Load /tmp/.../ncbi-tools6-6.1.20061015 into

branches/upstream/current.

7 files changed, 59 insertions, 27 deletions

diff --git a/network/id1arch/id1gen.c b/network/id1arch/id1gen.c
index 91fac52c..8ca03649 100644
--- a/network/id1arch/id1gen.c
+++ b/network/id1arch/id1gen.c
@@ -595,7 +595,6 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 ID1SeqHistAsnWrite(ID1SeqHistPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
-   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -1052,7 +1051,6 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 ID1SeqEntryInfoAsnWrite(ID1SeqEntryInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
-   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -1365,7 +1363,6 @@ NLM_EXTERN
 ID1serverDebugPtr LIBCALL
 ID1serverDebugAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 {
-   DataVal av;
    AsnTypePtr atp;
    Boolean isError = FALSE;
    AsnReadFunc func;
@@ -1421,7 +1418,6 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 ID1serverDebugAsnWrite(ID1serverDebugPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
-   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
diff --git a/network/id1arch/idfetch.c b/network/id1arch/idfetch.c
index 42f5adef..89316704 100644
--- a/network/id1arch/idfetch.c
+++ b/network/id1arch/idfetch.c
@@ -25,6 +25,9 @@
  * Author Karl Sirotkin
  *
  $Log: idfetch.c,v $
+ Revision 1.39  2006/08/02 15:16:04  vysokolo
+ Added features tRNA and microRNA
+
  Revision 1.38  2005/05/16 23:18:34  vysokolo
  Added features 'HPRD' and 'STS' to the key '-F'.
 
@@ -244,7 +247,7 @@ prf|acc|name pdb|entry|chain",
         {"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},
-        {"Add features delimited by ','. Allowed values are: 'CDD', 'SNP', 'SNP_graph', 'MGC', 'HPRD', 'STS'.", NULL,NULL,NULL,TRUE,'F',ARG_STRING,0.0,0,NULL}
+        {"Add features delimited by ','. Allowed values are: 'CDD', 'SNP', 'SNP_graph', 'MGC', 'HPRD', 'STS','tRNA','microRNA'.", NULL,NULL,NULL,TRUE,'F',ARG_STRING,0.0,0,NULL}
 };
 int Numarg = sizeof(myargs)/sizeof(myargs[0]);
 
@@ -1309,6 +1312,8 @@ select * from annot_types;
 5 "MGC"       feff 9
 6 "HPRD"      fdff 10
 7 "STS"       fbff 11
+8 "tRNA"      f7ff 12
+9 "microRNA"  efff 13
 */
 
 Boolean CreateMaxPlexParam()
@@ -1347,6 +1352,14 @@ Boolean CreateMaxPlexParam()
       {
 	maxplex_param &= 0xfffffbff;
       }
+      else if( !StringICmp( ptoken, "tRNA"))
+      {
+	maxplex_param &= 0xfffff7ff;
+      }
+      else if( !StringICmp( ptoken, "microRNA"))
+      {
+	maxplex_param &= 0xffffefff;
+      }
       else
       {
 	/* Error: unknown feature */
diff --git a/network/id2arch/id2.asn b/network/id2arch/id2.asn
index b367e57b..5f387dd1 100644
--- a/network/id2arch/id2.asn
+++ b/network/id2arch/id2.asn
@@ -1,4 +1,4 @@
---$Revision: 1.18 $
+--$Revision: 1.19 $
 --********************************************************************
 --
 --  Network Id server network access
@@ -20,9 +20,9 @@ IMPORTS Seq-id, Seq-loc                                 FROM NCBI-Seqloc
         ID2S-Chunk-Id, ID2S-Seq-annot-Info              FROM NCBI-Seq-split;
 
 
-----------------------------------------------------------------------------
+--*********************************************************************
 -- request types
-----------------------------------------------------------------------------
+--*********************************************************************
 
 -- Requests are sent in packets to allow sending several requests at once
 -- to avoid network latency, without possiblity of deadlock with server.
@@ -186,9 +186,9 @@ ID2-Get-Blob-Details ::= SEQUENCE {
 }
 
