
+    if(lpaccelNew == NULL)
+	/* failure */
+	return;
+ 
+    if(lpaccelNew != NULL && nAccelerators) 
+        CopyAcceleratorTable(haccel, lpaccelNew, nAccelerators); 
+ 
+    /* Find the accelerator that the user modified 
+       and change its flags and virtual-key code 
+       as appropriate. */
+ 
+    for(i = 0; i < nAccelerators; ++i) 
+    {
+	if(lpaccelNew[i].cmd == (WORD) id ||
+	   (lpaccelNew[i].fVirt == fAccelFlags &&
+            lpaccelNew[i].key == key))
+	    break;
+    } 
+ 
+    lpaccelNew[i].cmd = id; 
+    lpaccelNew[i].fVirt = fAccelFlags; 
+    lpaccelNew[i].key = key;
+
+    if(i == nAccelerators)
+	/* new accelerator added */
+	++nAccelerators;
+
+    /* Create the new accelerator table, and 
+       destroy the old one. */
+ 
+    if(haccelOld)
+        DestroyAcceleratorTable(haccelOld); 
+    haccel = CreateAcceleratorTable(lpaccelNew, nAccelerators);
+
+    Nlm_SetWindowHAccel(w, haccel);
+
+    Nlm_MemFree(lpaccelNew);
+}
+
+
+static void Nlm_PrepareTitleMsWin(Nlm_CharPtr temp, Nlm_CharPtr title,
+				  size_t siztemp, Nlm_CharPtr paccel,
+				  Nlm_Boolean isMenu)
+{
+    /* duplicate existing '&',
+       mark mnemo char with single '&',
+       add accelerator description */
+
+    Nlm_Char  accel = '\0';
+    Nlm_Char  mnemo = '\0';
+    Nlm_Uint4 mnemo_pos = 0;
+    Nlm_Uint4 src_pos = 0;
+    Nlm_Uint4 dest_pos = 0;
+
+    Nlm_TitleGetAccel(temp, &accel, &mnemo, &mnemo_pos);
+
+    if(isMenu)
+        accel = '\0';
+
+    if(paccel != NULL)
+	*paccel = accel;
+
+    for(src_pos = 0, dest_pos = 0;
+	title[src_pos] != '\0' && dest_pos+1 < siztemp;
+	++src_pos)
+    {
+	if(mnemo && src_pos == mnemo_pos)
+	{
+	    if(dest_pos + 2 < siztemp)
+	    {
+		temp[dest_pos++] = '&';
+		temp[dest_pos++] = title[src_pos];
+	    }
+	    else
+		break;
+	}
+	else
+	if(title[src_pos] == '&')
+	{
+	    if(dest_pos + 2 < siztemp)
+	    {
+		temp[dest_pos++] = '&';
+		temp[dest_pos++] = title[src_pos];
+	    }
+	    else
+		break;
+	}
+	else
+	if(title[src_pos] == '/')
+	    break;
+	else
+	    temp[dest_pos++] = title[src_pos];
+    }
+
+    temp[dest_pos] = '\0';
+
+    if(accel != '\0' && dest_pos + 7 < siztemp)
+    {
+	Nlm_StrCpy(temp+dest_pos, "\tCtrl- ");
+	if(IS_ALPHA(accel))
+	    temp[dest_pos+6] = TO_UPPER(accel);
+        else
+	    temp[dest_pos+6] = accel;
+    }
+}
+#endif /* WIN_MSWIN */
+
 
 static void Nlm_PrepareTitle(Nlm_CharPtr temp, Nlm_CharPtr title,
                              size_t siztemp, Nlm_Boolean isMenu)
@@ -3937,21 +4109,6 @@ static void Nlm_PrepareTitle(Nlm_CharPtr temp, Nlm_CharPtr title,
     }
   }}
 #endif
-
-#ifdef WIN_MSWIN
-  {{
-    Nlm_Char  mnemo;
-    Nlm_Uint4 pos;
-
-    if (Nlm_TitleGetAccel(temp, NULL, &mnemo, &pos)  &&  mnemo)
-      { /* temp := title[ 0..poslet-1 ] + '&' + title[ poslet..END ] */
-        Nlm_StringNCpy_0(temp+pos+1, title+pos, siztemp-pos-1);
-        temp[pos] = '&';
-      }
-
-    Nlm_StripTitleAccel( temp );
-  }}
-#endif
 }
 
 
@@ -3988,9 +4145,14 @@ static Nlm_ItemTool Nlm_AppendItems(Nlm_MenU m, Nlm_IteM i,
 #endif
 
 #ifdef WIN_MSWIN
+  {{
+  Nlm_Char accel;
+  Nlm_PrepareTitleMsWin(temp, itemNames, sizeof(temp), &accel, FALSE);
   AppendMenu(h, MF_ENABLED, nextMenuNum, temp);
+  Nlm_AddAccel(m, nextMenuNum, accel);
   if (nextMenuNum < 32767)
     nextMenuNum++;
+  }}
 #endif
 
 #ifdef WIN_MOTIF
@@ -4820,6 +4982,7 @@ static void Nlm_NewPopup (Nlm_MenU m, Nlm_CharPtr title, Nlm_RectPtr r)
   mb  = (Nlm_MenuBaR) Nlm_GetParent ((Nlm_GraphiC) m);
   mbh = Nlm_GetMenuBarHandle( mb );
   h = CreateMenu();
+  Nlm_PrepareTitleMsWin(temp, title, sizeof (temp), NULL, TRUE);
   AppendMenu(mbh, MF_POPUP | MF_ENABLED, (UINT)h, temp);
 #endif
 
