Load /tmp/.../ncbi-tools6-6.1.20051206 into

branches/upstream/current.

6 files changed, 84 insertions, 31 deletions

diff --git a/network/blast3/client/netblap3.c b/network/blast3/client/netblap3.c
index 2179f439..48bd3878 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 1.109  2005/10/12 19:49:46  kans
+* EntrezSetServer was removed, so commented out here
+*
+* Revision 1.108  2005/09/13 18:03:57  madden
+* Fix so that tweak_parameters cna be in other_options
+*
 * Revision 1.107  2005/08/04 15:54:41  kans
 * local variable defined before ASSERT in s_addTweakToOtherOptions for strict C compliance (CodeWarrior Carbon complained)
 *
@@ -755,7 +761,7 @@ s_addTweakToOtherOptions(Uint1 tweak_parameters, BlastParametersPtr parameters)
              {
                  other_options = MemNew((kBuffSize)*sizeof(char));
              }
-             sprintf(other_options+len, "t=%ld", (long) tweak_parameters);
+             sprintf(other_options+len, "-t%ld", (long) tweak_parameters);
              parameters->other_options = other_options;
         }
            
@@ -2883,8 +2889,8 @@ NLM_EXTERN Int4 BLASTGetUidsFromQuery(CharPtr       query,
         *uids = NULL;
     
     EntrezSetProgramName ("BLAST API");
-    EntrezSetServer ("www.ncbi.nlm.nih.gov", 80, 
-                     "/entrez/utils/entrez2server.fcgi");
+    /* EntrezSetServer ("www.ncbi.nlm.nih.gov", 80, 
+                     "/entrez/utils/entrez2server.fcgi"); */
     
     e2rq = EntrezCreateBooleanRequest (!count_only, FALSE, 
                                        is_na? "Nucleotide" : "Protein", 
diff --git a/network/id2arch/id2.asn b/network/id2arch/id2.asn
index b1c7a86a..00c6c411 100644
--- a/network/id2arch/id2.asn
+++ b/network/id2arch/id2.asn
@@ -1,4 +1,4 @@
---$Revision: 1.16 $
+--$Revision: 1.17 $
 --********************************************************************
 --
 --  Network Id server network access
@@ -446,7 +446,10 @@ ID2-Blob-Id ::= SEQUENCE {
                 snp         (1),
                 snp-graph   (4),
                 cdd         (8),
-                mgc         (16)
+                mgc         (16),
+                hprd        (32),
+                sts         (64),
+                trna        (128)
         } DEFAULT main,
         sat-key         INTEGER,
         -- version of blob, optional in some requests
diff --git a/network/taxon1/taxon2/tc2proc.c b/network/taxon1/taxon2/tc2proc.c
index d6c968d0..c088b815 100644
--- a/network/taxon1/taxon2/tc2proc.c
+++ b/network/taxon1/taxon2/tc2proc.c
@@ -1,5 +1,5 @@
 /*----------------*/
-/* $Id: tc2proc.c,v 1.38 2005/07/25 18:07:44 lavr Exp $           */
+/* $Id: tc2proc.c,v 1.39 2005/10/25 17:47:26 soussov Exp $           */
 /*----------------*/
 
 #include <stdlib.h>
@@ -1570,6 +1570,9 @@ static OrgModPtr copyOrgMod(OrgModPtr src)
 static int subtypeConflict(Int2 t1, Int2 t2)
 {
     if(t1 == t2) return 1;
+#if 1
+    if(t2 == 255) return 1;
+#else
     switch(t2) {
     case 2:
     case 6:
@@ -1582,6 +1585,7 @@ static int subtypeConflict(Int2 t1, Int2 t2)
     default:
         break;
     }
+#endif
     return 0;
 }
 
diff --git a/network/wwwblast/Src/Makefile b/network/wwwblast/Src/Makefile
index 54ca853e..4c27b01c 100644
--- a/network/wwwblast/Src/Makefile
+++ b/network/wwwblast/Src/Makefile
@@ -28,7 +28,7 @@ ALL_LIBS = -lncbidesk -lvibgif $(BLAST_LIBS) $(THREAD_LIBS)
 ALL_LIBS_CS = -lncbitxc2 -lncbiid1 -lnetblast -lnetcli $(ALL_LIBS)
 BL2_LIBS = $(BLAST_LIBS)
 # For Blast 2 sequences client/server
-BL2_LIBS_CS = -lncbiid1 -lnetcli $(BLAST_LIBS)
+BL2_LIBS_CS = -lncbiid1 -lnetcli $(BLAST_LIBS) -lblastcompadj
 
