Load ncbi (6.1.20041020) into ncbi-tools6/branches/upstream/current.

19 files changed, 2050 insertions, 1001 deletions

diff --git a/network/blast3/client/netblap3.h b/network/blast3/client/netblap3.h
index 239e34cc..73c8f66e 100644
--- a/network/blast3/client/netblap3.h
+++ b/network/blast3/client/netblap3.h
@@ -34,6 +34,9 @@
 *
 * RCS Modification History:
 * $Log: netblap3.h,v $
+* Revision 1.32  2004/06/30 12:34:14  madden
+* Add include for blfmtutl.h
+*
 * Revision 1.31  2003/01/10 21:45:06  bealer
 * - Modify to return errors from BLASTGetUidsFromQuery instead of logging them.
 *
@@ -133,6 +136,7 @@
 #include <ni_types.h>
 #include <blastdef.h>
 #include <blastpri.h>
+#include <blfmtutl.h>
 
 #undef NLM_EXTERN
 #ifdef NLM_IMPORT
diff --git a/network/id1arch/idfetch.c b/network/id1arch/idfetch.c
index 416f03e6..52992c2e 100644
--- a/network/id1arch/idfetch.c
+++ b/network/id1arch/idfetch.c
@@ -25,6 +25,15 @@
  * Author Karl Sirotkin
  *
  $Log: idfetch.c,v $
+ Revision 1.35  2004/10/12 21:39:28  vysokolo
+ Added intervals of accessions like: "ABC_000123-ABC_000456"
+
+ Revision 1.34  2004/10/04 19:30:25  vysokolo
+ The "strcasecmp" replaced by "StringICmp"
+
+ Revision 1.33  2004/09/30 17:59:26  vysokolo
+ Added key -F to enable features by name.
+
  Revision 1.32  2004/05/25 18:41:35  kans
  removed obsolete STREAM_SEQ_PORT_FIRST flag
 
@@ -160,7 +169,6 @@
  * Modified by Eugene Yaschenko for ID1 Server
  *
  */
-
 #include <ncbi.h>
 #include <objsset.h>
 #include <accid1.h>
@@ -224,7 +232,8 @@ prf|acc|name pdb|entry|chain",
         {"Log file", NULL,NULL,NULL,TRUE,'l',ARG_FILE_OUT,0.0,0,NULL},
         {"Generate gi list by entrez query", NULL,NULL,NULL,TRUE,'q',ARG_STRING,0.0,0,NULL},
         {"Generate gi list by entrez query", NULL,NULL,NULL,TRUE,'Q',ARG_FILE_IN,0.0,0,NULL},
-        {"Output only the list of gis, used with -q", NULL,NULL,NULL,TRUE,'n',ARG_BOOLEAN,0.0,0,NULL}
+        {"Output only the list of gis, used with -q", NULL,NULL,NULL,TRUE,'n',ARG_BOOLEAN,0.0,0,NULL},
+        {"Add features delimited by ','. Allowed values are: 'CDD', 'SNP', 'SNP_graph', 'MGC'.", NULL,NULL,NULL,TRUE,'F',ARG_STRING,0.0,0,NULL}
 };
 int Numarg = sizeof(myargs)/sizeof(myargs[0]);
 
@@ -241,13 +250,16 @@ int Numarg = sizeof(myargs)/sizeof(myargs[0]);
 static Nlm_Int2 Nlm_WhichArg PROTO(( Nlm_Char which, Nlm_Int2 numargs, Nlm_ArgPtr ap));
 static void MyBioseqToFasta(BioseqPtr bsp, Pointer userdata);
 
+static Boolean CreateMaxPlexParam();
+static Int4 GetIntervalAccession( const Char* pAccession, Char* pResult);
+
 Int4 giBuffer[1000];
 int giBufferPos = 0;
 
 DataVal Val;
 Int2 fileoutarg, logarg, outtypearg,maxplexarg,seqidarg,
   giarg, fastaarg, infotypearg, entarg, dbarg, gifilearg,
-  entrezqueryarg, entrezqueryfilearg, onlylistarg;
+  entrezqueryarg, entrezqueryfilearg, onlylistarg, showfeatures, maxplex_param;
 
 FILE * fp = NULL;
 AsnIoPtr asnout=NULL;
@@ -262,6 +274,8 @@ Int2 Main()
   FILE * fp_in = NULL;
   SeqIdPtr sip;
   Char tbuf[1024];
+  static CharPtr accession = NULL;
+  int type_int;
 
   /* check command line arguments */
 
@@ -289,6 +303,13 @@ Int2 Main()
   MACRO_SETARG('q', entrezqueryarg)
   MACRO_SETARG('Q', entrezqueryfilearg)
   MACRO_SETARG('n', onlylistarg)
+  MACRO_SETARG('F', showfeatures)
+
+  if( !CreateMaxPlexParam())
+  {
+    has_trouble=TRUE;
+    goto FATAL;
+  }
 
   if(! SeqEntryLoad())
     ErrShow();
@@ -462,9 +483,8 @@ Int2 Main()
      "flaTtened SeqId, format:
      type(name,accession,release,version) or type=accession",
      */
-    static CharPtr name = NULL, accession = NULL, release = NULL, version = NULL, number = NULL;
+    static CharPtr name = NULL, release = NULL, version = NULL, number = NULL;
     CharPtr p;
-    int type_int;
     static CharPtr PNTR fields [] = {&name, &accession, &release, &number};
     Boolean found_equals = FALSE, found_left = FALSE,
       found_colon = FALSE, flat_seqid_err = FALSE,
@@ -472,7 +492,6 @@ Int2 Main()
     int dex;
     TextSeqIdPtr tsip;
 
-    sip = ValNodeNew(NULL);
     type_int = atoi(myargs[seqidarg].strvalue);
     for(p = myargs[seqidarg].strvalue; *p; p++ )
     {
@@ -561,6 +580,7 @@ Int2 Main()
               "id1test: could not find \'(\' or \'=\' or \':\' in flattened seqid=%s",myargs[seqidarg].strvalue);  /* ) match */
       exit(1);
     }
+    sip = ValNodeNew(NULL);
     sip->choice = type_int;
     switch(type_int)
     {
@@ -595,6 +615,7 @@ Int2 Main()
     case SEQID_GENERAL :
     case SEQID_PDB :
     case SEQID_LOCAL :
+    default:
       ErrPost(CTX_NCBIIDRETRIEVE,30,
               "Sorry, this test program does not support %d patent, general, pdb, or local, try id2asn ",
               type_int);
@@ -605,24 +626,63 @@ Int2 Main()
 
   if(! fp_in && ! gi && ! (myargs[entrezqueryarg].strvalue || myargs[entrezqueryfilearg].strvalue))
   {
-    gi = ID1ArchGIGet (sip);
-    if(gi <= 0)
+    Char tacc[64];
+    if( sip->data.ptrvalue && GetIntervalAccession( accession, tacc) > 0 )
     {
-	if(sip->choice==SEQID_GENERAL){
-		Dbtag *db = (Dbtag*)sip->data.ptrvalue;
-		gi=myargs[entarg].intvalue=db->tag->str?atoi(db->tag->str):db->tag->id;
-		myargs[dbarg].strvalue=StringSave(db->db);
-	} else {
-	      SeqIdPrint(sip, tbuf, PRINTID_FASTA_SHORT);
-	      ErrPostEx(SEV_ERROR, 0, 0, "Couldn't find SeqId [%s]", tbuf);
-	      goto FATAL;	
+      do{ 
+      	Int4 tgi = TryGetGi( type_int, tacc, NULL, 0);
+	if(tgi <= 0)
+	{
+	  SeqIdPrint(sip, tbuf, PRINTID_FASTA_SHORT);
+	  ErrPostEx(SEV_ERROR, 0, 0, "Couldn't find SeqId [%s]", tbuf);
+	  has_trouble=TRUE;
+	  break;
 	}
+	if( !IdFetch_func(tgi,myargs[dbarg].strvalue, myargs[entarg].intvalue,maxplex_param))
+	{
+	  has_trouble=TRUE;
+	  break;
+	}
+
+	if(fp) fflush(fp);
+      }
+      while( GetIntervalAccession( NULL, tacc) > 0);
+      if(fp) fflush(fp);
+      if( has_trouble ) goto FATAL;
+    }
+    else
+    {
+      gi = ID1ArchGIGet (sip);
+      if(gi <= 0)
+      {
+	  if(sip->choice==SEQID_GENERAL){
+		  Dbtag *db = (Dbtag*)sip->data.ptrvalue;
+		  gi=myargs[entarg].intvalue=db->tag->str?atoi(db->tag->str):db->tag->id;
+		  myargs[dbarg].strvalue=StringSave(db->db);
+	  } else {
+		SeqIdPrint(sip, tbuf, PRINTID_FASTA_SHORT);
+		ErrPostEx(SEV_ERROR, 0, 0, "Couldn't find SeqId [%s]", tbuf);
+		goto FATAL;	
+	  }
+      }
     }
   }
   else if(fp_in)
   {
+    Char tacc[1024];
     while(fgets(tbuf,sizeof(tbuf)-1,fp_in)){
-      IdFetch_func1(tbuf, myargs[maxplexarg].intvalue);
+      if( GetIntervalAccession( tbuf, tacc) > 0 )
+      {
+	do{ 
+	  IdFetch_func1(tacc, maxplex_param); 
+	  if(fp) fflush(fp);
+	}
+	while( GetIntervalAccession( NULL, tacc) > 0);
+      }
+      else
+      {
+	IdFetch_func1(tbuf, maxplex_param);
+      }	      
       if(fp) fflush(fp);
     }
   }
@@ -652,7 +712,7 @@ Int2 Main()
     }
   }
 
-  if(gi>0 && !IdFetch_func(gi,myargs[dbarg].strvalue, myargs[entarg].intvalue,myargs[maxplexarg].intvalue))
+  if(gi>0 && !IdFetch_func(gi,myargs[dbarg].strvalue, myargs[entarg].intvalue,maxplex_param))
   {
     has_trouble=TRUE;
     goto FATAL;
@@ -699,7 +759,7 @@ void EntrezQuery(char *query)
       IdFetch_func(ids[i],
                    myargs[dbarg].strvalue,
                    myargs[entarg].intvalue,
-                   myargs[maxplexarg].intvalue);
+		   maxplex_param);
   }
 }
 
@@ -805,7 +865,7 @@ static Boolean IdFetch_func1(CharPtr data, Int2 maxplex)
       return IdFetch_func(gi,
                           myargs[dbarg].strvalue,
                           myargs[entarg].intvalue,
-                          myargs[maxplexarg].intvalue);
+                          maxplex_param);
 
     if(ver == INT2_MIN &&
        (
@@ -818,7 +878,7 @@ static Boolean IdFetch_func1(CharPtr data, Int2 maxplex)
       return IdFetch_func(gi,
                           myargs[dbarg].strvalue,
                           myargs[entarg].intvalue,
-                          myargs[maxplexarg].intvalue);
+                          maxplex_param);
     return 0;
   }
   else
@@ -1217,3 +1277,116 @@ MyBioseqToFasta(BioseqPtr bsp, Pointer userdata)
 		start=stop+1;
 	}
 }
+
+Boolean CreateMaxPlexParam()
+{
+  Char buf[1024];
+  Char *ptoken = NULL;
+  maxplex_param = 0xfffffff0 | myargs[maxplexarg].intvalue;
+
+  if(myargs[showfeatures].strvalue)
+  {
+    strncpy( buf, myargs[showfeatures].strvalue, 1024);
+    ptoken = strtok( buf, ",");
+    while( ptoken)
+    {
+      if( !StringICmp( ptoken, "CDD"))
+      {
+	maxplex_param &= 0xffffff7f;
+      }
+      else if( !StringICmp( ptoken, "SNP"))
+      {
+	maxplex_param &= 0xffffffef;
+      }
+      else if( !StringICmp( ptoken, "SNP_graph"))
+      {
+	maxplex_param &= 0xffffffbf;
+      }
+      else if( !StringICmp( ptoken, "MGC"))
+      {
+	maxplex_param &= 0xfffffeff;
+      }
+      else
+      {
+	/* Error: unknown feature */
+	ErrPostEx(SEV_ERROR,0,0,"Unknown feature type [%s]", ptoken);
+	return FALSE;
+      }
+      ptoken = strtok( NULL, ",");
+    }
+  }
+  return TRUE;
+}
+
+static Int4 GetPrefixIndexFromAcession( const Char* pSrc, Char* pDest, Int4* pDiditsLen)
+{
+  Int4 ret;
+  while( *pSrc )
+  {
+    if( isdigit( *pSrc)) break;
+    *pDest++ = *pSrc++;
+  }
+  *pDest = '\0';
+  if( !*pSrc ) return -1;
+  ret = atoi( pSrc);
+  *pDiditsLen = 0;
+  while( isdigit( *pSrc++)) ++(*pDiditsLen);
+  return ret;
+}
+
+/*************************************************
+* GetIntervalAccession parses string as 'ABC_0000123-ABC_0000456'
+* and *returns* in 'pResult' strings like 'ABC_0000123', 'ABC_0000124', 'ABC_0000125', ..., 'ABC_0000456'
+* iteratively using 'iterator'
+* First call 'pAccession' must be a string like 'ABC_0000123-ABC_0000456', and all other times NULL
+* returns: 0 if no more iterations
+*         -1 if wrong format of input string
+*         >0 if next iteration are present
+**************************************************/
+static Int4 GetIntervalAccession( const Char* pAccession, Char* pResult)
+{
+  static Int4 iterator=0, Start=0, End=0, DigitsStart=0;
+  static Char pStartPrefix[64]={'\0'};
+  static Char pFormat[64]={'\0'};
+  
+  if( pAccession )
+  {
+    Int4 DigitsEnd=0;
+    Char pBuff[64]={'\0'};
+    Char pEndPrefix[64];
+    Char *pEnd, *pStart;
+
+    iterator = 0;
+
+    strncpy( pBuff, pAccession, 64);
+    /*parse interval*/
+
+    /*find dash*/
+    pEnd = pStart = pBuff;
+    while( *pEnd++ )
+    {
+      if( *pEnd == '-' ) break;
+    }
+    if( !*pEnd ) return -1; /*no dash found*/
+
+    *pEnd++ = '\0';
+    
+    /*find index of start and end in the interval*/
+    Start = GetPrefixIndexFromAcession( pStart, pStartPrefix, &DigitsStart);
+    End = GetPrefixIndexFromAcession( pEnd, pEndPrefix, &DigitsEnd);
+
+    if( DigitsStart != DigitsEnd || strcmp( pStartPrefix, pEndPrefix) || Start >= End || DigitsStart < 1)
+    {
+      return -1; /* wrong interval format */
+    }
+    sprintf( pFormat, "%%s%%0%hdhd", DigitsStart);
+  }
+  
+  if( Start+iterator > End ) return 0; /*stop*/
+  
+  /* return next accession */
+  sprintf( pResult, pFormat, pStartPrefix, Start+iterator);
+
+  return ++iterator;
+}
+
diff --git a/network/id2arch/id2.asn b/network/id2arch/id2.asn
index d44755f7..b8ad3042 100644
--- a/network/id2arch/id2.asn
+++ b/network/id2arch/id2.asn
@@ -1,4 +1,4 @@
---$Revision: 1.12 $
+--$Revision: 1.14 $
 --********************************************************************
 --
 --  Network Id server network access
@@ -65,11 +65,11 @@ ID2-Request-Get-Packages ::= SEQUENCE {
 ID2-Request-Get-Seq-id ::= SEQUENCE {
         seq-id          ID2-Seq-id,
         seq-id-type     INTEGER {
-                any     (0),    -- return any one Seq-id
+                any     (0),    -- return any qualified Seq-id
                 gi      (1),    -- gi is preferred
                 text    (2),    -- text Seq-id (accession etc) is preferred
                 general (4),    -- general Seq-id is preferred
-                all     (127)   -- return all Seq-ids of the sequence
+                all     (127)   -- return all qualified Seq-ids of the sequence
         } DEFAULT any
 }
 
@@ -286,13 +286,23 @@ ID2-Reply-Get-Seq-id ::= SEQUENCE {
 }
 
 
+ID2-Blob-State ::= ENUMERATED {
+        live            (0),
+        suppressed-temp (1),
+        suppressed      (2),
+        dead            (3),
+        protected       (4),
+        withdrawn       (5)
+}
+
+
 -- Reply to ID2-Request-Get-Blob-Id.
 ID2-Reply-Get-Blob-Id ::= SEQUENCE {
         -- requested Seq-id
         seq-id          Seq-id,
 
         -- result
-        blob-id         ID2-Blob-Id,
+        blob-id         ID2-Blob-Id OPTIONAL,
 
         -- version of split data
         -- (0 for non split)
diff --git a/network/id2arch/id2.c b/network/id2arch/id2.c
index fe8c90a7..b2cf1384 100644
--- a/network/id2arch/id2.c
+++ b/network/id2arch/id2.c
@@ -32,7 +32,7 @@ id2genAsnLoad(void)
 
 /**************************************************
 *    Generated object loaders for Module NCBI-ID2Access
-*    Generated using ASNCODE Revision: 6.0 at May 3, 2004  6:18 PM
+*    Generated using ASNCODE Revision: 6.0 at Oct 18, 2004  1:24 AM
 *
 **************************************************/
 
@@ -2769,6 +2769,13 @@ ID2ReplyAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       }
       atp = AsnReadId(aip,amp, atp);
    }
+   if (atp == ID2_REPLY_discard) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> discard = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
 
    if (AsnReadVal(aip, atp, &av) <= 0) {
       goto erret;
@@ -2954,6 +2961,8 @@ ID2ReplyAsnWrite(ID2ReplyPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
          goto erret;
       }
    }
+   av.intvalue = ptr -> discard;
+   retval = AsnWrite(aip, ID2_REPLY_discard,  &av);
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
@@ -3497,6 +3506,13 @@ ID2ReplyGetSeqIdAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       }
       atp = AsnReadId(aip,amp, atp);
    }
+   if (atp == REPLY_GET_SEQ_ID_end_of_reply) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> end_of_reply = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
 
    if (AsnReadVal(aip, atp, &av) <= 0) {
       goto erret;
@@ -3554,6 +3570,8 @@ ID2ReplyGetSeqIdAsnWrite(ID2ReplyGetSeqIdPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
       }
    }
    AsnGenericChoiceSeqOfAsnWrite(ptr -> seq_id, (AsnWriteFunc) SeqIdAsnWrite, aip, ID2_REPLY_GET_SEQ_ID_seq_id, ID2_REPLY_GET_SEQ_ID_seq_id_E);
+   av.boolvalue = ptr -> end_of_reply;
+   retval = AsnWrite(aip, REPLY_GET_SEQ_ID_end_of_reply,  &av);
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
@@ -3678,6 +3696,13 @@ ID2ReplyGetBlobIdAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       }
       atp = AsnReadId(aip,amp, atp);
    }
+   if (atp == REPLY_GET_BLOB_ID_end_of_reply) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> end_of_reply = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
 
    if (AsnReadVal(aip, atp, &av) <= 0) {
       goto erret;
@@ -3742,6 +3767,8 @@ ID2ReplyGetBlobIdAsnWrite(ID2ReplyGetBlobIdPtr ptr, AsnIoPtr aip, AsnTypePtr ori
    av.intvalue = ptr -> split_version;
    retval = AsnWrite(aip, GET_BLOB_ID_split_version,  &av);
    AsnGenericUserSeqOfAsnWrite(ptr -> annot_info, (AsnWriteFunc) ID2SSeqAnnotInfoAsnWrite, aip, REPLY_GET_BLOB_ID_annot_info, REPLY_GET_BLOB_ID_annot_info_E);
+   av.boolvalue = ptr -> end_of_reply;
+   retval = AsnWrite(aip, REPLY_GET_BLOB_ID_end_of_reply,  &av);
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
diff --git a/network/id2arch/id2.h b/network/id2arch/id2.h
index 874c3e2c..4c2ff16a 100644
--- a/network/id2arch/id2.h
+++ b/network/id2arch/id2.h
@@ -9,8 +9,8 @@
 #include <asn.h>
 #endif
 
