Load ncbi (20011220) into ncbi-tools6/branches/upstream/current.

13 files changed, 989 insertions, 27 deletions

diff --git a/object/mapmime.h b/object/mapmime.h
index d7e69839..ff4ae0f2 100644
--- a/object/mapmime.h
+++ b/object/mapmime.h
@@ -3,3 +3,4 @@
 #include <objsset.h>
 #include <objmmdb1.h>
 #include <objcn3d.h>
+#include <objcdd.h>

diff --git a/object/objbibli.c b/object/objbibli.c
index 87f4ee8d..ce6c6f5e 100644
--- a/object/objbibli.c
+++ b/object/objbibli.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 1/1/91
 *
-* $Revision: 6.4 $
+* $Revision: 6.5 $
 *
 * File Description:  Object manager for module NCBI-Biblio
 *
@@ -41,6 +41,9 @@
 * 07-19-93 Ostell      Support for ASN30 added
 *
 * $Log: objbibli.c,v $
+* Revision 6.5  2001/10/09 15:57:38  kans
+* AuthListMatch does StringICmp if both are structured last names, StringNICmp otherwise
+*
 * Revision 6.4  2000/01/18 19:40:51  ostell
 * added support for PubStatusDate, ArticleIds
 *
@@ -3285,7 +3288,7 @@ NLM_EXTERN Int2 LIBCALL CitJourMatch (CitJourPtr a, CitJourPtr b)
 *****************************************************************************/
 NLM_EXTERN Int2 LIBCALL AuthListMatch(AuthListPtr a, AuthListPtr b, Boolean all)
 {
-	Int2 retval = 1, i;
+	Int2 retval = 1, lastnames = 0, i;
 	size_t len, tlen;
 	Char name[2][256];
 	ValNodePtr vnp[2];
@@ -3318,9 +3321,10 @@ NLM_EXTERN Int2 LIBCALL AuthListMatch(AuthListPtr a, AuthListPtr b, Boolean all)
 				if (pip->choice == 2)   /* std */
 				{
 					nsp = (NameStdPtr)pip->data;
-					if (nsp->names[0] != NULL)   /* last name */
+					if (nsp->names[0] != NULL) {  /* last name */
 						StringMove(name[i], nsp->names[0]);
-					else if (nsp->names[3] != NULL)  /* full name */
+						lastnames++;
+					} else if (nsp->names[3] != NULL)  /* full name */
 						StringMove(name[i], nsp->names[0]);
 				}
 				else if (pip->choice > 2)
@@ -3340,7 +3344,11 @@ NLM_EXTERN Int2 LIBCALL AuthListMatch(AuthListPtr a, AuthListPtr b, Boolean all)
 			else
 				return (Int2) 1;
 		}
-		retval = (Int2)StringNICmp(name[0], name[1], tlen);
+		if (lastnames == 2) {
+			retval = (Int2)StringICmp(name[0], name[1]);
+		} else {
+			retval = (Int2)StringNICmp(name[0], name[1], tlen);
+		}
 		if (retval < 0)
 			return (Int2) -1;
 		else if (retval > 0)
diff --git a/object/objfdef.c b/object/objfdef.c
index 6e46b747..f0d99583 100644
--- a/object/objfdef.c
+++ b/object/objfdef.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 9/94
 *
-* $Revision: 6.20 $
+* $Revision: 6.21 $
 *
 * File Description:  Object manager for feature definitions
 *
@@ -1267,8 +1267,28 @@ protref:    if (prp->name != NULL)
 					if (label == NULL)
 						label = typelabel;
 				}
-				else if (StringICmp("misc_feature", ifp->key))
-					label = typelabel;
+				else if (StringICmp("misc_feature", ifp->key)) {
+					for (gbp = sfp->qual; label == NULL && gbp != NULL; gbp = gbp->next) {
+						if (StringICmp ("standard_name", gbp->qual) == 0) {
+							label = gbp->val;
+						}
+					}
+					for (gbp = sfp->qual; label == NULL && gbp != NULL; gbp = gbp->next) {
+						if (StringICmp ("function", gbp->qual) == 0) {
+							label = gbp->val;
+						}
+					}
+					for (gbp = sfp->qual; label == NULL && gbp != NULL; gbp = gbp->next) {
+						if (StringICmp ("number", gbp->qual) == 0) {
+							label = gbp->val;
+						}
+					}
+					for (gbp = sfp->qual; label == NULL && gbp != NULL; gbp = gbp->next) {
+						label = gbp->val;
+					}
+					if (label == NULL)
+						label = typelabel;
+				}
 			}
 			break;
 		case SEQFEAT_REGION:
diff --git a/object/objfeat.c b/object/objfeat.c
index 3f53b566..583a6aa6 100644
--- a/object/objfeat.c
+++ b/object/objfeat.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.15 $
+* $Revision: 6.16 $
 *
 * File Description:  Object manager for module NCBI-SeqFeat
 *
@@ -523,8 +523,20 @@ erret:
 *****************************************************************************/
 NLM_EXTERN Boolean LIBCALL SeqFeatSetAsnWrite (SeqFeatPtr sfp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)
 {
+	return SeqFeatSetAsnWriteExtra(sfp, aip, set, element, (ValNodePtr) NULL);
+}
+
+/*****************************************************************************
+*
+*   SeqFeatSetAsnWriteExtra(sfp, aip, set, element, extras)
+*      this is to accomodate extra features from SeqEntryAsnOut()
+*
+*****************************************************************************/
+NLM_EXTERN Boolean LIBCALL SeqFeatSetAsnWriteExtra (SeqFeatPtr sfp, AsnIoPtr aip,
+				    AsnTypePtr set, AsnTypePtr element, ValNodePtr extras)
+{
 	AsnTypePtr atp;
-	SeqFeatPtr oldsfp;
+	SeqFeatPtr oldsfp, tsfp;
     Boolean retval = FALSE;
 	Int2 ctr = 0;
 
@@ -540,7 +552,10 @@ NLM_EXTERN Boolean LIBCALL SeqFeatSetAsnWrite (SeqFeatPtr sfp, AsnIoPtr aip, Asn
 	atp = AsnLinkType(element, SEQ_FEAT);   /* link local tree */
     if (atp == NULL)
         return FALSE;
+
 	oldsfp = sfp;
+	if (extras != NULL)   /* this is an extra set of feats */
+		oldsfp = (SeqFeatPtr)(extras->data.ptrvalue);
 
     if (! AsnOpenStruct(aip, set, (Pointer)oldsfp))
         goto erret;
@@ -560,6 +575,14 @@ NLM_EXTERN Boolean LIBCALL SeqFeatSetAsnWrite (SeqFeatPtr sfp, AsnIoPtr aip, Asn
 
