Load ncbi (6.1.20031028) into ncbi-tools6/branches/upstream/current.

36 files changed, 5567 insertions, 1342 deletions

diff --git a/api/alignmgr2.c b/api/alignmgr2.c
index 6afaf900..096953e2 100644
--- a/api/alignmgr2.c
+++ b/api/alignmgr2.c
@@ -28,13 +28,28 @@
 *
 * Version Creation Date:  10/01 
 *
-* $Revision: 6.44 $
+* $Revision: 6.49 $
 *
 * File Description: SeqAlign indexing, access, and manipulation functions 
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: alignmgr2.c,v $
+* Revision 6.49  2003/10/20 17:54:34  kans
+* AlnMgr2ComputeFreqMatrix protect against dereferencing NULL bsp
+*
+* Revision 6.48  2003/10/09 13:46:52  rsmith
+* Add AlnMgr2GetFirstNForSipList.
+*
+* Revision 6.47  2003/05/15 18:53:10  rsmith
+* in AlnMgr2GetSeqRangeForSipInStdSeg always return start & stop in coordinate order. Do not assume what minus strand will do or not.
+*
+* Revision 6.46  2003/04/24 20:28:48  rsmith
+* made AlnMgr2GetNthStdSeg use 1 based numbering like the other Nth functions.
+*
+* Revision 6.45  2003/04/23 20:36:13  rsmith
+* Added four functions in Section 11 to get information about Std-Seg alignments.
+*
 * Revision 6.44  2003/03/31 20:17:11  todorov
 * Added AlnMgr2IndexSeqAlignEx
 *
@@ -7159,6 +7174,29 @@ NLM_EXTERN Int4 AlnMgr2GetFirstNForSip(SeqAlignPtr sap, SeqIdPtr sip)
 
 /***************************************************************************
 *
+*  AlnMgr2GetFirstNForSipList returns the first row that one of a list of seqids occur on,
+*  or -1 if none of the seqids are in the alignment or if there is another
+*  error. 
+*  Handy if sip comes from a BioSeq, where it can point to a linked list
+*  of SeqIds.
+*
+***************************************************************************/
+NLM_EXTERN Int4 AlnMgr2GetFirstNForSipList(SeqAlignPtr sap, SeqIdPtr sip)
+{
+    Int4    i;
+    if (sap == NULL || sap->saip == NULL)
+        return -1;
+    
+    for (; sip; sip = sip->next) {
+        i = AlnMgr2GetFirstNForSip(sap, sip);
+        if (i != -1)
+            return i;
+    }
+    return -1;
+}
+
+/***************************************************************************
+*
 *  AlnMgr2GetParent returns the top-level seqalign associated with a given
 *  indexed alignment. It returns the actual pointer, not a copy.
 *
@@ -8392,30 +8430,32 @@ NLM_EXTERN AMFreqPtr AlnMgr2ComputeFreqMatrix(SeqAlignPtr sap, Int4 from, Int4 t
          {
             sip = AlnMgr2GetNthSeqIdPtr(sap, i+1);
             bsp = BioseqLockById(sip);
-            for (l=amp->from_row; l<=amp->to_row; l+=AM_SEQPORTSIZE)
-            {
-               counter = AlnMgr2SeqPortRead(&spp, buf, &bufpos, l, MIN(l+AM_SEQPORTSIZE, amp->to_row), amp->strand, code, bsp);
-               ctr = 0;
-               while (ctr < counter)
-               {
-                  res = buf[ctr];
-                  if (isna)
-                  {
-                     if (res == 1 || res == 2)
-                        afp->freq[res][j]++;
-                     else if (res == 4)
-                        afp->freq[3][j]++;
-                     else if (res == 8)
-                        afp->freq[4][j]++;
-                     else
-                        afp->freq[5][j]++;
-                  } else
-                     afp->freq[res][j]++;
-                  j++;
-                  ctr++;
-               }
+            if (bsp != NULL) {
+              for (l=amp->from_row; l<=amp->to_row; l+=AM_SEQPORTSIZE)
+              {
+                 counter = AlnMgr2SeqPortRead(&spp, buf, &bufpos, l, MIN(l+AM_SEQPORTSIZE, amp->to_row), amp->strand, code, bsp);
+                 ctr = 0;
+                 while (ctr < counter)
+                 {
+                    res = buf[ctr];
+                    if (isna)
+                    {
+                       if (res == 1 || res == 2)
+                          afp->freq[res][j]++;
+                       else if (res == 4)
+                          afp->freq[3][j]++;
+                       else if (res == 8)
+                          afp->freq[4][j]++;
+                       else
+                          afp->freq[5][j]++;
+                    } else
+                       afp->freq[res][j]++;
+                    j++;
+                    ctr++;
+                 }
+              }
+              BioseqUnlock(bsp);
             }
-            BioseqUnlock(bsp);
             SeqIdFree(sip);
          }
       }
@@ -9792,6 +9832,185 @@ NLM_EXTERN void AlnMgr2GetNthSeqRangeInSAStdSeg(SeqAlignPtr sap, Int4 n, Int4Ptr
       *stop = SeqLocStop(slp);
 }
 
+
+/***************************************************************************
+*
+*   AlnMgr2GetSeqRangeForSipInSAStdSeg  returns the smallest and largest sequence
+*  coordinates in in a Std-Seg seqalign for a given Sequence Id.  Also return the 
+*  strand type.  Either start, stop or strand can be NULL to only retrieve some of them.
+*  If start and stop are -1, there is an error (not a std-seg), the SeqID does not participate in this
+*  alignment or the alignment is one big insert on that id.  Returns true if the sip was found
+*  in the alignment with real coordinates, i.e. *start would not be -1.  RANGE
+*
+***************************************************************************/
+NLM_EXTERN Boolean AlnMgr2GetSeqRangeForSipInSAStdSeg(SeqAlignPtr sap, SeqIdPtr sip, Int4Ptr start, Int4Ptr stop, Uint1Ptr strand)
+{
+    Int4        c_start, c_stop;
+    Uint1       c_strand;
+    StdSegPtr   ssp;
+    Boolean     range_found = FALSE;
+    Boolean     strands_inconsistent = FALSE;
+
+    if (start) *start = -1;
+    if (stop)  *stop  = -1;
+    if (strand) *strand = Seq_strand_unknown;
+    
+    if (sap->segtype != SAS_STD)
+        return FALSE;
+
+    ssp = (StdSegPtr)(sap->segs);
+    while (ssp) { 
+        if (AlnMgr2GetSeqRangeForSipInStdSeg(ssp, sip, &c_start, &c_stop, &c_strand, NULL) &&
+            c_start != -1) /* skip inserts on our bioseq */
+        {
+             range_found = TRUE;
+                
+            if (start) {
+                if (*start == -1) {
+                    *start = c_start;
+                } else {
+                    *start = MIN(*start, c_start);
+                }
+            }
+            if (stop) {
+                *stop = MAX(*stop, c_stop);
+            }
+            if (strand && ! strands_inconsistent) {
+            /* if strands are different each time, ignore them. */
+                if (*strand != Seq_strand_unknown && *strand != c_strand) {
+                    *strand = Seq_strand_unknown;
+                    strands_inconsistent = TRUE;
+                } else {
+                    *strand = c_strand;
+                }
+            }
+        }
+        ssp = ssp->next;
+    }
+    return range_found;
+}
+
+
+/***************************************************************************
+*
+*   AlnMgr2GetSeqRangeForSipInStdSeg  returns the start and stop sequence
+*  coordinates in a Std-Segment for a given Sequence Id.  Also return the 
+*  strand type.  Either start, stop or strand can be NULL to only retrieve some of them.
+*  If start and stop are -1, the SeqID was not found in this segment.  
+*  Returns true if the sip was found, even if it is a gap (start, stop = -1).  RANGE
+*
+***************************************************************************/
+NLM_EXTERN Boolean AlnMgr2GetSeqRangeForSipInStdSeg(
+    StdSegPtr   ssp, 
+    SeqIdPtr    sip, 
+    Int4Ptr     start, 
+    Int4Ptr     stop, 
+    Uint1Ptr    strand,
+    Uint1Ptr    segType) /* AM_SEQ, AM_GAP, AM_INSERT */
+{
+    SeqLocPtr   loc;
+    Uint1       m_strand;
+    Int4        m_start, m_stop, m_swap;
+    Boolean     s_present = FALSE;
+    Boolean     m_present = FALSE;
+    Boolean     found_id = FALSE;
+    
+    for ( loc = ssp->loc;
+          loc != NULL;  
+          loc = loc->next ) {
+    /* One SeqLoc for each Sequence aligned by this segment. */
+        /* find the one that matches the sip parameter. */
+        if (SeqIdForSameBioseq(sip, SeqLocId(loc))) {
+            m_strand = SeqLocStrand(loc);
+            m_start  = SeqLocStart(loc);
+            m_stop   = SeqLocStop(loc);
+            /* Might have to reverse the order of start and stop on minus strands. 
+            /* so that start is less than stop. */
+            if (m_start > m_stop) {
+              m_swap  = m_start;
+              m_start = m_stop;
+              m_stop = m_swap;
+            }
+            if (start)  *start  = m_start;
+            if (stop)   *stop   = m_stop;
+            if (strand) *strand = m_strand;
+            if (m_start != -1)
+                m_present = TRUE;
+                
+            /* found our sequence in this segment. */
+            found_id = TRUE;
+        } else { /* a different sequence */
+            if (SeqLocStart(loc) != -1)
+                s_present = TRUE;
+        }
+    }
+    
+    if (segType) {
+        if (m_present && s_present)
+            *segType = AM_SEQ;
+        else if (!m_present && s_present)
+            *segType = AM_INSERT;
+        else if (m_present && !s_present)
+            *segType = AM_GAP;
+        else
+            *segType = AM_GAP; /* start will be -1 */
+    }
+    return found_id;
+}
+
+
+/***************************************************************************
+*
+*   AlnMgr2GetNthStdSeg  returns the a pointer to the Nth segment of
+*   a standard segment alignment.  Numbering starts with 1.
+*   returns NULL if not n segments or is not a std-seg aligment.
+*   Useful to pass its return value to AlnMgr2GetSeqRangeForSipInStdSeg()
+*
+***************************************************************************/
+NLM_EXTERN StdSegPtr AlnMgr2GetNthStdSeg(SeqAlignPtr sap, Int2 n)
+{
+    StdSegPtr   ssp;
+	Int2        i;
+
+    if (sap == NULL || sap->segtype != SAS_STD || n < 1)
+        return NULL;
+      
+    i = 1;
+    ssp = (StdSegPtr)(sap->segs);
+    while(ssp)
+    {
+        if (i == n)
+            return ssp;
+        ++i;
+        ssp = ssp->next;
+    }
+
+    return NULL;
+}
+
+/***************************************************************************
+*
+*  AlnMgr2GetNumStdSegs returns the number of segments in a standar-seg alignment.
+*   returns -1 if sap is null or not a standard-seg alignment.
+*
+***************************************************************************/
+NLM_EXTERN Int4 AlnMgr2GetNumStdSegs(SeqAlignPtr sap)
+{
+    Int4        seg_count = 0;
+    StdSegPtr   ssp;
+    
+    if (sap == NULL || sap->segtype != SAS_STD)
+        return -1;
+        
+    ssp = (StdSegPtr)(sap->segs);
+	while(ssp)
+	{
+		++seg_count;
+		ssp = ssp->next;
+	}
+	return seg_count;
+}   
+   
 static SeqLocPtr AlnMgr2GetLongestSeqLoc(SeqAlignPtr sap)
 {
    Int4       longest;
diff --git a/api/alignmgr2.h b/api/alignmgr2.h
index c71dccf4..2bd1dd3a 100644
--- a/api/alignmgr2.h
+++ b/api/alignmgr2.h
@@ -28,13 +28,19 @@
 *
 * Version Creation Date:  10/01 
 *
-* $Revision: 6.19 $
+* $Revision: 6.21 $
 *
 * File Description: SeqAlign indexing, access, and manipulation functions
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: alignmgr2.h,v $
+* Revision 6.21  2003/10/09 13:46:39  rsmith
+* Add AlnMgr2GetFirstNForSipList.
+*
+* Revision 6.20  2003/04/23 20:37:06  rsmith
+* Added four functions in section 11 to allow examination of Std-Seg alignments.
+*
 * Revision 6.19  2003/03/31 20:17:11  todorov
 * Added AlnMgr2IndexSeqAlignEx
 *
@@ -637,6 +643,17 @@ NLM_EXTERN Int4 AlnMgr2GetFirstNForSip(SeqAlignPtr sap, SeqIdPtr sip);
 
 /***************************************************************************
 *
+*  AlnMgr2GetFirstNForSipList returns the first row that one of a list of seqids occur on,
+*  or -1 if none of the seqids are in the alignment or if there is another
+*  error. 
+*  Handy if sip comes from a BioSeq, where it can point to a linked list
+*  of SeqIds.
+*
+***************************************************************************/
+NLM_EXTERN Int4 AlnMgr2GetFirstNForSipList(SeqAlignPtr sap, SeqIdPtr sip);
+
+/***************************************************************************
+*
 *  AlnMgr2GetParent returns the top-level seqalign associated with a given
 *  indexed alignment. It returns the actual pointer, not a copy.
 *
@@ -885,6 +902,62 @@ NLM_EXTERN SeqAlignPtr AlnMgr2FuseSet(SeqAlignPtr sap_head, Boolean returnall);
 NLM_EXTERN Int4 AlignMgr2GetFirstNForStdSeg(SeqAlignPtr sap, SeqIdPtr sip);
 NLM_EXTERN SeqIdPtr AlnMgr2GetNthSeqIdPtrStdSeg(SeqAlignPtr sap, Int4 n);
 NLM_EXTERN void AlnMgr2GetNthSeqRangeInSAStdSeg(SeqAlignPtr sap, Int4 n, Int4Ptr start, Int4Ptr stop);
+
+/***************************************************************************
+*
+*   AlnMgr2GetSeqRangeForSipInSAStdSeg  returns the smallest and largest sequence
+*  coordinates in in a Std-Seg seqalign for a given Sequence Id.  Also return the 
+*  strand type if it is the same on every segment, else set it to Seq_strand_unknown.
+*  Either start, stop or strand can be NULL to only retrieve some of them.
+*  If start and stop are -1, there is an error (not a std-seg), the SeqID does not participate in this
+*  alignment or the alignment is one big insert on that id.  Returns true if the sip was found
+*  in the alignment with real coordinates, i.e. *start would not be -1.  RANGE
+*
+***************************************************************************/
+NLM_EXTERN Boolean AlnMgr2GetSeqRangeForSipInSAStdSeg(SeqAlignPtr sap, SeqIdPtr sip, Int4Ptr start, Int4Ptr stop, Uint1Ptr strand);
+
+/***************************************************************************
+*
+*   AlnMgr2GetSeqRangeForSipInStdSeg  returns the start and stop sequence
+*  coordinates in a Std-Segment for a given Sequence Id.  Also return the 
+*  strand type.  Either start, stop, strand or segType can be NULL to only retrieve some of them.
+*  Returns false if the SeqID was not found in this segment, so no meaningful 
+*    data was passed back in other arguments.  
+*  Returns true if the sip was found, even if it is a gap (start, stop = -1).
+*  segType is set to AM_SEQ if the SeqID Sequence is not empty and one of 
+*  the other sequences aligned with it is also not empty.  To AM_GAP if
+*  the other sequences are all empty, and to AM_INSERT if the main sequence
+*  is empty. 
+*  RANGE
+*
+***************************************************************************/
+NLM_EXTERN Boolean AlnMgr2GetSeqRangeForSipInStdSeg(
+    StdSegPtr   ssp, 
+    SeqIdPtr    sip, 
+    Int4Ptr     start, 
+    Int4Ptr     stop, 
+    Uint1Ptr    strand,
+    Uint1Ptr    segType); /* AM_SEQ, AM_GAP, AM_INSERT */
+
+/***************************************************************************
+*
+*   AlnMgr2GetNthStdSeg  returns the a pointer to the Nth segment of
+*   a standard segment alignment.
+*   returns NULL if not n segments or is not a std-seg aligment.
+*   Useful to pass its return value to AlnMgr2GetSeqRangeForSipInStdSeg()
+*
+***************************************************************************/
+NLM_EXTERN StdSegPtr AlnMgr2GetNthStdSeg(SeqAlignPtr sap, Int2 n);
+
+/***************************************************************************
+*
+*  AlnMgr2GetNumStdSegs returns the number of segments in a standar-seg alignment.
+*   returns -1 if sap is null or not a standard-seg alignment.
+*   the Std-Seg version of AlnMgr2GetNumSegs
+*
+***************************************************************************/
+NLM_EXTERN Int4 AlnMgr2GetNumStdSegs(SeqAlignPtr sap);
+
 /***************************************************************************
 *
 *  The two mapping functions act a little differently for std-segs. The
diff --git a/api/alignval.c b/api/alignval.c
index 9b317c04..bf3a64b7 100644
--- a/api/alignval.c
+++ b/api/alignval.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/3/99
 *
-* $Revision: 6.35 $
+* $Revision: 6.37 $
 *
 * File Description:  To validate sequence alignment.
 *
@@ -443,7 +443,7 @@ static void ValMessage (SeqAlignPtr salp, Int1 MessageCode, ErrSev errlevel, Seq
       pos = valmsggetseqpos(salp, Intvalue, id);
       SeqIdWrite (idcontext, buf3, PRINTID_REPORT, sizeof (buf3));
       sprintf(string1, "Segs");
-      sprintf(string2, "Segment %ld (near alignment position %ld) contains only gaps.  Each segment must contain at least one actual sequence -- look for columns with all gaps and delete them.", (long) Intvalue, (long) pos);
+      sprintf(string2, "Segment %ld (near alignment position %ld) in the context of %s contains only gaps.  Each segment must contain at least one actual sequence -- look for columns with all gaps and delete them.", (long) Intvalue, (long) pos, buf3);
       break;
 
     case Err_Segs_Dim_One:
@@ -1495,7 +1495,7 @@ static Boolean Is_Fasta_Seqalign (SeqAlignPtr salp)
 		  /*if no more positive start value is found after the initial -1 start value, then it's  fasta like */
 		  if(k==dsp->numseg-1&&gap)
 		    {
-		      ValMessage (salp, Err_Fastalike, SEV_ERROR, siptemp, dsp->ids, 0); 
+		      ValMessage (salp, Err_Fastalike, SEV_WARNING, siptemp, dsp->ids, 0); 
 		      return TRUE;
 		    }
 		}
@@ -1541,7 +1541,7 @@ static Boolean Is_Fasta_Seqalign (SeqAlignPtr salp)
 		     /*if no more segment is found for this sequence, then it's  fasta like */
 		     if(k==psp->numseg-1&&gap)
 		       {
-			 ValMessage (salp, Err_Fastalike, SEV_ERROR, siptemp, psp->ids, 0); 
+			 ValMessage (salp, Err_Fastalike, SEV_WARNING, siptemp, psp->ids, 0); 
 			 return TRUE;
 		       }
 		   
@@ -1598,7 +1598,7 @@ static Boolean Is_Fasta_Seqalign (SeqAlignPtr salp)
 			      break;
 			    if(!ssptemp2->next&&gap)
 			      {
-				ValMessage (salp, Err_Fastalike, SEV_ERROR, sip, SipInSegs, 0);  
+				ValMessage (salp, Err_Fastalike, SEV_WARNING, sip, SipInSegs, 0);  
 				ValNodeFree(FinishedSip);
 				SeqIdSetFree(SipInSegs);
 				return TRUE;
diff --git a/api/asn2ff3.c b/api/asn2ff3.c
index ec9a8880..706036d0 100644
--- a/api/asn2ff3.c
+++ b/api/asn2ff3.c
@@ -35,6 +35,15 @@
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: asn2ff3.c,v $
+* Revision 6.118  2003/07/22 16:18:27  kans
+* added ZFIN as legal db_xref
+*
+* Revision 6.117  2003/06/10 18:44:10  kans
+* added GeneDB to list of legal db_xrefs
+*
+* Revision 6.116  2003/05/29 20:25:19  kans
+* added Interpro to list of legal dbxrefs
+*
 * Revision 6.115  2002/11/30 20:18:27  kans
 * added GOA to list of legal db_xrefs
 *
@@ -723,6 +732,7 @@ CharPtr dbtag[DBNUM] = {
   "FLYBASE",
   "GABI",
   "GDB",
+  "GeneDB",
   "GeneID",
   "GI",
   "GO",
@@ -731,6 +741,7 @@ CharPtr dbtag[DBNUM] = {
   "IMGT/LIGM",
   "IMGT/HLA",
   "InterimID",
+  "Interpro",
   "ISFinder",
   "JCM",
   "LocusID",
@@ -756,6 +767,7 @@ CharPtr dbtag[DBNUM] = {
   "UniSTS",
   "WorfDB",
   "WormBase",
+  "ZFIN",
   };
 
 
diff --git a/api/asn2ffp.h b/api/asn2ffp.h
index 87a8b726..f05a9b89 100644
--- a/api/asn2ffp.h
+++ b/api/asn2ffp.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/15/95
 *
-* $Revision: 6.30 $
+* $Revision: 6.33 $
 *
 * File Description: 
 *
@@ -45,6 +45,15 @@
 /*************************************
 *
  * $Log: asn2ffp.h,v $
+ * Revision 6.33  2003/07/22 16:18:27  kans
+ * added ZFIN as legal db_xref
+ *
+ * Revision 6.32  2003/06/10 18:44:10  kans
+ * added GeneDB to list of legal db_xrefs
+ *
+ * Revision 6.31  2003/05/29 20:25:19  kans
+ * added Interpro to list of legal dbxrefs
+ *
  * Revision 6.30  2002/11/30 20:18:27  kans
  * added GOA to list of legal db_xrefs
  *
@@ -192,6 +201,15 @@
 /*************************************
 *
 * $Log: asn2ffp.h,v $
+* Revision 6.33  2003/07/22 16:18:27  kans
+* added ZFIN as legal db_xref
+*
+* Revision 6.32  2003/06/10 18:44:10  kans
+* added GeneDB to list of legal db_xrefs
+*
+* Revision 6.31  2003/05/29 20:25:19  kans
+* added Interpro to list of legal dbxrefs
+*
 * Revision 6.30  2002/11/30 20:18:27  kans
 * added GOA to list of legal db_xrefs
 *
@@ -369,7 +387,7 @@ NLM_EXTERN  Boolean asn2ff_flags[13];
 #define ASN2FF_SHOW_ERROR_MSG	        asn2ff_flags[11]
 #define ASN2FF_SHOW_GB_STYLE	        asn2ff_flags[12]
 
-#define DBNUM 55
+#define DBNUM 58
 NLM_EXTERN CharPtr dbtag[DBNUM];
 
 NLM_EXTERN void FlatSpliceOff PROTO((SeqEntryPtr the_set, ValNodePtr desc));
diff --git a/api/asn2gnbk.c b/api/asn2gnbk.c
index 39e5c40d..deccca09 100644
--- a/api/asn2gnbk.c
+++ b/api/asn2gnbk.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 6.660 $
+* $Revision: 6.729 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -44,6 +44,7 @@
 #include <objsset.h>
 #include <objsub.h>
 #include <objfdef.h>
+#include <objpubme.h>
 #include <seqport.h>
 #include <sequtil.h>
 #include <sqnutils.h>
@@ -98,6 +99,7 @@ typedef struct asn2gbflags {
   Boolean             hideEmptySource;
   Boolean             goQualsToNote;
   Boolean             geneSynsToNote;
+  Boolean             selenocysteineToNote;
   Boolean             forGbRelease;
 } Asn2gbFlags, PNTR Asn2gbFlagsPtr;
 
@@ -137,6 +139,8 @@ typedef struct int_asn2gb_job {
   Boolean        newSourceOrg;
   ValNodePtr     lockedBspList;
   Boolean        relModeError;
+  Boolean        skipProts;
+  Boolean        skipMrnas;
   IndxPtr        index;
   GBSeqPtr       gbseq;
   StringItemPtr  pool;
@@ -195,6 +199,7 @@ typedef struct asn2gbwork {
   Boolean          citSubsFirst;
   Boolean          hideGeneFeats;
   Boolean          newLocusLine;
+  Boolean          showBaseCount;
 
   Boolean          hideImpFeats;
   Boolean          hideRemImpFeats;
@@ -209,6 +214,8 @@ typedef struct asn2gbwork {
   Boolean          onlyGeneRIFs;
   Boolean          latestGeneRIFs;
 
+  Boolean          showRefs;
+
   Boolean          isGPS;
   Boolean          copyGpsCdsUp;
   Boolean          copyGpsGeneDown;
@@ -516,6 +523,7 @@ static Uint1 source_qual_order [] = {
   SCQUAL_tissue_type,
   SCQUAL_clone_lib,
   SCQUAL_dev_stage,
+  SCQUAL_ecotype,
   SCQUAL_frequency,
 
   SCQUAL_germline,
@@ -565,7 +573,6 @@ static Uint1 source_desc_note_order [] = {
   SCQUAL_authority,
   SCQUAL_forma,
   SCQUAL_forma_specialis,
-  SCQUAL_ecotype,
   SCQUAL_synonym,
   SCQUAL_anamorph,
   SCQUAL_teleomorph,
@@ -607,7 +614,6 @@ static Uint1 source_feat_note_order [] = {
   SCQUAL_authority,
   SCQUAL_forma,
   SCQUAL_forma_specialis,
-  SCQUAL_ecotype,
   SCQUAL_synonym,
   SCQUAL_anamorph,
   SCQUAL_teleomorph,
@@ -805,6 +811,7 @@ typedef enum {
   FTQUAL_modelev,
   FTQUAL_note,
   FTQUAL_number,
+  FTQUAL_operon,
   FTQUAL_organism,
   FTQUAL_partial,
   FTQUAL_PCR_conditions,
@@ -833,12 +840,14 @@ typedef enum {
   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,
@@ -859,6 +868,10 @@ static Uint1 feat_qual_order [] = {
   FTQUAL_locus_tag,
   FTQUAL_gene_syn_refseq,
 
+  FTQUAL_gene_allele,
+
+  FTQUAL_operon,
+
   FTQUAL_product,
 
   FTQUAL_prot_EC_number,
@@ -881,6 +894,7 @@ static Uint1 feat_qual_order [] = {
   FTQUAL_number,
 
   FTQUAL_pseudo,
+  FTQUAL_selenocysteine,
 
   FTQUAL_codon_start,
 
@@ -895,7 +909,6 @@ static Uint1 feat_qual_order [] = {
   FTQUAL_frequency,
   FTQUAL_EC_number,
   FTQUAL_gene_map,
-  FTQUAL_gene_allele,
   FTQUAL_allele,
   FTQUAL_map,
   FTQUAL_mod_base,
@@ -944,6 +957,7 @@ pseudo after note - gi|6598562|gb|AC006419.3|AC006419
 */
 
 static Uint1 feat_note_order [] = {
+  FTQUAL_transcript_id_note, /* !!! remove October 15, 2003 !!! */
   FTQUAL_gene_desc,
   FTQUAL_gene_syn,
   FTQUAL_trna_codons,
@@ -958,7 +972,7 @@ static Uint1 feat_note_order [] = {
   FTQUAL_seqfeat_note,
   FTQUAL_exception_note,
   FTQUAL_region,
-  /* FTQUAL_selenocysteine, */
+  FTQUAL_selenocysteine_note,
   FTQUAL_prot_names,
   FTQUAL_bond,
   FTQUAL_site,
@@ -1023,6 +1037,7 @@ static FeaturQual asn2gnbk_featur_quals [ASN2GNBK_TOTAL_FEATUR] = {
   { "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         },
@@ -1050,6 +1065,7 @@ static FeaturQual asn2gnbk_featur_quals [ASN2GNBK_TOTAL_FEATUR] = {
   { "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          },
@@ -1057,6 +1073,7 @@ static FeaturQual asn2gnbk_featur_quals [ASN2GNBK_TOTAL_FEATUR] = {
   { "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   },
@@ -1098,7 +1115,7 @@ static Char doc_link [MAX_WWWBUF];
 #define DEF_LINK_DOC  "http://www.ncbi.nlm.nih.gov/genome/guide/build.html"
 
 static Char ev_link [MAX_WWWBUF];
-#define DEF_LINK_EV  "http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/evv.cgi?"
+#define DEF_LINK_EV  "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?"
 
 static Char ec_link [MAX_WWWBUF];
 #define DEF_LINK_EC "http://www.expasy.ch/cgi-bin/nicezyme.pl?"
@@ -1106,108 +1123,119 @@ static Char ec_link [MAX_WWWBUF];
 static 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];
+static Char link_ff [MAX_WWWBUF];
 #define DEF_LINK_FF  "/cgi-bin/Entrez/getfeat?"
 
-static Char link_muid[MAX_WWWBUF];
+static Char link_muid [MAX_WWWBUF];
 #define DEF_LINK_MUID  "/entrez/utils/qmap.cgi?"
 
-static Char link_ace[MAX_WWWBUF];
+static Char link_ace [MAX_WWWBUF];
 #define DEF_LINK_ACE  "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=gene&q="
 
-static Char link_code[MAX_WWWBUF];
+static 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];
+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];
+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];
+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];
+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];
+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];
+static Char link_gdb [MAX_WWWBUF];
 #define DEF_LINK_GDB "http://gdbwww.gdb.org/gdb-bin/genera/genera/hgd/DBObject/GDB:"
 
-static Char link_ck[MAX_WWWBUF];
+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];
+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];
+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];
+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];
+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];
+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];
+static Char link_dbEST [MAX_WWWBUF];
 #define DEF_LINK_dbEST "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?"
 
-static Char link_omim[MAX_WWWBUF];
+static Char link_omim [MAX_WWWBUF];
 #define DEF_LINK_OMIM "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id="
 
-static Char link_locus[MAX_WWWBUF];
+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];
+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];
+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];
+static Char link_rgd [MAX_WWWBUF];
 #define DEF_LINK_RGD "http://rgd.mcw.edu/query/query.cgi?id="
 
-static Char link_mgd[MAX_WWWBUF];
+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];
+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];
+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];
+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];
+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];
+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];
+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];
+static Char link_ifo [MAX_WWWBUF];
 #define DEF_LINK_IFO "http://www.ifo.or.jp/index_e.html"
 
-static Char link_jcm[MAX_WWWBUF];
+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];
+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];
+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];
+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_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/"
 
 /* utility functions */
 
@@ -1447,7 +1475,7 @@ static void FFAddPeriod (StringItemPtr sip) {
             FFRecycleString(ajp, riter);
             riter = prev;
             riter->next = NULL;
-	          sip->curr = riter;
+              sip->curr = riter;
             break;
           }
         }
@@ -2185,7 +2213,7 @@ static Int4 FFStringSearch (
       return shift;
     } else {
         shift += MAX( (Int4)good_suffix[j],
-		      (Int4)(j - last_occurance[FFCharAt(text,shift + j)]));
+              (Int4)(j - last_occurance[FFCharAt(text,shift + j)]));
     }
   }
 
@@ -2205,27 +2233,27 @@ static Boolean IsWholeWordSubstr (
   CharPtr subStr
 )
 {
-	Boolean left, right;
-	Char ch;
+    Boolean left, right;
+    Char ch;
 
 
-	/* check on the left only if there is a character there */
-	if (foundPos > 0) {
-		ch = FFCharAt(searchStr, foundPos - 1);
-		left = IS_WHITESP(ch) || ispunct(ch);
-	} else {
-		left = TRUE;
-	}
+    /* check on the left only if there is a character there */
+    if (foundPos > 0) {
+        ch = FFCharAt(searchStr, foundPos - 1);
+        left = IS_WHITESP(ch) || ispunct(ch);
+    } else {
+        left = TRUE;
+    }
 
-	foundPos += StringLen(subStr);
+    foundPos += StringLen(subStr);
   if ( foundPos == FFLength(searchStr) ) {
     right = TRUE;
   } else {
     ch = FFCharAt(searchStr, foundPos);
-	  right = IS_WHITESP(ch) || ispunct(ch);
+      right = IS_WHITESP(ch) || ispunct(ch);
   }
 
-	return left; /* see comment above */
+    return left; /* see comment above */
   /* return left && right;  this is how it should be!*/
 }
 
@@ -2297,6 +2325,10 @@ static void InitWWW (IntAsn2gbJobPtr ajp)
   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);
 }
 
 
@@ -2525,6 +2557,19 @@ static void FF_www_db_xref_gdb(
   }
 }
 
+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(
@@ -2536,67 +2581,75 @@ static void Do_www_db_xref(
   if ( ffstring == NULL || db == NULL || identifier == NULL ) return;
 
   if ( StringCmp(db, "FLYBASE") == 0) {
-	FF_www_db_xref_fly(ffstring, db, identifier);
+    FF_www_db_xref_fly(ffstring, db, identifier);
   } else if ( StringCmp(db , "COG") == 0) {
-	FF_www_db_xref_std(ffstring, db, identifier, link_cog);
+    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);
+    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);
+    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);
+    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);
+    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);
+    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);
+    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);
+    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);
+    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);
+    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);
+    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);
+    FF_www_db_xref_std(ffstring, db, identifier, link_rgd);
   } else if ( StringCmp(db , "MGD") == 0) {
-	FF_www_db_xref_mgd(ffstring, db, identifier);
+    FF_www_db_xref_mgd(ffstring, db, identifier);
   } else if ( StringCmp(db , "CDD") == 0) {
-	FF_www_db_xref_std(ffstring, db, identifier, link_cdd);
+    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);
+    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);
+    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);
+    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);
+    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);
+    FF_www_db_xref_pid(ffstring, db, identifier);
   } else if ( StringCmp(db , "dbEST") == 0) {
-	FF_www_db_xref_dbEST(ffstring, db, identifier);
+    FF_www_db_xref_dbEST(ffstring, db, identifier);
   } else if ( StringCmp(db , "dbSTS") == 0) {
-	FF_www_db_xref_dbSTS(ffstring, db, identifier);
+    FF_www_db_xref_dbSTS(ffstring, db, identifier);
   } else if ( StringCmp(db , "niaEST") == 0) {
-	FF_www_db_xref_niaEST(ffstring, db, identifier);
+    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);
+    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);
+    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);
+    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);
+    FF_www_db_xref_std(ffstring, db, identifier, link_nextdb);
   } else if ( StringCmp(db , "IFO") == 0) {
-	FF_www_db_xref_ifo(ffstring, db, identifier);
+    FF_www_db_xref_ifo(ffstring, db, identifier);
   } else if ( StringCmp(db , "GDB") == 0) {
-	FF_www_db_xref_gdb(ffstring, db, identifier);
+    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);
+    /* default: no link just the text */
+    FFAddTextToString(ffstring, db, ":", identifier, FALSE, FALSE, TILDE_IGNORE);
   }             
 }
 
@@ -2968,7 +3021,7 @@ static void FFAddString_NoRedund (
 
   if (StringNICmp (string, "tRNA-", 5) == 0) {
     str = string+5;
-	}
+    }
 
   while ( foundPos >= 0 && !wholeWord ) {
     foundPos = FFStringSearch(unique, str, foundPos);
@@ -3190,6 +3243,7 @@ static CharPtr legalDbXrefs [] = {
   "FLYBASE",
   "GABI",
   "GDB",
+  "GeneDB",
   "GeneID",
   "GI",
   "GO",
@@ -3224,10 +3278,12 @@ static CharPtr legalDbXrefs [] = {
   "UniSTS",
   "WorfDB",
   "WormBase",
+  "ZFIN",
   NULL
 };
 
 static CharPtr legalRefSeqDbXrefs [] = {
+  "REBASE",
   NULL
 };
 
@@ -3523,6 +3579,7 @@ static CharPtr FormatOrganismBlock (
   IntAsn2gbJobPtr    ajp;
   Asn2gbSectPtr      asp;
   BioSourcePtr       biop = NULL;
+  Char               ch;
   CharPtr            common = NULL;
   DbtagPtr           dbt;
   SeqMgrDescContext  dcontext;
@@ -3539,6 +3596,8 @@ static CharPtr FormatOrganismBlock (
   CharPtr            str;
   Int4               taxid = -1;
   CharPtr            taxname = NULL;
+  CharPtr            tmp;
+  CharPtr            ptr;
   ValNodePtr         vnp;
   StringItemPtr      ffstring, temp;
   Char               buf [16];
@@ -3631,8 +3690,20 @@ static CharPtr FormatOrganismBlock (
           FFAddOneString(temp, "<a href=", FALSE, FALSE, TILDE_IGNORE);
           FFAddOneString(temp, link_tax, FALSE, FALSE, TILDE_IGNORE);
           FFAddOneString(temp, "name=", FALSE, FALSE, TILDE_IGNORE);
-          sprintf (buf, "%ld", (long) taxid);
-          FFAddOneString(temp, taxname, 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);
@@ -5583,7 +5654,7 @@ static CharPtr FormatCitSub (
       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");
+          ValNodeCopyStr (&head, 0, " to the EMBL/GenBank/DDBJ databases.\n");
         } else {
           ValNodeCopyStr (&head, 0, " ");
         }
@@ -5593,7 +5664,7 @@ static CharPtr FormatCitSub (
       ValNodeCopyStr (&head, 0, affil);
       MemFree (affil);
     } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) {
-      ValNodeCopyStr (&head, 0, " to the EMBL/GenBank/DDBJ databases\n");
+      ValNodeCopyStr (&head, 0, " to the EMBL/GenBank/DDBJ databases.\n");
     }
   }
 
@@ -5929,6 +6000,21 @@ static void AddReferenceToGbseq (
   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
@@ -5958,12 +6044,15 @@ static CharPtr FormatReferenceBlock (
   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;
@@ -6047,6 +6136,30 @@ static CharPtr FormatReferenceBlock (
     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);
 
@@ -6304,7 +6417,9 @@ static CharPtr FormatReferenceBlock (
   if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
     needsPeriod = FALSE;
   } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-    needsPeriod = TRUE;
+    if (! IsCitSub (pdp, csp)) {
+      needsPeriod = TRUE;
+    }
   }
 
   FFAddOneString (temp, str, FALSE, FALSE, TILDE_IGNORE);
@@ -6386,6 +6501,13 @@ static CharPtr FormatReferenceBlock (
 
     FFRecycleString(ajp, ffstring);
     FFRecycleString(ajp, temp);
+    if (pep != NULL) {
+      PubmedEntryFree (pep);
+    }
+    if (pdpcopy != NULL) {
+      PubdescFree (pdpcopy);
+    }
+
     return str;
   }
 
@@ -6536,6 +6658,13 @@ static CharPtr FormatReferenceBlock (
 
   FFRecycleString(ajp, ffstring);
   FFRecycleString(ajp, temp);
+  if (pep != NULL) {
+    PubmedEntryFree (pep);
+  }
+  if (pdpcopy != NULL) {
+    PubdescFree (pdpcopy);
+  }
+
   return str;
 }
 
@@ -6552,8 +6681,8 @@ static Boolean IsTildeEOL(CharPtr str) {
 
   
   for ( ptr = str; 
-	IS_ALPHANUM(*ptr) || *ptr == '_' || *ptr == '-' || *ptr == '.';
-	++ptr) continue;
+    IS_ALPHANUM(*ptr) || *ptr == '_' || *ptr == '-' || *ptr == '.';
+    ++ptr) continue;
 
   return *ptr == '/' ? FALSE : TRUE;
 }
@@ -7455,7 +7584,6 @@ static CharPtr FlatLoc (
     order [SEQID_GENBANK] = num++;
     order [SEQID_EMBL] = num++;
     order [SEQID_DDBJ] = num++;
-    order [SEQID_LOCAL] = num++;
     order [SEQID_OTHER] = num++;
     order [SEQID_TPG] = num++;
     order [SEQID_TPE] = num++;
@@ -7469,6 +7597,7 @@ static CharPtr FlatLoc (
     order [SEQID_PATENT] = num++;
     order [SEQID_GI] = num++;;
     order [SEQID_GENERAL] = num++;
+    order [SEQID_LOCAL] = num++;
     order [SEQID_GIIM] = num++;
     order_initialized = TRUE;
   }
@@ -7521,6 +7650,114 @@ static CharPtr FlatLoc (
 }
 
 
+
+
+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.                          */
 /******************************************************************************/
@@ -7836,7 +8073,7 @@ static CharPtr GetMolTypeQual (
       }
       break;
     case MOLECULE_TYPE_PRE_MRNA :
-      return "pre-mRNA";
+      return "pre-RNA";
     case MOLECULE_TYPE_MRNA :
       return "mRNA";
     case MOLECULE_TYPE_RRNA :
@@ -8038,7 +8275,23 @@ static CharPtr FormatSourceFeatBlock (
     qvp [SCQUAL_focus].ble = TRUE;
   }
 
-  qvp [SCQUAL_mol_type].str = GetMolTypeQual (bsp);
+  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);
 
@@ -8450,7 +8703,7 @@ typedef struct qualfeatur {
   Uint1       featurclass;
 } QualFeatur, PNTR QualFeaturPtr;
 
-#define NUM_GB_QUALS 25
+#define NUM_GB_QUALS 26
 
 static QualFeatur qualToFeature [NUM_GB_QUALS] = {
   { "allele",         FTQUAL_allele         },
@@ -8467,6 +8720,7 @@ static QualFeatur qualToFeature [NUM_GB_QUALS] = {
   { "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      },
@@ -8581,6 +8835,7 @@ static CharPtr trnaList [] = {
   "tRNA-OTHER",
   "tRNA-Tyr",
   "tRNA-Glx",
+  "tRNA-TERM",
   NULL
 };
 
