Load ncbi (6.1.20030421) into ncbi-tools6/branches/upstream/current.

17 files changed, 1097 insertions, 232 deletions

diff --git a/network/blast3/client/netblap3.c b/network/blast3/client/netblap3.c
index 3b561e5b..191d5b13 100644
--- a/network/blast3/client/netblap3.c
+++ b/network/blast3/client/netblap3.c
@@ -34,6 +34,12 @@
 *
 * RCS Modification History:
 * $Log: netblap3.c,v $
+* Revision 1.104  2003/01/13 18:08:26  bealer
+* - Replace nonstandard snprintf() function with strcpy/strcat/strlen.
+*
+* Revision 1.103  2003/01/10 21:45:06  bealer
+* - Modify to return errors from BLASTGetUidsFromQuery instead of logging them.
+*
 * Revision 1.102  2002/10/30 18:54:58  madden
 * NULL out SeqLoc for lower-case masking
 *
@@ -2787,8 +2793,11 @@ parametersToOptions (BlastParametersPtr parameters, CharPtr program, ValNodePtr
    to get list of gis corresponding to the Entrez Boolean string or
    just number of such hits in the Entrez database */
 
-NLM_EXTERN Int4 BLASTGetUidsFromQuery(CharPtr query, Int4Ptr PNTR uids, 
-                                      Boolean is_na, Boolean count_only)
+NLM_EXTERN Int4 BLASTGetUidsFromQuery(CharPtr       query,
+				      Int4Ptr PNTR  uids,
+                                      Boolean       is_na,
+				      Boolean       count_only,
+				      BlastError ** blast_err)
 {
     Entrez2ReplyPtr e2ry;
     Entrez2RequestPtr  e2rq;
@@ -2811,20 +2820,55 @@ NLM_EXTERN Int4 BLASTGetUidsFromQuery(CharPtr query, Int4Ptr PNTR uids,
     e2ry = EntrezSynchronousQuery (e2rq);
     
     if (e2ry == NULL) {
-        ErrPostEx(SEV_ERROR, 0, 0, 
-                  "NULL returned from EntrezSynchronousQuery()");
+	if ( blast_err ) {
+	    *blast_err = BlastErrorNew();
+	    
+	    (*blast_err)->level = Blast_error_level_error;
+	    (*blast_err)->msg   = StrSave("NULL returned from EntrezSynchronousQuery()");
+	} else {
+	    ErrPostEx(SEV_ERROR, 0, 0, 
+		      "NULL returned from EntrezSynchronousQuery()");
+	}
+	
         return -1;
     }
-
+    
     if((e2rp = e2ry->reply) == NULL) {
-        ErrPostEx(SEV_ERROR, 0, 0, "Invalid ASN.1: E2ReplyPtr==NULL");
+	if ( blast_err ) {
+	    *blast_err = BlastErrorNew();
+	    
+	    (*blast_err)->level = Blast_error_level_error;
+	    (*blast_err)->msg   = StrSave("Invalid ASN.1: E2ReplyPtr==NULL");
+	} else {
+	    ErrPostEx(SEV_ERROR, 0, 0, "Invalid ASN.1: E2ReplyPtr==NULL");
+	}
         return -1;
     }
     
     switch(e2rp->choice) {
-        
     case E2Reply_error:
-        ErrPostEx(SEV_ERROR, 0, 0, (CharPtr) e2rp->data.ptrvalue);
+	if ( blast_err ) {
+	    const char * msg1 = "Error in request: ";
+	    const char * msg2 = (CharPtr) e2rp->data.ptrvalue;
+	    char       * msg3 = 0;
+	    
+	    int msglen1 = strlen(msg1);
+	    int msglen2 = strlen(msg2);
+	    
+	    msg3 = MemNew(msglen1 + msglen2 + 1);
+	    
+	    if ( msg3 ) {
+		strcpy(msg3, msg1);	
+		strcat(msg3, msg2);
+		
+		*blast_err = BlastErrorNew();
+		
+		(*blast_err)->level = Blast_error_level_error;
+		(*blast_err)->msg   = msg3;
+	    }
+	} else {
+	    ErrPostEx(SEV_ERROR, 0, 0, "Error in request: %s", (CharPtr) e2rp->data.ptrvalue);
+	}
         count = -1;
         break;
     case E2Reply_eval_boolean:
@@ -2840,15 +2884,36 @@ NLM_EXTERN Int4 BLASTGetUidsFromQuery(CharPtr query, Int4Ptr PNTR uids,
         }
         break;
     default:
-        ErrPostEx(SEV_ERROR, 0, 0, "Invalid reply type from the server: %d", e2rp->choice);
+	if ( blast_err ) {
+	    const char * msg1 = "Invalid reply type from the server: ";
+	    const char * msg2 = (CharPtr) e2rp->data.ptrvalue;
+	    char       * msg3 = 0;
+	    
+	    int msglen1 = strlen(msg1);
+	    int msglen2 = strlen(msg2);
+	    
+	    msg3 = MemNew(msglen1 + msglen2 + 1);
+	    
+	    if ( msg3 ) {
+		strcpy(msg3, msg1);	
+		strcat(msg3, msg2);
+		
+		*blast_err = BlastErrorNew();
+		
+		(*blast_err)->level = Blast_error_level_error;
+		(*blast_err)->msg   = msg3;
+	    }
+	} else {
+	    ErrPostEx(SEV_ERROR, 0, 0, "Invalid reply type from the server: %d", e2rp->choice);
+	}
         count = -1;
         break;
-        
     }
     
     Entrez2ReplyFree(e2ry);
     Entrez2RequestFree(e2rq);
-
+    
     return count;
 }
 #endif
+
diff --git a/network/blast3/client/netblap3.h b/network/blast3/client/netblap3.h
index d1c0124f..239e34cc 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 1.31  2003/01/10 21:45:06  bealer
+* - Modify to return errors from BLASTGetUidsFromQuery instead of logging them.
+*
 * Revision 1.30  2002/05/23 22:57:03  dondosha
 * Made GetResponsePtr external
 *
@@ -249,8 +252,11 @@ NLM_EXTERN BLAST_OptionsBlkPtr parametersToOptions (BlastParametersPtr parameter
 
 NLM_EXTERN BlastDbinfoPtr LIBCALL Blast3GetDbinfo(BlastNet3Hptr bl3hptr);
 
-NLM_EXTERN Int4 BLASTGetUidsFromQuery(CharPtr query, Int4Ptr PNTR uids, 
-                                      Boolean is_na, Boolean count_only);
+NLM_EXTERN Int4 BLASTGetUidsFromQuery(CharPtr       query, 
+				      Int4Ptr PNTR  uids, 
+                                      Boolean       is_na, 
+				      Boolean       count_only,
+				      BlastError ** err_ret);
 
 NLM_EXTERN Boolean SubmitRequest PROTO((BlastNet3Hptr bl3hptr, BlastRequestPtr blreqp, BlastResponsePtr PNTR response, NetProgressCallback callback, Boolean reestablish));
 
diff --git a/network/id1arch/id1.asn b/network/id1arch/id1.asn
index 7b8f9c5c..7f8d3cc1 100644
--- a/network/id1arch/id1.asn
+++ b/network/id1arch/id1.asn
@@ -1,4 +1,4 @@
---$Revision: 1.4 $
+--$Revision: 1.9 $
 --********************************************************************
 --
 --  Network Id server network access
@@ -32,8 +32,10 @@ ID1server-request ::= CHOICE {
 		getseqidsfromgi	INTEGER, --get all Seq-ids of given gi
 		getgihist	INTEGER, --get an historical list of gis 
 		getgirev	INTEGER, --get a revision history of gi
-		getgistate	INTEGER  --get a state of gi
- }
+		getgistate	INTEGER,  --get a state of gi
+		getsewithinfo	ID1server-maxcomplex,
+		getblobinfo	ID1server-maxcomplex
+}
 
 --  Complexity stuff will be for ID1
 
@@ -68,8 +70,29 @@ ID1server-back ::= CHOICE {
 		ids	SET OF Seq-id,
 		gihist	SET OF ID1Seq-hist,  -- because hand crafted Seq-hist does not follow 
 		                             -- same conventions 
-		girevhist SET OF ID1Seq-hist
- }
+		girevhist SET OF ID1Seq-hist,
+		gotsewithinfo   ID1SeqEntry-info,
+		gotblobinfo	ID1blob-info	
+}
 
 ID1server-debug ::= SET OF ID1server-back
+
+
+ID1blob-info ::= SEQUENCE {
+		gi INTEGER ,
+		sat INTEGER,
+                sat-key INTEGER,
+                satname VisibleString,
+		suppress	INTEGER,
+		withdrawn	INTEGER,
+		confidential	INTEGER,
+		blob-state	INTEGER,
+                comment         VisibleString OPTIONAL, -- public comment for withdrawn record 
+		extfeatmask	INTEGER	      OPTIONAL  -- mask for external features (SNP,...)
+}
+
+ID1SeqEntry-info ::= SEQUENCE {
+		blob-info	ID1blob-info,
+		blob		Seq-entry OPTIONAL
+}
 END
diff --git a/network/id1arch/id1.h b/network/id1arch/id1.h
index b7a5977b..a9596d75 100644
--- a/network/id1arch/id1.h
+++ b/network/id1arch/id1.h
@@ -9,7 +9,7 @@
 #include <asn.h>
 #endif
 