@@ -5525,6 +5688,7 @@ extern Nlm_MenU Nlm_SubMenu (Nlm_MenU m, Nlm_CharPtr title)
                                &r, sizeof(Nlm_ItemRec), subItemProcs);
   if (i != NULL) {
 #ifdef WIN_MSWIN
+    Nlm_PrepareTitleMsWin(temp, title, sizeof(temp), NULL, TRUE);
     Nlm_NewSubMenuAndItem(i, sub, temp);
 #else /* WIN_MOTIF */
     Nlm_NewCascadingMenu(m, i, sub, temp);
diff --git a/vibrant/vibprocs.h b/vibrant/vibprocs.h
index c77bc799..8287c03e 100644
--- a/vibrant/vibprocs.h
+++ b/vibrant/vibprocs.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.21 $
+* $Revision: 6.23 $
 *
 * File Description: 
 *       Vibrant procedure definitions
@@ -37,6 +37,12 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: vibprocs.h,v $
+* Revision 6.23  2004/01/05 17:08:09  kans
+* added functions to control use of dual screens
+*
+* Revision 6.22  2003/10/29 19:19:34  kans
+* added prototype for Nlm_SetTextColor
+*
 * Revision 6.21  2002/04/30 18:25:12  bazhin
 * Added function "Nlm_SetWindowConfigureCallback(WindoW w)", which
 * allows to catch events, when window just moved without resizing.
@@ -335,6 +341,14 @@ Nlm_VoidPtr Nlm_GetWindowExtra PROTO((Nlm_WindoW w));
 
 void        Nlm_SetWindowConfigureCallback PROTO((Nlm_WindoW w));
 
+/* Dual screen functions control centering where the window left parameter is negative */
+
+Nlm_Boolean Nlm_HasDualScreen (void);
+void Nlm_UseFullScreen (void);
+void Nlm_UseLeftScreen (void);
+void Nlm_UseRightScreen (void);
+
+
 /***  GROUPING OBJECT  ***/
 
 /*
@@ -537,6 +551,7 @@ size_t    Nlm_TextLength PROTO((Nlm_TexT t));
 void      Nlm_SelectText PROTO((Nlm_TexT t, Nlm_Int2 begin, Nlm_Int2 end));
 void      Nlm_SetTextEditable PROTO((Nlm_TexT t, Nlm_Boolean editable));
 void      Nlm_SetTextCursorBlinkRate PROTO((Nlm_TexT t, Nlm_Int2 msec));
+void      Nlm_SetTextColor PROTO((Nlm_TexT t, Nlm_Uint4 r, Nlm_Uint4 g, Nlm_Uint4 b));
 
 /* return the new insertion position in the text(it may differ from "pos"
  * if an error occured or "pos" is out of limits)
diff --git a/vibrant/vibtexts.c b/vibrant/vibtexts.c
index 79db447b..8d142f4d 100644
--- a/vibrant/vibtexts.c
+++ b/vibrant/vibtexts.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.14 $
+* $Revision: 6.17 $
 *
 * File Description: 
 *       Vibrant edit text functions
@@ -37,6 +37,16 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: vibtexts.c,v $
+* Revision 6.17  2003/11/17 17:03:30  kans
+* changed C++ style comments to C comments
+*
+* Revision 6.16  2003/11/03 21:51:34  sinyakov
+* WIN_MSWIN: bugfix: strlen(title) moved out of loop condition
+*
+* Revision 6.15  2003/10/29 19:10:08  bazhin
+* Added function Nlm_SetTextColor(Nlm_TexT t, Nlm_Uint4 r, Nlm_Uint4 g,
+*                                 Nlm_Uint4 b).
+*
 * Revision 6.14  2003/07/30 13:51:42  johnson
 * MSWIN: multi-line text boxes now respond to 'enter' key
 *
@@ -1790,6 +1800,7 @@ static void Nlm_SetScrollText (Nlm_GraphiC t, Nlm_Int2 item,
 #endif
 #ifdef WIN_MSWIN
   Nlm_Uint4	count;
+  Nlm_Uint4     len;
   Nlm_CharPtr	tmp, newTitle;
 #endif
 
@@ -1822,9 +1833,10 @@ static void Nlm_SetScrollText (Nlm_GraphiC t, Nlm_Int2 item,
   if (count == 0)
     SetWindowText (h, title);
   else { /* replace UNIX <lf> with DOS <cr><lf> */
-    newTitle = (Nlm_CharPtr) MemNew(strlen(title)+count+1);
+    len = Nlm_StringLen (title);
+    newTitle = (Nlm_CharPtr) MemNew(len+count+1);
     tmp = newTitle;
-    for (count=0; count < strlen(title); ++count) {
+    for (count=0; count < len; ++count) {
 	if (title[count] == '\n' && (count == 0 || title[count-1] != '\r'))
 	    *tmp++ = '\r';
 	*tmp++ = title[count];
@@ -1963,31 +1975,31 @@ extern Nlm_TexT Nlm_CurrentText (void)
 static void Clipboard_TEToDeskScrap()
 {
 	OSErr err;
-	// Copy the TE scrap to the desk scrap.
+	/* Copy the TE scrap to the desk scrap. */
 	err = TEToScrap();
 }
 
 static void Clipboard_TECut(TEHandle inTE)
 {
-	// Cut the text into the TE scrap.
+	/* Cut the text into the TE scrap. */
 	TECut(inTE);
-	// Update the desk scrap.
+	/* Update the desk scrap. */
 	Clipboard_TEToDeskScrap();
 }
 