@@ -8908,441 +9163,525 @@ typedef struct valqualstruc {
 
 static ValQual legalGbqualList [] = {
 
-  {FEATDEF_GENE ,  FTQUAL_allele},
-  {FEATDEF_GENE ,  FTQUAL_function},
-  {FEATDEF_GENE ,  FTQUAL_label},
-  {FEATDEF_GENE ,  FTQUAL_map},
-  {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_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_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_product},
-  {FEATDEF_mRNA ,  FTQUAL_standard_name},
-  {FEATDEF_mRNA ,  FTQUAL_usedin},
-
-  {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_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_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_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_function},
-  {FEATDEF_otherRNA ,  FTQUAL_label},
-  {FEATDEF_otherRNA ,  FTQUAL_map},
-  {FEATDEF_otherRNA ,  FTQUAL_product},
-  {FEATDEF_otherRNA ,  FTQUAL_standard_name},
-  {FEATDEF_otherRNA ,  FTQUAL_usedin},
-
-  {FEATDEF_attenuator ,  FTQUAL_label},
-  {FEATDEF_attenuator ,  FTQUAL_map},
-  {FEATDEF_attenuator ,  FTQUAL_phenotype},
-  {FEATDEF_attenuator ,  FTQUAL_usedin},
-
-  {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_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_product},
-  {FEATDEF_Imp_CDS ,  FTQUAL_standard_name},
-  {FEATDEF_Imp_CDS ,  FTQUAL_usedin},
-
-  {FEATDEF_conflict ,  FTQUAL_label},
-  {FEATDEF_conflict ,  FTQUAL_map},
-  {FEATDEF_conflict ,  FTQUAL_replace},
-  {FEATDEF_conflict ,  FTQUAL_usedin},
-
-  {FEATDEF_D_loop ,  FTQUAL_label},
-  {FEATDEF_D_loop ,  FTQUAL_map},
-  {FEATDEF_D_loop ,  FTQUAL_usedin},
-
-  {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_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_label},
-  {FEATDEF_GC_signal ,  FTQUAL_map},
-  {FEATDEF_GC_signal ,  FTQUAL_usedin},
-
-  {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_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_function},
-  {FEATDEF_LTR ,  FTQUAL_label},
-  {FEATDEF_LTR ,  FTQUAL_map},
-  {FEATDEF_LTR ,  FTQUAL_standard_name},
-  {FEATDEF_LTR ,  FTQUAL_usedin},
-
-  {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_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_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_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_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_function},
-  {FEATDEF_misc_signal ,  FTQUAL_label},
-  {FEATDEF_misc_signal ,  FTQUAL_map},
-  {FEATDEF_misc_signal ,  FTQUAL_phenotype},
-  {FEATDEF_misc_signal ,  FTQUAL_standard_name},
-  {FEATDEF_misc_signal ,  FTQUAL_usedin},
-
-  {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_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_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_label},
-  {FEATDEF_old_sequence ,  FTQUAL_map},
-  {FEATDEF_old_sequence ,  FTQUAL_replace},
-  {FEATDEF_old_sequence ,  FTQUAL_usedin},
-
-  {FEATDEF_polyA_signal ,  FTQUAL_label},
-  {FEATDEF_polyA_signal ,  FTQUAL_map},
-  {FEATDEF_polyA_signal ,  FTQUAL_usedin},
-
-  {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_standard_name},
-  {FEATDEF_prim_transcript ,  FTQUAL_usedin},
-
-  {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_function},
-  {FEATDEF_promoter ,  FTQUAL_label},
-  {FEATDEF_promoter ,  FTQUAL_map},
-  {FEATDEF_promoter ,  FTQUAL_phenotype},
-  {FEATDEF_promoter ,  FTQUAL_standard_name},
-  {FEATDEF_promoter ,  FTQUAL_usedin},
-
-  {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_label},
-  {FEATDEF_RBS ,  FTQUAL_map},
-  {FEATDEF_RBS ,  FTQUAL_standard_name},
-  {FEATDEF_RBS ,  FTQUAL_usedin},
-
-  {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_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_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_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_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_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_function},
-  {FEATDEF_stem_loop ,  FTQUAL_label},
-  {FEATDEF_stem_loop ,  FTQUAL_map},
-  {FEATDEF_stem_loop ,  FTQUAL_standard_name},
-  {FEATDEF_stem_loop ,  FTQUAL_usedin},
-
-  {FEATDEF_STS ,  FTQUAL_label},
-  {FEATDEF_STS ,  FTQUAL_map},
-  {FEATDEF_STS ,  FTQUAL_standard_name},
-  {FEATDEF_STS ,  FTQUAL_usedin},
-
-  {FEATDEF_TATA_signal ,  FTQUAL_label},
-  {FEATDEF_TATA_signal ,  FTQUAL_map},
-  {FEATDEF_TATA_signal ,  FTQUAL_usedin},
-
-  {FEATDEF_terminator ,  FTQUAL_label},
-  {FEATDEF_terminator ,  FTQUAL_map},
-  {FEATDEF_terminator ,  FTQUAL_standard_name},
-  {FEATDEF_terminator ,  FTQUAL_usedin},
-
-  {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_label},
-  {FEATDEF_unsure ,  FTQUAL_map},
-  {FEATDEF_unsure ,  FTQUAL_replace},
-  {FEATDEF_unsure ,  FTQUAL_usedin},
-
-  {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_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_label},
-  {FEATDEF_10_signal ,  FTQUAL_map},
-  {FEATDEF_10_signal ,  FTQUAL_standard_name},
-  {FEATDEF_10_signal ,  FTQUAL_usedin},
-
-  {FEATDEF_35_signal ,  FTQUAL_label},
-  {FEATDEF_35_signal ,  FTQUAL_map},
-  {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_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_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_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_function},
-  {FEATDEF_snoRNA ,  FTQUAL_label},
-  {FEATDEF_snoRNA ,  FTQUAL_map},
-  {FEATDEF_snoRNA ,  FTQUAL_product},
-  {FEATDEF_snoRNA ,  FTQUAL_standard_name},
-  {FEATDEF_snoRNA ,  FTQUAL_usedin}
-
+  { 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 */
@@ -9406,7 +9745,27 @@ static CharPtr validConsSpliceString [] = {
 };
 
 static CharPtr validExceptionString [] = {
-  "RNA editing", "reasons given in citation", NULL
+  "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) {
@@ -9580,6 +9939,7 @@ static Boolean ValidateRptUnit (
 )
 
 {
+#if 0
   CharPtr  str;
   Char     tmp [255];
 
@@ -9607,6 +9967,7 @@ static Boolean ValidateRptUnit (
     while (IS_DIGIT (*str)) str++;
     if (*str != '\0') return FALSE;  /* mustn't be anything after the yyy */
   }
+#endif
   return TRUE;
 }
 
@@ -10796,6 +11157,7 @@ static void AddLocusBlock (
 )
 
 {
+  size_t             acclen;
   IntAsn2gbJobPtr    ajp;
   Asn2gbSectPtr      asp;
   BaseBlockPtr       bbp;
@@ -10822,9 +11184,11 @@ static void AddLocusBlock (
   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];
@@ -10887,6 +11251,8 @@ static void AddLocusBlock (
         } 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;
@@ -10936,6 +11302,7 @@ static void AddLocusBlock (
     }
   }
   if (nm != NULL) {
+    /*
     sfp = SeqMgrGetNextFeature (nm, NULL, SEQFEAT_GENE, 0, &fcontext);
     if (sfp != NULL) {
       StringNCpy_0 (gene, fcontext.label, sizeof (gene));
@@ -10946,6 +11313,7 @@ static void AddLocusBlock (
         gene [0] = '\0';
       }
     }
+    */
   }
 
   /* more complicated code to get parent locus, if segmented, goes here */
@@ -10992,10 +11360,15 @@ static void AddLocusBlock (
             case SEQID_DDBJ :
               tsip = (TextSeqIdPtr) sip->data.ptrvalue;
               if (tsip != NULL && tsip->accession != NULL) {
-                if (StringLen (tsip->accession) == 12) {
+                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;
@@ -11060,7 +11433,7 @@ static void AddLocusBlock (
 
     if (awp->newLocusLine) {
 
-      if (wgsmaster) {
+      if (wgsmaster && (! is_nz)) {
         sprintf (len, "%ld rc", (long) length);
       } else {
         sprintf (len, "%ld bp", (long) length);
@@ -11333,7 +11706,10 @@ static void AddLocusBlock (
   } 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);
-    FFAddNChar(ffstring, ' ', 15 - 5 - StringLen(locus), FALSE);
+    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 {
@@ -11428,9 +11804,9 @@ static void AddDeflineBlock (
   Asn2gbSectPtr      asp;
   BaseBlockPtr       bbp;
   BioseqPtr          bsp;
-  Char               buf[1024]; 
+  Char               buf[4096]; 
   /*CharPtr          buf;
-  size_t             buflen = 1024;*/ 
+  size_t             buflen = 4096;*/ 
   SeqMgrDescContext  dcontext;
   GBSeqPtr           gbseq;
   ItemInfo           ii;
@@ -11506,6 +11882,7 @@ static void AddAccessionBlock (
 )
 
 {
+  size_t             acclen;
   SeqIdPtr           accn = NULL;
   IntAsn2gbJobPtr    ajp;
   Asn2gbSectPtr      asp;
@@ -11554,9 +11931,13 @@ static void AddAccessionBlock (
         accn = sip;
         tsip = (TextSeqIdPtr) sip->data.ptrvalue;
         if (tsip != NULL) {
-          if (StringLen (tsip->accession) == 12) {
+          acclen = StringLen (tsip->accession);
+          if (acclen == 12) {
             wgsaccn = tsip->accession;
             len = 12;
+          } else if (acclen == 13) {
+            wgsaccn = tsip->accession;
+            len = 13;
           }
         }
         break;
@@ -11661,9 +12042,12 @@ static void AddAccessionBlock (
       mip = (MolInfoPtr) sdp->data.ptrvalue;
       if (mip != NULL && mip->tech == MI_TECH_wgs) {
         StringNCpy_0 (buf, wgsaccn, sizeof (buf));
-        if (StringCmp (buf + len - 6, "000000") != 0) {
+        acclen = StringLen (buf);
+        if (acclen == 12 && StringCmp (buf + len - 6, "000000") != 0) {
           StringCpy (buf + len - 6, "000000");
-        } else if (StringCmp (buf + len - 8, "00000000") != 0) {
+        } 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';
@@ -13253,7 +13637,9 @@ static void AddSourceBlock (
   IntAsn2gbJobPtr    ajp;
   BaseBlockPtr       bbp;
   BioseqPtr          bsp;
+  SeqFeatPtr         cds;
   SeqMgrDescContext  dcontext;
+  BioseqPtr          dna;
   SeqMgrFeatContext  fcontext;
   GBBlockPtr         gbp;
   SeqDescrPtr        sdp;
@@ -13290,6 +13676,29 @@ static void AddSourceBlock (
       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;
+            }
+          }
+        }
+      }
     }
   }
 }
@@ -13360,7 +13769,7 @@ static RefBlockPtr AddPub (
 )
 
 {
-  Char            buf [121];
+  Char            buf [521]; /* increased for consortium in citsub */
   CitArtPtr       cap;
   CitBookPtr      cbp;
   CitGenPtr       cgp;
@@ -13665,6 +14074,7 @@ static int LIBCALLBACK SortReferences (
     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)) {
@@ -13794,6 +14204,20 @@ static CharPtr GetAuthorsPlusConsortium (
   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;
@@ -13810,6 +14234,7 @@ static Boolean LIBCALLBACK GetRefsOnCDS (
   Asn2gbWorkPtr   awp;
   CdsPubsPtr      cpp;
   IntRefBlockPtr  irp;
+  Boolean         okay;
   PubdescPtr      pdp;
   RefBlockPtr     rbp;
 
@@ -13818,21 +14243,30 @@ static Boolean LIBCALLBACK GetRefsOnCDS (
   awp = cpp->awp;
   if (awp == NULL) return TRUE;
 
+  okay = TRUE;
   pdp = (PubdescPtr) sfp->data.value.ptrvalue;
-  rbp = AddPub (awp, &(awp->pubhead), pdp);
-  if (rbp != NULL) {
+  if (awp->format == FTABLE_FMT) {
+    if (HasNoPmidOrMuid (pdp)) {
+      okay = FALSE;
+    }
+  }
 
-    rbp->entityID = context->entityID;
-    rbp->itemID = context->itemID;
-    rbp->itemtype = OBJ_SEQFEAT;
+  if (okay) {
+    rbp = AddPub (awp, &(awp->pubhead), pdp);
+    if (rbp != NULL) {
 
-    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);
+      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;
     }
-    irp->index = 0;
   }
 
   return TRUE;
@@ -13917,6 +14351,12 @@ static void GetRefsOnBioseq (
         }
       }
     }
+    if (awp->format == FTABLE_FMT) {
+      pdp = (PubdescPtr) sdp->data.ptrvalue;
+      if (HasNoPmidOrMuid (pdp)) {
+        okay = FALSE;
+      }
+    }
 
     if (okay) {
       pdp = (PubdescPtr) sdp->data.ptrvalue;
@@ -13939,8 +14379,6 @@ static void GetRefsOnBioseq (
     sdp = SeqMgrGetNextDescriptor (target, sdp, Seq_descr_pub, &dcontext);
   }
 
-  SeqIdFree (sint.id);
-
   /* if protein with no pubs, get pubs applicable to DNA location of CDS */
 
   if (cdsloc != NULL) {
@@ -13950,6 +14388,8 @@ static void GetRefsOnBioseq (
     SeqMgrGetAllOverlappingFeatures (cdsloc, FEATDEF_PUB, NULL, 0, LOCATION_SUBSET, (Pointer) &cp, GetRefsOnCDS);
   }
 
+  SeqIdFree (sint.id);
+
   /* features are indexed on parent if segmented */
 
   bsp = awp->parent;
@@ -13976,6 +14416,12 @@ static void GetRefsOnBioseq (
           takeIt = TRUE;
         }
       }
+      if (awp->format == FTABLE_FMT) {
+        pdp = (PubdescPtr) sdp->data.ptrvalue;
+        if (HasNoPmidOrMuid (pdp)) {
+          takeIt = FALSE;
+        }
+      }
 
       if (takeIt /* stop >= from && stop <= to */) {
 
@@ -13999,7 +14445,7 @@ static void GetRefsOnBioseq (
             right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END);
             strand = SeqLocStrand (ajp->ajp.slp);
             split = FALSE;
-            newloc = SeqLocReMap (sip, ajp->ajp.slp, irp->loc, 0, FALSE);
+            newloc = SeqLocReMapEx (sip, ajp->ajp.slp, irp->loc, 0, FALSE, ajp->masterStyle);
             /*
             newloc = SeqLocCopyRegion (sip, irp->loc, bsp, left, right, strand, &split);
             */
@@ -14089,6 +14535,7 @@ static Boolean AddReferenceBlock (
   ValNodePtr         head = NULL;
   Int2               i;
   IntRefBlockPtr     irp;
+  Boolean            is_aa;
   Boolean            is_embl = FALSE;
   Boolean            is_patent = FALSE;
   IntRefBlockPtr     lastirp;
@@ -14128,6 +14575,8 @@ static Boolean AddReferenceBlock (
     }
   }
 
+  is_aa = (Boolean) ISA_aa (bsp->mol);
+
   if (bsp->repr == Seq_repr_seg) {
 
     /* collect publication descriptors on local parts */
@@ -14254,9 +14703,14 @@ static Boolean AddReferenceBlock (
     if (rbp != NULL) {
       irp = (IntRefBlockPtr) rbp;
       if (irp->justuids) {
-        /* do not allow justuids reference to appear by itself - S79174.1 */
-        excise = TRUE;
-        /* justuids should still combine, even if no authors - S67070.1 */
+        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)) {
@@ -14563,6 +15017,7 @@ static void AddWGSMasterCommentString (
 )
 
 {
+  size_t             acclen;
   BioSourcePtr       biop;
   Char               buf [256];
   SeqMgrDescContext  dcontext;
@@ -14618,10 +15073,14 @@ static void AddWGSMasterCommentString (
     last = "?";
   }
   ver [0] = '\0';
-  if (StringLen (wgsname) == 12) {
+  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 (StringLen (wgsname) == 15) {
+  } else if (acclen == 15) {
     StringCpy (ver, wgsname + 7);
     ver [2] = '\0';
   }
@@ -14630,7 +15089,7 @@ static void AddWGSMasterCommentString (
   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, TRUE, FALSE, TILDE_EXPAND);
+  FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
 
   if (StringCmp (first, last) != 0) {
     sprintf (buf, " and consists of sequences %s-%s.", first, last);
@@ -14736,13 +15195,15 @@ static CharPtr GetStrForBankit (
   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 NCBI review. ";
+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 RefSeq record is provided to represent a collection of whole genome shotgun sequences. ";
+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
@@ -14762,7 +15223,7 @@ static CharPtr GetStatusForRefTrack (
       urf = ufp;
     }
   }
-  if (urf == NULL || urf->choice != 11) return NULL;
+  /* 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) {
@@ -14777,6 +15238,8 @@ static CharPtr GetStatusForRefTrack (
         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 ";
       }
@@ -14793,7 +15256,7 @@ static void AddStrForRefTrack (
 )
 
 {
-  CharPtr       accn, curator = NULL, st;
+  CharPtr       accn, curator = NULL, source = NULL, st;
   ObjectIdPtr   oip;
   UserFieldPtr  ufp, tmp, u, urf = NULL;
   Int2          i = 0;
@@ -14822,14 +15285,21 @@ static void AddStrForRefTrack (
         review = 4;
       } else if (StringICmp (st, "Reviewed") == 0) {
         review = 5;
-      } else if (StringICmp (st, "WGS") == 0) {
+      } 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) {
@@ -14842,74 +15312,120 @@ static void AddStrForRefTrack (
         }
       }
     }
-    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);
-    }
-    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 ( 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);
+      }
+      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, accn, FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString (ffstring, " and ", 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);
+            }
           }
         }
       }
-      FFAddOneString (ffstring, ".", FALSE, FALSE, TILDE_EXPAND);
     }
   }
+  return NULL;
 }
 
 
-static CharPtr reftxt11 = "This model reference sequence was predicted from NCBI contig";
-static CharPtr reftxt12 = "by automated computational analysis";
-static CharPtr reftxt13 = "using gene prediction method:";
+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,
@@ -15113,7 +15629,10 @@ static Boolean GetGeneAndLocus (
   return TRUE;
 }
 
-static CharPtr reftxt21 = "GENOME ANNOTATION REFSEQ:  NCBI contigs are derived from assembled genomic sequence data. They may include both draft and finished sequence.";
+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.";
 
@@ -15492,6 +16011,7 @@ static void AddCommentBlock (
 )
 
 {
+  size_t             acclen;
   IntAsn2gbJobPtr    ajp;
   BioseqPtr          bsp;
   Char               buf [128];
@@ -15508,15 +16028,19 @@ static void AddCommentBlock (
   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;
@@ -15545,31 +16069,137 @@ static void AddCommentBlock (
   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, "NT_", 3) == 0 || StringNCmp(tsip->accession, "NW_", 3) == 0) {
+        if (StringNCmp (tsip->accession, "NC_", 3) == 0) {
+          if (! StringHasNoText (genomeBuildNumber)) {
+            cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+            if (cbp != NULL) {
 
-          cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
-          if (cbp != NULL) {
+              cbp->first = first;
+              first = FALSE;
 
-            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);
+              }
 
-            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);
             }
+          }
 
-            FFAddOneString (ffstring, reftxt21, TRUE, FALSE, TILDE_EXPAND);
+        } else if (StringNCmp(tsip->accession, "NT_", 3) == 0 || StringNCmp(tsip->accession, "NW_", 3) == 0) {
 
-            cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "CC");
-            FFRecycleString(ajp, ffstring);
-            ffstring = FFGetString(ajp);
+          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 ||
@@ -15595,7 +16225,7 @@ static void AddCommentBlock (
                 FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
               }
 
-              FFAddOneString (ffstring, "GENOME ANNOTATION ", FALSE, FALSE, TILDE_IGNORE);
+              FFAddOneString (ffstring, "MODEL ", FALSE, FALSE, TILDE_IGNORE);
 
               if ( GetWWW(ajp) ) {
                 FFAddTextToString (ffstring, "<a href=", ref_link, ">", FALSE, FALSE, TILDE_IGNORE);
@@ -15606,7 +16236,7 @@ static void AddCommentBlock (
               }
               FFAddOneString (ffstring, ":  ", FALSE, FALSE, TILDE_IGNORE);
 
-              FFAddTextToString (ffstring, NULL, reftxt11, " ", 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);
@@ -15617,12 +16247,11 @@ static void AddCommentBlock (
                 FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
               }
 
-              FFAddOneString (ffstring, " ", FALSE, FALSE, TILDE_IGNORE);
-              FFAddOneString (ffstring, reftxt12, FALSE, FALSE, TILDE_IGNORE);
-
+              FFAddOneString (ffstring, ")", FALSE, FALSE, TILDE_IGNORE);
+ 
               if (method != NULL) {
                 FFAddOneString (ffstring, " ", FALSE, FALSE, TILDE_IGNORE);
-                FFAddOneString (ffstring, reftxt13, FALSE, FALSE, TILDE_IGNORE);
+                FFAddOneString (ffstring, reftxt12, FALSE, FALSE, TILDE_IGNORE);
                 FFAddOneString (ffstring, " ", FALSE, FALSE, TILDE_IGNORE);
                 FFAddOneString (ffstring, method, FALSE, FALSE, TILDE_IGNORE);
               }
@@ -15691,14 +16320,23 @@ static void AddCommentBlock (
 
     } 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) {
-        if (StringLen (tsip->accession) == 12) {
+        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') {
@@ -15726,6 +16364,45 @@ static void AddCommentBlock (
 
     } 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);
+        }
+      }
     }
   }
 
@@ -15933,7 +16610,7 @@ static void AddCommentBlock (
       }
     }
 
-    if (hist->replace_ids != NULL && hist->replace_date != NULL) {
+    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) {
@@ -16713,7 +17390,7 @@ static void GetSourcesOnBioseq (
               right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END);
               strand = SeqLocStrand (ajp->ajp.slp);
               split = FALSE;
-              newloc = SeqLocReMap (sip, ajp->ajp.slp, isp->loc, 0, FALSE);
+              newloc = SeqLocReMapEx (sip, ajp->ajp.slp, isp->loc, 0, FALSE, ajp->masterStyle);
               /*
               newloc = SeqLocCopyRegion (sip, isp->loc, bsp, left, right, strand, &split);
               */
@@ -17066,6 +17743,27 @@ static void AddSourceFeatBlock (
 #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));
@@ -17303,7 +18001,7 @@ static void GetFeatsOnCdsProduct (
             slp = SeqLocMerge (nbsp, location, NULL, FALSE, TRUE, FALSE);
             if (slp != NULL) {
               sip = SeqIdParse ("lcl|dummy");
-              newloc = SeqLocReMap (sip, ajp->ajp.slp, slp, 0, FALSE);
+              newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
               SeqIdFree (sip);
               SeqLocFree (slp);
               if (newloc == NULL) {
@@ -17532,7 +18230,7 @@ static Boolean LIBCALLBACK GetFeatsOnBioseq (
       slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, TRUE, FALSE);
       if (slp == NULL) return TRUE;
       sip = SeqIdParse ("lcl|dummy");
-      newloc = SeqLocReMap (sip, ajp->ajp.slp, slp, 0, FALSE);
+      newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
       SeqIdFree (sip);
       SeqLocFree (slp);
       if (newloc == NULL) return TRUE;
@@ -17600,7 +18298,8 @@ static Boolean LIBCALLBACK GetFeatsOnBioseq (
         } else if (sfp->product != NULL) {
           sip = SeqLocIdForProduct (sfp->product);
           if (sip != NULL) {
-            if (sip->choice == SEQID_GI && sip->data.intvalue > 0) {
+            if ((sip->choice == SEQID_GI && sip->data.intvalue > 0) ||
+                sip->choice == SEQID_LOCAL) {
               sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
               oldscope = SeqEntrySetScope (sep);
               prod = BioseqFind (sip);
@@ -17622,7 +18321,7 @@ static Boolean LIBCALLBACK GetFeatsOnBioseq (
                     }
                   }
                 }
-              } else {
+              } 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)) {
@@ -17649,6 +18348,12 @@ static Boolean LIBCALLBACK GetFeatsOnBioseq (
               }
             }
           }
+        } else {
+          if (sfp->excpt && (! StringHasNoText (sfp->except_text))) {
+            if (StringStr (sfp->except_text, "rearrangement required for product") != NULL) {
+              okay = TRUE;
+            }
+          }
         }
       } else {
         okay = TRUE;
@@ -17863,17 +18568,36 @@ static Boolean LIBCALLBACK GetFeatsOnSeg (
 )
 
 {
-  Asn2gbWorkPtr  awp;
-  BioseqPtr      bsp;
-  Uint2          entityID;
-  Int4           from;
-  SeqLocPtr      loc;
-  SeqIdPtr       sip;
-  Int4           to;
+  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;
 
@@ -18684,6 +19408,7 @@ static void DoOneSection (
 )
 
 {
+  size_t               acclen;
   IntAsn2gbJobPtr      ajp;
   Asn2gbSectPtr        asp;
   CharPtr              bases = NULL;
@@ -18785,10 +19510,15 @@ static void DoOneSection (
           sip->choice == SEQID_DDBJ) {
         tsip = (TextSeqIdPtr) sip->data.ptrvalue;
         if (tsip != NULL && tsip->accession != NULL) {
-          if (StringLen (tsip->accession) == 12) {
+          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;
+            }
           }
         }
      } else if (sip->choice == SEQID_OTHER) {
@@ -18818,11 +19548,20 @@ static void DoOneSection (
     }
   }
 
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice == SEQID_OTHER) {
+      isRefSeq = TRUE;
+    }
+  }
+
   /* start exploring and populating paragraphs */
 
   if (awp->format == FTABLE_FMT) {
 
     AddFeatHeaderBlock (awp);
+    if (awp->showRefs) {
+      AddReferenceBlock (awp, isRefSeq);
+    }
     AddFeatureBlock (awp);
 
   } else {
@@ -18875,11 +19614,6 @@ static void DoOneSection (
 
     /* !!! RELEASE_MODE should check return value of AddReferenceBlock !!! */
 
-    for (sip = bsp->id; sip != NULL; sip = sip->next) {
-      if (sip->choice == SEQID_OTHER) {
-        isRefSeq = TRUE;
-      }
-    }
     hasRefs = AddReferenceBlock (awp, isRefSeq);
     if (! hasRefs) {
       if (ajp->flags.needAtLeastOneRef) {
@@ -18916,7 +19650,9 @@ static void DoOneSection (
         }
 
         if (ISA_na (bsp->mol) && ajp->gbseq == NULL) {
-          AddBasecountBlock (awp, bases);
+          if (awp->showBaseCount) {
+            AddBasecountBlock (awp, bases);
+          }
         }
         AddOriginBlock (awp);
 
@@ -18941,7 +19677,9 @@ static void DoOneSection (
       }
 
       if (ISA_na (bsp->mol) && ajp->gbseq == NULL) {
-        AddBasecountBlock (awp, bases);
+        if (awp->showBaseCount) {
+          AddBasecountBlock (awp, bases);
+        }
       }
       AddOriginBlock (awp);
 
@@ -19125,6 +19863,7 @@ static void DoOneBioseq (
 {
   IntAsn2gbJobPtr       ajp;
   Asn2gbWorkPtr         awp;
+  BioseqSetPtr          bssp;
   SeqMgrSegmentContext  context;
   Boolean               contig = FALSE;
   Int4                  from;
@@ -19145,8 +19884,29 @@ static void DoOneBioseq (
 
   if (ISA_na (bsp->mol)) {
     if (ajp->format == GENPEPT_FMT || ajp->format == EMBLPEPT_FMT) return;
+
+    /* only do mRNA feature tables in GPS if targeted to a specific mRNA */
+
+    if (ajp->format == FTABLE_FMT && ajp->skipMrnas) {
+      if (bsp->idx.parenttype == OBJ_BIOSEQSET) {
+        bssp = (BioseqSetPtr) bsp->idx.parentptr;
+        if (bssp != NULL && bssp->_class == BioseqseqSet_class_nuc_prot) {
+          if (bsp->idx.parenttype == OBJ_BIOSEQSET) {
+            bssp = (BioseqSetPtr) bsp->idx.parentptr;
+            if (bssp != NULL && bssp->_class == BioseqseqSet_class_gen_prod_set) {
+              return;
+            }
+          }
+        }
+      }
+    }
+
   } else if (ISA_aa (bsp->mol)) {
     if (ajp->format == GENBANK_FMT || ajp->format == EMBL_FMT) return;
+
+    /* only do protein feature tables if targeted to a specific protein */
+
+    if (ajp->format == FTABLE_FMT && ajp->skipProts) return;
   }
 
   if (awp->style == SEGMENT_STYLE) {
@@ -19376,7 +20136,7 @@ static CharPtr GetGOtext (
         break;
     }
   }
-  if (StringHasNoText (textstr)) return NULL;
+  /* if (StringHasNoText (textstr)) return NULL; */
 
   str = (CharPtr) MemNew (StringLen (textstr) + StringLen (goid) + StringLen (evidence) + 50);
   if (str == NULL) return NULL;
@@ -19397,10 +20157,31 @@ static CharPtr GetGOtext (
     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?) */
@@ -19460,6 +20241,7 @@ static void FormatFeatureBlockQuals (
   ObjectIdPtr        oip;
   Boolean            okay;
   Boolean            only_digits;
+  BioseqPtr          pbsp;
   ValNodePtr         ppr;
   CharPtr            prefix;
   CharPtr            protein_seq = NULL;
@@ -19908,7 +20690,7 @@ static void FormatFeatureBlockQuals (
         }
 
         /* in release_mode, must be of the form 123..4567 or a single-token label,
-           or (technically illegal but common) letters and semicolons */
+           or (technically illegal but common) letters and semicolons - NO LONGER CHECKED */
 
         while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) {
           if (! StringHasNoText (gbq->val)) {
@@ -19927,18 +20709,22 @@ static void FormatFeatureBlockQuals (
                   ptr++;
                 }
                 if ((! ajp->flags.checkQualSyntax) || (ValidateRptUnit (str))) {
-                  FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                  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))) {
-                FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[idx].name, "=",
+                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);
               }
             }
@@ -20081,7 +20867,7 @@ static void FormatFeatureBlockQuals (
                 if (ajp->ajp.slp != NULL) {
                   sip = SeqIdParse ("lcl|dummy");
                   split = FALSE;
-                  newloc = SeqLocReMap (sip, ajp->ajp.slp, slp, 0, FALSE);
+                  newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
  
                   SeqIdFree (sip);
                   if (newloc != NULL) {
@@ -20114,10 +20900,10 @@ static void FormatFeatureBlockQuals (
       case Qual_class_anti_codon :
         slp = qvp [FTQUAL_anticodon].slp;
         newloc = NULL;
-        if (ajp->ajp.slp != NULL) {
+        if (slp != NULL && ajp->ajp.slp != NULL) {
           sip = SeqIdParse ("lcl|dummy");
           split = FALSE;
-          newloc = SeqLocReMap (sip, ajp->ajp.slp, slp, 0, FALSE);
+          newloc = SeqLocReMapEx (sip, ajp->ajp.slp, slp, 0, FALSE, ajp->masterStyle);
           /*
           newloc = SeqLocCopyRegion (sip, slp, bsp, left, right, strand, &split);
           */
@@ -20211,6 +20997,11 @@ static void FormatFeatureBlockQuals (
                   }
                 }
               }
+              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)) {
@@ -20290,6 +21081,16 @@ static void FormatFeatureBlockQuals (
                     }
                   }
                   */
+                } 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);
+                    }
+                  }
                 }
               }
             }
@@ -20497,7 +21298,7 @@ static void FormatFeatureBlockQuals (
               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;
+                    if (entry == NULL || entry->choice != 11) break;
                     ufp = (UserFieldPtr)  entry->data.ptrvalue;
                     str = GetGOtext (ufp);
                     if (! StringHasNoText (str)) {
@@ -20806,10 +21607,73 @@ static void FormatFeatureBlockQuals (
               }
               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);
@@ -20947,7 +21811,9 @@ static CharPtr FormatFeatureBlock (
   SeqLocPtr          newloc;
   Boolean            noLeft;
   Boolean            noRight;
+  SeqMgrFeatContext  ocontext;
   SeqEntryPtr        oldscope;
+  SeqFeatPtr         operon = NULL;
   Uint2              partial;
   SeqMgrFeatContext  pcontext;
   BioseqPtr          prd;
@@ -21135,7 +22001,7 @@ static CharPtr FormatFeatureBlock (
     }
   }
 
-  FFStartPrint(ffstring, afp->format, 5, 21, NULL, 0, 5, 21, "FT", ifp->firstfeat);
+  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 */ ) {
@@ -21161,7 +22027,7 @@ static CharPtr FormatFeatureBlock (
       right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END);
       strand = SeqLocStrand (ajp->ajp.slp);
       split = FALSE;
-      newloc = SeqLocReMap (sip, ajp->ajp.slp, location, 0, FALSE);
+      newloc = SeqLocReMapEx (sip, ajp->ajp.slp, location, 0, FALSE, ajp->masterStyle);
       /*
       newloc = SeqLocCopyRegion (sip, location, bsp, left, right, strand, &split);
       */
@@ -21216,8 +22082,12 @@ static CharPtr FormatFeatureBlock (
       }
     }
 
-    /* a few features cannot show /partial in RELEASE_MODE - later no features will */
+    /* 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:
@@ -21230,6 +22100,7 @@ static CharPtr FormatFeatureBlock (
         break;
       }
     }
+    */
   }
   if (ifp->mapToProt) {
     qvp [FTQUAL_partial].ble = FALSE;
@@ -21271,6 +22142,14 @@ static CharPtr FormatFeatureBlock (
       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 {
 
@@ -21318,10 +22197,26 @@ static CharPtr FormatFeatureBlock (
         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 */
 
@@ -21363,7 +22258,11 @@ static CharPtr FormatFeatureBlock (
                       residue = SeqMapTableConvert (smtp, residue);
                     }
                     if (residue == 'U') {
-                      qvp [FTQUAL_selenocysteine].str = "selenocysteine";
+                      if (ajp->flags.selenocysteineToNote) {
+                        qvp [FTQUAL_selenocysteine_note].str = "selenocysteine";
+                      } else {
+                        qvp [FTQUAL_selenocysteine].ble = TRUE;
+                      }
                     }
                   }
                 }
@@ -21504,6 +22403,43 @@ static CharPtr FormatFeatureBlock (
                 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;
@@ -21574,9 +22510,12 @@ static CharPtr FormatFeatureBlock (
           if (rrp->type == 2) {
             sip = SeqLocIdForProduct (sfp->product);
             if (sip != NULL) {
-              /* for RefSeq records or GenBank not release_mode */
-              if (is_other || (! ajp->flags.forGbRelease)) {
+              /* 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);
             }
@@ -21651,8 +22590,12 @@ static CharPtr FormatFeatureBlock (
                   } else {
                     shift = 1;
                   }
-                  idx = aa - (64 + shift);
-                  if (idx > 0 && idx < 25) {
+                  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) {
@@ -21830,14 +22773,22 @@ static CharPtr FormatFeatureBlock (
 
       /* !!! if ajp->flags.dropIllegalQuals, check CDS list here as well !!! */
       if (ajp->flags.dropIllegalQuals &&
-          (! StringInStringList (qvp [FTQUAL_seqfeat_note].str, validExceptionString)) ) {
+          (! StringInStringList (qvp [FTQUAL_seqfeat_note].str, validExceptionString))) {
         qvp [FTQUAL_exception].str = NULL;
       }
     }
-    if (ajp->flags.dropIllegalQuals &&
-        (! StringInStringList (qvp [FTQUAL_exception].str, validExceptionString))) {
-      qvp [FTQUAL_exception_note].str = qvp [FTQUAL_exception].str;
-      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;
@@ -22041,7 +22992,13 @@ static CharPtr FormatFeatureBlock (
   /* suppress selenocysteine note if already in comment */
 
   if (StringStr (sfp->comment, "selenocysteine") != NULL) {
-    qvp [FTQUAL_selenocysteine].str = 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 */
@@ -22443,7 +23400,7 @@ static Boolean IsSepRefseq (
 }
 
 typedef struct modeflags {
-  Boolean  flags [24];
+  Boolean  flags [25];
 } ModeFlags, PNTR ModeFlagsPtr;
 
 static ModeFlags flagTable [] = {
@@ -22453,28 +23410,28 @@ static ModeFlags flagTable [] = {
    TRUE,  TRUE,  TRUE,  TRUE,  TRUE,
    TRUE,  TRUE,  TRUE,  TRUE,  TRUE,
    TRUE,  TRUE,  TRUE,  TRUE,  TRUE,
-   TRUE,  TRUE,  TRUE,  TRUE},
+   TRUE,  TRUE,  TRUE,  TRUE,  TRUE},
 
   /* ENTREZ_MODE */
   {FALSE, TRUE,  TRUE,  TRUE,  TRUE,
    FALSE, TRUE,  TRUE,  TRUE,  TRUE,
    TRUE,  TRUE,  FALSE, TRUE,  TRUE,
    TRUE,  TRUE,  FALSE, FALSE, TRUE,
-   TRUE,  TRUE,  TRUE,  FALSE},
+   TRUE,  TRUE,  TRUE,  TRUE,  FALSE},
 
   /* SEQUIN_MODE */
   {FALSE, FALSE, FALSE, FALSE, FALSE,
    FALSE, FALSE, TRUE,  FALSE, FALSE,
    FALSE, FALSE, FALSE, FALSE, FALSE,
    FALSE, FALSE, FALSE, FALSE, FALSE,
-   FALSE, FALSE, FALSE, FALSE},
+   FALSE, FALSE, FALSE, FALSE, FALSE},
 
   /* DUMP_MODE */
   {FALSE, FALSE, FALSE, FALSE, FALSE,
    FALSE, FALSE, FALSE, FALSE, FALSE,
    FALSE, FALSE, FALSE, FALSE, FALSE,
    FALSE, FALSE, FALSE, FALSE, FALSE,
-   FALSE, FALSE, FALSE, FALSE}
+   FALSE, FALSE, FALSE, FALSE, FALSE}
 };
 
 static void SetFlagsFromMode (
@@ -22521,6 +23478,7 @@ static void SetFlagsFromMode (
   ajp->flags.hideEmptySource = *(bp++);
   ajp->flags.goQualsToNote = *(bp++);
   ajp->flags.geneSynsToNote = *(bp++);
+  ajp->flags.selenocysteineToNote = *(bp++);
   ajp->flags.forGbRelease = *(bp++);
 
   /* unapproved qualifiers suppressed for flatfile, okay for GBSeq XML */
@@ -22537,7 +23495,13 @@ static void SetFlagsFromMode (
     */
 
     sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID);
-    if (! IsSepRefseq (sep)) {
+    if (IsSepRefseq (sep)) {
+
+      /* selenocysteine always a separate qualifier for RefSeq */
+
+      ajp->flags.selenocysteineToNote = FALSE;
+
+    } else {
 
       /* collaboration unapproved Gene Ontology quals on their own line only for RefSeq */
 
@@ -22583,6 +23547,82 @@ static void CheckVersionWithGi (BioseqPtr bsp, Pointer userdata)
 }
 
 
+typedef struct lookforids {
+  Boolean isGED;
+  Boolean isNTorNW;
+  Boolean isNC;
+  Boolean isTPA;
+  Boolean isNuc;
+  Boolean isProt;
+} LookForIDs, PNTR LookForIDsPtr;
+
+static void LookForSeqIDs (BioseqPtr bsp, Pointer userdata)
+
+{
+  LookForIDsPtr  lfip;
+  SeqIdPtr       sip;
+  TextSeqIdPtr   tsip;
+
+  lfip = (LookForIDsPtr) userdata;
+  if (ISA_na (bsp->mol)) {
+    lfip->isNuc = TRUE;
+  }
+  if (ISA_aa (bsp->mol)) {
+    lfip->isProt = TRUE;
+  }
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    switch (sip->choice) {
+      case SEQID_GENBANK :
+      case SEQID_EMBL :
+      case SEQID_DDBJ :
+        lfip->isGED = TRUE;
+        break;
+      case SEQID_TPG :
+      case SEQID_TPE :
+      case SEQID_TPD :
+        lfip->isTPA = TRUE;
+        break;
+      case SEQID_OTHER :
+        tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+        if (tsip != NULL) {
+          if (StringNCmp (tsip->accession, "NC_", 3) == 0) {
+            lfip->isNC = TRUE;
+          } else if (StringNCmp (tsip->accession, "NT_", 3) == 0) {
+            lfip->isNTorNW = TRUE;
+          } else if (StringNCmp (tsip->accession, "NW_", 3) == 0) {
+            lfip->isNTorNW = TRUE;
+          }
+        }
+        break;
+      default :
+        break;
+    }
+  }
+}
+
+static void LookForGEDetc (
+  SeqEntryPtr topsep,
+  BoolPtr isGED,
+  BoolPtr isNTorNW,
+  BoolPtr isNC,
+  BoolPtr isTPA,
+  BoolPtr isNuc,
+  BoolPtr isProt
+)
+
+{
+  LookForIDs  lfi;
+
+  MemSet ((Pointer) &lfi, 0, sizeof (LookForIDs));
+  VisitBioseqsInSep (topsep, (Pointer) &lfi, LookForSeqIDs);
+  *isGED = lfi.isGED;
+  *isNTorNW = lfi.isNTorNW;
+  *isNC = lfi.isNC;
+  *isTPA = lfi.isTPA;
+  *isNuc = lfi.isNuc;
+  *isProt = lfi.isProt;
+}
+
 #define FEAT_FETCH_MASK (ONLY_NEAR_FEATURES | FAR_FEATURES_SUPPRESS | NEAR_FEATURES_SUPPRESS)
 #define HTML_XML_ASN_MASK (CREATE_HTML_FLATFILE | CREATE_XML_GBSEQ_FILE | CREATE_ASN_GBSEQ_FILE)
 #define GENE_RIF_MASK (HIDE_GENE_RIFS | ONLY_GENE_RIFS | LATEST_GENE_RIFS)
@@ -22610,6 +23650,12 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   GBSeqPtr         gbseq = NULL;
   Int4             i;
   IndxPtr          index = NULL;
+  Boolean          isGED;
+  Boolean          isNTorNW;
+  Boolean          isNC;
+  Boolean          isNuc;
+  Boolean          isProt;
+  Boolean          isTPA;
   Int4             j;
   Int4             k;
   Boolean          lockFarComp;
@@ -22631,6 +23677,8 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   SubmitBlockPtr   sbp;
   SeqEntryPtr      sep;
   SeqIntPtr        sintp;
+  Boolean          skipMrnas = FALSE;
+  Boolean          skipProts = FALSE;
   SeqSubmitPtr     ssp;
   BioseqSetPtr     topbssp;
   ValNodePtr       vnp;
@@ -22668,6 +23716,14 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
     entityID = ObjMgrGetEntityIDForPointer (bsp);
   } else if (bssp != NULL) {
     entityID = ObjMgrGetEntityIDForPointer (bssp);
+    if (format == FTABLE_FMT) {
+      skipProts = TRUE;
+      skipMrnas = TRUE;
+    }
+  }
+  if ((Boolean) ((custom & SHOW_PROT_FTABLE) != 0)) {
+    skipProts = FALSE;
+    skipMrnas = FALSE;
   }
 
   if (entityID == 0) return NULL;
@@ -22727,7 +23783,11 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
     /* lock all bioseqs in advance, including remote genome components */
 
     sep = GetTopSeqEntryForEntityID (entityID);
-    ajp->lockedBspList = LockFarComponentsEx (sep, lockFarComp, lockFarLocs, lockFarProd);
+    if (ajp->ajp.slp != NULL && lockFarComp) {
+      ajp->lockedBspList = LockFarComponentsEx (sep, FALSE, lockFarLocs, lockFarProd, ajp->ajp.slp);
+    } else {
+      ajp->lockedBspList = LockFarComponentsEx (sep, lockFarComp, lockFarLocs, lockFarProd, NULL);
+    }
   }
 
   lookupFarComp = (Boolean) ((locks & LOOKUP_FAR_COMPONENTS) != 0);
@@ -22753,6 +23813,8 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   }
 
   ajp->relModeError = FALSE;
+  ajp->skipProts = skipProts;
+  ajp->skipMrnas = skipMrnas;
 