-static char * asnfilename = "id1.h13";
+static char * asnfilename = "id1.h18";
 static AsnValxNode avnx[5] = {
     {20,"entry" ,0,0.0,&avnx[1] } ,
     {20,"bioseq" ,1,0.0,&avnx[2] } ,
@@ -17,18 +17,18 @@ static AsnValxNode avnx[5] = {
     {20,"nuc-prot" ,3,0.0,&avnx[4] } ,
     {20,"pub-set" ,4,0.0,NULL } };
 
-static AsnType atx[42] = {
+static AsnType atx[60] = {
   {401, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1]} ,
   {402, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[2]} ,
   {403, "Seq-hist" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[3]} ,
-  {404, "ID1server-request" ,1,0,0,0,0,0,0,0,NULL,&atx[22],&atx[4],0,&atx[8]} ,
+  {404, "ID1server-request" ,1,0,0,0,0,0,0,0,NULL,&atx[24],&atx[4],0,&atx[8]} ,
   {0, "init" ,128,0,0,0,0,0,0,0,NULL,&atx[5],NULL,0,&atx[6]} ,
   {305, "NULL" ,0,5,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "getgi" ,128,1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[7]} ,
   {0, "getsefromgi" ,128,2,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[17]} ,
   {405, "ID1server-maxcomplex" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[9],0,&atx[10]} ,
   {0, "maxplex" ,128,0,0,0,0,0,0,0,NULL,&atx[10],NULL,0,&atx[12]} ,
-  {406, "Entry-complexities" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[0],0,&atx[23]} ,
+  {406, "Entry-complexities" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[0],0,&atx[25]} ,
   {302, "INTEGER" ,0,2,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "gi" ,128,1,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[13]} ,
   {0, "ent" ,128,2,0,1,0,0,0,0,NULL,&atx[11],NULL,0,&atx[14]} ,
@@ -39,30 +39,48 @@ static AsnType atx[42] = {
   {0, "getseqidsfromgi" ,128,4,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[19]} ,
   {0, "getgihist" ,128,5,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[20]} ,
   {0, "getgirev" ,128,6,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[21]} ,
-  {0, "getgistate" ,128,7,0,0,0,0,0,0,NULL,&atx[11],NULL,0,NULL} ,
+  {0, "getgistate" ,128,7,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[22]} ,
+  {0, "getsewithinfo" ,128,8,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[23]} ,
+  {0, "getblobinfo" ,128,9,0,0,0,0,0,0,NULL,&atx[8],NULL,0,NULL} ,
   {315, "CHOICE" ,0,-1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {407, "ID1Seq-hist" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[24],0,&atx[25]} ,
+  {407, "ID1Seq-hist" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[26],0,&atx[27]} ,
   {0, "hist" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {408, "ID1server-back" ,1,0,0,0,0,0,0,0,NULL,&atx[22],&atx[26],0,&atx[40]} ,
-  {0, "init" ,128,0,0,0,0,0,0,0,NULL,&atx[5],NULL,0,&atx[27]} ,
-  {0, "error" ,128,1,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[28]} ,
-  {0, "gotgi" ,128,2,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[29]} ,
-  {0, "gotseqentry" ,128,3,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[30]} ,
-  {0, "gotdeadseqentry" ,128,4,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[31]} ,
-  {0, "fini" ,128,5,0,0,0,0,0,0,NULL,&atx[5],NULL,0,&atx[32]} ,
-  {0, "gistate" ,128,6,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[33]} ,
-  {0, "ids" ,128,7,0,0,0,0,0,0,NULL,&atx[35],&atx[34],0,&atx[36]} ,
+  {408, "ID1server-back" ,1,0,0,0,0,0,0,0,NULL,&atx[24],&atx[28],0,&atx[43]} ,
+  {0, "init" ,128,0,0,0,0,0,0,0,NULL,&atx[5],NULL,0,&atx[29]} ,
+  {0, "error" ,128,1,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[30]} ,
+  {0, "gotgi" ,128,2,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[31]} ,
+  {0, "gotseqentry" ,128,3,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[32]} ,
+  {0, "gotdeadseqentry" ,128,4,0,0,0,0,0,0,NULL,&atx[1],NULL,0,&atx[33]} ,
+  {0, "fini" ,128,5,0,0,0,0,0,0,NULL,&atx[5],NULL,0,&atx[34]} ,
+  {0, "gistate" ,128,6,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[35]} ,
+  {0, "ids" ,128,7,0,0,0,0,0,0,NULL,&atx[37],&atx[36],0,&atx[38]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,NULL} ,
   {314, "SET OF" ,0,17,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {0, "gihist" ,128,8,0,0,0,0,0,0,NULL,&atx[35],&atx[37],0,&atx[38]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[23],NULL,0,NULL} ,
-  {0, "girevhist" ,128,9,0,0,0,0,0,0,NULL,&atx[35],&atx[39],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[23],NULL,0,NULL} ,
-  {409, "ID1server-debug" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[41],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[25],NULL,0,NULL} };
+  {0, "gihist" ,128,8,0,0,0,0,0,0,NULL,&atx[37],&atx[39],0,&atx[40]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[25],NULL,0,NULL} ,
+  {0, "girevhist" ,128,9,0,0,0,0,0,0,NULL,&atx[37],&atx[41],0,&atx[42]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[25],NULL,0,NULL} ,
+  {0, "gotsewithinfo" ,128,10,0,0,0,0,0,0,NULL,&atx[43],NULL,0,&atx[57]} ,
+  {409, "ID1SeqEntry-info" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[44],0,&atx[45]} ,
+  {0, "blob-info" ,128,0,0,0,0,0,0,0,NULL,&atx[45],NULL,0,&atx[56]} ,
+  {410, "ID1blob-info" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[46],0,&atx[58]} ,
+  {0, "gi" ,128,0,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[47]} ,
+  {0, "sat" ,128,1,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[48]} ,
+  {0, "sat-key" ,128,2,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[49]} ,
+  {0, "satname" ,128,3,0,0,0,0,0,0,NULL,&atx[15],NULL,0,&atx[50]} ,
+  {0, "suppress" ,128,4,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[51]} ,
+  {0, "withdrawn" ,128,5,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[52]} ,
+  {0, "confidential" ,128,6,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[53]} ,
+  {0, "blob-state" ,128,7,0,0,0,0,0,0,NULL,&atx[11],NULL,0,&atx[54]} ,
+  {0, "comment" ,128,8,0,1,0,0,0,0,NULL,&atx[15],NULL,0,&atx[55]} ,
+  {0, "extfeatmask" ,128,9,0,1,0,0,0,0,NULL,&atx[11],NULL,0,NULL} ,
+  {0, "blob" ,128,1,0,1,0,0,0,0,NULL,&atx[1],NULL,0,NULL} ,
+  {0, "gotblobinfo" ,128,11,0,0,0,0,0,0,NULL,&atx[45],NULL,0,NULL} ,
+  {411, "ID1server-debug" ,1,0,0,0,0,0,0,0,NULL,&atx[37],&atx[59],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[27],NULL,0,NULL} };
 
 static AsnModule ampx[1] = {
-  { "NCBI-ID1Access" , "id1.h13",&atx[0],NULL,NULL,0,0} };
+  { "NCBI-ID1Access" , "id1.h18",&atx[0],NULL,NULL,0,0} };
 
 static AsnValxNodePtr avn = avnx;
 static AsnTypePtr at = atx;
@@ -85,6 +103,8 @@ static AsnModulePtr amp = ampx;
 #define ID1SERVER_REQUEST_getgihist &at[19]
 #define ID1SERVER_REQUEST_getgirev &at[20]
 #define ID1SERVER_REQUEST_getgistate &at[21]
+#define ID1SERVER_REQUEST_getsewithinfo &at[22]
+#define ID1SERVER_REQUEST_getblobinfo &at[23]
 
 #define ID1SERVER_MAXCOMPLEX &at[8]
 #define ID1SERVER_MAXCOMPLEX_maxplex &at[9]
@@ -94,23 +114,41 @@ static AsnModulePtr amp = ampx;
 
 #define ENTRY_COMPLEXITIES &at[10]
 