 static void Clipboard_TECopy(TEHandle inTE)
 {
-	// Copy the text into the TE scrap.
+	/* Copy the text into the TE scrap. */
 	TECopy(inTE);
-	// Update the desk scrap.
+	/* Update the desk scrap. */
 	Clipboard_TEToDeskScrap();
 }
 
 static void Clipboard_TEPaste(TEHandle inTE)
 {
-//#if TARGET_API_MAC_CARBON
-	//ScrapRef scrap;
-	//OSStatus status = GetCurrentScrap(&scrap);
+    /* #if TARGET_API_MAC_CARBON */
+	/* ScrapRef scrap; */
+	/* OSStatus status = GetCurrentScrap(&scrap); */
 	OSErr err = TEFromScrap();
 	TEPaste(inTE);
 }
@@ -3977,3 +3989,20 @@ extern void Nlm_SetTextCursorBlinkRate(Nlm_TexT t, Nlm_Int2 msec)
 #endif
     return;
 }
+
+extern void Nlm_SetTextColor(Nlm_TexT t, Nlm_Uint4 r, Nlm_Uint4 g, Nlm_Uint4 b)
+{
+#ifdef WIN_MOTIF
+    Nlm_TextTool h;
+    Arg          args[2];
+
+    if(t == NULL)
+        return;
+    h = Nlm_GetTextHandle(t);
+    if(h == NULL)
+        return;
+    XtSetArg(args[0], XmNforeground, Nlm_GetColorRGB(r, g, b));
+    XtSetValues(h, args, 1);
+#endif
+    return;
+}
diff --git a/vibrant/vibutils.c b/vibrant/vibutils.c
index e414f523..f0992619 100644
--- a/vibrant/vibutils.c
+++ b/vibrant/vibutils.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.55 $
+* $Revision: 6.57 $
 *
 * File Description:
 *       Vibrant miscellaneous functions
@@ -37,6 +37,12 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: vibutils.c,v $
+* Revision 6.57  2003/11/17 17:03:30  kans
+* changed C++ style comments to C comments
+*
+* Revision 6.56  2003/11/07 16:06:58  rsmith
+* Changed Mac printing system calls from deprecated ones to modern ones primarily to ease building with precompiled headers.
+*
 * Revision 6.55  2003/05/05 12:38:07  rsmith
 * casts to make call to RegQueryValueEx safer in Nlm_GetExecPath. Needed by Codewarrior when compiling to Win32.
 *
@@ -391,27 +397,25 @@ either.
 */
 
 #include <ncbilcl.h>
-#include <vibtypes.h>
-#include <vibprocs.h>
-#include <vibincld.h>
-#include <ncbiport.h>
 
 #ifdef WIN_MAC
-# include <Navigation.h>
 # if TARGET_API_MAC_CARBON
-// Use non-session APIs of the Carbon Printing Manager, for easy porting
-#ifdef PM_USE_SESSION_APIS
-#undef PM_USE_SESSION_APIS
-#endif
-#  define PM_USE_SESSION_APIS 0
+/* Use non-session APIs of the Carbon Printing Manager, for easy porting */
 #  include <PMApplication.h>
 #  include <FullPath.h>
 # endif
 # ifdef OS_UNIX_DARWIN
 #  include <LaunchServices.h>
 # endif
+# include <Navigation.h>
 #endif
 
+#include <vibtypes.h>
+#include <vibprocs.h>
+#include <vibincld.h>
+#include <ncbiport.h>
+
+
 #ifdef WIN_MOTIF
 #include <sys/times.h>
 #include <limits.h>
@@ -455,6 +459,8 @@ static Nlm_BoxData      recentBoxData;
 
 #ifdef WIN_MAC
 # if TARGET_API_MAC_CARBON
+static PMPrintSession  printSession;
+
 static PMPageFormat    pageFormat = kPMNoPageFormat;
 static PMPrintSettings printSettings = kPMNoPrintSettings;
 static PMPrintContext  thePrintingPort = kPMNoReference;
@@ -3961,29 +3967,38 @@ static void Nlm_SetupPrinterDeviceContext(HDC prHDC)
 
 #ifdef WIN_MAC
 # if TARGET_API_MAC_CARBON
+
 extern Nlm_WindoW Nlm_StartPrinting (void)
 {
   OSStatus status;
   Boolean accepted;
   
-  status = PMBegin();
+/*  status = PMBegin(); */
+  status = PMCreateSession(&printSession);
   if (status != noErr) return NULL;
-  status = PMNewPageFormat(&pageFormat);
+/*  status = PMNewPageFormat(&pageFormat); */
+  status = PMCreatePageFormat(&pageFormat);
   if (status != noErr || pageFormat == kPMNoPageFormat) return NULL;
-  status = PMDefaultPageFormat(pageFormat);
+/*  status = PMDefaultPageFormat(pageFormat); */
+  status = PMSessionDefaultPageFormat(printSession, pageFormat);
   if (status != noErr) return NULL;
-  status = PMPageSetupDialog(pageFormat, &accepted);
+/*  status = PMPageSetupDialog(pageFormat, &accepted); */
+  status = PMSessionPageSetupDialog(printSession, pageFormat, &accepted);
   if (status != noErr) return NULL;
-  status = PMNewPrintSettings(&printSettings);
+/*  status = PMNewPrintSettings(&printSettings); */
+  status = PMCreatePrintSettings(&printSettings);
   if (status != noErr || printSettings == kPMNoPrintSettings) return NULL;
-  status = PMDefaultPrintSettings(printSettings);
+/*  status = PMDefaultPrintSettings(printSettings); */
+  status = PMSessionDefaultPrintSettings (printSession, printSettings);
   if (status != noErr) return NULL;
-  status = PMPrintDialog(printSettings, pageFormat, &accepted);
+/*  status = PMPrintDialog(printSettings, pageFormat, &accepted); */
+  status = PMSessionPrintDialog(printSession, printSettings, pageFormat, &accepted);
   if (!accepted) status = kPMCancel;
   if (status != noErr) return NULL;
   