   MemSet ((Pointer) (&aw), 0, sizeof (Asn2gbWork));
   aw.ajp = ajp;
@@ -22767,9 +23829,40 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   aw.showconfeats = (Boolean) ((flags & SHOW_CONTIG_FEATURES) != 0);
   aw.showconsource = (Boolean) ((flags & SHOW_CONTIG_SOURCES) != 0);
 
-  aw.onlyNearFeats = (Boolean) ((flags & FEAT_FETCH_MASK) == ONLY_NEAR_FEATURES);
-  aw.farFeatsSuppress = (Boolean) ((flags & FEAT_FETCH_MASK) == FAR_FEATURES_SUPPRESS);
-  aw.nearFeatsSuppress = (Boolean) ((flags & FEAT_FETCH_MASK) == NEAR_FEATURES_SUPPRESS);
+  aw.format = format;
+  aw.mode = mode;
+  aw.style = style;
+
+  sep = GetTopSeqEntryForEntityID (entityID);
+
+  /* special types of records override feature fetching parameters */
+
+  aw.onlyNearFeats = FALSE;
+  aw.farFeatsSuppress = FALSE;
+  aw.nearFeatsSuppress = FALSE;
+  LookForGEDetc (sep, &isGED, &isNTorNW, &isNC, &isTPA, &isNuc, &isProt);
+  if (ajp->ajp.slp != NULL) {
+    /* specified location obeys fetching parameters, for now */
+    aw.onlyNearFeats = (Boolean) ((flags & FEAT_FETCH_MASK) == ONLY_NEAR_FEATURES);
+    aw.farFeatsSuppress = (Boolean) ((flags & FEAT_FETCH_MASK) == FAR_FEATURES_SUPPRESS);
+    aw.nearFeatsSuppress = (Boolean) ((flags & FEAT_FETCH_MASK) == NEAR_FEATURES_SUPPRESS);
+  } else if (mode == ENTREZ_MODE) {
+    /* entrez_mode overrides settings to avoid far fetches */
+    aw.onlyNearFeats = TRUE;
+    aw.showconfeats = TRUE;
+  } else if (isNTorNW || isTPA) {
+    aw.onlyNearFeats = TRUE;
+  } else if (isNC) {
+    if ((Boolean) ((flags & FEAT_FETCH_MASK) == ONLY_NEAR_FEATURES)) {
+      aw.onlyNearFeats = TRUE;
+    } else {
+      aw.nearFeatsSuppress = TRUE;
+    }
+  } else {
+    aw.onlyNearFeats = (Boolean) ((flags & FEAT_FETCH_MASK) == ONLY_NEAR_FEATURES);
+    aw.farFeatsSuppress = (Boolean) ((flags & FEAT_FETCH_MASK) == FAR_FEATURES_SUPPRESS);
+    aw.nearFeatsSuppress = (Boolean) ((flags & FEAT_FETCH_MASK) == NEAR_FEATURES_SUPPRESS);
+  }
 
   aw.hideImpFeats = (Boolean) ((custom & HIDE_IMP_FEATS) != 0);
   aw.hideRemImpFeats = (Boolean) ((custom & HIDE_REM_IMP_FEATS) != 0);
@@ -22789,8 +23882,9 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   aw.onlyGeneRIFs = (Boolean) ((custom & GENE_RIF_MASK) == ONLY_GENE_RIFS);
   aw.latestGeneRIFs = (Boolean) ((custom & GENE_RIF_MASK) == LATEST_GENE_RIFS);
 
+  aw.showRefs = (Boolean) ((custom & SHOW_FTABLE_REFS) != 0);
+
   aw.isGPS = FALSE;
-  sep = GetTopSeqEntryForEntityID (entityID);
   if (sep != NULL && IS_Bioseq_set (sep)) {
     topbssp = (BioseqSetPtr) sep->data.ptrvalue;
     if (topbssp != NULL && topbssp->_class == BioseqseqSet_class_gen_prod_set) {
@@ -22808,17 +23902,18 @@ NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup (
   */
 
   aw.newLocusLine = TRUE;
+  aw.showBaseCount = FALSE;
 
-  if ((Boolean) (flags & DDBJ_VARIANT_FORMAT) != 0) {
+  if ((Boolean) ((flags & DDBJ_VARIANT_FORMAT) != 0)) {
     aw.citSubsFirst = TRUE;
     aw.hideGeneFeats = TRUE;
     aw.newLocusLine = FALSE;
+    aw.showBaseCount = TRUE;
     ajp->newSourceOrg = FALSE;
   }
-
-  aw.format = format;
-  aw.mode = mode;
-  aw.style = style;
+  if (mode == SEQUIN_MODE || mode == DUMP_MODE) {
+    aw.showBaseCount = TRUE;
+  }
 
   aw.hup = FALSE;
   aw.ssp = NULL;
@@ -22952,17 +24047,32 @@ static void PrintFtableIntervals (
 )
 
 {
-  Boolean    partial5;
-  Boolean    partial3;
-  SeqLocPtr  slp;
-  Int4       start;
-  Int4       stop;
-  Char       str [64];
-  Char       str1 [32];
-  Char       str2 [32];
+  IntFuzzPtr  ifp;
+  Boolean     partial5;
+  Boolean     partial3;
+  SeqLocPtr   slp;
+  SeqPntPtr   spp;
+  Int4        start;
+  Int4        stop;
+  Char        str [64];
+  Char        str1 [32];
+  Char        str2 [32];
 
   if (head == NULL || target == NULL || location == NULL || label == NULL) return;
 
+  if (location->choice == SEQLOC_PNT) {
+    spp = (SeqPntPtr) location->data.ptrvalue;
+    if (spp != NULL) {
+      ifp = spp->fuzz;
+      if (ifp != NULL && ifp->choice == 4 && ifp->a == 3) {
+        sprintf (str, "%ld^\t%ld\t%s\n", (long) (spp->point + 1),
+                 (long) (spp->point + 2), label);
+        ValNodeCopyStr (head, 0, str);
+        return;
+      }
+    }
+  }
+
   slp = SeqLocFindNext (location, NULL);
   if (slp == NULL) return;
 
@@ -23074,7 +24184,7 @@ static void PrintFTUserFld (
           break;
       }
     }
-    if (StringHasNoText (textstr)) break;
+    /* if (StringHasNoText (textstr)) break; */
   
     str = (CharPtr) MemNew (StringLen (textstr) + StringLen (goid) + StringLen (evidence) + 40);
     if (str == NULL) return;
@@ -23182,6 +24292,33 @@ static void PrintFTCodeBreak (
   }
 }
 
+static SeqIdPtr SeqIdFindForTable (SeqIdPtr sip)
+
+{
+  Uint1  order [NUM_SEQID];
+
+  SeqIdBestRank (order, NUM_SEQID);
+  order [SEQID_LOCAL] = 20;
+  order [SEQID_GENBANK] = 5;
+  order [SEQID_EMBL] = 5;
+  order [SEQID_PIR] = 5;
+  order [SEQID_SWISSPROT] = 5;
+  order [SEQID_DDBJ] = 5;
+  order [SEQID_PRF] = 5;
+  order [SEQID_PDB] = 5;
+  order [SEQID_TPG] = 5;
+  order [SEQID_TPE] = 5;
+  order [SEQID_TPD] = 5;
+  order [SEQID_PATENT] = 10;
+  order [SEQID_OTHER] = 8;
+  order [SEQID_GENERAL] = 15;
+  order [SEQID_GIBBSQ] = 15;
+  order [SEQID_GIBBMT] = 15;
+  order [SEQID_GIIM] = 20;
+  order [SEQID_GI] = 20;
+  return SeqIdSelect (sip, order, NUM_SEQID);
+}
+
 /* #define MAKE_MRNA_GPS_FEAT */
 
 static void PrintFtableLocAndQuals (
@@ -23193,28 +24330,39 @@ static void PrintFtableLocAndQuals (
 )
 
 {
-  CodeBreakPtr  cbp;
-  CdRegionPtr   crp;
-  DbtagPtr      dbt;
-  GBQualPtr     gbq;
-  ValNodePtr    geneorprotdb;
-  GeneRefPtr    grp;
-  CharPtr       label;
-  ObjectIdPtr   oip;
-  BioseqPtr     prod;
-  SeqFeatPtr    prot;
-  ProtRefPtr    prp;
-  Boolean       pseudo;
-  RnaRefPtr     rrp;
-  SeqIdPtr      sip;
-  SeqIdPtr      sip2;
-  Char          str [256];
-  Char          tmp [300];
-  tRNAPtr       trp;
-  ValNodePtr    vnp;
+  Int2               bondidx;
+  BioseqSetPtr       bssp;
+  CodeBreakPtr       cbp;
+  BioseqPtr          cdna;
+  SeqFeatPtr         cds;
+  CdRegionPtr        crp;
+  SeqMgrDescContext  dcontext;
+  DbtagPtr           dbt;
+  SeqMgrFeatContext  fcontext;
+  GBQualPtr          gbq;
+  ValNodePtr         geneorprotdb;
+  GeneRefPtr         grp;
+  Boolean            is_gps_genomic = FALSE;
+  CharPtr            label;
+  MolInfoPtr         mip;
+  ObjectIdPtr        oip;
+  BioseqPtr          prod;
+  SeqFeatPtr         prot;
+  ProtRefPtr         prp;
+  Boolean            pseudo;
+  RnaRefPtr          rrp;
+  SeqDescrPtr        sdp;
+  Int4               sec_str;
+  SeqIdPtr           sip;
+  SeqIdPtr           sip2;
+  Int2               siteidx;
+  Char               str [256];
+  Char               tmp [300];
+  tRNAPtr            trp;
+  ValNodePtr         vnp;
 #ifdef MAKE_MRNA_GPS_FEAT
-  CharPtr       rnaid;
-  CharPtr       rnaprod;
+  CharPtr            rnaid;
+  CharPtr            rnaprod;
 #endif
 
   if (head == NULL || target == NULL || sfp == NULL || context == NULL) return;
@@ -23227,6 +24375,23 @@ static void PrintFtableLocAndQuals (
     label = "???";
   }
 
+  /* check if genomic sequence in genomic product set */
+
+  if (target->idx.parenttype == OBJ_BIOSEQSET) {
+    bssp = (BioseqSetPtr) target->idx.parentptr;
+    if (bssp != NULL && bssp->_class == BioseqseqSet_class_gen_prod_set) {
+      sdp = SeqMgrGetNextDescriptor (target, NULL, Seq_descr_molinfo, &dcontext);
+      if (sdp != NULL) {
+        mip = (MolInfoPtr) sdp->data.ptrvalue;
+        if (mip != NULL && mip->biomol == MOLECULE_TYPE_GENOMIC) {
+#ifndef MAKE_MRNA_GPS_FEAT
+          is_gps_genomic = TRUE;
+#endif
+        }
+      }
+    }
+  }
+
   PrintFtableIntervals (head, target, sfp->location, label);
 
   geneorprotdb = NULL;
@@ -23335,7 +24500,8 @@ static void PrintFtableLocAndQuals (
         }
       }
       if (prod != NULL) {
-        for (sip = prod->id; sip != NULL; sip = sip->next) {
+        sip = SeqIdFindForTable (prod->id);
+        if (sip != NULL) {
           if (sip->choice == SEQID_GENBANK ||
               sip->choice == SEQID_EMBL ||
               sip->choice == SEQID_DDBJ ||
@@ -23380,6 +24546,39 @@ static void PrintFtableLocAndQuals (
             }
           }
         }
+        if (is_gps_genomic) {
+          cds = SeqMgrGetCDSgivenProduct (prod, NULL);
+          if (cds != NULL) {
+            cdna = BioseqFindFromSeqLoc (cds->location);
+            if (cdna != NULL) {
+              sip = SeqIdFindWorst (cdna->id);
+              if (sip != NULL) {
+                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) {
+                  if (SeqIdWrite (sip, str, PRINTID_TEXTID_ACC_VER, sizeof (str)) != NULL) {
+                    sprintf (tmp, "\t\t\ttranscript_id\t%s\n", str);
+                    ValNodeCopyStr (head, 0, tmp);
+                  }
+                } else if (sip->choice == SEQID_LOCAL && (! ajp->flags.suppressLocalID)) {
+                  if (SeqIdWrite (sip, str, PRINTID_TEXTID_ACC_VER, sizeof (str)) != NULL) {
+                    sprintf (tmp, "\t\t\ttranscript_id\tlcl|%s\n", str);
+                    ValNodeCopyStr (head, 0, tmp);
+                  }
+                } else if (sip->choice == SEQID_GENERAL) {
+                  if (SeqIdWrite (sip, str, PRINTID_FASTA_GENERAL, sizeof (str)) != NULL) {
+                    sprintf (tmp, "\t\t\ttranscript_id\t%s\n", str);
+                    ValNodeCopyStr (head, 0, tmp);
+                  }
+                }
+              }
+            }
+          }
+        }
       } else if (sfp->product != NULL) {
         sip = SeqLocId (sfp->product);
         if (sip != NULL) {
@@ -23441,7 +24640,8 @@ static void PrintFtableLocAndQuals (
         }
       }
       if (prod != NULL) {
-        for (sip = prod->id; sip != NULL; sip = sip->next) {
+        sip = SeqIdFindForTable (prod->id);
+        if (sip != NULL) {
           if (sip->choice == SEQID_GENBANK ||
               sip->choice == SEQID_EMBL ||
               sip->choice == SEQID_DDBJ ||
@@ -23465,6 +24665,39 @@ static void PrintFtableLocAndQuals (
             }
           }
         }
+        if (is_gps_genomic) {
+          cds = SeqMgrGetNextFeature (prod, NULL, SEQFEAT_CDREGION, 0, &fcontext);
+          if (cds != NULL && SeqMgrGetNextFeature (prod, cds, SEQFEAT_CDREGION, 0, &fcontext) == NULL) {
+            prod = BioseqFindFromSeqLoc (cds->product);
+            if (prod != NULL) {
+              sip = SeqIdFindWorst (prod->id);
+              if (sip != NULL) {
+                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) {
+                  if (SeqIdWrite (sip, str, PRINTID_TEXTID_ACC_VER, sizeof (str)) != NULL) {
+                    sprintf (tmp, "\t\t\tprotein_id\t%s\n", str);
+                    ValNodeCopyStr (head, 0, tmp);
+                  }
+                } else if (sip->choice == SEQID_LOCAL && (! ajp->flags.suppressLocalID)) {
+                  if (SeqIdWrite (sip, str, PRINTID_TEXTID_ACC_VER, sizeof (str)) != NULL) {
+                    sprintf (tmp, "\t\t\tprotein_id\tlcl|%s\n", str);
+                    ValNodeCopyStr (head, 0, tmp);
+                  }
+                } else if (sip->choice == SEQID_GENERAL) {
+                  if (SeqIdWrite (sip, str, PRINTID_FASTA_GENERAL, sizeof (str)) != NULL) {
+                    sprintf (tmp, "\t\t\tprotein_id\t%s\n", str);
+                    ValNodeCopyStr (head, 0, tmp);
+                  }
+                }
+              }
+            }
+          }
+        }
       } else if (sfp->product != NULL) {
         sip = SeqLocId (sfp->product);
         if (sip != NULL) {
@@ -23499,6 +24732,87 @@ static void PrintFtableLocAndQuals (
         }
       }
       break;
+    case SEQFEAT_PROT :
+      prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+      if (prp != NULL) {
+        if (prp->name != NULL) {
+          for (vnp = prp->name; vnp != NULL; vnp = vnp->next) {
+            StringNCpy_0 (str, (CharPtr) vnp->data.ptrvalue, sizeof (str));
+            if (! StringHasNoText (str)) {
+              sprintf (tmp, "\t\t\tproduct\t%s\n", str);
+              ValNodeCopyStr (head, 0, tmp);
+            }
+          }
+        }
+        if (prp->desc != NULL) {
+          StringNCpy_0 (str, prp->desc, sizeof (str));
+          if (! StringHasNoText (str)) {
+            sprintf (tmp, "\t\t\tprot_desc\t%s\n", str);
+            ValNodeCopyStr (head, 0, tmp);
+          }
+        }
+        for (vnp = prp->activity; vnp != NULL; vnp = vnp->next) {
+          StringNCpy_0 (str, (CharPtr) vnp->data.ptrvalue, sizeof (str));
+          if (! StringHasNoText (str)) {
+            sprintf (tmp, "\t\t\tfunction\t%s\n", str);
+            ValNodeCopyStr (head, 0, tmp);
+          }
+        }
+        for (vnp = prp->ec; vnp != NULL; vnp = vnp->next) {
+          StringNCpy_0 (str, (CharPtr) vnp->data.ptrvalue, sizeof (str));
+          if (! StringHasNoText (str)) {
+            sprintf (tmp, "\t\t\tEC_number\t%s\n", str);
+            ValNodeCopyStr (head, 0, tmp);
+          }
+        }
+      }
+      StringNCpy_0 (str, sfp->comment, sizeof (str));
+      if (! StringHasNoText (str)) {
+        sprintf (tmp, "\t\t\tprot_note\t%s\n", str);
+        ValNodeCopyStr (head, 0, tmp);
+      }
+      break;
+    case SEQFEAT_REGION :
+      StringNCpy_0 (str, (CharPtr) sfp->data.value.ptrvalue, sizeof (str));
+      if (! StringHasNoText (str)) {
+        sprintf (tmp, "\t\t\tregion\t%s\n", str);
+        ValNodeCopyStr (head, 0, tmp);
+      }
+      break;
+    case SEQFEAT_BOND :
+      bondidx = (Int2) sfp->data.value.intvalue;
+      if (bondidx == 255) {
+        bondidx = 5;
+      }
+      if (bondidx > 0 && bondidx < 6) {
+        sprintf (tmp, "\t\t\tbond_type\t%s\n", bondList [bondidx]);
+        ValNodeCopyStr (head, 0, tmp);
+      }
+      break;
+    case SEQFEAT_SITE :
+      siteidx = (Int2) sfp->data.value.intvalue;
+      if (siteidx == 255) {
+        siteidx = 26;
+      }
+      if (siteidx > 0 && siteidx < 27) {
+        sprintf (tmp, "\t\t\tsite_type\t%s\n", siteList [siteidx]);
+        ValNodeCopyStr (head, 0, tmp);
+      }
+      break;
+    case SEQFEAT_PSEC_STR :
+      sec_str = (Int2) sfp->data.value.intvalue;
+      if (sec_str > 0 && sec_str <= 3) {
+        sprintf (tmp, "\t\t\tsec_str_type\t%s\n", secStrText [sec_str]);
+        ValNodeCopyStr (head, 0, tmp);
+      }
+      break;
+    case SEQFEAT_HET :
+      StringNCpy_0 (str, (CharPtr) sfp->data.value.ptrvalue, sizeof (str));
+      if (! StringHasNoText (str)) {
+        sprintf (tmp, "\t\t\theterogen\t%s\n", str);
+        ValNodeCopyStr (head, 0, tmp);
+      }
+      break;
     default :
       break;
   }
@@ -23655,6 +24969,7 @@ NLM_EXTERN CharPtr asn2gnbk_format (
   ValNodePtr         head;
   IntAsn2gbJobPtr    iajp;
   Char               id [42];
+  IntRefBlockPtr     irp;
   size_t             max;
   SeqEntryPtr        oldscope;
   QualValPtr         qv;
@@ -23662,6 +24977,7 @@ NLM_EXTERN CharPtr asn2gnbk_format (
   SeqEntryPtr        sep;
   SeqFeatPtr         sfp;
   SeqIdPtr           sip;
+  SeqIdPtr           sip2;
   CharPtr            str = NULL;
   BioseqPtr          target;
   Char               tmp [53];
@@ -23717,12 +25033,37 @@ NLM_EXTERN CharPtr asn2gnbk_format (
 
       if (blocktype == FEATHEADER_BLOCK) {
         sip = SeqIdFindBest (target->id, 0);
+        if (sip != NULL && sip->choice == SEQID_GI) {
+          sip2 = GetSeqIdForGI (sip->data.intvalue);
+          if (sip2 != NULL) {
+            sip = sip2;
+          }
+        }
         SeqIdWrite (sip, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
         if (! StringHasNoText (id)) {
           sprintf (tmp, ">Feature %s\n", id);
           str = StringSave (tmp);
         }
 
+      } else if (blocktype == REFERENCE_BLOCK) {
+
+        irp = (IntRefBlockPtr) bbp;
+        if (irp->loc != NULL) {
+          if (irp->rb.pmid != 0 || irp->rb.muid != 0) {
+            head = NULL;
+            PrintFtableIntervals (&head, target, irp->loc, "REFERENCE");
+            if (irp->rb.pmid != 0) {
+              sprintf (tmp, "\t\t\tpmid\t%ld\n", (long) irp->rb.pmid);
+              ValNodeCopyStr (&head, 0, tmp);
+            } else if (irp->rb.muid != 0) {
+              sprintf (tmp, "\t\t\tmuid\t%ld\n", (long) irp->rb.muid);
+              ValNodeCopyStr (&head, 0, tmp);
+            }
+            str = MergeValNodeStrings (head);
+            ValNodeFreeData (head);
+          }
+        }
+
       } else if (blocktype == FEATURE_BLOCK) {
 
         sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext);
@@ -23968,7 +25309,11 @@ NLM_EXTERN Boolean SeqEntryToGnbk (
 
   if (lockFarComp || lockFarLocs || lockFarProd) {
     locks = locks ^ (LOCK_FAR_COMPONENTS | LOCK_FAR_LOCATIONS | LOCK_FAR_PRODUCTS);
-    bsplist = LockFarComponentsEx (sep, lockFarComp, lockFarLocs, lockFarProd);
+    if (slp != NULL && lockFarComp) {
+      bsplist = LockFarComponentsEx (sep, FALSE, lockFarLocs, lockFarProd, slp);
+    } else {
+      bsplist = LockFarComponentsEx (sep, lockFarComp, lockFarLocs, lockFarProd, NULL);
+    }
   }
 
   lookupFarComp = (Boolean) ((locks & LOOKUP_FAR_COMPONENTS) != 0);
diff --git a/api/asn2gnbk.h b/api/asn2gnbk.h
index 0a1c056e..1c2bfc61 100644
--- a/api/asn2gnbk.h
+++ b/api/asn2gnbk.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 6.52 $
+* $Revision: 6.53 $
 *
 * File Description:  New GenBank flatfile generator
 *
@@ -142,6 +142,9 @@ typedef unsigned long CstType;
 #define ONLY_GENE_RIFS         2048
 #define LATEST_GENE_RIFS       3072
 
+#define SHOW_PROT_FTABLE       4096
+#define SHOW_FTABLE_REFS       8192
+
 /* opaque pointer for special extensions */
 
 struct XtraData;
diff --git a/api/edutil.c b/api/edutil.c
index b0227a9a..b6ea951e 100644
--- a/api/edutil.c
+++ b/api/edutil.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 2/4/94
 *
-* $Revision: 6.19 $
+* $Revision: 6.20 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -39,6 +39,9 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: edutil.c,v $
+* Revision 6.20  2003/06/03 20:25:34  kans
+* SeqLocReplaceID works on bonds if both ends bonded to the same Seq-id
+*
 * Revision 6.19  2003/02/10 22:57:45  kans
 * added BioseqCopyEx, which takes a BioseqPtr instead of a SeqIdPtr for the source
 *
@@ -3490,6 +3493,7 @@ NLM_EXTERN SeqLocPtr SeqLocReplaceID (SeqLocPtr slp, SeqIdPtr new_sip)
   SeqLocPtr        curr;
   PackSeqPntPtr    pspp;
   SeqIntPtr        target_sit;
+  SeqBondPtr       sbp;
   SeqPntPtr        spp;
 
   switch (slp->choice) {
@@ -3519,10 +3523,23 @@ NLM_EXTERN SeqLocPtr SeqLocReplaceID (SeqLocPtr slp, SeqIdPtr new_sip)
         target_sit->id = SeqIdDup (new_sip);
         break;
      case SEQLOC_PNT :
-        spp = (SeqPntPtr)slp->data.ptrvalue;
+        spp = (SeqPntPtr) slp->data.ptrvalue;
         SeqIdFree(spp->id);
         spp->id = SeqIdDup(new_sip);
         break;
+     case SEQLOC_BOND :
+        sbp = (SeqBondPtr) slp->data.ptrvalue;
+        if (sbp == NULL || sbp->a == NULL || sbp->b == NULL) break;
+        /* only do this if both ends bonded to same Seq-id */
+        if (SeqIdMatch (sbp->a->id, sbp->b->id)) {
+          spp = sbp->a;
+          SeqIdFree(spp->id);
+          spp->id = SeqIdDup(new_sip);
+          spp = sbp->b;
+          SeqIdFree(spp->id);
+          spp->id = SeqIdDup(new_sip);
+        }
+        break;
      default :
         break;
   }
diff --git a/api/explore.h b/api/explore.h
index a4923d10..5d8ed27d 100644
--- a/api/explore.h
+++ b/api/explore.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 6/30/98
 *
-* $Revision: 6.43 $
+* $Revision: 6.45 $
 *
 * File Description:  Reengineered and optimized exploration functions
 *                      to be used for future code
@@ -208,6 +208,11 @@ NLM_EXTERN SeqFeatPtr LIBCALL SeqMgrGetOverlappingGene (
   SeqMgrFeatContext PNTR context
 );
 
+NLM_EXTERN SeqFeatPtr LIBCALL SeqMgrGetOverlappingOperon (
+  SeqLocPtr slp,
+  SeqMgrFeatContext PNTR context
+);
+
 /*****************************************************************************
 *
 *   SeqMgrGetOverlappingXXX returns the overlapping mRNA/CDS/publication/biosource
@@ -482,6 +487,7 @@ NLM_EXTERN Boolean LIBCALL SeqMgrGetBioseqContext (
 #define LOCATION_SUBSET  2 /* SeqLocAinB must be satisfied, no boundary checking */
 #define CHECK_INTERVALS  3 /* SeqLocAinB plus internal exon-intron boundaries must match */
 #define INTERVAL_OVERLAP 4 /* at least one pair of intervals must overlap */
+#define COMMON_INTERVAL  5 /* at least one pair of intervals must match */
 
 NLM_EXTERN VoidPtr LIBCALL SeqMgrBuildFeatureIndex (
   BioseqPtr bsp,
diff --git a/api/fdlKludge.h b/api/fdlKludge.h
index 13d3c8bf..96783f80 100644
--- a/api/fdlKludge.h
+++ b/api/fdlKludge.h
@@ -28,13 +28,25 @@
 *
 * Version Creation Date:   10/15/01
 *
-* $Revision: 6.8 $
+* $Revision: 6.12 $
 *
 * File Description:
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: fdlKludge.h,v $
+* Revision 6.12  2003/06/11 20:15:45  jianye
+* changed unigene linkout
+*
+* Revision 6.11  2003/06/02 20:02:23  jianye
+* Added geo linkout
+*
+* Revision 6.10  2003/05/05 19:33:54  jianye
+* Change url for structure linkout
+*
+* Revision 6.9  2003/04/21 21:49:37  jianye
+* changed some url
+*
 * Revision 6.8  2003/04/14 20:43:22  jianye
 * Adde geo url and modified structure linkout url
 *
@@ -63,7 +75,6 @@
 
 #include <objloc.h>
 
-#define total_linkout 4
 
 #define linkout_locuslink (1<<0)
 #define linkout_unigene   (1<<1)
@@ -72,12 +83,12 @@
 
 /* url for linkout*/
 #define URL_LocusLink "<a href=\"http://www.ncbi.nlm.nih.gov/LocusLink/list.cgi?Q=%d%s\"><img border=0 height=16 width=16 src=\"/blast/images/L.gif\" alt=\"LocusLink info\"></a>"
-#define URL_Unigene "<a href=\"http://www.ncbi.nlm.nih.gov/UniGene/query.cgi?ORG=%s&TEXT=@gi(%d)\"><img border=0 height=16 width=16 src=\"/blast/images/U.gif\" alt=\"UniGene info\"></a>"
-
-#define URL_Structure "<a href=\"http://ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi?blast_RID=%s&blast_rep_gi=%d&hit=%d&blast_CD_RID=%s&blast_view=%s&hsp=0&taxname=%s&client=blast\"><img border=0 height=16 width=16 src=\"http://ncbi.nlm.nih.gov/Structure/cblast/str_link.gif\" alt=\"Related structures\"></a>"
+#define URL_Unigene "<a href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=%d[Nucleotide+UID]\"><img border=0 height=16 width=16 src=\"/blast/images/U.gif\" alt=\"UniGene info\"></a>"
 
-#define URL_Structure_Overview "<a href=\"http://ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi?blast_RID=%s&blast_rep_gi=%d&hit=%d&blast_CD_RID=%s&blast_view=%s&hsp=0&taxname=%s&client=blast\">Related Structures</a>"
+#define URL_Structure "<a href=\"http://www.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi?blast_RID=%s&blast_rep_gi=%d&hit=%d&blast_CD_RID=%s&blast_view=%s&hsp=0&taxname=%s&client=blast\"><img border=0 height=16 width=16 src=\"http://www.ncbi.nlm.nih.gov/Structure/cblast/str_link.gif\" alt=\"Related structures\"></a>"
 
-#define URL_Geo "<a href=\"http://boris.ncbi.nlm.nih.gov:2441/entrez/testers/edgar/query.fcgi?term=%d[gi]&db=geo\"><img border=0 height=16 width=16 src=\"/blast/images/G.gif\" alt=\"Geo\"></a>"
+#define URL_Structure_Overview "<a href=\"http://www.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi?blast_RID=%s&blast_rep_gi=%d&hit=%d&blast_CD_RID=%s&blast_view=%s&hsp=0&taxname=%s&client=blast\">Related Structures</a>"
 
+#define URL_Geo "<a href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo&term=%d[gi]\"><img border=0 height=16 width=16 src=\"/blast/images/G.gif\" alt=\"Geo\"></a>"
+ 
 #endif
diff --git a/api/ffprint.c b/api/ffprint.c
index dfe12693..b0fa78ce 100644
--- a/api/ffprint.c
+++ b/api/ffprint.c
@@ -29,13 +29,16 @@
 *
 * Version Creation Date:   7/15/95
 *
-* $Revision: 6.7 $
+* $Revision: 6.8 $
 *
 * File Description: 
 *
 * Modifications:  
 * --------------------------------------------------------------------------
  * $Log: ffprint.c,v $
+ * Revision 6.8  2003/07/15 14:35:56  dondosha
+ * Added #defines for substitutes to fprintf and fflush, needed for gzip compression of Web BLAST results
+ *
  * Revision 6.7  2002/08/26 22:06:57  kans
  * ff_RecalculateLinks (MS) to fix hotlink artifact
  *
@@ -125,6 +128,11 @@ parameters combined into Asn2ffJobPtr structure
 #include <ffprint.h>
 #include <ncbithr.h>
 
+int (*ff_fprintf)(FILE*, const char *, ...) = fprintf;
+int (*ff_fflush)(FILE*) = fflush;
+
+#define fprintf ff_fprintf
+#define fflush ff_fflush
 
 static TNlmTls ffprint_tls = NULL;
 
diff --git a/api/findrepl.c b/api/findrepl.c
index 43b5ca45..37e91158 100644
--- a/api/findrepl.c
+++ b/api/findrepl.c
@@ -44,6 +44,15 @@
 * RCS Modification History:
 * -------------------------
 * $Log: findrepl.c,v $
+* Revision 6.10  2003/07/31 20:54:54  kans
+* FindReplaceString does not need do_replace argument
+*
+* Revision 6.9  2003/07/31 18:18:03  kans
+* added FindReplaceString
+*
+* Revision 6.8  2003/05/11 21:12:50  kans
+* FindReplAligns loops through StdSegPtr chain, also does ssp->ids within
+*
 * Revision 6.7  2002/06/11 14:41:20  kans
 * added support for locus_tag
 *
@@ -1214,9 +1223,13 @@ static void FindReplAligns (
       }
       break;
     case SAS_STD :
-      ssp = (StdSegPtr) sap->segs;
-      for (slp = ssp->loc; slp != NULL; slp = slp->next) {
-        VisitSeqIdsInSeqLoc (slp, userdata, FindReplSeqId);
+      for (ssp = (StdSegPtr) sap->segs; ssp != NULL; ssp = ssp->next) {
+        for (sip = ssp->ids; sip != NULL; sip = sip->next) {
+          FindReplSeqId (sip, userdata);
+        }
+        for (slp = ssp->loc; slp != NULL; slp = slp->next) {
+          VisitSeqIdsInSeqLoc (slp, userdata, FindReplSeqId);
+        }
       }
       break;
     case SAS_DISC :
@@ -1699,3 +1712,56 @@ NLM_EXTERN void FindReplaceInEntity (
   }
 }
 
+/*=======================================================================*/
+/*                                                                       */
+/*  FindReplaceString() - find/replace just one string.                  */
+/*                                                                       */
+/*=======================================================================*/
+
+NLM_EXTERN void FindReplaceString (
+  CharPtr PNTR strp,
+  CharPtr find_string,
+  CharPtr replace_string,
+  Boolean case_counts,
+  Boolean whole_word
+)
+
+{
+  int         ch;
+  FindStruct  fs;
+  int         j;
+
+  if (strp == NULL || StringHasNoText (find_string)) return;
+
+  MemSet ((Pointer) &fs, 0, sizeof (FindStruct));
+
+  fs.entityID = 0;
+  fs.find_string = find_string;
+  fs.replace_string = replace_string;
+  fs.case_counts = case_counts;
+  fs.whole_word = whole_word;
+  fs.do_replace = TRUE;
+  fs.select_item = FALSE;
+  fs.send_update = FALSE;
+
+  fs.did_find = FALSE;
+  fs.did_replace = FALSE;
+  fs.dirty = FALSE;
+
+  /* build Boyer-Moore displacement array in advance */
+
+  fs.subLen = StringLen (find_string);
+
+  for (ch = 0; ch < 256; ch++) {
+    fs.d [ch] = fs.subLen;
+  }
+  for (j = 0; j < (int) (fs.subLen - 1); j++) {
+    ch = (int) (case_counts ? find_string [j] : TO_UPPER (find_string [j]));
+    if (ch >= 0 && ch <= 255) {
+      fs.d [ch] = fs.subLen - j - 1;
+    }
+  }
+
+  FindReplString (strp, &fs);
+}
+
diff --git a/api/findrepl.h b/api/findrepl.h
index 84f16c72..20df8b12 100644
--- a/api/findrepl.h
+++ b/api/findrepl.h
@@ -44,6 +44,12 @@
 * RCS Modification History:
 * -------------------------
 * $Log: findrepl.h,v $
+* Revision 6.3  2003/07/31 20:54:54  kans
+* FindReplaceString does not need do_replace argument
+*
+* Revision 6.2  2003/07/31 18:18:03  kans
+* added FindReplaceString
+*
 * Revision 6.1  2000/11/03 20:36:00  kans
 * FindReplaceInEntity replaces FindInEntity and FindInEntityX - complete redesign, no longer using AsnExpOptExplore because of the difficulty of replacing with a larger string (TF + JK)
 *
@@ -112,6 +118,14 @@ NLM_EXTERN void FindReplaceInEntity (
   Boolean do_seqid_local
 );
 
+NLM_EXTERN void FindReplaceString (
+  CharPtr PNTR strp,
+  CharPtr find_string,
+  CharPtr replace_string,
+  Boolean case_counts,
+  Boolean whole_word
+);
+
 
 #ifdef __cplusplus
 extern "C" }
diff --git a/api/gbfeat.c b/api/gbfeat.c
index dd2fa347..55eeac51 100644
--- a/api/gbfeat.c
+++ b/api/gbfeat.c
@@ -3,9 +3,13 @@
 *   -- all routines for checking genbank feature table
 *   -- all extern variables are in gbftglob.c
 *                                                                  10-11-93
-$Revision: 6.8 $
+$Revision: 6.9 $
 *
 * $Log: gbfeat.c,v $
+* Revision 6.9  2003/10/09 15:35:51  bazhin
+* Qualifier "rpt_unit" is removed from the list of ones to be splitted
+* by commas.
+*
 * Revision 6.8  2001/12/06 17:00:41  kans
 * TextSave takes size_t, not Int2, otherwise titin protein tries to allocate negative number
 *
@@ -74,9 +78,9 @@ $Revision: 6.8 $
 #include <gbfeat.h>
 #include <errdefn.h>
 
-#define ParFlat_SPLIT_IGNORE 5
+#define ParFlat_SPLIT_IGNORE 4
 CharPtr GBQual_names_split_ignore[ParFlat_SPLIT_IGNORE] = {
-"citation", "EC_number", "rpt_type", "rpt_unit", "usedin"};
+"citation", "EC_number", "rpt_type", "usedin"};
 
 /*------------------------- GBQualNameValid() ------------------------*/
 /****************************************************************************
diff --git a/api/gbftdef.h b/api/gbftdef.h
index fa06de1a..f9d5df3c 100644
--- a/api/gbftdef.h
+++ b/api/gbftdef.h
@@ -3,6 +3,15 @@
 *   -- GenBank Feature table define file
 *
 * $Log: gbftdef.h,v $
+* Revision 6.17  2003/10/07 13:50:36  kans
+* added gap, operon, oriT features and ecotype, estimated_length and operon qualifiers
+*
+* Revision 6.16  2003/08/19 15:18:37  kans
+* added GBQUAL_segment, increased ParFlat_TOTAL_GBQUAL and opt_qual array size
+*
+* Revision 6.15  2003/05/07 22:03:31  kans
+* added GBQUAL_mol_type, raised opt_qual array to 51 elements
+*
 * Revision 6.14  2003/02/22 21:20:05  kans
 * added GBQUAL_locus_tag, legal for now in gene features
 *
@@ -175,13 +184,18 @@
 #define GBQUAL_isolation_source  79
 #define GBQUAL_serovar           80
 #define GBQUAL_locus_tag         81
+#define GBQUAL_mol_type          82
+#define GBQUAL_segment           83
+#define GBQUAL_ecotype           84
+#define GBQUAL_estimated_length  85
+#define GBQUAL_operon            86
 
-#define ParFlat_TOTAL_GBQUAL     82
+#define ParFlat_TOTAL_GBQUAL     87
 #define ParFlat_TOTAL_IntOr       3
 #define ParFlat_TOTAL_LRB         3
 #define ParFlat_TOTAL_Exp         2
 #define ParFlat_TOTAL_Rpt         7
-#define ParFlat_TOTAL_GBFEAT     64
+#define ParFlat_TOTAL_GBFEAT     67
 