     }
 
+    while (extras != NULL)
+    {
+	tsfp = (SeqFeatPtr)(extras->data.ptrvalue);
+	if (! SeqFeatAsnWrite(tsfp, aip, atp))
+		goto erret;
+	extras = extras->next;
+    }
+
     if (! AsnCloseStruct(aip, set, (Pointer)oldsfp))
         goto erret;
     retval = TRUE;
@@ -5646,3 +5669,4 @@ erret:
 
 
 
+
diff --git a/object/objfeat.h b/object/objfeat.h
index ddfdc6f0..81937ae2 100644
--- a/object/objfeat.h
+++ b/object/objfeat.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.9 $
+* $Revision: 6.10 $
 *
 * File Description:  Object manager interface for module NCBI-SeqFeat
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: objfeat.h,v $
+* Revision 6.10  2001/10/02 21:47:54  kans
+* added hooks for writing extra descriptors or features (JO)
+*
 * Revision 6.9  2000/09/28 11:40:19  ostell
 * added endogenous_virus (19) to MolInfo.genome
 *
@@ -305,6 +308,9 @@ NLM_EXTERN Boolean LIBCALL SeqFeatDataAsnRead PROTO((AsnIoPtr aip, AsnTypePtr or
 NLM_EXTERN Boolean    LIBCALL SeqFeatSetAsnWrite PROTO((SeqFeatPtr anp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element));
 NLM_EXTERN SeqFeatPtr LIBCALL SeqFeatSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element));
 
+/** used only SeqAnnotAsnWriteExtra **/
+NLM_EXTERN Boolean    LIBCALL SeqFeatSetAsnWriteExtra PROTO((SeqFeatPtr anp, AsnIoPtr aip,
+					AsnTypePtr set, AsnTypePtr element, ValNodePtr extras));
 /*****************************************************************************
 *
 *   CodeBreak
@@ -694,3 +700,4 @@ NLM_EXTERN TxinitPtr LIBCALL TxinitFree PROTO((TxinitPtr txp));
 #endif
 
 #endif
+
diff --git a/object/objloc.c b/object/objloc.c
index 97ecf8ee..22210c5e 100644
--- a/object/objloc.c
+++ b/object/objloc.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.5 $
+* $Revision: 6.6 $
 *
 * File Description:  Object manager for module NCBI-Seqloc
 *
@@ -41,6 +41,9 @@
 *
 *
 * $Log: objloc.c,v $
+* Revision 6.6  2001/08/06 20:07:26  ostell
+* added SEQID_TPG, TPE, TPD types
+*
 * Revision 6.5  2001/01/31 15:24:20  kans
 * PatentSeqId.seqid is now an Int4 (JO)
 *
@@ -287,6 +290,9 @@ NLM_EXTERN Boolean LIBCALL SeqLocAsnLoad (void)
     13 = ddbj Textseq-id    -- ddbj
 	14 = prf Textseq-id ,         -- PRF SEQDB
 	15 = pdb PDB-seq-id          -- PDB sequence
+    16 = tpg Textseq-id ,         -- Third Party Annot/Seq Genbank
+    17 = tpe Textseq-id ,         -- Third Party Annot/Seq EMBL
+    18 = tpd Textseq-id }         -- Third Party Annot/Seq DDBJ
 *
 *****************************************************************************/
 /*****************************************************************************
@@ -321,6 +327,9 @@ NLM_EXTERN SeqIdPtr LIBCALL SeqIdFree (SeqIdPtr anp)
         case SEQID_OTHER:     /* other */
         case SEQID_DDBJ:
 		case SEQID_PRF:
+	case SEQID_TPG:
+	case SEQID_TPE:
+	case SEQID_TPD:
             TextSeqIdFree((TextSeqIdPtr)pnt);
             break;
         case SEQID_PATENT:      /* patent seq id */
@@ -436,6 +445,18 @@ NLM_EXTERN Boolean LIBCALL SeqIdAsnWrite (SeqIdPtr anp, AsnIoPtr aip, AsnTypePtr
             writetype = SEQ_ID_pdb;
             func = (AsnWriteFunc) PDBSeqIdAsnWrite;
             break;
+        case SEQID_TPG:      /* tpg   */
+            writetype = SEQ_ID_tpg;
+            func = (AsnWriteFunc) TextSeqIdAsnWrite;
+            break;
+        case SEQID_TPE:      /* tpe   */
+            writetype = SEQ_ID_tpe;
+            func = (AsnWriteFunc) TextSeqIdAsnWrite;
+            break;
+        case SEQID_TPD:      /* tpd   */
+            writetype = SEQ_ID_tpd;
+            func = (AsnWriteFunc) TextSeqIdAsnWrite;
+            break;
     }
     if (writetype != NULL)
         retval = (* func)(pnt, aip, writetype);   /* write it out */
@@ -566,6 +587,21 @@ NLM_EXTERN SeqIdPtr LIBCALL SeqIdAsnRead (AsnIoPtr aip, AsnTypePtr orig)
         choice = SEQID_PDB;
         func = (AsnReadFunc) PDBSeqIdAsnRead;
     }
+    else if (atp == SEQ_ID_tpg)
+    {
+        choice = SEQID_TPG;
+        func = (AsnReadFunc) TextSeqIdAsnRead;
+    }
+    else if (atp == SEQ_ID_tpe)
+    {
+        choice = SEQID_TPE;
+        func = (AsnReadFunc) TextSeqIdAsnRead;
+    }
+    else if (atp == SEQ_ID_tpd)
+    {
+        choice = SEQID_TPD;
+        func = (AsnReadFunc) TextSeqIdAsnRead;
+    }
     else
         goto erret;
 