-  status = PMBeginDocument(printSettings, pageFormat, &thePrintingPort);
-  if ((status != noErr) || (thePrintingPort == kPMNoReference)) return NULL;
+/*  status = PMBeginDocument(printSettings, pageFormat, &thePrintingPort); */
+  status = PMSessionBeginDocument(printSession, printSettings, pageFormat);
+  if (status != noErr) return NULL;
   
   return Nlm_CurrentWindow();
 }
@@ -4091,35 +4106,28 @@ extern void Nlm_EndPrinting (Nlm_WindoW w)
 
   Nlm_nowPrinting = FALSE;
   if (w != NULL) {
-    (void)PMEndDocument(thePrintingPort);
-    status = PMError();
+    status = PMSessionError(printSession);
     if (status != noErr) {
-      Nlm_Message (MSG_ERROR, "PMEndDocument error %d", status);
-    }
-// This call is not supported under Carbon, need to figure out
-// how Apple wants us to deal with this ...  churchill 12/28/99
-#if 0
-    PrPicFile (prHdl, 0L, 0L, 0L, &prStat);
-    prerr = PrError ();
-    if (prerr != noErr) {
-      Nlm_Message (MSG_ERROR, "PrPicFile error %d", prerr);
+      Nlm_Message (MSG_ERROR, "PM Session error %d", status);
     }
-    prPort = NULL;
-    Nlm_UseWindow (w);
-#endif
+    /* (void)PMEndDocument(thePrintingPort); */
+    PMSessionEndDocument (printSession);
   }
   if (pageFormat != kPMNoPageFormat) {
-    (void)PMDisposePageFormat(pageFormat);
+   /* (void)PMDisposePageFormat(pageFormat); */
+    PMRelease(pageFormat);
     pageFormat = kPMNoPageFormat;
   }
   if (printSettings != kPMNoPrintSettings) {
-    (void)PMDisposePrintSettings(printSettings);
+  /*  (void)PMDisposePrintSettings(printSettings); */
+    PMRelease(printSettings);
     printSettings = kPMNoPrintSettings;
   }
-  (void)PMEnd();
+  /* (void)PMEnd(); */
+  PMRelease(printSession);
 }
 
-# else  // not TARGET_API_MAC_CARBON
+# else  /* not TARGET_API_MAC_CARBON */
 
 extern void Nlm_EndPrinting (Nlm_WindoW w)
 {
@@ -4132,8 +4140,8 @@ extern void Nlm_EndPrinting (Nlm_WindoW w)
     if (prerr != noErr) {
       Nlm_Message (MSG_ERROR, "PrCloseDoc error %d", prerr);
     }
-// This call is not supported under Carbon, need to figure out
-// how Apple wants us to deal with this ...  churchill 12/28/99
+    /* This call is not supported under Carbon, need to figure out
+    how Apple wants us to deal with this ...  churchill 12/28/99 */
     PrPicFile (prHdl, 0L, 0L, 0L, &prStat);
     prerr = PrError ();
     if (prerr != noErr) {
@@ -4363,8 +4371,9 @@ extern Nlm_Boolean Nlm_StartPage (void)
 {
   OSStatus status;
   
-  status = PMBeginPage(thePrintingPort, NULL);
-  if (status != noErr) return false;  // ??
+/*  status = PMBeginPage(thePrintingPort, NULL); */
+  status = PMSessionBeginPage(printSession, pageFormat, NULL);
+  if (status != noErr) return false;  /* ?? */
   
   return true;
 }
@@ -4432,8 +4441,9 @@ extern Nlm_Boolean Nlm_EndPage (void)
 {
   OSStatus status;
   
-  status = PMEndPage(thePrintingPort);
-  if (status != noErr) return false;  // ??
+/*  status = PMEndPage(thePrintingPort); */
+  status = PMSessionEndPage(printSession);
+  if (status != noErr) return false;  /* ?? */
   
   return true;
 }
@@ -4502,10 +4512,12 @@ static OSType Nlm_GetOSType (Nlm_CharPtr str, OSType dfault)
   return rsult;
 }
 
-// 2001-03-22:  Joshua Juran
-// Working directory records are gone in Carbon.
-// However, so is Standard File.  The code which calls Nav Services instead of SF
-// doesn't need this function, so we don't define it.
+/*
+ 2001-03-22:  Joshua Juran
+ Working directory records are gone in Carbon.
+ However, so is Standard File.  The code which calls Nav Services instead of SF
+ doesn't need this function, so we don't define it.
+*/
 # if !TARGET_API_MAC_CARBON
 static void Nlm_GetFilePath (Nlm_Int2 currentVol, Nlm_CharPtr path, size_t maxsize)
 
@@ -4773,14 +4785,14 @@ static Nlm_Boolean Nlm_NavServGetInputFileName (Nlm_CharPtr fileName, size_t max
         filterProc = NewNavObjectFilterUPP(MyNavFilterProc);
     }
 