-static char * asnfilename = "id2.h10";
-static AsnValxNode avnx[48] = {
+static char * asnfilename = "id2.h14";
+static AsnValxNode avnx[57] = {
     {20,"set-value" ,1,0.0,&avnx[1] } ,
     {20,"get-value" ,2,0.0,&avnx[2] } ,
     {20,"force-value" ,3,0.0,&avnx[3] } ,
@@ -58,9 +58,18 @@ static AsnValxNode avnx[48] = {
     {20,"nlmzip" ,2,0.0,&avnx[45] } ,
     {20,"bzip2" ,3,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {3,NULL,0,0.0,NULL } };
-
-static AsnType atx[142] = {
+    {3,NULL,0,0.0,NULL } ,
+    {20,"reply" ,0,0.0,&avnx[49] } ,
+    {20,"last-octet-string" ,1,0.0,&avnx[50] } ,
+    {20,"nothing" ,2,0.0,NULL } ,
+    {20,"live" ,0,0.0,&avnx[52] } ,
+    {20,"suppressed-temp" ,1,0.0,&avnx[53] } ,
+    {20,"suppressed" ,2,0.0,&avnx[54] } ,
+    {20,"dead" ,3,0.0,&avnx[55] } ,
+    {20,"protected" ,4,0.0,&avnx[56] } ,
+    {20,"withdrawn" ,5,0.0,NULL } };
+
+static AsnType atx[146] = {
   {401, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1]} ,
   {402, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[2]} ,
   {403, "ID2S-Chunk-Id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[3]} ,
@@ -73,7 +82,7 @@ static AsnType atx[142] = {
   {0, "params" ,128,1,0,1,0,0,0,0,NULL,&atx[10],NULL,0,&atx[21]} ,
   {407, "ID2-Params" ,1,0,0,0,0,0,0,0,NULL,&atx[17],&atx[11],0,&atx[25]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[12],NULL,0,NULL} ,
-  {430, "ID2-Param" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[13],0,NULL} ,
+  {431, "ID2-Param" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[13],0,NULL} ,
   {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[14],NULL,0,&atx[15]} ,
   {323, "VisibleString" ,0,26,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "value" ,128,1,0,1,0,0,0,0,NULL,&atx[17],&atx[16],0,&atx[18]} ,
@@ -147,65 +156,69 @@ static AsnType atx[142] = {
   {0, "retry-delay" ,128,1,0,1,0,0,0,0,NULL,&atx[8],NULL,0,&atx[84]} ,
   {0, "message" ,128,2,0,1,0,0,0,0,NULL,&atx[14],NULL,0,NULL} ,
   {0, "end-of-reply" ,128,3,0,1,0,0,0,0,NULL,&atx[23],NULL,0,&atx[86]} ,
-  {0, "reply" ,128,4,0,0,0,0,0,0,NULL,&atx[35],&atx[87],0,NULL} ,
+  {0, "reply" ,128,4,0,0,0,0,0,0,NULL,&atx[35],&atx[87],0,&atx[139]} ,
   {0, "init" ,128,0,0,0,0,0,0,0,NULL,&atx[23],NULL,0,&atx[88]} ,
   {0, "empty" ,128,1,0,0,0,0,0,0,NULL,&atx[23],NULL,0,&atx[89]} ,
   {0, "get-package" ,128,2,0,0,0,0,0,0,NULL,&atx[90],NULL,0,&atx[93]} ,
   {419, "ID2-Reply-Get-Package" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[91],0,&atx[94]} ,
   {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[14],NULL,0,&atx[92]} ,
   {0, "params" ,128,1,0,1,0,0,0,0,NULL,&atx[10],NULL,0,NULL} ,
-  {0, "get-seq-id" ,128,3,0,0,0,0,0,0,NULL,&atx[94],NULL,0,&atx[98]} ,
-  {420, "ID2-Reply-Get-Seq-id" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[95],0,&atx[99]} ,
+  {0, "get-seq-id" ,128,3,0,0,0,0,0,0,NULL,&atx[94],NULL,0,&atx[99]} ,
+  {420, "ID2-Reply-Get-Seq-id" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[95],0,&atx[100]} ,
   {0, "request" ,128,0,0,0,0,0,0,0,NULL,&atx[30],NULL,0,&atx[96]} ,
-  {0, "seq-id" ,128,1,0,1,0,0,0,0,NULL,&atx[17],&atx[97],0,NULL} ,
+  {0, "seq-id" ,128,1,0,1,0,0,0,0,NULL,&atx[17],&atx[97],0,&atx[98]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,NULL} ,
-  {0, "get-blob-id" ,128,4,0,0,0,0,0,0,NULL,&atx[99],NULL,0,&atx[105]} ,
-  {421, "ID2-Reply-Get-Blob-Id" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[100],0,&atx[106]} ,
-  {0, "seq-id" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[101]} ,
-  {0, "blob-id" ,128,1,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[102]} ,
-  {0, "split-version" ,128,2,0,0,1,0,0,0,&avnx[32],&atx[8],NULL,0,&atx[103]} ,
-  {0, "annot-info" ,128,3,0,1,0,0,0,0,NULL,&atx[17],&atx[104],0,NULL} ,
+  {0, "end-of-reply" ,128,2,0,1,0,0,0,0,NULL,&atx[23],NULL,0,NULL} ,
+  {0, "get-blob-id" ,128,4,0,0,0,0,0,0,NULL,&atx[100],NULL,0,&atx[107]} ,
+  {421, "ID2-Reply-Get-Blob-Id" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[101],0,&atx[108]} ,
+  {0, "seq-id" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[102]} ,
+  {0, "blob-id" ,128,1,0,1,0,0,0,0,NULL,&atx[47],NULL,0,&atx[103]} ,
+  {0, "split-version" ,128,2,0,0,1,0,0,0,&avnx[32],&atx[8],NULL,0,&atx[104]} ,
+  {0, "annot-info" ,128,3,0,1,0,0,0,0,NULL,&atx[17],&atx[105],0,&atx[106]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[3],NULL,0,NULL} ,
-  {0, "get-blob-seq-ids" ,128,5,0,0,0,0,0,0,NULL,&atx[106],NULL,0,&atx[116]} ,
-  {422, "ID2-Reply-Get-Blob-Seq-ids" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[107],0,&atx[117]} ,
-  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[108]} ,
-  {0, "ids" ,128,1,0,1,0,0,0,0,NULL,&atx[109],NULL,0,NULL} ,
-  {427, "ID2-Reply-Data" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[110],0,&atx[137]} ,
-  {0, "data-type" ,128,0,0,0,1,0,0,0,&avnx[37],&atx[8],&avnx[33],0,&atx[111]} ,
-  {0, "data-format" ,128,1,0,0,1,0,0,0,&avnx[41],&atx[8],&avnx[38],0,&atx[112]} ,
-  {0, "data-compression" ,128,2,0,0,1,0,0,0,&avnx[46],&atx[8],&avnx[42],0,&atx[113]} ,
-  {0, "data" ,128,3,0,0,0,0,0,0,NULL,&atx[17],&atx[114],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[115],NULL,0,NULL} ,
+  {0, "end-of-reply" ,128,4,0,1,0,0,0,0,NULL,&atx[23],NULL,0,NULL} ,
+  {0, "get-blob-seq-ids" ,128,5,0,0,0,0,0,0,NULL,&atx[108],NULL,0,&atx[118]} ,
+  {422, "ID2-Reply-Get-Blob-Seq-ids" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[109],0,&atx[119]} ,
+  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[110]} ,
+  {0, "ids" ,128,1,0,1,0,0,0,0,NULL,&atx[111],NULL,0,NULL} ,
+  {428, "ID2-Reply-Data" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[112],0,&atx[141]} ,
+  {0, "data-type" ,128,0,0,0,1,0,0,0,&avnx[37],&atx[8],&avnx[33],0,&atx[113]} ,
+  {0, "data-format" ,128,1,0,0,1,0,0,0,&avnx[41],&atx[8],&avnx[38],0,&atx[114]} ,
+  {0, "data-compression" ,128,2,0,0,1,0,0,0,&avnx[46],&atx[8],&avnx[42],0,&atx[115]} ,
+  {0, "data" ,128,3,0,0,0,0,0,0,NULL,&atx[17],&atx[116],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[117],NULL,0,NULL} ,
   {304, "OCTET STRING" ,0,4,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {0, "get-blob" ,128,6,0,0,0,0,0,0,NULL,&atx[117],NULL,0,&atx[121]} ,
-  {423, "ID2-Reply-Get-Blob" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[118],0,&atx[122]} ,
-  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[119]} ,
-  {0, "split-version" ,128,1,0,0,1,0,0,0,&avnx[47],&atx[8],NULL,0,&atx[120]} ,
-  {0, "data" ,128,2,0,1,0,0,0,0,NULL,&atx[109],NULL,0,NULL} ,
-  {0, "reget-blob" ,128,7,0,0,0,0,0,0,NULL,&atx[122],NULL,0,&atx[127]} ,
-  {424, "ID2-Reply-ReGet-Blob" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[123],0,&atx[128]} ,
-  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[124]} ,
-  {0, "split-version" ,128,1,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[125]} ,
-  {0, "offset" ,128,2,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[126]} ,
-  {0, "data" ,128,3,0,1,0,0,0,0,NULL,&atx[109],NULL,0,NULL} ,
-  {0, "get-split-info" ,128,8,0,0,0,0,0,0,NULL,&atx[128],NULL,0,&atx[132]} ,
-  {425, "ID2S-Reply-Get-Split-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[129],0,&atx[133]} ,
-  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[130]} ,
-  {0, "split-version" ,128,1,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[131]} ,
-  {0, "data" ,128,2,0,1,0,0,0,0,NULL,&atx[109],NULL,0,NULL} ,
-  {0, "get-chunk" ,128,9,0,0,0,0,0,0,NULL,&atx[133],NULL,0,NULL} ,
-  {426, "ID2S-Reply-Get-Chunk" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[134],0,&atx[109]} ,
-  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[135]} ,
-  {0, "chunk-id" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[136]} ,
-  {0, "data" ,128,2,0,1,0,0,0,0,NULL,&atx[109],NULL,0,NULL} ,
-  {428, "ID2-Blob-Seq-ids" ,1,0,0,0,0,0,0,0,NULL,&atx[17],&atx[138],0,&atx[139]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[139],NULL,0,NULL} ,
-  {429, "ID2-Blob-Seq-id" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[140],0,&atx[12]} ,
-  {0, "seq-id" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[141]} ,
+  {0, "get-blob" ,128,6,0,0,0,0,0,0,NULL,&atx[119],NULL,0,&atx[123]} ,
+  {423, "ID2-Reply-Get-Blob" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[120],0,&atx[124]} ,
+  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[121]} ,
+  {0, "split-version" ,128,1,0,0,1,0,0,0,&avnx[47],&atx[8],NULL,0,&atx[122]} ,
+  {0, "data" ,128,2,0,1,0,0,0,0,NULL,&atx[111],NULL,0,NULL} ,
+  {0, "reget-blob" ,128,7,0,0,0,0,0,0,NULL,&atx[124],NULL,0,&atx[129]} ,
+  {424, "ID2-Reply-ReGet-Blob" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[125],0,&atx[130]} ,
+  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[126]} ,
+  {0, "split-version" ,128,1,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[127]} ,
+  {0, "offset" ,128,2,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[128]} ,
+  {0, "data" ,128,3,0,1,0,0,0,0,NULL,&atx[111],NULL,0,NULL} ,
+  {0, "get-split-info" ,128,8,0,0,0,0,0,0,NULL,&atx[130],NULL,0,&atx[134]} ,
+  {425, "ID2S-Reply-Get-Split-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[131],0,&atx[135]} ,
+  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[132]} ,
+  {0, "split-version" ,128,1,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[133]} ,
+  {0, "data" ,128,2,0,1,0,0,0,0,NULL,&atx[111],NULL,0,NULL} ,
+  {0, "get-chunk" ,128,9,0,0,0,0,0,0,NULL,&atx[135],NULL,0,NULL} ,
+  {426, "ID2S-Reply-Get-Chunk" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[136],0,&atx[140]} ,
+  {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[137]} ,
+  {0, "chunk-id" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[138]} ,
+  {0, "data" ,128,2,0,1,0,0,0,0,NULL,&atx[111],NULL,0,NULL} ,
+  {0, "discard" ,128,5,0,1,0,0,0,0,NULL,&atx[19],&avnx[48],0,NULL} ,
+  {427, "ID2-Blob-State" ,1,0,0,0,0,0,0,0,NULL,&atx[19],&avnx[51],0,&atx[111]} ,
+  {429, "ID2-Blob-Seq-ids" ,1,0,0,0,0,0,0,0,NULL,&atx[17],&atx[142],0,&atx[143]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[143],NULL,0,NULL} ,
+  {430, "ID2-Blob-Seq-id" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[144],0,&atx[12]} ,
+  {0, "seq-id" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[145]} ,
   {0, "replaced" ,128,1,0,1,0,0,0,0,NULL,&atx[23],NULL,0,NULL} };
 
 static AsnModule ampx[1] = {
-  { "NCBI-ID2Access" , "id2.h10",&atx[0],NULL,NULL,0,0} };
+  { "NCBI-ID2Access" , "id2.h14",&atx[0],NULL,NULL,0,0} };
 
 static AsnValxNodePtr avn = avnx;
 static AsnTypePtr at = atx;
@@ -302,12 +315,13 @@ static AsnModulePtr amp = ampx;
 #define ID2_REPLY_reply_empty &at[88]
 #define ID2_REPLY_reply_get_package &at[89]
 #define ID2_REPLY_reply_get_seq_id &at[93]
-#define ID2_REPLY_reply_get_blob_id &at[98]
-#define REPLY_reply_get_blob_seq_ids &at[105]
-#define ID2_REPLY_reply_get_blob &at[116]
-#define ID2_REPLY_reply_reget_blob &at[121]
-#define ID2_REPLY_reply_get_split_info &at[127]
-#define ID2_REPLY_reply_get_chunk &at[132]
+#define ID2_REPLY_reply_get_blob_id &at[99]
+#define REPLY_reply_get_blob_seq_ids &at[107]
+#define ID2_REPLY_reply_get_blob &at[118]
+#define ID2_REPLY_reply_reget_blob &at[123]
+#define ID2_REPLY_reply_get_split_info &at[129]
+#define ID2_REPLY_reply_get_chunk &at[134]
+#define ID2_REPLY_discard &at[139]
 
 #define ID2_ERROR &at[81]
 #define ID2_ERROR_severity &at[82]
@@ -322,52 +336,56 @@ static AsnModulePtr amp = ampx;
 #define ID2_REPLY_GET_SEQ_ID_request &at[95]
 #define ID2_REPLY_GET_SEQ_ID_seq_id &at[96]
 #define ID2_REPLY_GET_SEQ_ID_seq_id_E &at[97]
-
-#define ID2_REPLY_GET_BLOB_ID &at[99]
-#define ID2_REPLY_GET_BLOB_ID_seq_id &at[100]
-#define ID2_REPLY_GET_BLOB_ID_blob_id &at[101]
-#define GET_BLOB_ID_split_version &at[102]
-#define REPLY_GET_BLOB_ID_annot_info &at[103]
-#define REPLY_GET_BLOB_ID_annot_info_E &at[104]
-
-#define ID2_REPLY_GET_BLOB_SEQ_IDS &at[106]
-#define REPLY_GET_BLOB_SEQ_IDS_blob_id &at[107]
-#define ID2_REPLY_GET_BLOB_SEQ_IDS_ids &at[108]
-
-#define ID2_REPLY_GET_BLOB &at[117]
-#define ID2_REPLY_GET_BLOB_blob_id &at[118]
-#define REPLY_GET_BLOB_split_version &at[119]
-#define ID2_REPLY_GET_BLOB_data &at[120]
-
-#define ID2_REPLY_REGET_BLOB &at[122]
-#define ID2_REPLY_REGET_BLOB_blob_id &at[123]
-#define REPLY_REGET_BLOB_split_version &at[124]
-#define ID2_REPLY_REGET_BLOB_offset &at[125]
-#define ID2_REPLY_REGET_BLOB_data &at[126]
-
-#define ID2S_REPLY_GET_SPLIT_INFO &at[128]
-#define REPLY_GET_SPLIT_INFO_blob_id &at[129]
-#define GET_SPLIT_INFO_split_version &at[130]
-#define ID2S_REPLY_GET_SPLIT_INFO_data &at[131]
-
-#define ID2S_REPLY_GET_CHUNK &at[133]
-#define ID2S_REPLY_GET_CHUNK_blob_id &at[134]
-#define ID2S_REPLY_GET_CHUNK_chunk_id &at[135]
-#define ID2S_REPLY_GET_CHUNK_data &at[136]
-
-#define ID2_REPLY_DATA &at[109]
-#define ID2_REPLY_DATA_data_type &at[110]
-#define ID2_REPLY_DATA_data_format &at[111]
-#define ID2_REPLY_DATA_data_compression &at[112]
-#define ID2_REPLY_DATA_data &at[113]
-#define ID2_REPLY_DATA_data_E &at[114]
-
-#define ID2_BLOB_SEQ_IDS &at[137]
-#define ID2_BLOB_SEQ_IDS_E &at[138]
-
-#define ID2_BLOB_SEQ_ID &at[139]
-#define ID2_BLOB_SEQ_ID_seq_id &at[140]
-#define ID2_BLOB_SEQ_ID_replaced &at[141]
+#define REPLY_GET_SEQ_ID_end_of_reply &at[98]
+
+#define ID2_REPLY_GET_BLOB_ID &at[100]
+#define ID2_REPLY_GET_BLOB_ID_seq_id &at[101]
+#define ID2_REPLY_GET_BLOB_ID_blob_id &at[102]
+#define GET_BLOB_ID_split_version &at[103]
+#define REPLY_GET_BLOB_ID_annot_info &at[104]
+#define REPLY_GET_BLOB_ID_annot_info_E &at[105]
+#define REPLY_GET_BLOB_ID_end_of_reply &at[106]
+
+#define ID2_REPLY_GET_BLOB_SEQ_IDS &at[108]
+#define REPLY_GET_BLOB_SEQ_IDS_blob_id &at[109]
+#define ID2_REPLY_GET_BLOB_SEQ_IDS_ids &at[110]
+
+#define ID2_REPLY_GET_BLOB &at[119]
+#define ID2_REPLY_GET_BLOB_blob_id &at[120]
+#define REPLY_GET_BLOB_split_version &at[121]
+#define ID2_REPLY_GET_BLOB_data &at[122]
+
+#define ID2_REPLY_REGET_BLOB &at[124]
+#define ID2_REPLY_REGET_BLOB_blob_id &at[125]
+#define REPLY_REGET_BLOB_split_version &at[126]
+#define ID2_REPLY_REGET_BLOB_offset &at[127]
+#define ID2_REPLY_REGET_BLOB_data &at[128]
+
+#define ID2S_REPLY_GET_SPLIT_INFO &at[130]
+#define REPLY_GET_SPLIT_INFO_blob_id &at[131]
+#define GET_SPLIT_INFO_split_version &at[132]
+#define ID2S_REPLY_GET_SPLIT_INFO_data &at[133]
+
+#define ID2S_REPLY_GET_CHUNK &at[135]
+#define ID2S_REPLY_GET_CHUNK_blob_id &at[136]
+#define ID2S_REPLY_GET_CHUNK_chunk_id &at[137]
+#define ID2S_REPLY_GET_CHUNK_data &at[138]
+
+#define ID2_BLOB_STATE &at[140]
+
+#define ID2_REPLY_DATA &at[111]
+#define ID2_REPLY_DATA_data_type &at[112]
+#define ID2_REPLY_DATA_data_format &at[113]
+#define ID2_REPLY_DATA_data_compression &at[114]
+#define ID2_REPLY_DATA_data &at[115]
+#define ID2_REPLY_DATA_data_E &at[116]
+
+#define ID2_BLOB_SEQ_IDS &at[141]
+#define ID2_BLOB_SEQ_IDS_E &at[142]
+
+#define ID2_BLOB_SEQ_ID &at[143]
+#define ID2_BLOB_SEQ_ID_seq_id &at[144]
+#define ID2_BLOB_SEQ_ID_replaced &at[145]
 
 #define ID2_PARAM &at[12]
 #define ID2_PARAM_name &at[13]
diff --git a/network/id2arch/id2gen.h b/network/id2arch/id2gen.h
index c88e6c92..97df398d 100644
--- a/network/id2arch/id2gen.h
+++ b/network/id2arch/id2gen.h
@@ -17,7 +17,7 @@ extern "C" { /* } */
 /**************************************************
 *
 *    Generated objects for Module NCBI-ID2Access
-*    Generated using ASNCODE Revision: 6.0 at May 3, 2004  6:18 PM
+*    Generated using ASNCODE Revision: 6.0 at Oct 18, 2004  1:24 AM
 *
 **************************************************/
 
@@ -334,6 +334,12 @@ typedef struct struct_ID2_Reply {
    struct struct_ID2_Error PNTR   error;
    Uint1   end_of_reply;
    ValNodePtr   Reply_reply;
+   Uint2   discard;
+   /* following #defines are for enumerated type, not used by object loaders */
+#define ID2_Reply_discard_reply 0
+#define ID2_Reply_discard_last_octet_string 1
+#define ID2_Reply_discard_nothing 2
+
 } ID2Reply, PNTR ID2ReplyPtr;
 
 
@@ -427,6 +433,7 @@ NLM_EXTERN Boolean LIBCALL ID2ReplyGetPackageAsnWrite PROTO (( ID2ReplyGetPackag
 typedef struct struct_ID2_Reply_Get_Seq_id {
    struct struct_ID2_Request_Get_Seq_id PNTR   request;
    ValNodePtr   seq_id;
+   Uint1   end_of_reply;
 } ID2ReplyGetSeqId, PNTR ID2ReplyGetSeqIdPtr;
 
 
@@ -447,6 +454,7 @@ typedef struct struct_ID2_Reply_Get_Blob_Id {
    struct struct_ID2_Blob_Id PNTR   blob_id;
    Int4   split_version;
    struct struct_ID2S_Seq_annot_Info PNTR   annot_info;
+   Uint1   end_of_reply;
 } ID2ReplyGetBlobId, PNTR ID2ReplyGetBlobIdPtr;
 
 
@@ -550,6 +558,14 @@ NLM_EXTERN ID2SReplyGetChunkPtr LIBCALL ID2SReplyGetChunkNew PROTO (( void ));
 NLM_EXTERN ID2SReplyGetChunkPtr LIBCALL ID2SReplyGetChunkAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
 NLM_EXTERN Boolean LIBCALL ID2SReplyGetChunkAsnWrite PROTO (( ID2SReplyGetChunkPtr , AsnIoPtr, AsnTypePtr));
 