@@ -641,6 +677,9 @@ NLM_EXTERN SeqIdPtr LIBCALL SeqIdDup (SeqIdPtr oldid)
 		case SEQID_OTHER:
 		case SEQID_DDBJ:
 		case SEQID_PRF:
+		case SEQID_TPG:
+		case SEQID_TPE:
+		case SEQID_TPD:
 			at = (TextSeqIdPtr)oldid->data.ptrvalue;
             bt = TextSeqIdNew();
 			if (bt == NULL) return NULL;
diff --git a/object/objloc.h b/object/objloc.h
index a1d5d73e..441bb05b 100644
--- a/object/objloc.h
+++ b/object/objloc.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.2 $
+* $Revision: 6.3 $
 *
 * File Description:  Object manager interface for module NCBI-Seqloc
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: objloc.h,v $
+* Revision 6.3  2001/08/06 20:07:26  ostell
+* added SEQID_TPG, TPE, TPD types
+*
 * Revision 6.2  2001/01/31 15:24:20  kans
 * PatentSeqId.seqid is now an Int4 (JO)
 *
@@ -128,6 +131,10 @@ NLM_EXTERN Boolean	LIBCALL SeqLocAsnLoad PROTO((void));
     13 = ddbj Textseq-id
 	14 = prf Textseq-id ,         -- PRF SEQDB
 	15 = pdb PDB-seq-id          -- PDB sequence
+    16 = tpg Textseq-id ,         -- Third Party Annot/Seq Genbank
+    17 = tpe Textseq-id ,         -- Third Party Annot/Seq EMBL
+    18 = tpd Textseq-id }         -- Third Party Annot/Seq DDBJ
+
 
 	WARNING: Some routines in sequtil.c (e.g. SeqIdPrint, SeqIdParse)
         and tofasta.c  use
@@ -136,7 +143,7 @@ NLM_EXTERN Boolean	LIBCALL SeqLocAsnLoad PROTO((void));
 *
 *****************************************************************************/
 
-#define NUM_SEQID 16     /* total number of SeqId types */
+#define NUM_SEQID 19     /* total number of SeqId types */
 
 #define SEQID_NOT_SET ( (Uint1)0)
 #define SEQID_LOCAL ( (Uint1)1)
@@ -158,6 +165,10 @@ NLM_EXTERN Boolean	LIBCALL SeqLocAsnLoad PROTO((void));
 #define SEQID_PRF ((Uint1)14)
 #define SEQID_PDB ((Uint1)15)
 
+#define SEQID_TPG ((Uint1)16)
+#define SEQID_TPE ((Uint1)17)
+#define SEQID_TPD ((Uint1)18)
+
 NLM_EXTERN Boolean	 LIBCALL SeqIdAsnWrite PROTO((SeqIdPtr anp, AsnIoPtr aip, AsnTypePtr atp));
 NLM_EXTERN SeqIdPtr LIBCALL SeqIdAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
 NLM_EXTERN SeqIdPtr LIBCALL SeqIdFree PROTO((SeqIdPtr anp));
diff --git a/object/objmime.c b/object/objmime.c
index 616c9971..2c8b8277 100644
--- a/object/objmime.c
+++ b/object/objmime.c
@@ -31,6 +31,18 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: objmime.c,v $
+* Revision 6.11  2001/11/21 16:38:23  thiessen
+* move cn3d stuff into bundle
+*
+* Revision 6.10  2001/11/21 14:25:41  thiessen
+* remove BisotrucOrId
+*
+* Revision 6.9  2001/11/20 15:59:34  thiessen
+* add imports to BundleSeqsAligns
+*
+* Revision 6.8  2001/11/16 14:54:26  thiessen
+* add new general type
+*
 * Revision 6.7  2001/06/21 14:44:29  thiessen
 * add new user annotations
 *
@@ -122,6 +134,9 @@ NcbiMimeAsn1Free(ValNodePtr anp)
    case NcbiMimeAsn1_strucseqs:
       BiostrucSeqsFree(anp -> data.ptrvalue);
       break;
+   case NcbiMimeAsn1_general:
+      BiostrucSeqsAlignsCddFree(anp -> data.ptrvalue);
+      break;
    }
    return MemFree(anp);
 }
@@ -198,6 +213,10 @@ NcbiMimeAsn1AsnRead(AsnIoPtr aip, AsnTypePtr orig)
       choice = NcbiMimeAsn1_strucseqs;
       func = (AsnReadFunc) BiostrucSeqsAsnRead;
    }
+   else if (atp == NCBI_MIME_ASN1_general) {
+      choice = NcbiMimeAsn1_general;
+      func = (AsnReadFunc) BiostrucSeqsAlignsCddAsnRead;
+   }
    anp->choice = choice;
    if (func != NULL)
    {
@@ -279,6 +298,10 @@ NcbiMimeAsn1AsnWrite(NcbiMimeAsn1Ptr anp, AsnIoPtr aip, AsnTypePtr orig)
       writetype = NCBI_MIME_ASN1_strucseqs;
       func = (AsnWriteFunc) BiostrucSeqsAsnWrite;
       break;
+   case NcbiMimeAsn1_general:
+      writetype = NCBI_MIME_ASN1_general;
+      func = (AsnWriteFunc) BiostrucSeqsAlignsCddAsnWrite;
+      break;
    }
    if (writetype != NULL) {
       retval = (* func)(pnt, aip, writetype);   /* write it out */
@@ -1521,3 +1544,548 @@ erret:
    return retval;
 }
 