-#define ID1SEQ_HIST &at[23]
-#define ID1SEQ_HIST_hist &at[24]
-
-#define ID1SERVER_BACK &at[25]
-#define ID1SERVER_BACK_init &at[26]
-#define ID1SERVER_BACK_error &at[27]
-#define ID1SERVER_BACK_gotgi &at[28]
-#define ID1SERVER_BACK_gotseqentry &at[29]
-#define ID1SERVER_BACK_gotdeadseqentry &at[30]
-#define ID1SERVER_BACK_fini &at[31]
-#define ID1SERVER_BACK_gistate &at[32]
-#define ID1SERVER_BACK_ids &at[33]
-#define ID1SERVER_BACK_ids_E &at[34]
-#define ID1SERVER_BACK_gihist &at[36]
-#define ID1SERVER_BACK_gihist_E &at[37]
-#define ID1SERVER_BACK_girevhist &at[38]
-#define ID1SERVER_BACK_girevhist_E &at[39]
-
-#define ID1SERVER_DEBUG &at[40]
-#define ID1SERVER_DEBUG_E &at[41]
+#define ID1SEQ_HIST &at[25]
+#define ID1SEQ_HIST_hist &at[26]
+
+#define ID1SERVER_BACK &at[27]
+#define ID1SERVER_BACK_init &at[28]
+#define ID1SERVER_BACK_error &at[29]
+#define ID1SERVER_BACK_gotgi &at[30]
+#define ID1SERVER_BACK_gotseqentry &at[31]
+#define ID1SERVER_BACK_gotdeadseqentry &at[32]
+#define ID1SERVER_BACK_fini &at[33]
+#define ID1SERVER_BACK_gistate &at[34]
+#define ID1SERVER_BACK_ids &at[35]
+#define ID1SERVER_BACK_ids_E &at[36]
+#define ID1SERVER_BACK_gihist &at[38]
+#define ID1SERVER_BACK_gihist_E &at[39]
+#define ID1SERVER_BACK_girevhist &at[40]
+#define ID1SERVER_BACK_girevhist_E &at[41]
+#define ID1SERVER_BACK_gotsewithinfo &at[42]
+#define ID1SERVER_BACK_gotblobinfo &at[57]
+
+#define ID1SEQENTRY_INFO &at[43]
+#define ID1SEQENTRY_INFO_blob_info &at[44]
+#define ID1SEQENTRY_INFO_blob &at[56]
+
+#define ID1BLOB_INFO &at[45]
+#define ID1BLOB_INFO_gi &at[46]
+#define ID1BLOB_INFO_sat &at[47]
+#define ID1BLOB_INFO_sat_key &at[48]
+#define ID1BLOB_INFO_satname &at[49]
+#define ID1BLOB_INFO_suppress &at[50]
+#define ID1BLOB_INFO_withdrawn &at[51]
+#define ID1BLOB_INFO_confidential &at[52]
+#define ID1BLOB_INFO_blob_state &at[53]
+#define ID1BLOB_INFO_comment &at[54]
+#define ID1BLOB_INFO_extfeatmask &at[55]
+
+#define ID1SERVER_DEBUG &at[58]
+#define ID1SERVER_DEBUG_E &at[59]
diff --git a/network/id1arch/id1arch.c b/network/id1arch/id1arch.c
index 0b9ffab0..39c58afd 100644
--- a/network/id1arch/id1arch.c
+++ b/network/id1arch/id1arch.c
@@ -134,7 +134,11 @@ s_ID1ArchSeqEntryGet (Int4 uid, CharPtr db, Int4 ent,Int4Ptr status, Int2 maxple
     AsnIoReset(asnout);
     ID1serverRequestFree (id1reqp);
 
-    if ((id1bp = NetID1servReadAsn()) == NULL)
+    SeqMgrHoldIndexing(TRUE);
+    id1bp = NetID1servReadAsn();
+    SeqMgrHoldIndexing(FALSE);
+
+    if (id1bp == NULL)
         return NULL;
 
     if (id1bp->choice != ID1serverBack_gotseqentry &&
diff --git a/network/id1arch/id1gen.c b/network/id1arch/id1gen.c
index cecce98d..a5a2fa4f 100644
--- a/network/id1arch/id1gen.c
+++ b/network/id1arch/id1gen.c
@@ -32,7 +32,7 @@ id1genAsnLoad(void)
 
 /**************************************************
 *    Generated object loaders for Module NCBI-ID1Access
-*    Generated using ASNCODE Revision: 6.0 at Jul 30, 1998  4:04 PM
+*    Generated using ASNCODE Revision: 6.0 at Mar 18, 2003 12:08 PM
 *
 **************************************************/
 
@@ -63,6 +63,12 @@ ID1serverRequestFree(ValNodePtr anp)
    case ID1serverRequest_getsefromgi:
       ID1serverMaxcomplexFree(anp -> data.ptrvalue);
       break;
+   case ID1serverRequest_getsewithinfo:
+      ID1serverMaxcomplexFree(anp -> data.ptrvalue);
+      break;
+   case ID1serverRequest_getblobinfo:
+      ID1serverMaxcomplexFree(anp -> data.ptrvalue);
+      break;
    }
    return MemFree(anp);
 }
@@ -169,6 +175,14 @@ ID1serverRequestAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       }
       anp->data.intvalue = av.intvalue;
    }
+   else if (atp == ID1SERVER_REQUEST_getsewithinfo) {
+      choice = ID1serverRequest_getsewithinfo;
+      func = (AsnReadFunc) ID1serverMaxcomplexAsnRead;
+   }
+   else if (atp == ID1SERVER_REQUEST_getblobinfo) {
+      choice = ID1serverRequest_getblobinfo;
+      func = (AsnReadFunc) ID1serverMaxcomplexAsnRead;
+   }
    anp->choice = choice;
    if (func != NULL)
    {
@@ -262,6 +276,14 @@ ID1serverRequestAsnWrite(ID1serverRequestPtr anp, AsnIoPtr aip, AsnTypePtr orig)
       av.intvalue = anp->data.intvalue;
       retval = AsnWrite(aip, ID1SERVER_REQUEST_getgistate, &av);
       break;
+   case ID1serverRequest_getsewithinfo:
+      writetype = ID1SERVER_REQUEST_getsewithinfo;
+      func = (AsnWriteFunc) ID1serverMaxcomplexAsnWrite;
+      break;
+   case ID1serverRequest_getblobinfo:
+      writetype = ID1SERVER_REQUEST_getblobinfo;
+      func = (AsnWriteFunc) ID1serverMaxcomplexAsnWrite;
+      break;
    }
    if (writetype != NULL) {
       retval = (* func)(pnt, aip, writetype);   /* write it out */
@@ -650,6 +672,12 @@ ID1serverBackFree(ValNodePtr anp)
    case ID1serverBack_girevhist:
       AsnGenericUserSeqOfFree((Pointer) pnt, (AsnOptFreeFunc) ID1SeqHistFree);
       break;
+   case ID1serverBack_gotsewithinfo:
+      ID1SeqEntryInfoFree(anp -> data.ptrvalue);
+      break;
+   case ID1serverBack_gotblobinfo:
+      ID1blobInfoFree(anp -> data.ptrvalue);
+      break;
    }
    return MemFree(anp);
 }
@@ -773,6 +801,14 @@ ID1serverBackAsnRead(AsnIoPtr aip, AsnTypePtr orig)
          goto erret;
       }
    }
+   else if (atp == ID1SERVER_BACK_gotsewithinfo) {
+      choice = ID1serverBack_gotsewithinfo;
+      func = (AsnReadFunc) ID1SeqEntryInfoAsnRead;
+   }
+   else if (atp == ID1SERVER_BACK_gotblobinfo) {
+      choice = ID1serverBack_gotblobinfo;
+      func = (AsnReadFunc) ID1blobInfoAsnRead;
+   }
    anp->choice = choice;
    if (func != NULL)
    {
@@ -871,6 +907,14 @@ ID1serverBackAsnWrite(ID1serverBackPtr anp, AsnIoPtr aip, AsnTypePtr orig)
    case ID1serverBack_girevhist:
       retval = AsnGenericUserSeqOfAsnWrite((Pointer) pnt, (AsnWriteFunc) ID1SeqHistAsnWrite, aip, ID1SERVER_BACK_girevhist, ID1SERVER_BACK_girevhist_E);
       break;
+   case ID1serverBack_gotsewithinfo:
+      writetype = ID1SERVER_BACK_gotsewithinfo;
+      func = (AsnWriteFunc) ID1SeqEntryInfoAsnWrite;
+      break;
+   case ID1serverBack_gotblobinfo:
+      writetype = ID1SERVER_BACK_gotblobinfo;
+      func = (AsnWriteFunc) ID1blobInfoAsnWrite;
+      break;
    }
    if (writetype != NULL) {
       retval = (* func)(pnt, aip, writetype);   /* write it out */
@@ -888,6 +932,414 @@ erret:
 