+/* following #defines are for enumerated type, not used by object loaders */
+#define ID2_Blob_State_live 0
+#define ID2_Blob_State_suppressed_temp 1
+#define ID2_Blob_State_suppressed 2
+#define ID2_Blob_State_dead 3
+#define ID2_Blob_State_protected__ 4
+#define ID2_Blob_State_withdrawn 5
+
 
 
 /**************************************************
diff --git a/network/id2arch/id2sgen.c b/network/id2arch/id2sgen.c
index c6c866df..00bfba67 100644
--- a/network/id2arch/id2sgen.c
+++ b/network/id2arch/id2sgen.c
@@ -32,7 +32,7 @@ id2sgenAsnLoad(void)
 
 /**************************************************
 *    Generated object loaders for Module NCBI-Seq-split
-*    Generated using ASNCODE Revision: 6.0 at May 3, 2004  6:18 PM
+*    Generated using ASNCODE Revision: 6.0 at Oct 18, 2004  1:24 AM
 *
 **************************************************/
 
@@ -1267,6 +1267,9 @@ ID2SChunkContentFree(ValNodePtr anp)
    case ID2SChunkContent_seq_annot_place:
       ID2SSeqAnnotPlaceInfoFree(anp -> data.ptrvalue);
       break;
+   case ID2SChunkContent_bioseq_place:
+      AsnGenericUserSeqOfFree((Pointer) pnt, (AsnOptFreeFunc) ID2SBioseqPlaceInfoFree);
+      break;
    }
    return MemFree(anp);
 }
@@ -1347,6 +1350,14 @@ ID2SChunkContentAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       choice = ID2SChunkContent_seq_annot_place;
       func = (AsnReadFunc) ID2SSeqAnnotPlaceInfoAsnRead;
    }
+   else if (atp == ID2S_CHUNK_CONTENT_bioseq_place) {
+      choice = ID2SChunkContent_bioseq_place;
+      anp -> data.ptrvalue =
+      AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SBioseqPlaceInfoAsnRead,             (AsnOptFreeFunc) ID2SBioseqPlaceInfoFree);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
    anp->choice = choice;
    if (func != NULL)
    {
@@ -1432,6 +1443,9 @@ ID2SChunkContentAsnWrite(ID2SChunkContentPtr anp, AsnIoPtr aip, AsnTypePtr orig)
       writetype = CHUNK_CONTENT_seq_annot_place;
       func = (AsnWriteFunc) ID2SSeqAnnotPlaceInfoAsnWrite;
       break;
+   case ID2SChunkContent_bioseq_place:
+      retval = AsnGenericUserSeqOfAsnWrite((Pointer) pnt, (AsnWriteFunc) ID2SBioseqPlaceInfoAsnWrite, aip, ID2S_CHUNK_CONTENT_bioseq_place, CHUNK_CONTENT_bioseq_place_E);
+      break;
    }
    if (writetype != NULL) {
       retval = (* func)(pnt, aip, writetype);   /* write it out */
@@ -1476,8 +1490,8 @@ ID2SSeqDescrInfoFree(ID2SSeqDescrInfoPtr ptr)
    if(ptr == NULL) {
       return NULL;
    }
-   AsnGenericUserSeqOfFree(ptr -> bioseqs, (AsnOptFreeFunc) ID2IdRangeFree);
-   AsnGenericUserSeqOfFree(ptr -> bioseq_sets, (AsnOptFreeFunc) ID2IdRangeFree);
+   ID2BioseqIdsFree(ptr -> bioseqs);
+   ID2BioseqSetIdsFree(ptr -> bioseq_sets);
    return MemFree(ptr);
 }
 
@@ -1537,15 +1551,15 @@ ID2SSeqDescrInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == ID2S_SEQ_DESCR_INFO_bioseqs) {
-      ptr -> bioseqs = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2IdRangeAsnRead, (AsnOptFreeFunc) ID2IdRangeFree);
-      if (isError && ptr -> bioseqs == NULL) {
+      ptr -> bioseqs = ID2BioseqIdsAsnRead(aip, atp);
+      if (aip -> io_failure) {
          goto erret;
       }
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == ID2S_SEQ_DESCR_INFO_bioseq_sets) {
-      ptr -> bioseq_sets = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2IdRangeAsnRead, (AsnOptFreeFunc) ID2IdRangeFree);
-      if (isError && ptr -> bioseq_sets == NULL) {
+      ptr -> bioseq_sets = ID2BioseqSetIdsAsnRead(aip, atp);
+      if (aip -> io_failure) {
          goto erret;
       }
       atp = AsnReadId(aip,amp, atp);
@@ -1603,8 +1617,16 @@ ID2SSeqDescrInfoAsnWrite(ID2SSeqDescrInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 
    av.intvalue = ptr -> type_mask;
    retval = AsnWrite(aip, ID2S_SEQ_DESCR_INFO_type_mask,  &av);
-   AsnGenericUserSeqOfAsnWrite(ptr -> bioseqs, (AsnWriteFunc) ID2IdRangeAsnWrite, aip, ID2S_SEQ_DESCR_INFO_bioseqs, ID2S_SEQ_DESCR_INFO_bioseqs_E);
-   AsnGenericUserSeqOfAsnWrite(ptr -> bioseq_sets, (AsnWriteFunc) ID2IdRangeAsnWrite, aip, ID2S_SEQ_DESCR_INFO_bioseq_sets, SEQ_DESCR_INFO_bioseq_sets_E);
+   if (ptr -> bioseqs != NULL) {
+      if ( ! ID2BioseqIdsAsnWrite(ptr -> bioseqs, aip, ID2S_SEQ_DESCR_INFO_bioseqs)) {
+         goto erret;
+      }
+   }
+   if (ptr -> bioseq_sets != NULL) {
+      if ( ! ID2BioseqSetIdsAsnWrite(ptr -> bioseq_sets, aip, ID2S_SEQ_DESCR_INFO_bioseq_sets)) {
+         goto erret;
+      }
+   }
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
@@ -1646,7 +1668,7 @@ ID2SSeqAssemblyInfoFree(ID2SSeqAssemblyInfoPtr ptr)
    if(ptr == NULL) {
       return NULL;
    }
-   AsnGenericUserSeqOfFree(ptr -> bioseqs, (AsnOptFreeFunc) ID2IdRangeFree);
+   ID2BioseqIdsFree(ptr -> bioseqs);
    return MemFree(ptr);
 }
 
@@ -1699,8 +1721,8 @@ ID2SSeqAssemblyInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
    func = NULL;
 
    if (atp == ID2S_SEQ_ASSEMBLY_INFO_bioseqs) {
-      ptr -> bioseqs = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2IdRangeAsnRead, (AsnOptFreeFunc) ID2IdRangeFree);
-      if (isError && ptr -> bioseqs == NULL) {
+      ptr -> bioseqs = ID2BioseqIdsAsnRead(aip, atp);
+      if (aip -> io_failure) {
          goto erret;
       }
       atp = AsnReadId(aip,amp, atp);
@@ -1756,7 +1778,11 @@ ID2SSeqAssemblyInfoAsnWrite(ID2SSeqAssemblyInfoPtr ptr, AsnIoPtr aip, AsnTypePtr
       goto erret;
    }
 
-   AsnGenericUserSeqOfAsnWrite(ptr -> bioseqs, (AsnWriteFunc) ID2IdRangeAsnWrite, aip, ID2S_SEQ_ASSEMBLY_INFO_bioseqs, SEQ_ASSEMBLY_INFO_bioseqs_E);
+   if (ptr -> bioseqs != NULL) {
+      if ( ! ID2BioseqIdsAsnWrite(ptr -> bioseqs, aip, ID2S_SEQ_ASSEMBLY_INFO_bioseqs)) {
+         goto erret;
+      }
+   }
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
@@ -1799,8 +1825,8 @@ ID2SSeqAnnotPlaceInfoFree(ID2SSeqAnnotPlaceInfoPtr ptr)
       return NULL;
    }
    MemFree(ptr -> name);
-   AsnGenericUserSeqOfFree(ptr -> bioseqs, (AsnOptFreeFunc) ID2IdRangeFree);
-   AsnGenericUserSeqOfFree(ptr -> bioseq_sets, (AsnOptFreeFunc) ID2IdRangeFree);
+   ID2BioseqIdsFree(ptr -> bioseqs);
+   ID2BioseqSetIdsFree(ptr -> bioseq_sets);
    return MemFree(ptr);
 }
 
@@ -1860,15 +1886,15 @@ ID2SSeqAnnotPlaceInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == SEQ_ANNOT_PLACE_INFO_bioseqs) {
-      ptr -> bioseqs = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2IdRangeAsnRead, (AsnOptFreeFunc) ID2IdRangeFree);
-      if (isError && ptr -> bioseqs == NULL) {
+      ptr -> bioseqs = ID2BioseqIdsAsnRead(aip, atp);
+      if (aip -> io_failure) {
          goto erret;
       }
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == ANNOT_PLACE_INFO_bioseq_sets) {
-      ptr -> bioseq_sets = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2IdRangeAsnRead, (AsnOptFreeFunc) ID2IdRangeFree);
-      if (isError && ptr -> bioseq_sets == NULL) {
+      ptr -> bioseq_sets = ID2BioseqSetIdsAsnRead(aip, atp);
+      if (aip -> io_failure) {
          goto erret;
       }
       atp = AsnReadId(aip,amp, atp);
@@ -1928,8 +1954,177 @@ ID2SSeqAnnotPlaceInfoAsnWrite(ID2SSeqAnnotPlaceInfoPtr ptr, AsnIoPtr aip, AsnTyp
       av.ptrvalue = ptr -> name;
       retval = AsnWrite(aip, ID2S_SEQ_ANNOT_PLACE_INFO_name,  &av);
    }
-   AsnGenericUserSeqOfAsnWrite(ptr -> bioseqs, (AsnWriteFunc) ID2IdRangeAsnWrite, aip, SEQ_ANNOT_PLACE_INFO_bioseqs, SEQ_ANNOT_PLACE_INFO_bioseqs_E);
-   AsnGenericUserSeqOfAsnWrite(ptr -> bioseq_sets, (AsnWriteFunc) ID2IdRangeAsnWrite, aip, ANNOT_PLACE_INFO_bioseq_sets, ANNOT_PLACE_INFO_bioseq_sets_E);
+   if (ptr -> bioseqs != NULL) {
+      if ( ! ID2BioseqIdsAsnWrite(ptr -> bioseqs, aip, SEQ_ANNOT_PLACE_INFO_bioseqs)) {
+         goto erret;
+      }
+   }
+   if (ptr -> bioseq_sets != NULL) {
+      if ( ! ID2BioseqSetIdsAsnWrite(ptr -> bioseq_sets, aip, ANNOT_PLACE_INFO_bioseq_sets)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2SBioseqPlaceInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SBioseqPlaceInfoPtr LIBCALL
+ID2SBioseqPlaceInfoNew(void)
+{
+   ID2SBioseqPlaceInfoPtr ptr = MemNew((size_t) sizeof(ID2SBioseqPlaceInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SBioseqPlaceInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SBioseqPlaceInfoPtr LIBCALL
+ID2SBioseqPlaceInfoFree(ID2SBioseqPlaceInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericChoiceSeqOfFree(ptr -> seq_ids, (AsnOptFreeFunc) SeqIdFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SBioseqPlaceInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SBioseqPlaceInfoPtr LIBCALL
+ID2SBioseqPlaceInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SBioseqPlaceInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2sgenAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SBioseqPlaceInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_BIOSEQ_PLACE_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID2S_BIOSEQ_PLACE_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SBioseqPlaceInfoNew();
+   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 == BIOSEQ_PLACE_INFO_bioseq_set) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> bioseq_set = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_BIOSEQ_PLACE_INFO_seq_ids) {
+      ptr -> seq_ids = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqIdAsnRead, (AsnOptFreeFunc) SeqIdFree);
+      if (isError && ptr -> seq_ids == 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 = ID2SBioseqPlaceInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SBioseqPlaceInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SBioseqPlaceInfoAsnWrite(ID2SBioseqPlaceInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2sgenAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_BIOSEQ_PLACE_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> bioseq_set;
+   retval = AsnWrite(aip, BIOSEQ_PLACE_INFO_bioseq_set,  &av);
+   AsnGenericChoiceSeqOfAsnWrite(ptr -> seq_ids, (AsnWriteFunc) SeqIdAsnWrite, aip, ID2S_BIOSEQ_PLACE_INFO_seq_ids, BIOSEQ_PLACE_INFO_seq_ids_E);
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
@@ -1944,6 +2139,234 @@ erret:
 
 /**************************************************
 *
+*    ID2BioseqIdsFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2BioseqIdsPtr LIBCALL
+ID2BioseqIdsFree(ID2BioseqIdsPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr,  (AsnOptFreeFunc) ID2IdRangeFree);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    ID2BioseqIdsAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2BioseqIdsPtr LIBCALL
+ID2BioseqIdsAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2BioseqIdsPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2sgenAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2BioseqIds ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_BIOSEQ_IDS);
+   } else {
+      atp = AsnLinkType(orig, ID2_BIOSEQ_IDS);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2IdRangeAsnRead, (AsnOptFreeFunc) ID2IdRangeFree);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2BioseqIdsFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2BioseqIdsAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2BioseqIdsAsnWrite(ID2BioseqIdsPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2sgenAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_BIOSEQ_IDS);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericUserSeqOfAsnWrite(ptr , (AsnWriteFunc) ID2IdRangeAsnWrite, aip, atp, ID2_BIOSEQ_IDS_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID2BioseqSetIdsFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2BioseqSetIdsPtr LIBCALL
+ID2BioseqSetIdsFree(ID2BioseqSetIdsPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericBaseSeqOfFree(ptr,ASNCODE_INTVAL_SLOT);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    ID2BioseqSetIdsAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2BioseqSetIdsPtr LIBCALL
+ID2BioseqSetIdsAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2BioseqSetIdsPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2sgenAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2BioseqSetIds ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2_BIOSEQ_SET_IDS);
+   } else {
+      atp = AsnLinkType(orig, ID2_BIOSEQ_SET_IDS);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_INTVAL_SLOT, &isError);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2BioseqSetIdsFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2BioseqSetIdsAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2BioseqSetIdsAsnWrite(ID2BioseqSetIdsPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2sgenAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2_BIOSEQ_SET_IDS);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr, ASNCODE_INTVAL_SLOT, aip, atp, ID2_BIOSEQ_SET_IDS_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
 *    ID2SFeatTypeInfoNew()
 *
 **************************************************/
@@ -2509,8 +2932,9 @@ ID2SChunkDataFree(ID2SChunkDataPtr ptr)
    AsnGenericChoiceSeqOfFree(ptr -> descrs, (AsnOptFreeFunc) SeqDescrFree);
    AsnGenericUserSeqOfFree(ptr -> annots, (AsnOptFreeFunc) SeqAnnotFree);
    AsnGenericUserSeqOfFree(ptr -> assembly, (AsnOptFreeFunc) SeqAlignFree);
-   AsnGenericUserSeqOfFree(ptr -> seq_map, (AsnOptFreeFunc) SeqLiteralFree);
-   AsnGenericUserSeqOfFree(ptr -> seq_data, (AsnOptFreeFunc) SeqLiteralFree);
+   AsnGenericUserSeqOfFree(ptr -> seq_map, (AsnOptFreeFunc) ID2SSequencePieceFree);
+   AsnGenericUserSeqOfFree(ptr -> seq_data, (AsnOptFreeFunc) ID2SSequencePieceFree);
+   AsnGenericUserSeqOfFree(ptr -> bioseqs, (AsnOptFreeFunc) BioseqFree);
    return MemFree(ptr);
 }
 
@@ -2535,6 +2959,9 @@ Id_idFree(ValNodePtr anp)
    {
    default:
       break;
+   case Id_id_seq_id:
+      SeqIdFree(anp -> data.ptrvalue);
+      break;
    }
    return MemFree(anp);
 }
@@ -2616,19 +3043,26 @@ ID2SChunkDataAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == ID2S_CHUNK_DATA_seq_map) {
-      ptr -> seq_map = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqLiteralAsnRead, (AsnOptFreeFunc) SeqLiteralFree);
+      ptr -> seq_map = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SSequencePieceAsnRead, (AsnOptFreeFunc) ID2SSequencePieceFree);
       if (isError && ptr -> seq_map == NULL) {
          goto erret;
       }
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == ID2S_CHUNK_DATA_seq_data) {
-      ptr -> seq_data = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqLiteralAsnRead, (AsnOptFreeFunc) SeqLiteralFree);
+      ptr -> seq_data = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ID2SSequencePieceAsnRead, (AsnOptFreeFunc) ID2SSequencePieceFree);
       if (isError && ptr -> seq_data == NULL) {
          goto erret;
       }
       atp = AsnReadId(aip,amp, atp);
    }
+   if (atp == ID2S_CHUNK_DATA_bioseqs) {
+      ptr -> bioseqs = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) BioseqAsnRead, (AsnOptFreeFunc) BioseqFree);
+      if (isError && ptr -> bioseqs == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
 
    if (AsnReadVal(aip, atp, &av) <= 0) {
       goto erret;
@@ -2712,6 +3146,10 @@ Id_idAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       }
       anp->data.intvalue = av.intvalue;
    }
+   else if (atp == ID2S_CHUNK_DATA_id_seq_id) {
+      choice = Id_id_seq_id;
+      func = (AsnReadFunc) SeqIdAsnRead;
+   }
    anp->choice = choice;
    if (func != NULL)
    {
@@ -2775,8 +3213,9 @@ ID2SChunkDataAsnWrite(ID2SChunkDataPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
    AsnGenericChoiceSeqOfAsnWrite(ptr -> descrs, (AsnWriteFunc) SeqDescrAsnWrite, aip, ID2S_CHUNK_DATA_descrs, ID2S_CHUNK_DATA_descrs_E);
    AsnGenericUserSeqOfAsnWrite(ptr -> annots, (AsnWriteFunc) SeqAnnotAsnWrite, aip, ID2S_CHUNK_DATA_annots, ID2S_CHUNK_DATA_annots_E);
    AsnGenericUserSeqOfAsnWrite(ptr -> assembly, (AsnWriteFunc) SeqAlignAsnWrite, aip, ID2S_CHUNK_DATA_assembly, ID2S_CHUNK_DATA_assembly_E);
-   AsnGenericUserSeqOfAsnWrite(ptr -> seq_map, (AsnWriteFunc) SeqLiteralAsnWrite, aip, ID2S_CHUNK_DATA_seq_map, ID2S_CHUNK_DATA_seq_map_E);
-   AsnGenericUserSeqOfAsnWrite(ptr -> seq_data, (AsnWriteFunc) SeqLiteralAsnWrite, aip, ID2S_CHUNK_DATA_seq_data, ID2S_CHUNK_DATA_seq_data_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> seq_map, (AsnWriteFunc) ID2SSequencePieceAsnWrite, aip, ID2S_CHUNK_DATA_seq_map, ID2S_CHUNK_DATA_seq_map_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> seq_data, (AsnWriteFunc) ID2SSequencePieceAsnWrite, aip, ID2S_CHUNK_DATA_seq_data, ID2S_CHUNK_DATA_seq_data_E);
+   AsnGenericUserSeqOfAsnWrite(ptr -> bioseqs, (AsnWriteFunc) BioseqAsnWrite, aip, ID2S_CHUNK_DATA_bioseqs, ID2S_CHUNK_DATA_bioseqs_E);
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
@@ -2836,6 +3275,10 @@ Id_idAsnWrite(Id_idPtr anp, AsnIoPtr aip, AsnTypePtr orig)
       av.intvalue = anp->data.intvalue;
       retval = AsnWrite(aip, ID2S_CHUNK_DATA_id_gi, &av);
       break;
+   case Id_id_seq_id:
+      writetype = ID2S_CHUNK_DATA_id_seq_id;
+      func = (AsnWriteFunc) SeqIdAsnWrite;
+      break;
    }
    if (writetype != NULL) {
       retval = (* func)(pnt, aip, writetype);   /* write it out */
@@ -2853,6 +3296,167 @@ erret:
 
 /**************************************************
 *
+*    ID2SSequencePieceNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSequencePiecePtr LIBCALL
+ID2SSequencePieceNew(void)
+{
+   ID2SSequencePiecePtr ptr = MemNew((size_t) sizeof(ID2SSequencePiece));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID2SSequencePieceFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSequencePiecePtr LIBCALL
+ID2SSequencePieceFree(ID2SSequencePiecePtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr -> data, (AsnOptFreeFunc) SeqLiteralFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID2SSequencePieceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID2SSequencePiecePtr LIBCALL
+ID2SSequencePieceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID2SSequencePiecePtr ptr;
+
+   if (! loaded)
+   {
+      if (! id2sgenAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID2SSequencePiece ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID2S_SEQUENCE_PIECE);
+   } else {
+      atp = AsnLinkType(orig, ID2S_SEQUENCE_PIECE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID2SSequencePieceNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == ID2S_SEQUENCE_PIECE_start) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> start = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID2S_SEQUENCE_PIECE_data) {
+      ptr -> data = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqLiteralAsnRead, (AsnOptFreeFunc) SeqLiteralFree);
+      if (isError && ptr -> data == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID2SSequencePieceFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID2SSequencePieceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID2SSequencePieceAsnWrite(ID2SSequencePiecePtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id2sgenAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID2S_SEQUENCE_PIECE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> start;
+   retval = AsnWrite(aip, ID2S_SEQUENCE_PIECE_start,  &av);
+   AsnGenericUserSeqOfAsnWrite(ptr -> data, (AsnWriteFunc) SeqLiteralAsnWrite, aip, ID2S_SEQUENCE_PIECE_data, ID2S_SEQUENCE_PIECE_data_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
 *    ID2IntervalNew()
 *
 **************************************************/
diff --git a/network/id2arch/id2sgen.h b/network/id2arch/id2sgen.h
index 77c3d001..dd043526 100644
--- a/network/id2arch/id2sgen.h
+++ b/network/id2arch/id2sgen.h
@@ -17,7 +17,7 @@ extern "C" { /* } */
 /**************************************************
 *
 *    Generated objects for Module NCBI-Seq-split
-*    Generated using ASNCODE Revision: 6.0 at May 3, 2004  6:18 PM
+*    Generated using ASNCODE Revision: 6.0 at Oct 18, 2004  1:24 AM
 *
 **************************************************/
 