 #define  Class_pos_aa             1
 #define  Class_text               2
@@ -214,7 +228,7 @@ typedef struct sematic_gbfeature {
     Int2     mand_num;
     Int2     mand_qual[5];
     Int2     opt_num;
-    Int2     opt_qual[50];
+    Int2     opt_qual[55];
 } SematicFeat, PNTR SematicFeatPtr;
 
 typedef struct gbfeat_name {
diff --git a/api/gbftglob.c b/api/gbftglob.c
index 894ed6b6..e9b26887 100644
--- a/api/gbftglob.c
+++ b/api/gbftglob.c
@@ -4,6 +4,31 @@
 *   -- all the defined variables in the gbfeat.h
 *
 * $Log: gbftglob.c,v $
+* Revision 6.37  2003/10/07 17:05:58  kans
+* added allele and operon to many features
+*
+* Revision 6.36  2003/10/07 13:50:36  kans
+* added gap, operon, oriT features and ecotype, estimated_length and operon qualifiers
+*
+* Revision 6.35  2003/10/06 16:19:45  kans
+* rpt_unit went from Class_token to Class_text
+*
+* Revision 6.34  2003/10/03 15:16:14  bazhin
+* Numeric value "opt_num" in STATIC__ParFlat_GBFeat array changed
+* from 13 to 15 for feature "allele" to cover "usedin" and "locus_tag"
+* qualifiers.
+*
+* Revision 6.33  2003/10/03 12:44:27  bazhin
+* Numeric value "opt_num" in STATIC__ParFlat_GBFeat array changed
+* from 13 to 14 for feature "precursor_RNA" to cover "locus_tag"
+* qualifier.
+*
+* Revision 6.32  2003/08/19 15:19:04  kans
+* added GBQUAL_segment, increased ParFlat_TOTAL_GBQUAL and opt_qual array size
+*
+* Revision 6.31  2003/05/07 22:03:31  kans
+* added GBQUAL_mol_type, raised opt_qual array to 51 elements
+*
 * Revision 6.30  2003/03/06 16:23:13  kans
 * when gene qualifier was removed as required on gene feature, it was not put back as optional qualifier
 *
@@ -181,7 +206,7 @@ static GbFeatName STATIC__ParFlat_GBQual_names[ParFlat_TOTAL_GBQUAL] = {
  {"proviral", Class_none}, {"pseudo", Class_none},
  {"rearranged", Class_none}, { "replace", Class_text}, 
  {"rpt_family", Class_text}, {"rpt_type", Class_rpt},
- { "rpt_unit", Class_token}, { "sex", Class_text},
+ { "rpt_unit", Class_text}, { "sex", Class_text},
  {"sequenced_mol", Class_text}, { "serotype", Class_text},
  {"specific_host", Class_text}, {"standard_name", Class_text}, 
  {"strain", Class_text}, {"sub_clone", Class_text}, 
@@ -195,8 +220,9 @@ static GbFeatName STATIC__ParFlat_GBQual_names[ParFlat_TOTAL_GBQUAL] = {
  {"organelle", Class_text}, {"transcript_id", Class_text},   
  {"transgenic", Class_none}, {"environmental_sample", Class_none},
  {"isolation_source", Class_text}, {"serovar", Class_text},
- {"locus_tag", Class_text},
- };
+ {"locus_tag", Class_text}, {"mol_type", Class_text},
+ {"segment", Class_text},{"ecotype", Class_text},
+ {"estimated_length", Class_text}, {"operon", Class_text} };
 
 NLM_EXTERN GbFeatNamePtr x_ParFlat_GBQual_names(void) {
   return STATIC__ParFlat_GBQual_names;
@@ -214,70 +240,72 @@ CharPtr ParFlat_RptString[ParFlat_TOTAL_Rpt] = {
        "dispersed", "other"};
 
 static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
-   {"allele", 0, {-1, -1, -1, -1, -1}, 13,
+   {"allele", 0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_frequency, 
      GBQUAL_gene,GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
       GBQUAL_phenotype, GBQUAL_product, GBQUAL_replace, GBQUAL_standard_name, 
       GBQUAL_usedin,
       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"attenuator", 0, {-1, -1, -1, -1, -1}, 11,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"attenuator", 0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_label, 
      GBQUAL_gene, GBQUAL_map,
       GBQUAL_note, GBQUAL_partial, GBQUAL_phenotype, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, GBQUAL_operon,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"C_region", 0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"C_region", 0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, 
      GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
      GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"CAAT_signal", 0, {-1, -1, -1, -1, -1}, 10,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"CAAT_signal", 0, {-1, -1, -1, -1, -1}, 11,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_label, 
      GBQUAL_gene, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"CDS", 0, {-1, -1, -1, -1, -1}, 25,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"CDS", 0, {-1, -1, -1, -1, -1}, 26,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_codon, GBQUAL_codon_start, GBQUAL_db_xref, 
      GBQUAL_EC_number,GBQUAL_evidence, GBQUAL_exception, GBQUAL_function, 
      GBQUAL_gdb_xref, GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, 
      GBQUAL_number, GBQUAL_partial, GBQUAL_product, GBQUAL_pseudo, 
      GBQUAL_standard_name, GBQUAL_translation, GBQUAL_transl_except, 
      GBQUAL_transl_table, GBQUAL_usedin, GBQUAL_protein_id,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"conflict",  1, {GBQUAL_citation, -1, -1, -1, -1}, 8,
+      GBQUAL_locus_tag, GBQUAL_operon,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"conflict",  1, {GBQUAL_citation, -1, -1, -1, -1}, 9,
      {GBQUAL_db_xref,GBQUAL_evidence, GBQUAL_map, GBQUAL_note, GBQUAL_gene, GBQUAL_usedin,
-     GBQUAL_replace, 
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 
+     GBQUAL_replace, GBQUAL_locus_tag, GBQUAL_allele,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"D-loop",  0, {-1, -1, -1, -1}, 10,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"D-loop",  0, {-1, -1, -1, -1}, 11,
      {GBQUAL_evidence, GBQUAL_citation, GBQUAL_label, GBQUAL_gene,
      GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_usedin, GBQUAL_db_xref, 
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"D_segment", 0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"D_segment", 0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_evidence, GBQUAL_gene, 
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_product,
       GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin, GBQUAL_db_xref, 
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"enhancer",  0, {-1, -1, -1, -1, -1}, 11,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"enhancer",  0, {-1, -1, -1, -1, -1}, 12,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_label, 
      GBQUAL_gene, GBQUAL_map, 
       GBQUAL_note, GBQUAL_partial, GBQUAL_standard_name,  GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"exon", 0, {-1, -1, -1, -1, -1}, 17,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_EC_number,
       GBQUAL_evidence, GBQUAL_function, GBQUAL_gene, GBQUAL_label,
@@ -285,28 +313,34 @@ static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
       GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name, 
       GBQUAL_usedin,GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"GC_signal", 0, {-1, -1, -1, -1, -1}, 10,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"gap",  1, {GBQUAL_estimated_length, -1, -1, -1, -1}, 0,
+     {-1, -1,  -1,  -1, -1,  -1, -1, -1,  -1,  -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"GC_signal", 0, {-1, -1, -1, -1, -1}, 11,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_label, 
      GBQUAL_gene, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"gene", 0, {-1, -1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"gene", 0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, 
      GBQUAL_function, GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
      GBQUAL_pseudo, GBQUAL_phenotype, GBQUAL_usedin, GBQUAL_locus_tag,
+     GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-	{"iDNA", 0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+	{"iDNA", 0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function, 
      GBQUAL_label,
       GBQUAL_gene, GBQUAL_map, GBQUAL_note, GBQUAL_number, GBQUAL_partial,
       GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"intron", 0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_cons_splice, GBQUAL_db_xref,
      GBQUAL_evidence,  GBQUAL_function, 
@@ -314,244 +348,259 @@ static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
       GBQUAL_partial, GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1,}},
-   {"J_segment", 0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"J_segment", 0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene, 
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_product, 
       GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"LTR", 0, {-1, -1, -1, -1, -1}, 11,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"LTR", 0, {-1, -1, -1, -1, -1}, 12,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function, 
-     GBQUAL_gene, 
-      GBQUAL_label, GBQUAL_note, GBQUAL_partial, GBQUAL_standard_name,
-      GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+     GBQUAL_gene, GBQUAL_label, GBQUAL_note, GBQUAL_partial, GBQUAL_standard_name,
+      GBQUAL_usedin, GBQUAL_locus_tag, GBQUAL_allele,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"mat_peptide",  0, {-1, -1, -1, -1, -1}, 16,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"mat_peptide",  0, {-1, -1, -1, -1, -1}, 17,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_EC_number,
       GBQUAL_evidence, GBQUAL_function, GBQUAL_gene, GBQUAL_label,
       GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_pseudo, 
       GBQUAL_product, GBQUAL_standard_name, GBQUAL_usedin,
-       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+       GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"misc_binding",  1, {GBQUAL_bound_moiety, -1, -1, -1, -1}, 11,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"misc_binding",  1, {GBQUAL_bound_moiety, -1, -1, -1, -1}, 12,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function, 
      GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
       GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"misc_difference", 0, {-1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"misc_difference", 0, {-1, -1, -1, -1}, 15,
      {GBQUAL_phenotype, GBQUAL_citation, GBQUAL_clone, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene, 
      GBQUAL_label, GBQUAL_map, GBQUAL_partial, GBQUAL_replace, 
       GBQUAL_note, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1}},
-   {"misc_feature",  0, {-1, -1, -1, -1, -1}, 16,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"misc_feature",  0, {-1, -1, -1, -1, -1}, 17,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function, 
      GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_number, 
       GBQUAL_phenotype, GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name,
-      GBQUAL_usedin, GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_usedin, GBQUAL_locus_tag, GBQUAL_allele,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"misc_recomb", 0, {-1, -1, -1, -1, -1}, 12,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"misc_recomb", 0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene, 
      GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_organism, 
      GBQUAL_partial, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"misc_RNA",  0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"misc_RNA",  0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function, 
      GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_product, 
       GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"misc_signal",  0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"misc_signal",  0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function, 
      GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_phenotype, 
       GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"misc_structure",  0, {-1, -1, -1, -1, -1}, 12,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"misc_structure",  0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function, 
      GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
       GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"modified_base",  1, {GBQUAL_mod_base, -1, -1, -1, -1}, 10,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"modified_base",  1, {GBQUAL_mod_base, -1, -1, -1, -1}, 11,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_frequency, 
      GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"mRNA",  0, {-1, -1, -1, -1, -1}, 16,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"mRNA",  0, {-1, -1, -1, -1, -1}, 17,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function, 
      GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 	
      GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_transcript_id, GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 
+      GBQUAL_transcript_id, GBQUAL_locus_tag, GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, 
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"mutation",  0, {-1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_frequency,
      GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_phenotype,
      GBQUAL_product, GBQUAL_replace, GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"N_region",  0, {-1, -1, -1, -1, -1}, 12,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_product, 
       GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"old_sequence",   1, {GBQUAL_citation, -1, -1, -1}, 9,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"old_sequence",   1, {GBQUAL_citation, -1, -1, -1}, 10,
      {GBQUAL_db_xref, GBQUAL_gene, GBQUAL_evidence, GBQUAL_map, GBQUAL_note, 
      GBQUAL_partial, GBQUAL_replace, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"polyA_signal", 0, {-1, -1, -1, -1, -1}, 10,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"operon", 1, {GBQUAL_operon, -1, -1, -1, -1}, 12,
+     {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, 
+     GBQUAL_function, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
+     GBQUAL_pseudo, GBQUAL_phenotype, GBQUAL_usedin,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"oriT", 0, {-1, -1, -1, -1, -1}, 16,
+     {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_direction, GBQUAL_evidence, 
+     GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
+     GBQUAL_rpt_family, GBQUAL_rpt_type, GBQUAL_rpt_unit, GBQUAL_standard_name,
+     GBQUAL_usedin, GBQUAL_locus_tag, GBQUAL_allele,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"polyA_signal", 0, {-1, -1, -1, -1, -1}, 11,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"polyA_site", 0, {-1, -1, -1, -1, -1}, 9,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"polyA_site", 0, {-1, -1, -1, -1, -1}, 10,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"precursor_RNA",  0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"precursor_RNA",  0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
       GBQUAL_product, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"prim_transcript",  0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"prim_transcript",  0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
       GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"primer_bind",  0, {-1, -1, -1, -1, -1}, 12,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"primer_bind",  0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_standard_name,
       GBQUAL_PCR_conditions,GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"promoter",  0, {-1, -1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"promoter",  0, {-1, -1, -1, -1, -1}, 16,
      {GBQUAL_citation,GBQUAL_db_xref,  GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
       GBQUAL_phenotype, GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"protein_bind",  1, {GBQUAL_bound_moiety, -1, -1, -1, -1}, 12,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"protein_bind",  1, {GBQUAL_bound_moiety, -1, -1, -1, -1}, 13,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
       GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"RBS",  0, {-1, -1, -1, -1, -1}, 11,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"RBS",  0, {-1, -1, -1, -1, -1}, 12,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
       GBQUAL_label, GBQUAL_map,GBQUAL_note, GBQUAL_partial, GBQUAL_standard_name,
-      GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_usedin, GBQUAL_locus_tag, GBQUAL_allele,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"repeat_region",  0, {-1, -1, -1, -1, -1}, 17,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"repeat_region",  0, {-1, -1, -1, -1, -1}, 18,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, GBQUAL_insertion_seq, GBQUAL_label, GBQUAL_map, GBQUAL_note,
       GBQUAL_partial, GBQUAL_rpt_type, GBQUAL_rpt_family, GBQUAL_rpt_unit,
       GBQUAL_standard_name,
       GBQUAL_transposon, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
-      -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"repeat_unit",  0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"repeat_unit",  0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, 
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_rpt_family,
       GBQUAL_rpt_type, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"rep_origin",  0, {-1, -1, -1, -1, -1}, 12,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"rep_origin",  0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_citation, GBQUAL_direction, GBQUAL_db_xref, GBQUAL_evidence,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
       GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"rRNA",  0, {-1, -1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"rRNA",  0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function, 
      GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_product,
       GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"S_region",  0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"S_region",  0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_product,
       GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"satellite",  0, {-1, -1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"satellite",  0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
       GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_rpt_type,
       GBQUAL_rpt_family,GBQUAL_rpt_unit, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"scRNA",  0, {-1, -1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"scRNA",  0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene,GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
       GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"sig_peptide", 0, {-1, -1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"sig_peptide", 0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
      GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
      GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"snoRNA",  0, {-1, -1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"snoRNA",  0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene,GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
       GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"snRNA",  0, {-1, -1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"snRNA",  0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene,GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial,
       GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"source", 1, {GBQUAL_organism, -1, -1, -1, -1}, 50,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"source", 1, {GBQUAL_organism, -1, -1, -1, -1}, 53,
      {GBQUAL_cell_line, GBQUAL_cell_type, GBQUAL_chloroplast, 
       GBQUAL_chromoplast, GBQUAL_chromosome,
       GBQUAL_citation, GBQUAL_clone, GBQUAL_clone_lib, GBQUAL_country, GBQUAL_cultivar,
@@ -566,70 +615,75 @@ static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
       GBQUAL_tissue_type, GBQUAL_transposon, GBQUAL_usedin, 
       GBQUAL_specimen_voucher, GBQUAL_variety, GBQUAL_virion,
       GBQUAL_organelle, GBQUAL_transgenic, GBQUAL_environmental_sample,
-      GBQUAL_isolation_source, GBQUAL_serovar}},
-   {"stem_loop",  0, {-1, -1, -1, -1, -1}, 12,
+      GBQUAL_isolation_source, GBQUAL_serovar, GBQUAL_mol_type, GBQUAL_segment,
+      GBQUAL_ecotype, -1, -1}},
+   {"stem_loop",  0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
       GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, GBQUAL_operon,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"STS",  0, {-1, -1, -1, -1, -1}, 11,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"STS",  0, {-1, -1, -1, -1, -1}, 12,
      {GBQUAL_citation, GBQUAL_standard_name, GBQUAL_db_xref, GBQUAL_gene,
       GBQUAL_label, GBQUAL_usedin, GBQUAL_note, GBQUAL_partial, GBQUAL_map, 
-      GBQUAL_evidence, GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_evidence, GBQUAL_locus_tag, GBQUAL_allele,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"TATA_signal",  0, {-1, -1, -1, -1, -1}, 10,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"TATA_signal",  0, {-1, -1, -1, -1, -1}, 11,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
       GBQUAL_label, GBQUAL_map,
       GBQUAL_note, GBQUAL_partial, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"terminator",  0, {-1, -1, -1, -1, -1}, 11,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"terminator",  0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
       GBQUAL_label, GBQUAL_map,GBQUAL_note, GBQUAL_partial,
        GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, GBQUAL_operon,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"transit_peptide",  0, {-1, -1, -1, -1, -1}, 14,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"transit_peptide",  0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref,
       GBQUAL_evidence, GBQUAL_function, GBQUAL_gene, GBQUAL_label, GBQUAL_map,
        GBQUAL_note,GBQUAL_partial, GBQUAL_product, GBQUAL_pseudo, 	
        GBQUAL_standard_name, GBQUAL_usedin,
-       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+       GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"tRNA",  0, {-1, -1, -1, -1, -1}, 15,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"tRNA",  0, {-1, -1, -1, -1, -1}, 16,
      {GBQUAL_anticodon, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence,
       GBQUAL_function, GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, 
       GBQUAL_partial, GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name,
        GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"unsure",  0, {-1, -1, -1, -1}, 10,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"unsure",  0, {-1, -1, -1, -1}, 11,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene, GBQUAL_usedin, 
      GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_replace, 
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"V_region",  0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"V_region",  0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
       GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"V_segment",  0, {-1, -1, -1, -1, -1}, 13,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"V_segment",  0, {-1, -1, -1, -1, -1}, 14,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
       GBQUAL_product, GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_allele, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"variation",  0, {-1, -1, -1, -1}, 16,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, 
      GBQUAL_frequency, GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note,
@@ -637,49 +691,49 @@ static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
      GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"3'clip",  0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
       GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"3'UTR",  0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
       GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"5'clip",  0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_function, GBQUAL_gene,
       GBQUAL_evidence, GBQUAL_label, GBQUAL_map,  
       GBQUAL_note, GBQUAL_partial, GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"5'UTR",  0, {-1, -1, -1, -1, -1}, 13,
      {GBQUAL_allele, GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, 
       GBQUAL_note, GBQUAL_partial, GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"-10_signal",  0, {-1, -1, -1, -1, -1}, 11,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"-10_signal",  0, {-1, -1, -1, -1, -1}, 12,
      {GBQUAL_citation,GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
      GBQUAL_label, GBQUAL_map,GBQUAL_note,GBQUAL_partial, 
      GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"-35_signal",  0, {-1, -1, -1, -1, -1}, 11,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
+   {"-35_signal",  0, {-1, -1, -1, -1, -1}, 12,
      {GBQUAL_citation,GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_gene,
      GBQUAL_label, GBQUAL_map,GBQUAL_note,GBQUAL_partial, 
      GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}}
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 -1, -1, -1, -1}}
       };
 
 NLM_EXTERN SematicFeatPtr x_ParFlat_GBFeat(void) {
diff --git a/api/lsqfetch.c b/api/lsqfetch.c
index fb778990..68378ca3 100644
--- a/api/lsqfetch.c
+++ b/api/lsqfetch.c
@@ -37,6 +37,12 @@
 * Date     Name        Description of modification
 *
 * $Log: lsqfetch.c,v $
+* Revision 6.16  2003/08/27 21:24:05  kans
+* enable alt indexed fasta looks up previously registered function, changes settings for new path
+*
+* Revision 6.15  2003/08/27 19:27:43  kans
+* added AltIndexedFastaLibFetch functions for chimpanzee genome project
+*
 * Revision 6.14  2002/11/13 23:07:37  johnson
 * Changed make_lib such that it looks to see if it matches the *whole* seq-id
 * (defined by the next character being non-alphanumeric).
@@ -81,6 +87,12 @@
 * Revision changed to 6.0
 *
 * $Log: lsqfetch.c,v $
+* Revision 6.16  2003/08/27 21:24:05  kans
+* enable alt indexed fasta looks up previously registered function, changes settings for new path
+*
+* Revision 6.15  2003/08/27 19:27:43  kans
+* added AltIndexedFastaLibFetch functions for chimpanzee genome project
+*
 * Revision 6.14  2002/11/13 23:07:37  johnson
 * Changed make_lib such that it looks to see if it matches the *whole* seq-id
 * (defined by the next character being non-alphanumeric).
@@ -1240,12 +1252,13 @@ static FastaIndexPtr ReadFastaIndex (
   return fip;
 }
 
-/* object manager registerable fetch function */
+/* human genome object manager registerable fetch function */
 
 static CharPtr fastalibfetchproc = "IndexedFastaLibBioseqFetch";
 
 typedef struct flibftch {
   CharPtr        path;
+  CharPtr        fastaname;
   FastaIndexPtr  currentfip;
 } FastaLibFetchData, PNTR FastaLibFetchPtr;
 
@@ -1352,10 +1365,145 @@ NLM_EXTERN void IndexedFastaLibFetchDisable (void)
   flfp = (FastaLibFetchPtr) ompp->procdata;
   if (flfp == NULL) return;
   MemFree (flfp->path);
+  /* MemFree (flfp->fastaname); */
+  FreeFastaIndex (flfp->currentfip);
+  MemFree (flfp);
+}
+
+/* chimpanzee genome object manager registerable fetch function */
+
+static CharPtr altfastalibfetchproc = "AltIndexedFastaLibBioseqFetch";
+
+static void ChangeLocalToGenbank (BioseqPtr bsp, Pointer userdata)
+
+{
+  Char      id [41], tmp [41];
+  SeqIdPtr  sip;
+
+  for (sip = bsp->id; sip != NULL && sip->choice != SEQID_LOCAL; sip = sip->next) continue;
+  if (sip == NULL) return;
+  SeqIdWrite (sip, id, PRINTID_REPORT, sizeof (id));
+  sprintf (tmp, "gb|%s", id);
+  sip = SeqIdParse (tmp);
+  bsp->id = SeqIdSetFree (bsp->id);
+  bsp->id = sip;
+  SeqMgrReplaceInBioseqIndex (bsp);
+}
+
+static Int2 LIBCALLBACK AltIndexedFastaLibBioseqFetchFunc (Pointer data)
+
+{
+  BioseqPtr         bsp;
+  Pointer           dataptr = NULL;
+  Uint2             datatype, entityID = 0;
+  Char              file [FILENAME_MAX], path [PATH_MAX], id [41];
+  FastaLibFetchPtr  flfp;
+  FILE              *fp;
+  Int4              offset;
+  OMProcControlPtr  ompcp;
+  ObjMgrProcPtr     ompp;
+  SeqEntryPtr       sep = NULL;
+  SeqIdPtr          sip;
+
+  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;
+  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);
+      if (offset < 0) return OM_MSG_RET_ERROR;
+      sprintf (file, "%s.fsa", flfp->fastaname);
+      StringNCpy_0 (path, flfp->path, sizeof (path));
+      FileBuildPath (path, NULL, file);
+      fp = FileOpen (path, "r");
+      if (fp == NULL) return OM_MSG_RET_ERROR;
+      fseek (fp, offset, SEEK_SET);
+      dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID,
+                                        FALSE, FALSE, TRUE, FALSE);
+      if (dataptr != NULL) {
+        sep = GetTopSeqEntryForEntityID (entityID);
+      }
+      FileClose (fp);
+    }
+  }
+
+  if (sep == NULL) return OM_MSG_RET_ERROR;
+  VisitBioseqsInSep (sep, NULL, ChangeLocalToGenbank);
+  bsp = BioseqFindInSeqEntry (sip, sep);
+  ompcp->output_data = (Pointer) bsp;
+  ompcp->output_entityID = ObjMgrGetEntityIDForChoice (sep);
+  return OM_MSG_RET_DONE;
+}
+
+NLM_EXTERN Boolean AltIndexedFastaLibFetchEnable (CharPtr path, CharPtr fastaname)
+
+{
+  Char              file [FILENAME_MAX];
+  FastaLibFetchPtr  flfp = NULL;
+  Boolean           is_new = FALSE;
+  ObjMgrPtr         omp;
+  ObjMgrProcPtr     ompp;
+  Char              str [PATH_MAX];
+
+  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);
+    }
+  } else {
+    flfp = (FastaLibFetchPtr) MemNew (sizeof (FastaLibFetchData));
+    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 (is_new) {
+    ObjMgrProcLoad (OMPROC_FETCH, altfastalibfetchproc, altfastalibfetchproc,
+                    OBJ_SEQID, 0, OBJ_BIOSEQ, 0, (Pointer) flfp,
+                    AltIndexedFastaLibBioseqFetchFunc, PROC_PRIORITY_DEFAULT);
+  }
+  return TRUE;
+}
+
+NLM_EXTERN void AltIndexedFastaLibFetchDisable (void)
+
+{
+  FastaLibFetchPtr  flfp;
+  ObjMgrPtr         omp;
+  ObjMgrProcPtr     ompp;
+
+  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);
 }
 
+/* common function for creating indexes of fasta library files */
+
 NLM_EXTERN void CreateFastaIndex (
   CharPtr file
 )
diff --git a/api/lsqfetch.h b/api/lsqfetch.h
index a0e9daac..52a59363 100644
--- a/api/lsqfetch.h
+++ b/api/lsqfetch.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 5/25/95
 *
-* $Revision: 6.2 $
+* $Revision: 6.3 $
 *
 * File Description:  Utilities for fetching local sequences
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: lsqfetch.h,v $
+* Revision 6.3  2003/08/27 19:27:43  kans
+* added AltIndexedFastaLibFetch functions for chimpanzee genome project
+*
 * Revision 6.2  2001/03/12 23:19:33  kans
 * added IndexedFastaLib functions - currently uses genome contig naming conventions
 *
@@ -246,10 +249,18 @@ NLM_EXTERN Boolean CheckDnaResidue PROTO((CharPtr seq_ptr, Int4 ck_len, Int4Ptr
 
 /**********************************************************************/
 
-/* indexed FASTA lib functions - currently uses genome contig naming convention */
+/* indexed FASTA lib functions - currently uses human genome contig naming convention */
 
 NLM_EXTERN Boolean IndexedFastaLibFetchEnable (CharPtr path);
 NLM_EXTERN void IndexedFastaLibFetchDisable (void);
+
+/* alternative indexed FASTA lib functions - currently uses chimpanzee genome contig naming convention */
+
+NLM_EXTERN Boolean AltIndexedFastaLibFetchEnable (CharPtr path, CharPtr fastaname);
+NLM_EXTERN void AltIndexedFastaLibFetchDisable (void);
+
+/* common function for creating indexes of fasta library files */
+
 NLM_EXTERN void CreateFastaIndex (CharPtr file);
 
 
diff --git a/api/salpstat.c b/api/salpstat.c
index 68ca2aae..4f741ace 100644
--- a/api/salpstat.c
+++ b/api/salpstat.c
@@ -631,7 +631,7 @@ NLM_EXTERN Int4Ptr LIBCALL SeqAlignListGapList(SeqAlignPtr sap,Int4Ptr gap_num){
 
   /* Utility subroutine for SeqAlignWindowStats */
 
-static void LIBCALL UpdateWindow(Int4 win_size,Int4 cur_pos,Uint1Ptr win_buf1,Uint1Ptr win_buf2,Uint1 res_1,Uint1 res_2,Uint1 code,Int4Ptr win_gap,Int4Ptr win_gapmismatch,Int4Ptr win_mismatch,Int4Ptr win_match,Boolean N_are_not_mismatches){ 
+static void LIBCALL UpdateWindowStats(Int4 win_size,Int4 cur_pos,Uint1Ptr win_buf1,Uint1Ptr win_buf2,Uint1 res_1,Uint1 res_2,Uint1 code,Int4Ptr win_gap,Int4Ptr win_gapmismatch,Int4Ptr win_mismatch,Int4Ptr win_match,Boolean N_are_not_mismatches){ 
   Uint1 exit_char1,exit_char2;
   Int4 loc;
   if(win_size<=0) return; /* For case where user didn't care about window */
@@ -828,7 +828,7 @@ NLM_EXTERN Int4 LIBCALL SeqAlignWindowStats(SeqAlignPtr align, BioseqPtr bsp_1,
 		  res_1 =  SeqPortGetResidue(spp_1);
 		  res_2= '-';
 		}
-	      UpdateWindow(win_size,cur_pos,win_buf1,win_buf2,res_1,res_2,code,&win_gap,&win_gapmismatch,&win_mismatch,&win_match,N_are_not_mismatches);
+	      UpdateWindowStats(win_size,cur_pos,win_buf1,win_buf2,res_1,res_2,code,&win_gap,&win_gapmismatch,&win_mismatch,&win_match,N_are_not_mismatches);
 	      CheckMinMax(win_size,cur_pos,win_gap,
 			  win_gapmismatch,win_mismatch,win_match,
 			  mmin_mismatch,mmax_mismatch,
@@ -864,7 +864,7 @@ NLM_EXTERN Int4 LIBCALL SeqAlignWindowStats(SeqAlignPtr align, BioseqPtr bsp_1,
 		}
 	      else
 		++mismatches;
-	      UpdateWindow(win_size,cur_pos,win_buf1,win_buf2,res_1,res_2,code,&win_gap,&win_gapmismatch,&win_mismatch,&win_match,N_are_not_mismatches);
+	      UpdateWindowStats(win_size,cur_pos,win_buf1,win_buf2,res_1,res_2,code,&win_gap,&win_gapmismatch,&win_mismatch,&win_match,N_are_not_mismatches);
 	      CheckMinMax(win_size,cur_pos,win_gap,
 			  win_gapmismatch,win_mismatch,win_match,
 			  mmin_mismatch,mmax_mismatch,
diff --git a/api/seqmgr.c b/api/seqmgr.c
index 65f24262..9994a256 100644
--- a/api/seqmgr.c
+++ b/api/seqmgr.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 9/94
 *
-* $Revision: 6.203 $
+* $Revision: 6.210 $
 *
 * File Description:  Manager for Bioseqs and BioseqSets
 *
@@ -39,6 +39,27 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: seqmgr.c,v $
+* Revision 6.210  2003/10/24 19:49:11  kans
+* operon feature of equal range sorted before gene, mRNA, CDS
+*
+* Revision 6.209  2003/10/23 17:40:01  kans
+* added SeqMgrGetOverlappingOperon and bspextra operonsByPos and numoperons fields
+*
+* Revision 6.208  2003/10/02 16:12:31  bollin
+* added COMMON_INTERVAL overlap type to TestForOverlap
+*
+* Revision 6.207  2003/09/22 17:27:29  kans
+* strip RNA- prefix, not just - on RNAs
+*
+* Revision 6.206  2003/09/22 16:13:20  kans
+* LockFarComponentsEx takes new SeqLocPtr parameter
+*
+* Revision 6.205  2003/09/22 15:55:06  kans
+* all rna context labels were searched for dash, now just trna
+*
+* Revision 6.204  2003/08/04 20:41:20  kans
+* SeqMgrProcessNonIndexedBioseq needed to reset version to 0 each time through outer loop (EY)
+*
 * Revision 6.203  2003/04/03 22:40:09  kans
 * feature index location problem now reports latest identifier in record to make it easier to find problem
 *
@@ -3420,7 +3441,7 @@ static Boolean NEAR SeqMgrProcessNonIndexedBioseq(Boolean force_it)
 	Boolean indexed;
 	TextSeqIdPtr tsip;
 	SeqMgrPtr smp;
-	Int2 version = 0;
+	Int2 version;
 	Boolean sort_now = TRUE;
 
 	smp = SeqMgrReadLock();
@@ -3456,6 +3477,7 @@ static Boolean NEAR SeqMgrProcessNonIndexedBioseq(Boolean force_it)
 			if (bsp->id != NULL)
 			{
 				indexed = TRUE;
+				version = 0;
 				for (sip = bsp->id; sip != NULL; sip = sip->next)
 				{
 					oldchoice = 0;
@@ -4041,6 +4063,7 @@ static Boolean SeqMgrClearBioseqExtraData (ObjMgrDataPtr omdp)
   bspextra->CDSsByPos = MemFree (bspextra->CDSsByPos);
   bspextra->pubsByPos = MemFree (bspextra->pubsByPos);
   bspextra->orgsByPos = MemFree (bspextra->orgsByPos);
+  bspextra->operonsByPos = MemFree (bspextra->operonsByPos);
 
   /* free list of descriptor information */
 
@@ -4104,6 +4127,7 @@ static Boolean SeqMgrClearBioseqExtraData (ObjMgrDataPtr omdp)
   bspextra->numCDSs = 0;
   bspextra->numpubs = 0;
   bspextra->numorgs = 0;
+  bspextra->numoperons = 0;
   bspextra->numsegs = 0;
 
   bspextra->min = INT4_MAX;
@@ -5467,9 +5491,9 @@ static void RecordOneFeature (BioseqExtraPtr bspextra, ObjMgrDataPtr omdp,
         FeatDefLabel (sfp, buf, sizeof (buf) - 1, OM_LABEL_CONTENT);
         ptr = buf;
         if (sfp->data.choice == SEQFEAT_RNA) {
-          ptr = StringChr (buf, '-');
+          ptr = StringStr (buf, "RNA-");
           if (ptr != NULL) {
-            ptr++;
+            ptr += 4;
           } else {
             ptr = buf;
           }
@@ -6163,10 +6187,19 @@ static int LIBCALLBACK SortFeatItemListByPos (VoidPtr vp1, VoidPtr vp2)
     return -1; /* was 1 */
   } else if (sp1->right < sp2->right) {
     return 1; /* was -1 */
+  }
+
+  /* given identical extremes, put operon features first */
+
+  if (sp1->subtype == FEATDEF_operon && sp2->subtype != FEATDEF_operon) {
+    return -1;
+  } else if (sp2->subtype == FEATDEF_operon && sp1->subtype != FEATDEF_operon) {
+    return 1;
+  }
 
-  /* given identical extremes, put gene features first */
+  /* then gene features */
 
-  } else if (sp1->subtype == FEATDEF_GENE && sp2->subtype != FEATDEF_GENE) {
+  if (sp1->subtype == FEATDEF_GENE && sp2->subtype != FEATDEF_GENE) {
     return -1;
   } else if (sp2->subtype == FEATDEF_GENE && sp1->subtype != FEATDEF_GENE) {
     return 1;
@@ -6324,10 +6357,19 @@ static int LIBCALLBACK SortFeatItemListByRev (VoidPtr vp1, VoidPtr vp2)
     return -1;
   } else if (sp1->left > sp2->left) {
     return 1;
+  }
+
+  /* given identical extremes, put operon features first */
+
+  if (sp1->subtype == FEATDEF_operon && sp2->subtype != FEATDEF_operon) {
+    return -1;
+  } else if (sp2->subtype == FEATDEF_operon && sp1->subtype != FEATDEF_operon) {
+    return 1;
+  }
 
-  /* given identical extremes, put gene features first */
+  /* then gene features */
 
-  } else if (sp1->subtype == FEATDEF_GENE && sp2->subtype != FEATDEF_GENE) {
+  if (sp1->subtype == FEATDEF_GENE && sp2->subtype != FEATDEF_GENE) {
     return -1;
   } else if (sp2->subtype == FEATDEF_GENE && sp1->subtype != FEATDEF_GENE) {
     return 1;
@@ -6703,6 +6745,7 @@ static void IndexRecordedFeatures (SeqEntryPtr sep, Boolean dorevfeats)
         bspextra->CDSsByPos = SeqMgrBuildFeatureIndex (bsp, &(bspextra->numCDSs), 0, FEATDEF_CDS);
         bspextra->pubsByPos = SeqMgrBuildFeatureIndex (bsp, &(bspextra->numpubs), 0, FEATDEF_PUB);
         bspextra->orgsByPos = SeqMgrBuildFeatureIndex (bsp, &(bspextra->numorgs), 0, FEATDEF_BIOSRC);
+        bspextra->operonsByPos = SeqMgrBuildFeatureIndex (bsp, &(bspextra->numoperons), 0, FEATDEF_operon);
       }
 
       if (dorevfeats) {
@@ -7679,9 +7722,10 @@ static Int4 TestForOverlap (SMFeatItemPtr feat, SeqLocPtr slp,
       }
     }
 
-  } else if (overlapType == INTERVAL_OVERLAP) {
+  } else if (overlapType == INTERVAL_OVERLAP || overlapType == COMMON_INTERVAL) {
 
-    /* requires overlap between at least one pair of intervals */
+    /* requires overlap between at least one pair of intervals (INTERVAL_OVERLAP) */
+    /* or one complete shared interval (COMMON_INTERVAL) */
 
     if (feat->right >= left && feat->left <= right) {
       sfp = feat->sfp;
@@ -7690,7 +7734,11 @@ static Int4 TestForOverlap (SMFeatItemPtr feat, SeqLocPtr slp,
         while (a != NULL) {
           b = SeqLocFindNext (sfp->location, NULL);
           while (b != NULL) {
-            if (SeqLocCompare (a, b) != SLC_NO_MATCH) {
+            if ((overlapType == INTERVAL_OVERLAP
+                && SeqLocCompare (a, b) != SLC_NO_MATCH) 
+              || (overlapType == COMMON_INTERVAL
+                && SeqLocCompare (a, b) == SLC_A_EQ_B))
+            {
               diff = ABS (left - feat->left) + ABS (feat->right - right);
               return diff;
             }
@@ -7825,6 +7873,9 @@ static SeqFeatPtr SeqMgrGetBestOverlappingFeat (SeqLocPtr slp, Uint2 subtype,
       array = bspextra->orgsByPos;
       num = bspextra->numorgs;
       break;
+  	case FEATDEF_operon :
+      array = bspextra->operonsByPos;
+      num = bspextra->numoperons;
     default :
       break;
   }
@@ -8058,6 +8109,12 @@ NLM_EXTERN SeqFeatPtr LIBCALL SeqMgrGetOverlappingSource (SeqLocPtr slp, SeqMgrF
   return SeqMgrGetBestOverlappingFeat (slp, FEATDEF_BIOSRC, NULL, 0, NULL, CONTAINED_WITHIN, context, NULL, NULL, NULL);
 }
 
+NLM_EXTERN SeqFeatPtr LIBCALL SeqMgrGetOverlappingOperon (SeqLocPtr slp, SeqMgrFeatContext PNTR context)
+
+{
+  return SeqMgrGetBestOverlappingFeat (slp, FEATDEF_operon, NULL, 0, NULL, CONTAINED_WITHIN, context, NULL, NULL, NULL);
+}
+
 /*****************************************************************************
 *
 *   SeqMgrGetFeatureByLabel returns the a feature with the desired label
@@ -9542,7 +9599,24 @@ static void LockAllProducts (SeqFeatPtr sfp, Pointer userdata)
   }
 }
 
-NLM_EXTERN ValNodePtr LockFarComponentsEx (SeqEntryPtr sep, Boolean components, Boolean locations, Boolean products)
+static void LockAllSublocs (SeqLocPtr loc, Pointer userdata)
+
+{
+  SeqLocPtr        slp = NULL;
+  ValNodePtr PNTR  vnpp;
+
+  if (loc == NULL) return;
+  vnpp = (ValNodePtr PNTR) userdata;
+  if (vnpp == NULL) return;
+
+  while ((slp = SeqLocFindNext (loc, slp)) != NULL) {
+    if (slp != NULL && slp->choice != SEQLOC_NULL) {
+      LockAllSegments (slp, vnpp);
+    }
+  }
+}
+
+NLM_EXTERN ValNodePtr LockFarComponentsEx (SeqEntryPtr sep, Boolean components, Boolean locations, Boolean products, SeqLocPtr loc)
 
 {
   ValNodePtr   bsplist = NULL;
@@ -9559,6 +9633,9 @@ NLM_EXTERN ValNodePtr LockFarComponentsEx (SeqEntryPtr sep, Boolean components,
   if (products) {
     VisitFeaturesInSep (sep, (Pointer) &bsplist, LockAllProducts);
   }
+  if (loc != NULL) {
+    LockAllSublocs (sep, (Pointer) &bsplist);
+  }
   SeqEntrySetScope (oldsep);
   return bsplist;
 }
@@ -9566,7 +9643,7 @@ NLM_EXTERN ValNodePtr LockFarComponentsEx (SeqEntryPtr sep, Boolean components,
 NLM_EXTERN ValNodePtr LockFarComponents (SeqEntryPtr sep)
 
 {
-  return LockFarComponentsEx (sep, TRUE, FALSE, FALSE);
+  return LockFarComponentsEx (sep, TRUE, FALSE, FALSE, NULL);
 }
 
 NLM_EXTERN ValNodePtr UnlockFarComponents (ValNodePtr bsplist)
diff --git a/api/seqmgr.h b/api/seqmgr.h
index 6a2d8b4e..86731995 100644
--- a/api/seqmgr.h
+++ b/api/seqmgr.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 9/94
 *
-* $Revision: 6.50 $
+* $Revision: 6.52 $
 *
 * File Description:  Manager for Bioseqs and BioseqSets
 *
@@ -40,6 +40,12 @@
 *
 *
 * $Log: seqmgr.h,v $
+* Revision 6.52  2003/10/23 17:40:01  kans
+* added SeqMgrGetOverlappingOperon and bspextra operonsByPos and numoperons fields
+*
+* Revision 6.51  2003/09/22 16:13:20  kans
+* LockFarComponentsEx takes new SeqLocPtr parameter
+*
 * Revision 6.50  2003/02/12 14:20:47  kans
 * added IsNonGappedLiteral, used to allow compressed deltas as (previously always raw) parts of segsets
 *
@@ -931,6 +937,7 @@ typedef struct bioseqextra {
   SMFeatItemPtr PNTR  CDSsByPos;      /* subset of featsByPos array containing only CDS features */
   SMFeatItemPtr PNTR  pubsByPos;      /* subset of featsByPos array containing only publication features */
   SMFeatItemPtr PNTR  orgsByPos;      /* subset of featsByPos array containing only biosource features */
+  SMFeatItemPtr PNTR  operonsByPos;   /* subset of featsByPos array containing only operon features */
 
   BioseqPtr           parentBioseq;   /* segmented parent of this raw part all packaged together */
   SMSeqIdxPtr         segparthead;    /* linked list to speed mapping from parts to segmented bioseq */
@@ -946,6 +953,7 @@ typedef struct bioseqextra {
   Int4                numCDSs;        /* number of elements in CDSsByPos array */
   Int4                numpubs;        /* number of elements in pubsByPos array */
   Int4                numorgs;        /* number of elements in orgsByPos array */
+  Int4                numoperons;     /* number of elements in operonsByPos array */
 
   Int4                numsegs;        /* number of segments in partslist array */
 
@@ -1048,7 +1056,7 @@ NLM_EXTERN SeqAlignPtr LIBCALL SeqMgrFindSeqAlignByID PROTO((Uint2 entityID, Uin
 
 NLM_EXTERN ValNodePtr LockFarComponents (SeqEntryPtr sep);
 
-NLM_EXTERN ValNodePtr LockFarComponentsEx (SeqEntryPtr sep, Boolean components, Boolean locations, Boolean products);
+NLM_EXTERN ValNodePtr LockFarComponentsEx (SeqEntryPtr sep, Boolean components, Boolean locations, Boolean products, SeqLocPtr loc);
 