-    //  Specify default options for dialog box
+    /*  Specify default options for dialog box */
     anErr = NavGetDefaultDialogOptions(&dialogOptions);
     if (anErr == noErr)
     {
-        //  Adjust the options to fit our needs
-        //  Set this option
+        /*  Adjust the options to fit our needs */
+        /*  Set this option */
         dialogOptions.dialogOptionFlags |= kNavSelectDefaultLocation;
-        //  Clear this one
+        /*  Clear this one */
         dialogOptions.dialogOptionFlags ^= kNavAllowPreviews;
 
         anErr = AECreateDesc(typeFSS, &fss,
@@ -4788,8 +4800,8 @@ static Nlm_Boolean Nlm_NavServGetInputFileName (Nlm_CharPtr fileName, size_t max
                              &defaultLocation );
         if (anErr == noErr)
         {
-            // Get 'open' resource. A nil handle being returned is OK,
-            // this simply means no automatic file filtering.
+            /* Get 'open' resource. A nil handle being returned is OK,
+               this simply means no automatic file filtering. */
             NavTypeListHandle typeList = (NavTypeListHandle)GetResource(
                                         'open', 128);
             NavReplyRecord reply;
@@ -4799,7 +4811,7 @@ static Nlm_Boolean Nlm_NavServGetInputFileName (Nlm_CharPtr fileName, size_t max
                                    typeList, 0);
             if (anErr == noErr && reply.validRecord)
             {
-                //  Deal with multiple file selection
+                /*  Deal with multiple file selection */
                 long    count;
 
                 anErr = AECountItems(&(reply.selection), &count);
@@ -4830,7 +4842,7 @@ static Nlm_Boolean Nlm_NavServGetInputFileName (Nlm_CharPtr fileName, size_t max
                         }
                     }
                 }
-                //  Dispose of NavReplyRecord, resources, descriptors
+                /*  Dispose of NavReplyRecord, resources, descriptors */
                 anErr = NavDisposeReply(&reply);
             }
             if (typeList != NULL)
@@ -5120,10 +5132,10 @@ static Nlm_Boolean Nlm_NavServGetOutputFileName (Nlm_CharPtr fileName, size_t ma
     anErr = NavGetDefaultDialogOptions (&dialogOptions);
     if (anErr == noErr)
     {
-        //  Adjust the options to fit our needs
-        //  Set this option
+        /*  Adjust the options to fit our needs */
+        /*  Set this option */
         dialogOptions.dialogOptionFlags |= kNavNoTypePopup;
-        //  Clear this one
+        /*  Clear this one */
         dialogOptions.dialogOptionFlags ^= kNavAllowStationery;
 
         anErr = AECreateDesc(typeFSS, &fss,
@@ -5131,7 +5143,7 @@ static Nlm_Boolean Nlm_NavServGetOutputFileName (Nlm_CharPtr fileName, size_t ma
                              &defaultLocation );
         if (anErr == noErr) {
 
-            //  One way to get the name for the file to be saved.
+            /*  One way to get the name for the file to be saved. */
             Nlm_StringNCpy_0 ((Nlm_CharPtr) dialogOptions.savedFileName, dfault, 255);
             Nlm_CtoPstr ((Nlm_CharPtr) dialogOptions.savedFileName);
 
@@ -5153,10 +5165,12 @@ static Nlm_Boolean Nlm_NavServGetOutputFileName (Nlm_CharPtr fileName, size_t ma
                 {
                     if (reply.replacing)
                     {
-                        // Make sure you save a temporary file
-                        // so you can check for problems before replacing
-                        // an existing file. Once the save is confirmed,
-                        // swap the files and delete the original.
+                        /*
+                         Make sure you save a temporary file
+                         so you can check for problems before replacing
+                         an existing file. Once the save is confirmed,
+                         swap the files and delete the original.
+                        */
                         Nlm_ConvertFilename (&documentFSSpec, filename);
                         Nlm_StringNCpy_0 (fileName, filename, maxsize);
                         rsult = TRUE;
@@ -5170,7 +5184,7 @@ static Nlm_Boolean Nlm_NavServGetOutputFileName (Nlm_CharPtr fileName, size_t ma
 
                     if ( anErr == noErr)
                     {
-                        // DO NOT call NavCompleteSave() to complete
+                        /* DO NOT call NavCompleteSave() to complete */
                         /* anErr = NavCompleteSave(&reply,
                                                 kNavTranslateInPlace); */
                     }
diff --git a/vibrant/vibwndws.c b/vibrant/vibwndws.c
index 125fc302..3e78ad9a 100644
--- a/vibrant/vibwndws.c
+++ b/vibrant/vibwndws.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.54 $
+* $Revision: 6.60 $
 *
 * File Description:
 *       Vibrant main, event loop, and window functions
@@ -37,6 +37,28 @@
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: vibwndws.c,v $
+* Revision 6.60  2004/01/20 23:35:38  sinyakov
+* [WIN_MSWIN] implemented menu accelerators
+*
+* Revision 6.59  2004/01/05 18:42:40  kans
+* record screen mode at time of window creation
+*
+* Revision 6.58  2004/01/05 17:08:09  kans
+* added functions to control use of dual screens
+*
+* Revision 6.57  2003/12/03 17:45:21  kans
+* For OS_MAC, always include Profiler.h
+*
+* Revision 6.56  2003/11/17 17:03:30  kans
+* changed C++ style comments to C comments
+*
+* Revision 6.55  2003/11/03 21:57:48  sinyakov
+* WIN_MSWIN: added ability to put a message into message processing loop
+* to call a callback function within the main GUI thread
+* callback function address is passed in WPARAM,
+* callback function parameter is passed in LPARAM
+* this functionality is used by Win32 implementation of smartnet.c module
+*
 * Revision 6.54  2003/04/09 18:16:53  kans
 * motif version of Nlm_ProcessKeyPress sets ctrlKey and shftKey, clears cmmdKey and optKey, leaves dblClick alone
 *
@@ -619,10 +641,10 @@
 #ifdef WIN_MAC
 #include <Appearance.h>
 #include <Navigation.h>
-# if !defined(OS_UNIX_DARWIN)
-#  include <Profiler.h>
-# endif
-# include "MoreCarbonAccessors.h"
+#if __profile__
+#include <Profiler.h>
+#endif
+#include "MoreCarbonAccessors.h"
 #endif
 