@@ -165,6 +165,7 @@ typedef ValNode ID2SChunkContent;
 #define ID2SChunkContent_seq_map 4
 #define ID2SChunkContent_seq_data 5
 #define ID2SChunkContent_seq_annot_place 6
+#define ID2SChunkContent_bioseq_place 7
 
 
 NLM_EXTERN ID2SChunkContentPtr LIBCALL ID2SChunkContentFree PROTO ((ID2SChunkContentPtr ));
@@ -181,7 +182,7 @@ NLM_EXTERN Boolean LIBCALL ID2SChunkContentAsnWrite PROTO (( ID2SChunkContentPtr
 typedef struct struct_ID2S_Seq_descr_Info {
    Int4   type_mask;
    struct struct_ID2_Id_Range PNTR   bioseqs;
-   struct struct_ID2_Id_Range PNTR   bioseq_sets;
+   ValNodePtr   bioseq_sets;
 } ID2SSeqDescrInfo, PNTR ID2SSeqDescrInfoPtr;
 
 
@@ -243,7 +244,7 @@ NLM_EXTERN Boolean LIBCALL ID2SSeqAssemblyInfoAsnWrite PROTO (( ID2SSeqAssemblyI
 typedef struct struct_ID2S_Seq_annot_place_Info {
    CharPtr   name;
    struct struct_ID2_Id_Range PNTR   bioseqs;
-   struct struct_ID2_Id_Range PNTR   bioseq_sets;
+   ValNodePtr   bioseq_sets;
 } ID2SSeqAnnotPlaceInfo, PNTR ID2SSeqAnnotPlaceInfoPtr;
 
 
@@ -256,6 +257,65 @@ NLM_EXTERN Boolean LIBCALL ID2SSeqAnnotPlaceInfoAsnWrite PROTO (( ID2SSeqAnnotPl
 
 /**************************************************
 *
+*    ID2SBioseqPlaceInfo
+*
+**************************************************/
+typedef struct struct_ID2S_Bioseq_place_Info {
+   struct struct_ID2S_Bioseq_place_Info PNTR next;
+   Int4   bioseq_set;
+   ValNodePtr   seq_ids;
+} ID2SBioseqPlaceInfo, PNTR ID2SBioseqPlaceInfoPtr;
+
+
+NLM_EXTERN ID2SBioseqPlaceInfoPtr LIBCALL ID2SBioseqPlaceInfoFree PROTO ((ID2SBioseqPlaceInfoPtr ));
+NLM_EXTERN ID2SBioseqPlaceInfoPtr LIBCALL ID2SBioseqPlaceInfoNew PROTO (( void ));
+NLM_EXTERN ID2SBioseqPlaceInfoPtr LIBCALL ID2SBioseqPlaceInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SBioseqPlaceInfoAsnWrite PROTO (( ID2SBioseqPlaceInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID2BioseqIds
+*
+**************************************************/
+typedef struct struct_ID2IdRange ID2BioseqIds;
+typedef struct struct_ID2IdRange PNTR ID2BioseqIdsPtr;
+#define ID2BioseqIdsNew() ID2IdRangeNew() 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN ID2BioseqIdsPtr LIBCALL ID2BioseqIdsFree PROTO ((ID2BioseqIdsPtr ));
+NLM_EXTERN ID2BioseqIdsPtr LIBCALL ID2BioseqIdsNew PROTO (( void ));
+NLM_EXTERN ID2BioseqIdsPtr LIBCALL ID2BioseqIdsAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2BioseqIdsAsnWrite PROTO (( ID2BioseqIdsPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    ID2BioseqSetIds
+*
+**************************************************/
+typedef ValNode ID2BioseqSetIds;
+typedef ValNodePtr ID2BioseqSetIdsPtr;
+#define ID2BioseqSetIdsNew() ValNodeNew(NULL) 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN ID2BioseqSetIdsPtr LIBCALL ID2BioseqSetIdsFree PROTO ((ID2BioseqSetIdsPtr ));
+NLM_EXTERN ID2BioseqSetIdsPtr LIBCALL ID2BioseqSetIdsNew PROTO (( void ));
+NLM_EXTERN ID2BioseqSetIdsPtr LIBCALL ID2BioseqSetIdsAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2BioseqSetIdsAsnWrite PROTO (( ID2BioseqSetIdsPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
 *    ID2SFeatTypeInfo
 *
 **************************************************/
@@ -315,8 +375,9 @@ typedef struct struct_ID2S_Chunk_Data {
    ValNodePtr   descrs;
    struct struct_Seq_annot PNTR   annots;
    struct struct_Seq_align PNTR   assembly;
-   struct struct_Seq_literal PNTR   seq_map;
-   struct struct_Seq_literal PNTR   seq_data;
+   struct struct_ID2S_Sequence_Piece PNTR   seq_map;
+   struct struct_ID2S_Sequence_Piece PNTR   seq_data;
+   struct struct_Bioseq PNTR   bioseqs;
 } ID2SChunkData, PNTR ID2SChunkDataPtr;
 
 
@@ -335,6 +396,7 @@ typedef ValNode Id_id;
 
 #define Id_id_bioseq_set 1
 #define Id_id_gi 2
+#define Id_id_seq_id 3
 
 #ifdef NLM_GENERATED_CODE_PROTO
 
@@ -348,6 +410,25 @@ static Boolean LIBCALL Id_idAsnWrite PROTO (( Id_idPtr , AsnIoPtr, AsnTypePtr));
 
 /**************************************************
 *
+*    ID2SSequencePiece
+*
+**************************************************/
+typedef struct struct_ID2S_Sequence_Piece {
+   struct struct_ID2S_Sequence_Piece PNTR next;
+   Int4   start;
+   struct struct_Seq_literal PNTR   data;
+} ID2SSequencePiece, PNTR ID2SSequencePiecePtr;
+
+
+NLM_EXTERN ID2SSequencePiecePtr LIBCALL ID2SSequencePieceFree PROTO ((ID2SSequencePiecePtr ));
+NLM_EXTERN ID2SSequencePiecePtr LIBCALL ID2SSequencePieceNew PROTO (( void ));
+NLM_EXTERN ID2SSequencePiecePtr LIBCALL ID2SSequencePieceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID2SSequencePieceAsnWrite PROTO (( ID2SSequencePiecePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
 *    ID2Interval
 *
 **************************************************/
diff --git a/network/id2arch/seqsplit.asn b/network/id2arch/seqsplit.asn
index 0b047a7e..451170c8 100644
--- a/network/id2arch/seqsplit.asn
+++ b/network/id2arch/seqsplit.asn
@@ -1,4 +1,4 @@
---$Revision: 1.4 $
+--$Revision: 1.6 $
 --********************************************************************
 --
 --  Network Id server network access
@@ -7,9 +7,9 @@
 --
 --*********************************************************************
 --
---  ID2.asn
+--  seqsplit.asn
 --
---     messages for id server network access
+--     representation of split sequences
 --
 --*********************************************************************
 
@@ -18,14 +18,17 @@ BEGIN
 
 EXPORTS ID2S-Chunk-Id, ID2S-Seq-annot-Info;
 
-IMPORTS Seq-loc                                 FROM NCBI-Seqloc
-        Seq-annot, Seq-descr, Seq-literal       FROM NCBI-Sequence
-        Seq-align                               FROM NCBI-Seqalign;
+IMPORTS Seq-id                                      FROM NCBI-Seqloc
+        Bioseq, Seq-annot, Seq-descr, Seq-literal   FROM NCBI-Sequence
+        Seq-align                                   FROM NCBI-Seqalign;
 
 ----------------------------------------------------------------------------
 -- Blob split info types
 ----------------------------------------------------------------------------
 
+----------------------------------------------------------------------------
+-- Chunks split description
+
 
 ID2S-Split-Info ::= SEQUENCE {
         bioseqs-info    SET OF ID2S-Bioseqs-Info OPTIONAL,
@@ -35,21 +38,13 @@ ID2S-Split-Info ::= SEQUENCE {
 
 ID2S-Bioseqs-Info ::= SEQUENCE {
         info            ID2S-Bioseq-Info,
-        bioseqs         ID2-Id-Range
+        bioseqs         ID2S-Bioseq-Ids
 }
 
 
 ID2S-Bioseq-Info ::= SEQUENCE {
         gap-count       INTEGER OPTIONAL,
-        seq-map-has-ref BOOLEAN OPTIONAL,
-        sequence-split  ID2S-Sequence-Split-Info OPTIONAL
-}
-
-
-ID2S-Sequence-Split-Info ::= SEQUENCE {
-        block-size      INTEGER,
-        chunk-start     ID2S-Chunk-Id,
-        chunk-blocks    SEQUENCE OF INTEGER
+        seq-map-has-ref BOOLEAN OPTIONAL
 }
 
 
@@ -59,20 +54,36 @@ ID2S-Chunk-Info ::= SEQUENCE {
 }
 
 
+-- Description of information in this chunk
+-- Place means id of Bioseq or Bioseq-set
 ID2S-Chunk-Content ::= CHOICE {
+        -- place of Seq-descrs
         seq-descr       ID2S-Seq-descr-Info,
+
+        -- locations and types of annotations
         seq-annot       ID2S-Seq-annot-Info,
+
+        -- place of assembly history
         seq-assembly    ID2S-Seq-assembly-Info,
+
+        -- place of sequence map
         seq-map         ID2S-Seq-map-Info,
+        
+        -- place of sequence data
         seq-data        ID2S-Seq-data-Info,
-        seq-annot-place ID2S-Seq-annot-place-Info
+
+        -- place of Seq-annots
+        seq-annot-place ID2S-Seq-annot-place-Info,
+
+        -- place of Bioseqs
+        bioseq-place    SET OF ID2S-Bioseq-place-Info
 }
 
 
 ID2S-Seq-descr-Info ::= SEQUENCE {
         type-mask       INTEGER, -- mask of Seq-descr types,
-        bioseqs         SET OF ID2-Id-Range OPTIONAL,
-        bioseq-sets     SET OF ID2-Id-Range OPTIONAL
+        bioseqs         ID2S-Bioseq-Ids OPTIONAL,
+        bioseq-sets     ID2S-Bioseq-set-Ids OPTIONAL
 }
 
 
@@ -83,14 +94,14 @@ ID2S-Seq-annot-Info ::= SEQUENCE {
         align           NULL OPTIONAL,
         graph           NULL OPTIONAL,
         feat            SET OF ID2S-Feat-type-Info OPTIONAL,
-        seq-loc         ID2-Seq-loc OPTIONAL
+        seq-loc         ID2S-Seq-loc OPTIONAL
 }
 
 
 ID2S-Seq-annot-place-Info ::= SEQUENCE {
         name            VisibleString OPTIONAL,
-        bioseqs         SET OF ID2-Id-Range OPTIONAL,
-        bioseq-sets     SET OF ID2-Id-Range OPTIONAL
+        bioseqs         ID2S-Bioseq-Ids OPTIONAL,
+        bioseq-sets     ID2S-Bioseq-set-Ids OPTIONAL
 }
 
 
@@ -101,14 +112,20 @@ ID2S-Feat-type-Info ::=  SEQUENCE {
 
 
 ID2S-Seq-assembly-Info ::= SEQUENCE {
-        bioseqs         SET OF ID2-Id-Range
+        bioseqs         ID2S-Bioseq-Ids
 }
 
 
-ID2S-Seq-map-Info ::= ID2-Seq-loc
+ID2S-Seq-map-Info ::= ID2S-Seq-loc
 
 
-ID2S-Seq-data-Info ::= ID2-Seq-loc
+ID2S-Seq-data-Info ::= ID2S-Seq-loc
+
+
+ID2S-Bioseq-place-Info ::= SEQUENCE {
+        bioseq-set      INTEGER,
+        seq-ids         ID2S-Bioseq-Ids
+}
 
 
 ID2S-Chunk ::= SEQUENCE {
@@ -117,15 +134,27 @@ ID2S-Chunk ::= SEQUENCE {
 
 
 ID2S-Chunk-Data ::= SEQUENCE {
+        -- place of data to insert
         id              CHOICE {
+                -- Bioseq-set id
                 bioseq-set      INTEGER,
-                gi              INTEGER
+                -- Bioseq id
+                gi              INTEGER,
+                -- Bioseq id
+                seq-id          Seq-id
         },
-        descrs          SET OF Seq-descr OPTIONAL,
+        -- Seq-descr, for Bioseq and Bioseq-set
+        descr           Seq-descr OPTIONAL,
+        -- Seq-annot, for Bioseq and Bioseq-set
         annots          SET OF Seq-annot OPTIONAL,
+        -- assembly history Seq-align, for Bioseq
         assembly        SET OF Seq-align OPTIONAL,
+        -- sequence map, for Bioseq
         seq-map         SEQUENCE OF ID2S-Sequence-Piece OPTIONAL,
-        seq-data        SEQUENCE OF ID2S-Sequence-Piece OPTIONAL
+        -- sequence data, for Bioseq
+        seq-data        SEQUENCE OF ID2S-Sequence-Piece OPTIONAL,
+        -- Bioseq, for Bioseq-set
+        bioseqs         SET OF Bioseq OPTIONAL
 }
 
 
@@ -143,38 +172,70 @@ ID2S-Sequence-Piece ::= SEQUENCE {
 ID2S-Chunk-Id ::= INTEGER
 
 
-ID2-Id-Range ::= SEQUENCE {
-        start           INTEGER,  -- gi for Bioseq, local id for Bioseq-set
-        count           INTEGER DEFAULT 1
+ID2S-Bioseq-set-Ids ::= SET OF INTEGER
+
+
+ID2S-Bioseq-Ids ::= SET OF CHOICE {
+        gi              INTEGER,
+        seq-id          Seq-id,
+        gi-range        ID2S-Gi-Range
 }
 
 
-ID2-Seq-loc ::= CHOICE {
-        gi-whole        INTEGER,
-        interval        ID2-Interval,
-        packed-ints     ID2-Packed-Seq-ints,
-        gi-whole-range  ID2-Id-Range,
-        loc-set         SET OF ID2-Seq-loc,
-        seq-loc         Seq-loc
+ID2S-Gi-Range ::= SEQUENCE {
+        start           INTEGER,             -- start gi in this gi range
+        count           INTEGER DEFAULT 1    -- number of sequential gis
 }
 
 
-ID2-Interval ::= SEQUENCE {
+-- ID2S-Seq-loc is used to represent unordered and unstranded
+-- set of intervals on set of sequences.
+-- It's optimized for compact encoding of several common cases:
+--    Seq-ids of type gi,
+--    intervals covering whole sequences,
+--    whole sequences with sequential gis,
+--    set of intervals on the same sequence (Seq-id sharing).
+ID2S-Seq-loc ::= CHOICE {
+        whole-gi        INTEGER,             -- whole sequence by gi
+        whole-seq-id    Seq-id,              -- whole sequence by Seq-id
+        whole-gi-range  ID2S-Gi-Range,       -- set of whole sequences by gis
+        gi-interval     ID2S-Gi-Interval,    -- interval on sequence by gi
+        seq-id-interval ID2S-Seq-id-Interval,-- interval on sequence by Seq-id
+        gi-ints         ID2S-Gi-Ints,        -- set of intervals on the same gi
+        seq-id-ints     ID2S-Seq-id-Ints,    -- set of intervals on the same id
+        loc-set         SET OF ID2S-Seq-loc  -- combination of locations
+}
+
+
+ID2S-Gi-Interval ::= SEQUENCE {
         gi              INTEGER,
         start           INTEGER,
         length          INTEGER DEFAULT 1
 }
 
 
-ID2-Seq-range ::= SEQUENCE {
+ID2S-Seq-id-Interval ::= SEQUENCE {
+        seq-id          Seq-id,
         start           INTEGER,
         length          INTEGER DEFAULT 1
 }
 
 
-ID2-Packed-Seq-ints ::= SEQUENCE {
+ID2S-Interval ::= SEQUENCE {
+        start           INTEGER,
+        length          INTEGER DEFAULT 1
+}
+
+
+ID2S-Gi-Ints ::= SEQUENCE {
         gi              INTEGER,
-        intervals       SET OF ID2-Seq-range
+        ints            SET OF ID2S-Interval
+}
+
+
+ID2S-Seq-id-Ints ::= SEQUENCE {
+        seq-id          Seq-id,
+        ints            SET OF ID2S-Interval
 }
 
 
diff --git a/network/id2arch/seqsplit.h b/network/id2arch/seqsplit.h
index 1a6dbde2..f68d3b98 100644
--- a/network/id2arch/seqsplit.h
+++ b/network/id2arch/seqsplit.h
@@ -9,16 +9,16 @@
 #include <asn.h>
 #endif
 
-static char * asnfilename = "seqsplit.h13";
+static char * asnfilename = "seqsplit.h15";
 static AsnValxNode avnx[3] = {
     {3,NULL,1,0.0,NULL } ,
     {3,NULL,1,0.0,NULL } ,
     {3,NULL,1,0.0,NULL } };
 