 NLM_EXTERN ValNodePtr UnlockFarComponents (ValNodePtr bsplist);
 
diff --git a/api/seqport.c b/api/seqport.c
index e19eb81e..a42d70d3 100644
--- a/api/seqport.c
+++ b/api/seqport.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/13/91
 *
-* $Revision: 6.79 $
+* $Revision: 6.82 $
 *
 * File Description:  Ports onto Bioseqs
 *
@@ -39,6 +39,15 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: seqport.c,v $
+* Revision 6.82  2003/08/18 21:07:35  kans
+* RevCompStr was stepping on str variable
+*
+* Revision 6.81  2003/08/18 20:09:46  kans
+* SeqPortStreamLoc calls SeqPortStream recursively to local buffer, reverse complements if necessary, and passes appropriate subsequence to callback - speeds up far deltas that point to other far deltas
+*
+* Revision 6.80  2003/08/07 19:54:33  kans
+* TransTableTranslateCommon turns on no_start only if CDS location is 5prime partial, not if product is missing the amino end
+*
 * Revision 6.79  2002/11/11 18:02:40  kans
 * added SeqPortStream to efficiently stream through a sequence
 *
@@ -2202,6 +2211,84 @@ static void SeqPortStreamLit (
   BioseqFree (bsp);
 }
 
+static void RevCompStr (
+  CharPtr str
+)
+
+{
+  Char     ch;
+  CharPtr  complementBase = " TVGH  CD  M KN   YSAABW R ";
+  Int2     i;
+  Uint1    letterToComp [256];
+  Char     lttr;
+  CharPtr  nd;
+  CharPtr  tmp;
+
+  if (str == NULL) return;
+
+  /* set up complementation lookup table */
+
+  for (i = 0; i < 256; i++) {
+    letterToComp [i] = '\0';
+  }
+  for (ch = 'A', i = 1; ch <= 'Z'; ch++, i++) {
+    lttr = complementBase [i];
+    if (lttr != ' ') {
+      letterToComp [(int) (Uint1) ch] = lttr;
+    }
+  }
+  for (ch = 'a', i = 1; ch <= 'z'; ch++, i++) {
+    lttr = complementBase [i];
+    if (lttr != ' ') {
+      letterToComp [(int) (Uint1) ch] = lttr;
+    }
+  }
+
+  /* reverse string */
+
+  nd = str;
+  while (*nd != '\0') {
+    nd++;
+  }
+  nd--;
+
+  tmp = str;
+  while (nd > tmp) {
+    ch = *nd;
+    *nd = *tmp;
+    *tmp = ch;
+    nd--;
+    tmp++;
+  }
+
+  /* complement string */
+
+  nd = str;
+  ch = *nd;
+  while (ch != '\0') {
+    *nd = letterToComp [(int) (Uint1) ch];
+    nd++;
+    ch = *nd;
+  }
+}
+
+static void LIBCALLBACK SaveLocStream (
+  CharPtr sequence,
+  Pointer userdata
+)
+
+{
+  CharPtr       tmp;
+  CharPtr PNTR  tmpp;
+
+  tmpp = (CharPtr PNTR) userdata;
+  tmp = *tmpp;
+
+  tmp = StringMove (tmp, sequence);
+
+  *tmpp = tmp;
+}
+
 static void SeqPortStreamLoc (
   SeqLocPtr slp,
   Boolean expandGaps,
@@ -2212,7 +2299,9 @@ static void SeqPortStreamLoc (
 {
   BioseqPtr  bsp;
   Int4       from;
+  CharPtr    str;
   Uint1      strand;
+  CharPtr    tmp;
   Int4       to;
 
   if (slp == NULL || proc == NULL) return;
@@ -2224,7 +2313,28 @@ static void SeqPortStreamLoc (
   to = SeqLocStop (slp);
   strand = SeqLocStrand (slp);
 
-  SeqPortStreamRaw (bsp, from, to, strand, expandGaps, userdata, proc);
+  str = str = MemNew (sizeof (Char) * (bsp->length + 10));
+  if (str != NULL) {
+    tmp = str;
+    SeqPortStream (bsp, TRUE, (Pointer) &tmp, SaveLocStream);
+
+    if (to > 0 && to < bsp->length) {
+      str [to + 1] = '\0';
+    }
+    tmp = str;
+    if (from > 0 && from < bsp->length) {
+      tmp += from;
+    }
+    if (strand == Seq_strand_minus && ISA_na (bsp->mol)) {
+      RevCompStr (tmp);
+    }
+
+    proc (tmp, userdata);
+
+    MemFree (str);
+  }
+
+  /* SeqPortStreamRaw (bsp, from, to, strand, expandGaps, userdata, proc); */
 
   BioseqUnlock (bsp);
 }
@@ -4906,7 +5016,7 @@ static ByteStorePtr TransTableTranslateCommon (
   no_start = FALSE;
   part_loc = SeqLocPartialCheck (location);
   part_prod = SeqLocPartialCheck (product);
-  if ((part_loc & SLP_START) || (part_prod & SLP_START)) {
+  if ((part_loc & SLP_START) /* || (part_prod & SLP_START) */) {
     no_start = TRUE;
   }
   if (StringHasNoText (tbl->sncbieaa) || no_start || frame > 1) {
diff --git a/api/sequtil.c b/api/sequtil.c
index 722119e6..6b014789 100644
--- a/api/sequtil.c
+++ b/api/sequtil.c
@@ -29,13 +29,37 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.131 $
+* $Revision: 6.139 $
 *
 * File Description:  Sequence Utilities for objseq and objsset
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: sequtil.c,v $
+* Revision 6.139  2003/10/24 14:36:12  kans
+* added CH as GenBank CONN to WHICH_db_accession
+*
+* Revision 6.138  2003/09/09 20:08:18  kans
+* SeqLocPartialCheck locks bioseq if seqloc_whole and far
+*
+* Revision 6.137  2003/09/02 15:11:50  kans
+* WHICH_db_accession takes ZP_ with 8 digits as refseq_prot_predicted
+*
+* Revision 6.136  2003/08/11 13:45:18  kans
+* added CG as ncbi gss
+*
+* Revision 6.135  2003/07/14 20:17:53  kans
+* added CF as ncbi est to WHICH_db_accession
+*
+* Revision 6.134  2003/07/02 14:35:21  kans
+* added CE as ncbi gss
+*
+* Revision 6.133  2003/05/20 22:15:24  yaschenk
+* SeqIdSelect loops indefinitely on corrupted memory
+*
+* Revision 6.132  2003/04/30 16:40:41  kans
+* added CD as GenBank EST
+*
 * Revision 6.131  2003/03/25 13:32:22  kans
 * added CC as ncbi gss accession prefix
 *
@@ -3063,10 +3087,12 @@ NLM_EXTERN SeqIdPtr SeqIdSelect (SeqIdPtr sip, Uint1Ptr order, Int2 num)
 				else if (order[sip->choice] < order[bestid->choice])
 					bestid = sip;
 			}
-		}
-		else
+		} else {
 			ErrPostEx(SEV_ERROR, 0,0, "SeqIdSelect: choice [%d] out of range [%d]",
 				(int)(sip->choice), (int)num);
+			if(sip->choice > NUM_SEQID) /*** something is really wrong ***/
+				return NULL;
+		}
     }
 
     return bestid;
@@ -5974,68 +6000,82 @@ NLM_EXTERN Uint2 SeqLocPartialCheck(SeqLocPtr head)
 				break;
 			case SEQLOC_WHOLE:
 				found_molinfo = FALSE;
-				bsp = BioseqFind((SeqIdPtr)(slp->data.ptrvalue));
-				if (bsp == NULL) break;
-				bcp = BioseqContextNew(bsp);
-				if (bcp == NULL) break;
-				vnp = NULL;
-				while ((vnp = BioseqContextGetSeqDescr(bcp, Seq_descr_molinfo, vnp, NULL)) != NULL)
+				locked = FALSE;
+				bsp = BioseqFindCore((SeqIdPtr)(slp->data.ptrvalue));
+				if (bsp == NULL)
 				{
-					found_molinfo = TRUE;
-					mip = (MolInfoPtr)(vnp->data.ptrvalue);
-					switch (mip->completeness)
-					{
-						case 3:	/* no left */
-							if (slp == first)
-								retval |= SLP_START;
-							else
-								retval |= SLP_INTERNAL;
-							break;
-						case 4:    /* no right */
-							if (slp == last)
-								retval |= SLP_STOP;
-							else
-								retval |= SLP_INTERNAL;
-							break;
-						case 2:    /* partial */
-							retval |= SLP_OTHER;
-							break;
-						case 5:    /* no ends */
-							retval |= SLP_START;
-							retval |= SLP_STOP;
-							break;
-						default:
-							break;
-					}
+					bsp = BioseqLockById((SeqIdPtr)(slp->data.ptrvalue));
+					if (bsp != NULL)
+						locked = TRUE;
 				}
-				if (! found_molinfo)
-				{
-				while ((vnp = BioseqContextGetSeqDescr(bcp, Seq_descr_modif, vnp, NULL)) != NULL)
-				{
-					for (vnp2 = (ValNodePtr)(vnp->data.ptrvalue); vnp2 != NULL; vnp2 = vnp2->next)
+				if (bsp == NULL) break;
+				bcp = BioseqContextNew(bsp);
+				if (bcp != NULL) {
+					vnp = NULL;
+					while ((vnp = BioseqContextGetSeqDescr(bcp, Seq_descr_molinfo, vnp, NULL)) != NULL)
 					{
-						switch (vnp2->data.intvalue)
+						found_molinfo = TRUE;
+						mip = (MolInfoPtr)(vnp->data.ptrvalue);
+						switch (mip->completeness)
 						{
-							case 16:	/* no left */
+							case 3:	/* no left */
 								if (slp == first)
 									retval |= SLP_START;
 								else
 									retval |= SLP_INTERNAL;
 								break;
-							case 17:    /* no right */
+							case 4:    /* no right */
 								if (slp == last)
 									retval |= SLP_STOP;
 								else
 									retval |= SLP_INTERNAL;
 								break;
-							case 10:    /* partial */
+							case 2:    /* partial */
 								retval |= SLP_OTHER;
 								break;
+							case 5:    /* no ends */
+								retval |= SLP_START;
+								retval |= SLP_STOP;
+								break;
+							default:
+								break;
 						}
 					}
+					if (! found_molinfo)
+					{
+						while ((vnp = BioseqContextGetSeqDescr(bcp, Seq_descr_modif, vnp, NULL)) != NULL)
+						{
+							for (vnp2 = (ValNodePtr)(vnp->data.ptrvalue); vnp2 != NULL; vnp2 = vnp2->next)
+							{
+								switch (vnp2->data.intvalue)
+								{
+						
+									case 16:	/* no left */
+							
+										if (slp == first)
+								
+											retval |= SLP_START;
+									
+										else
+											retval |= SLP_INTERNAL;
+										break;
+									case 17:    /* no right */
+										if (slp == last)
+											retval |= SLP_STOP;
+										else
+											retval |= SLP_INTERNAL;
+										break;
+									case 10:    /* partial */
+										retval |= SLP_OTHER;
+										break;
+								}
+							}
+						}
+					}
+					BioseqContextFree(bcp);
 				}
-				}
-				BioseqContextFree(bcp);
+				if (locked)
+					BioseqUnlock (bsp);
 				break;
 			default:
 				break;
@@ -8723,7 +8763,9 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
 	      (StringICmp(temp,"BQ") == 0) || 
 	      (StringICmp(temp,"BU") == 0) || 
 	      (StringICmp(temp,"CA") == 0) || 
-	      (StringICmp(temp,"CB") == 0) ) {             /* NCBI EST */
+	      (StringICmp(temp,"CB") == 0) || 
+	      (StringICmp(temp,"CD") == 0) || 
+	      (StringICmp(temp,"CF") == 0) ) {                /* NCBI EST */
               retcode = ACCN_NCBI_EST;
           } else if ((StringICmp(temp,"BV") == 0)) {      /* NCBI STS */
               retcode = ACCN_NCBI_STS;
@@ -8734,7 +8776,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
               retcode = ACCN_NCBI_DIRSUB;
           } else if ((StringICmp(temp,"AE") == 0)) {      /* NCBI genome project data */
               retcode = ACCN_NCBI_GENOME;
-          } else if ((StringICmp(temp,"AH") == 0)) {      /* NCBI segmented set header Bioseq */
+          } else if ((StringICmp(temp,"AH") == 0) ||
+                     (StringICmp(temp,"CH") == 0)) {      /* NCBI segmented set header Bioseq */
               retcode = ACCN_NCBI_SEGSET | ACCN_AMBIGOUS_MOL; /* A few segmented
                                                                  proteins are AH */
           } else if ((StringICmp(temp,"AS") == 0)) {      /* NCBI "other" */
@@ -8745,7 +8788,9 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
                      (StringICmp(temp,"AZ") == 0) ||
                      (StringICmp(temp,"BH") == 0) ||
                      (StringICmp(temp,"BZ") == 0) ||
-                     (StringICmp(temp,"CC") == 0) )  {     /* NCBI GSS */
+                     (StringICmp(temp,"CC") == 0) ||
+                     (StringICmp(temp,"CE") == 0) ||
+                     (StringICmp(temp,"CG") == 0) )  {     /* NCBI GSS */
               retcode = ACCN_NCBI_GSS;
           } else if ((StringICmp(temp,"AR") == 0)) {      /* NCBI patent */
               retcode = ACCN_NCBI_PATENT;
@@ -8845,6 +8890,27 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
           s++;
       }
       break;
+    case 11: /* New 11-character accession, two letters +"_"+ 8 digits */
+      if(!IS_ALPHA(*s) || !IS_ALPHA(*(s+1)))
+          break;
+      if(*(s+2)!='_')
+          break;
+      temp[0] = *s; s++;
+      temp[1] = *s; s++;
+      temp[2] = NULLB; s++;
+      
+      if ((StringICmp(temp,"ZP") == 0)) { 
+          retcode = ACCN_REFSEQ_PROT_PREDICTED;
+      } else
+          retval = FALSE;
+      while (*s) {
+          if (! IS_DIGIT(*s)) {
+              retval = FALSE;
+              break;
+          }
+          s++;
+      }
+      break;
     case 12: /* whole genome shotgun 12-character accession, four letters + 8 digits */
       if(!IS_ALPHA(*s) || !IS_ALPHA(*(s+1)) || !IS_ALPHA(*(s+2)) || !IS_ALPHA(*(s+3)))
           break;
diff --git a/api/sqnutil1.c b/api/sqnutil1.c
index c22f7a65..41e84d32 100644
--- a/api/sqnutil1.c
+++ b/api/sqnutil1.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.271 $
+* $Revision: 6.283 $
 *
 * File Description: 
 *
@@ -1643,12 +1643,9 @@ NLM_EXTERN void PromoteXrefsEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID, B
   Char                 ch;
   CdRegionPtr          crp;
   Int2                 ctr = 1;
-  DbtagPtr             dbt;
   ValNodePtr           descr;
   SeqFeatPtr           first;
   GBQualPtr            gbq;
-  SeqFeatPtr           gene;
-  GeneRefPtr           grp;
   Int4                 i;
   Char                 id [64];
   SeqEntryPtr          last;
@@ -1680,6 +1677,11 @@ NLM_EXTERN void PromoteXrefsEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID, B
   long int             val;
   ValNodePtr           vnp;
   SeqFeatXrefPtr       xref;
+  /*
+  DbtagPtr             dbt;
+  SeqFeatPtr           gene;
+  GeneRefPtr           grp;
+  */
 
   if (sfp == NULL || bsp == NULL) return;
 
@@ -1693,8 +1695,9 @@ NLM_EXTERN void PromoteXrefsEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID, B
     sfp = sfp->next;
   }
 
-  /* expand genes specified by qualifiers on other features (except repeat_region) */
+  /* no longer expand genes specified by qualifiers on other features (except repeat_region) */
 
+  /*
   sfp = first;
   while (sfp != NULL) {
     prev = &(sfp->xref);
@@ -1720,7 +1723,6 @@ NLM_EXTERN void PromoteXrefsEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID, B
                 gene->location = AsnIoMemCopy (sfp->location,
                                                (AsnReadFunc) SeqLocAsnRead,
                                                (AsnWriteFunc) SeqLocAsnWrite);
-                /* copy dbxrefs from parent feature */
                 for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next) {
                   dbt = (DbtagPtr) vnp->data.ptrvalue;
                   if (dbt == NULL) continue;
@@ -1741,6 +1743,7 @@ NLM_EXTERN void PromoteXrefsEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID, B
     }
     sfp = sfp->next;
   }
+  */
 
   /* expand mRNA features into cDNA product sequences */
 
@@ -2739,7 +2742,7 @@ static void CleanupTrna (SeqFeatPtr sfp, tRNAPtr trp)
     if (aa == 0 && curraa != 0) {
       aa = curraa;
       trp->aa = curraa;
-      trp->aatype = Seq_code_ncbieaa;
+      trp->aatype = 2;
     }
     if (aa != 0 && aa == curraa) {
       if (justTrnaText) {
@@ -2758,7 +2761,7 @@ static void CleanupTrna (SeqFeatPtr sfp, tRNAPtr trp)
   aa = ParseTRnaString (sfp->comment, &justTrnaText, trpcodon, TRUE);
   if (aa == 0) return;
   trp->aa = aa;
-  trp->aatype = Seq_code_ncbieaa;
+  trp->aatype = 2;
   if (justTrnaText) {
     for (j = 0; j < 6; j++) {
       if (trp->codon [j] == 255) {
@@ -3241,7 +3244,7 @@ static Boolean HandledGBQualOnImp (SeqFeatPtr sfp, GBQualPtr gbq)
       ptr++;
       ch = *ptr;
     }
-    return TRUE;
+    /* return TRUE; */
   }
   return FALSE;
 }
@@ -5468,6 +5471,27 @@ static void CopyProtXrefToProtFeat (ProtRefPtr prp, ProtRefPtr prx)
   }
 }
 
+static Boolean InGpsGenomic (SeqFeatPtr sfp)
+
+{
+  BioseqPtr     bsp;
+  BioseqSetPtr  bssp;
+
+  if (sfp == NULL) return FALSE;
+  bsp = BioseqFindFromSeqLoc (sfp->location);
+  if (bsp == NULL) return FALSE;
+  if (bsp->idx.parenttype == OBJ_BIOSEQSET) {
+    bssp = (BioseqSetPtr) bsp->idx.parentptr;
+    while (bssp != NULL) {
+      if (bssp->_class == BioseqseqSet_class_nuc_prot) return FALSE;
+      if (bssp->_class == BioseqseqSet_class_gen_prod_set) return TRUE;
+      if (bssp->idx.parenttype != OBJ_BIOSEQSET) return FALSE;
+      bssp = (BioseqSetPtr) bssp->idx.parentptr;
+    }
+  }
+  return FALSE;
+}
+
 static void HandleXrefOnCDS (SeqFeatPtr sfp)
 
 {
@@ -5479,6 +5503,7 @@ static void HandleXrefOnCDS (SeqFeatPtr sfp)
   SeqFeatXrefPtr       xref;
 
   if (sfp != NULL && sfp->product != NULL) {
+    if (InGpsGenomic (sfp)) return;
     prot = GetBestProteinFeatureUnindexed (sfp->product);
     if (prot != NULL) {
       prp = (ProtRefPtr) prot->data.value.ptrvalue;
@@ -5737,6 +5762,10 @@ static void CleanupFeatureStrings (SeqFeatPtr sfp, Boolean stripSerial, ValNodeP
       CleanDoubleQuoteList (grp->syn);
       grp->db = ValNodeSort (grp->db, SortDbxref);
       CleanupDuplicateDbxrefs (&(grp->db));
+      /* now move grp->dbxref to sfp->dbxref */
+      vnp = grp->db;
+      grp->db = NULL;
+      ValNodeLink ((&sfp->dbxref), vnp);
       if (grp->locus != NULL && grp->syn != NULL) {
         vnp = grp->syn;
         str = (CharPtr) vnp->data.ptrvalue;
@@ -5772,6 +5801,10 @@ static void CleanupFeatureStrings (SeqFeatPtr sfp, Boolean stripSerial, ValNodeP
       CleanDoubleQuoteList (prp->activity);
       prp->db = ValNodeSort (prp->db, SortDbxref);
       CleanupDuplicateDbxrefs (&(prp->db));
+      /* now move prp->dbxref to sfp->dbxref */
+      vnp = prp->db;
+      prp->db = NULL;
+      ValNodeLink ((&sfp->dbxref), vnp);
       if (prp->processed != 3 && prp->processed != 4 &&
           prp->name == NULL && sfp->comment != NULL) {
         if (StringICmp (sfp->comment, "putative") != 0) {
@@ -6563,6 +6596,8 @@ static void BasicSeqEntryCleanupInternal (SeqEntryPtr sep, ValNodePtr PNTR publi
   OrgRefPtr     orp;
   Boolean       partial5;
   Boolean       partial3;
+  Uint1         processed;
+  ProtRefPtr    prp;
   ValNodePtr    psp;
   RnaRefPtr     rrp;
   Uint1         rrptype;
@@ -6659,6 +6694,28 @@ static void BasicSeqEntryCleanupInternal (SeqEntryPtr sep, ValNodePtr PNTR publi
                 sfp->data.value.ptrvalue = rrp;
                 rrp->type = rrptype;
                 sfp->idx.subtype = FindFeatDefType (sfp);
+              } else {
+                processed = 0;
+                if (StringCmp (ifp->key, "proprotein") == 0 || StringCmp (ifp->key, "preprotein") == 0) {
+                  processed = 1;
+                } else if (StringCmp (ifp->key, "mat_peptide") == 0) {
+                  processed = 2;
+                } else if (StringCmp (ifp->key, "sig_peptide") == 0) {
+                  processed = 3;
+                } else if (StringCmp (ifp->key, "transit_peptide") == 0) {
+                  processed = 4;
+                }
+                if (processed != 0 || StringCmp (ifp->key, "Protein") == 0) {
+                  bsp = BioseqFind (SeqLocId (sfp->location));
+                  if (bsp != NULL && ISA_aa (bsp->mol)) {
+                    sfp->data.value.ptrvalue = ImpFeatFree (ifp);
+                    sfp->data.choice = SEQFEAT_PROT;
+                    prp = ProtRefNew ();
+                    sfp->data.value.ptrvalue = prp;
+                    prp->processed = processed;
+                    sfp->idx.subtype = FindFeatDefType (sfp);
+                  }
+                }
               }
             }
           }
@@ -7267,6 +7324,83 @@ NLM_EXTERN void ResynchMessengerRNAPartials (SeqEntryPtr sep)
   VisitFeaturesInSep (sep, NULL, ResynchMRNAPartials);
 }
 
+NLM_EXTERN void ResynchPeptidePartials (SeqFeatPtr sfp, Pointer userdata)
+
+{
+  SeqFeatPtr   bestprot;
+  BioseqPtr    bsp;
+  MolInfoPtr   mip;
+  Boolean      partial5;
+  Boolean      partial3;
+  ProtRefPtr   prp;
+  SeqEntryPtr  sep;
+  SeqIdPtr     sip;
+  SeqLocPtr    slp;
+  ValNodePtr   vnp;
+
+  if (sfp->data.choice != SEQFEAT_PROT) return;
+  prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+  if (prp == NULL) return;
+  if (prp->processed < 1 || prp->processed > 4) return;
+  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+  sfp->partial = (Boolean) (sfp->partial || partial5 || partial3);
+  slp = SeqLocFindNext (sfp->location, NULL);
+  if (slp == NULL) return;
+  sip = SeqLocId (sfp->product);
+  if (sip == NULL) return;
+  bsp = BioseqFind (sip);
+  if (bsp != NULL && ISA_aa (bsp->mol) && bsp->repr == Seq_repr_raw) {
+    sep = SeqMgrGetSeqEntryForData (bsp);
+    if (sep == NULL) return;
+    bestprot = SeqMgrGetBestProteinFeature (bsp, NULL);
+    if (bestprot == NULL) {
+      bestprot = GetBestProteinFeatureUnindexed (sfp->product);
+    }
+    if (bestprot != NULL) {
+      bestprot->location = SeqLocFree (bestprot->location);
+      bestprot->location = CreateWholeInterval (sep);
+      SetSeqLocPartial (bestprot->location, partial5, partial3);
+      bestprot->partial = (partial5 || partial3);
+    }
+    vnp = SeqEntryGetSeqDescr (sep, Seq_descr_molinfo, NULL);
+    if (vnp == NULL) {
+      vnp = CreateNewDescriptor (sep, Seq_descr_molinfo);
+      if (vnp != NULL) {
+        mip = MolInfoNew ();
+        vnp->data.ptrvalue = (Pointer) mip;
+        if (mip != NULL) {
+          mip->biomol = 8;
+          mip->tech = 13;
+        }
+      }
+    }
+    if (vnp != NULL) {
+      mip = (MolInfoPtr) vnp->data.ptrvalue;
+      if (mip != NULL) {
+        if (partial5 && partial3) {
+          mip->completeness = 5;
+        } else if (partial5) {
+          mip->completeness = 3;
+        } else if (partial3) {
+          mip->completeness = 4;
+        /*
+        } else if (partial) {
+          mip->completeness = 2;
+        */
+        } else {
+          mip->completeness = 0;
+        }
+      }
+    }
+  }
+}
+
+NLM_EXTERN void ResynchProteinPartials (SeqEntryPtr sep)
+
+{
+  VisitFeaturesInSep (sep, NULL, ResynchPeptidePartials);
+}
+
 /* SeqIdStripLocus removes the SeqId.name field if accession is set */
 
 NLM_EXTERN SeqIdPtr SeqIdStripLocus (SeqIdPtr sip)
@@ -7479,9 +7613,12 @@ NLM_EXTERN Boolean UseLocalAsnloadDataAndErrMsg (void)
 {
   Boolean  dataFound;
   Char     path [PATH_MAX];
+  Char     appPath[PATH_MAX];
   CharPtr  ptr;
 
-  ProgramPath (path, sizeof (path));
+  ProgramPath (appPath, sizeof (path));
+  StrCpy(path, appPath);
+  /* data a sibling of our application? */
   ptr = StringRChr (path, DIRDELIMCHR);
   if (ptr != NULL) {
     ptr++;
@@ -7489,6 +7626,7 @@ NLM_EXTERN Boolean UseLocalAsnloadDataAndErrMsg (void)
   }
   dataFound = CheckDataPath (path, "data");
   if (! (dataFound)) {
+  /* data an uncle of our application? */
     if (ptr != NULL) {
       ptr--;
       *ptr = '\0';
@@ -7501,50 +7639,12 @@ NLM_EXTERN Boolean UseLocalAsnloadDataAndErrMsg (void)
     }
   }
 #ifdef OS_UNIX_DARWIN
-  /* Mac OS X package has application in Programname.app/Contents/MacOS/Programname */
-  if (! (dataFound)) {
-    if (ptr != NULL) {
-      /* check within Contents/Resources */
+  if (! (dataFound) &&  IsApplicationPackage(appPath)) {
+      /* is data inside our application within Contents/Resources? */
+      StrCpy(path, appPath);
+      FileBuildPath(path, "Contents", NULL);
       FileBuildPath (path, "Resources", NULL);
       dataFound = CheckDataPath (path, "data");
-      /* did not change ptr, so if it failed just go up to next higher level */
-    }
-  }
-  if (! (dataFound)) {
-    if (ptr != NULL) {
-      ptr--;
-      *ptr = '\0';
-      ptr = StringRChr (path, DIRDELIMCHR);
-      if (ptr != NULL) {
-        ptr++;
-        *ptr = '\0';
-      }
-      dataFound = CheckDataPath (path, "data");
-    }
-  }
-  if (! (dataFound)) {
-    if (ptr != NULL) {
-      ptr--;
-      *ptr = '\0';
-      ptr = StringRChr (path, DIRDELIMCHR);
-      if (ptr != NULL) {
-        ptr++;
-        *ptr = '\0';
-      }
-      dataFound = CheckDataPath (path, "data");
-    }
-  }
-  if (! (dataFound)) {
-    if (ptr != NULL) {
-      ptr--;
-      *ptr = '\0';
-      ptr = StringRChr (path, DIRDELIMCHR);
-      if (ptr != NULL) {
-        ptr++;
-        *ptr = '\0';
-      }
-      dataFound = CheckDataPath (path, "data");
-    }
   }
 #endif
   if (dataFound) {
@@ -7941,9 +8041,18 @@ NLM_EXTERN Uint2 FindFeatFromFeatDefType (Uint2 subtype)
       if (subtype >= FEATDEF_IMP && subtype <= FEATDEF_site_ref) {
         return SEQFEAT_IMP;
       }
+      if (subtype == FEATDEF_oriT) {
+        return SEQFEAT_IMP;
+      }
       if (subtype >= FEATDEF_preprotein && subtype <= FEATDEF_transit_peptide_aa) {
         return SEQFEAT_PROT;
       }
+      if (subtype == FEATDEF_operon) {
+        return SEQFEAT_IMP;
+      }
+      if (subtype == FEATDEF_gap) {
+        return SEQFEAT_IMP;
+      }
   }
   return 0;
 }
@@ -8263,6 +8372,7 @@ NLM_EXTERN Int4 VisitSeqIdsInSeqLoc (SeqLocPtr slp, Pointer userdata, VisitSeqId
   SeqPntPtr      spp;
 
   if (slp == NULL) return index;
+
   while (slp != NULL) {
     switch (slp->choice) {
       case SEQLOC_NULL :
@@ -8324,6 +8434,155 @@ NLM_EXTERN Int4 VisitSeqIdsInSeqLoc (SeqLocPtr slp, Pointer userdata, VisitSeqId
     }
     slp = slp->next;
   }
+
+  return index;
+}
+
+NLM_EXTERN Int4 VisitSeqIdsInSeqFeat (SeqFeatPtr sfp, Pointer userdata, VisitSeqIdFunc callback)
+
+{
+  CodeBreakPtr  cbp;
+  CdRegionPtr   crp;
+  Int4          index = 0;
+  RnaRefPtr     rrp;
+  tRNAPtr       trp;
+
+  if (sfp == NULL) return index;
+
+  index += VisitSeqIdsInSeqLoc (sfp->location, userdata, callback);
+  index += VisitSeqIdsInSeqLoc (sfp->product, userdata, callback);
+
+  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) {
+          index += VisitSeqIdsInSeqLoc (cbp->loc, userdata, callback);
+        }
+      }
+      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) {
+          index += VisitSeqIdsInSeqLoc (trp->anticodon, userdata, callback);
+        }
+      }
+      break;
+    default :
+      break;
+  }
+
+  return index;
+}
+
+NLM_EXTERN Int4 VisitSeqIdsInSeqAlign (SeqAlignPtr sap, Pointer userdata, VisitSeqIdFunc callback)
+
+{
+  DenseDiagPtr  ddp;
+  DenseSegPtr   dsp;
+  Int4          index = 0;
+  SeqIdPtr      sip;
+  SeqLocPtr     slp = NULL;
+  StdSegPtr     ssp;
+
+  if (sap == NULL) return index;
+
+  if (sap->bounds != NULL) {
+    sip = SeqLocId (sap->bounds);
+    index += VisitSeqIdList (sip, userdata, callback);
+  }
+
+  if (sap->segs == NULL) return index;
+
+  switch (sap->segtype) {
+    case SAS_DENDIAG :
+      ddp = (DenseDiagPtr) sap->segs;
+      if (ddp != NULL) {
+        for (sip = ddp->id; sip != NULL; sip = sip->next) {
+          index += VisitSeqIdList (sip, userdata, callback);
+        }
+      }
+      break;
+    case SAS_DENSEG :
+      dsp = (DenseSegPtr) sap->segs;
+      if (dsp != NULL) {
+        for (sip = dsp->ids; sip != NULL; sip = sip->next) {
+          index += VisitSeqIdList (sip, userdata, callback);
+        }
+      }
+      break;
+    case SAS_STD :
+      ssp = (StdSegPtr) sap->segs;
+      for (slp = ssp->loc; slp != NULL; slp = slp->next) {
+        sip = SeqLocId (slp);
+        index += VisitSeqIdList (sip, userdata, callback);
+      }
+      break;
+    case SAS_DISC :
+      /* recursive */
+      for (sap = (SeqAlignPtr) sap->segs; sap != NULL; sap = sap->next) {
+        index += VisitSeqIdsInSeqAlign (sap, userdata, callback);
+      }
+      break;
+    default :
+      break;
+  }
+
+  return index;
+}
+
+NLM_EXTERN Int4 VisitSeqIdsInSeqGraph (SeqGraphPtr sgp, Pointer userdata, VisitSeqIdFunc callback)
+
+{
+  Int4      index = 0;
+  SeqIdPtr  sip;
+
+  if (sgp == NULL) return index;
+
+  if (sgp->loc != NULL) {
+    sip = SeqLocId (sgp->loc);
+    index += VisitSeqIdList (sip, userdata, callback);
+  }
+
+  return index;
+}
+
+NLM_EXTERN Int4 VisitSeqIdsInSeqAnnot (SeqAnnotPtr annot, Pointer userdata, VisitSeqIdFunc callback)
+
+{
+  Int4         index = 0;
+  SeqAlignPtr  sap;
+  SeqFeatPtr   sfp;
+  SeqGraphPtr  sgp;
+
+  if (annot == NULL || annot->data == NULL) return index;
+
+  switch (annot->type) {
+
+    case 1 :
+      for (sfp = (SeqFeatPtr) annot->data; sfp != NULL; sfp = sfp->next) {
+        index += VisitSeqIdsInSeqFeat (sfp, userdata, callback);
+      }
+      break;
+
+    case 2 :
+      for (sap = (SeqAlignPtr) annot->data; sap != NULL; sap = sap->next) {
+        index += VisitSeqIdsInSeqAlign (sap, userdata, callback);
+      }
+      break;
+
+    case 3 :
+      for (sgp = (SeqGraphPtr) annot->data; sgp != NULL; sgp = sgp->next) {
+        index += VisitSeqIdsInSeqGraph (sgp, userdata, callback);
+      }
+      break;
+
+    default :
+      break;
+  }
+
   return index;
 }
 
diff --git a/api/sqnutil2.c b/api/sqnutil2.c
index f2e27242..a5817f57 100644
--- a/api/sqnutil2.c
+++ b/api/sqnutil2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.144 $
+* $Revision: 6.152 $
 *
 * File Description: 
 *
@@ -3054,14 +3054,17 @@ static SimpleSeqPtr ByteStoreToSimpleSeq (ByteStorePtr bs, CharPtr seqid, CharPt
 #define strandStr  field [STRAND_TAG]
 
 static Boolean ParseFeatTableLine (CharPtr line, Int4Ptr startP, Int4Ptr stopP,
-                                   BoolPtr partial5P, BoolPtr partial3P,
-                                   CharPtr PNTR featP, CharPtr PNTR qualP,
+                                   BoolPtr partial5P, BoolPtr partial3P, BoolPtr ispointP,
+                                   BoolPtr isminusP, CharPtr PNTR featP, CharPtr PNTR qualP,
                                    CharPtr PNTR valP, Int4 offset)
 
 {
   Boolean     badNumber;
   CharPtr     field [NUM_FTABLE_COLUMNS];
   Int2        i;
+  Boolean     isminus = FALSE;
+  Boolean     ispoint = FALSE;
+  size_t      len;
   ValNodePtr  parsed;
   Boolean     partial5 = FALSE;
   Boolean     partial3 = FALSE;
@@ -3098,6 +3101,11 @@ static Boolean ParseFeatTableLine (CharPtr line, Int4Ptr startP, Int4Ptr stopP,
     partial5 = TRUE;
     str++;
   }
+  len = StringLen (str);
+  if (len > 1 && str [len - 1] == '^') {
+    ispoint = TRUE;
+    str [len - 1] = '\0';
+  }
   if (str != NULL && sscanf (str, "%ld", &val) == 1) {
     start = val;
   } else {
@@ -3131,6 +3139,7 @@ static Boolean ParseFeatTableLine (CharPtr line, Int4Ptr startP, Int4Ptr stopP,
           start = stop;
           stop = tmp;
         }
+        isminus = TRUE;
       }
     }
   }
@@ -3139,6 +3148,8 @@ static Boolean ParseFeatTableLine (CharPtr line, Int4Ptr startP, Int4Ptr stopP,
   *stopP = stop + offset;
   *partial5P = partial5;
   *partial3P = partial3;
+  *ispointP = ispoint;
+  *isminusP = isminus;
   *featP = featType;
   *qualP = qualType;
   *valP = qualVal;
@@ -3297,7 +3308,8 @@ NLM_EXTERN Uint1 ParseTRnaString (CharPtr strx, BoolPtr justTrnaText, Uint1Ptr c
       }
     } else if (StringICmp ("tRNA", str) != 0 &&
                StringICmp ("transfer", str) != 0 &&
-               StringICmp ("RNA", str) != 0) {
+               StringICmp ("RNA", str) != 0 &&
+               StringICmp ("product", str) != 0) {
       if (cdP != NULL && StringLen (str) == 3) {
         StringCpy (codon, str);
         for (i = 0; i < 3; i++) {
@@ -3323,7 +3335,8 @@ NLM_EXTERN Uint1 ParseTRnaString (CharPtr strx, BoolPtr justTrnaText, Uint1Ptr c
     if (curraa != 0) {
     } else if (StringICmp ("tRNA", str) != 0 &&
                StringICmp ("transfer", str) != 0 &&
-               StringICmp ("RNA", str) != 0) {
+               StringICmp ("RNA", str) != 0 &&
+               StringICmp ("product", str) != 0) {
       if (cdP != NULL && StringLen (str) == 3) {
         StringCpy (codon, str);
         for (i = 0; i < 3; i++) {
@@ -4127,6 +4140,12 @@ NLM_EXTERN void AddQualifierToFeature (SeqFeatPtr sfp, CharPtr qual, CharPtr val
       prp->desc = StringSaveNoNull (val);
     } else if (sfp->data.choice == SEQFEAT_CDREGION && StringCmp (qual, "prot_note") == 0) {
       bail = FALSE;
+    } else if (sfp->data.choice == SEQFEAT_PROT && StringCmp (qual, "prot_desc") == 0) {
+      prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+      if (prp != NULL) {
+        prp->desc = MemFree (prp->desc);
+        prp->desc = StringSaveNoNull (val);
+      }
     } 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)) {
@@ -4313,6 +4332,20 @@ NLM_EXTERN void AddQualifierToFeature (SeqFeatPtr sfp, CharPtr qual, CharPtr val
         }
       }
     }
+  } else if (sfp->data.choice == SEQFEAT_PROT) {
+    if (qnum == GBQUAL_function || qnum == GBQUAL_EC_number || qnum == GBQUAL_product) {
+      prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+      if (prp != NULL) {
+        if (qnum == GBQUAL_function) {
+          ValNodeCopyStr (&(prp->activity), 0, val);
+        } else if (qnum == GBQUAL_EC_number) {
+          ValNodeCopyStr (&(prp->ec), 0, val);
+        } else if (qnum == GBQUAL_product) {
+          ValNodeCopyStr (&(prp->name), 0, val);
+        }
+        return;
+      }
+    }
   } else if (sfp->data.choice == SEQFEAT_RNA) {
     if (qnum == GBQUAL_product) {
       rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
@@ -4485,16 +4518,94 @@ NLM_EXTERN SeqLocPtr AddIntervalToLocation (SeqLocPtr loc, SeqIdPtr sip,
   return rsult;
 }
 
+static CharPtr TokenizeAtWhiteSpace (CharPtr str)
+
+{
+  Char     ch;
+  CharPtr  ptr;
+
+  if (str == NULL) return NULL;
+  ptr = str;
+  ch = *ptr;
+
+  while (ch != '\0' && (IS_WHITESP (ch))) {
+    ptr++;
+    ch = *ptr;
+  }
+  while (ch != '\0' && (! IS_WHITESP (ch))) {
+    ptr++;
+    ch = *ptr;
+  }
+  if (ch != '\0') {
+    *ptr = '\0';
+    ptr++;
+  }
+
+  return ptr;
+}
+
+static void ParseWhitespaceIntoTabs (CharPtr line)
+
+{
+  Char     ch;
+  size_t   len;
+  CharPtr  ptr;
+  CharPtr  str;
+  CharPtr  tmp;
+
+  if (StringHasNoText (line)) return;
+  len = StringLen (line) + 10;
+
+  str = MemNew (len);
+  if (str == NULL) return;
+
+  ptr = line;
+  ch = *ptr;
+  if (IS_WHITESP (ch)) {
+    /* qualifier value line */
+    StringCat (str, "\t\t\t");
+    TrimSpacesAroundString (ptr);
+    tmp = TokenizeAtWhiteSpace (ptr);
+    StringCat (str, ptr);
+    StringCat (str, "\t");
+    StringCat (str, tmp);
+  } else {
+    /* location and possible feature key line */
+    TrimSpacesAroundString (ptr);
+    tmp = TokenizeAtWhiteSpace (ptr);
+    StringCat (str, ptr);
+    StringCat (str, "\t");
+    ptr = tmp;
+    tmp = TokenizeAtWhiteSpace (ptr);
+    StringCat (str, ptr);
+    ptr = tmp;
+    if (! StringHasNoText (ptr)) {
+      tmp = TokenizeAtWhiteSpace (ptr);
+      StringCat (str, "\t");
+      StringCat (str, ptr);
+    }
+  }
+
+  /* replace original with tab-delimited table */
+  StringCpy (line, str);
+
+  MemFree (str);
+}
+
 static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
 