 /**************************************************
 *
+*    ID1SeqEntryInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID1SeqEntryInfoPtr LIBCALL
+ID1SeqEntryInfoNew(void)
+{
+   ID1SeqEntryInfoPtr ptr = MemNew((size_t) sizeof(ID1SeqEntryInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID1SeqEntryInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID1SeqEntryInfoPtr LIBCALL
+ID1SeqEntryInfoFree(ID1SeqEntryInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ID1blobInfoFree(ptr -> blob_info);
+   SeqEntryFree(ptr -> blob);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID1SeqEntryInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID1SeqEntryInfoPtr LIBCALL
+ID1SeqEntryInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID1SeqEntryInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id1genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID1SeqEntryInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID1SEQENTRY_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID1SEQENTRY_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID1SeqEntryInfoNew();
+   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 == ID1SEQENTRY_INFO_blob_info) {
+      ptr -> blob_info = ID1blobInfoAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1SEQENTRY_INFO_blob) {
+      ptr -> blob = SeqEntryAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID1SeqEntryInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID1SeqEntryInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID1SeqEntryInfoAsnWrite(ID1SeqEntryInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id1genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID1SEQENTRY_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> blob_info != NULL) {
+      if ( ! ID1blobInfoAsnWrite(ptr -> blob_info, aip, ID1SEQENTRY_INFO_blob_info)) {
+         goto erret;
+      }
+   }
+   if (ptr -> blob != NULL) {
+      if ( ! SeqEntryAsnWrite(ptr -> blob, aip, ID1SEQENTRY_INFO_blob)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ID1blobInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+ID1blobInfoPtr LIBCALL
+ID1blobInfoNew(void)
+{
+   ID1blobInfoPtr ptr = MemNew((size_t) sizeof(ID1blobInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ID1blobInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+ID1blobInfoPtr LIBCALL
+ID1blobInfoFree(ID1blobInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> satname);
+   MemFree(ptr -> comment);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ID1blobInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ID1blobInfoPtr LIBCALL
+ID1blobInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ID1blobInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! id1genAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ID1blobInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, ID1BLOB_INFO);
+   } else {
+      atp = AsnLinkType(orig, ID1BLOB_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ID1blobInfoNew();
+   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 == ID1BLOB_INFO_gi) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> gi = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1BLOB_INFO_sat) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> sat = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1BLOB_INFO_sat_key) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> sat_key = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1BLOB_INFO_satname) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> satname = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1BLOB_INFO_suppress) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> suppress = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1BLOB_INFO_withdrawn) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> withdrawn = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1BLOB_INFO_confidential) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> confidential = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1BLOB_INFO_blob_state) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> blob_state = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1BLOB_INFO_comment) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> comment = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ID1BLOB_INFO_extfeatmask) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> extfeatmask = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ID1blobInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ID1blobInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ID1blobInfoAsnWrite(ID1blobInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! id1genAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, ID1BLOB_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 -> gi;
+   retval = AsnWrite(aip, ID1BLOB_INFO_gi,  &av);
+   av.intvalue = ptr -> sat;
+   retval = AsnWrite(aip, ID1BLOB_INFO_sat,  &av);
+   av.intvalue = ptr -> sat_key;
+   retval = AsnWrite(aip, ID1BLOB_INFO_sat_key,  &av);
+   if (ptr -> satname != NULL) {
+      av.ptrvalue = ptr -> satname;
+      retval = AsnWrite(aip, ID1BLOB_INFO_satname,  &av);
+   }
+   av.intvalue = ptr -> suppress;
+   retval = AsnWrite(aip, ID1BLOB_INFO_suppress,  &av);
+   av.intvalue = ptr -> withdrawn;
+   retval = AsnWrite(aip, ID1BLOB_INFO_withdrawn,  &av);
+   av.intvalue = ptr -> confidential;
+   retval = AsnWrite(aip, ID1BLOB_INFO_confidential,  &av);
+   av.intvalue = ptr -> blob_state;
+   retval = AsnWrite(aip, ID1BLOB_INFO_blob_state,  &av);
+   if (ptr -> comment != NULL) {
+      av.ptrvalue = ptr -> comment;
+      retval = AsnWrite(aip, ID1BLOB_INFO_comment,  &av);
+   }
+   av.intvalue = ptr -> extfeatmask;
+   retval = AsnWrite(aip, ID1BLOB_INFO_extfeatmask,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
 *    ID1serverDebugFree()
 *
 **************************************************/
@@ -913,7 +1365,7 @@ NLM_EXTERN
 ID1serverDebugPtr LIBCALL
 ID1serverDebugAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 {
-   
+   DataVal av;
    AsnTypePtr atp;
    Boolean isError = FALSE;
    AsnReadFunc func;
@@ -969,7 +1421,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 ID1serverDebugAsnWrite(ID1serverDebugPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
-
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
diff --git a/network/id1arch/id1gen.h b/network/id1arch/id1gen.h
index cb0988d2..f7cc4209 100644
--- a/network/id1arch/id1gen.h
+++ b/network/id1arch/id1gen.h
@@ -17,7 +17,7 @@ extern "C" { /* } */
 /**************************************************
 *
 *    Generated objects for Module NCBI-ID1Access
-*    Generated using ASNCODE Revision: 6.0 at Jul 30, 1998  4:04 PM
+*    Generated using ASNCODE Revision: 6.0 at Mar 18, 2003 12:08 PM
 *
 **************************************************/
 
@@ -33,6 +33,8 @@ typedef ValNode ID1serverRequest;
 #define ID1serverRequest_getgihist 6
 #define ID1serverRequest_getgirev 7
 #define ID1serverRequest_getgistate 8
+#define ID1serverRequest_getsewithinfo 9
+#define ID1serverRequest_getblobinfo 10
 
 
 NLM_EXTERN ID1serverRequestPtr LIBCALL ID1serverRequestFree PROTO ((ID1serverRequestPtr ));
@@ -89,6 +91,8 @@ typedef ValNode ID1serverBack;
 #define ID1serverBack_ids 8
 #define ID1serverBack_gihist 9
 #define ID1serverBack_girevhist 10
+#define ID1serverBack_gotsewithinfo 11
+#define ID1serverBack_gotblobinfo 12
 
 
 NLM_EXTERN ID1serverBackPtr LIBCALL ID1serverBackFree PROTO ((ID1serverBackPtr ));
@@ -99,6 +103,50 @@ NLM_EXTERN Boolean LIBCALL ID1serverBackAsnWrite PROTO (( ID1serverBackPtr , Asn
 
 /**************************************************
 *
+*    ID1SeqEntryInfo
+*
+**************************************************/
+typedef struct struct_ID1SeqEntry_info {
+   struct struct_ID1blob_info PNTR   blob_info;
+   ValNodePtr   blob;
+} ID1SeqEntryInfo, PNTR ID1SeqEntryInfoPtr;
+
+
+NLM_EXTERN ID1SeqEntryInfoPtr LIBCALL ID1SeqEntryInfoFree PROTO ((ID1SeqEntryInfoPtr ));
+NLM_EXTERN ID1SeqEntryInfoPtr LIBCALL ID1SeqEntryInfoNew PROTO (( void ));
+NLM_EXTERN ID1SeqEntryInfoPtr LIBCALL ID1SeqEntryInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID1SeqEntryInfoAsnWrite PROTO (( ID1SeqEntryInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ID1blobInfo
+*
+**************************************************/
+typedef struct struct_ID1blob_info {
+   Int4   gi;
+   Int4   sat;
+   Int4   sat_key;
+   CharPtr   satname;
+   Int4   suppress;
+   Int4   withdrawn;
+   Int4   confidential;
+   Int4   blob_state;
+   CharPtr   comment;
+   Int4   extfeatmask;
+} ID1blobInfo, PNTR ID1blobInfoPtr;
+
+
+NLM_EXTERN ID1blobInfoPtr LIBCALL ID1blobInfoFree PROTO ((ID1blobInfoPtr ));
+NLM_EXTERN ID1blobInfoPtr LIBCALL ID1blobInfoNew PROTO (( void ));
+NLM_EXTERN ID1blobInfoPtr LIBCALL ID1blobInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ID1blobInfoAsnWrite PROTO (( ID1blobInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
 *    ID1serverDebug
 *
 **************************************************/
diff --git a/network/id1arch/idfetch.c b/network/id1arch/idfetch.c
index 3cd1d240..ce439e7a 100644
--- a/network/id1arch/idfetch.c
+++ b/network/id1arch/idfetch.c
@@ -25,6 +25,18 @@
  * Author Karl Sirotkin
  *
  $Log: idfetch.c,v $
+ Revision 1.27  2003/03/28 18:48:39  yaschenk
+ tuning ObjMgr, adding STREAM_SEQ_PORT_FIRST to SeqEntryToGnbk
+
+ Revision 1.26  2003/01/29 23:08:19  yaschenk
+ fixing FASTA on far pointers
+
+ Revision 1.25  2003/01/21 22:27:23  kans
+ new CstType parameter for flatfile generator
+
+ Revision 1.24  2002/12/30 22:36:53  yaschenk
+ optimizing..
+
  Revision 1.23  2002/11/07 17:21:55  yaschenk
  switching ID1 to new displatcher
 
@@ -137,7 +149,13 @@
 #include <ncbi.h>
 #include <objsset.h>
 #include <accid1.h>
+
+#if 0
 #include <asn2ff.h>
+#else
+#include <asn2gnbk.h>
+#endif
+
 #include <tofasta.h>
 #include <ni_types.h>
 #include <ni_lib.h>
@@ -206,6 +224,7 @@ 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);
 
 Int4 giBuffer[1000];
 int giBufferPos = 0;
@@ -338,6 +357,16 @@ Int2 Main()
     has_trouble=TRUE;
     goto FATAL;
   }
+
+  {  /** tuning ObjMgr **/
+	ObjMgrPtr	omp;
+        omp=ObjMgrGet();
+        omp->maxtemp=500;
+        /*omp->maxobj=64000;*/
+        omp->autoclean = TRUE;
+
+  }
+
   if(myargs[infotypearg].intvalue != 1)
   {
     outmode = "w";
@@ -375,14 +404,19 @@ Int2 Main()
   if( has_trouble )
     exit (1);
 