-static AsnType atx[109] = {
+static AsnType atx[123] = {
   {401, "ID2S-Chunk-Id" ,1,0,0,0,0,1,0,0,NULL,&atx[1],NULL,0,&atx[2]} ,
   {302, "INTEGER" ,0,2,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {402, "ID2S-Seq-annot-Info" ,1,0,0,0,0,1,0,0,NULL,&atx[15],&atx[3],0,&atx[39]} ,
+  {402, "ID2S-Seq-annot-Info" ,1,0,0,0,0,1,0,0,NULL,&atx[15],&atx[3],0,&atx[41]} ,
   {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[4],NULL,0,&atx[5]} ,
   {323, "VisibleString" ,0,26,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "align" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[7]} ,
@@ -26,108 +26,122 @@ static AsnType atx[109] = {
   {0, "graph" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[8]} ,
   {0, "feat" ,128,3,0,1,0,0,0,0,NULL,&atx[14],&atx[9],0,&atx[16]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[10],NULL,0,NULL} ,
-  {420, "ID2S-Feat-type-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[11],0,&atx[17]} ,
+  {425, "ID2S-Feat-type-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[11],0,&atx[17]} ,
   {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[12]} ,
   {0, "subtypes" ,128,1,0,1,0,0,0,0,NULL,&atx[14],&atx[13],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1],NULL,0,NULL} ,
   {314, "SET OF" ,0,17,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {311, "SEQUENCE" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "seq-loc" ,128,4,0,1,0,0,0,0,NULL,&atx[17],NULL,0,NULL} ,
-  {421, "ID2-Seq-loc" ,1,0,0,0,0,0,0,0,NULL,&atx[40],&atx[18],0,&atx[92]} ,
+  {426, "ID2-Seq-loc" ,1,0,0,0,0,0,0,0,NULL,&atx[40],&atx[18],0,&atx[99]} ,
   {0, "gi-whole" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[19]} ,
   {0, "interval" ,128,1,0,0,0,0,0,0,NULL,&atx[20],NULL,0,&atx[24]} ,
-  {424, "ID2-Interval" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[21],0,&atx[25]} ,
+  {430, "ID2-Interval" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[21],0,&atx[25]} ,
   {0, "gi" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[22]} ,
   {0, "start" ,128,1,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[23]} ,
   {0, "length" ,128,2,0,0,1,0,0,0,&avnx[0],&atx[1],NULL,0,NULL} ,
   {0, "packed-ints" ,128,2,0,0,0,0,0,0,NULL,&atx[25],NULL,0,&atx[32]} ,
-  {425, "ID2-Packed-Seq-ints" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[26],0,&atx[29]} ,
+  {431, "ID2-Packed-Seq-ints" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[26],0,&atx[29]} ,
   {0, "gi" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[27]} ,
   {0, "intervals" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[28],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[29],NULL,0,NULL} ,
-  {426, "ID2-Seq-range" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[30],0,NULL} ,
+  {432, "ID2-Seq-range" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[30],0,NULL} ,
   {0, "start" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[31]} ,
   {0, "length" ,128,1,0,0,1,0,0,0,&avnx[1],&atx[1],NULL,0,NULL} ,
   {0, "gi-whole-range" ,128,3,0,0,0,0,0,0,NULL,&atx[33],NULL,0,&atx[36]} ,
-  {412, "ID2-Id-Range" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[34],0,&atx[55]} ,
+  {414, "ID2-Id-Range" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[34],0,&atx[57]} ,
   {0, "start" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[35]} ,
   {0, "count" ,128,1,0,0,1,0,0,0,&avnx[2],&atx[1],NULL,0,NULL} ,
   {0, "loc-set" ,128,4,0,0,0,0,0,0,NULL,&atx[14],&atx[37],0,&atx[38]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[17],NULL,0,NULL} ,
   {0, "seq-loc" ,128,5,0,0,0,0,0,0,NULL,&atx[39],NULL,0,NULL} ,
-  {403, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[41]} ,
+  {404, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[42]} ,
   {315, "CHOICE" ,0,-1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {404, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[42]} ,
-  {405, "Seq-descr" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[43]} ,
-  {406, "Seq-literal" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[44]} ,
-  {407, "Seq-align" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[45]} ,
-  {408, "ID2S-Split-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[46],0,&atx[48]} ,
-  {0, "bioseqs-info" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[47],0,&atx[62]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[48],NULL,0,NULL} ,
-  {409, "ID2S-Bioseqs-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[49],0,&atx[64]} ,
-  {0, "info" ,128,0,0,0,0,0,0,0,NULL,&atx[50],NULL,0,&atx[61]} ,
-  {411, "ID2S-Bioseq-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[51],0,&atx[33]} ,
-  {0, "gap-count" ,128,0,0,1,0,0,0,0,NULL,&atx[1],NULL,0,&atx[52]} ,
-  {0, "seq-map-has-ref" ,128,1,0,1,0,0,0,0,NULL,&atx[53],NULL,0,&atx[54]} ,
+  {403, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[39]} ,
+  {405, "Bioseq" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[43]} ,
+  {406, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[44]} ,
+  {407, "Seq-descr" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[45]} ,
+  {408, "Seq-literal" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[46]} ,
+  {409, "Seq-align" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[47]} ,
+  {410, "ID2S-Split-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[48],0,&atx[50]} ,
+  {0, "bioseqs-info" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[49],0,&atx[64]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[50],NULL,0,NULL} ,
+  {411, "ID2S-Bioseqs-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[51],0,&atx[66]} ,
+  {0, "info" ,128,0,0,0,0,0,0,0,NULL,&atx[52],NULL,0,&atx[63]} ,
+  {413, "ID2S-Bioseq-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[53],0,&atx[33]} ,
+  {0, "gap-count" ,128,0,0,1,0,0,0,0,NULL,&atx[1],NULL,0,&atx[54]} ,
+  {0, "seq-map-has-ref" ,128,1,0,1,0,0,0,0,NULL,&atx[55],NULL,0,&atx[56]} ,
   {301, "BOOLEAN" ,0,1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {0, "sequence-split" ,128,2,0,1,0,0,0,0,NULL,&atx[55],NULL,0,NULL} ,
-  {413, "ID2S-Sequence-Split-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[56],0,&atx[68]} ,
-  {0, "block-size" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[57]} ,
-  {0, "chunk-start" ,128,1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[58]} ,
-  {0, "chunk-blocks" ,128,2,0,0,0,0,0,0,NULL,&atx[60],&atx[59],0,NULL} ,
+  {0, "sequence-split" ,128,2,0,1,0,0,0,0,NULL,&atx[57],NULL,0,NULL} ,
+  {415, "ID2S-Sequence-Split-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[58],0,&atx[70]} ,
+  {0, "block-size" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[59]} ,
+  {0, "chunk-start" ,128,1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[60]} ,
+  {0, "chunk-blocks" ,128,2,0,0,0,0,0,0,NULL,&atx[62],&atx[61],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1],NULL,0,NULL} ,
   {312, "SEQUENCE OF" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "bioseqs" ,128,1,0,0,0,0,0,0,NULL,&atx[33],NULL,0,NULL} ,
-  {0, "chunks" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[63],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[64],NULL,0,NULL} ,
-  {410, "ID2S-Chunk-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[65],0,&atx[50]} ,
-  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[66]} ,
-  {0, "content" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[67],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[68],NULL,0,NULL} ,
-  {414, "ID2S-Chunk-Content" ,1,0,0,0,0,0,0,0,NULL,&atx[40],&atx[69],0,&atx[70]} ,
-  {0, "seq-descr" ,128,0,0,0,0,0,0,0,NULL,&atx[70],NULL,0,&atx[76]} ,
-  {415, "ID2S-Seq-descr-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[71],0,&atx[78]} ,
-  {0, "type-mask" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[72]} ,
-  {0, "bioseqs" ,128,1,0,1,0,0,0,0,NULL,&atx[14],&atx[73],0,&atx[74]} ,
+  {0, "chunks" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[65],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[66],NULL,0,NULL} ,
+  {412, "ID2S-Chunk-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[67],0,&atx[52]} ,
+  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[68]} ,
+  {0, "content" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[69],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[70],NULL,0,NULL} ,
+  {416, "ID2S-Chunk-Content" ,1,0,0,0,0,0,0,0,NULL,&atx[40],&atx[71],0,&atx[72]} ,
+  {0, "seq-descr" ,128,0,0,0,0,0,0,0,NULL,&atx[72],NULL,0,&atx[80]} ,
+  {417, "ID2S-Seq-descr-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[73],0,&atx[82]} ,
+  {0, "type-mask" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[74]} ,
+  {0, "bioseqs" ,128,1,0,1,0,0,0,0,NULL,&atx[75],NULL,0,&atx[77]} ,
+  {423, "ID2-Bioseq-Ids" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[76],0,&atx[78]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[33],NULL,0,NULL} ,
-  {0, "bioseq-sets" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[75],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[33],NULL,0,NULL} ,
-  {0, "seq-annot" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[77]} ,
-  {0, "seq-assembly" ,128,2,0,0,0,0,0,0,NULL,&atx[78],NULL,0,&atx[81]} ,
-  {416, "ID2S-Seq-assembly-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[79],0,&atx[82]} ,
-  {0, "bioseqs" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[80],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[33],NULL,0,NULL} ,
-  {0, "seq-map" ,128,3,0,0,0,0,0,0,NULL,&atx[82],NULL,0,&atx[83]} ,
-  {417, "ID2S-Seq-map-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[17],NULL,0,&atx[84]} ,
-  {0, "seq-data" ,128,4,0,0,0,0,0,0,NULL,&atx[84],NULL,0,&atx[85]} ,
-  {418, "ID2S-Seq-data-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[17],NULL,0,&atx[86]} ,
-  {0, "seq-annot-place" ,128,5,0,0,0,0,0,0,NULL,&atx[86],NULL,0,NULL} ,
-  {419, "ID2S-Seq-annot-place-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[87],0,&atx[10]} ,
-  {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[4],NULL,0,&atx[88]} ,
-  {0, "bioseqs" ,128,1,0,1,0,0,0,0,NULL,&atx[14],&atx[89],0,&atx[90]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[33],NULL,0,NULL} ,
-  {0, "bioseq-sets" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[91],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[33],NULL,0,NULL} ,
-  {422, "ID2S-Chunk" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[93],0,&atx[95]} ,
-  {0, "data" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[94],0,NULL} ,
+  {0, "bioseq-sets" ,128,2,0,1,0,0,0,0,NULL,&atx[78],NULL,0,NULL} ,
+  {424, "ID2-Bioseq-set-Ids" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[79],0,&atx[10]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1],NULL,0,NULL} ,
+  {0, "seq-annot" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[81]} ,
+  {0, "seq-assembly" ,128,2,0,0,0,0,0,0,NULL,&atx[82],NULL,0,&atx[84]} ,
+  {418, "ID2S-Seq-assembly-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[83],0,&atx[85]} ,
+  {0, "bioseqs" ,128,0,0,0,0,0,0,0,NULL,&atx[75],NULL,0,NULL} ,
+  {0, "seq-map" ,128,3,0,0,0,0,0,0,NULL,&atx[85],NULL,0,&atx[86]} ,
+  {419, "ID2S-Seq-map-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[17],NULL,0,&atx[87]} ,
+  {0, "seq-data" ,128,4,0,0,0,0,0,0,NULL,&atx[87],NULL,0,&atx[88]} ,
+  {420, "ID2S-Seq-data-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[17],NULL,0,&atx[89]} ,
+  {0, "seq-annot-place" ,128,5,0,0,0,0,0,0,NULL,&atx[89],NULL,0,&atx[93]} ,
+  {421, "ID2S-Seq-annot-place-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[90],0,&atx[95]} ,
+  {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[4],NULL,0,&atx[91]} ,
+  {0, "bioseqs" ,128,1,0,1,0,0,0,0,NULL,&atx[75],NULL,0,&atx[92]} ,
+  {0, "bioseq-sets" ,128,2,0,1,0,0,0,0,NULL,&atx[78],NULL,0,NULL} ,
+  {0, "bioseq-place" ,128,6,0,0,0,0,0,0,NULL,&atx[14],&atx[94],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[95],NULL,0,NULL} ,
-  {423, "ID2S-Chunk-Data" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[96],0,&atx[20]} ,
-  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[40],&atx[97],0,&atx[99]} ,
-  {0, "bioseq-set" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[98]} ,
-  {0, "gi" ,128,1,0,0,0,0,0,0,NULL,&atx[1],NULL,0,NULL} ,
-  {0, "descrs" ,128,1,0,1,0,0,0,0,NULL,&atx[14],&atx[100],0,&atx[101]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[42],NULL,0,NULL} ,
-  {0, "annots" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[102],0,&atx[103]} ,
+  {422, "ID2S-Bioseq-place-Info" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[96],0,&atx[75]} ,
+  {0, "bioseq-set" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[97]} ,
+  {0, "seq-ids" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[98],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[41],NULL,0,NULL} ,
-  {0, "assembly" ,128,3,0,1,0,0,0,0,NULL,&atx[14],&atx[104],0,&atx[105]} ,
+  {427, "ID2S-Chunk" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[100],0,&atx[102]} ,
+  {0, "data" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[101],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[102],NULL,0,NULL} ,
+  {428, "ID2S-Chunk-Data" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[103],0,&atx[115]} ,
+  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[40],&atx[104],0,&atx[107]} ,
+  {0, "bioseq-set" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[105]} ,
+  {0, "gi" ,128,1,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[106]} ,
+  {0, "seq-id" ,128,2,0,0,0,0,0,0,NULL,&atx[41],NULL,0,NULL} ,
+  {0, "descrs" ,128,1,0,1,0,0,0,0,NULL,&atx[14],&atx[108],0,&atx[109]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[44],NULL,0,NULL} ,
-  {0, "seq-map" ,128,4,0,1,0,0,0,0,NULL,&atx[60],&atx[106],0,&atx[107]} ,
+  {0, "annots" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[110],0,&atx[111]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[43],NULL,0,NULL} ,
-  {0, "seq-data" ,128,5,0,1,0,0,0,0,NULL,&atx[60],&atx[108],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[43],NULL,0,NULL} };
+  {0, "assembly" ,128,3,0,1,0,0,0,0,NULL,&atx[14],&atx[112],0,&atx[113]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[46],NULL,0,NULL} ,
+  {0, "seq-map" ,128,4,0,1,0,0,0,0,NULL,&atx[62],&atx[114],0,&atx[119]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[115],NULL,0,NULL} ,
+  {429, "ID2S-Sequence-Piece" ,1,0,0,0,0,0,0,0,NULL,&atx[15],&atx[116],0,&atx[20]} ,
+  {0, "start" ,128,0,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[117]} ,
+  {0, "data" ,128,1,0,0,0,0,0,0,NULL,&atx[62],&atx[118],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[45],NULL,0,NULL} ,
+  {0, "seq-data" ,128,5,0,1,0,0,0,0,NULL,&atx[62],&atx[120],0,&atx[121]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[115],NULL,0,NULL} ,
+  {0, "bioseqs" ,128,6,0,1,0,0,0,0,NULL,&atx[14],&atx[122],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[42],NULL,0,NULL} };
 
 static AsnModule ampx[1] = {
-  { "NCBI-Seq-split" , "seqsplit.h13",&atx[0],NULL,NULL,0,0} };
+  { "NCBI-Seq-split" , "seqsplit.h15",&atx[0],NULL,NULL,0,0} };
 
 static AsnValxNodePtr avn = avnx;
 static AsnTypePtr at = atx;
@@ -151,65 +165,73 @@ static AsnModulePtr amp = ampx;
 #define ID2S_SEQ_ANNOT_INFO_feat_E &at[9]
 #define ID2S_SEQ_ANNOT_INFO_seq_loc &at[16]
 
-#define ID2S_SPLIT_INFO &at[45]
-#define ID2S_SPLIT_INFO_bioseqs_info &at[46]
-#define ID2S_SPLIT_INFO_bioseqs_info_E &at[47]
-#define ID2S_SPLIT_INFO_chunks &at[62]
-#define ID2S_SPLIT_INFO_chunks_E &at[63]
+#define ID2S_SPLIT_INFO &at[47]
+#define ID2S_SPLIT_INFO_bioseqs_info &at[48]
+#define ID2S_SPLIT_INFO_bioseqs_info_E &at[49]
+#define ID2S_SPLIT_INFO_chunks &at[64]
+#define ID2S_SPLIT_INFO_chunks_E &at[65]
 
-#define ID2S_BIOSEQS_INFO &at[48]
-#define ID2S_BIOSEQS_INFO_info &at[49]
-#define ID2S_BIOSEQS_INFO_bioseqs &at[61]
+#define ID2S_BIOSEQS_INFO &at[50]
+#define ID2S_BIOSEQS_INFO_info &at[51]
+#define ID2S_BIOSEQS_INFO_bioseqs &at[63]
 
-#define ID2S_CHUNK_INFO &at[64]
-#define ID2S_CHUNK_INFO_id &at[65]
-#define ID2S_CHUNK_INFO_content &at[66]
-#define ID2S_CHUNK_INFO_content_E &at[67]
+#define ID2S_CHUNK_INFO &at[66]
+#define ID2S_CHUNK_INFO_id &at[67]
+#define ID2S_CHUNK_INFO_content &at[68]
+#define ID2S_CHUNK_INFO_content_E &at[69]
 
-#define ID2S_BIOSEQ_INFO &at[50]
-#define ID2S_BIOSEQ_INFO_gap_count &at[51]
-#define BIOSEQ_INFO_seq_map_has_ref &at[52]
-#define ID2S_BIOSEQ_INFO_sequence_split &at[54]
+#define ID2S_BIOSEQ_INFO &at[52]
+#define ID2S_BIOSEQ_INFO_gap_count &at[53]
+#define BIOSEQ_INFO_seq_map_has_ref &at[54]
+#define ID2S_BIOSEQ_INFO_sequence_split &at[56]
 
 #define ID2_ID_RANGE &at[33]
 #define ID2_ID_RANGE_start &at[34]
 #define ID2_ID_RANGE_count &at[35]
 
-#define ID2S_SEQUENCE_SPLIT_INFO &at[55]
-#define SEQUENCE_SPLIT_INFO_block_size &at[56]
-#define SPLIT_INFO_chunk_start &at[57]
-#define SPLIT_INFO_chunk_blocks &at[58]
-#define SPLIT_INFO_chunk_blocks_E &at[59]
-
-#define ID2S_CHUNK_CONTENT &at[68]
-#define ID2S_CHUNK_CONTENT_seq_descr &at[69]
-#define ID2S_CHUNK_CONTENT_seq_annot &at[76]
-#define ID2S_CHUNK_CONTENT_seq_assembly &at[77]
-#define ID2S_CHUNK_CONTENT_seq_map &at[81]
-#define ID2S_CHUNK_CONTENT_seq_data &at[83]
-#define CHUNK_CONTENT_seq_annot_place &at[85]
-
-#define ID2S_SEQ_DESCR_INFO &at[70]
-#define ID2S_SEQ_DESCR_INFO_type_mask &at[71]
-#define ID2S_SEQ_DESCR_INFO_bioseqs &at[72]
-#define ID2S_SEQ_DESCR_INFO_bioseqs_E &at[73]
-#define ID2S_SEQ_DESCR_INFO_bioseq_sets &at[74]
-#define SEQ_DESCR_INFO_bioseq_sets_E &at[75]
-
-#define ID2S_SEQ_ASSEMBLY_INFO &at[78]
-#define ID2S_SEQ_ASSEMBLY_INFO_bioseqs &at[79]
-#define SEQ_ASSEMBLY_INFO_bioseqs_E &at[80]
-
-#define ID2S_SEQ_MAP_INFO &at[82]
-
-#define ID2S_SEQ_DATA_INFO &at[84]
-
-#define ID2S_SEQ_ANNOT_PLACE_INFO &at[86]
-#define ID2S_SEQ_ANNOT_PLACE_INFO_name &at[87]
-#define SEQ_ANNOT_PLACE_INFO_bioseqs &at[88]
-#define SEQ_ANNOT_PLACE_INFO_bioseqs_E &at[89]
-#define ANNOT_PLACE_INFO_bioseq_sets &at[90]
-#define ANNOT_PLACE_INFO_bioseq_sets_E &at[91]
+#define ID2S_SEQUENCE_SPLIT_INFO &at[57]
+#define SEQUENCE_SPLIT_INFO_block_size &at[58]
+#define SPLIT_INFO_chunk_start &at[59]
+#define SPLIT_INFO_chunk_blocks &at[60]
+#define SPLIT_INFO_chunk_blocks_E &at[61]
+
+#define ID2S_CHUNK_CONTENT &at[70]
+#define ID2S_CHUNK_CONTENT_seq_descr &at[71]
+#define ID2S_CHUNK_CONTENT_seq_annot &at[80]
+#define ID2S_CHUNK_CONTENT_seq_assembly &at[81]
+#define ID2S_CHUNK_CONTENT_seq_map &at[84]
+#define ID2S_CHUNK_CONTENT_seq_data &at[86]
+#define CHUNK_CONTENT_seq_annot_place &at[88]
+#define ID2S_CHUNK_CONTENT_bioseq_place &at[93]
+#define CHUNK_CONTENT_bioseq_place_E &at[94]
+
+#define ID2S_SEQ_DESCR_INFO &at[72]
+#define ID2S_SEQ_DESCR_INFO_type_mask &at[73]
+#define ID2S_SEQ_DESCR_INFO_bioseqs &at[74]
+#define ID2S_SEQ_DESCR_INFO_bioseq_sets &at[77]
+
+#define ID2S_SEQ_ASSEMBLY_INFO &at[82]
+#define ID2S_SEQ_ASSEMBLY_INFO_bioseqs &at[83]
+
+#define ID2S_SEQ_MAP_INFO &at[85]
+
+#define ID2S_SEQ_DATA_INFO &at[87]
+
+#define ID2S_SEQ_ANNOT_PLACE_INFO &at[89]
+#define ID2S_SEQ_ANNOT_PLACE_INFO_name &at[90]
+#define SEQ_ANNOT_PLACE_INFO_bioseqs &at[91]
+#define ANNOT_PLACE_INFO_bioseq_sets &at[92]
+
+#define ID2S_BIOSEQ_PLACE_INFO &at[95]
+#define BIOSEQ_PLACE_INFO_bioseq_set &at[96]
+#define ID2S_BIOSEQ_PLACE_INFO_seq_ids &at[97]
+#define BIOSEQ_PLACE_INFO_seq_ids_E &at[98]
+
+#define ID2_BIOSEQ_IDS &at[75]
+#define ID2_BIOSEQ_IDS_E &at[76]
+
+#define ID2_BIOSEQ_SET_IDS &at[78]
+#define ID2_BIOSEQ_SET_IDS_E &at[79]
 
 #define ID2S_FEAT_TYPE_INFO &at[10]
 #define ID2S_FEAT_TYPE_INFO_type &at[11]
@@ -225,24 +247,32 @@ static AsnModulePtr amp = ampx;
 #define ID2_SEQ_LOC_loc_set_E &at[37]
 #define ID2_SEQ_LOC_seq_loc &at[38]
 
-#define ID2S_CHUNK &at[92]
-#define ID2S_CHUNK_data &at[93]
-#define ID2S_CHUNK_data_E &at[94]
-
-#define ID2S_CHUNK_DATA &at[95]
-#define ID2S_CHUNK_DATA_id &at[96]
-#define ID2S_CHUNK_DATA_id_bioseq_set &at[97]
-#define ID2S_CHUNK_DATA_id_gi &at[98]
-#define ID2S_CHUNK_DATA_descrs &at[99]
-#define ID2S_CHUNK_DATA_descrs_E &at[100]
-#define ID2S_CHUNK_DATA_annots &at[101]
-#define ID2S_CHUNK_DATA_annots_E &at[102]
-#define ID2S_CHUNK_DATA_assembly &at[103]
-#define ID2S_CHUNK_DATA_assembly_E &at[104]
-#define ID2S_CHUNK_DATA_seq_map &at[105]
-#define ID2S_CHUNK_DATA_seq_map_E &at[106]
-#define ID2S_CHUNK_DATA_seq_data &at[107]
-#define ID2S_CHUNK_DATA_seq_data_E &at[108]
+#define ID2S_CHUNK &at[99]
+#define ID2S_CHUNK_data &at[100]
+#define ID2S_CHUNK_data_E &at[101]
+
+#define ID2S_CHUNK_DATA &at[102]
+#define ID2S_CHUNK_DATA_id &at[103]
+#define ID2S_CHUNK_DATA_id_bioseq_set &at[104]
+#define ID2S_CHUNK_DATA_id_gi &at[105]
+#define ID2S_CHUNK_DATA_id_seq_id &at[106]
+#define ID2S_CHUNK_DATA_descrs &at[107]
+#define ID2S_CHUNK_DATA_descrs_E &at[108]
+#define ID2S_CHUNK_DATA_annots &at[109]
+#define ID2S_CHUNK_DATA_annots_E &at[110]
+#define ID2S_CHUNK_DATA_assembly &at[111]
+#define ID2S_CHUNK_DATA_assembly_E &at[112]
+#define ID2S_CHUNK_DATA_seq_map &at[113]
+#define ID2S_CHUNK_DATA_seq_map_E &at[114]
+#define ID2S_CHUNK_DATA_seq_data &at[119]
+#define ID2S_CHUNK_DATA_seq_data_E &at[120]
+#define ID2S_CHUNK_DATA_bioseqs &at[121]
+#define ID2S_CHUNK_DATA_bioseqs_E &at[122]
+
+#define ID2S_SEQUENCE_PIECE &at[115]
+#define ID2S_SEQUENCE_PIECE_start &at[116]
+#define ID2S_SEQUENCE_PIECE_data &at[117]
+#define ID2S_SEQUENCE_PIECE_data_E &at[118]
 