 BL2_DEFINE = -DBL2SEQ_STANDALONE
 
diff --git a/network/wwwblast/Src/wblast2.c b/network/wwwblast/Src/wblast2.c
index ec6830ed..9db717d0 100644
--- a/network/wwwblast/Src/wblast2.c
+++ b/network/wwwblast/Src/wblast2.c
@@ -1,4 +1,4 @@
-/* $Id: wblast2.c,v 1.25 2005/08/19 15:53:50 coulouri Exp $
+/* $Id: wblast2.c,v 1.30 2005/12/05 16:14:48 coulouri Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -27,12 +27,27 @@
 *
 * Initial Creation Date: 10/23/2000
 *
-* $Revision: 1.25 $
+* $Revision: 1.30 $
 *
 * File Description:
 *        BLAST 2 Sequences CGI program
 *
 * $Log: wblast2.c,v $
+* Revision 1.30  2005/12/05 16:14:48  coulouri
+* c99 variable declaration breaks irix and solaris compilers
+*
+* Revision 1.29  2005/10/21 14:12:37  zaretska
+* Added code to treat NCBI_SEQID seq type the same way as  ACCESSION_GI to fix bug for Blast2Seq when called from 'Search trace archive...'
+*
+* Revision 1.28  2005/10/19 15:27:16  zaretska
+* Fixed disappearing version number in accession. Strip carriage return from accession/gi enetred in GUI.
+*
+* Revision 1.27  2005/10/04 15:55:21  coulouri
+* correct broken urls
+*
+* Revision 1.26  2005/09/07 14:21:41  coulouri
+* correct broken link
+*
 * Revision 1.25  2005/08/19 15:53:50  coulouri
 * correct grammar
 *
@@ -606,9 +621,9 @@ static void	Blast2SeqMainPage(CharPtr warning, CharPtr seq1, CharPtr seq2, CharP
            printf("<TD><B><I>\n");
            printf("<A HREF=http://www.ncbi.nlm.nih.gov/Entrez><font color=#ffffff>Entrez</font></A>\n");
            printf("</I></B></TD>\n");
-           printf("<TD><B><I><A HREF=bl2.html><font color=#ffffff>BLAST 2 sequences</font></A></I></B></TD>\n");
+           printf("<TD><B><I><A HREF=wblast2.cgi><font color=#ffffff>BLAST 2 sequences</font></A></I></B></TD>\n");
            printf("<TD><B><I><A HREF=http://www.ncbi.nlm.nih.gov/blast><font color=#ffffff>BLAST</font></A></I></B></TD>\n");
-           printf("<TD><B><I><A HREF=bl2_seg.html><font color=#ffffff>Example</font></A></I></B></TD>\n");
+           printf("<TD><B><I><A HREF=example.html><font color=#ffffff>Example</font></A></I></B></TD>\n");
            printf("<TD><B><I>\n");
            printf("<A HREF=http://www.ncbi.nlm.nih.gov/blast/blast_help.html><font color=#ffffff>Help</font></A>\n");
            printf("</I></B></TD></TR></TABLE></CENTER>\n");
@@ -649,7 +664,7 @@ static void	Blast2SeqMainPage(CharPtr warning, CharPtr seq1, CharPtr seq2, CharP
         if (!options) {
            printf("This tool produces the alignment of two given sequences using "
 #ifndef BL2SEQ_STANDALONE
-"<A HREF=http://www.ncbi.nlm.nih.gov/blast/newblast.html TARGET=one>BLAST</A> engine for local alignment. <BR>The stand-alone executable for blasting two sequences (bl2seq) can be retrieved from <A HREF=ftp://ncbi.nlm.nih.gov/blast/executables> NCBI ftp site</A><br><b><A HREF=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10339815&dopt=Abstract>Reference:</A></b> Tatiana A. Tatusova, Thomas L. Madden (1999), \"Blast 2 sequences - a new tool for comparing protein and nucleotide sequences\", FEMS Microbiol Lett. 174:247-250 \
+"<A HREF=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9254694&dopt=Citation\" TARGET=one>BLAST</A> engine for local alignment. <BR>The stand-alone executable for blasting two sequences (bl2seq) can be retrieved from <A HREF=ftp://ftp.ncbi.nlm.nih.gov/blast/executables> NCBI ftp site</A><br><b><A HREF=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10339815&dopt=Abstract>Reference:</A></b> Tatiana A. Tatusova, Thomas L. Madden (1999), \"Blast 2 sequences - a new tool for comparing protein and nucleotide sequences\", FEMS Microbiol Lett. 174:247-250 \
 <br><BR>"
 #else
 "BLAST<BR>engine for local alignment.<P>\n"
@@ -1368,9 +1383,10 @@ static void DrawRectAlign(PrymPtr PNTR rect, Int2 k, Int2 color, Int2 height, In
 }
 
 #define LOCAL_BUFLEN 255
+
 static BioseqPtr 
 
-FindSeqByAccession(CharPtr accver, Int2 id_num)
+FindSeqByAccession(CharPtr accessionOrGi, Int2 id_num)
 {
    BioseqPtr bsp = NULL;
 
@@ -1386,18 +1402,22 @@ FindSeqByAccession(CharPtr accver, Int2 id_num)
    ByteStorePtr old_seq_data = NULL;
 