 #if defined(WIN_MOTIF) && defined(_DEBUG) && !defined(__hpux)
@@ -690,6 +712,14 @@ extern void Nlm_ConvertFilename ( FSSpec *fss, Nlm_CharPtr filename );
 #endif
 #endif
 
+typedef enum {
+  USE_FULL_SCREEN = 1,
+  USE_LEFT_SCREEN,
+  USE_RIGHT_SCREEN
+} Nlm_ScreenMode;
+
+static Nlm_ScreenMode Nlm_screenMode = USE_FULL_SCREEN;
+
 typedef  struct  Nlm_shelldata {
   struct Nlm_shelldata PNTR next;
   Nlm_ShellTool             shell;
@@ -720,6 +750,7 @@ typedef  struct  Nlm_windowdata {
   Nlm_WndFreeProc  cleanup;
   Nlm_WndActnProc  timer;
   Nlm_WindoW       modalOwner; /* esl++ to support nested modal dialogs */
+  Nlm_ScreenMode   screenMode;
 #ifdef WIN_MOTIF
   Visual      *visual;
   Nlm_Boolean cMap_fixed;
@@ -727,6 +758,7 @@ typedef  struct  Nlm_windowdata {
 #ifdef WIN_MSWIN
   Nlm_Uint4        style;
   Nlm_Uint4        ex_style;
+  Nlm_Handle	   haccel;
 #endif
 } Nlm_WindowData;
 
@@ -758,7 +790,7 @@ AEEventHandlerUPP HandleAEQuitAppPtr;
 AEEventHandlerUPP HandleAEAnswerPtr;
 #endif
 typedef SInt32 AERefCon;
-//typedef UInt32 AERefCon;
+/* typedef UInt32 AERefCon; */
 #endif
 
 #ifdef WIN_MSWIN
@@ -932,6 +964,7 @@ static void Nlm_LoadWindowData (Nlm_WindoW w, Nlm_WindowTool hdl,
     wdptr->cleanup = cln;
     wdptr->timer = tmr;
     wdptr->modalOwner = NULL; /* esl++ */
+    wdptr->screenMode = Nlm_screenMode; /* jk */
 #ifdef WIN_MOTIF
     wdptr->visual = NULL;
     wdptr->cMap_fixed = FALSE;
@@ -1204,6 +1237,32 @@ extern Nlm_Boolean Nlm_IsWindowDying (Nlm_WindoW w)
   return rsult;
 }
 
+static void Nlm_SetScreenMode (Nlm_WindoW w, Nlm_ScreenMode screenMode)
+
+{
+  Nlm_WindowData  wdata;
+
+  if (w != NULL) {
+    Nlm_GetWindowData (w, &wdata);
+    wdata.screenMode = screenMode;
+    Nlm_SetWindowData (w, &wdata);
+  }
+}
+
+static Nlm_ScreenMode Nlm_GetScreenMode (Nlm_WindoW w)
+
+{
+  Nlm_ScreenMode  rsult;
+  Nlm_WindowData  wdata;
+
+  rsult = USE_FULL_SCREEN;
+  if (w != NULL) {
+    Nlm_GetWindowData (w, &wdata);
+    rsult = wdata.screenMode;
+  }
+  return rsult;
+}
+
 extern Nlm_WindoW Nlm_GetParentWindow (Nlm_GraphiC a)
 
 {
@@ -2152,10 +2211,10 @@ extern void Nlm_SetUpdateRegion (WindowPtr wptr)
 
   if (wptr != NULL) {
     GetPortVisibleRegion(GetWindowPort(wptr), Nlm_updateRgn);
-    //HLock ((Handle) Nlm_updateRgn);
+    /* HLock ((Handle) Nlm_updateRgn); */
     GetRegionBounds(Nlm_updateRgn, &bounds);
     Nlm_RectToolToRecT (&bounds, &Nlm_updateRect);
-    //HUnlock ((Handle) Nlm_updateRgn);
+    /* HUnlock ((Handle) Nlm_updateRgn); */
   }
 }
 #endif
@@ -2797,6 +2856,7 @@ static void Nlm_NewWindow (Nlm_WindoW w, Nlm_Int2 type, Nlm_Int2 procID,
   Nlm_GetWindowData(w, &wdata);
   wdata.style    = style;
   wdata.ex_style = ex_style;
+  wdata.haccel   = 0;
   Nlm_SetWindowData(w, &wdata);
   }}
 #endif
@@ -3047,6 +3107,35 @@ static void Nlm_RemoveWindow (Nlm_GraphiC w, Nlm_Boolean savePort)
   Nlm_Update ();
 }
 