 #define ID2_INTERVAL &at[20]
 #define ID2_INTERVAL_gi &at[21]
diff --git a/network/medarch/client/mdrcherr.h b/network/medarch/client/mdrcherr.h
index 69889082..e5332548 100644
--- a/network/medarch/client/mdrcherr.h
+++ b/network/medarch/client/mdrcherr.h
@@ -3,6 +3,9 @@
 *
 * RCS Modification History:
 * $Log: mdrcherr.h,v $
+* Revision 6.2  2004/08/17 15:21:31  bazhin
+* Added a few error messages to report PubMed id problems.
+*
 * Revision 6.1  2003/10/01 13:07:50  bazhin
 * Added a couple of new warning messages ERR_REFERENCE_NoConsortAuthors
 * and ERR_REFERENCE_DiffConsortAuthors. The severity of message
@@ -36,6 +39,10 @@
 #define ERR_REFERENCE_MuidMissmatch  1,8
 #define ERR_REFERENCE_NoConsortAuthors 1,9
 #define ERR_REFERENCE_DiffConsortAuthors 1,10
+#define ERR_REFERENCE_PmidMissmatch 1,11
+#define ERR_REFERENCE_Multiple_pmid 1,12
+#define ERR_REFERENCE_FailedToGetPub 1,13
+
 #define ERR_PRINT  2,0
 #define ERR_PRINT_Failed  2,1
 
diff --git a/network/medarch/client/medarch.msg b/network/medarch/client/medarch.msg
index 9df68937..b583241b 100644
--- a/network/medarch/client/medarch.msg
+++ b/network/medarch/client/medarch.msg
@@ -10,6 +10,9 @@ $^   MedlineMatchIgnored, 7, SEV_ERROR
 $^   MuidMissmatch, 8, SEV_WARNING
 $^   NoConsortAuthors, 9, SEV_WARNING
 $^   DiffConsortAuthors, 10, SEV_WARNING
+$^   PmidMismatch, 11, SEV_WARNING
+$^   Multiple_pmid, 12, SEV_WARNING
+$^   FailedToGetPub, 13, SEV_ERROR
 
 $$ PRINT, 2
 $^   Failed, 1, SEV_WARNING
diff --git a/network/medarch/client/medutil.c b/network/medarch/client/medutil.c
index fc6b5199..efe601ae 100644
--- a/network/medarch/client/medutil.c
+++ b/network/medarch/client/medutil.c
@@ -28,7 +28,7 @@
 *   
 * Version Creation Date: 8/31/93
 *
-* $Revision: 6.14 $
+* $Revision: 6.15 $
 *
 * File Description:  Medline Utilities for MedArch
 *   Assumes user calls MedArchInit and Fini
@@ -44,6 +44,9 @@
 *
 * RCS Modification History:
 * $Log: medutil.c,v $
+* Revision 6.15  2004/08/18 17:00:56  bazhin
+* Fixed bug with medline lookup if both PubMed and Medline ids are present.
+*
 * Revision 6.14  2004/03/19 18:32:03  bazhin
 * One more patch related to the previous one.
 *
@@ -722,7 +725,7 @@ static Boolean if_inpress_set(CitArtPtr cap)
 }
 
 /**********************************************************/
-static void PropogateInPress(Boolean inpress, ValNodePtr vnp)
+static void PropagateInPress(Boolean inpress, ValNodePtr vnp)
 {
     CitJourPtr jour;
     CitBookPtr book;
@@ -749,491 +752,503 @@ static void PropogateInPress(Boolean inpress, ValNodePtr vnp)
     }
 }
 
-/*****************************************************************************
-*
-*   FixPubEquiv()
-*
-*****************************************************************************/
-ValNodePtr FixPubEquiv(ValNodePtr pube, FindPubOptionPtr fpop)
+/**********************************************************/
+static ValNodePtr PubEquivAdd(ValNodePtr headvnp, ValNodePtr addvnp)
 {
-	ValNodePtr tmp, muidptr=NULL, pmidptr=NULL, citartptr=NULL, mepptr = NULL,
-		otherptr = NULL, tmp2, next, new;
-	Int2 muidctr = 0, pmidctr = 0, citartctr = 0, mepctr = 0, otherctr = 0;
-	Int4 muid = 0, oldmuid=0, pmid = 0, oldpmid=0;
-	CitArtPtr	cit;
-	Boolean		got;
-	Boolean		inpress;
+    ValNodePtr vnp;
 
-	if (pube == NULL) return NULL;
+    if(headvnp == NULL)
+        return(addvnp);
+    for(vnp = headvnp; vnp->next != NULL;)
+        vnp = vnp->next;
+    vnp->next = addvnp;
+    return(headvnp);
+}
 
-	for(got = FALSE, tmp = pube; tmp != NULL; tmp = tmp->next)
-	{
-		if(tmp->choice == PUB_Muid || tmp->choice == PUB_PMid)
-		{
-			got = TRUE;
-			break;
-		}
-	}
+/**********************************************************/
+static ValNodePtr PubEquivPutBack(ValNodePtr headvnp, ValNodePtr addvnp)
+{
+    ValNodePtr vnp;
 
-	for (tmp = pube; tmp != NULL; tmp = next)
-	{
-		next = tmp->next;
-		tmp->next = NULL;
-		switch (tmp->choice)
-		{
-			case PUB_Muid:
-				muidctr++;
-				if (muidptr == NULL)
-					muidptr = tmp;
-				else
-				{
-					for (tmp2 = muidptr; tmp2->next != NULL; tmp2 = tmp2->next)
-						continue;
-					tmp2->next = tmp;
-				}
-				break;
-			case PUB_PMid:
-				pmidctr++;
-				if (pmidptr == NULL)
-					pmidptr = tmp;
-				else
-				{
-					for (tmp2 = pmidptr; tmp2->next != NULL; tmp2 = tmp2->next)
-						continue;
-					tmp2->next = tmp;
-				}
-				break;
-			case PUB_Article:
-				cit = tmp->data.ptrvalue;
-				if (cit->from == 2 || (in_press(cit) && got == FALSE)) {
-					otherctr++;
-					if (otherptr == NULL)
-						otherptr = tmp;
-					else
-					{
-						for (tmp2 = otherptr; tmp2->next != NULL; tmp2 = tmp2->next)
-							continue;
-						tmp2->next = tmp;
-					}
-				} else {
-					citartctr++;
-					if (citartptr == NULL)
-						citartptr = tmp;
-					else
-					{
-						for (tmp2 = citartptr; tmp2->next != NULL;
-													tmp2 = tmp2->next)
-							continue;
-						tmp2->next = tmp;
-					}
-				}
-				break;
-			case PUB_Medline:
-				mepctr++;
-				if (mepptr == NULL)
-					mepptr = tmp;
-				else
-				{
-					for (tmp2 = mepptr; tmp2->next != NULL; tmp2 = tmp2->next)
-						continue;
-					tmp2->next = tmp;
-				}
-				break;
-			default:
-				otherctr++;
-				if (otherptr == NULL)
-					otherptr = tmp;
-				else
-				{
-					for (tmp2 = otherptr; tmp2->next != NULL; tmp2 = tmp2->next)
-						continue;
-					tmp2->next = tmp;
-				}
-				break;
-		}
-	}
+    if(headvnp == NULL)
+        return(addvnp);
+    if(addvnp == NULL)
+        return(headvnp);
 
-	pube = otherptr;   /* put back others */
-	tmp2 = otherptr;
-	if (tmp2 != NULL)
-	{
-		for (tmp2 = otherptr; tmp2->next != NULL; tmp2 = tmp2->next)
-			continue;
-	}
-	
-	if ((muidctr != 0 || pmidctr != 0) && (! fpop->always_look))   /* got an muid */
-	{
-		if (mepptr != NULL)
-		{
-			if (tmp2 == NULL)
-			{
-				tmp2 = mepptr;
-				pube = tmp2;
-			}
-			else
-				tmp2->next = mepptr;
-			
-			while (tmp2->next != NULL)
-				tmp2 = tmp2->next;
-		}
-		if (pmidptr != NULL) {
-			if (tmp2 == NULL)
-			{
-				tmp2 = pmidptr;
-				pube = tmp2;
-			}
-			else
-				tmp2->next = pmidptr;
-			
-			while (tmp2->next != NULL)
-				tmp2 = tmp2->next;
-		}
-		if (muidptr != NULL)
-		{
-			if (tmp2 == NULL)
-			{
-				tmp2 = muidptr;
-				pube = tmp2;
-			}
-			else
-				tmp2->next = muidptr;
-			
-			while (tmp2->next != NULL)
-				tmp2 = tmp2->next;
-		}
-		if (citartptr != NULL)
-		{
-			if (tmp2 == NULL)
-			{
-				tmp2 = citartptr;
-				pube = tmp2;
-			}
-			else
-				tmp2->next = citartptr;
-		}
-		return pube;   /* no changes */
-	}
+    for(vnp = addvnp; vnp->next != NULL;)
+        vnp = vnp->next;
+    vnp->next = headvnp;
+    return(addvnp);
+}
 
-	if (mepctr != 0)    /* have a medline entry, take it first */
-	{
-		if (mepctr > 1)
-		{
-			ErrPostEx(SEV_WARNING, ERR_REFERENCE_Multiple_ref, "More than one Medline entry in Pub-equiv");
-			mepptr->next = PubEquivFree(mepptr->next);
-		}
-		PubEquivFree(muidptr);   /* ditch others */
-		PubEquivFree(pmidptr);
-		PubEquivFree(citartptr);
-		tmp = SplitMedlineEntry((MedlineEntryPtr)(mepptr->data.ptrvalue));
-		ValNodeFree(mepptr);
-		if (tmp2 == NULL)
-			pube = tmp;
-		else
-			tmp2->next = tmp;
-		return pube;
-	}
+/**********************************************************/
+static ValNodePtr FixPubEquivAppend(ValNodePtr pube, ValNodePtr tmp2,
+                                    ValNodePtr tmp)
+{
+    if(tmp2 == NULL)
+        return(tmp);
+    tmp2->next = tmp;
+    return(pube);
+}
 
-	if (pmidctr != 0)    /* have a pmid */
-	{
-		oldpmid = pmidptr->data.intvalue;
-		if (pmidctr > 1)     /* more than one, just take the first */
-		{
-			for (tmp = pmidptr->next; tmp != NULL; tmp = tmp->next)
-			{
-				if (tmp->data.intvalue != pmid)
-				{
-					ErrPostEx(SEV_WARNING, ERR_REFERENCE_Multiple_muid, "Two different pmids in Pub-equiv [%ld] [%ld]\n",
-						(long) oldpmid, (long) (tmp->data.intvalue));
-				}
-			}
-		 	pmidptr->next = PubEquivFree(pmidptr->next);
-		}
-	}
+/**********************************************************/
+static ValNodePtr FixPubEquivAppendPmid(ValNodePtr tmp, Int4 muid,
+                                        ValNodePtr pmidptr)
+{
+    Int4 oldpmid;
+    Int4 newpmid;
 
-	if (muidctr != 0)    /* have an muid */
-	{
-		oldmuid = muidptr->data.intvalue;
-		if (muidctr > 1)     /* more than one, just take the first */
-		{
-			for (tmp = muidptr->next; tmp != NULL; tmp = tmp->next)
-			{
-				if (tmp->data.intvalue != muid)
-				{
-					ErrPostEx(SEV_WARNING, ERR_REFERENCE_Multiple_muid, "Two different muids in Pub-equiv [%ld] [%ld]\n",
-						(long) oldmuid, (long) (tmp->data.intvalue));
-				}
-			}
-		 	muidptr->next = PubEquivFree(muidptr->next);
-		}
-	}
+    oldpmid = (pmidptr == NULL) ? 0 : pmidptr->data.intvalue;
 
-	if (citartctr > 0)
-	{
-		if (citartctr > 1)  /* ditch extras */
-		{
-			ErrPostEx(SEV_WARNING, ERR_REFERENCE_Multiple_ref, "More than one Cit-art in Pub-equiv");
-			citartptr->next = PubEquivFree(citartptr->next);
-		}
+    newpmid = MedArchMu2Pm(muid);
+    if(oldpmid < 1 && newpmid < 1)
+        return(tmp);
 
-		inpress = if_inpress_set(citartptr->data.ptrvalue);
-		fpop->lookups_attempted++;
-		muid = MedArchCitMatch(citartptr);
-		if (muid != 0)   /* success */
-		{
-			print_pub(citartptr, TRUE, FALSE, muid);
-			fpop->lookups_succeeded++;
-			if (oldmuid)   /* already had an muid */
-			{
-				if (oldmuid != muid)
-				{
-					ErrPostEx(SEV_ERROR, ERR_REFERENCE_MuidMissmatch, "OldMUID=%ld doesn't match lookup (%ld). Keeping lookup.",
-						(long)oldmuid, (long)muid);
-				}
-			}
-			if (fpop->replace_cit)
-			{
-				fpop->fetches_attempted++;
-				new = FetchPub(muid);
-				if (new != NULL) 
-				{
-					fpop->fetches_succeeded++;
+    if(oldpmid > 0 && newpmid > 0 && oldpmid != newpmid)
+        ErrPostEx(SEV_ERROR, ERR_REFERENCE_PmidMissmatch,
+                  "OldPMID=%ld doesn't match lookup (%ld). Keeping lookup.",
+                  (long) oldpmid, (long) newpmid);
 
-					if (ten_authors(citartptr->data.ptrvalue,
-											new->data.ptrvalue))
-					{
-						if (muidptr != NULL)
-							tmp = muidptr;
-						else
-						{
-							tmp = ValNodeNew(tmp2);
-							tmp->choice = PUB_Muid;
-						}
-						if (tmp2 == NULL) {
-							pube = tmp;
-						} else {
-							tmp2->next = tmp;
-						}
-						tmp->data.intvalue = muid;
-						tmp->next = new;
-						
-						PubFree(citartptr);
-						citartptr = new;
-					} else {
-						print_pub(citartptr, FALSE, TRUE, muid);
-						PubFree(new);
-						if (tmp2 == NULL) {
-							pube = citartptr;
-						} else {
-							tmp2->next = citartptr;
-						}
-						if (muidptr != NULL)
-							citartptr->next = muidptr;
-					}
-				}
-				else
-				{
-					ErrPostEx(SEV_ERROR, 0, 0, "Failed to get pub from MedArch server for muid = %ld. Input one is preserved.", muid);
-					if (muidptr != NULL)
-						tmp = muidptr;
-					else
-					{
-						tmp = ValNodeNew(tmp2);
-						tmp->choice = PUB_Muid;
-					}
-					if (tmp2 == NULL)
-						pube = tmp;
-					tmp->data.intvalue = muid;
-					tmp2 = tmp;
-					tmp->next = citartptr;
-					MedlineToISO(citartptr);
-				}
-			}
-			else
-			{
-				if (muidptr != NULL)
-					tmp = muidptr;
-				else
-				{
-					tmp = ValNodeNew(tmp2);
-					tmp->choice = PUB_Muid;
-				}
-				if (tmp2 == NULL)
-					pube = tmp;
-				tmp->data.intvalue = muid;
-				tmp2 = tmp;
-				tmp->next = citartptr;
-				MedlineToISO(citartptr);
-			}
-			PropogateInPress(inpress, citartptr);
-			return pube;
-		}
+    if(pmidptr != NULL)
+        tmp->next = pmidptr;
+    else
+    {
+        tmp->next = ValNodeNew(NULL);
+        tmp->next->choice = PUB_PMid;
+    }
 
-		/* muid lookup failed */
+    tmp = tmp->next;
+    tmp->data.intvalue = (newpmid > 0) ? newpmid : oldpmid;
 
-		pmid = MedArchCitMatchPmId(citartptr);
-		if (pmid != 0)   /* success */
-		{
-			print_pub(citartptr, TRUE, FALSE, pmid);
-			fpop->lookups_succeeded++;
-			if (oldpmid)   /* already had an muid */
-			{
-				if (oldpmid != pmid)
-				{
-					ErrPostEx(SEV_ERROR, ERR_REFERENCE_MuidMissmatch, "OldPMID=%ld doesn't match lookup (%ld). Keeping lookup.",
-						(long)oldpmid, (long)pmid);
-				}
-			}
-			if (fpop->replace_cit)
-			{
-				fpop->fetches_attempted++;
-				new = FetchPubPmId(pmid);
-				if (new != NULL) 
-				{
-					fpop->fetches_succeeded++;
+    return(tmp);
+}
 
-					if (ten_authors(citartptr->data.ptrvalue,
-											new->data.ptrvalue))
-					{
-						if (pmidptr != NULL)
-							tmp = pmidptr;
-						else
-						{
-							tmp = ValNodeNew(tmp2);
-							tmp->choice = PUB_PMid;
-						}
-						if (tmp2 == NULL) {
-							pube = tmp;
-						} else {
-							tmp2->next = tmp;
-						}
-						tmp->data.intvalue = pmid;
-						tmp->next = new;
-						
-						PubFree(citartptr);
-						citartptr = new;
-					} else {
-						print_pub(citartptr, FALSE, TRUE, pmid);
-						PubFree(new);
-						if (tmp2 == NULL) {
-							pube = citartptr;
-						} else {
-							tmp2->next = citartptr;
-						}
-						if (pmidptr != NULL)
-							citartptr->next = pmidptr;
-					}
-				}
-				else
-				{
-					ErrPostEx(SEV_ERROR, 0, 0, "Failed to get pub from MedArch server for pmid = %ld. Input one is preserved.", pmid);
-					if (pmidptr != NULL)
-						tmp = pmidptr;
-					else
-					{
-						tmp = ValNodeNew(tmp2);
-						tmp->choice = PUB_PMid;
-					}
-					if (tmp2 == NULL)
-						pube = tmp;
-					tmp->data.intvalue = pmid;
-					tmp2 = tmp;
-					tmp->next = citartptr;
-					MedlineToISO(citartptr);
-				}
-			}
-			else
-			{
-				if (pmidptr != NULL)
-					tmp = pmidptr;
-				else
-				{
-					tmp = ValNodeNew(tmp2);
-					tmp->choice = PUB_PMid;
-				}
-				if (tmp2 == NULL)
-					pube = tmp;
-				tmp->data.intvalue = pmid;
-				tmp2 = tmp;
-				tmp->next = citartptr;
-				MedlineToISO(citartptr);
-			}
-			PropogateInPress(inpress, citartptr);
-			return pube;
-		}
+/**********************************************************/
+static ValNodePtr FixPubEquivAppendMuid(ValNodePtr tmp, Int4 pmid,
+                                        ValNodePtr muidptr)
+{
+    Int4 oldmuid;
+    Int4 newmuid;
 
-		print_pub(citartptr, FALSE, FALSE, oldmuid);
-		if (tmp2 == NULL)
-			pube = citartptr;
-		else
-			tmp2->next = citartptr;
-		if (muidptr != NULL)   /* ditch the mismatched muid */
-			PubFree(muidptr);
-		PropogateInPress(inpress, citartptr);
-		return pube;
+    oldmuid = (muidptr == NULL) ? 0 : muidptr->data.intvalue;
 
-	}
-		
-	if (oldpmid != 0)    /* have a pmid but no cit-art */
-	{
-		fpop->fetches_attempted++;
-		tmp = MedArchGetPubPmId(oldpmid);
-		if (tmp == NULL)
-		{
-			ErrPostEx(SEV_WARNING, ERR_REFERENCE_No_reference, "Cant find article for pmid [%ld]", (long) oldpmid);
-		}
-		else
-		{
-			fpop->fetches_succeeded++;
-			if (fpop->replace_cit)
-			{
-				tmp = MedlineToISO(tmp);
-				if (tmp2 == NULL)
-				 	pube = tmp;
-				else
-					tmp2->next = tmp;
-				tmp2 = tmp;
-			} else {
-				PubFree(tmp);
-			}
-		}
-		if (tmp2 == NULL)
-		 	pube = pmidptr;
-		else
-			tmp2->next = pmidptr;
-	}
+    newmuid = MedArchPm2Mu(pmid);
+    if(oldmuid < 1 && newmuid < 1)
+        return(tmp);
 