+/**************************************************
+*
+*    BiostrucSeqsAlignsCddNew()
+*
+**************************************************/
+NLM_EXTERN
+BiostrucSeqsAlignsCddPtr LIBCALL
+BiostrucSeqsAlignsCddNew(void)
+{
+   BiostrucSeqsAlignsCddPtr ptr = MemNew((size_t) sizeof(BiostrucSeqsAlignsCdd));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    BiostrucSeqsAlignsCddFree()
+*
+**************************************************/
+NLM_EXTERN
+BiostrucSeqsAlignsCddPtr LIBCALL
+BiostrucSeqsAlignsCddFree(BiostrucSeqsAlignsCddPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   SeqAlignData_seq_align_dataFree(ptr -> SeqAlignData_seq_align_data);
+   AsnGenericUserSeqOfFree(ptr -> structures, (AsnOptFreeFunc) BiostrucFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    SeqAlignData_seq_align_dataFree()
+*
+**************************************************/
+static
+SeqAlignData_seq_align_dataPtr LIBCALL
+SeqAlignData_seq_align_dataFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case SeqAlignData_seq_align_data_bundle:
+      BundleSeqsAlignsFree(anp -> data.ptrvalue);
+      break;
+   case SeqAlignData_seq_align_data_cdd:
+      CddFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    BiostrucSeqsAlignsCddAsnRead()
+*
+**************************************************/
+NLM_EXTERN
+BiostrucSeqsAlignsCddPtr LIBCALL
+BiostrucSeqsAlignsCddAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   BiostrucSeqsAlignsCddPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmimeAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* BiostrucSeqsAlignsCdd ::= (self contained) */
+      atp = AsnReadId(aip, amp, BIOSTRUC_SEQS_ALIGNS_CDD);
+   } else {
+      atp = AsnLinkType(orig, BIOSTRUC_SEQS_ALIGNS_CDD);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = BiostrucSeqsAlignsCddNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == SEQS_ALIGNS_CDD_seq_align_data) {
+      ptr -> SeqAlignData_seq_align_data = SeqAlignData_seq_align_dataAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQS_ALIGNS_CDD_structures) {
+      ptr -> structures = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) BiostrucAsnRead, (AsnOptFreeFunc) BiostrucFree);
+      if (isError && ptr -> structures == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = BiostrucSeqsAlignsCddFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    SeqAlignData_seq_align_dataAsnRead()
+*
+**************************************************/
+static
+SeqAlignData_seq_align_dataPtr LIBCALL
+SeqAlignData_seq_align_dataAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmimeAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SeqAlignData_seq_align_data ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQS_ALIGNS_CDD_seq_align_data);
+   } else {
+      atp = AsnLinkType(orig, SEQS_ALIGNS_CDD_seq_align_data);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == CDD_seq_align_data_bundle) {
+      choice = SeqAlignData_seq_align_data_bundle;
+      func = (AsnReadFunc) BundleSeqsAlignsAsnRead;
+   }
+   else if (atp == ALIGNS_CDD_seq_align_data_cdd) {
+      choice = SeqAlignData_seq_align_data_cdd;
+      func = (AsnReadFunc) CddAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    BiostrucSeqsAlignsCddAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL
+BiostrucSeqsAlignsCddAsnWrite(BiostrucSeqsAlignsCddPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmimeAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, BIOSTRUC_SEQS_ALIGNS_CDD);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> SeqAlignData_seq_align_data != NULL) {
+      if ( ! SeqAlignData_seq_align_dataAsnWrite(ptr -> SeqAlignData_seq_align_data, aip, SEQS_ALIGNS_CDD_seq_align_data)) {
+         goto erret;
+      }
+   }
+   AsnGenericUserSeqOfAsnWrite(ptr -> structures, (AsnWriteFunc) BiostrucAsnWrite, aip, SEQS_ALIGNS_CDD_structures, SEQS_ALIGNS_CDD_structures_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    SeqAlignData_seq_align_dataAsnWrite()
+*
+**************************************************/
+static Boolean LIBCALL
+SeqAlignData_seq_align_dataAsnWrite(SeqAlignData_seq_align_dataPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmimeAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, SEQS_ALIGNS_CDD_seq_align_data);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case SeqAlignData_seq_align_data_bundle:
+      writetype = CDD_seq_align_data_bundle;
+      func = (AsnWriteFunc) BundleSeqsAlignsAsnWrite;
+      break;
+   case SeqAlignData_seq_align_data_cdd:
+      writetype = ALIGNS_CDD_seq_align_data_cdd;
+      func = (AsnWriteFunc) CddAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    BundleSeqsAlignsNew()
+*
+**************************************************/
+NLM_EXTERN
+BundleSeqsAlignsPtr LIBCALL
+BundleSeqsAlignsNew(void)
+{
+   BundleSeqsAlignsPtr ptr = MemNew((size_t) sizeof(BundleSeqsAligns));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    BundleSeqsAlignsFree()
+*
+**************************************************/
+NLM_EXTERN
+BundleSeqsAlignsPtr LIBCALL
+BundleSeqsAlignsFree(BundleSeqsAlignsPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericChoiceSeqOfFree(ptr -> sequences, (AsnOptFreeFunc) SeqEntryFree);
+   AsnGenericUserSeqOfFree(ptr -> seqaligns, (AsnOptFreeFunc) SeqAnnotFree);
+   BiostrucAnnotSetFree(ptr -> strucaligns);
+   AsnGenericUserSeqOfFree(ptr -> imports, (AsnOptFreeFunc) SeqAnnotFree);
+   Cn3dStyleDictionaryFree(ptr -> style_dictionary);
+   Cn3dUserAnnotationsFree(ptr -> user_annotations);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    BundleSeqsAlignsAsnRead()
+*
+**************************************************/
+NLM_EXTERN
+BundleSeqsAlignsPtr LIBCALL
+BundleSeqsAlignsAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   BundleSeqsAlignsPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmimeAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* BundleSeqsAligns ::= (self contained) */
+      atp = AsnReadId(aip, amp, BUNDLE_SEQS_ALIGNS);
+   } else {
+      atp = AsnLinkType(orig, BUNDLE_SEQS_ALIGNS);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = BundleSeqsAlignsNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == BUNDLE_SEQS_ALIGNS_sequences) {
+      ptr -> sequences = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqEntryAsnRead, (AsnOptFreeFunc) SeqEntryFree);
+      if (isError && ptr -> sequences == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == BUNDLE_SEQS_ALIGNS_seqaligns) {
+      ptr -> seqaligns = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqAnnotAsnRead, (AsnOptFreeFunc) SeqAnnotFree);
+      if (isError && ptr -> seqaligns == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == BUNDLE_SEQS_ALIGNS_strucaligns) {
+      ptr -> strucaligns = BiostrucAnnotSetAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == BUNDLE_SEQS_ALIGNS_imports) {
+      ptr -> imports = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqAnnotAsnRead, (AsnOptFreeFunc) SeqAnnotFree);
+      if (isError && ptr -> imports == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQS_ALIGNS_style_dictionary) {
+      ptr -> style_dictionary = Cn3dStyleDictionaryAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQS_ALIGNS_user_annotations) {
+      ptr -> user_annotations = Cn3dUserAnnotationsAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = BundleSeqsAlignsFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    BundleSeqsAlignsAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL
+BundleSeqsAlignsAsnWrite(BundleSeqsAlignsPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmimeAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, BUNDLE_SEQS_ALIGNS);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   AsnGenericChoiceSeqOfAsnWrite(ptr -> sequences, (AsnWriteFunc) SeqEntryAsnWrite, aip, BUNDLE_SEQS_ALIGNS_sequences, BUNDLE_SEQS_ALIGNS_sequences_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> seqaligns, (AsnWriteFunc) SeqAnnotAsnWrite, aip, BUNDLE_SEQS_ALIGNS_seqaligns, BUNDLE_SEQS_ALIGNS_seqaligns_E);
+   if (ptr -> strucaligns != NULL) {
+      if ( ! BiostrucAnnotSetAsnWrite(ptr -> strucaligns, aip, BUNDLE_SEQS_ALIGNS_strucaligns)) {
+         goto erret;
+      }
+   }
+   AsnGenericUserSeqOfAsnWrite(ptr -> imports, (AsnWriteFunc) SeqAnnotAsnWrite, aip, BUNDLE_SEQS_ALIGNS_imports, BUNDLE_SEQS_ALIGNS_imports_E);
+   if (ptr -> style_dictionary != NULL) {
+      if ( ! Cn3dStyleDictionaryAsnWrite(ptr -> style_dictionary, aip, SEQS_ALIGNS_style_dictionary)) {
+         goto erret;
+      }
+   }
+   if (ptr -> user_annotations != NULL) {
+      if ( ! Cn3dUserAnnotationsAsnWrite(ptr -> user_annotations, aip, SEQS_ALIGNS_user_annotations)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
diff --git a/object/objmime.h b/object/objmime.h
index 9c97929c..302f9380 100644
--- a/object/objmime.h
+++ b/object/objmime.h
@@ -31,6 +31,18 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: objmime.h,v $
+* Revision 6.11  2001/11/21 16:38:23  thiessen
+* move cn3d stuff into bundle
+*
+* Revision 6.10  2001/11/21 14:25:41  thiessen
+* remove BisotrucOrId
+*
+* Revision 6.9  2001/11/20 15:59:34  thiessen
+* add imports to BundleSeqsAligns
+*
+* Revision 6.8  2001/11/16 14:54:26  thiessen
+* add new general type
+*
 * Revision 6.7  2001/06/21 14:44:29  thiessen
 * add new user annotations
 *
@@ -77,6 +89,7 @@ typedef ValNode NcbiMimeAsn1;
 #define NcbiMimeAsn1_alignseq 3     /* yanli added */
 #define NcbiMimeAsn1_strucseq 4     /* yanli added */
 #define NcbiMimeAsn1_strucseqs 5    /* yanli added */
+#define NcbiMimeAsn1_general 6      /* paul */
 