+NLM_EXTERN void Nlm_UseFullScreen (void)
+
+{
+  Nlm_screenMode = USE_FULL_SCREEN;
+}
+
+NLM_EXTERN void Nlm_UseLeftScreen (void)
+
+{
+  Nlm_screenMode = USE_LEFT_SCREEN;
+}
+
+NLM_EXTERN void Nlm_UseRightScreen (void)
+
+{
+  Nlm_screenMode = USE_RIGHT_SCREEN;
+}
+
+NLM_EXTERN Nlm_Boolean Nlm_HasDualScreen (void)
+
+{
+  if (screenBitBounds.right > 2000 && screenBitBounds.bottom < 800) {
+    return TRUE;
+  } else if (screenBitBounds.right > 2500 && screenBitBounds.bottom < 1100) {
+    return TRUE;
+  }
+  return FALSE;
+}
+
 /* esl: extraWidth parameter added */
 static void Nlm_ResizeWindow (Nlm_GraphiC w, Nlm_Int2 dragHeight,
                               Nlm_Int2 scrollWidth, Nlm_Int2 minWidth,
@@ -3062,6 +3151,7 @@ static void Nlm_ResizeWindow (Nlm_GraphiC w, Nlm_Int2 dragHeight,
   Nlm_RecT        r;
   Nlm_Int4        rleft;
   Nlm_Int4        rtop;
+  Nlm_ScreenMode  screenMode;
   Nlm_Int4        toppix;
   Nlm_WindowTool  wptr;
 #ifdef WIN_MOTIF
@@ -3104,10 +3194,31 @@ static void Nlm_ResizeWindow (Nlm_GraphiC w, Nlm_Int2 dragHeight,
       height = r.bottom + extraHeight;
     if (r.left < 0)
       {
-        free = screenBitBounds.right - width;
-        rleft = (Nlm_Int4)r.left;
-        leftpix = free * (-rleft) / 100;
-        r.left = (Nlm_Int2)leftpix;
+        if (Nlm_HasDualScreen ()) {
+          screenMode = Nlm_GetScreenMode ((Nlm_WindoW) w);
+          if (screenMode == USE_LEFT_SCREEN) {
+            free = screenBitBounds.right / 2 - width;
+            rleft = (Nlm_Int4)r.left;
+            leftpix = free * (-rleft) / 100;
+            r.left = (Nlm_Int2)leftpix;
+          } else if (screenMode == USE_RIGHT_SCREEN) {
+            free = screenBitBounds.right / 2 - width;
+            rleft = (Nlm_Int4)r.left;
+            leftpix = free * (-rleft) / 100;
+            r.left = (Nlm_Int2)leftpix;
+            r.left += screenBitBounds.right / 2;
+          } else {
+            free = screenBitBounds.right - width;
+            rleft = (Nlm_Int4)r.left;
+            leftpix = free * (-rleft) / 100;
+            r.left = (Nlm_Int2)leftpix;
+          }
+        } else {
+          free = screenBitBounds.right - width;
+          rleft = (Nlm_Int4)r.left;
+          leftpix = free * (-rleft) / 100;
+          r.left = (Nlm_Int2)leftpix;
+        }
       }
     if (r.top < 0)
       {
@@ -3929,7 +4040,7 @@ static Nlm_Boolean Nlm_ZoomClick (Nlm_GraphiC w, Nlm_PoinT pt)
     
     if (TrackBox (wptr, ptool, windowLoc)) {
       Rect bounds;
-      // WindowPeek::dataHandle is not supported under Carbon.
+      /* WindowPeek::dataHandle is not supported under Carbon. */
 #if OPAQUE_TOOLBOX_STRUCTS
       ZoomWindowIdeal(wptr, part, &idealSize);
 #else
@@ -5418,7 +5529,7 @@ static void Nlm_HandleEvent (void)
       mess = (Nlm_currentEvent.message & osEvtMessageMask) >> 24;
       if (mess == suspendResumeMessage) {
         if (Nlm_currentEvent.message & resumeFlag) {
-          // Resume
+          /* Resume */
 #if !TARGET_API_MAC_CARBON
           if (Nlm_currentEvent.message & convertClipboardFlag) {
             /* 2001-05-14:  JDJ
@@ -6421,11 +6532,13 @@ void main ()
 #endif
 
 #if TARGET_API_MAC_CARBON >= 1
-  // carbon changes the API: pass the number of master pointers to allocate
-  //MoreMasters (1280);
-  // 2001-03-22:  Joshua Juran
-  // CarbonDater report says to use MoreMasterPointers() instead of MoreMasters().
-  // Universal Interfaces 3.3.2 declares MoreMasters(void) under Carbon.
+  /*
+   carbon changes the API: pass the number of master pointers to allocate
+   MoreMasters (1280);
+   2001-03-22:  Joshua Juran
+   CarbonDater report says to use MoreMasterPointers() instead of MoreMasters().
+   Universal Interfaces 3.3.2 declares MoreMasters(void) under Carbon.
+  */
   MoreMasterPointers(1280);
   FlushEvents (everyEvent, 0);
   /* the rest of the toolbox is done for us can't init them...
@@ -6836,8 +6949,8 @@ extern void Nlm_RemoveDyingWindows (void)
     Nlm_currentWindowTool = GetWindowFromPort(tempPort);
     Nlm_SetUpdateRegion (GetWindowFromPort(tempPort));
     SetPenState (&state);
-    // 2001-03-22:  Joshua Juran
-    // Carbon does not support application-supplied storage for windows.
+    /* 2001-03-22:  Joshua Juran
+       Carbon does not support application-supplied storage for windows. */
     DisposeWindow(wptr);
 #endif
 #ifdef WIN_MSWIN
@@ -6845,6 +6958,10 @@ extern void Nlm_RemoveDyingWindows (void)
       DeleteObject( wdata.cMap );
       wdata.cMap = NULL;
     }
+    if ( wdata.haccel != NULL ){
+      DestroyAcceleratorTable(wdata.haccel);
+      wdata.haccel = NULL;
+    }
     Nlm_currentHDC = tempPort;
     RemoveProp (wptr, (LPSTR) "Nlm_VibrantProp");
     DestroyWindow (wptr);
@@ -6988,6 +7105,93 @@ static void Nlm_ProcessKeyPress (XEvent *event)
 }
 #endif
 