 {
+  Boolean        allowWhitesp  = TRUE;
   BioSourcePtr   biop;
   CdRegionPtr    crp;
   AnnotDescrPtr  desc;
   CharPtr        feat;
+  IntFuzzPtr     fuzz;
   GeneRefPtr     grp;
   Int2           idx;
   ImpFeatPtr     ifp;
+  Boolean        isminus;
+  Boolean        ispoint;
   Int2           j;
   CharPtr        label;
   Char           line [2047];
@@ -4508,12 +4619,15 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
   PubdescPtr     pdp;
   Int4           pos;
   SeqFeatPtr     prev = NULL;
+  ProtRefPtr     prp;
   CharPtr        qual;
   Uint1          rnatype;
   RnaRefPtr      rrp;
   SeqAnnotPtr    sap = NULL;
   SeqFeatPtr     sfp = NULL;
   SeqIdPtr       sip;
+  SeqLocPtr      slp;
+  SeqPntPtr      spp;
   Int4           start;
   Int4           stop;
   SqnTagPtr      stp;
@@ -4543,7 +4657,11 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
         return sap;
       }
 
-      if (ParseFeatTableLine (line, &start, &stop, &partial5, &partial3, &feat, &qual, &val, offset)) {
+      if (allowWhitesp) {
+        ParseWhitespaceIntoTabs (line);
+      }
+
+      if (ParseFeatTableLine (line, &start, &stop, &partial5, &partial3, &ispoint, &isminus, &feat, &qual, &val, offset)) {
         if (feat != NULL && start >= 0 && stop >= 0) {
 
           if (sap == NULL) {
@@ -4620,6 +4738,23 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
                 rrp->type = rnatype;
               }
 
+            } else if (StringCmp (feat, "Protein") == 0) {
+
+              sfp->data.choice = SEQFEAT_PROT;
+              prp = ProtRefNew ();
+              if (prp != NULL) {
+                sfp->data.value.ptrvalue = (Pointer) prp;
+              }
+
+            } else if (StringCmp (feat, "proprotein") == 0) {
+
+              sfp->data.choice = SEQFEAT_PROT;
+              prp = ProtRefNew ();
+              if (prp != NULL) {
+                sfp->data.value.ptrvalue = (Pointer) prp;
+                prp->processed = 1;
+              }
+
             } else if (StringCmp (feat, "source") == 0) {
 
               sfp->data.choice = SEQFEAT_BIOSRC;
@@ -4672,7 +4807,30 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
               }
             }
 
-            sfp->location = AddIntervalToLocation (NULL, sip, start, stop, partial5, partial3);
+            if (ispoint) {
+              spp = SeqPntNew ();
+              if (spp != NULL) {
+                spp->point = start;
+                if (isminus) {
+                  spp->strand = Seq_strand_minus;
+                }
+                spp->id = SeqIdDup (sip);
+                fuzz = IntFuzzNew ();
+                if (fuzz != NULL) {
+                  fuzz->choice = 4;
+                  fuzz->a = 3;
+                  spp->fuzz = fuzz;
+                }
+                slp = ValNodeNew (NULL);
+                if (slp != NULL) {
+                  slp->choice = SEQLOC_PNT;
+                  slp->data.ptrvalue = (Pointer) spp;
+                  sfp->location = slp;
+                }
+              }
+            } else {
+              sfp->location = AddIntervalToLocation (NULL, sip, start, stop, partial5, partial3);
+            }
 
             if (partial5 || partial3) {
               sfp->partial = TRUE;
@@ -5250,7 +5408,7 @@ NLM_EXTERN Pointer ReadAsnFastaOrFlatFile (FILE *fp, Uint2Ptr datatypeptr, Uint2
   Boolean        inLetters;
   Boolean        isProt = FALSE;
   Int4           j;
-  Char           line [1023];
+  Char           line [4096];
   Boolean        mayBeAccessionList = TRUE;
   Boolean        mayBePlainFasta = TRUE;
   SeqFeatPtr     nextsfp;
diff --git a/api/sqnutil3.c b/api/sqnutil3.c
index 76bcdcc8..c1554dcd 100644
--- a/api/sqnutil3.c
+++ b/api/sqnutil3.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   2/7/00
 *
-* $Revision: 6.23 $
+* $Revision: 6.28 $
 *
 * File Description: 
 *
@@ -977,6 +977,7 @@ static FeatdefNameData featdefWithName [] = {
   { FEATDEF_D_segment ,          "D_segment"          },
   { FEATDEF_enhancer ,           "enhancer"           },
   { FEATDEF_exon ,               "exon"               },
+  { FEATDEF_gap ,                "gap"                },
   { FEATDEF_GC_signal ,          "GC_signal"          },
   { FEATDEF_GENE ,               "Gene"               },
   { FEATDEF_HET ,                "Het"                },
@@ -1001,6 +1002,8 @@ static FeatdefNameData featdefWithName [] = {
   { FEATDEF_NUM ,                "Num"                },
   { FEATDEF_N_region ,           "N_region"           },
   { FEATDEF_old_sequence ,       "old_sequence"       },
+  { FEATDEF_operon ,             "operon"             },
+  { FEATDEF_oriT ,               "oriT"               },
   { FEATDEF_polyA_signal ,       "polyA_signal"       },
   { FEATDEF_polyA_site ,         "polyA_site"         },
   { FEATDEF_preRNA ,             "precursor_RNA"      },
@@ -1159,11 +1162,14 @@ static CharPtr featurekeys [] = {
   "NonStdRes" ,
   "Het" ,
   "Src" ,
-  "pro_peptide" ,
+  "proprotein" ,
   "mat_peptide" ,
   "sig_peptide" ,
   "transit_peptide",
-  "snoRNA"
+  "snoRNA",
+  "gap",
+  "operon",
+  "oriT"
 };
 
 NLM_EXTERN CharPtr FindKeyFromFeatDefType (Uint1 type, Boolean forGBFF)
@@ -1527,3 +1533,23 @@ NLM_EXTERN void SegOrDeltaBioseqToRaw (BioseqPtr bsp)
   bsp->seq_data_type = Seq_code_iupacna;
 }
 
+
+static PubMedFetchFunc pmf_pubfetch = NULL;
+
+NLM_EXTERN void LIBCALL PubMedSetFetchFunc (PubMedFetchFunc func)
+
+{
+  pmf_pubfetch = func;
+}
+
+NLM_EXTERN PubmedEntryPtr LIBCALL GetPubMedForUid (Int4 uid)
+
+{
+  PubMedFetchFunc  func;
+
+  if (uid < 1) return NULL;
+  func = pmf_pubfetch;
+  if (func == NULL) return NULL;
+  return func (uid);
+}
+
diff --git a/api/sqnutils.h b/api/sqnutils.h
index 20b6e762..e3a061e3 100644
--- a/api/sqnutils.h
+++ b/api/sqnutils.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.87 $
+* $Revision: 6.92 $
 *
 * File Description: 
 *
@@ -47,6 +47,7 @@
 
 #include <ncbi.h>
 #include <sequtil.h>
+#include <objpubme.h>
 
 #undef NLM_EXTERN
 #ifdef NLM_IMPORT
@@ -195,10 +196,15 @@ NLM_EXTERN void ResynchCodingRegionPartials (SeqEntryPtr sep);
 
 NLM_EXTERN void ResynchMessengerRNAPartials (SeqEntryPtr sep);
 
+/* resynchronizes protein feature with product peptide bioseq */
+
+NLM_EXTERN void ResynchProteinPartials (SeqEntryPtr sep);
+
 /* individual feature callbacks for above functions */
 
 NLM_EXTERN void ResynchMRNAPartials (SeqFeatPtr sfp, Pointer userdata);
 NLM_EXTERN void ResynchCDSPartials (SeqFeatPtr sfp, Pointer userdata);
+NLM_EXTERN void ResynchPeptidePartials (SeqFeatPtr sfp, Pointer userdata);
 
 /* functions to parse [org=Drosophila melanogaster] and [gene=lacZ] from titles */
 /* for example, passing "gene" to SqnTagFind returns "lacZ" */
@@ -493,11 +499,16 @@ NLM_EXTERN Int4 VisitSetsInSet (BioseqSetPtr bssp, Pointer userdata, VisitSetsFu
 typedef void (*VisitElementsFunc) (SeqEntryPtr sep, Pointer userdata);
 NLM_EXTERN Int4 VisitElementsInSep (SeqEntryPtr sep, Pointer userdata, VisitElementsFunc callback);
 
-/* visits all SeqIds within a SeqLoc */
+/* visits all SeqIds within a SeqLoc, or within features, alignments, graphs, or annots */
 
 typedef void (*VisitSeqIdFunc) (SeqIdPtr sip, Pointer userdata);
 NLM_EXTERN Int4 VisitSeqIdsInSeqLoc (SeqLocPtr slp, Pointer userdata, VisitSeqIdFunc callback);
 
+NLM_EXTERN Int4 VisitSeqIdsInSeqFeat (SeqFeatPtr sfp, Pointer userdata, VisitSeqIdFunc callback);
+NLM_EXTERN Int4 VisitSeqIdsInSeqAlign (SeqAlignPtr sap, Pointer userdata, VisitSeqIdFunc callback);
+NLM_EXTERN Int4 VisitSeqIdsInSeqGraph (SeqGraphPtr sgp, Pointer userdata, VisitSeqIdFunc callback);
+NLM_EXTERN Int4 VisitSeqIdsInSeqAnnot (SeqAnnotPtr annot, Pointer userdata, VisitSeqIdFunc callback);
+
 /* visits all sub UserFields - if the data type is 11, VisitUserFieldsInUfp recurses */
 
 typedef void (*VisitUserFieldsFunc) (UserFieldPtr ufp, Pointer userdata);
@@ -538,6 +549,17 @@ NLM_EXTERN Int4 VisitBioSourcesInSep (SeqEntryPtr sep, Pointer userdata, VisitBi
 typedef void (*ScanBioseqSetFunc) (SeqEntryPtr sep, Pointer userdata);
 NLM_EXTERN Int4 ScanBioseqSetRelease (CharPtr inputFile, Boolean binary, Boolean compressed, Pointer userdata, ScanBioseqSetFunc callback);
 
+/* PubMed registered fetch functionality */
+
+NLM_EXTERN PubmedEntryPtr LIBCALL GetPubMedForUid (Int4 uid);
+
+/* internal support type, registration function */
+
+typedef PubmedEntryPtr (LIBCALLBACK * PubMedFetchFunc) (Int4 uid);
+
+NLM_EXTERN void LIBCALL PubMedSetFetchFunc (PubMedFetchFunc func);
+
+
 
 #ifdef __cplusplus
 }
diff --git a/api/subutil.c b/api/subutil.c
index ff5c748d..a4cbcaed 100644
--- a/api/subutil.c
+++ b/api/subutil.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 11/3/93
 *
-* $Revision: 6.52 $
+* $Revision: 6.55 $
 *
 * File Description: Utilities for creating ASN.1 submissions
 *
@@ -40,6 +40,17 @@
 *
 *
 * $Log: subutil.c,v $
+* Revision 6.55  2003/10/16 17:16:33  mjohnson
+*
+* Added ORG_* and IS_ORG_* defines for origins. Use these constants
+* and macros instead of small integers.
+*
+* Revision 6.54  2003/10/08 16:46:44  kans
+* fix in AddCompleteness (KT)
+*
+* Revision 6.53  2003/07/11 18:22:45  kans
+* AddSourceToRefGeneTrackUserObject
+*
 * Revision 6.52  2002/11/05 17:01:55  kans
 * refgene tracking user object uses comment as name if accession is empty
 *
@@ -2570,7 +2581,7 @@ NLM_EXTERN Boolean AddGenomeToEntry (
 		bio = BioSourceNew();
 	}
 	bio->genome = (Uint1)type;
-	bio->origin = 0;               /* unknown */
+	bio->origin = ORG_DEFAULT;	/* unknown */
 	vnp->data.ptrvalue = (Pointer) bio;
 	
 	return TRUE;
@@ -2732,19 +2743,19 @@ NLM_EXTERN void AddCompleteness(NCBISubPtr submission, SeqEntryPtr sep, SeqFeatP
 	Boolean	partial = FALSE;
 
 	retval = SeqLocPartialCheck(sfp->location);
-	if (retval & SLP_START) {
+	if ((retval & SLP_START) && (retval & SLP_STOP)) {
+		AddCompleteToEntry(submission, sep, 5);   /* no_ends */
+		partial = TRUE;
+	} else if (retval & SLP_START) {
 		AddCompleteToEntry(submission, sep, 3);   /* no_left */
 		partial = TRUE;
-	}
-	if (retval & SLP_STOP) {
+	} else if (retval & SLP_STOP) {
 		AddCompleteToEntry(submission, sep, 4);  /* no_right */
 		partial = TRUE;
-	}
-	if (retval & (SLP_OTHER | SLP_INTERNAL)) {
+	} else if (retval & (SLP_OTHER | SLP_INTERNAL)) {
 		AddCompleteToEntry(submission, sep, 2);  /* partial */
 		partial = TRUE;
-	}
-	if (!partial && sfp->partial) {
+	} else if (!partial && sfp->partial) {
 		AddCompleteToEntry(submission, sep, 2);  /* partial */
 	}
 }
@@ -4420,6 +4431,7 @@ NLM_EXTERN void AddCuratorToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr c
 {
   UserFieldPtr  curr;
   ObjectIdPtr   oip;
+  UserFieldPtr  prev = NULL;
 
   if (uop == NULL || collaborator == NULL) return;
   oip = uop->type;
@@ -4430,6 +4442,7 @@ NLM_EXTERN void AddCuratorToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr c
     if (oip != NULL && StringICmp (oip->str, "Collaborator") == 0) {
       break;
     }
+    prev = curr;
   }
 
   if (curr == NULL) {
@@ -4439,10 +4452,13 @@ NLM_EXTERN void AddCuratorToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr c
     curr->label = oip;
     curr->choice = 1; /* visible string */
 
-    /* link status at beginning of list */
+    /* link curator at end of list */
 
-    curr->next = uop->data;
-    uop->data = curr;
+    if (prev != NULL) {
+      prev->next = curr;
+    } else {
+      uop->data = curr;
+    }
   }
 
   if (curr == NULL || curr->choice != 1) return;
@@ -4454,6 +4470,50 @@ NLM_EXTERN void AddCuratorToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr c
   curr->data.ptrvalue = (Pointer) StringSave (collaborator);
 }
 
+NLM_EXTERN void AddSourceToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr genomicSource)
+
+{
+  UserFieldPtr  curr;
+  ObjectIdPtr   oip;
+  UserFieldPtr  prev = NULL;
+
+  if (uop == NULL || genomicSource == NULL) return;
+  oip = uop->type;
+  if (oip == NULL || StringICmp (oip->str, "RefGeneTracking") != 0) return;
+
+  for (curr = uop->data; curr != NULL; curr = curr->next) {
+    oip = curr->label;
+    if (oip != NULL && StringICmp (oip->str, "GenomicSource") == 0) {
+      break;
+    }
+    prev = curr;
+  }
+
+  if (curr == NULL) {
+    curr = UserFieldNew ();
+    oip = ObjectIdNew ();
+    oip->str = StringSave ("GenomicSource");
+    curr->label = oip;
+    curr->choice = 1; /* visible string */
+
+    /* link source at end of list */
+
+    if (prev != NULL) {
+      prev->next = curr;
+    } else {
+      uop->data = curr;
+    }
+  }
+
+  if (curr == NULL || curr->choice != 1) return;
+
+  /* replace any existing source indication */
+
+  curr->data.ptrvalue = MemFree (curr->data.ptrvalue);
+
+  curr->data.ptrvalue = (Pointer) StringSave (genomicSource);
+}
+
 NLM_EXTERN void AddAccessionToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr field,
                                                       CharPtr accn, Int4 gi,
                                                       Boolean sequenceChange,
diff --git a/api/subutil.h b/api/subutil.h
index 480c5157..41645047 100644
--- a/api/subutil.h
+++ b/api/subutil.h
@@ -31,7 +31,7 @@
 *   
 * Version Creation Date: 11/3/93
 *
-* $Revision: 6.43 $
+* $Revision: 6.46 $
 *
 * File Description: Utilities for creating ASN.1 submissions
 *
@@ -42,6 +42,17 @@
 *
 *
 * $Log: subutil.h,v $
+* Revision 6.46  2003/10/21 18:16:05  bazhin
+* Replaced C++ comments with C ones.
+*
+* Revision 6.45  2003/10/16 17:16:33  mjohnson
+*
+* Added ORG_* and IS_ORG_* defines for origins. Use these constants
+* and macros instead of small integers.
+*
+* Revision 6.44  2003/07/11 18:22:45  kans
+* AddSourceToRefGeneTrackUserObject
+*
 * Revision 6.43  2002/07/09 16:17:35  kans
 * AddAccessionToTpaAssemblyUserObject takes from and to parameters
 *
@@ -949,6 +960,26 @@ NLM_EXTERN Boolean AddSubSourceToEntry (
 #define ORGMOD_old_name 254
 #define ORGMOD_other 255 
 
+/* Defines for BioSrc.origin
+ */
+#define ORG_UNKNOWN 0
+#define ORG_NATURAL 1
+#define ORG_NATMUT 2
+#define ORG_MUT 3
+#define ORG_ARTIFICIAL 4
+#define ORG_SYNTHETIC 5
+#define ORG_OTHER 255
+#define ORG_DEFAULT ORG_UNKNOWN
+
+#define IS_ORG_UNKNOWN(S) ((S).origin == ORG_UNKNOWN)
+#define IS_ORG_NATURAL(S) ((S).origin == ORG_NATURAL)
+#define IS_ORG_NATMUT(S) ((S).origin == ORG_NATMUT)
+#define IS_ORG_MUT(S) ((S).origin == ORG_MUT)
+#define IS_ORG_ARTIFICIAL(S) ((S).origin == ORG_ARTIFICIAL)
+#define IS_ORG_SYNTHETIC(S) ((S).origin == ORG_SYNTHETIC)
+#define IS_ORG_OTHER(S) ((S).origin == ORG_OTHER)
+
+
 /*********************************************
 *  OrgMod defines subclasses of organism names
 *    (also see SubSource above for subclasses of source material)
@@ -1557,6 +1588,7 @@ NLM_EXTERN Boolean AddPhrapGraphToSeqLit (
 NLM_EXTERN UserObjectPtr CreateRefGeneTrackUserObject (void);
 NLM_EXTERN void AddStatusToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr status);
 NLM_EXTERN void AddCuratorToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr collaborator);
+NLM_EXTERN void AddSourceToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr genomicSource);
 NLM_EXTERN void AddAccessionToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr field,
                                                       CharPtr accn, Int4 gi,
                                                       Boolean sequenceChange,
diff --git a/api/tofasta.c b/api/tofasta.c
index bba0ed88..c605b2a0 100644
--- a/api/tofasta.c
+++ b/api/tofasta.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/12/91
 *
-* $Revision: 6.114 $
+* $Revision: 6.121 $
 *
 * File Description:  various sequence objects to fasta output
 *
@@ -39,6 +39,27 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: tofasta.c,v $
+* Revision 6.121  2003/08/04 19:51:02  kans
+* for complete chromosome title, if > 3 clones (by counting semicolons) then just display count, not full text of clones
+*
+* Revision 6.120  2003/07/25 16:15:25  kans
+* FindProtDefLine of hypothetical protein only needs to look for locus_tag
+*
+* Revision 6.119  2003/07/25 15:34:07  kans
+* protect FindProtDefLine against no parent CDS (e.g., SWISS-PROT segmented record P33072)
+*
+* Revision 6.118  2003/07/24 21:51:04  kans
+* if hypothetical protein, find gene and add to name
+*
+* Revision 6.117  2003/07/23 20:37:02  kans
+* if making htgs title, do not set iip values
+*
+* Revision 6.116  2003/07/22 18:31:44  kans
+* Added support for EMBLBlockPtr keywords in addition to GBBlockPtr keywords in suppressing sequencing in progress message
+*
+* Revision 6.115  2003/05/02 16:22:24  kans
+* added FindNRDefLine to make NR_ deflines on the fly
+*
 * Revision 6.114  2003/03/25 17:00:53  kans
 * CreateDefLine htgs suffix only shows if delta seq with more than 0 gaps
 *
@@ -2603,6 +2624,7 @@ static ValNodePtr IndexedGatherDescrOnBioseq (ItemInfoPtr iip, BioseqPtr bsp, Ui
 	SeqDescrPtr        sdp;
 
 	sdp = SeqMgrGetNextDescriptor (bsp, NULL, choice, &dcontext);
+	if (sdp == NULL) return NULL;
 	if (ISA_aa(bsp->mol) && !is_pdb(bsp)) {
 		if (dcontext.level != 0) return NULL;
 	}
@@ -2836,6 +2858,89 @@ static CharPtr FindNMDefLine (BioseqPtr bsp)
   return str;
 }
 
+static CharPtr FindNRDefLine (BioseqPtr bsp)
+
+{
+  BioSourcePtr  biop;
+  Char          buf [512];
+  Uint2         entityID;
+  CharPtr       gene;
+  size_t        len;
+  MolInfoPtr    mip;
+  NMDef         nd;
+  OrgRefPtr     orp;
+  CharPtr       rna = "miscRNA";
+  SeqEntryPtr   sep;
+  CharPtr       str;
+  ValNodePtr    vnp;
+
+  MemSet ((Pointer) &nd, 0, sizeof (NMDef));
+  entityID = ObjMgrGetEntityIDForPointer (bsp);
+  sep = GetBestTopParentForDataEx (entityID, bsp, TRUE);
+
+  VisitFeaturesInSep (sep, (Pointer) &nd, FindNMFeats);
+  if (nd.numgenes < 1) return NULL;
+
+  vnp = GatherDescrOnBioseq (NULL, bsp, Seq_descr_source, FALSE);
+  if (vnp == NULL) return NULL;
+  biop = (BioSourcePtr) vnp->data.ptrvalue;
+  orp = biop->org;
+  if (orp == NULL || StringHasNoText (orp->taxname)) return NULL;
+
+  FeatDefLabel (nd.gene, buf, sizeof (buf) - 1, OM_LABEL_CONTENT);
+  gene = StringSaveNoNull (buf);
+
+  vnp = GatherDescrOnBioseq (NULL, bsp, Seq_descr_molinfo,TRUE);
+  if (vnp != NULL) {
+    mip = (MolInfoPtr) vnp->data.ptrvalue;
+    if (mip != NULL) {
+      switch (mip->biomol) {
+        case MOLECULE_TYPE_PRE_MRNA :
+          rna = "precursorRNA";
+          break;
+        case MOLECULE_TYPE_MRNA :
+          rna = "mRNA";
+          break;
+        case MOLECULE_TYPE_RRNA :
+          rna = "rRNA";
+          break;
+        case MOLECULE_TYPE_TRNA :
+          rna = "tRNA";
+          break;
+        case MOLECULE_TYPE_SNRNA :
+          rna = "snRNA";
+          break;
+        case MOLECULE_TYPE_SCRNA :
+          rna = "scRNA";
+          break;
+        case MOLECULE_TYPE_CRNA :
+          rna = "cRNA";
+          break;
+        case MOLECULE_TYPE_SNORNA :
+          rna = "snoRNA";
+          break;
+        case MOLECULE_TYPE_TRANSCRIBED_RNA :
+          rna = "miscRNA";
+          break;
+        default :
+          break;
+      }
+    }
+  }
+
+  len = StringLen (orp->taxname) + StringLen (gene) +
+        StringLen (", ") + 30;
+
+  str = (CharPtr) MemNew (len);
+  if (str != NULL) {
+    sprintf (str, "%s %s, %s", orp->taxname, gene, rna);
+  }
+
+  MemFree (gene);
+
+  return str;
+}
+
 static CharPtr FindProtDefLine(BioseqPtr bsp)
 {
 	SeqFeatPtr sfp = NULL, f;
@@ -2880,6 +2985,58 @@ static CharPtr FindProtDefLine(BioseqPtr bsp)
                                         (CharPtr) vnp->data.ptrvalue);
 				s += StringLen((CharPtr)vnp->data.ptrvalue) + 2;
 			}
+			/* if hypothetical protein, append locus_tag */
+			if (StringICmp (title, "hypothetical protein") == 0) {
+				sfp = NULL;
+				if (indexed) {
+					sfp = SeqMgrGetCDSgivenProduct (bsp, NULL);
+				} else {
+					sfp = GatherProtCDS(bsp);
+				}
+				if (sfp != NULL) {
+					grp = SeqMgrGetGeneXref (sfp);
+					if (grp == NULL) {
+						loc = sfp->location;
+						best_gene = NULL;
+						if (indexed) {
+							best_gene = SeqMgrGetOverlappingGene (loc, NULL);
+						} else {
+							vnp = GatherGenesForCDS(loc);
+							for (v=vnp; v; v=v->next) {
+								f = (SeqFeatPtr) v->data.ptrvalue;
+								diff_current = SeqLocAinB(loc, f->location);
+								if (! diff_current) {
+									best_gene = f;
+									break;
+								} else if (diff_current > 0) {
+									if ((diff_lowest == -1) || (diff_current<diff_lowest)) {
+										diff_lowest = diff_current;
+										best_gene = f;
+									}
+								}
+							}
+							ValNodeFree(vnp);
+						}
+						if (best_gene != NULL) {
+							grp = (GeneRefPtr) best_gene->data.value.ptrvalue;
+						}
+					}
+				}
+				if (grp != NULL) {
+					geneprod = NULL;
+					if (grp->locus_tag != NULL) {
+						geneprod = grp->locus_tag;
+					}
+					if (geneprod != NULL) {
+						s = (CharPtr) MemNew (StringLen (geneprod) + StringLen (title) + 20);
+						if (s != NULL) {
+							sprintf (s, "%s %s", title, geneprod);
+							MemFree (title);
+							title = s;
+						}
+					}
+				}
+			}
 		} else if (prp->desc) {
 			title = StringSave(prp->desc);
 		}
@@ -3084,6 +3241,27 @@ static Boolean StrainNotAtEndOfTaxname (CharPtr name, CharPtr strain)
   return FALSE;
 }
 
+static Int2 GetNumClones (CharPtr str)
+
+{
+  Char  ch;
+  Int2  count;
+
+  if (StringHasNoText (str)) return 0;
+
+  count = 1;
+  ch = *str;
+  while (ch != '\0') {
+    if (ch == ';') {
+      count++;
+    }
+    str++;
+    ch = *str;
+  }
+
+  return count;
+}
+
 static CharPtr UseOrgMods(BioseqPtr bsp, CharPtr suffix)
 {
 	ItemInfoPtr 		iip = NULL;
@@ -3096,6 +3274,7 @@ static CharPtr UseOrgMods(BioseqPtr bsp, CharPtr suffix)
 	CharPtr				name = NULL, chr = NULL, str = NULL,
 						cln = NULL, map = NULL, def=NULL;
 	Int2 				deflen = 0;
+	Int2                numclones;
 		
 	if (bsp == NULL) {
 		return NULL;
@@ -3119,9 +3298,16 @@ static CharPtr UseOrgMods(BioseqPtr bsp, CharPtr suffix)
 		}
 		if (ssp->subtype == 3) { /* clone */
 			if (ssp->name != NULL) {
-				cln = (CharPtr) MemNew(StringLen(ssp->name) + 8);
-				deflen += StringLen(ssp->name) + 8;
-				sprintf(cln, " clone %s", ssp->name);		
+				numclones = GetNumClones (ssp->name);
+				if (numclones > 3) {
+					cln = (CharPtr) MemNew (20);
+					sprintf (cln, ", %d clones,", (int) numclones);
+					deflen += StringLen (cln) + 2;
+				} else {
+					cln = (CharPtr) MemNew(StringLen(ssp->name) + 8);
+					deflen += StringLen(ssp->name) + 8;
+					sprintf(cln, " clone %s", ssp->name);
+				}		
 			}
 		}
 		if (ssp->subtype == 2) { /* map */
@@ -3446,9 +3632,11 @@ NLM_EXTERN Boolean CreateDefLineEx (ItemInfoPtr iip, BioseqPtr bsp, CharPtr buf,
 		"WORKING DRAFT SEQUENCE",
 		"*** SEQUENCING IN PROGRESS ***" };
 	Boolean htg_tech = FALSE, htgs_draft = FALSE, htgs_cancelled = FALSE,
-	        is_nc = FALSE, is_nm = FALSE, is_tpa = FALSE;
+	        is_nc = FALSE, is_nm = FALSE, is_nr = FALSE, is_tpa = FALSE;
 	MolInfoPtr mip;
 	GBBlockPtr gbp = NULL;
+	EMBLBlockPtr ebp = NULL;
+	ValNodePtr keywords = NULL;
 	Boolean wgsmaster = FALSE;
 	CharPtr suffix = NULL;
 	SeqIdPtr sip;
@@ -3474,6 +3662,8 @@ NLM_EXTERN Boolean CreateDefLineEx (ItemInfoPtr iip, BioseqPtr bsp, CharPtr buf,
 						is_nc = TRUE;
 					} else if (StringNICmp (tsip->accession, "NM_", 3) == 0) {
 						is_nm = TRUE;
+					} else if (StringNICmp (tsip->accession, "NR_", 3) == 0) {
+						is_nr = TRUE;
 					}
 				}
 				break;
@@ -3519,6 +3709,16 @@ NLM_EXTERN Boolean CreateDefLineEx (ItemInfoPtr iip, BioseqPtr bsp, CharPtr buf,
 		vnp=GatherDescrOnBioseq(iip, bsp, Seq_descr_genbank,TRUE);
 		if (vnp != NULL) {
 			gbp = (GBBlockPtr) vnp->data.ptrvalue;
+			if (gbp != NULL) {
+			  keywords = gbp->keywords;
+			}
+		}
+		vnp=GatherDescrOnBioseq(iip, bsp, Seq_descr_embl,TRUE);
+		if (vnp != NULL) {
+			ebp = (EMBLBlockPtr) vnp->data.ptrvalue;
+			if (ebp != NULL) {
+			  keywords = ebp->keywords;
+			}
 		}
 	}
 	if (! ignoreTitle)
@@ -3528,8 +3728,13 @@ NLM_EXTERN Boolean CreateDefLineEx (ItemInfoPtr iip, BioseqPtr bsp, CharPtr buf,
               title = StringSaveNoNull((CharPtr)vnp->data.ptrvalue);
           }
 	if (tech == MI_TECH_htgs_0 || tech == MI_TECH_htgs_1 || tech == MI_TECH_htgs_2) {
-                MemFree(title);  /* manufacture all HTG titles */
-                title = NULL;
+        MemFree(title);  /* manufacture all HTG titles */
+        title = NULL;
+        if (iip != NULL) {
+          iip->entityID = 0;
+          iip->itemID = 0;
+          iip->itemtype = 0;
+        }
 		if (title == NULL || *title == '\0') {
 			title = UseOrgMods(bsp, NULL);
 			organism = NULL;
@@ -3578,6 +3783,13 @@ NLM_EXTERN Boolean CreateDefLineEx (ItemInfoPtr iip, BioseqPtr bsp, CharPtr buf,
         iip->itemID = 0;
         iip->itemtype = 0;
 	  }
+	} else if (is_nr && title == NULL) {
+	  title = FindNRDefLine (bsp);
+	  if (title != NULL && iip != NULL) {
+        iip->entityID = 0;
+        iip->itemID = 0;
+        iip->itemtype = 0;
+	  }
 	}
 /* some titles may have zero length */
 	if (title != NULL && *title != '\0') {
@@ -3736,8 +3948,8 @@ NLM_EXTERN Boolean CreateDefLineEx (ItemInfoPtr iip, BioseqPtr bsp, CharPtr buf,
 					i = 0;
 				}
 			} else {
-				if (gbp != NULL) {
-					for (vnp = gbp->keywords; vnp != NULL; vnp = vnp->next) {
+				if (keywords != NULL) {
+					for (vnp = keywords; vnp != NULL; vnp = vnp->next) {
 						if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_DRAFT") == 0) {
 							htgs_draft = TRUE;
 						} else if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_CANCELLED") == 0) {
diff --git a/api/tomedlin.c b/api/tomedlin.c
index 3a39dab6..0f779966 100644
--- a/api/tomedlin.c
+++ b/api/tomedlin.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 10/15/91
 *
-* $Revision: 6.8 $
+* $Revision: 6.10 $
 *
 * File Description:  conversion to medlars format
 *
@@ -40,6 +40,12 @@
 *
 *
 * $Log: tomedlin.c,v $
+* Revision 6.10  2003/09/28 20:22:47  kans
+* added PubmedEntryToXXXFile functions
+*
+* Revision 6.9  2003/09/26 18:57:51  kans
+* MedlineEntryToDataFile calls MakeMLAuthString for structured author
+*
 * Revision 6.8  2001/10/29 20:37:06  kans
 * MakeAuthorString for structured authors
 *
@@ -187,15 +193,66 @@ static ColData table [2] = {{0, 6, 0, 'l', TRUE, TRUE, FALSE},
 static Char *months[13] = {"", "Jan", "Feb", "Mar", "Apr", "May", "Jun",
                            "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"};
 
-NLM_EXTERN Boolean MedlineEntryToDataFile (MedlineEntryPtr mep, FILE *fp)
+static CharPtr MakeMLAuthString (
+  CharPtr name,
+  CharPtr initials,
+  CharPtr suffix
+)
+
+{
+  Char     ch;
+  size_t   len;
+  CharPtr  ptr;
+  CharPtr  str;
+  CharPtr  tmp;
+
+  if (name == NULL) return NULL;
+
+  len = StringLen (name) + StringLen (initials) * 3 + StringLen (suffix);
+  str = MemNew (sizeof (Char) * (len + 4));
+  if (str == NULL) return NULL;
+
+  tmp = str;
+
+  tmp = StringMove (tmp, name);
+
+  ptr = initials;
+  if (! StringHasNoText (initials)) {
+    tmp = StringMove (tmp, " ");
+    ch = *ptr;
+    while (ch != '\0') {
+      if (ch == '-') {
+        *tmp = '-';
+        tmp++;
+      } else if (ch != '.') {
+        *tmp = ch;
+        tmp++;
+      }
+      ptr++;
+      ch = *ptr;
+    }
+    *tmp = '\0';
+  }
+
+  if (! StringHasNoText (suffix)) {
+    tmp = StringMove (tmp, " ");
+    tmp = StringMove (tmp, suffix);
+  }
+
+  return str;
+}
+
+static Boolean MedlineEntryToDataFileEx (MedlineEntryPtr mep, Int4 pmid, FILE *fp)
 
 {
   CharPtr         abstract;
   AffilPtr        affil;
+  AuthorPtr       ap;
   AuthListPtr     authors = NULL;
   CitArtPtr       cit;
   CitJourPtr      citjour;
   Int2            count;
+  CharPtr         curr;
   DatePtr         date = NULL;
   ValNodePtr      gene;
   Int2            i;
@@ -204,9 +261,11 @@ NLM_EXTERN Boolean MedlineEntryToDataFile (MedlineEntryPtr mep, FILE *fp)
   size_t          len;
   MedlineMeshPtr  mesh;
   ValNodePtr      names;
+  NameStdPtr      nsp;
   CharPtr         p;
   CharPtr         pages = NULL;
   ParData         para;
+  PersonIdPtr     pid;
   CharPtr         ptr;
   ValNodePtr      qual;
   Boolean         rsult;
@@ -255,20 +314,59 @@ NLM_EXTERN Boolean MedlineEntryToDataFile (MedlineEntryPtr mep, FILE *fp)
     cit = mep->cit;
     if (cit != NULL) {
       authors = cit->authors;
-      if (authors != NULL && (authors->choice == 2 || authors->choice == 3)) {
-        names = authors->names;
-        count = 0;
-        while (names != NULL) {
-          if (count >= 20) {
-            rsult = (Boolean) (SendTextToFile (fp, buffer, &para, table) && rsult);
-            ClearString ();
-            count = 0;
+      if (authors != NULL) {
+        if (authors->choice == 1) {
+          names = authors->names;
+          count = 0;
+          while (names != NULL) {
+            if (count >= 20) {
+              rsult = (Boolean) (SendTextToFile (fp, buffer, &para, table) && rsult);
+              ClearString ();
+              count = 0;
+            }
+            curr = NULL;
+            ap = (AuthorPtr) names->data.ptrvalue;
+            if (ap != NULL) {
+              pid = ap->name;
+              if (pid != NULL) {
+                if (pid->choice == 2) {
+                  nsp = (NameStdPtr) pid->data;
+                  if (nsp != NULL) {
+                    if (! StringHasNoText (nsp->names [0])) {
+                      curr = MakeMLAuthString (nsp->names [0], nsp->names [4], nsp->names [5]);
+                    } else if (! StringHasNoText (nsp->names [3])) {
+                      curr = MakeMLAuthString (nsp->names [3], NULL, NULL);
+                    }
+                  }
+                } else if (pid->choice == 3 || pid->choice == 4) {
+                  curr = MakeMLAuthString ((CharPtr) pid->data, NULL, NULL);
+                }
+              }
+            }
+            if (curr != NULL) {
+              AddString ("AU  -\t");
+              AddString (curr);
+              AddString ("\n");
+              curr = MemFree (curr);
+            }
+            names = names->next;
+            count++;
+          }
+        } else if (authors->choice == 2 || authors->choice == 3) {
+          names = authors->names;
+          count = 0;
+          while (names != NULL) {
+            if (count >= 20) {
+              rsult = (Boolean) (SendTextToFile (fp, buffer, &para, table) && rsult);
+              ClearString ();
+              count = 0;
+            }
+            AddString ("AU  -\t");
+            AddString (names->data.ptrvalue);
+            AddString ("\n");
+            names = names->next;
+            count++;
           }
-          AddString ("AU  -\t");
-          AddString (names->data.ptrvalue);
-          AddString ("\n");
-          names = names->next;
-          count++;
         }
       }
       rsult = (Boolean) (SendTextToFile (fp, buffer, &para, table) && rsult);
@@ -581,6 +679,23 @@ NLM_EXTERN Boolean MedlineEntryToDataFile (MedlineEntryPtr mep, FILE *fp)
   return rsult;
 }
 
+NLM_EXTERN Boolean MedlineEntryToDataFile (MedlineEntryPtr mep, FILE *fp)
+
+{
+  return MedlineEntryToDataFileEx (mep, 0, fp);
+}
+
+NLM_EXTERN Boolean PubmedEntryToDataFile (PubmedEntryPtr pep, FILE *fp)
+
+{
+  MedlineEntryPtr  mep;
+
+  if (pep == NULL || fp == NULL) return FALSE;
+  mep = (MedlineEntryPtr) pep->medent;
+  if (mep == NULL) return FALSE;
+  return MedlineEntryToDataFileEx (mep, pep->pmid, fp);
+}
+
 #ifdef VAR_ARGS
 static CharPtr CDECL StrngAppend (first, va_alist)
 CharPtr first;
@@ -1036,7 +1151,7 @@ static ColData  colFmt [3] = {{0, 0, 0, 'l', TRUE, TRUE, FALSE},
 
 static ColData  mshFmt [1] = {{0, 80, 0, 'l', FALSE, FALSE, TRUE}};
 
-static Boolean MedlineEntryToDocOrAbsFile (MedlineEntryPtr mep, FILE *fp, Boolean showMesh)
+static Boolean MedlineEntryToDocOrAbsFile (MedlineEntryPtr mep, Int4 pmid, FILE *fp, Boolean showMesh)
 
 {
   size_t      len;
@@ -1122,13 +1237,35 @@ static Boolean MedlineEntryToDocOrAbsFile (MedlineEntryPtr mep, FILE *fp, Boolea
 NLM_EXTERN Boolean MedlineEntryToDocFile (MedlineEntryPtr mep, FILE *fp)
 
 {
-  return MedlineEntryToDocOrAbsFile (mep, fp, TRUE);
+  return MedlineEntryToDocOrAbsFile (mep, 0, fp, TRUE);
 }
 
 NLM_EXTERN Boolean MedlineEntryToAbsFile (MedlineEntryPtr mep, FILE *fp)
 
 {
-  return MedlineEntryToDocOrAbsFile (mep, fp, FALSE);
+  return MedlineEntryToDocOrAbsFile (mep, 0, fp, FALSE);
+}
+
+NLM_EXTERN Boolean PubmedEntryToDocFile (PubmedEntryPtr pep, FILE *fp)
+
+{
+  MedlineEntryPtr  mep;
+
+  if (pep == NULL || fp == NULL) return FALSE;
+  mep = (MedlineEntryPtr) pep->medent;
+  if (mep == NULL) return FALSE;
+  return MedlineEntryToDocOrAbsFile (mep, pep->pmid, fp, TRUE);
+}
+
+NLM_EXTERN Boolean PubmedEntryToAbsFile (PubmedEntryPtr pep, FILE *fp)
+
+{
+  MedlineEntryPtr  mep;
+
+  if (pep == NULL || fp == NULL) return FALSE;
+  mep = (MedlineEntryPtr) pep->medent;
+  if (mep == NULL) return FALSE;
+  return MedlineEntryToDocOrAbsFile (mep, pep->pmid, fp, FALSE);
 }
 
 #define IBM_MEDLINE_DIVSS '$'
diff --git a/api/tomedlin.h b/api/tomedlin.h
index 487bb1c1..1be1818f 100644
--- a/api/tomedlin.h
+++ b/api/tomedlin.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 10/15/91
 *
-* $Revision: 6.1 $
+* $Revision: 6.2 $
 *
 * File Description:  conversion to medlars format
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: tomedlin.h,v $
+* Revision 6.2  2003/09/28 20:22:47  kans
+* added PubmedEntryToXXXFile functions
+*
 * Revision 6.1  1997/12/22 18:51:23  grisha
 * update unit-record number for PmId to 969
 *
@@ -78,6 +81,7 @@
 
 #include <objmedli.h>
 #include <objmdrs.h>
+#include <objpubme.h>
 
 #define MEDLINE_BADCODE 0 /* BAD                             */
 #define MEDLINE_EOF -1  /* END OF ENTRY                      */
@@ -163,6 +167,10 @@ NLM_EXTERN Boolean MedlarsEntryToDataFile PROTO((MedlarsEntryPtr mep, FILE *fp))
 NLM_EXTERN Boolean MedlarsEntryToDocFile PROTO((MedlarsEntryPtr mep, FILE *fp));
 NLM_EXTERN Boolean MedlarsEntryToAbsFile PROTO((MedlarsEntryPtr mep, FILE *fp));
 