 
 NLM_EXTERN NcbiMimeAsn1Ptr LIBCALL NcbiMimeAsn1Free PROTO ((NcbiMimeAsn1Ptr ));
@@ -225,6 +238,65 @@ NLM_EXTERN Boolean LIBCALL BiostrucSeqsAsnWrite PROTO (( BiostrucSeqsPtr , AsnIo
 #define Entrez_style_pdb 12
 #define Entrez_style_kinemage 13
 
+
+/**************************************************
+*
+*    BiostrucSeqsAlignsCdd
+*
+**************************************************/
+typedef struct struct_Biostruc_seqs_aligns_cdd {
+   ValNodePtr   SeqAlignData_seq_align_data;
+   struct struct_Biostruc PNTR   structures;
+} BiostrucSeqsAlignsCdd, PNTR BiostrucSeqsAlignsCddPtr;
+
+
+NLM_EXTERN BiostrucSeqsAlignsCddPtr LIBCALL BiostrucSeqsAlignsCddFree PROTO ((BiostrucSeqsAlignsCddPtr ));
+NLM_EXTERN BiostrucSeqsAlignsCddPtr LIBCALL BiostrucSeqsAlignsCddNew PROTO (( void ));
+NLM_EXTERN BiostrucSeqsAlignsCddPtr LIBCALL BiostrucSeqsAlignsCddAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL BiostrucSeqsAlignsCddAsnWrite PROTO (( BiostrucSeqsAlignsCddPtr , AsnIoPtr, AsnTypePtr));
+
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+typedef ValNodePtr SeqAlignData_seq_align_dataPtr;
+typedef ValNode SeqAlignData_seq_align_data;
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+#define SeqAlignData_seq_align_data_bundle 1
+#define SeqAlignData_seq_align_data_cdd 2
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr ));
+static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    BundleSeqsAligns
+*
+**************************************************/
+typedef struct struct_Bundle_seqs_aligns {
+   ValNodePtr   sequences;
+   struct struct_Seq_annot PNTR   seqaligns;
+   struct struct_Biostruc_annot_set PNTR   strucaligns;
+   struct struct_Seq_annot PNTR   imports;
+   struct struct_Cn3d_style_dictionary PNTR   style_dictionary;
+   struct struct_Cn3d_user_annotations PNTR   user_annotations;
+} BundleSeqsAligns, PNTR BundleSeqsAlignsPtr;
+
+
+NLM_EXTERN BundleSeqsAlignsPtr LIBCALL BundleSeqsAlignsFree PROTO ((BundleSeqsAlignsPtr ));
+NLM_EXTERN BundleSeqsAlignsPtr LIBCALL BundleSeqsAlignsNew PROTO (( void ));
+NLM_EXTERN BundleSeqsAlignsPtr LIBCALL BundleSeqsAlignsAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL BundleSeqsAlignsAsnWrite PROTO (( BundleSeqsAlignsPtr , AsnIoPtr, AsnTypePtr));
+
+
 #ifdef __cplusplus
 /* { */ }
 #endif
diff --git a/object/objpub.c b/object/objpub.c
index 62504eff..8d8fcf61 100644
--- a/object/objpub.c
+++ b/object/objpub.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.3 $
+* $Revision: 6.4 $
 *
 * File Description:  Object manager for module NCBI-Pub
 *
@@ -41,6 +41,9 @@
 *
 *
 * $Log: objpub.c,v $
+* Revision 6.4  2001/11/20 14:50:54  kans
+* PubLabelUnique return immediately if PMID or MUID, already unique
+*
 * Revision 6.3  2000/06/15 19:13:28  yaschenk
 * PubAsnWrite should not fail when pmid is stripped
 *
@@ -1348,11 +1351,13 @@ NLM_EXTERN Int2 LIBCALL PubLabelUnique (ValNodePtr pub, CharPtr buf, Int2 buflen
 			sprintf(tbuf, "NLM%ld", (long)(pub->data.intvalue));
 			diff = LabelCopy(buf, tbuf, buflen);
 			buflen -= diff;
+			return (len - buflen); /* already unique */
 			break;
 		case PUB_PMid:
 			sprintf(tbuf, "PM%ld", (long)(pub->data.intvalue));
 			diff = LabelCopy(buf, tbuf, buflen);
 			buflen -= diff;
+			return (len - buflen); /* already unique */
 			break;
 		case PUB_Equiv:
 			for (i = 0; i < 5; i++)
diff --git a/object/objseq.c b/object/objseq.c
index ec0fcced..15065b84 100644
--- a/object/objseq.c
+++ b/object/objseq.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.10 $
+* $Revision: 6.15 $
 *
 * File Description:  Object manager for module NCBI-Seq
 *
@@ -91,6 +91,13 @@ static char *this_file = __FILE__;
 #include <objmgr.h>
 #include <sequtil.h>
 