 
-----------------------------------------------------------------------------
+--*********************************************************************
 -- reply types
-----------------------------------------------------------------------------
+--*********************************************************************
 
 
 ID2-Reply ::= SEQUENCE {
@@ -437,9 +437,9 @@ ID2-Blob-Seq-id ::= SEQUENCE {
 }
 
 
-----------------------------------------------------------------------------
+--*********************************************************************
 -- utility types
-----------------------------------------------------------------------------
+--*********************************************************************
 
 
 ID2-Blob-Id ::= SEQUENCE {
diff --git a/network/taxon1/common/taxon1.asn b/network/taxon1/common/taxon1.asn
index 7b28cb39..1d8cffcc 100644
--- a/network/taxon1/common/taxon1.asn
+++ b/network/taxon1/common/taxon1.asn
@@ -1,4 +1,4 @@
---$Revision: 6.6 $
+--$Revision: 6.7 $
 --**********************************************************************
 --
 --  NCBI Taxonomy Server
@@ -38,7 +38,8 @@ Taxon1-req ::= CHOICE {
         maxtaxid        NULL,           -- get max taxid
         getproptypes    NULL,           -- get property types
         getorgprop      Taxon1-info,    -- get properties for organism
-        searchname      Taxon1-info}    -- fancy search (token set, wild card)
+        searchname      Taxon1-info,    -- fancy search (token set, wild card)
+        dumpnames4class INTEGER}        -- all names of certain name class
 
 Taxon1-resp ::= CHOICE {
 	error		Taxon1-error,	-- sent on any error
@@ -65,7 +66,8 @@ Taxon1-resp ::= CHOICE {
         maxtaxid        INTEGER,
 	getproptypes    SET OF Taxon1-info,
         getorgprop      SET OF Taxon1-info,
-        searchname      SET OF Taxon1-name}
+        searchname      SET OF Taxon1-name,
+        dumpnames4class SET OF Taxon1-name}
 
 Taxon1-info ::= SEQUENCE {
 	ival1	INTEGER,
diff --git a/network/taxon1/taxon2/txcdproc.c b/network/taxon1/taxon2/txcdproc.c
index f8055068..b7a11b97 100644
--- a/network/taxon1/taxon2/txcdproc.c
+++ b/network/taxon1/taxon2/txcdproc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   07/15/97
 *
-* $Revision: 1.16 $
+* $Revision: 1.17 $
 *
 * File Description: 
 *       API for Taxonomy service
@@ -44,6 +44,9 @@
 *
 * RCS Modification History:
 * $Log: txcdproc.c,v $
+* Revision 1.17  2006/07/13 17:14:49  bollin
+* use Uint4 instead of Uint2 for itemID values
+*
 * Revision 1.16  2003/11/04 17:13:58  soussov
 * adds NetFini() call if service can not start properly
 *
@@ -185,7 +188,6 @@ static Taxon1RespPtr NetTaxArchReadAsn(void)
 
 static Boolean TaxServInit(void)
 {
-    DataVal    av;
     Taxon1ReqPtr taxrp;
     Taxon1RespPtr taxbp;
 
diff --git a/network/vibnet/docsum.c b/network/vibnet/docsum.c
index be09ca80..60a334aa 100644
--- a/network/vibnet/docsum.c
+++ b/network/vibnet/docsum.c
@@ -29,13 +29,16 @@
 *
 * Version Creation Date:   9/13/96
 *
-* $Revision: 6.56 $
+* $Revision: 6.57 $
 *
 * File Description: 
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: docsum.c,v $
+* Revision 6.57  2006/07/13 17:14:49  bollin
+* use Uint4 instead of Uint2 for itemID values
+*
 * Revision 6.56  2003/12/02 20:42:06  kans
 * fixed sprintf calls in SetDefaultFailureMessae
 *
@@ -494,7 +497,7 @@ static SeqEntryPtr SeqEntryLockByGi (Int4 uid)
   return sep;
 }
 
-static Uint2 BioseqFindEntityByGi (Int4 uid, Uint2Ptr itemIDptr)
+static Uint2 BioseqFindEntityByGi (Int4 uid, Uint4Ptr itemIDptr)
 