-	if (oldmuid != 0)    /* have an muid but no cit-art */
-	{
-		fpop->fetches_attempted++;
-		tmp = MedArchGetPub(oldmuid);
-		if (tmp == NULL)
-		{
-			ErrPostEx(SEV_WARNING, ERR_REFERENCE_No_reference, "Cant find article for muid [%ld]", (long) oldmuid);
-		}
-		else
-		{
-			fpop->fetches_succeeded++;
-			if (fpop->replace_cit)
-			{
-				tmp = MedlineToISO(tmp);
-				if (tmp2 == NULL)
-				 	pube = tmp;
-				else
-					tmp2->next = tmp;
-				tmp2 = tmp;
-			} else {
-				PubFree(tmp);
-			}
-		}
-		if (tmp2 == NULL)
-		 	pube = muidptr;
-		else
-			tmp2->next = muidptr;
-	}
+    if(oldmuid > 0 && newmuid > 0 && oldmuid != newmuid)
+        ErrPostEx(SEV_ERROR, ERR_REFERENCE_MuidMissmatch,
+                  "OldMUID=%ld doesn't match lookup (%ld). Keeping lookup.",
+                  (long) oldmuid, (long) newmuid);
+
+    if(muidptr != NULL)
+        tmp->next = muidptr;
+    else
+    {
+        tmp->next = ValNodeNew(NULL);
+        tmp->next->choice = PUB_Muid;
+    }
 
-	return pube;
+    tmp = tmp->next;
+    tmp->data.intvalue = (newmuid > 0) ? newmuid : oldmuid;
+
+    return(tmp);
 }
 
+/**********************************************************/
+ValNodePtr FixPubEquiv(ValNodePtr pube, FindPubOptionPtr fpop)
+{
+    ValNodePtr tmp;
+    ValNodePtr muidptr = NULL;
+    ValNodePtr pmidptr = NULL;
+    ValNodePtr citartptr = NULL;
+    ValNodePtr mepptr = NULL;
+    ValNodePtr otherptr = NULL;
+    ValNodePtr tmp2;
+    ValNodePtr next;
+    ValNodePtr new;
+    Int4       muid = 0;
+    Int4       oldmuid = 0;
+    Int4       pmid = 0;
+    Int4       oldpmid = 0;
+    CitArtPtr  cit;
+    Boolean    got;
+    Boolean    inpress;
+
+    if(pube == NULL)
+        return(NULL);
+
+    for(got = FALSE, tmp = pube; tmp != NULL; tmp = tmp->next)
+    {
+        if(tmp->choice == PUB_Muid || tmp->choice == PUB_PMid)
+        {
+            got = TRUE;
+            break;
+        }
+    }
+
+    for(tmp = pube; tmp != NULL; tmp = next)
+    {
+        next = tmp->next;
+        tmp->next = NULL;
+        if(tmp->choice == PUB_Muid)
+            muidptr = PubEquivAdd(muidptr, tmp);
+        else if(tmp->choice == PUB_PMid)
+            pmidptr = PubEquivAdd(pmidptr, tmp);
+        else if(tmp->choice == PUB_Article)
+        {
+            cit = tmp->data.ptrvalue;
+            if(cit->from == 2 || (in_press(cit) != FALSE && got == FALSE))
+                otherptr = PubEquivAdd(otherptr, tmp);
+            else
+                citartptr = PubEquivAdd(citartptr, tmp);
+        }
+        else if(tmp->choice == PUB_Medline)
+            mepptr = PubEquivAdd(mepptr, tmp);
+        else
+            otherptr = PubEquivAdd(otherptr, tmp);
+    }
+
+    if((muidptr != NULL || pmidptr != NULL) &&  /* got a muid or pmid */
+       fpop->always_look == FALSE)
+    {
+        pube = PubEquivPutBack(NULL, citartptr);
+        pube = PubEquivPutBack(pube, muidptr);
+        pube = PubEquivPutBack(pube, pmidptr);
+        pube = PubEquivPutBack(pube, mepptr);
+        pube = PubEquivPutBack(pube, otherptr);
+        return(pube);                   /* no changes */
+    }
+
+    pube = otherptr;                    /* put back others */
+    tmp2 = otherptr;
+    if(tmp2 != NULL)
+        while(tmp2->next != NULL)
+            tmp2 = tmp2->next;
+
+    if(mepptr != NULL)                  /* have a medline entry,
+                                           take it first */
+    {
+        if(mepptr->next != NULL)
+        {
+            ErrPostEx(SEV_WARNING, ERR_REFERENCE_Multiple_ref,
+                      "More than one Medline entry in Pub-equiv");
+            mepptr->next = PubEquivFree(mepptr->next);
+        }
+        PubEquivFree(muidptr);          /* ditch others */
+        PubEquivFree(pmidptr);
+        PubEquivFree(citartptr);
+        tmp = SplitMedlineEntry((MedlineEntryPtr) mepptr->data.ptrvalue);
+        ValNodeFree(mepptr);
+        pube = FixPubEquivAppend(pube, tmp2, tmp);
+        return(pube);
+    }
+
+    if(pmidptr != NULL)                 /* have a pmid */
+    {
+        oldpmid = pmidptr->data.intvalue;
+        if(pmidptr->next != NULL)       /* more than one, just take
+                                           the first */
+        {
+            for(tmp = pmidptr->next; tmp != NULL; tmp = tmp->next)
+                if(tmp->data.intvalue != pmid)
+                    ErrPostEx(SEV_WARNING, ERR_REFERENCE_Multiple_pmid,
+                              "Two different pmids in Pub-equiv [%ld] [%ld]",
+                              (long) oldpmid, (long) tmp->data.intvalue);
+            pmidptr->next = PubEquivFree(pmidptr->next);
+        }
+    }
+
+    if(muidptr != NULL)                 /* have an muid */
+    {
+        oldmuid = muidptr->data.intvalue;
+        if(muidptr->next != NULL)       /* more than one, just take
+                                           the first */
+        {
+            for(tmp = muidptr->next; tmp != NULL; tmp = tmp->next)
+                if(tmp->data.intvalue != muid)
+                    ErrPostEx(SEV_WARNING, ERR_REFERENCE_Multiple_muid,
+                              "Two different muids in Pub-equiv [%ld] [%ld]",
+                              (long) oldmuid, (long) tmp->data.intvalue);
+            muidptr->next = PubEquivFree(muidptr->next);
+        }
+    }
+
+    if(citartptr != NULL)
+    {
+        if(citartptr->next != NULL)     /* ditch extras */
+        {
+            ErrPostEx(SEV_WARNING, ERR_REFERENCE_Multiple_ref,
+                      "More than one Cit-art in Pub-equiv");
+            citartptr->next = PubEquivFree(citartptr->next);
+        }
+
+        inpress = if_inpress_set(citartptr->data.ptrvalue);
+        fpop->lookups_attempted++;
+        muid = MedArchCitMatch(citartptr);
+        if(muid != 0)                   /* success */
+        {
+            print_pub(citartptr, TRUE, FALSE, muid);
+            fpop->lookups_succeeded++;
+            if(oldmuid > 0 && oldmuid != muid)  /* already had an muid */
+                ErrPostEx(SEV_ERROR, ERR_REFERENCE_MuidMissmatch,
+                          "OldMUID=%ld doesn't match lookup (%ld). Keeping lookup.",
+                          (long) oldmuid, (long) muid);
+            if(fpop->replace_cit != FALSE)
+            {
+                fpop->fetches_attempted++;
+                new = FetchPub(muid);
+                if(new != NULL) 
+                {
+                    fpop->fetches_succeeded++;
+
+                    if(ten_authors(citartptr->data.ptrvalue,
+                                   new->data.ptrvalue) != FALSE)
+                    {
+                        if(muidptr != NULL)
+                            tmp = muidptr;
+                        else
+                        {
+                            tmp = ValNodeNew(tmp2);
+                            tmp->choice = PUB_Muid;
+                        }
+                        tmp->data.intvalue = muid;
+                        pube = FixPubEquivAppend(pube, tmp2, tmp);
+                        tmp = FixPubEquivAppendPmid(tmp, muid, pmidptr);
+                        tmp->next = new;
+
+                        PubFree(citartptr);
+                        citartptr = new;
+                    }
+                    else
+                    {
+                        if(muidptr != NULL)
+                            tmp = muidptr;
+                        else
+                        {
+                            tmp = ValNodeNew(tmp2);
+                            tmp->choice = PUB_Muid;
+                        }
+                        tmp->data.intvalue = muid;
+                        pube = FixPubEquivAppend(pube, tmp2, tmp);
+                        tmp = FixPubEquivAppendPmid(tmp, muid, pmidptr);
+
+                        print_pub(citartptr, FALSE, TRUE, muid);
+                        PubFree(new);
+                        tmp->next = citartptr;
+                    }
+                }
+                else
+                {
+                    ErrPostEx(SEV_ERROR, ERR_REFERENCE_FailedToGetPub,
+                              "Failed to get pub from MedArch server for muid = %ld. Input one is preserved.",
+                              muid);
+                    if(muidptr != NULL)
+                        tmp = muidptr;
+                    else
+                    {
+                        tmp = ValNodeNew(tmp2);
+                        tmp->choice = PUB_Muid;
+                    }
+                    if(tmp2 == NULL)
+                        pube = tmp;
+                    tmp->data.intvalue = muid;
+                    tmp = FixPubEquivAppendPmid(tmp, muid, pmidptr);
+/*                    tmp2 = tmp;*/
+                    tmp->next = citartptr;
+                    MedlineToISO(citartptr);
+                }
+            }
+            else
+            {
+                if(muidptr != NULL)
+                    tmp = muidptr;
+                else
+                {
+                    tmp = ValNodeNew(tmp2);
+                    tmp->choice = PUB_Muid;
+                }
+                if(tmp2 == NULL)
+                    pube = tmp;
+                tmp->data.intvalue = muid;
+                tmp = FixPubEquivAppendPmid(tmp, muid, pmidptr);
+/*                tmp2 = tmp;*/
+                tmp->next = citartptr;
+                MedlineToISO(citartptr);
+            }
+            PropagateInPress(inpress, citartptr);
+            return(pube);
+        }
+
+        /* muid lookup failed
+         */
+        pmid = MedArchCitMatchPmId(citartptr);
+        if(pmid != 0)                   /* success */
+        {
+            print_pub(citartptr, TRUE, FALSE, pmid);
+            fpop->lookups_succeeded++;
+            if(oldpmid > 0 && oldpmid != pmid)  /* already had a pmid */
+                ErrPostEx(SEV_ERROR, ERR_REFERENCE_PmidMissmatch,
+                          "OldPMID=%ld doesn't match lookup (%ld). Keeping lookup.",
+                          (long) oldpmid, (long) pmid);
+
+            if(fpop->replace_cit != FALSE)
+            {
+                fpop->fetches_attempted++;
+                new = FetchPubPmId(pmid);
+                if(new != NULL) 
+                {
+                    fpop->fetches_succeeded++;
+
+                    if(ten_authors(citartptr->data.ptrvalue,
+                                   new->data.ptrvalue) != FALSE)
+                    {
+                        if(pmidptr != NULL)
+                            tmp = pmidptr;
+                        else
+                        {
+                            tmp = ValNodeNew(tmp2);
+                            tmp->choice = PUB_PMid;
+                        }
+                        tmp->data.intvalue = pmid;
+                        pube = FixPubEquivAppend(pube, tmp2, tmp);
+                        tmp = FixPubEquivAppendMuid(tmp, pmid, muidptr);
+                        tmp->next = new;
+
+                        PubFree(citartptr);
+                        citartptr = new;
+                    }
+                    else
+                    {
+                        if(pmidptr != NULL)
+                            tmp = pmidptr;
+                        else
+                        {
+                            tmp = ValNodeNew(tmp2);
+                            tmp->choice = PUB_PMid;
+                        }
+                        tmp->data.intvalue = pmid;
+                        pube = FixPubEquivAppend(pube, tmp2, tmp);
+                        tmp = FixPubEquivAppendMuid(tmp, pmid, muidptr);
+
+                        print_pub(citartptr, FALSE, TRUE, pmid);
+                        PubFree(new);
+                        tmp->next = citartptr;
+                    }
+                }
+                else
+                {
+                    ErrPostEx(SEV_ERROR, ERR_REFERENCE_FailedToGetPub,
+                              "Failed to get pub from MedArch server for pmid = %ld. Input one is preserved.",
+                              pmid);
+                    if(pmidptr != NULL)
+                        tmp = pmidptr;
+                    else
+                    {
+                        tmp = ValNodeNew(tmp2);
+                        tmp->choice = PUB_PMid;
+                    }
+                    if(tmp2 == NULL)
+                        pube = tmp;
+                    tmp->data.intvalue = pmid;
+/*                    tmp2 = tmp;*/
+                    tmp = FixPubEquivAppendMuid(tmp, pmid, muidptr);
+                    tmp->next = citartptr;
+                    MedlineToISO(citartptr);
+                }
+            }
+            else
+            {
+                if(pmidptr != NULL)
+                    tmp = pmidptr;
+                else
+                {
+                    tmp = ValNodeNew(tmp2);
+                    tmp->choice = PUB_PMid;
+                }
+                if(tmp2 == NULL)
+                    pube = tmp;
+                tmp->data.intvalue = pmid;
+/*                tmp2 = tmp;*/
+                tmp = FixPubEquivAppendMuid(tmp, pmid, muidptr);
+                tmp->next = citartptr;
+                MedlineToISO(citartptr);
+            }
+            PropagateInPress(inpress, citartptr);
+            return(pube);
+        }
+
+        print_pub(citartptr, FALSE, FALSE, oldmuid);
+        pube = FixPubEquivAppend(pube, tmp2, citartptr);
+        if(muidptr != NULL)             /* ditch the mismatched muid */
+            PubFree(muidptr);
+        if(pmidptr != NULL)             /* ditch the mismatched pmid */
+            PubFree(pmidptr);
+        PropagateInPress(inpress, citartptr);
+        return(pube);
+    }
+
+    if(oldpmid != 0)                    /* have a pmid but no cit-art */
+    {
+        fpop->fetches_attempted++;
+        tmp = MedArchGetPubPmId(oldpmid);
+        if(tmp != NULL)
+        {
+            fpop->fetches_succeeded++;
+            if(fpop->replace_cit != FALSE)
+            {
+                tmp = MedlineToISO(tmp);
+                pube = FixPubEquivAppend(pube, tmp2, tmp);
+                tmp2 = tmp;
+            }
+            else
+                PubFree(tmp);
+            pube = FixPubEquivAppend(pube, tmp2, pmidptr);
+            FixPubEquivAppendMuid(pmidptr, oldpmid, muidptr);
+            return(pube);
+        }
+        ErrPostEx(SEV_WARNING, ERR_REFERENCE_No_reference,
+                  "Cant find article for pmid [%ld]", (long) oldpmid);
+/*        pube = FixPubEquivAppend(pube, tmp2, pmidptr);*/
+    }
+
+    if(oldmuid != 0)                    /* have a muid but no cit-art */
+    {
+        fpop->fetches_attempted++;
+        tmp = MedArchGetPub(oldmuid);
+        if(tmp != NULL)
+        {
+            fpop->fetches_succeeded++;
+            if(fpop->replace_cit != FALSE)
+            {
+                tmp = MedlineToISO(tmp);
+                pube = FixPubEquivAppend(pube, tmp2, tmp);
+                tmp2 = tmp;
+            }
+            else
+                PubFree(tmp);
+            pube = FixPubEquivAppend(pube, tmp2, muidptr);
+            FixPubEquivAppendPmid(muidptr, oldmuid, pmidptr);
+            return(pube);
+        }
+        ErrPostEx(SEV_WARNING, ERR_REFERENCE_No_reference,
+                  "Cant find article for muid [%ld]", (long) oldmuid);
+/*        pube = FixPubEquivAppend(pube, tmp2, muidptr);*/
+    }
+
+    if(oldpmid > 0)
+    {
+        pube = FixPubEquivAppend(pube, tmp2, pmidptr);
+        FixPubEquivAppendMuid(pmidptr, oldpmid, muidptr);
+    }
+    else if(oldmuid > 0)
+    {
+        pube = FixPubEquivAppend(pube, tmp2, muidptr);
+        FixPubEquivAppendPmid(muidptr, oldmuid, pmidptr);
+    }
+
+    return(pube);
+}
 
 /*****************************************************************************
 *
diff --git a/network/nsclilib/ni_service.c b/network/nsclilib/ni_service.c
index ed78575b..9cade6b4 100644
--- a/network/nsclilib/ni_service.c
+++ b/network/nsclilib/ni_service.c
@@ -1,4 +1,4 @@
-/*  $RCSfile: ni_service.c,v $  $Revision: 6.18 $  $Date: 2004/02/23 17:00:39 $
+/*  $RCSfile: ni_service.c,v $  $Revision: 6.19 $  $Date: 2004/07/12 16:34:05 $
  * ==========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -30,6 +30,10 @@
  *
  * --------------------------------------------------------------------------
  * $Log: ni_service.c,v $
+ * Revision 6.19  2004/07/12 16:34:05  lavr
+ * Add "SRV_CONN_MODE" for alternate FIREWALL switching
+ * (Thanks to Svetlana Karamycheva for reporting this..)
+ *
  * Revision 6.18  2004/02/23 17:00:39  lavr
  * Fix n_written variable name typo
  *
@@ -105,6 +109,7 @@
 
 #define SRV_SECTION         "NET_SERV"
 
+#define ENV_CONN_MODE       "SRV_CONN_MODE"
 #define ENV_ENGINE_HOST     "SRV_ENGINE_HOST"
 #define ENV_ENGINE_PORT     "SRV_ENGINE_PORT"
 #define ENV_ENGINE_URL      "SRV_ENGINE_URL"
@@ -196,6 +201,12 @@ static NI_HandPtr s_GenericGetService
     /* Now override default parameters with legacy parameters
      * of older WWW service dispatcher -- should go obsolete soon... */
 
+    /* alternate firewall mode request */
+    NI_GetEnvParam(configFile, SRV_SECTION, ENV_CONN_MODE,
+                   str, sizeof(str), "");
+    if (*str  &&  StringICmp(str, "FIREWALL") == 0)
+        net_info->firewall = 1/*true*/;
+
     /* alternate dispatcher's host name & port */
     NI_GetEnvParam(configFile, SRV_SECTION, ENV_ENGINE_HOST,
                    net_info->host, sizeof(net_info->host), def_info->host);
@@ -248,6 +259,7 @@ static NI_HandPtr s_GenericGetService
     if ((val = atoi(str)) != 0)
         net_info->max_try = val;
 
+    /* alternate debug printout request */
     NI_GetEnvParam(configFile, SRV_SECTION, ENV_DEBUG_PRINTOUT,
                    str, sizeof(str), "");
     if (*str  &&  (StringICmp(str, "1"   ) == 0 ||
diff --git a/network/nsclilib/ni_www.c b/network/nsclilib/ni_www.c
index a451d963..1b2855c0 100644
--- a/network/nsclilib/ni_www.c
+++ b/network/nsclilib/ni_www.c
@@ -1,4 +1,4 @@
-/*  $Id: ni_www.c,v 4.26 2000/09/28 17:53:24 vakatov Exp $
+/*  $Id: ni_www.c,v 4.27 2004/09/28 15:17:32 lavr Exp $
 * ==========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -31,6 +31,9 @@
 *
 * --------------------------------------------------------------------------
 * $Log: ni_www.c,v $
+* Revision 4.27  2004/09/28 15:17:32  lavr
+* Retire LB_DIRECT unconditionally
+*
 * Revision 4.26  2000/09/28 17:53:24  vakatov
 * NI_WWW_SetNcbidPort() -- yet another fix
 *
@@ -110,6 +113,9 @@
 #include <ncbicli.h>
 
 #ifdef LB_DIRECT
+#  undef LB_DIRECT
+#endif
+#ifdef LB_DIRECT
 #  include <lbapi.h>
 #  include <ncbithr.h>
 #endif
diff --git a/network/taxon1/common/taxutil.c b/network/taxon1/common/taxutil.c
index b92c9b14..d57c63e2 100644
--- a/network/taxon1/common/taxutil.c
+++ b/network/taxon1/common/taxutil.c
@@ -357,13 +357,19 @@ OrgRefPtr replace_org_err(OrgRefPtr orp, Boolean replace)
 ****************************************************************************/
 OrgRefPtr replace_org(OrgRefPtr orp, Boolean replace)
 {
+    CharPtr         common = NULL;
 	OrgRefPtr		new;	
 	Taxon1DataPtr	tax;
 
 	if (orp == NULL) {
 		return NULL;
 	}
+	common = orp->common;
+	if (StringDoesHaveText (orp->taxname) && StringDoesHaveText (orp->common)) {
+	    orp->common = NULL;
+	}
 	tax = tax1_lookup(orp, 1);
+	orp->common = common;
 	if (tax && tax->org) {
 		if (replace) {
 	         new = AsnIoMemCopy(tax->org, (AsnReadFunc) OrgRefAsnRead, 
diff --git a/network/taxon1/taxon2/tc2proc.c b/network/taxon1/taxon2/tc2proc.c
index 0b2ca9f1..bd2f26c0 100644
--- a/network/taxon1/taxon2/tc2proc.c
+++ b/network/taxon1/taxon2/tc2proc.c
@@ -1,5 +1,5 @@
 /*----------------*/
-/* $Id: tc2proc.c,v 1.34 2004/02/25 19:21:21 soussov Exp $           */
+/* $Id: tc2proc.c,v 1.35 2004/10/06 20:34:26 soussov Exp $           */
 /*----------------*/
 