-  if(fp_in || myargs[entrezqueryarg].strvalue || myargs[entrezqueryfilearg].strvalue)
-  { /*** Statefull mode ***/
-        putenv("CONN_STATELESS=FALSE");  /***NI_SetInterface(eNII_WWW);***/
-  }
-  else
-  { /*** Stateless mode ***/
-	putenv("CONN_STATELESS=TRUE");   /***NI_SetInterface(eNII_WWWDirect);***/
-  }
+
+	if(   fp_in 
+	   || myargs[entrezqueryarg].strvalue
+           || myargs[entrezqueryfilearg].strvalue
+           || myargs[outtypearg].intvalue == 3
+           || myargs[outtypearg].intvalue == 4
+           || myargs[outtypearg].intvalue == 5
+              ) { /*** Statefull mode ***/
+		putenv("CONN_STATELESS=FALSE"); 
+	}
+	else { /*** Stateless mode ***/
+		putenv("CONN_STATELESS=TRUE"); 
+	}
 
   if(!ID1BioseqFetchEnable("idfetch",TRUE))
   {
@@ -939,6 +973,7 @@ static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex)
   }
   else
   {
+    putenv("CONN_STATELESS=FALSE");  /*** some formats may ask a lot of information ***/
     switch(myargs[outtypearg].intvalue)
     {
     case 1:
@@ -952,7 +987,12 @@ static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex)
       }
       break;
     case 3:
+#if 0
       if(!SeqEntryToFlat(sep, fp, GENBANK_FMT, RELEASE_MODE)){
+#else 
+      AssignIDsInEntity(0,OBJ_SEQENTRY,sep);
+      if(!SeqEntryToGnbk(sep,NULL,GENBANK_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES,STREAM_SEQ_PORT_FIRST,0,NULL,fp)){
+#endif
         ErrPostEx(SEV_WARNING,0,0,
                   "GenBank Format does not exist for this sequence ");
         retval=FALSE;
@@ -960,7 +1000,12 @@ static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex)
       }
       break;
     case 4:
+#if 0
       if(!SeqEntryToFlat(sep, fp, GENPEPT_FMT, RELEASE_MODE))
+#else 
+      AssignIDsInEntity(0,OBJ_SEQENTRY,sep);
+      if(!SeqEntryToGnbk(sep,NULL,GENPEPT_FMT,ENTREZ_MODE,0,SHOW_CONTIG_FEATURES|ONLY_NEAR_FEATURES,STREAM_SEQ_PORT_FIRST,0,NULL,fp))
+#endif
       {
         ErrPostEx(SEV_WARNING,0,0,
                   "GenPept Format does not exist for this sequence");
@@ -975,12 +1020,21 @@ static Boolean IdFetch_func(Int4 gi,CharPtr db, Int4 ent,Int2 maxplex)
       switch(myargs[infotypearg].intvalue){
       case 0:
         if(bsp){
+#if 0
           SeqEntrysToFasta (sep, fp, ISA_na (bsp->mol), group_segs);
+#else
+		MyBioseqToFasta(bsp,(Pointer)fp);
+#endif
         }
         else
         {
+#if 0
           SeqEntryToFasta(sep, fp, TRUE);  /* nuc acids */
           SeqEntryToFasta(sep, fp, FALSE); /* proteins */
+#else
+		VisitBioseqsInSep(sep,(Pointer)fp, MyBioseqToFasta);
+
+#endif
         }
         break;
       case 2:
@@ -1001,11 +1055,13 @@ DONE:
   {
     static Uint2  reap_cnt;
     BioseqUnlock(bsp);
+#if 0
     reap_cnt++;
     if(reap_cnt > 128){
       ObjMgrFreeCache(0);
       reap_cnt=0;
     }
+#endif
   }
   else if(sep)
   {
@@ -1108,3 +1164,42 @@ static Int4 BEGetUidsFromQuery(CharPtr query, Uint4Ptr PNTR uids,
   return count;
 }
 
+#define FASTA_LINE_SIZE         70
+#define FASTA_LINES_IN_CHUNK    5000
+
+static void
+MyBioseqToFasta(BioseqPtr bsp, Pointer userdata)
+{
+        SeqPortPtr      spp=NULL;
+        Char            buf[2048];
+        Char         	str[200];
+        ValNodePtr      vnp;
+        MolInfoPtr      mip=NULL;
+	FILE PNTR fp=(FILE PNTR)userdata;
+	Int4    start=0,step=FASTA_LINE_SIZE*FASTA_LINES_IN_CHUNK,stop;
+
+	for(vnp=bsp->descr;vnp;vnp=vnp->next){
+                if(vnp->choice==Seq_descr_molinfo){
+                        mip = (MolInfoPtr)(vnp->data.ptrvalue);
+                }
+        }
+	SeqIdWrite(bsp->id,str,PRINTID_FASTA_LONG,199);
+	if(!CreateDefLine(NULL, bsp, buf, sizeof(buf), mip?mip->tech:0, NULL, NULL)) return;
+	fprintf(fp, ">%s %s\n", str,buf);
+	while(start < bsp->length){
+		stop=start+step-1;
+		if(stop >= bsp->length) stop=bsp->length-1;
+		spp = SeqPortNew(bsp,start,stop,0, (ISA_na(bsp->mol))?Seq_code_iupacna:Seq_code_ncbieaa);
+		if(spp==NULL) return;
+		SeqPortSet_do_virtual(spp, TRUE);
+		while (FastaSeqLineEx(spp, buf, FASTA_LINE_SIZE, ISA_na(bsp->mol),TRUE)) {
+			fprintf(fp,"%s\n", buf);
+			buf[0] = '\0';
+		}
+		if(spp) {
+			SeqPortFree(spp);
+			spp=NULL;
+		}
+		start=stop+1;
+	}
+}
diff --git a/network/medarch/client/medutil.c b/network/medarch/client/medutil.c
index 4cb50b0a..7914ea5e 100644
--- a/network/medarch/client/medutil.c
+++ b/network/medarch/client/medutil.c
@@ -28,7 +28,7 @@
 *   
 * Version Creation Date: 8/31/93
 *
-* $Revision: 6.6 $
+* $Revision: 6.8 $
 *
 * File Description:  Medline Utilities for MedArch
 *   Assumes user calls MedArchInit and Fini
@@ -44,6 +44,12 @@
 *
 * RCS Modification History:
 * $Log: medutil.c,v $
+* Revision 6.8  2003/03/25 19:14:59  bazhin
+* Function "ten_authors()" became public (from static).
+*
+* Revision 6.7  2003/03/12 20:35:02  bazhin
+* "ten_authors()" function now can handle consortiums.
+*
 * Revision 6.6  2001/03/08 12:47:44  ostell
 * made FixPub work if no medline uid returned, but pmid is returned.
 *
@@ -248,7 +254,7 @@ void print_pub(ValNodePtr pub, Boolean found, Boolean auth, Int4 muid)
 *    ten_authors   
 * 											
 ****************************************************************************/
-static Boolean ten_authors(CitArtPtr art, CitArtPtr art_tmp) 
+Boolean ten_authors(CitArtPtr art, CitArtPtr art_tmp) 
 {
 	Int2 num, numnew, i, match, n;
 	ValNodePtr v;
@@ -273,8 +279,13 @@ static Boolean ten_authors(CitArtPtr art, CitArtPtr art_tmp)
 			for (v = art_tmp->authors->names; v != NULL && numnew < 10;
 								v = v->next, numnew++) {
 				aup = v->data.ptrvalue;
-				namestd	= aup->name->data;
-				mu[numnew] = namestd->names[0];	
+				if(aup->name->choice == 2)
+				{
+					namestd = aup->name->data;
+					mu[numnew] = namestd->names[0];
+				}
+				else if(aup->name->choice == 5)
+					mu[numnew] = aup->name->data;
 			}
 		}
 
@@ -283,8 +294,15 @@ static Boolean ten_authors(CitArtPtr art, CitArtPtr art_tmp)
 				no_compare = FALSE;
 				for (v = art->authors->names; v != NULL; v = v->next) {
 					aup = v->data.ptrvalue;
-					namestd	= aup->name->data;
-					ptr = namestd->names[0];
+					if(aup->name->choice == 2)
+					{
+						namestd = aup->name->data;
+						ptr = namestd->names[0];
+					}
+					else if(aup->name->choice == 5)
+						ptr = aup->name->data;
+					else
+						continue;
 					for (i = 0; i < numnew; i++) {
 						if (StringICmp(ptr, mu[i]) == 0) {
 							match++;
diff --git a/network/medarch/client/medutil.h b/network/medarch/client/medutil.h
index da27786a..daf20b22 100644
--- a/network/medarch/client/medutil.h
+++ b/network/medarch/client/medutil.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 8/31/93
 *
-* $Revision: 6.1 $
+* $Revision: 6.2 $
 *
 * File Description:  * File Description:  Medline Utilities for MedArch
 *   Assumes user calls MedArchInit and Fini
@@ -45,6 +45,9 @@
 *
 * RCS Modification History:
 * $Log: medutil.h,v $
+* Revision 6.2  2003/03/25 19:14:50  bazhin
+* Function "ten_authors()" became public (from static).
+*
 * Revision 6.1  2000/08/18 17:01:02  kans
 * added FetchPubPmId, enhanced FixPubEquiv to handle records with pmid but no muid
 *
@@ -127,6 +130,7 @@ ValNodePtr MedlineToISO PROTO((ValNodePtr tmp));
 ValNodePtr get_std_auth PROTO((CharPtr token, Uint1 format));
 
 Boolean in_press PROTO ((CitArtPtr cit));
+Boolean ten_authors PROTO((CitArtPtr art, CitArtPtr art_tmp));
 
 #ifdef __cplusplus
 }
diff --git a/network/nsclilib/ni_msg.c b/network/nsclilib/ni_msg.c
index 5f43dba5..326392e7 100644
--- a/network/nsclilib/ni_msg.c
+++ b/network/nsclilib/ni_msg.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:        1/1/92
 *
-* $Revision: 6.2 $
+* $Revision: 6.3 $
 *
 * File Description: 
 *   This file consists mostly of functions for creating, destroying, reading,
@@ -138,6 +138,9 @@
 *
 * RCS Modification History:
 * $Log: ni_msg.c,v $
+* Revision 6.3  2002/12/17 23:01:36  kans
+* support for OS_UNIX_DARWIN for Mach-O executables (RGS)
+*
 * Revision 6.2  2001/08/29 18:00:01  juran
 * Under Carbon, define missing POSIX macros in terms of Mac counterparts.
 *
@@ -191,7 +194,7 @@ static char *  _this_file = __FILE__;
 #include "ni_msg.h"
 #include "ni_asn.h"   /* produced by ASNTOOL */
 