 {
   ValNode  vn;
@@ -803,7 +806,7 @@ static CharPtr FileToString (CharPtr path)
 {
   Int2     actual;
   FILE     *fp;
-  Int4     len;
+  Int8     len;
   CharPtr  ptr;
 
   if (path == NULL) return NULL;
@@ -3945,7 +3948,7 @@ static void LaunchSequenceViewer (Int4 uid, Int2 numAlign, Int4Ptr alignuids, In
   EntrezGlobalsPtr  egp;
   Uint2             entityID;
   Int2              handled;
-  Uint2             itemID;
+  Uint4             itemID;
   SeqEntryPtr       sep;
 
   WatchCursor ();
@@ -3992,7 +3995,7 @@ static void LaunchGenomeViewer (Int4 uid, Int2 numAlign, Int4Ptr alignuids, Int2
   Uint2        datatype;
   Uint2        entityID;
   Int2         handled;
-  Uint2        itemID;
+  Uint4        itemID;
   SeqEntryPtr  sep;
 
   WatchCursor ();
diff --git a/network/wwwblast/Src/wblast2.c b/network/wwwblast/Src/wblast2.c
index 6e54ecdc..e3183a9c 100644
--- a/network/wwwblast/Src/wblast2.c
+++ b/network/wwwblast/Src/wblast2.c
@@ -1,4 +1,4 @@
-/* $Id: wblast2.c,v 1.37 2006/04/26 14:48:23 jianye Exp $
+/* $Id: wblast2.c,v 1.39 2006/07/05 15:59:21 jianye Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -27,12 +27,18 @@
 *
 * Initial Creation Date: 10/23/2000
 *
-* $Revision: 1.37 $
+* $Revision: 1.39 $
 *
 * File Description:
 *        BLAST 2 Sequences CGI program
 *
 * $Log: wblast2.c,v $
+* Revision 1.39  2006/07/05 15:59:21  jianye
+* limit the defline length to 512
+*
+* Revision 1.38  2006/06/07 23:44:48  jianye
+* fix short identical user id collision
+*
 * Revision 1.37  2006/04/26 14:48:23  jianye
 * force printing out accession in defline
 *
@@ -295,6 +301,8 @@
 
 #define NR_SIZE_NA 2385885539
 #define NR_SIZE_AA 181542687
+#define DEFLINE_LENGTH 512
+Char defline_buf[DEFLINE_LENGTH+4];
 
 typedef struct prym{
 	Int2		len;
@@ -1717,7 +1725,11 @@ static void PrintParam(Boolean is_prot, Int2 mtrx, Int2 ma, Int2 ms, BLAST_Optio
  
     defline = BioseqGetTitle(query_bsp);
     if(defline) {
-        printf("%s", defline);
+        StringNCpy(defline_buf, defline, DEFLINE_LENGTH);
+        if(StringLen(defline) > DEFLINE_LENGTH) {
+            StringCat(defline_buf, "...");
+        }
+        printf("%s", defline_buf);
     } 
 
     printf("<BR>");
@@ -1738,7 +1750,11 @@ static void PrintParam(Boolean is_prot, Int2 mtrx, Int2 ma, Int2 ms, BLAST_Optio
    
     defline = BioseqGetTitle(subject_bsp);
     if(defline) {
-        printf("%s", defline);
+        StringNCpy(defline_buf, defline, DEFLINE_LENGTH - 3);
+        if(StringLen(defline) > DEFLINE_LENGTH) {
+            StringCat(defline_buf, "...");
+        }
+        printf("%s", defline_buf);
     } 
     printf("<BR>\n");
 
@@ -2328,7 +2344,7 @@ Int2 Main(void)
     
     if(seq1EntryData && seq2EntryData && 
             seq_1_type != ACCESSION_GI && seq_2_type != ACCESSION_GI &&
-                            StrNCmp(seq1EntryData, seq2EntryData, 6) == 0 ) {
+                            StrNCmp(seq1EntryData, seq2EntryData, 2) == 0 ) {
         AdjustSubjectLine(&seq1EntryData,&seq2EntryData);
     }