 #include <stdlib.h>
@@ -904,9 +904,11 @@ static OrgModPtr bldOrgMod(TreeCursorPtr cursor)
         else if(rank == tax_getRankId("forma")) {
             orgMdf->subtype= 25; /* forma */
         }
+#if 0
         else if((parent != NULL) && (prank == SubspeciesRank)) {
             orgMdf->subtype= 2; /* strain */
         }
+#endif
         else {
             orgMdf->subtype= 0; /* other */
         }
diff --git a/network/wwwblast/Src/wblast2.c b/network/wwwblast/Src/wblast2.c
index 61da2167..264f8fda 100644
--- a/network/wwwblast/Src/wblast2.c
+++ b/network/wwwblast/Src/wblast2.c
@@ -1,4 +1,4 @@
-/* $Id: wblast2.c,v 1.9 2004/05/14 17:25:07 dondosha Exp $
+/* $Id: wblast2.c,v 1.14 2004/10/12 20:49:55 dondosha Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -27,12 +27,27 @@
 *
 * Initial Creation Date: 10/23/2000
 *
-* $Revision: 1.9 $
+* $Revision: 1.14 $
 *
 * File Description:
 *        BLAST 2 Sequences CGI program
 *
 * $Log: wblast2.c,v $
+* Revision 1.14  2004/10/12 20:49:55  dondosha
+* Correction due to change in SummaryReturn structure name and contents
+*
+* Revision 1.13  2004/08/16 19:39:35  dondosha
+* Use CreateMaskByteStore function from txalign.h; fixed bug in masking filtered locations for translated queries
+*
+* Revision 1.12  2004/08/09 15:40:51  dondosha
+* Propagated change in progotype for BLAST_TwoSeqLocSets
+*
+* Revision 1.11  2004/06/28 16:11:17  dondosha
+* Fixed constant name
+*
+* Revision 1.10  2004/06/24 21:17:07  dondosha
+* Boolean argument in ScoreAndEvalueToBuffers changed to Uint1
+*
 * Revision 1.9  2004/05/14 17:25:07  dondosha
 * Allow use of new BLAST engine
 *
@@ -182,6 +197,8 @@
 #include <tofasta.h>
 #include <wwwblast.h>
 #include <id1arch.h>
+#include <txalign.h>
+
 /* For rlimit stuff. */
 #if defined(OS_UNIX)
 #include <sys/resource.h>
@@ -198,11 +215,7 @@
 #include <qblastnet.h>
 #endif
 
-#if 1
-#define USE_NEW_BLAST
-#endif
-
-#ifdef USE_NEW_BLAST
+#ifndef USE_OLD_BLAST
 #include <algo/blast/api/twoseq_api.h>
 #endif
 
@@ -578,7 +591,7 @@ static void	Blast2SeqMainPage(CharPtr warning, CharPtr seq1, CharPtr seq2, CharP
            printf("</tr></table>\n");
         } else {
            printf("<CENTER><TABLE CELLSPACING=2 CELLPADDING=2 WIDTH=100%%>\n");
-           printf("<TR ALIGN=CENTER BaGCOLOR=#8dc7cc BGCOLOR=#0000ff><TD><B><I>\n");
+           printf("<TR ALIGN=CENTER BGCOLOR=#8dc7cc BGCOLOR=#0000ff><TD><B><I>\n");
            printf("<A HREF=http://www.ncbi.nlm.nih.gov/><font color=#ffffff>NCBI</font></A></I></B></TD>\n");
            printf("<TD><B><I>\n");
            printf("<A HREF=http://www.ncbi.nlm.nih.gov/Entrez><font color=#ffffff>Entrez</font></A>\n");
@@ -1052,109 +1065,27 @@ static Boolean sum_for_DenseSeg(DenseSegPtr dsp, AlignSumPtr asp)
 	return TRUE;
 }
 
-/* static functions from txalign.c needed for SEG masking */
-static void MaskWithLowComplexity(ByteStorePtr bsp, SeqLocPtr maskloc, Uint1 mol)
-{
-	SeqLocPtr slp = NULL;
-	Int4 start, stop;
-	Uint1 res = 'N';
-	
-
-	if(mol == Seq_mol_aa)
-		res = 'X';
-
-	while(maskloc)
-	{
-		slp = NULL;
- 		while((slp = SeqLocFindNext(maskloc, slp))!=NULL)
-		{
-			start = SeqLocStart(slp);
-			stop = SeqLocStop(slp);
-			BSSeek(bsp, start, SEEK_SET);
-			for(; start <=stop; ++start)
-                BSPutByte(bsp, (Int2)res);
-		}
-		maskloc = maskloc->next;
-	}
-}
-
-static ByteStorePtr create_byte_store_from_bsp (BioseqPtr bsp)
+/** Frees the part of the byte store list that has not been used for replacement
+ * of Bioseq data.
+ */
+static void 
+ByteStoreListFreeUnused (ValNodePtr bs_list, Uint1 frame_to_skip)
 {
-	SeqPortPtr spp;
-	Uint1 code;
-	ByteStorePtr b_store;
-	Uint1 residue;
-
-	if(bsp == NULL)
-		return NULL;
-	if(bsp->mol == Seq_mol_aa)
-		code = Seq_code_iupacaa;
-	else
-		code = Seq_code_iupacna;
-
-	spp = SeqPortNew(bsp, 0, bsp->length-1, Seq_strand_plus, code);
-	b_store = BSNew(bsp->length +1);
-	BSSeek(b_store, 0, SEEK_SET);
-	while((residue = SeqPortGetResidue(spp)) != SEQPORT_EOF)
-		BSPutByte(b_store, (Int2)residue);
-	SeqPortFree(spp);
-	return b_store;
-}
-
-static ValNodePtr CreateMaskByteStore (ValNodePtr mask_list)
-{
-	BioseqPtr bsp;
-	SeqLocPtr slp;
-	SeqIdPtr sip;
-	ValNodePtr list, curr;
-	ByteStorePtr b_store, c_store;
-	Uint1 mol;
-
-	list = NULL;
-	b_store = NULL;
-	while(mask_list)
-	{
-		curr = ValNodeNew(list);
-		curr->choice = mask_list->choice;
-		if(list == NULL)
-			list = curr;
-		slp = mask_list->data.ptrvalue;
-		if(slp != NULL)
-		{
-			if(b_store == NULL)
-			{
-				sip = SeqLocId(slp);
-				if(sip != NULL)
-				{
-					bsp = BioseqLockById(sip);
-					if(bsp != NULL)
-					{
-						b_store = create_byte_store_from_bsp (bsp);
-						mol = bsp->mol;
-						BioseqUnlock(bsp);
-					}
-				}
-			}
-			if(b_store != NULL)
-			{
-				if(mask_list->next == NULL)
-				{
-					c_store = b_store;
-					b_store = NULL;
-				}
-				else
-					c_store = BSDup(b_store);
-				MaskWithLowComplexity(c_store, slp, mol);
-				curr->data.ptrvalue = c_store;
-			}
-		}
-
-		mask_list = mask_list->next;
-	}
-
-	if(b_store != NULL)
-		BSFree(b_store);
-	return list;
+   ByteStorePtr bsp;
+   ValNodePtr bs_next = NULL;
+   Boolean skip_done = FALSE;
+
+   for( ; bs_list; bs_list = bs_next) {
+      bs_next = bs_list->next;
+      if (skip_done || bs_list->choice != frame_to_skip) {
+         bsp = (ByteStorePtr) bs_list->data.ptrvalue;
+         if(bsp != NULL)
+            BSFree(bsp);
+      } else {
+         skip_done = TRUE;
+      }
+      MemFree(bs_list);
+   }
 }
 
 /*******************************************************/
@@ -1167,12 +1098,14 @@ static void PrintOutScore(SeqAlignPtr sap, Boolean is_aa, Int4Ptr PNTR matrix, V
 	Char eval_buff[10], bit_score_buff[10];
 	AlignSumPtr asp;
 	Int2 percent_identical, percent_positive;
-        ValNodePtr bs_list;
-        BioseqPtr q_bsp;
-        Int4 frame;
-        Uint1 code;
-        Uint1 repr;
-        ByteStorePtr seq_data;
+   ValNodePtr bs_list;
+   BioseqPtr q_bsp;
+   Int4 frame;
+   Uint1 code=0;
+   Uint1 repr=0;
+   ByteStorePtr seq_data=NULL;
+   Boolean local_matrix = FALSE;     
+   Boolean seq_data_replaced = FALSE;
 
 	printf("<pre>\n");
 	GetScoreAndEvalue(sap, &score, &bit_score, &evalue, &number);
@@ -1181,7 +1114,7 @@ static void PrintOutScore(SeqAlignPtr sap, Boolean is_aa, Int4Ptr PNTR matrix, V
       before e. */
 	eval_buff_ptr = eval_buff;
    ScoreAndEvalueToBuffers(bit_score, evalue, bit_score_buff, 
-                           &eval_buff_ptr, TRUE);
+                           &eval_buff_ptr, TX_KNOCK_OFF_ALLOWED);
 
 	if (number == 1) {
 		printf("Score = %s bits (%ld), Expect = %s<BR>", 
@@ -1192,46 +1125,58 @@ static void PrintOutScore(SeqAlignPtr sap, Boolean is_aa, Int4Ptr PNTR matrix, V
 	}
 	asp = MemNew(sizeof(AlignSum));
 	asp->matrix = NULL;
-        if (is_aa) {
-           if (matrix != NULL)
-              asp->matrix = matrix;
-           else
-              asp->matrix = load_default_matrix();
+   if (is_aa) {
+      if (matrix != NULL)
+         asp->matrix = matrix;
+      else {
+         asp->matrix = load_default_matrix();
+         local_matrix = TRUE;
+      }
 	}
 	asp->is_aa = is_aa;
 	asp->totlen = 0;
 	asp->positive = 0;
 	asp->identical = 0;
 	asp->gaps = 0;
-        asp->master_sip = SeqIdDup(TxGetQueryIdFromSeqAlign(sap));
-        asp->target_sip = TxGetSubjectIdFromSeqAlign(sap);
-
-        if (mask_loc) { /* Mask the query sequence */
-           bs_list = CreateMaskByteStore (mask_loc);
-           q_bsp = BioseqLockById(asp->master_sip);
-           if (ISA_na(q_bsp->mol) && sap->segtype == SAS_STD) {
-              StdSegPtr ssp = (StdSegPtr) sap->segs;
-              frame = SeqLocStart(ssp->loc);
-              if (SeqLocStrand(ssp->loc) == Seq_strand_minus) {
-                 frame += SeqLocLen(ssp->loc);
-                 frame = -(1+(q_bsp->length - frame)%3);
-              } else {
-                 frame = (1+frame%3);
-              }
-           } else
-              frame = 0;
-           repr = q_bsp->repr;
-           seq_data = q_bsp->seq_data;
-           code = q_bsp->seq_data_type;
-           if (!replace_bytestore_data(q_bsp, bs_list, (Uint1)frame)) {
-              q_bsp->repr = repr;
-              q_bsp->seq_data = seq_data;
-              q_bsp->seq_data_type = code;
-           }
-           BioseqUnlock(q_bsp);
-        }
-
-        find_score_in_align(sap, 1, asp);
+   asp->master_sip = SeqIdDup(TxGetQueryIdFromSeqAlign(sap));
+   asp->target_sip = TxGetSubjectIdFromSeqAlign(sap);
+
+   if (mask_loc) { /* Mask the query sequence */
+      bs_list = CreateMaskByteStore (mask_loc);
+      q_bsp = BioseqLockById(asp->master_sip);
+      if (ISA_na(q_bsp->mol) && sap->segtype == SAS_STD) {
+         StdSegPtr ssp = (StdSegPtr) sap->segs;
+         frame = SeqLocStart(ssp->loc);
+         if (SeqLocStrand(ssp->loc) == Seq_strand_minus) {
+            frame += SeqLocLen(ssp->loc);
+            frame = -(1+(q_bsp->length - frame)%3);
+         } else {
+            frame = (1+frame%3);
+         }
+      } else
+         frame = 0;
+      repr = q_bsp->repr;
+      seq_data = q_bsp->seq_data;
+      code = q_bsp->seq_data_type;
+      seq_data_replaced = replace_bytestore_data(q_bsp, bs_list, (Uint1)frame);
+      if (!seq_data_replaced) {
+         q_bsp->repr = repr;
+         q_bsp->seq_data = seq_data;
+         q_bsp->seq_data_type = code;
+      }
+      BioseqUnlock(q_bsp);
+      ByteStoreListFreeUnused(bs_list, (Uint1)frame);
+   }
+   
+   find_score_in_align(sap, 1, asp);
+
+   /* Restore the unmasked sequence data. */
+   if (seq_data_replaced) {
+      q_bsp = BioseqLockById(asp->master_sip);
+      q_bsp->repr = repr;
+      q_bsp->seq_data = seq_data;
+      q_bsp->seq_data_type = code;
+   }
 
 	if (asp && asp->totlen > 0) {
            Char sign1, sign2;           
@@ -1273,8 +1218,11 @@ static void PrintOutScore(SeqAlignPtr sap, Boolean is_aa, Int4Ptr PNTR matrix, V
            printf("<BR><BR>");
 	}
 	printf("</pre>\n");		
-        SeqIdFree(asp->master_sip);
-        MemFree(asp);
+   
+   SeqIdFree(asp->master_sip);
+   if (local_matrix)
+      free_default_matrix(asp->matrix);
+   MemFree(asp);
 }
 
 static Int2 CreateRectAlign(SeqAlignPtr sap, PrymPtr PNTR rect, PrymPtr PNTR rectY, FloatHi scalex, FloatHi scaley, Int4 l1, Int4 l2, Int2 color, Int4 from, Int4 ffrom, Int4 to, Int4 tto)
@@ -1721,6 +1669,7 @@ static BioseqPtr FindSeqByAccession(CharPtr accver, Int2 id_num, Boolean is_na)
    if (gi > 0) {
       ValNodeAddInt(&sip, SEQID_GI, gi);
       bsp = BioseqLockById(sip);
+      SeqIdFree(sip);
    } 
 
    if (bsp == NULL)
@@ -1982,12 +1931,14 @@ static void* ConnectionThreadRun(void *p)
       if (run_status != WBLAST2_DONE) /* Sleep 4 seconds */
          poll(NULL, 0, 4000);
    }
-   
+
+   MemFree(fds);
+
    return NULL;
 }
 #endif
 
-#ifdef USE_NEW_BLAST
+#ifndef USE_OLD_BLAST
 static void BLASTOptions2SummaryOptions(BLAST_OptionsBlk* options,
                                         Char* progname,
                                         BLAST_SummaryOptions* s_options)
@@ -2031,9 +1982,8 @@ static void BLASTOptions2SummaryOptions(BLAST_OptionsBlk* options,
    s_options->gap_x_dropoff = options->gap_x_dropoff;
    s_options->db_length = options->db_length;
    s_options->word_threshold = options->threshold_second;
-   /* If window size is set to 0, enforce single hit method for initial 
-      words */
-   if (options->window_size == 0)
+
+   if (!options->multiple_hits_only)
       s_options->init_seed_method = eOneHit;
 }
 #endif
@@ -2076,7 +2026,6 @@ Int2 Main(void)
     static PrymPtr PNTR rectY;
     SeqLocPtr    slp1=NULL, slp2=NULL, slp, sl, qslp = NULL;
     Uint1        align_type;
-    
     ValNodePtr	   other_returns, mask, mask_head;
     CharPtr		   buffer = NULL;
     BLAST_KarlinBlkPtr ka_params=NULL, ka_gap_params=NULL;
@@ -2100,9 +2049,11 @@ Int2 Main(void)
     int pid, time_start, results_size = 0;
 #endif
 
-#ifdef USE_NEW_BLAST 
+#ifndef USE_OLD_BLAST 
     BLAST_SummaryOptions* s_options = NULL;
-    BLAST_SummaryReturn* s_return = NULL;
+    Blast_SummaryReturn* s_return = NULL;
+    Boolean mask_at_hash;
+    EBlastProgramType program_number; 
 #endif
 
 #ifdef RLIMIT_CPU
@@ -2462,10 +2413,14 @@ Int2 Main(void)
 
         StringCpy(options->matrix, mbuf);
         
-        /* one-pass non-multiple hits search with low threshold */		
-        options->two_pass_method  = FALSE;                      			
-        options->multiple_hits_only  = FALSE;
-        options->threshold_second = 9;
+        /* Use one-pass initial word search with low threshold, except for 
+           tblastx. Also do not use multiple hits approach for finding initial 
+           seeds. */
+        options->two_pass_method  = FALSE;  
+        if (StrCmp(progname, "tblastx")) {
+           options->threshold_second = 9;
+           options->multiple_hits_only  = FALSE;
+        }
     } else {
         if (gopen == -1) 
             gopen = (is_megablast) ? 0 : 5;
@@ -2597,13 +2552,24 @@ Int2 Main(void)
     logmsg(0);
 #endif
 
-#ifndef USE_NEW_BLAST
+#ifndef USE_OLD_BLAST
+    BLAST_SummaryOptionsInit(&s_options);
+    BLASTOptions2SummaryOptions(options, progname, s_options);
+    BLAST_TwoSeqLocSets(s_options, slp1, slp2, NULL, &seqalign, &mask, &mask_at_hash,
+                        &s_return);
+    if (mask_at_hash) {
+       /* If masking was done for lookup table only, do not use mask locations
+          for formatting. */
+       while (mask) {
+          SeqLocSetFree(mask->data.ptrvalue);
+          mask = mask->next;
+       }
+    }
+        
+    BLAST_SummaryOptionsFree(s_options);
+#else
     seqalign =  BlastTwoSequencesByLocEx(slp1, slp2, progname, 
                                          options, &other_returns, NULL);
-#else
-       BLAST_SummaryOptionsInit(&s_options);
-       BLASTOptions2SummaryOptions(options, progname, s_options);
-       BLAST_TwoSeqLocSets(s_options, slp1, slp2, &seqalign, &mask, &s_return);
 #endif
     run_status = WBLAST2_FORMAT;    
     /*	seqalign =  BlastTwoSequencesEx(query_bsp, subject_bsp, progname, 
@@ -2633,7 +2599,7 @@ Int2 Main(void)
         return 0;
     }
 
-#ifndef USE_NEW_BLAST
+#ifdef USE_OLD_BLAST
     mask = NULL;
     for (vnp=other_returns; vnp; vnp = vnp->next) {
         switch (vnp->choice) {
@@ -3023,7 +2989,22 @@ Int2 Main(void)
     if (txmatrix)
         txmatrix = TxMatrixDestruct(txmatrix);
     dbinfo = TxDfDbInfoDestruct(dbinfo);
-#ifndef USE_NEW_BLAST
+#ifndef USE_OLD_BLAST
+    if (s_return->ka_params) {
+       PrintKAParameters(s_return->ka_params->Lambda, s_return->ka_params->K, 
+                         s_return->ka_params->H, 70, stdout, FALSE);
+    }
+    if (s_return->ka_params_gap) {
+       PrintKAParameters(s_return->ka_params_gap->Lambda, 
+                         s_return->ka_params_gap->K, 
+                         s_return->ka_params_gap->H, 70, stdout, TRUE);
+    }
+    BlastProgram2Number(progname, &program_number);
+    buffer = Blast_GetParametersBuffer(program_number, s_return);
+    PrintTildeSepLines(buffer, 70, stdout);
+    sfree(buffer);
+    Blast_SummaryReturnFree(s_return);
+#else
     if (ka_params) {
         PrintKAParameters(ka_params->Lambda, ka_params->K, ka_params->H, 
                           70, stdout, FALSE);
@@ -3037,25 +3018,14 @@ Int2 Main(void)
     PrintTildeSepLines(buffer, 70, stdout);
     MemFree(buffer);
     free_buff();
+#endif
     mask_head = mask;
     while (mask) {
         SeqLocSetFree(mask->data.ptrvalue);
         mask = mask->next;
     }
     ValNodeFree(mask_head);
-#else
-    if (s_return->ka_params) {
-       PrintKAParameters(s_return->ka_params->Lambda, s_return->ka_params->K, 
-                         s_return->ka_params->H, 70, stdout, FALSE);
-    }
-    if (s_return->ka_params_gap) {
-       PrintKAParameters(s_return->ka_params_gap->Lambda, 
-                         s_return->ka_params_gap->K, 
-                         s_return->ka_params_gap->H, 70, stdout, TRUE);
-    }
-    PrintTildeSepLines(s_return->params_buffer, 70, stdout);
-    
-#endif
+
     CreateTailHTML();
     run_status = WBLAST2_DONE;
     options = BLASTOptionDelete(options);
diff --git a/network/wwwblast/Src/wwwblast.h b/network/wwwblast/Src/wwwblast.h
index 7df7f90c..657dca15 100644
--- a/network/wwwblast/Src/wwwblast.h
+++ b/network/wwwblast/Src/wwwblast.h
@@ -1,4 +1,4 @@
-/* $Id: wwwblast.h,v 1.2 2003/05/13 22:00:37 dondosha Exp $
+/* $Id: wwwblast.h,v 1.3 2004/06/30 21:06:21 madden Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,12 +29,15 @@
 *
 * Initial Creation Date: 03/15/2000
 *
-* $Revision: 1.2 $
+* $Revision: 1.3 $
 *
 * File Description:
 *        Definitions for standalone WWW Blast CGI program.
 *
 * $Log: wwwblast.h,v $
+* Revision 1.3  2004/06/30 21:06:21  madden
+* Add include for blfmtutl.h
+*
 * Revision 1.2  2003/05/13 22:00:37  dondosha
 * More changes to make alternative links work
 *
@@ -85,6 +88,7 @@
 #include <ddvcreate.h>
 #include <objblst3.h>
 #include <mblast.h>
+#include <blfmtutl.h>
 
 #ifdef NCBI_CLIENT_SERVER
 #include <netblap3.h>