+NLM_EXTERN Boolean PubmedEntryToDataFile PROTO((PubmedEntryPtr pep, FILE *fp));
+NLM_EXTERN Boolean PubmedEntryToDocFile PROTO((PubmedEntryPtr pep, FILE *fp));
+NLM_EXTERN Boolean PubmedEntryToAbsFile PROTO((PubmedEntryPtr pep, FILE *fp));
+
 NLM_EXTERN MedlinePtr ParseMedline PROTO((MedlineEntryPtr mep));
 NLM_EXTERN MedlinePtr FreeMedline PROTO((MedlinePtr mPtr));
 
diff --git a/api/txalign.c b/api/txalign.c
index 3253529f..127cc1a5 100644
--- a/api/txalign.c
+++ b/api/txalign.c
@@ -1,4 +1,4 @@
-/* $Id: txalign.c,v 6.72 2003/01/23 23:31:58 dondosha Exp $
+/* $Id: txalign.c,v 6.79 2003/09/26 20:54:10 dondosha Exp $
 ***************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -27,13 +27,34 @@
 *
 * File Name:  txalign.c
 *
-* $Revision: 6.72 $
+* $Revision: 6.79 $
 * 
 * File Description:  Formating of text alignment for the BLAST output
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: txalign.c,v $
+* 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
+*
+* Revision 6.78  2003/08/20 21:29:13  dondosha
+* Correction for OOF alignments with nucleotide coordinates starting at 1
+*
+* Revision 6.77  2003/07/30 14:07:36  dondosha
+* Changed hrefs to trace.cgi in accordance with the new taxonomy web interface
+*
+* Revision 6.76  2003/07/21 22:15:23  dondosha
+* Added support for out-of-frame tblastn alignments
+*
+* Revision 6.75  2003/07/15 14:36:06  dondosha
+* Added a #define for fprintf substitute, needed for gzip compression of Web BLAST results
+*
+* Revision 6.74  2003/06/11 20:15:35  jianye
+* changed unigene linkout
+*
+* Revision 6.73  2003/06/02 20:02:15  jianye
+* Added geo linkout
+*
 * Revision 6.72  2003/01/23 23:31:58  dondosha
 * Added a global variable for the query number, needed in make_dumpgnl_links
 *
@@ -511,6 +532,9 @@ int query_number_glb;
 /*Indicate if db contains sequence with gi*/
 Boolean DbHasGi=FALSE;
 
+int (*tx_fprintf)(FILE*, const char *, ...) = fprintf;
+#define fprintf tx_fprintf
+
 /*
 	Used by the functions that format the one-line descriptions.
 */
@@ -643,6 +667,7 @@ static void addLinkoutForDefline(BioseqPtr bsp, SeqIdPtr sip, FILE* fp){
 	/*add space in front of linkout*/
 	fprintf(fp, " ");
 	bdlpTemp=bdlp;
+	
 	while(bdlpTemp){
 	  if(checkLinkoutType(bdlpTemp, linkout_locuslink)){
 	    hasLinkout=TRUE;
@@ -654,20 +679,10 @@ static void addLinkoutForDefline(BioseqPtr bsp, SeqIdPtr sip, FILE* fp){
 	}
 	bdlpTemp=bdlp;
 	while(bdlpTemp){ 	
-	  if(checkLinkoutType(bdlpTemp, linkout_unigene)){
-         
+	  if(checkLinkoutType(bdlpTemp, linkout_unigene)){         
 	    hasLinkout=TRUE;
 	    gi=GetGIForSeqId(bdlpTemp->seqid);
-	    rnp=FDGetTaxNamesFromBioseq(bsp, bdlpTemp->taxid);
-	    if(rnp&&rnp->sci_name){
-	      unigeneName=getNameInitials(rnp->sci_name);
-	      if(unigeneName){
-		fprintf(fp, URL_Unigene, unigeneName, gi);
-	      }
-	      MemFree(unigeneName);
-	    }
-	    
-	    RDBTaxNamesFree(rnp);
+	    fprintf(fp, URL_Unigene,  gi); 
 	    break;
 	  }
 	  bdlpTemp=bdlpTemp->next;
@@ -682,6 +697,16 @@ static void addLinkoutForDefline(BioseqPtr bsp, SeqIdPtr sip, FILE* fp){
 	  }
 	  bdlpTemp=bdlpTemp->next;
 	}
+	bdlpTemp=bdlp;
+	while(bdlpTemp){
+	  if(checkLinkoutType(bdlpTemp, linkout_geo)){
+	    gi=GetGIForSeqId(bdlpTemp->seqid);
+	    fprintf(fp, URL_Geo, gi);
+	    break;
+	  }
+	  bdlpTemp=bdlpTemp->next;
+	}
+	
       }
       BlastDefLineSetFree(bdlp);
     }
@@ -722,21 +747,16 @@ static void addLinkoutForBioseq(BioseqPtr bsp, SeqIdPtr sip, SeqIdPtr firstSip,
 	
 	if(checkLinkoutType(actualBdlp, linkout_unigene)){	
 	  hasLinkout=TRUE;	
-	  rnp=FDGetTaxNamesFromBioseq(bsp, actualBdlp->taxid);
-	  if(rnp&&rnp->sci_name){
-	    unigeneName=getNameInitials(rnp->sci_name);
-	    if(unigeneName){
-	      fprintf(fp, URL_Unigene, unigeneName, gi);
-	    }
-	    MemFree(unigeneName);
-	  }
-	 
-	  RDBTaxNamesFree(rnp);
+	  fprintf(fp, URL_Unigene,  gi);
 	}
 	if(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");
 	}
+	
+	if(checkLinkoutType(actualBdlp, linkout_geo)){
+	  fprintf(fp, URL_Geo, gi);
+	}
       }
       BlastDefLineSetFree(bdlp);
     }
@@ -1722,7 +1742,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
 					    		tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon);
                                             load = TRUE;
                                          } else if (!StringICmp(db_tag->db, "TI")) {
-                                            sprintf(HTML_buffer, "<a name = TI%ld></a><a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?val=%ld&cmd=retrieve&dopt=fasta\">", (long) oip->id, (long) oip->id);
+                                            sprintf(HTML_buffer, "<a name = TI%ld></a><a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\">", (long) oip->id, (long) oip->id);
                                             
                                             html_len = StringLen(HTML_buffer);
                                             sprintf(docbuf+pos, HTML_buffer);
@@ -2616,8 +2636,13 @@ static Boolean load_align_sum_for_StdSeg(StdSegPtr ssp, AlignSumPtr asp)
         return FALSE;
 
     if(asp->ooframe) {
-        master_is_translated = TRUE;
-        target_is_translated = FALSE;	
+       if (SeqLocStrand(ssp->loc) != Seq_strand_unknown) {
+          master_is_translated = TRUE;
+          target_is_translated = FALSE;	
+       } else {
+          master_is_translated = FALSE;
+          target_is_translated = TRUE;	
+       }
     } else {
         /* Check for valid sequence. */
         if (SeqLocLen(ssp->loc) == 3*SeqLocLen(ssp->loc->next))
@@ -2748,10 +2773,17 @@ static Boolean load_align_sum_for_StdSeg(StdSegPtr ssp, AlignSumPtr asp)
         }
 
         if(asp->ooframe) {
-            if(ssp->loc->next->choice != SEQLOC_EMPTY)
-                asp->totlen += SeqLocLen(ssp->loc->next);
-            else
-                asp->totlen += SeqLocLen(ssp->loc)/3;
+           if (master_is_translated) {
+              if(ssp->loc->next->choice != SEQLOC_EMPTY)
+                 asp->totlen += SeqLocLen(ssp->loc->next);
+              else
+                 asp->totlen += SeqLocLen(ssp->loc)/3;
+           } else {
+              if(ssp->loc->choice != SEQLOC_EMPTY)
+                 asp->totlen += SeqLocLen(ssp->loc);
+              else
+                 asp->totlen += SeqLocLen(ssp->loc->next)/3;
+           }
         } else {
         
             if (ssp->loc->choice != SEQLOC_EMPTY) {
@@ -4589,7 +4621,7 @@ PrintDefLinesFromSeqAlignEx2(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp
 #endif
     
     if(!StringICmp(blast_type, "fruitfly")) {
-        fprintf(stdout, "<IMG SRC=\"/BLAST/images/map_mark.gif\" BORDER=0> - please follow this image for the map location of the sequence<P>\n");
+        fprintf(outfp, "<IMG SRC=\"/BLAST/images/map_mark.gif\" BORDER=0> - please follow this image for the map location of the sequence<P>\n");
     }
     
     asn2ff_set_output(outfp, NULL);
@@ -4884,7 +4916,7 @@ PrintDefLinesFromSeqAlignEx2(SeqAlignPtr seqalign, Int4 line_length, FILE *outfp
                         } else if (db_tag->db && StringICmp(db_tag->db, "TI") == 0) {
                            oip = db_tag->tag;
                            if(oip->id != 0) {
-                              fprintf(outfp, "<a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?val=%ld&cmd=retrieve&dopt=fasta\">", (long) oip->id);
+                              fprintf(outfp, "<a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\">", (long) oip->id);
                            }
                         } else {
                             make_dumpgnl_links(txsp->id, blast_type, txsp->segs_str, db_name, txsp->is_na, outfp, txsp->buffer_id, FALSE);
@@ -5417,7 +5449,7 @@ static CharPtr FSFPrintOneDefline(AlignStatOptionPtr asop, Boolean is_na,
                     } else if (db_tag->db && StringICmp(db_tag->db, "TI") == 0) {
                        oip = db_tag->tag;
                        if(oip->id != 0) {
-                          fprintf(asop->fp, "<a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?val=%ld&cmd=retrieve&dopt=fasta\">", (long) oip->id);
+                          fprintf(asop->fp, "<a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\">", (long) oip->id);
                        }
                     } else {
                         /** * links to incomplete genomes */
@@ -5960,22 +5992,27 @@ NLM_EXTERN Uint4 GetTxAlignOptionValue (Uint1 tx_option, BoolPtr hide_feature,
 	return option;
 }
 
-Int4 OOFGetDNAStrand(StdSegPtr sseg)
+/** The following function assumes that neither of the locations in
+ * the first link in StdSeg is empty.
+ * @param sseg Alignment segments [in]
+ * @param dna_strand The strand of the nucleotide sequence [out]
+ * @return TRUE for tblastn, FALSE for blastx.
+ */
+static Boolean OOFGetDNAStrand(StdSegPtr sseg, Int4Ptr dna_strand)
 {
-    Int4 dna_strand;
-    SeqIntPtr seq_int1;
-    SeqLocPtr slp1;
+    Uint1 strand;
+    Boolean reverse;
 
-    for(; sseg != NULL; sseg= sseg->next) {
-        slp1 = sseg->loc;
-        
-        if(slp1->choice == SEQLOC_INT) {
-            seq_int1 = (SeqIntPtr) slp1->data.ptrvalue;
-            return seq_int1->strand;
-        }
+    if ((strand = SeqLocStrand(sseg->loc)) != Seq_strand_unknown) {
+       *dna_strand = (Int4) strand;
+       reverse = FALSE;
+    } else {
+       *dna_strand = (Int4) SeqLocStrand(sseg->loc->next);
+       reverse = TRUE;
     }
-    return Seq_strand_unknown;
+    return reverse;
 }
+
 static Int4 SetDNALineEnd(Int4 dna_index, Int4 dna_strand)
 {
     Int4 dna_line_end;
@@ -6041,6 +6078,7 @@ static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
     Int4 i, lines, k, shift_info = 0;
     Char  c1, c2, c3;
     Int4 dna_strand, max_digits, num_pad;
+    Boolean reverse = FALSE;
 
     if(sap == NULL || sap->segtype != 3) /* Should be StdSeg here! */
         return FALSE;
@@ -6051,8 +6089,8 @@ static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
     pro_index = 0;
     pro_line_end = 0;
     dna_line_end = 0;
-    
-    dna_strand = OOFGetDNAStrand((StdSegPtr) sap->segs);
+   
+    reverse = OOFGetDNAStrand((StdSegPtr) sap->segs, &dna_strand);
 
     /* Needed for printing nice alignment with normal spacing */
     max_digits = GetMaxFROMDigits((StdSegPtr) sap->segs);
@@ -6065,8 +6103,18 @@ static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
         length_pro = 0;
         b_store = NULL;
         
-        slp1 = sseg->loc;
-        
+        if (reverse) {
+           slp2 = sseg->loc;
+           slp1 = sseg->loc->next;
+           sip2 = sseg->ids;       /* Protein */
+           sip1 = sseg->ids->next; /* DNA */
+        } else {
+           slp1 = sseg->loc;
+           slp2 = sseg->loc->next;
+           sip1 = sseg->ids;       /* DNA */
+           sip2 = sseg->ids->next; /* Protein */
+        }
+
         if(slp1->choice == SEQLOC_INT) 
             seq_int1 = (SeqIntPtr) slp1->data.ptrvalue;
         else if (slp1->choice == SEQLOC_EMPTY)
@@ -6074,7 +6122,6 @@ static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
         else
             return FALSE;       /* Invalid SeqLoc */
         
-        slp2 = sseg->loc->next;
         
         if(slp2->choice == SEQLOC_INT)
             seq_int2 = (SeqIntPtr) slp2->data.ptrvalue;
@@ -6087,9 +6134,6 @@ static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
         if(seq_int1 == NULL && seq_int2 == NULL)
             continue;
         
-        sip1 = sseg->ids;       /* DNA */
-        sip2 = sseg->ids->next; /* Protein */
-
         /* printf("shift_info = %d\n", shift_info); */
 
         if(shift_info%3)
@@ -6171,12 +6215,12 @@ static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
         }
 
         if(line_index == 0) {
-            dna_line_start = dna_index; 
+            dna_line_start = dna_index + 1; 
             pro_line_start = pro_index + 1;
         }
 
         if (dna_line_start == 0)
-            dna_line_start = dna_index; 
+            dna_line_start = dna_index + 1; 
         
         if(pro_line_start == 0)
             pro_line_start = pro_index + 1;
@@ -6293,37 +6337,64 @@ static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
 
                 /* ------- Printout of the alignment ------------- */ 
 
-                fprintf(fp, "Query: %d", dna_line_start+1);
+                if (reverse) {
+                   fprintf(fp, "Query: %d", pro_line_start);
+                   num_pad = 
+                      max_digits - GetDigitsInINT(pro_line_start) + 1;
+
+                   for(k=0; k < num_pad; k++)
+                      fprintf(fp, " ");
+                   
+                   fprintf(fp, "%s %d\n", line2, pro_line_end);
                 
-                num_pad = max_digits - GetDigitsInINT(dna_line_start+1) + 1;
+                   num_pad = 8 + max_digits;
+                   
+                   for(k=0; k < num_pad; k++)
+                      fprintf(fp, " ");
 
-                for(k=0; k < num_pad; k++)
-                    fprintf(fp, " ");
+                   fprintf(fp, "%s\nSbjct: %d", line3, dna_line_start);
 
-                fprintf(fp, "%s %d\n", line1, dna_line_end+3);
-                
-                num_pad = 8 + max_digits;
-                
-                for(k=0; k < num_pad; k++)
-                    fprintf(fp, " ");
+                   num_pad = 
+                      max_digits - GetDigitsInINT(dna_line_start) + 1;
 
-                fprintf(fp, "%s\nSbjct: %d", line3, pro_line_start);
+                   for(k=0; k < num_pad; k++)
+                      fprintf(fp, " ");
+                   
+                   fprintf(fp, "%s %d\n\n", line1, dna_line_end+3);
 
-                num_pad = max_digits - GetDigitsInINT(pro_line_start) + 1;
+                } else {
+                   fprintf(fp, "Query: %d", dna_line_start);
+                   num_pad = 
+                      max_digits - GetDigitsInINT(dna_line_start) + 1;
+
+                   for(k=0; k < num_pad; k++)
+                      fprintf(fp, " ");
+                   
+                   fprintf(fp, "%s %d\n", line1, dna_line_end+3);
+                
+                   num_pad = 8 + max_digits;
+                   
+                   for(k=0; k < num_pad; k++)
+                      fprintf(fp, " ");
 
-                for(k=0; k < num_pad; k++)
-                    fprintf(fp, " ");
+                   fprintf(fp, "%s\nSbjct: %d", line3, pro_line_start);
 
-                fprintf(fp, "%s %d\n\n", line2, pro_line_end);
+                   num_pad = 
+                      max_digits - GetDigitsInINT(pro_line_start) + 1;
 
+                   for(k=0; k < num_pad; k++)
+                      fprintf(fp, " ");
+                   
+                   fprintf(fp, "%s %d\n\n", line2, pro_line_end);
+                }
                 /* --------------------------------------------------- */
 
                 if(dna_line_end != 0) {
 
                     if(dna_strand != Seq_strand_minus)
-                        dna_line_start = dna_line_end+3; /*takes 3 bases*/
+                        dna_line_start = dna_line_end+4; /*takes 3 bases*/
                     else
-                        dna_line_start = dna_line_end+1; /*takes 3 bases*/
+                        dna_line_start = dna_line_end+2; /*takes 3 bases*/
                 }
                 if(pro_line_end != 0) 
                     pro_line_start = pro_line_end+1;
@@ -6357,35 +6428,58 @@ static Boolean OOFShowSingleAlignment(SeqAlignPtr sap, ValNodePtr mask,
 
 
     /* ------- Printout of the alignment remainder ------- */ 
+    if (reverse) {
+       fprintf(fp, "Query: %d", pro_line_start);
     
-    fprintf(fp, "Query: %d", dna_line_start+1);
-    
-    num_pad = max_digits - GetDigitsInINT(dna_line_start+1) + 1;
-    
-    for(k=0; k < num_pad; k++)
-        fprintf(fp, " ");
-    
-    fprintf(fp, "%s %d\n", line1, dna_line_end+3);
-    
-    num_pad = 8 + max_digits;
-    
-    for(k=0; k < num_pad; k++)
-        fprintf(fp, " ");
-    
-    fprintf(fp, "%s\nSbjct: %d", line3, pro_line_start);
-    
-    num_pad = max_digits - GetDigitsInINT(pro_line_start) + 1;
-    
-    for(k=0; k < num_pad; k++)
-        fprintf(fp, " ");
-    
-    fprintf(fp, "%s %d\n\n\n", line2, pro_line_end);
+       num_pad = max_digits - GetDigitsInINT(pro_line_start) + 1;
+       
+       for(k=0; k < num_pad; k++)
+          fprintf(fp, " ");
+       
+       fprintf(fp, "%s %d\n", line2, pro_line_end);
+       
+       num_pad = 8 + max_digits;
+       
+       for(k=0; k < num_pad; k++)
+          fprintf(fp, " ");
+       
+       fprintf(fp, "%s\nSbjct: %d", line3, dna_line_start);
+       
+       num_pad = max_digits - GetDigitsInINT(dna_line_start) + 1;
+       
+       for(k=0; k < num_pad; k++)
+          fprintf(fp, " ");
+       
+       fprintf(fp, "%s %d\n\n\n", line1, dna_line_end+3);
+    } else {
+       fprintf(fp, "Query: %d", dna_line_start);
     
+       num_pad = max_digits - GetDigitsInINT(dna_line_start) + 1;
+       
+       for(k=0; k < num_pad; k++)
+          fprintf(fp, " ");
+       
+       fprintf(fp, "%s %d\n", line1, dna_line_end+3);
+       
+       num_pad = 8 + max_digits;
+       
+       for(k=0; k < num_pad; k++)
+          fprintf(fp, " ");
+       
+       fprintf(fp, "%s\nSbjct: %d", line3, pro_line_start);
+       
+       num_pad = max_digits - GetDigitsInINT(pro_line_start) + 1;
+       
+       for(k=0; k < num_pad; k++)
+          fprintf(fp, " ");
+       
+       fprintf(fp, "%s %d\n\n\n", line2, pro_line_end);
+    }
     /* --------------------------------------------------- */
     
     /*    fprintf(fp, "\nQuery: %-5d %s %-5d\n             "
           "%s\nSbjct: %-5d %s %-5d\n\n", 
-          dna_line_start+1, line1, dna_line_end+3, line3, 
+          dna_line_start, line1, dna_line_end+3, line3, 
           pro_line_start, line2, pro_line_end); */
     
     return TRUE;
diff --git a/api/valid.c b/api/valid.c
index 1b52746f..667a2876 100644
--- a/api/valid.c
+++ b/api/valid.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 1/1/94
 *
-* $Revision: 6.364 $
+* $Revision: 6.403 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -39,6 +39,123 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: valid.c,v $
+* Revision 6.403  2003/10/24 21:31:00  kans
+* added test for ERR_SEQ_FEAT_UTRdoesNotAbutCDS on mRNA
+*
+* Revision 6.402  2003/10/24 17:50:35  kans
+* added ERR_SEQ_INST_SeqLitGapLength0
+*
+* Revision 6.401  2003/10/24 04:41:50  kans
+* ValidateImpFeat warns if repeat_region /rpt_unit has same length as sfp->location but does not have matching sequence
+*
+* Revision 6.400  2003/10/23 20:29:38  kans
+* warn about allele gbqual when inheriting allele from gene
+*
+* Revision 6.399  2003/10/20 19:44:47  kans
+* added * Terminator codon
+*
+* Revision 6.398  2003/10/20 16:53:05  kans
+* suppress validator warning for synthetic sequences with molinfo other genetic when origin is artificial
+*
+* Revision 6.397  2003/10/17 21:12:27  kans
+* added ERR_SEQ_FEAT_OnlyGeneXrefs test
+*
+* Revision 6.396  2003/10/10 22:38:39  kans
+* added tests for BadTrnaCodon and BadTrnaAA
+*
+* Revision 6.395  2003/10/06 16:19:26  kans
+* commented out check on rpt_unit content - now any text will be allowed
+*
+* Revision 6.394  2003/10/01 19:46:39  kans
+* suppress partial not at end warning for CDD region
+*
+* Revision 6.393  2003/09/30 20:35:30  kans
+* fixed IsSynthetic to look at div if origin was not set
+*
+* Revision 6.392  2003/09/23 12:33:37  kans
+* Check DeltaLitOnly and allow test for terminal Ns
+*
+* Revision 6.391  2003/09/18 18:28:53  kans
+* fixed IsMicroRNA - was using continue statements in while loop instead of for loop
+*
+* Revision 6.390  2003/09/11 15:24:35  kans
+* duplicate feat severity warning check was only done for cds, not mrna
+*
+* Revision 6.389  2003/09/10 14:29:13  kans
+* IsMicroRNA feature test for molinfo-biomol.other, do mrnatrans base comparison even if polyA test fails
+*
+* Revision 6.388  2003/09/09 20:09:21  kans
+* lower severity for far product partial inconsistency and mrnatranscheck, also check for 95% polyA
+*
+* Revision 6.387  2003/08/13 21:45:30  kans
+*  added ERR_SEQ_DESCR_RefGeneTrackingWithoutStatus
+*
+* Revision 6.386  2003/08/11 15:08:08  kans
+* REBASE is legal refseq dbxref
+*
+* Revision 6.385  2003/08/01 21:33:38  kans
+* ERR_SEQ_INST_InternalNsInSeqLit dropped to warning, cutoff still at 80
+*
+* Revision 6.384  2003/08/01 21:30:28  kans
+* added CountAdjacentNsInSeqLit for htgs 1 and 2
+*
+* Revision 6.383  2003/07/30 21:44:31  kans
+* comment out archaic locations messages because TMSMART thinks it should not promote locations
+*
+* Revision 6.382  2003/07/29 15:59:11  kans
+* use new ERR_SEQ_PKG_ArchaicFeatureLocation and ERR_SEQ_PKG_ArchaicFeatureProduct tokens, also do not complain if location or product is local and Bioseq has TMSMART or BankIt general
+*
+* Revision 6.381  2003/07/28 22:11:04  kans
+* check for archaic feature locations and products
+*
+* Revision 6.380  2003/07/22 16:18:07  kans
+* added Kerguelen Archipelago to country list
+*
+* Revision 6.379  2003/07/15 16:46:02  kans
+* suppress BadDeltaSeq - HTGS 2 delta seq has no gaps and no graphs - if HTGS_ACTIVEFIN keyword present
+*
+* Revision 6.378  2003/07/07 15:35:01  kans
+* ERR_SEQ_INST_TerminalNs is SEV_ERROR if 10 or more Ns at either end
+*
+* Revision 6.377  2003/07/02 19:36:47  kans
+* added CheckCDSPartial to check cds->location partials against product molinfo
+*
+* Revision 6.376  2003/06/17 21:15:46  kans
+* germline and rearranged are mutually exclusive - proviral and virion are because there is only one biop->genome
+*
+* Revision 6.375  2003/06/17 21:05:13  kans
+* synthetic biosource should have molinfo biomol other
+*
+* Revision 6.374  2003/06/17 20:03:38  kans
+* NT-036298 (dash instead of underscore) gives REJECT level BadSeqIdFormat error
+*
+* Revision 6.373  2003/06/02 21:42:11  kans
+* allow 4 + 2 + 7 wgs master accessions
+*
+* Revision 6.372  2003/05/09 18:46:47  kans
+* severity of first and last delta seq component is gap message lowered if not HTGS
+*
+* Revision 6.371  2003/05/02 19:19:28  kans
+* added rearrangement exception to list that suppressed CdTransCheck
+*
+* Revision 6.370  2003/05/01 20:08:57  kans
+* Serbia and Montenegro restored to list of countries, but Yugoslavia also remains
+*
+* Revision 6.369  2003/04/30 16:38:37  kans
+* added CdsProductIdCheck
+*
+* Revision 6.368  2003/04/27 20:16:23  kans
+* ribosomal slippage exception suppresses CDSmRNArange warning
+*
+* Revision 6.367  2003/04/24 19:51:47  kans
+* rearrangement required okay for all records, not just refseq, at least for now
+*
+* Revision 6.366  2003/04/24 19:19:12  kans
+* added support for new rearrangement required for product exception
+*
+* Revision 6.365  2003/04/23 16:56:16  kans
+* ERR_GENERIC_BadPageNumbering dropped to SEV_WARNING
+*
 * Revision 6.364  2003/04/21 16:39:22  kans
 * CheckRnaProductType was doing the wrong thing for rRNAs
 *
@@ -1337,6 +1454,7 @@ NLM_EXTERN void SpellCheckSeqFeat (GatherContextPtr gcp);
 NLM_EXTERN void SpellCheckString (ValidStructPtr vsp, CharPtr str);
 NLM_EXTERN void SpliceCheck (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);
 static void     ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, PubdescPtr pdp);
 static void     ValidateSfpCit (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPtr sfp);
@@ -1929,6 +2047,14 @@ static void LookForAnyPubAndOrg (SeqEntryPtr sep, BoolPtr no_pub, BoolPtr no_bio
   }
 }
 
+typedef struct ftprob {
+  Uint4  num_misplaced_features;
+  Uint4  num_archaic_locations;
+  Uint4  num_archaic_products;
+  Uint4  num_gene_feats;
+  Uint4  num_gene_xrefs;
+} FeatProb, PNTR FeatProbPtr;
+
 static void CheckFeatPacking (BioseqPtr bsp, SeqFeatPtr sfp, Uint4Ptr num_misplaced_features)
 {
   SeqAnnotPtr     sap;
@@ -1967,22 +2093,101 @@ static void CheckFeatPacking (BioseqPtr bsp, SeqFeatPtr sfp, Uint4Ptr num_mispla
   }
 }
 
+static Boolean IdIsArchaic (SeqIdPtr sip)
+
+{
+  BioseqPtr  bsp;
+  DbtagPtr   dbt;
+  SeqIdPtr   id;
+
+  if (sip == NULL) return FALSE;
+  if (sip->choice != SEQID_LOCAL && sip->choice != SEQID_GENERAL) return FALSE;
+  bsp = BioseqFind (sip);
+  if (bsp == NULL) return FALSE;
+  for (id = bsp->id; id != NULL; id = id->next) {
+    switch (id->choice) {
+      case SEQID_GENERAL :
+        if (sip->choice == SEQID_LOCAL) {
+          dbt = (DbtagPtr) id->data.ptrvalue;
+          if (dbt != NULL) {
+            if (StringICmp (dbt->db, "TMSMART") != 0 && StringICmp (dbt->db, "BankIt") != 0) {
+              return TRUE;
+            }
+          }
+        }
+        break;
+      case SEQID_GI :
+      case SEQID_GENBANK :
+      case SEQID_EMBL :
+      case SEQID_PATENT :
+      case SEQID_OTHER :
+      case SEQID_DDBJ :
+      case SEQID_TPG :
+      case SEQID_TPE :
+      case SEQID_TPD :
+        return TRUE;
+      default :
+        break;
+    }
+  }
+  return FALSE;
+}
+
+static void CheckFeatLocAndProd (SeqFeatPtr sfp, FeatProbPtr fpp)
+
+{
+  SeqLocPtr  slp;
+
+  if (sfp == NULL || fpp == NULL) return;
+  if (sfp->product != NULL && IdIsArchaic (SeqLocId (sfp->product))) {
+    (fpp->num_archaic_products)++;
+  }
+  slp = SeqLocFindNext (sfp->location, NULL);
+  while (slp != NULL) {
+    if (IdIsArchaic (SeqLocId (slp))) {
+      (fpp->num_archaic_locations)++;
+      return;
+    }
+    slp = SeqLocFindNext (sfp->location, slp);
+  }
+}
+
 static Boolean LIBCALLBACK CountMisplacedFeatures (BioseqPtr bsp, SeqMgrBioseqContextPtr bcontext)
 {
-  Uint4Ptr        num_misplaced_features;
+  FeatProbPtr     fpp;
   SeqFeatPtr      sfp;
   SeqMgrFeatContext fcontext;
 
-  num_misplaced_features = (Uint4Ptr) bcontext->userdata;
+  fpp = (FeatProbPtr) bcontext->userdata;
   sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
   while (sfp != NULL) {
-    CheckFeatPacking (bsp, sfp, num_misplaced_features);
+    CheckFeatPacking (bsp, sfp, &(fpp->num_misplaced_features));
+    CheckFeatLocAndProd (sfp, fpp);
     sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
   }
 
   return TRUE;
 }
 
+static void CountGeneXrefs (SeqFeatPtr sfp, Pointer userdata)
+
+{
+  FeatProbPtr  fpp;
+  GeneRefPtr   grp;
+
+  if (sfp == NULL || userdata == NULL) return;
+  fpp = (FeatProbPtr) userdata;
+
+  if (sfp->data.choice == SEQFEAT_GENE) {
+    (fpp->num_gene_feats)++;
+  }
+
+  grp = SeqMgrGetGeneXref (sfp);
+  if (grp == NULL || SeqMgrGeneIsSuppressed (grp)) return;
+
+  (fpp->num_gene_xrefs)++;
+}
+
 static Boolean IsNoncuratedRefSeq (BioseqPtr bsp, ErrSev *sev)
 
 {
@@ -2020,7 +2225,7 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
   Int2            errors[6], i;
   Boolean         suppress_no_pubs = TRUE;
   Boolean         suppress_no_biosrc = TRUE;
-  Uint4           num_misplaced_features = 0;
+  FeatProb        featprob;
   GatherContextPtr gcp = NULL;
   GatherContext   gc;
   SeqEntryPtr     fsep;
@@ -2040,6 +2245,8 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
   for (i = 0; i < 6; i++)       /* keep errors between clears */
     errors[i] = 0;
 
+  MemSet ((Pointer) &featprob, 0, sizeof (FeatProb));
+
   if (vsp->useSeqMgrIndexes) {
     entityID = ObjMgrGetEntityIDForChoice (sep);
 
@@ -2048,7 +2255,10 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
       SeqMgrIndexFeatures (entityID, NULL);
       ErrSetMessageLevel (oldsev);
     }
-    SeqMgrExploreBioseqs (entityID, NULL, (Pointer) &num_misplaced_features, CountMisplacedFeatures, TRUE, TRUE, TRUE);
+    SeqMgrExploreBioseqs (entityID, NULL, (Pointer) &featprob, CountMisplacedFeatures, TRUE, TRUE, TRUE);
+
+    topsep = GetTopSeqEntryForEntityID (entityID);
+    VisitFeaturesInSep (topsep, (Pointer) &featprob, CountGeneXrefs);
   } else {
 
     /* if not using indexing, still need feature->idx.subtype now */
@@ -2169,11 +2379,30 @@ NLM_EXTERN Boolean ValidateSeqEntry (SeqEntryPtr sep, ValidStructPtr vsp)
         }
       }
 
-      if (num_misplaced_features > 1) {
-        ValidErr (vsp, SEV_REJECT, ERR_SEQ_PKG_FeaturePackagingProblem, "There are %d mispackaged features in this record.", (int) num_misplaced_features);
-      } else if (num_misplaced_features == 1) {
-        ValidErr (vsp, SEV_REJECT, ERR_SEQ_PKG_FeaturePackagingProblem, "There is %d mispackaged feature in this record.", (int) num_misplaced_features);
+      if (featprob.num_misplaced_features > 1) {
+        ValidErr (vsp, SEV_REJECT, ERR_SEQ_PKG_FeaturePackagingProblem, "There are %d mispackaged features in this record.", (int) featprob.num_misplaced_features);
+      } else if (featprob.num_misplaced_features == 1) {
+        ValidErr (vsp, SEV_REJECT, ERR_SEQ_PKG_FeaturePackagingProblem, "There is %d mispackaged feature in this record.", (int) featprob.num_misplaced_features);
       }
+
+      /*
+      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);
+      } else if (featprob.num_archaic_locations == 1) {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_PKG_ArchaicFeatureLocation, "There is %d archaic feature location in this record.", (int) featprob.num_archaic_locations);
+      }
+
+      if (featprob.num_archaic_products > 1) {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_PKG_ArchaicFeatureProduct, "There are %d archaic feature products in this record.", (int) featprob.num_archaic_products);
+      } else if (featprob.num_archaic_products == 1) {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_PKG_ArchaicFeatureProduct, "There is %d archaic feature product in this record.", (int) featprob.num_archaic_products);
+      }
+      */
+
+      if (featprob.num_gene_feats == 0 && featprob.num_gene_xrefs > 0) {
+        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);
+      }
+
       first = FALSE;
     }
 
@@ -3034,6 +3263,89 @@ static void ValidateIDSetAgainstDb (GatherContextPtr gcp, ValidStructPtr vsp, Bi
   }
 }
 
+typedef struct enrun {
+  Int4  ncount;
+  Int4  maxrun;
+} RunOfNs, PNTR RunOfNsPtr;
+
+static void LIBCALLBACK CountAdjacentProc (CharPtr sequence, Pointer userdata)
+
+{
+  Char        ch;
+  RunOfNsPtr  ronp;
+  CharPtr     str;
+
+  ronp = (RunOfNsPtr) userdata;
+  if (sequence == NULL || ronp == NULL) return;
+
+  str = sequence;
+  ch = *str;
+  while (ch != '\0') {
+    if (ch == 'N') {
+      (ronp->ncount)++;
+      if (ronp->ncount > ronp->maxrun) {
+        ronp->maxrun = ronp->ncount;
+      }
+    } else {
+      ronp->ncount = 0;
+    }
+    str++;
+    ch = *str;
+  }
+}
+
+static Int4 CountAdjacentNsInSeqLit (SeqLitPtr slitp, Boolean is_na)
+
+{
+  BioseqPtr  bsp;
+  RunOfNs    ron;
+
+  if (slitp == NULL || slitp->length < 1 || slitp->seq_data == NULL) return 0;
+
+  bsp = BioseqNew ();
+  if (bsp == NULL) return 0;
+
+  if (slitp->seq_data != NULL) {
+    bsp->repr = Seq_repr_raw;
+  } else {
+    bsp->repr = Seq_repr_virtual;
+  }
+  if (is_na) {
+    bsp->mol = Seq_mol_dna;
+  } else {
+    bsp->mol = Seq_mol_aa;
+  }
+  bsp->seq_data_type = slitp->seq_data_type;
+  bsp->seq_data = slitp->seq_data;
+  bsp->length = slitp->length;
+  bsp->id = SeqIdParse ("lcl|countseqlitns");
+
+  ron.ncount = 0;
+  ron.maxrun = 0;
+
+  SeqPortStream (bsp, TRUE, (Pointer) &ron, CountAdjacentProc);
+
+  bsp->seq_data = NULL;
+
+  BioseqFree (bsp);
+
+  return ron.maxrun;
+}
+
+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 void ValidateBioseqInst (GatherContextPtr gcp)
 {
   Boolean         retval = TRUE;
@@ -3061,6 +3373,7 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
   Boolean         litHasData;
   SeqMgrDescContext context;
   SeqFeatPtr      cds;
+  GBBlockPtr      gbp;
   GeneRefPtr      grp;
   SeqFeatPtr      gene;
   SeqMgrFeatContext genectxt;
@@ -3075,6 +3388,7 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
   Boolean         multitoken;
   Boolean         hasGi = FALSE;
   SeqHistPtr      hist;
+  Boolean         isActiveFin = FALSE;
   Boolean         isGenBankEMBLorDDBJ;
   Boolean         isPatent = FALSE;
   Boolean         isPDB = FALSE;
@@ -3091,7 +3405,6 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
   Int2            trailingX = 0;
   Int2            numletters, numdigits, numunderscores;
   Boolean         letterAfterDigit, badIDchars;
-  GBBlockPtr      gbp;
   EMBLBlockPtr    ebp;
   SeqDescrPtr     sdp;
   SeqMgrDescContext dcontext;
@@ -3103,9 +3416,12 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
   ObjValNodePtr   ovp;
   BioseqSetPtr    bssp;
   UserObjectPtr   uop;
+  UserFieldPtr    ufp;
   ObjectIdPtr     oip;
+  Boolean         hasRefTrackStatus;
   Int2            accn_count = 0;
   Int2            gi_count = 0;
+  Int4            runsofn;
 
   /* set up data structures */
 
@@ -3192,6 +3508,8 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
         } else if (numletters == 2 && numdigits == 6 && ISA_aa (bsp->mol) && bsp->repr == Seq_repr_seg) {
         } else if (numletters == 4 && numdigits == 8 && ISA_na (bsp->mol) &&
                    (sip1->choice == SEQID_GENBANK || sip1->choice == SEQID_EMBL || sip1->choice == SEQID_DDBJ)) {
+        } else if (numletters == 4 && numdigits == 9 && ISA_na (bsp->mol) &&
+                   (sip1->choice == SEQID_GENBANK || sip1->choice == SEQID_EMBL || sip1->choice == SEQID_DDBJ)) {
         } else {
           ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadSeqIdFormat, "Bad accession %s", tsip->accession);
         }
@@ -3260,7 +3578,7 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
           }
         }
         if (letterAfterDigit || badIDchars) {
-          ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadSeqIdFormat, "Bad accession %s", tsip->accession);
+          ValidErr (vsp, SEV_REJECT, ERR_SEQ_INST_BadSeqIdFormat, "Bad accession %s", tsip->accession);
         } else if (isNZ && numletters == 4 && numdigits == 8 && numunderscores == 0) {
         } else if (numletters == 2 && numdigits == 6 && numunderscores == 1) {
         } else if (numletters == 2 && numdigits == 8 && numunderscores == 1) {
@@ -3347,6 +3665,23 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
             gcp->itemID = olditemid;
             gcp->thistype = olditemtype;
           }
+        } else if (oip != NULL && StringICmp (oip->str, "RefGeneTracking") == 0) {
+          hasRefTrackStatus = FALSE;
+          for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+            oip = ufp->label;
+            if (oip != NULL && StringCmp (oip->str, "Status") == 0) {
+              hasRefTrackStatus = TRUE;
+            }
+          }
+          if (! hasRefTrackStatus) {
+            olditemid = gcp->itemID;
+            olditemtype = gcp->thistype;
+            gcp->itemID = context.itemID;
+            gcp->thistype = OBJ_SEQDESC;
+            ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_RefGeneTrackingWithoutStatus, "RefGeneTracking object needs to have Status set");
+            gcp->itemID = olditemid;
+            gcp->thistype = olditemtype;
+          }
         }
       }
       vnp = SeqMgrGetNextDescriptor (bsp, vnp, Seq_descr_user, &context);
@@ -3727,6 +4062,39 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
   mip = NULL;
 
   if (bsp->repr == Seq_repr_delta) {
+    vnp = NULL;
+    if (vsp->useSeqMgrIndexes) {
+      vnp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &context);
+    } else {
+      bcp = BioseqContextNew (bsp);
+      vnp = BioseqContextGetSeqDescr (bcp, Seq_descr_genbank, NULL, NULL);
+      BioseqContextFree (bcp);
+    }
+    if (vnp != NULL) {
+      gbp = (GBBlockPtr) vnp->data.ptrvalue;
+      if (gbp != NULL) {
+        for (vnp = gbp->keywords; vnp != NULL; vnp = vnp->next) {
+          str = (CharPtr) vnp->data.ptrvalue;
+          if (StringICmp (str, "HTGS_ACTIVEFIN") == 0) {
+            isActiveFin = TRUE;
+          }
+        }
+      }
+    }
+  }
+
+  if (bsp->repr == Seq_repr_delta) {
+    vnp = NULL;
+    if (vsp->useSeqMgrIndexes) {
+      vnp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &context);
+    } else {
+      bcp = BioseqContextNew (bsp);
+      vnp = BioseqContextGetSeqDescr (bcp, Seq_descr_molinfo, NULL, NULL);
+      BioseqContextFree (bcp);
+    }
+    if (vnp != NULL) {
+      mip = (MolInfoPtr) vnp->data.ptrvalue;
+    }
     len = 0;
     for (vnp = (ValNodePtr) (bsp->seq_ext); vnp != NULL; vnp = vnp->next) {
       if (vnp->data.ptrvalue == NULL)
@@ -3778,6 +4146,16 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
             default:
               break;
             }
+            if (mip != NULL) {
+              if (mip->tech == MI_TECH_htgs_1 || mip->tech == MI_TECH_htgs_2) {
+                runsofn = CountAdjacentNsInSeqLit (slitp, (Boolean) ISA_na (bsp->mol));
+                if (runsofn > 80) {
+                  ValidErr (vsp, SEV_WARNING, ERR_SEQ_INST_InternalNsInSeqLit, "Run of %ld Ns in delta chain", (long) runsofn);
+                }
+              }
+            }
+          } else if (slitp->length == 0) {
+            ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_SeqLitGapLength0, "Gap of length 0 in delta chain");
           }
           len += slitp->length;
           break;
@@ -3792,31 +4170,28 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
     } else if (bsp->length < len) {
       ValidErr (vsp, SEV_REJECT, ERR_SEQ_INST_SeqDataLenWrong, "Bioseq.seq_data is larger [%ld] than given length [%ld]", (long) (len), (long) bsp->length);
     }
-    vnp = NULL;
-    if (vsp->useSeqMgrIndexes) {
-      vnp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &context);
-    } else {
-      bcp = BioseqContextNew (bsp);
-      vnp = BioseqContextGetSeqDescr (bcp, Seq_descr_molinfo, NULL, NULL);
-      BioseqContextFree (bcp);
-    }
-    if (vnp != NULL) {
-      mip = (MolInfoPtr) vnp->data.ptrvalue;
-      if (mip != NULL) {
-        is_gps = FALSE;
-        sep = vsp->sep;
-        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 ((!isNTorNC) && (! is_gps) && mip->tech != MI_TECH_htgs_0 && mip->tech != MI_TECH_htgs_1 &&
-            mip->tech != MI_TECH_htgs_2 && mip->tech != MI_TECH_htgs_3 && mip->tech != MI_TECH_wgs &&
-            mip->tech != MI_TECH_unknown && mip->tech != MI_TECH_standard) {
-          ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadDeltaSeq, "Delta seq technique should not be [%d]", (int) (mip->tech));
+    if (mip != NULL) {
+      is_gps = FALSE;
+      sep = vsp->sep;
+      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 ((!isNTorNC) && (! is_gps) && mip->tech != MI_TECH_htgs_0 && mip->tech != MI_TECH_htgs_1 &&
+          mip->tech != MI_TECH_htgs_2 && mip->tech != MI_TECH_htgs_3 && mip->tech != MI_TECH_wgs &&
+          mip->tech != MI_TECH_unknown && mip->tech != MI_TECH_standard) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadDeltaSeq, "Delta seq technique should not be [%d]", (int) (mip->tech));
+      }
+    }
+  }
+
+  sev = SEV_ERROR;
+  if (mip != NULL) {
+    if (mip->tech != MI_TECH_htgs_0 && mip->tech != MI_TECH_htgs_1 &&
+        mip->tech != MI_TECH_htgs_2 && mip->tech != MI_TECH_htgs_3) {
+      sev = SEV_WARNING;
     }
   }
 