+#ifdef WIN_MSWIN
+
+typedef void (LIBCALLBACK *CallbackProc)(void* data);
+static UINT idWMVibrantCallback = 0;
+
+static void Nlm_InitVibrantCallback ()
+
+{
+    idWMVibrantCallback = RegisterWindowMessage("VibrantCallback");
+}
+
+
+static Nlm_Boolean Nlm_ProcessVibrantCallback (LPMSG lpMsg)
+
+{
+    if(idWMVibrantCallback && idWMVibrantCallback == lpMsg->message)
+    {
+	CallbackProc proc = (CallbackProc)lpMsg->wParam;
+	proc((void*)(lpMsg->lParam));
+	return TRUE;
+    }
+    else
+	return FALSE;
+}
+#endif
+
+#ifdef WIN_MSWIN
+
+extern Nlm_Handle Nlm_GetWindowHAccel (Nlm_WindoW w)
+
+{
+  Nlm_Handle      rsult;
+  Nlm_WindowData  wdata;
+
+  rsult = (Nlm_Handle) 0;
+  if (w != NULL) {
+    Nlm_GetWindowData (w, &wdata);
+    rsult = wdata.haccel;
+  }
+  return rsult;
+}
+
+
+extern void Nlm_SetWindowHAccel (Nlm_WindoW w, Nlm_Handle h)
+
+{
+  Nlm_WindowData  wdata;
+
+  if (w != NULL) {
+    Nlm_GetWindowData (w, &wdata);
+    wdata.haccel = h;
+    Nlm_SetWindowData (w, &wdata);
+  }
+}
+
+
+static Nlm_Boolean Nlm_ProcessAccelerator (LPMSG lpMsg)
+
+{
+    if(lpMsg->hwnd != NULL &&
+       (lpMsg->message == WM_KEYDOWN ||
+        lpMsg->message == WM_KEYUP ||
+	lpMsg->message == WM_SYSKEYDOWN ||
+	lpMsg->message == WM_SYSKEYUP ||
+	lpMsg->message == WM_CHAR))
+    {
+        Nlm_WindoW w = (Nlm_WindoW) GetProp (lpMsg->hwnd, (LPSTR) "Nlm_VibrantProp");
+	if(w != NULL)
+	{
+	    Nlm_WindoW p = Nlm_GetParentWindow((Nlm_GraphiC)w);
+	    if(p != NULL)
+	    {
+		Nlm_WindowData wdata;
+		Nlm_GetWindowData(p, &wdata);
+		if(wdata.haccel != NULL)
+		{
+		    int ret = TranslateAccelerator(wdata.handle, wdata.haccel, lpMsg);
+		    return ret != 0;
+		}
+	    }
+	}
+    }
+
+    return FALSE;
+}
+#endif
+
 extern void Nlm_ProcessAnEvent (void)
 
 {
@@ -7003,6 +7207,7 @@ extern void Nlm_ProcessAnEvent (void)
     if (GetMessage (&Nlm_currentMssg, NULL, 0, 0)) {
       TranslateMessage (&Nlm_currentMssg);
       Nlm_ProcessKeyPress (&Nlm_currentMssg);
+      Nlm_ProcessVibrantCallback(&Nlm_currentMssg);
       DispatchMessage (&Nlm_currentMssg);
     }
   }
@@ -7076,6 +7281,7 @@ extern void Nlm_ProcessEventOrIdle (void)
     if (GetMessage (&Nlm_currentMssg, NULL, 0, 0)) {
       TranslateMessage (&Nlm_currentMssg);
       Nlm_ProcessKeyPress (&Nlm_currentMssg);
+      Nlm_ProcessVibrantCallback(&Nlm_currentMssg);
       DispatchMessage (&Nlm_currentMssg);
     }
   }
@@ -7115,6 +7321,7 @@ extern void Nlm_ProcessExternalEvent (void)
     if (GetMessage (&Nlm_currentMssg, NULL, 0, 0)) {
       TranslateMessage (&Nlm_currentMssg);
       Nlm_ProcessKeyPress (&Nlm_currentMssg);
+      Nlm_ProcessVibrantCallback(&Nlm_currentMssg);
       DispatchMessage (&Nlm_currentMssg);
     }
   }
@@ -7150,6 +7357,7 @@ extern void Nlm_ProcessEvents (void)
   }
 #endif
 #ifdef WIN_MSWIN
+  Nlm_InitVibrantCallback ();
   if (registeredDropProc != NULL) {
     DragAcceptFiles(Nlm_currentHWnd, TRUE);
   }
@@ -7162,9 +7370,12 @@ extern void Nlm_ProcessEvents (void)
       }
     }
     if (GetMessage (&Nlm_currentMssg, NULL, 0, 0)) {
-      TranslateMessage (&Nlm_currentMssg);
-      Nlm_ProcessKeyPress (&Nlm_currentMssg);
-      DispatchMessage (&Nlm_currentMssg);
+      if(!Nlm_ProcessAccelerator(&Nlm_currentMssg)) {
+	TranslateMessage (&Nlm_currentMssg);
+	Nlm_ProcessKeyPress (&Nlm_currentMssg);
+	Nlm_ProcessVibrantCallback(&Nlm_currentMssg);
+	DispatchMessage (&Nlm_currentMssg);
+      }
       Nlm_RemoveDyingWindows ();
     }
   }