-#if TARGET_API_MAC_CARBON
+#if TARGET_API_MAC_CARBON && !defined(O_NDELAY)
 #define O_NDELAY kO_NDELAY
 #endif
 
diff --git a/network/nsclilib/readme b/network/nsclilib/readme
index 8b3894d8..15a8a0b0 100644
--- a/network/nsclilib/readme
+++ b/network/nsclilib/readme
@@ -81,14 +81,15 @@ Value:
 | on your proxy firewall server to those of NCBI
 | (see in http://www.ncbi.nlm.nih.gov/cpp/network/firewall.html).
 | Thus the mapping on your non-transparent firewall server
-| shoul look like this:
+| should look like this:
 | 
-| SRV_PROXY_HOST:5853    -->    130.14.22.1:5853  RETIRED -- DO NOT USE!
-| SRV_PROXY_HOST:5859    -->    130.14.22.2:5859  RETIRED -- DO NOT USE!
-| SRV_PROXY_HOST:5840    -->    130.14.22.8:5840  RETIRED -- DO NOT USE!
-| SRV_PROXY_HOST:5810    -->    130.14.22.30:5810 RETIRED -- DO NOT USE!
-| SRV_PROXY_HOST:5812    -->    130.14.22.31:5812
-| SRV_PROXY_HOST:5811    -->    130.14.22.32:5811
+| SRV_PROXY_HOST:5853       --> 130.14.22.1:5853  RETIRED -- DO NOT USE!
+| SRV_PROXY_HOST:5859       --> 130.14.22.2:5859  RETIRED -- DO NOT USE!
+| SRV_PROXY_HOST:5840       --> 130.14.22.8:5840  RETIRED -- DO NOT USE!
+| SRV_PROXY_HOST:5810       --> 130.14.22.30:5810 RETIRED -- DO NOT USE!
+| SRV_PROXY_HOST:5812       --> 130.14.22.31:5812
+| SRV_PROXY_HOST:5811       --> 130.14.22.32:5811
+| SRV_PROXY_HOST:5850..5860 --> 130.14.29.112:5850..5860(for future extensions)
 | 
 | NOTE:  It's pretty rare (if ever) when you have to use
 |        "SRV_PROXY_HOST" as most of firewalls are "transparent"
@@ -187,4 +188,4 @@ Solaris or IRIX. Then, the client must run on the host that:
 a) belongs to one of NCBI subnets and
 b) has "lbdaemon"(load-balance daemon) application running on it.
 
-$Date: 2002/09/07 02:00:28 $
+$Date: 2003/02/08 17:51:14 $
diff --git a/network/taxon1/common/taxinc.h b/network/taxon1/common/taxinc.h
index ae2017bf..f96ecbae 100644
--- a/network/taxon1/common/taxinc.h
+++ b/network/taxon1/common/taxinc.h
@@ -187,6 +187,14 @@ Int4 tax1_getTaxId4GI(Int4 gi);
  */
 CharPtr tax1m_getBlastName(Int4 tax_id);
 
+/*---------------------------------------------
+ * Find out is taxonomy lookup system inited or not
+ * Returns: TRUE - alive
+ *          FALSE - dead
+ */
+
+Boolean tax1_inited(void);
+
 
 #ifdef __cplusplus
 /* { */ }
diff --git a/network/taxon1/taxon2/tc2proc.c b/network/taxon1/taxon2/tc2proc.c
index f7b24cbc..7861336f 100644
--- a/network/taxon1/taxon2/tc2proc.c
+++ b/network/taxon1/taxon2/tc2proc.c
@@ -1,5 +1,5 @@
 /*----------------*/
-/* $Id: tc2proc.c,v 1.23 2002/10/18 19:48:51 soussov Exp $           */
+/* $Id: tc2proc.c,v 1.28 2003/03/05 21:32:00 soussov Exp $           */
 /*----------------*/
 
 #include <stdlib.h>
@@ -17,6 +17,8 @@
 #define ORGMOD_gb_acronym 32
 #define ORGMOD_gb_anamorph 33
 #define ORGMOD_gb_synonym 34
+#define ORGMOD_anamorph 29
+#define ORGMOD_synonym 28
 
 
 static TreePtr tax_tree= NULL;
@@ -204,6 +206,7 @@ int CloseTaxDB(void)
             }
         }
     }
+    tax_tree= NULL;
     return 1;
 }
 
@@ -766,74 +769,79 @@ static Int2 getSubtypeFromName(CharPtr name)
 {
     CharPtr c;
     if(strchr(name, '.') == NULL) return 0;
+
+    /* ignore subsp. cf. and subsp. aff. */
+    if (StringStr (name, "subsp. cf.") != NULL) return 0;
+    if (StringStr (name, "subsp. aff.") != NULL) return 0;
+
     /* check for subsp */
     c= StringStr(name, "subsp.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 6);
         return 22;
     }
     c= StringStr(name, "ssp.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 4);
         return 22;
     }
     c= StringStr(name, "f. sp.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 6);
         return 26;
     }
     c= StringStr(name, "f.sp.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 5);
         return 26;
     }
     c= StringStr(name, "str.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 4);
         return 2;
     }
     c= StringStr(name, "substr.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 7);
         return 3;
     }
     c= StringStr(name, "var.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 4);
         return 6;
     }
     c= StringStr(name, "sv.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 3);
         return 9;
     }
     c= StringStr(name, "cv.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 3);
         return 10;
     }
     c= StringStr(name, "pv.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 3);
         return 11;
     }
     c= StringStr(name, "bv.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 3);
         return 13;
     }
     c= StringStr(name, "f.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 2);
         return 25;
     }
     c= StringStr(name, "fo.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 3);
         return 25;
     }
     c= StringStr(name, "grp.");
-    if(c) {
+    if(c == name) {
         rmWord(name, c, 4);
         return 15;
     }
@@ -1380,7 +1388,7 @@ static OrgRefPtr getFromBuff(Int4 id, int* is_sp, int* is_uncult, NameListPtr* b
     return orp;
 }
 
-static OrgModPtr fixModifier(Int4 tax_id, OrgModPtr omp)
+static OrgModPtr fixModifier(Int4 tax_id, OrgModPtr omp, CharPtr taxname)
 {
     _subspec src_ss;
     _subspecPtr ss= NULL;
@@ -1395,7 +1403,15 @@ static OrgModPtr fixModifier(Int4 tax_id, OrgModPtr omp)
         OrgModFree(omp);
         return NULL;
     }
-      
+
+    if((omp->subtype == ORGMOD_anamorph ||
+        omp->subtype == ORGMOD_synonym) && 
+       StringICmp(omp->subname, taxname) == 0) {
+        omp->next= NULL;
+        OrgModFree(omp);
+        return NULL;
+    }
+        
 
     if((omp->subname != NULL) && (omp->subtype != 0)) {
         src_ss.stype= omp->subtype;
@@ -1426,13 +1442,13 @@ static OrgModPtr fixModifier(Int4 tax_id, OrgModPtr omp)
     return omp;
 }
 
-static void CleanOrgMod(Int4 tax_id, OrgNamePtr onp)
+static void CleanOrgMod(Int4 tax_id, OrgNamePtr onp, CharPtr taxname)
 {
     OrgModPtr omp, omp_p, omp_n;
 
     for(omp_p= NULL, omp= onp->mod; omp != NULL; omp= omp_n) {
         omp_n= omp->next;
-        if((omp= fixModifier(tax_id, omp)) == NULL) {
+        if((omp= fixModifier(tax_id, omp, taxname)) == NULL) {
             /* exclude this modifier */
             if(omp_p == NULL) {
                 onp->mod= omp_n;
@@ -1443,13 +1459,13 @@ static void CleanOrgMod(Int4 tax_id, OrgNamePtr onp)
     }
 }
 	    
-static void cleanOrgName(Int4 tax_id, OrgNamePtr onp)
+static void cleanOrgName(Int4 tax_id, OrgNamePtr onp, CharPtr taxname)
 {
     if(onp->lineage != NULL) onp->lineage= MemFree(onp->lineage);
     if(onp->div != NULL) onp->div= MemFree(onp->div);
 #if 1
     /* #if 0 means that we will trust to initial modifier */
-    if(onp->mod != NULL) CleanOrgMod(tax_id, onp);
+    if(onp->mod != NULL) CleanOrgMod(tax_id, onp, taxname);
 #endif
     if(onp->next != NULL) OrgNameSetFree(onp->next);
     if(onp->data != NULL) {
@@ -1536,7 +1552,7 @@ static int subtypeConflict(Int2 t1, Int2 t2)
     return 0;
 }
 
-static void mergeOrgMod(OrgModPtr omp, OrgModPtr src)
+static void mergeOrgMod(OrgModPtr omp, OrgModPtr src, int need_copy)
 {
     if(src == NULL) return;
     else {
@@ -1544,18 +1560,31 @@ static void mergeOrgMod(OrgModPtr omp, OrgModPtr src)
         for(dst= omp; dst != NULL; dst= dst->next) {
             lst= dst;
             if(subtypeConflict((Int2)dst->subtype, (Int2)src->subtype)) {
-                mergeOrgMod(omp, src->next);
+                lst= src->next;
+                if(!need_copy) {
+                    src->next= NULL;
+                    OrgModFree(src);
+                }
+                mergeOrgMod(omp, lst, need_copy);
                 return;
             }
         }
 