@@ -3825,7 +4200,7 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
     if (vnp != NULL && vnp->choice == 2) {
       slitp = (SeqLitPtr) vnp->data.ptrvalue;
       if (slitp != NULL && slitp->seq_data == NULL) {
-        ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadDeltaSeq, "First delta seq component is a gap");
+        ValidErr (vsp, sev, ERR_SEQ_INST_BadDeltaSeq, "First delta seq component is a gap");
       }
     }
     last_is_gap = FALSE;
@@ -3856,13 +4231,15 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
     if (vnp != NULL && vnp->choice == 2) {
       slitp = (SeqLitPtr) vnp->data.ptrvalue;
       if (slitp != NULL && slitp->seq_data == NULL) {
-        ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadDeltaSeq, "Last delta seq component is a gap");
+        ValidErr (vsp, sev, ERR_SEQ_INST_BadDeltaSeq, "Last delta seq component is a gap");
       }
     }
     if (num_gaps == 0 && mip != NULL) {
       if (/* mip->tech == MI_TECH_htgs_1 || */ mip->tech == MI_TECH_htgs_2) {
         if (VisitGraphsInSep (sep, NULL, NULL) == 0) {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_INST_BadDeltaSeq, "HTGS 2 delta seq has no gaps and no graphs");
+          if (! isActiveFin) {
+            ValidErr (vsp, SEV_WARNING, ERR_SEQ_INST_BadDeltaSeq, "HTGS 2 delta seq has no gaps and no graphs");
+          }
         }
       }
     }
@@ -3993,28 +4370,38 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
     }
   }
 
-  if (ISA_na (bsp->mol) && bsp->repr == Seq_repr_raw && bsp->length > 5) {
+  if (ISA_na (bsp->mol) && (bsp->repr == Seq_repr_raw || (bsp->repr == Seq_repr_delta && DeltaLitOnly (bsp))) && bsp->length > 10) {
     /* check for N bases at start or stop of sequence */
     sfp = (SeqFeatPtr) MemNew (sizeof (SeqFeat));
     if (sfp == NULL) return;
     sfp->data.choice = SEQFEAT_COMMENT;
 
-    sfp->location = AddIntervalToLocation (NULL, bsp->id, 0, 2, FALSE, FALSE);
+    sfp->location = AddIntervalToLocation (NULL, bsp->id, 0, 9, FALSE, FALSE);
     str = GetSequenceByFeature (sfp);
     if (str != NULL) {
       if (str [0] == 'n' || str [0] == 'N') {
-        ValidErr (vsp, SEV_WARNING, ERR_SEQ_INST_TerminalNs, "N at beginning of sequence");
+        if (StringICmp (str, "NNNNNNNNNN") == 0) {
+          sev = SEV_ERROR;
+        } else {
+          sev = SEV_WARNING;
+        }
+        ValidErr (vsp, sev, ERR_SEQ_INST_TerminalNs, "N at beginning of sequence");
       }
     }
     MemFree (str);
     sfp->location = SeqLocFree (sfp->location);
 
-    sfp->location = AddIntervalToLocation (NULL, bsp->id, bsp->length - 3, bsp->length - 1, FALSE, FALSE);
+    sfp->location = AddIntervalToLocation (NULL, bsp->id, bsp->length - 10, bsp->length - 1, FALSE, FALSE);
     str = GetSequenceByFeature (sfp);
     len = StringLen (str);
     if (str != NULL && len > 0) {
       if (str [len - 1] == 'n' || str [len - 1] == 'N') {
-        ValidErr (vsp, SEV_WARNING, ERR_SEQ_INST_TerminalNs, "N at end of sequence");
+        if (StringICmp (str, "NNNNNNNNNN") == 0) {
+          sev = SEV_ERROR;
+        } else {
+          sev = SEV_WARNING;
+        }
+        ValidErr (vsp, sev, ERR_SEQ_INST_TerminalNs, "N at end of sequence");
       }
     }
     MemFree (str);
@@ -4226,6 +4613,7 @@ static void ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, PubdescPt
                 ValidErr (vsp, sev, ERR_GENERIC_MissingPubInfo, "Journal pages missing");
               }
               if (! noPages) {
+                sev = SEV_WARNING;
                 StringNCpy_0 (temp, imp->pages, sizeof (temp));
                 ptr = StringChr (temp, '-');
                 if (ptr != NULL) {
@@ -4295,9 +4683,10 @@ static void ValidateSfpCit (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPtr
 typedef struct bioseqvalid
 {
   ValidStructPtr  vsp;
-  Boolean         is_aa;        /* bioseq is protein? */
-  Boolean         is_mrna;      /* molinfo is mrna? */
-  Boolean         is_prerna;    /* molinfo is precursor rna? */
+  Boolean         is_aa;         /* bioseq is protein? */
+  Boolean         is_mrna;       /* molinfo is mrna? */
+  Boolean         is_prerna;     /* molinfo is precursor rna? */
+  Boolean         is_artificial; /* biosource origin is artificial? */
   Boolean         got_a_pub;
   int             last_na_mol, last_na_mod, last_organelle, last_partialness, last_left_right, last_biomol, last_tech, last_completeness, num_full_length_src_feat,     /* number full length src feats */
                   num_full_length_prot_ref;
@@ -4729,6 +5118,7 @@ static CharPtr  countrycodes[] = {
   "Juan de Nova Island",
   "Kazakhstan",
   "Kenya",
+  "Kerguelen Archipelago",
   "Kingman Reef",
   "Kiribati",
   "Kuwait",
@@ -4811,6 +5201,7 @@ static CharPtr  countrycodes[] = {
   "Sao Tome and Principe",
   "Saudi Arabia",
   "Senegal",
+  "Serbia and Montenegro",
   "Seychelles",
   "Sierra Leone",
   "Singapore",
@@ -5028,11 +5419,13 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
   CharPtr         countryname;
   ValNodePtr      db;
   DbtagPtr        dbt;
+  Boolean         germline = FALSE;
   Int2            i;
   Int4            id;
   OrgNamePtr      onp;
   OrgModPtr       omp;
   OrgRefPtr       orp;
+  Boolean         rearranged = FALSE;
   SubSourcePtr    ssp;
 
   if (vsp->sourceQualTags == NULL) {
@@ -5070,9 +5463,16 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
       ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadSubSource, "Unknown subsource subtype %d", (int) (ssp->subtype));
     } else if (ssp->subtype == SUBSRC_other) {
       ValidateSourceQualTags (vsp, gcp, biop, ssp->name);
+    } else if (ssp->subtype == SUBSRC_germline) {
+      germline = TRUE;
+    } else if (ssp->subtype == SUBSRC_rearranged) {
+      rearranged = TRUE;
     }
     ssp = ssp->next;
   }
+  if (germline && rearranged) {
+    ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadSubSource, "Germline and rearranged should not both be present");
+  }
   if (chromcount > 1) {
     if (chromconf) {
       ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_MultipleChromosomes, "Multiple conflicting chromosome qualifiers");
@@ -5166,6 +5566,65 @@ static Boolean IsXr (ValNodePtr sdp)
   return FALSE;
 }
 
+static Boolean IsSynthetic (BioseqPtr bsp)
+
+{
+  BioSourcePtr       biop;
+  SeqMgrDescContext  dcontext;
+  OrgNamePtr         onp;
+  OrgRefPtr          orp;
+  SeqDescrPtr        sdp;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  if (sdp == NULL) return FALSE;
+  biop = (BioSourcePtr) sdp->data.ptrvalue;
+  if (biop == NULL) return FALSE;
+  if (biop->origin == 5) return TRUE;
+  orp = biop->org;
+  if (orp == NULL) return FALSE;
+  onp = orp->orgname;
+  if (onp == NULL) return FALSE;
+  if (StringICmp (onp->div, "SYN") == 0) return TRUE;
+  return FALSE;
+}
+
+static Boolean IsMicroRNA (BioseqPtr bsp)
+
+{
+  SeqMgrFeatContext  fcontext;
+  RnaRefPtr          rrp;
+  SeqFeatPtr         sfp;
+  CharPtr            str;
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_otherRNA, &fcontext);
+  while (sfp != NULL) {
+    if (sfp->data.choice == SEQFEAT_RNA) {
+      rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+      if (rrp != NULL && rrp->ext.choice == 1) {
+        str = (CharPtr) rrp->ext.value.ptrvalue;
+        if (StringStr (str, "microRNA") != NULL) return TRUE;
+      }
+    }
+    sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_otherRNA, &fcontext);
+  }
+  return FALSE;
+}
+
+static Boolean IsOtherDNA (BioseqPtr bsp)
+
+{
+  SeqMgrDescContext  dcontext;
+  MolInfoPtr         mip;
+  SeqDescrPtr        sdp;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp == NULL) return FALSE;
+  mip = (MolInfoPtr) sdp->data.ptrvalue;
+  if (mip == NULL) return FALSE;
+  if (mip->biomol == 255) return TRUE;
+  return FALSE;
+}
+
 static Boolean ValidateSeqDescrCommon (ValNodePtr sdp, BioseqValidStrPtr bvsp, ValidStructPtr vsp, Uint2 descitemid)
 {
   ValNodePtr      vnp, vnp2;
@@ -5371,6 +5830,12 @@ static Boolean ValidateSeqDescrCommon (ValNodePtr sdp, BioseqValidStrPtr bvsp, V
         }
       }
     }
+    if (biop != NULL && biop->origin == 5) {
+      bsp = bvsp->bsp;
+      if (! IsOtherDNA (bsp)) {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_InvalidForType, "Molinfo-biomol other should be used if Biosource-location is synthetic");
+      }
+    }
     /* ValidateBioSource (vsp, gcp, biop); */
     this_org = biop->org;
     /* fall into Seq_descr_org */
@@ -5415,18 +5880,25 @@ static Boolean ValidateSeqDescrCommon (ValNodePtr sdp, BioseqValidStrPtr bvsp, V
       switch (mip->biomol) {
       case MOLECULE_TYPE_PEPTIDE:      /* peptide */
         if (!bvsp->is_aa) {
-          ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_InvalidForType, "Nucleic acid with Molinfo-biomol = peptide");
+          ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_InvalidForType, "Nucleic acid with Molinfo-biomol = peptide");          
         }
         break;
       case MOLECULE_TYPE_OTHER_GENETIC_MATERIAL:
-        ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_InvalidForType, "Molinfo-biomol = other genetic");
+        if (! bvsp->is_artificial) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_InvalidForType, "Molinfo-biomol = other genetic");
+        }
         break;
       case 0:                  /* unknown */
         ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_InvalidForType, "Molinfo-biomol unknown used");
         break;
       case 255:                /* other */
         if (! IsXr (vnp)) {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_InvalidForType, "Molinfo-biomol other used");
+          bsp = bvsp->bsp;
+          if (! IsSynthetic (bsp)) {
+            if (! IsMicroRNA (bsp)) {
+              ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_InvalidForType, "Molinfo-biomol other used");
+            }
+          }
         }
         break;
       default:                 /* the rest are nucleic acid */
@@ -5776,6 +6248,8 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
   int             overlapPepSev;
   BioSourcePtr    biop = NULL;
   OrgRefPtr       orp = NULL;
+  Int4            fiveUTRright;
+  Int4            cdsRight;
 
   gcp = bvsp->gcp;
   vsp = bvsp->vsp;
@@ -5858,9 +6332,9 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
                   }
                 }
               }
-              if (GPSorNTorNC (vsp->sep, sfp->location)) {
-                severity = SEV_WARNING;
-              }
+            }
+            if (GPSorNTorNC (vsp->sep, sfp->location)) {
+              severity = SEV_WARNING;
             }
             if (FlybaseDbxrefs (last->dbxref) || FlybaseDbxrefs (sfp->dbxref)) {
               severity = SEV_ERROR;
@@ -5960,6 +6434,52 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
     sfp = SeqMgrGetNextFeatureByLabel (bsp, sfp, SEQFEAT_GENE, 0, &fcontext);
   }
 
+  if (bvsp->is_mrna) {
+    fiveUTRright = 0;
+    cdsRight = 0;
+    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 + 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, "5'UTR does not abut CDS");
+            vsp->sfp = NULL;
+            if (gcp != NULL) {
+              gcp->itemID = olditemid;
+              gcp->thistype = olditemtype;
+            }
+          }
+        }
+      } else if (sfp->idx.subtype == FEATDEF_3UTR) {
+        if (cdsRight > 0) {
+          if (cdsRight + 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, "CDS does not abut 3'UTR");
+            if (gcp != NULL) {
+              gcp->itemID = olditemid;
+              gcp->thistype = olditemtype;
+            }
+          }
+        }
+      }
+      sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
+    }
+  }
+
   SeqMgrExploreDescriptors (bsp, (Pointer) bvsp, ValidateSeqDescrIndexed, NULL);
 
   omdp = ObjMgrGetData (gcp->entityID);
@@ -6019,6 +6539,7 @@ static Boolean ValidateBioseqContextGather (GatherContextPtr gcp)
 *****************************************************************************/
 static void ValidateBioseqContext (GatherContextPtr gcp)
 {
+  size_t          acclen;
   ValidStructPtr  vsp;
   BioseqPtr       bsp;
   GatherScope     gs;
@@ -6038,6 +6559,7 @@ static void ValidateBioseqContext (GatherContextPtr gcp)
   Boolean         is_gb = FALSE;
   ErrSev          sev;
   TextSeqIdPtr    tsip;
+  BioSourcePtr    biop;
 
   vsp = (ValidStructPtr) (gcp->userdata);
   bsp = (BioseqPtr) (gcp->thisitem);
@@ -6081,6 +6603,15 @@ static void ValidateBioseqContext (GatherContextPtr gcp)
     if (vnp != NULL) {
       mip = (MolInfoPtr) vnp->data.ptrvalue;
     }
+    vnp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &context);
+    if (vnp != NULL) {
+      biop = (BioSourcePtr) vnp->data.ptrvalue;
+      if (biop != NULL) {
+        if (biop->origin == ORG_ARTIFICIAL) {
+          bvs.is_artificial = TRUE;
+        }
+      }
+    }
   }
 
   bvs.is_mrna = FALSE;
@@ -6179,7 +6710,10 @@ static void ValidateBioseqContext (GatherContextPtr gcp)
       is_gb = TRUE;
       tsip = (TextSeqIdPtr) sip->data.ptrvalue;
       if (tsip != NULL && tsip->accession != NULL) {
-        if (StringLen (tsip->accession) == 12) {
+        acclen = StringLen (tsip->accession);
+        if (acclen == 12) {
+          is_wgs = TRUE;
+        } else if (acclen == 13) {
           is_wgs = TRUE;
         }
       }
@@ -6321,6 +6855,7 @@ static void ValidateImpFeat (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPt
   GeneRefPtr      grp;
   Int2            i;
   Int2            index;
+  Boolean         just_nuc_letters;
   CharPtr         key;
   Boolean         multi_rpt_unit;
   Boolean         no_white_space;
@@ -6472,11 +7007,34 @@ static void ValidateImpFeat (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPt
               multi_rpt_unit = FALSE;
             }
           }
+          /*
           if (found) {
             ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_InvalidQualifierValue, "Illegal value for qualifier %s", gbqual->qual);
           } else if ((!multi_rpt_unit) && StringLen (gbqual->val) > 48) {
             ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_InvalidQualifierValue, "Illegal value for qualifier %s", gbqual->qual);
           }
+          */
+          if (StringICmp (key,"repeat_region") == 0) {
+            if (! multi_rpt_unit) {
+              if (StringLen (gbqual->val) == SeqLocLen (sfp->location)) {
+                just_nuc_letters = TRUE;
+                for (ptr = gbqual->val, ch = *ptr; ch != '\0'; ptr++, ch = *ptr) {
+                  if (StringChr ("ACGTNacgtn", ch) == NULL) {
+                    just_nuc_letters = FALSE;
+                  }
+                }
+                if (just_nuc_letters) {
+                  tmp = GetSequenceByFeature (sfp);
+                  if (tmp != NULL) {
+                    if (StringICmp (tmp, gbqual->val) != 0) {
+                      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_InvalidQualifierValue, "repeat_region /rpt_unit and underlying sequence do not match");
+                    }
+                    MemFree (tmp);
+                  }
+                }
+              }
+            }
+          }
         } else if (val == GBQUAL_label) {
           no_white_space = TRUE;
           only_digits = TRUE;
@@ -6641,21 +7199,54 @@ static Boolean PartialAtSpliceSite (SeqLocPtr head, Uint2 slpTag)
 
 static void CheckTrnaCodons (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPtr sfp, tRNAPtr trp)
 {
-  Uint1           aa;
+  Uint1           aa = 0;
   BioseqPtr       bsp;
   Int2            code;
   CharPtr         codes = NULL;
   Uint1           from;
   GeneticCodePtr  gncp;
+  Uint2           idx;
   Int2            j;
   SeqEntryPtr     sep;
   ErrSev          sev = SEV_ERROR;
+  Uint1           shift;
   SeqMapTablePtr  smtp;
   Uint1           taa;
   ValNodePtr      vnp;
 
   if (vsp == NULL || gcp == NULL || sfp == NULL || trp == NULL)
     return;
+
+  aa = 0;
+  if (trp->aatype == 2) {
+    aa = trp->aa;
+  } else {
+    from = 0;
+    switch (trp->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;
+    }
+    smtp = SeqMapTableFind (Seq_code_ncbieaa, from);
+    if (smtp != NULL) {
+      aa = SeqMapTableConvert (smtp, trp->aa);
+    }
+  }
+
   for (j = 0; j < 6; j++) {
     if (trp->codon[j] < 64) {
       if (codes == NULL) {
@@ -6677,35 +7268,6 @@ static void CheckTrnaCodons (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPt
       if (codes == NULL)
         return;
       taa = codes[trp->codon[j]];
-      aa = 0;
-      if (trp->aatype == 2) {
-        aa = trp->aa;
-      } else {
-        from = 0;
-        switch (trp->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;
-        }
-        smtp = SeqMapTableFind (Seq_code_ncbieaa, from);
-        if (smtp != NULL) {
-          aa = SeqMapTableConvert (smtp, trp->aa);
-        }
-      }
       if (aa > 0 && aa != 255) {
         if (taa != aa) {
           if (aa == 'U') {
@@ -6714,6 +7276,28 @@ static void CheckTrnaCodons (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPt
           ValidErr (vsp, sev, ERR_SEQ_FEAT_TrnaCodonWrong, "tRNA codon does not match genetic code");
         }
       }
+    } else if (trp->codon [j] < 255) {
+      ValidErr (vsp, sev, ERR_SEQ_FEAT_BadTrnaCodon, "tRNA codon value %d is greater than maximum 63", (int) trp->codon [j]);
+    }
+  }
+
+  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) {
+      /* valid trna amino acid */
+    } else {
+      ValidErr (vsp, sev, ERR_SEQ_FEAT_BadTrnaAA, "Invalid tRNA amino acid");
     }
   }
 }
@@ -6780,6 +7364,71 @@ static Boolean NucAndProtNotInNPS (BioseqPtr nuc, BioseqPtr prot)
   return FALSE;
 }
 
+static void CheckCDSPartial (ValidStructPtr vsp, SeqFeatPtr sfp)
+
+{
+  BioseqPtr          bsp;
+  SeqMgrDescContext  context;
+  MolInfoPtr         mip;
+  Boolean            partial5;
+  Boolean            partial3;
+  SeqDescrPtr        sdp;
+
+  if (vsp == NULL || sfp == NULL) return;
+  if (sfp->product == NULL) return;
+  if (!vsp->useSeqMgrIndexes) return;
+  bsp = BioseqFindFromSeqLoc (sfp->product);
+  if (bsp == NULL) return;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &context);
+  if (sdp == NULL) return;
+  mip = (MolInfoPtr) sdp->data.ptrvalue;
+  if (mip == NULL) return;
+  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+  switch (mip->completeness) {
+    case 0 : /* unknown */
+      break;
+    case 1 : /* complete */
+      if (partial5 || partial3) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "CDS is partial but protein is complete");
+      }
+      break;
+    case 2 : /* partial */
+      break;
+    case 3 : /* no-left */
+      if (! partial5) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "CDS is 5' complete but protein is NH2 partial");
+      }
+      if (partial3) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "CDS is 3' partial but protein is NH2 partial");
+      }
+      break;
+    case 4 : /* no-right */
+      if (! partial3) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "CDS is 3' complete but protein is CO2 partial");
+      }
+      if (partial5) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "CDS is 5' partial but protein is CO2 partial");
+      }
+      break;
+    case 5 : /* no-ends */
+      if (partial5 && partial3) {
+      } else if (partial5) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "CDS is 5' partial but protein has neither end");
+      } else if (partial3) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "CDS is 3' partial but protein has neither end");
+      } else {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "CDS is complete but protein has neither end");
+      }
+      break;
+    case 6 : /* has-left */
+      break;
+    case 7 : /* has-right */
+      break;
+    default :
+      break;
+  }
+}
+
 static void CheckForCommonCDSProduct (ValidStructPtr vsp, SeqFeatPtr sfp)
 {
   BioseqPtr       bsp;
@@ -6988,7 +7637,10 @@ static void CheckForBadMRNAOverlap (ValidStructPtr vsp, SeqFeatPtr sfp)
   }
   mrna = SeqMgrGetOverlappingFeature (sfp->location, FEATDEF_mRNA, NULL, 0, NULL, LOCATION_SUBSET, &fcontext);
   if (mrna != NULL) {
-    ValidErr (vsp, sev, ERR_SEQ_FEAT_CDSmRNArange, "mRNA contains CDS but internal intron-exon boundaries do not match");
+    if (StringISearch (sfp->except_text, "ribosomal slippage") == NULL &&
+        StringISearch (sfp->except_text, "ribosome slippage") == NULL) {
+      ValidErr (vsp, sev, ERR_SEQ_FEAT_CDSmRNArange, "mRNA contains CDS but internal intron-exon boundaries do not match");
+    }
   } else {
     ValidErr (vsp, sev, ERR_SEQ_FEAT_CDSmRNArange, "mRNA overlaps or contains CDS but does not completely contain intervals");
   }
@@ -7044,6 +7696,7 @@ static CharPtr legalDbXrefOnRefSeq [] = {
   "GenBank",
   "EMBL",
   "DDBJ",
+  "REBASE",
   NULL
 };
 
@@ -7112,6 +7765,7 @@ static CharPtr legal_exception_strings [] = {
   "artificial frameshift",
   "non-consensus splice site",
   "nonconsensus splice site",
+  "rearrangement required for product",
   NULL
 };
 
@@ -7279,6 +7933,24 @@ NLM_EXTERN Boolean IsNuclAcc (CharPtr name)
   return TRUE;
 }
 
+static Boolean IsCddFeat (
+  SeqFeatPtr sfp
+)
+
+{
+  DbtagPtr    dbt;
+  ValNodePtr  vnp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_REGION) return FALSE;
+
+  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;
+}
+
 NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
 {
   Int2            type, i, j;
@@ -7322,6 +7994,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
   SeqMgrDescContext context;
   GeneRefPtr      grpx;
   SeqFeatPtr      sfpx;
+  SeqFeatPtr      operon;
   Boolean         redundantgenexref;
   SeqMgrFeatContext fcontext;
   CharPtr         syn1, syn2, label = NULL;
@@ -7329,6 +8002,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
   SeqIdPtr        sip;
   TextSeqIdPtr    tsip;
   BioseqPtr       protBsp;
+  ErrSev          sev;
 
   vsp = (ValidStructPtr) (gcp->userdata);
   sfp = (SeqFeatPtr) (gcp->thisitem);
@@ -7358,8 +8032,35 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_PartialProblem, "Gene of 'order' with otherwise complete location should have partial flag set");
       }
     }
-    /* inconsistent combination of partial/complete product,location,partial flag */
-    else if (((partials[0] == SLP_COMPLETE) && (sfp->product != NULL)) || (partials[1] == SLP_COMPLETE) || (!sfp->partial)) {
+    /* inconsistent combination of partial/complete product,location,partial flag - part 1 */
+    else if (((partials[0] == SLP_COMPLETE) && (sfp->product != NULL))) {
+      sev = SEV_WARNING;
+      bsp = GetBioseqGivenSeqLoc (sfp->product, gcp->entityID);
+      /* if not local bioseq product, lower severity */
+      if (bsp == NULL) {
+        sev = SEV_INFO;
+      }
+      tmp = StringMove (buf, "Inconsistent: ");
+      if (sfp->product != NULL) {
+        tmp = StringMove (tmp, "Product= ");
+        if (partials[0])
+          tmp = StringMove (tmp, "partial, ");
+        else
+          tmp = StringMove (tmp, "complete, ");
+      }
+      tmp = StringMove (tmp, "Location= ");
+      if (partials[1])
+        tmp = StringMove (tmp, "partial, ");
+      else
+        tmp = StringMove (tmp, "complete, ");
+      tmp = StringMove (tmp, "Feature.partial= ");
+      if (sfp->partial)
+        tmp = StringMove (tmp, "TRUE");
+      else
+        tmp = StringMove (tmp, "FALSE");
+      ValidErr (vsp, sev, ERR_SEQ_FEAT_PartialProblem, buf);
+    /* inconsistent combination of partial/complete product,location,partial flag - part 2 */
+    } else if ((partials[1] == SLP_COMPLETE) || (!sfp->partial)) {
       tmp = StringMove (buf, "Inconsistent: ");
       if (sfp->product != NULL) {
         tmp = StringMove (tmp, "Product= ");
@@ -7390,7 +8091,9 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
       errtype = SLP_NOSTART;
       for (j = 0; j < 4; j++) {
         if (partials[i] & errtype) {
-          if (i == 1 && j < 2 && PartialAtSpliceSite (sfp->location, errtype)) {
+          if (i == 1 && j < 2 && IsCddFeat (sfp)) {
+            /* suppresses  warning */
+          } else if (i == 1 && j < 2 && PartialAtSpliceSite (sfp->location, errtype)) {
             ValidErr (vsp, SEV_INFO, ERR_SEQ_FEAT_PartialProblem,
 		      "%s: %s (but is at consensus splice site)",
 		      parterr[i], parterrs[j]);
@@ -7411,7 +8114,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
           } else {
             ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_PartialProblem,
 		      "%s: %s", parterr[i], parterrs[j]);
-	  }
+          }
         }
         errtype <<= 1;
       }
@@ -7513,6 +8216,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
       CdTransCheck (vsp, sfp);
       SpliceCheck (vsp, sfp);
     }
+    CdsProductIdCheck (vsp, sfp);
     crp = (CdRegionPtr) (sfp->data.value.ptrvalue);
     if (crp != NULL) {
       for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
@@ -7591,6 +8295,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
     CheckForBadGeneOverlap (vsp, sfp);
     CheckForBadMRNAOverlap (vsp, sfp);
     CheckForCommonCDSProduct (vsp, sfp);
+    CheckCDSPartial (vsp, sfp);
     break;
   case 4:                      /* Prot-ref */
     prp = (ProtRefPtr) (sfp->data.value.ptrvalue);
@@ -7852,6 +8557,26 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
   }
   if (type != SEQFEAT_GENE) {
     grp = SeqMgrGetGeneXref (sfp);
+    if (grp == NULL) {
+      sfpx = SeqMgrGetOverlappingGene (sfp->location, &fcontext);
+      if (sfpx != NULL) {
+        grp = (GeneRefPtr) sfpx->data.value.ptrvalue;
+      }
+    }
+    if (grp != NULL && (! SeqMgrGeneIsSuppressed (grp))) {
+      if (! StringHasNoText (grp->allele)) {
+        for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
+          if (StringCmp (gbq->qual, "allele") == 0) {
+            if (StringICmp (gbq->val, grp->allele) == 0) {
+              ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_InvalidQualifierValue, "Redundant allele qualifier (%s) on gene and feature", gbq->val);
+            } else {
+              ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_InvalidQualifierValue, "Mismatched allele qualifier on gene (%s) and feature (%s)", grp->allele, gbq->val);
+            }
+          }
+        }
+      }
+    }
+    grp = SeqMgrGetGeneXref (sfp);
     if (grp == NULL || SeqMgrGeneIsSuppressed (grp))
       return;
     sfpx = SeqMgrGetOverlappingGene (sfp->location, &fcontext);
@@ -7883,8 +8608,22 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
       }
       ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_UnnecessaryGeneXref, "Unnecessary gene cross-reference %s", label);
     }
+  } else {
+    operon = SeqMgrGetOverlappingOperon (sfp->location, &fcontext);
+    if (operon != NULL) {
+      if (SeqMgrGetDesiredFeature (sfp->idx.entityID, 0, 0, 0, sfp, &fcontext) == sfp) {
+        if (! StringHasNoText (fcontext.label)) {
+          for (gbq = operon->qual; gbq != NULL; gbq = gbq->next) {
+            if (StringCmp (gbq->qual, "operon") == 0) {
+              if (StringICmp (gbq->val, fcontext.label) == 0) {
+                ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_InvalidQualifierValue, "Operon is same as gene - %s", gbq->val);
+              }
+            }
+          }
+        }
+      }
+    }
   }
-  return;
 }
 
 /*****************************************************************************
@@ -7903,11 +8642,16 @@ static CharPtr bypass_mrna_trans_check [] = {
 
 NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
 {
+  BioseqPtr       bsp;
+  Char            ch;
+  Int4            counta, countnona;
+  GatherContextPtr  gcp;
   Int2            i;
   Int4            mismatch, total;
   CharPtr         mrseq, pdseq;
   Int4            mlen, plen;
   CharPtr         ptr1, ptr2;
+  ErrSev          sev;
   SeqFeat         sf;
   SeqIdPtr        sip;
   ValNode         vn;
@@ -7929,6 +8673,16 @@ NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
   if (sip == NULL)
     return;
 
+  sev = SEV_ERROR;
+  gcp = vsp->gcp;
+  if (gcp != NULL) {
+    bsp = GetBioseqGivenSeqLoc (sfp->product, gcp->entityID);
+    /* if not local bioseq product, lower severity */
+    if (bsp == NULL) {
+      sev = SEV_WARNING;
+    }
+  }
+
   mrseq = GetSequenceByFeature (sfp);
   if (mrseq == NULL)
     return;
@@ -7946,8 +8700,32 @@ NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
     mlen = StringLen (mrseq);
     plen = StringLen (pdseq);
     if (mlen != plen) {
-      ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_TranscriptLen, "Transcript length [%ld] does not match product length [%ld]", (long) mlen, (long) plen);
-    } else if (mlen > 0 && StringICmp (mrseq, pdseq) != 0) {
+      if (mlen < plen) {
+        ptr1 = pdseq + mlen;
+        counta = 0;
+        countnona = 0;
+        ch = *ptr1;
+        while (ch != '\0') {
+          if (ch == 'A' || ch == 'a') {
+            counta++;
+          } else {
+            countnona++;
+          }
+          ptr1++;
+          ch = *ptr1;
+        }
+        if (counta < 19 * countnona) {
+          ValidErr (vsp, sev, ERR_SEQ_FEAT_TranscriptLen, "Transcript length [%ld] less than product length [%ld], and tail < 95%s polyA", (long) mlen, (long) plen, "%");
+          plen = mlen; /* even if it fails polyA test, allow base-by-base comparison on common length */
+        } else {
+          ValidErr (vsp, SEV_INFO, ERR_SEQ_FEAT_TranscriptLen, "Transcript length [%ld] less than product length [%ld], but tail >= 95%s polyA", (long) mlen, (long) plen, "%");
+          plen = mlen; /* if it passes polyA test, allow base-by-base comparison on common length */
+        }
+      } else {
+        ValidErr (vsp, sev, ERR_SEQ_FEAT_TranscriptLen, "Transcript length [%ld] greater than product length [%ld]", (long) mlen, (long) plen);
+      }
+    }
+    if (mlen == plen && mlen > 0 && StringICmp (mrseq, pdseq) != 0) {
       mismatch = 0;
       total = 0;
       ptr1 = mrseq;
@@ -7960,7 +8738,7 @@ NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
         ptr2++;
         total++;
       }
-      ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_TranscriptMismatches,
+      ValidErr (vsp, sev, ERR_SEQ_FEAT_TranscriptMismatches,
                 "There are %ld mismatches out of %ld bases between the transcript and product sequence", (long) mismatch, (long) total);
     }
     MemFree (pdseq);
@@ -8035,6 +8813,7 @@ static CharPtr bypass_cds_trans_check [] = {
   "reasons given in citation",
   "artificial frameshift",
   "unclassified translation discrepancy",
+  "rearrangement required for product",
   NULL
 };
 
@@ -8628,6 +9407,115 @@ NLM_EXTERN void SpliceCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
 
 /*****************************************************************************
 *
+*   CdsProductIdCheck (vsp, sfp)
+*      code taken from asn2gnbk.c - release mode expects CDS product Bioseqs
+*
+*****************************************************************************/
+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 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 void CdsProductIdCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
+
+{
+  SeqFeatPtr         gene;
+  GeneRefPtr         grp;
+  Boolean            juststop = FALSE;
+  Boolean            okay = FALSE;
+  SeqEntryPtr        oldscope;
+  Boolean            partial5;
+  Boolean            partial3;
+  Boolean            pseudo = FALSE;
+  SeqEntryPtr        sep;
+
+   /* non-pseudo CDS must have /product */
+   if (sfp->pseudo) {
+	 pseudo = TRUE;
+   }
+   grp = SeqMgrGetGeneXref (sfp);
+   if (grp == NULL) {
+	 sep = GetTopSeqEntryForEntityID (sfp->idx.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) {
+	 okay = TRUE;
+   } else {
+	 if (sfp->excpt && (! StringHasNoText (sfp->except_text))) {
+	   if (StringStr (sfp->except_text, "rearrangement required for product") != NULL) {
+		 okay = TRUE;
+	   }
+	 }
+   }
+   if (! okay) {
+    ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_MissingCDSproduct, "Expected CDS product absent");
+   }
+}
+
+/*****************************************************************************
+*
 *   ValidateSeqLoc(vsp, slp, prefix)
 *
 *****************************************************************************/
diff --git a/api/valid.msg b/api/valid.msg
index 4bb11461..a7923795 100644
--- a/api/valid.msg
+++ b/api/valid.msg
@@ -152,6 +152,13 @@ $^   UnexpectedIdentifierChange, 41
 The set of sequence identifiers on a Bioseq are not consistent with the previous version
 of the record in the database.
 
+$^   InternalNsInSeqLit, 42
+There are runs of many Ns inside the SeqLit component of a delta Bioseq.
+
+$^   SeqLitGapLength0, 43
+A SeqLit component of a delta Bioseq can specify a gap, but it should not be a gap
+of 0 length.
+
 $$ SEQ_DESCR, 2
 
 $^   BioSourceMissing, 1
@@ -252,6 +259,9 @@ $^   UnnecessaryBioSourceFocus, 24
 Focus should not be set on a BioSource descriptor in records where there is no
 BioSource feature.
 
+$^   RefGeneTrackingWithoutStatus, 25
+The RefGeneTracking user object does not have the required Status field set.
+
 $$ GENERIC, 3
 
 $^   NonAsciiAsn, 1
@@ -318,6 +328,12 @@ however be referenced remotely.
 $^   InconsistentMolInfoBiomols, 12
 Mol-info.biomol is inconsistent within a segset or parts set.
 
+$^   ArchaicFeatureLocation, 13
+A feature location should refer to the accession or gi number, not a local or general ID.
+
+$^   ArchaicFeatureProduct, 14
+A feature product should refer to the accession or gi number, not a local or general ID.
+
 $$ SEQ_FEAT, 5
 
 $^   InvalidForType, 1
@@ -573,6 +589,25 @@ $^   RnaProductMismatch, 61
 The RNA feature product type does not correspond to the RNA feature type.  These
 need to be consistent.
 
+$^   MissingCDSproduct, 62
+The CDS should have a product, but does not.  Pseudo or short CDSs (less than 6
+amino acids), or those marked with a rearrangement required for product exception,
+are exempt from needing a product.
+
+$^   BadTrnaCodon, 63
+The tRNA codon recognized is an illegal value.
+
+$^   BadTrnaAA, 64
+The tRNA encoded amino acid is an illegal value.
+
+$^   OnlyGeneXrefs, 65
+There are gene xrefs but no gene features.  Records should normally have single-interval
+gene features covering other biological features.  Gene xrefs are used only to override
+the inheritance by overlap.
+
+$^   UTRdoesNotAbutCDS, 66
+The 5'UTR and 3'UTR features should exactly abut the CDS feature.
+
 $$ SEQ_ALIGN, 6
 
 $^   SeqIdProblem, 1
diff --git a/api/validerr.h b/api/validerr.h
index 5ac8939a..b4ced162 100644
--- a/api/validerr.h
+++ b/api/validerr.h
@@ -43,6 +43,8 @@
 #define ERR_SEQ_INST_HistAssemblyMissing  1,39
 #define ERR_SEQ_INST_TerminalNs  1,40
 #define ERR_SEQ_INST_UnexpectedIdentifierChange  1,41
+#define ERR_SEQ_INST_InternalNsInSeqLit  1,42
+#define ERR_SEQ_INST_SeqLitGapLength0  1,43
 #define ERR_SEQ_DESCR  2,0
 #define ERR_SEQ_DESCR_BioSourceMissing  2,1
 #define ERR_SEQ_DESCR_InvalidForType  2,2
@@ -68,6 +70,7 @@
 #define ERR_SEQ_DESCR_ObsoleteSourceQual  2,22
 #define ERR_SEQ_DESCR_StructuredSourceNote  2,23
 #define ERR_SEQ_DESCR_UnnecessaryBioSourceFocus  2,24
+#define ERR_SEQ_DESCR_RefGeneTrackingWithoutStatus  2,25
 #define ERR_GENERIC  3,0
 #define ERR_GENERIC_NonAsciiAsn  3,1
 #define ERR_GENERIC_Spell  3,2
@@ -88,6 +91,8 @@
 #define ERR_SEQ_PKG_FeaturePackagingProblem  4,10
 #define ERR_SEQ_PKG_GenomicProductPackagingProblem  4,11
 #define ERR_SEQ_PKG_InconsistentMolInfoBiomols  4,12
+#define ERR_SEQ_PKG_ArchaicFeatureLocation  4,13
+#define ERR_SEQ_PKG_ArchaicFeatureProduct  4,14
 #define ERR_SEQ_FEAT  5,0
 #define ERR_SEQ_FEAT_InvalidForType  5,1
 #define ERR_SEQ_FEAT_PartialProblem  5,2
@@ -150,6 +155,11 @@
 #define ERR_SEQ_FEAT_FeatContentDup  5,59
 #define ERR_SEQ_FEAT_BadProductSeqId  5,60
 #define ERR_SEQ_FEAT_RnaProductMismatch  5,61
+#define ERR_SEQ_FEAT_MissingCDSproduct  5,62
+#define ERR_SEQ_FEAT_BadTrnaCodon  5,63
+#define ERR_SEQ_FEAT_BadTrnaAA  5,64
+#define ERR_SEQ_FEAT_OnlyGeneXrefs  5,65
+#define ERR_SEQ_FEAT_UTRdoesNotAbutCDS  5,66
 #define ERR_SEQ_ALIGN  6,0
 #define ERR_SEQ_ALIGN_SeqIdProblem  6,1
 #define ERR_SEQ_ALIGN_StrandRev  6,2