+static Boolean SeqDescrAsnWriteExtra (ValNodePtr anp, AsnIoPtr aip, AsnTypePtr orig,
+					Boolean anp_not_null);
+static Boolean SeqAnnotSetAsnWriteExtra (SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr set,
+					 AsnTypePtr element, Boolean sap_not_null);
+static Boolean SeqAnnotAsnWriteExtra (SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr orig,
+						  ValNodePtr extras);
+
 /*****************************************************************************
 *
 *   Bioseq ObjMgr Routines
@@ -609,15 +616,28 @@ NLM_EXTERN BioseqPtr LIBCALL BioseqNew (void)
 *****************************************************************************/
 NLM_EXTERN BioseqPtr LIBCALL BioseqFree (BioseqPtr bsp)
 {
+	Boolean top = FALSE;
+
     if (bsp == NULL)
         return bsp;
 
+	if (bsp->idx.parentptr == NULL || bsp->idx.parenttype == OBJ_SEQSUB) {
+		if (bsp->seqentry != NULL) {
+			SeqMgrDeleteIndexesInRecord (bsp->seqentry);
+			top = TRUE;
+		}
+	}
+
 	if (! SeqMgrDelete(SM_BIOSEQ, (Pointer)bsp))
 	    ErrPostEx(SEV_ERROR, 0,0, "BioseqFree: pointer not registered");
 
     SeqIdSetFree(bsp->id);
 	BioseqFreeComponents(bsp);
 
+	if (top) {
+		ObjMgrDeleteAllInRecord ();
+	}
+
 	return (BioseqPtr)MemFree(bsp);
 }
 
@@ -730,6 +750,10 @@ NLM_EXTERN Boolean LIBCALL BioseqAsnWrite (BioseqPtr bsp, AsnIoPtr aip, AsnTypeP
     {
         if (! SeqDescrAsnWrite(bsp->descr, aip, BIOSEQ_descr)) goto erret;
     }
+    else
+    {
+        if (! SeqDescrExtraCheck(aip, BIOSEQ_descr)) goto erret;
+    }
 
 	if (! BioseqInstAsnWrite(bsp, aip, BIOSEQ_inst)) goto erret;
 
@@ -738,6 +762,10 @@ NLM_EXTERN Boolean LIBCALL BioseqAsnWrite (BioseqPtr bsp, AsnIoPtr aip, AsnTypeP
         if (! SeqAnnotSetAsnWrite(bsp->annot, aip, BIOSEQ_annot, BIOSEQ_annot_E))
             goto erret;
     }
+    else   /* look for extra features from SeqEntryAsnOut() */
+    {
+        if (! SeqAnnotSetExtraCheck(aip, BIOSEQ_annot, BIOSEQ_annot_E)) goto erret;
+    }
 
     if (! AsnCloseStruct(aip, atp, (Pointer)bsp)) goto erret;
     retval = TRUE;
@@ -1348,6 +1376,7 @@ NLM_EXTERN SeqDescPtr LIBCALL SeqDescFree (SeqDescPtr anp)
 	return anp;
 }
 
+
 /*****************************************************************************
 *
 *   SeqDescrAsnWrite(anp, aip, atp)
@@ -1357,9 +1386,38 @@ NLM_EXTERN SeqDescPtr LIBCALL SeqDescFree (SeqDescPtr anp)
 *****************************************************************************/
 NLM_EXTERN Boolean LIBCALL SeqDescrAsnWrite (ValNodePtr anp, AsnIoPtr aip, AsnTypePtr orig)
 {
+	return SeqDescrAsnWriteExtra(anp, aip, orig, TRUE);
+}
+
+/*****************************************************************************
+*
+*   SeqDescrExtraCheck(aip, atp)
+*   	atp is the current type (if identifier of a parent struct)
+*       if atp == NULL, then assumes it stands alone (SeqDescr ::=)
+*       checks for extra descriptors from SeqEntryAsnOut, when descr is NULL
+*
+*****************************************************************************/
+NLM_EXTERN Boolean LIBCALL SeqDescrExtraCheck (AsnIoPtr aip, AsnTypePtr orig)
+{
+	return SeqDescrAsnWriteExtra((ValNodePtr)NULL, aip, orig, FALSE);
+}
+/*****************************************************************************
+*
+*   SeqDescrAsnWriteExtra(anp, aip, atp, anp_not_null)
+*   	atp is the current type (if identifier of a parent struct)
+*       if atp == NULL, then assumes it stands alone (SeqDescr ::=)
+*       either anp or extras from SeqEntryAsnOut can be written
+*       if anp_not_null, means anp cannot be NULL
+*
+*****************************************************************************/
+static Boolean SeqDescrAsnWriteExtra (ValNodePtr anp, AsnIoPtr aip, AsnTypePtr orig,
+					Boolean anp_not_null)
+{
 	AsnTypePtr atp;
-    ValNodePtr oldanp;
-    Boolean retval = FALSE;
+    ValNodePtr oldanp = NULL, tanp;
+    Boolean retval = FALSE, had_extra = FALSE, had_anp = FALSE;
+	AsnOptionPtr aopp;
+	ValNodePtr extras = NULL;
 
 	if (! loaded)
 	{
@@ -1370,17 +1428,39 @@ NLM_EXTERN Boolean LIBCALL SeqDescrAsnWrite (ValNodePtr anp, AsnIoPtr aip, AsnTy
 	if (aip == NULL)
 		return FALSE;
 
+	if (anp != NULL) had_anp = TRUE;
+	aopp = AsnIoOptionGet(aip, OP_NCBIOBJSEQ, CHECK_EXTRA_DESC, NULL);
+	if (aopp != NULL)
+	{
+		had_extra = TRUE;
+		extras = (ValNodePtr)(aopp->data.ptrvalue);
+	}
+	else if ((anp == NULL) && (! anp_not_null))  /* nothing to write */
+		return TRUE;
+
 	if (! ProgMon("Write SeqDescr"))
 		return FALSE;
 
 	atp = AsnLinkType(orig, SEQ_DESCR);   /* link local tree */
     if (atp == NULL) return FALSE;
 