-        lst->next= dst= OrgModNew();
-        dst->subtype= src->subtype;
-        dst->subname= (src->subname != NULL)? StringSave(src->subname) : NULL;
-        dst->attrib= (src->attrib != NULL)? StringSave(src->attrib) : NULL;
-        dst->next= NULL;
+        if(need_copy) {
+            lst->next= dst= OrgModNew();
+            dst->subtype= src->subtype;
+            dst->subname= (src->subname != NULL)? StringSave(src->subname) : NULL;
+            dst->attrib= (src->attrib != NULL)? StringSave(src->attrib) : NULL;
+            dst->next= NULL;
+            lst= src->next;
+        }
+        else {
+            lst->next= src;
+            lst= src->next;
+            src->next= NULL;
+        }
         
-        mergeOrgMod(omp, src->next);
+        mergeOrgMod(omp, lst, need_copy);
     }
 
 }
@@ -1644,7 +1673,7 @@ static void bldOrgRefOut(OrgRefPtr dst, OrgRefPtr src, Int4 tax_id)
   
     if(onp->mod == NULL) onp->mod= copyOrgMod(src->orgname->mod);
     else {
-        mergeOrgMod(onp->mod, src->orgname->mod);
+        mergeOrgMod(onp->mod, src->orgname->mod, 1);
     }
     onp->lineage= (src->orgname->lineage != NULL)? StringSave(src->orgname->lineage) : NULL;
     onp->gcode= src->orgname->gcode;
@@ -1652,33 +1681,80 @@ static void bldOrgRefOut(OrgRefPtr dst, OrgRefPtr src, Int4 tax_id)
     onp->div= StringSave(src->orgname->div);
 }
 
-static void populateReplaced(OrgRefPtr orp, CharPtr oldName)
+static void populateReplaced(OrgRefPtr orp, OrgModPtr hitName)
 {
-    OrgNamePtr onp;
-    OrgModPtr omp;
+    OrgModPtr omp, srv_mod;
 
-    if((orp->taxname != NULL) && (StringICmp(orp->taxname, oldName) == 0)) {
-        MemFree(oldName);
-        return;
-    }
+    if(hitName == NULL) return;
 
-    if((orp->common != NULL) && (StringICmp(orp->common, oldName) == 0)) {
-        MemFree(oldName);
-        return;
+    /* find the real hitName */
+    if (hitName->subtype == 254) {
+        srv_mod= hitName->next;
+        hitName->next= NULL;
     }
+    else {
+        srv_mod= hitName;
+        for(omp= hitName, hitName= hitName->next; hitName; hitName= hitName->next) {
+            if(hitName->subtype == 254) {
+                omp->next= hitName->next;
+                hitName->next= NULL;
+                break;
+            }
+            else {
+                omp= hitName;
+            }
+        }
+    }
+                
 
-    /* organism name was changed */
-    onp= orp->orgname;
-    if(onp != NULL) {
-        omp= OrgModNew();
-        omp->next= onp->mod;
-        omp->subtype= 254;
-        omp->subname= oldName;
-        onp->mod= omp;
+    if(orp->orgname->mod) {
+        mergeOrgMod(orp->orgname->mod, srv_mod, 0);
     }
     else {
-        MemFree(oldName);
+        orp->orgname->mod= srv_mod;
     }
+
+
+    if(hitName == NULL) return;
+
+    for(omp= orp->orgname->mod; omp != NULL; omp= omp->next) {
+        if(omp->subtype == 254) { /* search name is populated already */
+            if((omp->attrib == NULL) && (hitName->attrib != NULL) &&
+               (StringICmp(omp->subname, hitName->subname) == 0)) { 
+                omp->attrib= hitName->attrib;
+                hitName->attrib= NULL;
+            }
+            OrgModFree(hitName);
+            return;
+        }
+    }
+
+    if((orp->taxname != NULL) && (StringICmp(orp->taxname, hitName->subname) == 0)) {
+        /* we probably don't need to populate search name */
+        if(hitName->attrib == NULL) {
+            OrgModFree(hitName);
+            return;
+        }
+        else {
+            Uint1 st= atoi(hitName->attrib+1);
+            char* sn= strchr(hitName->attrib, '=');
+            if(sn == NULL) {
+                OrgModFree(hitName);
+                return;
+            }
+            ++sn;
+            for(omp= orp->orgname->mod; omp != NULL; omp= omp->next) {
+                if((omp->subtype == st) && (StringICmp(omp->subname, sn) == 0)) {
+                    OrgModFree(hitName);
+                    return;
+                }
+            }
+        }
+    }
+
+    /* adding this modifier */
+    hitName->next= orp->orgname->mod;
+    orp->orgname->mod= hitName;
 }
 
 Taxon2DataPtr tax1m_lookup(OrgRefPtr inp_orgRef, int merge)
@@ -1689,10 +1765,9 @@ Taxon2DataPtr tax1m_lookup(OrgRefPtr inp_orgRef, int merge)
     int is_species;
     int is_uncultured;
     NameListPtr bl;
-    Boolean need_search_name= TRUE;
-    CharPtr hit_name;
+    OrgModPtr hitName;
 
-    tax_id= tax1_getTaxIdByOrgRef(inp_orgRef);
+    tax_id= txc_findByOrg(inp_orgRef, &hitName);
     if(tax_id <= 0) return NULL;
     db_orgRef= s_tax1_getOrgRef(tax_id, &is_species, &is_uncultured, &bl);
     if(db_orgRef == NULL) return NULL;
@@ -1702,47 +1777,6 @@ Taxon2DataPtr tax1m_lookup(OrgRefPtr inp_orgRef, int merge)
     res->is_uncultured= is_uncultured;
     res->blast_name= make_blast_name(bl);
 
-    /* populate search name if necessary */
-    if(inp_orgRef->taxname != NULL) {
-        if((db_orgRef->taxname != NULL) && (StringICmp(inp_orgRef->taxname, db_orgRef->taxname) == 0)) {
-            need_search_name= FALSE;
-        }
-        else if((db_orgRef->common != NULL) && (StringICmp(inp_orgRef->taxname, db_orgRef->common) == 0)) {
-            need_search_name= FALSE;
-        }
-    }
-
-    if(need_search_name && (inp_orgRef->common != NULL)) {
-        if((db_orgRef->taxname != NULL) && (StringICmp(inp_orgRef->common, db_orgRef->taxname) == 0)) {
-            need_search_name= FALSE;
-        }
-        else if((db_orgRef->common != NULL) && (StringICmp(inp_orgRef->common, db_orgRef->common) == 0)) {
-            need_search_name= FALSE;
-        }
-    }
-
-    if(need_search_name && (inp_orgRef->orgname != NULL)) {
-        /* check if search name already exists */
-        OrgModPtr omp;
-
-        for(omp= inp_orgRef->orgname->mod; omp != NULL; omp= omp->next) {
-            if(omp->subtype == 254) {
-                need_search_name= FALSE;
-                break;
-            }
-        }
-    }
-
-    hit_name= NULL;
-    if(need_search_name) {
-        if((inp_orgRef->taxname != NULL) && (inp_orgRef->taxname[0] != '\0')) {
-            hit_name= StringSave(inp_orgRef->taxname);
-        }
-        else if((inp_orgRef->common != NULL) && (inp_orgRef->common[0] != '\0')) {
-            hit_name= StringSave(inp_orgRef->common);
-        }
-    }
-
     if(merge) {
         /* we have to merge old orgref with the new one */
         res->org= inp_orgRef;
@@ -1750,7 +1784,8 @@ Taxon2DataPtr tax1m_lookup(OrgRefPtr inp_orgRef, int merge)
         if(inp_orgRef->taxname != NULL) MemFree(inp_orgRef->taxname);
         if(inp_orgRef->common != NULL) MemFree(inp_orgRef->common);
         if(inp_orgRef->syn != NULL) ValNodeFreeData(inp_orgRef->syn);
-        if(inp_orgRef->orgname != NULL) cleanOrgName(tax_id, inp_orgRef->orgname);
+        if(inp_orgRef->orgname != NULL) cleanOrgName(tax_id, inp_orgRef->orgname,
+                                                     db_orgRef->taxname);
     }
     else {
         /* make new orgref */
@@ -1760,7 +1795,7 @@ Taxon2DataPtr tax1m_lookup(OrgRefPtr inp_orgRef, int merge)
     }
     /* fill-up orgref based on db_orgRef */
     bldOrgRefOut(res->org, db_orgRef, tax_id);
-    if(need_search_name && (hit_name != NULL)) populateReplaced(res->org, hit_name);
+    populateReplaced(res->org, hitName);
     return res;
 }
 
@@ -1770,10 +1805,11 @@ Taxon1DataPtr tax1_lookup(OrgRefPtr inp_orgRef, int merge)
     Int4 tax_id;
     OrgRefPtr db_orgRef;
     int is_species;
-    Boolean need_search_name= TRUE;
-    CharPtr hit_name;
+    OrgModPtr hitName;
 
-    tax_id= tax1_getTaxIdByOrgRef(inp_orgRef);
+    tax_id= txc_findByOrg(inp_orgRef, &hitName);
+
+    //tax_id= tax1_getTaxIdByOrgRef(inp_orgRef);
     if(tax_id <= 0) return NULL;
     db_orgRef= s_tax1_getOrgRef(tax_id, &is_species, NULL, NULL);
     if(db_orgRef == NULL) return NULL;
@@ -1783,47 +1819,6 @@ Taxon1DataPtr tax1_lookup(OrgRefPtr inp_orgRef, int merge)
     res->embl_code= NULL;
     res->div= (db_orgRef->orgname != NULL)? StringSave(db_orgRef->orgname->div) : NULL;
 
-    /* populate search name if necessary */
-    if(inp_orgRef->taxname != NULL) {
-        if((db_orgRef->taxname != NULL) && (StringICmp(inp_orgRef->taxname, db_orgRef->taxname) == 0)) {
-            need_search_name= FALSE;
-        }
-        else if((db_orgRef->common != NULL) && (StringICmp(inp_orgRef->taxname, db_orgRef->common) == 0)) {
-            need_search_name= FALSE;
-        }
-    }
-
-    if(need_search_name && (inp_orgRef->common != NULL)) {
-        if((db_orgRef->taxname != NULL) && (StringICmp(inp_orgRef->common, db_orgRef->taxname) == 0)) {
-            need_search_name= FALSE;
-        }
-        else if((db_orgRef->common != NULL) && (StringICmp(inp_orgRef->common, db_orgRef->common) == 0)) {
-            need_search_name= FALSE;
-        }
-    }
-
-    if(need_search_name && (inp_orgRef->orgname != NULL)) {
-        /* check if search name already exists */
-        OrgModPtr omp;
-
-        for(omp= inp_orgRef->orgname->mod; omp != NULL; omp= omp->next) {
-            if(omp->subtype == 254) {
-                need_search_name= FALSE;
-                break;
-            }
-        }
-    }
-
-    hit_name= NULL;
-    if(need_search_name) {
-        if((inp_orgRef->taxname != NULL) && (inp_orgRef->taxname[0] != '\0')) {
-            hit_name= StringSave(inp_orgRef->taxname);
-        }
-        else if((inp_orgRef->common != NULL) && (inp_orgRef->common[0] != '\0')) {
-            hit_name= StringSave(inp_orgRef->common);
-        }
-    }
-
     if(merge) {
         /* we have to merge old orgref with the new one */
         res->org= inp_orgRef;
@@ -1831,7 +1826,8 @@ Taxon1DataPtr tax1_lookup(OrgRefPtr inp_orgRef, int merge)
         if(inp_orgRef->taxname != NULL) MemFree(inp_orgRef->taxname);
         if(inp_orgRef->common != NULL) MemFree(inp_orgRef->common);
         if(inp_orgRef->syn != NULL) ValNodeFreeData(inp_orgRef->syn);
-        if(inp_orgRef->orgname != NULL) cleanOrgName(tax_id, inp_orgRef->orgname);
+        if(inp_orgRef->orgname != NULL) cleanOrgName(tax_id, inp_orgRef->orgname, 
+                                                     db_orgRef->taxname);
     }
     else {
         /* make new orgref */
@@ -1841,7 +1837,7 @@ Taxon1DataPtr tax1_lookup(OrgRefPtr inp_orgRef, int merge)
     }
     /* fill-up orgref based on db_orgRef */
     bldOrgRefOut(res->org, db_orgRef, tax_id);
-    if(need_search_name && (hit_name != NULL)) populateReplaced(res->org, hit_name);
+    populateReplaced(res->org, hitName);
     return res;
 }
   
@@ -2162,6 +2158,7 @@ Int4 tax1e_needUpdate(OrgRefPtr inp_orgRef)
 
 Boolean tax1_isAlive(void)
 {
+    if(!tax1_inited()) return FALSE;
     return (tax1_getTaxIdByName("dog") > 1)? TRUE : FALSE;
 }
 
@@ -2204,3 +2201,8 @@ CharPtr tax1m_getBlastName(Int4 tax_id)
     tree_closeCursor(cursor);
     return res;
 }
+
+Boolean tax1_inited()
+{
+    return (tax_tree != NULL)? TRUE : FALSE;
+}
diff --git a/network/taxon1/taxon2/txcdproc.c b/network/taxon1/taxon2/txcdproc.c
index 760ff7d1..ca27b0bb 100644
--- a/network/taxon1/taxon2/txcdproc.c
+++ b/network/taxon1/taxon2/txcdproc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   07/15/97
 *
-* $Revision: 1.12 $
+* $Revision: 1.14 $
 *
 * File Description: 
 *       API for Taxonomy service
@@ -44,6 +44,12 @@
 *
 * RCS Modification History:
 * $Log: txcdproc.c,v $
+* Revision 1.14  2003/03/06 16:30:32  kans
+* tdp->org needed a cast to (OrgRefPtr) due to Mac compiler complaint
+*
+* Revision 1.13  2003/03/05 21:32:00  soussov
+* new lookup procedure
+*
 * Revision 1.12  2001/09/28 15:53:15  soussov
 * tax1e_maxTaxId() added
 *
@@ -1453,3 +1459,81 @@ Int4 tax1e_maxTaxId()
 
     return tax_id;
 }
+
+static OrgRefPtr s_findbyorg(OrgRefPtr orgRef)
+{
+    Taxon1ReqPtr taxrp;
+    Taxon1RespPtr taxbp;
+    Taxon1DataPtr tdp;
+
+    if((taxrp= ValNodeNew(NULL)) == NULL) return 0;
+    taxrp->choice= Taxon1Req_lookup;
+    taxrp->data.ptrvalue= orgRef;
+    Taxon1ReqAsnWrite(taxrp, asnout, NULL);
+    AsnIoReset(asnout);
+    taxrp->data.ptrvalue= NULL;
+    Taxon1ReqFree(taxrp);
+
+    if((taxbp= NetTaxArchReadAsn()) == NULL) return 0;
+    
+    if(taxbp->choice != Taxon1Resp_lookup) {
+        report_service_error("txc_getTaxIdByOrgRef", taxbp);
+        Taxon1RespFree(taxbp);
+        return NULL;
+    }
+    
+    tdp= taxbp->data.ptrvalue;
+    orgRef= (OrgRefPtr) tdp->org;
+    tdp->org= NULL;
+    Taxon1RespFree(taxbp);
+    
+    return orgRef;
+}
+
+Int4 txc_findByOrg(OrgRefPtr inp_orgRef, OrgModPtr* hitName)
+{
+    Int4 i;
+    short erract;
+    ErrDesc err;
+    OrgRefPtr orp= NULL;
+    Int4 tax_id= 0;
+
+    if(tax_track) tax_time1= clock();
+    for (i= TAXARCH_SERV_RETRIES; i >= 0; --i) {
+        ErrGetOpts(&erract, NULL);
+        ErrSetOpts(ERR_IGNORE, 0);
+        ErrFetch(&err);
+
+        orp = s_findbyorg(inp_orgRef);
+
+        ErrSetOpts(erract, 0);
+        if (!ErrFetch(&err))  break; /* success */
+        
+        if(!ReestablishNetTaxArch()) break;
+    }
+    
+    if(tax_track) {
+        double diff= (double)(clock() - tax_time1)/CLOCKS_PER_SEC;
+        printf("tax1_getTaxIdByOrgRef() %f\n", diff);
+    }
+    
+    if(orp && orp->db) {
+        ValNodePtr vnp= orp->db;
+        DbtagPtr dbtag= vnp->data.ptrvalue;
+        ObjectIdPtr object_id= dbtag->tag;
+        tax_id= object_id->id;
+        
+        if(hitName) {
+            if(orp->orgname) {
+                *hitName= orp->orgname->mod;
+                orp->orgname->mod= NULL;
+            }
+            else *hitName= NULL;
+        }
+    }
+
+    if(orp) OrgRefFree(orp);
+
+    return tax_id;
+}
+
diff --git a/network/taxon1/taxon2/txclient.h b/network/taxon1/taxon2/txclient.h
index 711614c9..8060d02f 100644
--- a/network/taxon1/taxon2/txclient.h
+++ b/network/taxon1/taxon2/txclient.h
@@ -31,6 +31,9 @@
 *
 *
 * $Log: txclient.h,v $
+* Revision 1.7  2003/03/05 21:32:00  soussov
+* new lookup procedure
+*
 * Revision 1.6  1998/07/23 18:27:01  soussov
 * one prototype added
 *
@@ -168,6 +171,7 @@ Boolean te_saveEditWindows(void);
 
 #ifdef TAXSERVICE
 Int4 txc_getTaxIdByOrgRef(OrgRefPtr orgRef);
+Int4 txc_findByOrg(OrgRefPtr inp_orgRef, OrgModPtr* hitName);
 #endif
 
 _subspecPtr tax_SSgetAll(Int4 tax_id);
@@ -175,4 +179,5 @@ _subspecPtr tax_SSget(Int4 tax_id, _subspecPtr ssrec);
 tax_OrgModPtr tax_SSgetLegal(Int4 tax_id);
 Int4 tax_SSgetNodes(Uint1 stype, CharPtr sname, Uint1 mode, Int4Ptr* ids);
 
+
 #endif
diff --git a/network/taxon1/taxon2/txcproc.c b/network/taxon1/taxon2/txcproc.c
index 122ea296..e9fc9481 100644
--- a/network/taxon1/taxon2/txcproc.c
+++ b/network/taxon1/taxon2/txcproc.c
@@ -31,6 +31,9 @@
 *
 *
 * $Log: txcproc.c,v $
+* Revision 1.7  2003/03/05 21:32:00  soussov
+* new lookup procedure
+*
 * Revision 1.6  1999/12/20 17:05:17  soussov
 * taxid4gi added
 *
@@ -2592,3 +2595,9 @@ Int4 tax_getTaxId4GI(Int4 gi)
     ct_cmd_drop(cmd);
     return tax_id;		
 }
+
+Int4 txc_findByOrg(OrgRefPtr inp_orgRef, OrgModPtr* hitName)
+{
+    if(hitName) *hitName= NULL;
+    return tax1_getTaxIdByOrgRef(inp_orgRef);
+}