-	if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+	if (anp_not_null)
+		oldanp = anp;
+	else if (extras != NULL)
+		oldanp = (ValNodePtr)(extras->data.ptrvalue);
+
+	if (oldanp == NULL)
+		{ AsnNullValueMsg(aip, atp); goto erret; }
 
-	oldanp = anp;
     if (! AsnOpenStruct(aip, atp, (Pointer)oldanp)) goto erret; /* SET OF */
 
+    while (extras != NULL)    /* extras first */
+    {
+	tanp = (ValNodePtr)(extras->data.ptrvalue);
+	if (! SeqDescAsnWrite(tanp, aip, SEQ_DESCR_E)) goto erret;
+	extras = extras->next;
+    }
+
     while (anp != NULL)
     {
 		if (! SeqDescAsnWrite (anp, aip, SEQ_DESCR_E)) goto erret;
@@ -1389,6 +1469,10 @@ NLM_EXTERN Boolean LIBCALL SeqDescrAsnWrite (ValNodePtr anp, AsnIoPtr aip, AsnTy
     if (! AsnCloseStruct(aip, atp, oldanp)) goto erret;
     retval = TRUE;
 erret:
+	if (had_extra)
+	{
+		AsnIoOptionFree(aip, OP_NCBIOBJSEQ, CHECK_EXTRA_DESC);
+	}
 	AsnUnlinkType(orig);       /* unlink local tree */
 	return retval;
 }
@@ -2662,6 +2746,25 @@ NLM_EXTERN SeqAnnotPtr LIBCALL SeqAnnotFree (SeqAnnotPtr sap)
 *****************************************************************************/
 NLM_EXTERN Boolean LIBCALL SeqAnnotAsnWrite (SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr orig)
 {
+	return SeqAnnotAsnWriteExtra(sap, aip, orig, (ValNodePtr)NULL);
+}
+
+/*****************************************************************************
+*
+*   SeqAnnotAsnWriteExtra(sap, aip, atp, extras)
+*   	atp is the current type (if identifier of a parent struct)
+*       if atp == NULL, then assumes it stands alone (SeqAnnot ::=)
+*       if extras != NULL
+*           assumes sap has no data ptr
+*           assumes extras is a ValNode chain pointing to SeqFeats from
+*              SeqEntryAsnOut()
+*       else
+*           ignores extras and writes the SeqAnnot
+*
+*****************************************************************************/
+static Boolean SeqAnnotAsnWriteExtra (SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr orig,
+						  ValNodePtr extras)
+{
 	DataVal av;
 	AsnTypePtr atp;
     Boolean retval = FALSE;
@@ -2715,7 +2818,15 @@ NLM_EXTERN Boolean LIBCALL SeqAnnotAsnWrite (SeqAnnotPtr sap, AsnIoPtr aip, AsnT
     switch (sap->type)
     {
         case 1:
-            if (! SeqFeatSetAsnWrite((SeqFeatPtr)sap->data, aip, SEQ_ANNOT_data_ftable, SEQ_ANNOT_data_ftable_E)) goto erret;
+	    if (extras != NULL)  /* from SeqEntryAsnOut */
+	    {
+		if (! SeqFeatSetAsnWriteExtra((SeqFeatPtr)sap->data, aip, SEQ_ANNOT_data_ftable,
+					      SEQ_ANNOT_data_ftable_E, extras)) goto erret;
+	    }
+	    else
+	    {
+		if (! SeqFeatSetAsnWrite((SeqFeatPtr)sap->data, aip, SEQ_ANNOT_data_ftable, SEQ_ANNOT_data_ftable_E)) goto erret;
+	    }
             break;
         case 2:
             if (! SeqAlignSetAsnWrite((SeqAlignPtr)sap->data, aip, SEQ_ANNOT_data_align, SEQ_ANNOT_data_align_E)) goto erret;
@@ -2865,9 +2976,38 @@ erret:
 *****************************************************************************/
 NLM_EXTERN Boolean LIBCALL SeqAnnotSetAsnWrite (SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)
 {
+	return SeqAnnotSetAsnWriteExtra(sap, aip, set, element, TRUE);
+}
+
+/*****************************************************************************
+*
+*   SeqAnnotSetExtraCheck(aip, set, element)
+*   	atp is the current type (if identifier of a parent struct)
+*       if atp == NULL, then assumes it stands alone (SeqAnnot ::=)
+*       called to check for extra features from SeqEntryAsnOut when sap is NULL
+*
+*****************************************************************************/
+NLM_EXTERN Boolean LIBCALL SeqAnnotSetExtraCheck (AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)
+{
+	return SeqAnnotSetAsnWriteExtra((SeqAnnotPtr)NULL, aip, set, element, FALSE);
+}
+
+/*****************************************************************************
+*
+*   SeqAnnotSetAsnWriteExtra(sap, aip, set, element, sap_not_null)
+*   	atp is the current type (if identifier of a parent struct)
+*       if atp == NULL, then assumes it stands alone (SeqAnnot ::=)
+*
+*****************************************************************************/
+static Boolean SeqAnnotSetAsnWriteExtra (SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr set,
+					 AsnTypePtr element, Boolean sap_not_null)
+{
 	AsnTypePtr atp;
-	SeqAnnotPtr oldsap;
-    Boolean retval = FALSE;
+	SeqAnnotPtr oldsap = NULL, tsap = NULL;
+    Boolean retval = FALSE, had_sap = FALSE, had_extra = FALSE;
+	AsnOptionPtr aopp;
+	ValNodePtr extras = NULL;
+	SeqAnnot sa;
 
 	if (! loaded)
 	{
@@ -2878,12 +3018,28 @@ NLM_EXTERN Boolean LIBCALL SeqAnnotSetAsnWrite (SeqAnnotPtr sap, AsnIoPtr aip, A
 	if (aip == NULL)
 		return FALSE;
 
+	aopp = AsnIoOptionGet(aip, OP_NCBIOBJSEQ, CHECK_EXTRA_FEAT, NULL);
+	if (aopp != NULL)
+	{
+		had_extra = TRUE;
+		extras = aopp->data.ptrvalue;
+		tsap = &sa;
+		MemSet(tsap, 0, sizeof(SeqAnnot));
+		tsap->type = 1;  /* feature table */
+	}
+	else if ((sap == NULL) && (! sap_not_null))  /* nothing to write */
+		return TRUE;
+		
 	atp = AsnLinkType(element, SEQ_ANNOT);   /* link local tree */
     if (atp == NULL) return FALSE;
 
-	if (sap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+	if (sap_not_null)
+		oldsap = sap;
+	else
+		oldsap = tsap;
+
+	if (oldsap == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
 
-	oldsap = sap;
     if (! AsnOpenStruct(aip, set, (Pointer)oldsap)) goto erret;
 
     while (sap != NULL)
@@ -2891,9 +3047,17 @@ NLM_EXTERN Boolean LIBCALL SeqAnnotSetAsnWrite (SeqAnnotPtr sap, AsnIoPtr aip, A
         if (! SeqAnnotAsnWrite(sap, aip, atp)) goto erret;
         sap = sap->next;
     }
+
+    if (tsap != NULL)
+    {
+	if (! SeqAnnotAsnWriteExtra(tsap, aip, atp, extras)) goto erret;
+    }
+
     if (! AsnCloseStruct(aip, set, (Pointer)oldsap)) goto erret;
     retval = TRUE;
 erret:
+	if (had_extra)
+		AsnIoOptionFree(aip, OP_NCBIOBJSEQ, CHECK_EXTRA_FEAT);
 	AsnUnlinkType(element);       /* unlink local tree */
 	return retval;
 }
@@ -4525,3 +4689,4 @@ erret:
     goto ret;
 }
 
+
diff --git a/object/objseq.h b/object/objseq.h
index cfcce33c..2ca38054 100644
--- a/object/objseq.h
+++ b/object/objseq.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.4 $
+* $Revision: 6.5 $
 *
 * File Description:  Object manager interface for module NCBI-Seq
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: objseq.h,v $
+* Revision 6.5  2001/10/02 21:47:54  kans
+* added hooks for writing extra descriptors or features (JO)
+*
 * Revision 6.4  1999/09/27 17:48:38  kans
 * using GatherIndex structure
 *
@@ -284,6 +287,11 @@ NLM_EXTERN Int2 LIBCALL SeqAnnotLabel PROTO((SeqAnnotPtr sap, CharPtr buffer, In
 NLM_EXTERN Boolean     LIBCALL SeqAnnotSetAsnWrite PROTO((SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element));
 NLM_EXTERN SeqAnnotPtr LIBCALL SeqAnnotSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element));
 
+/** SeqAnnotSetExtraCheck looks for extra Features from SeqEntryAsnOut
+    and adds them to the stream when the annot pointer is NULL
+*********/
+NLM_EXTERN Boolean LIBCALL SeqAnnotSetExtraCheck (AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element);
+
 
 /*****************************************************************************
 *
@@ -467,6 +475,8 @@ typedef struct op_objseq {
 
 /* types for AsnIoOption OP_NCBIOBJSEQ */
 #define BIOSEQ_CHECK_ID 1    /* match Op_objseq.sip */
+#define CHECK_EXTRA_DESC 2   /* used by SeqEntryAsnOut */
+#define CHECK_EXTRA_FEAT 3   /* used by SeqEntryAsnOut */
 
 /*****************************************************************************
 *
@@ -548,6 +558,11 @@ NLM_EXTERN SeqDescPtr LIBCALL SeqDescAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp
 NLM_EXTERN SeqDescPtr LIBCALL SeqDescFree PROTO((SeqDescPtr anp));
 NLM_EXTERN Int2 LIBCALL SeqDescLabel PROTO((SeqDescPtr vnp, CharPtr buffer, Int2 buflen, Boolean content));
 
+/** SeqDescrExtraCheck looks for extra Descriptors from SeqEntryAsnOut
+    and adds them to the stream when the descr pointer is NULL
+*********/
+NLM_EXTERN Boolean LIBCALL SeqDescrExtraCheck (AsnIoPtr aip, AsnTypePtr atp);
+
 /*****************************************************************************
 *
 *   Pubdesc, Numbering, MolInfo, BioSource types defined in objpubd.h
@@ -567,3 +582,4 @@ NLM_EXTERN Int2 LIBCALL SeqDescLabel PROTO((SeqDescPtr vnp, CharPtr buffer, Int2
 
 #endif
 
+
diff --git a/object/objsset.c b/object/objsset.c
index e12e4500..9d2f5611 100644
--- a/object/objsset.c
+++ b/object/objsset.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.1 $
+* $Revision: 6.4 $
 *
 * File Description:  Object manager for module NCBI-Seqset
 *
@@ -41,6 +41,15 @@
 *
 *
 * $Log: objsset.c,v $
+* Revision 6.4  2001/11/30 12:20:18  kans
+* ObjMgrDeleteAllInRecord called when freeing top bsp or bssp
+*
+* Revision 6.3  2001/11/16 19:31:09  kans
+* BioseqFree and BioseqSetFree on top-level object call SeqMgrDeleteIndexesInRecord
+*
+* Revision 6.2  2001/08/07 17:22:27  kans
+* added third party annotation SeqIDs to FindBestBioseqLabel
+*
 * Revision 6.1  1998/08/24 18:28:11  kans
 * removed solaris -v -fd warnings
 *
@@ -143,6 +152,10 @@ static void FindBestBioseqLabel (SeqEntryPtr sep, Pointer data, Int4 index, Int2
 			case SEQID_GENBANK:
 			case SEQID_EMBL:
 			case SEQID_DDBJ:
+			case SEQID_OTHER:
+			case SEQID_TPG:
+			case SEQID_TPE:
+			case SEQID_TPD:
 				has_gb = TRUE;
 			case SEQID_PIR:
 			case SEQID_SWISSPROT:
@@ -378,14 +391,27 @@ NLM_EXTERN BioseqSetPtr LIBCALL BioseqSetNew (void)
 *****************************************************************************/
 NLM_EXTERN BioseqSetPtr LIBCALL BioseqSetFree (BioseqSetPtr bsp)
 {
+	Boolean top = FALSE;
+
     if (bsp == NULL)
         return bsp;
 
+	if (bsp->idx.parentptr == NULL || bsp->idx.parenttype == OBJ_SEQSUB) {
+		if (bsp->seqentry != NULL) {
+			SeqMgrDeleteIndexesInRecord (bsp->seqentry);
+			top = TRUE;
+		}
+	}
+
 	if (! SeqMgrDelete(SM_BIOSEQSET, (Pointer)bsp))
 	    ErrPostEx(SEV_ERROR, 0,0, "BioseqSetFree: pointer not registered");
 
 	BioseqSetFreeComponents(bsp, TRUE);
 
+	if (top) {
+		ObjMgrDeleteAllInRecord ();
+	}
+
 	return (BioseqSetPtr)MemFree(bsp);
 }