    ID1BioseqFetchEnable ("wblast2", TRUE);
-      
-   if ((gi = atoi(accver)) == 0) {
-      accession = StringTokMT(accver, ".", &accver);
-      
-      if (accver)
-         version = atoi(accver);
+   
+   if ((gi = atoi(accessionOrGi)) == 0) {
+      Char accver[LOCAL_BUFLEN];
+      CharPtr ptrVersion = NULL;
 
       if((sip = ValNodeNew (NULL)) == NULL)
          return NULL;
       if((tsip = TextSeqIdNew ()) == NULL)
          return NULL;
+
+      StringCpy(accver, accessionOrGi);
+      accession = StringTokMT(accver, ".", &ptrVersion);
       
+      if (ptrVersion)
+         version = atoi(ptrVersion);
+
       tsip->accession = StringSave(accession);
       tsip->version = version;
       /* GenBank, EMBL, and DDBJ. */
@@ -1777,6 +1797,7 @@ typedef enum {
     ACCESSION_GI
 } BlastQuerySequenceType;
 
+
 #define MAX_ALLOWED_ID_LEN 20
 #define IS_NEWLINE(a) ((a)=='\0' || (a)=='\n' || (a)=='\r')
 static int get_sequence_type(char *querystr)
@@ -1886,6 +1907,8 @@ static char * GetAndFormatEnteredSequence(WWWBlastInfoPtr theInfo,int seqNbr,int
 
     if(c) {
         *seq_type = get_sequence_type(c);
+        //Treat NCBI_SEQID seq type the same way as  ACCESSION_GI
+        *seq_type = (*seq_type == NCBI_SEQID) ? ACCESSION_GI : *seq_type;
         //Check here if sequence is enetered with subjetc line !!!
         if(*seq_type != ACCESSION_GI && *seq_type != FASTA_WITH_DEFLINE) {        
         // if (c1 && *c1 != '>') {
@@ -1895,7 +1918,10 @@ static char * GetAndFormatEnteredSequence(WWWBlastInfoPtr theInfo,int seqNbr,int
             MemFree(c);
             c = seq;
             MemFree(sbuf);
-        }        
+        }
+        if(*seq_type == ACCESSION_GI) {
+            StringTok(c, "\n\r\t");
+        }
     }
     return c;
 }
diff --git a/network/wwwblast/Src/wwwbutl.c b/network/wwwblast/Src/wwwbutl.c
index 94387037..2732555c 100644
--- a/network/wwwblast/Src/wwwbutl.c
+++ b/network/wwwblast/Src/wwwbutl.c
@@ -1,4 +1,4 @@
-/* $Id: wwwbutl.c,v 1.21 2004/01/16 17:35:20 dondosha Exp $
+/* $Id: wwwbutl.c,v 1.22 2005/08/31 20:35:22 coulouri Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,12 +29,24 @@
 *
 * Initial Version Creation Date: 04/21/2000
 *
-* $Revision: 1.21 $
+* $Revision: 1.22 $
 *
 * File Description:
 *         WWW BLAST/PSI/PHI utilities
 *
 * $Log: wwwbutl.c,v $
+* Revision 1.22  2005/08/31 20:35:22  coulouri
+* From Mike Gertz:
+* in WWWCreateSearchOptions:
+*   - Replaced outmoded adjustment of options->expect_value when
+*     compostion-based statistics is used with the newer behavior
+*     implemented in blastpgp - increase the expect_value only when
+*     mode > 1 composition-based statistics is being used.
+*   - By taking no action to modify the hitlist size, implicitly use the
+*     default action defined in the BlastSingleQueryResultSize routine;
+*     previously it was a bug to not modify the hitlist size in
+*     WWWCreateSearchOptions.
+*
 * Revision 1.21  2004/01/16 17:35:20  dondosha
 * Fixed mouseover problems
 *
@@ -201,6 +213,10 @@
 
 #include <wwwblast.h>
 
+/* Multiplier by which to increase the evalue when mode > 1 composition-based
+ * statistics is being used. */
+#define EVALUE_EXPAND 10
+
 void WWWBlastInfoFree(WWWBlastInfoPtr theInfo)
 {
     Int4 i;
@@ -1486,16 +1502,14 @@ Boolean WWWCreateSearchOptions(WWWBlastInfoPtr theInfo)
         options->tweak_parameters = TRUE;
 
     /* Adjustment of expect value and hitlist size */
-    if (options->tweak_parameters) {
-        options->hitlist_size *= 2; /*allows for extra matches*/
-        options->original_expect_value = 
-            options->expect_value;
-        if (options->expect_value < 0.1) {
-            options->expect_value = 
-                MIN(0.1, 10 * options->expect_value);
-        }
+    options->kappa_expect_value = options->expect_value;
+    if (options->tweak_parameters > 1) {
+        /* relax the cutoff evalue so that we don't loose too many
+         * hits for which compositional adjustment improves the
+         * evalue. */
+        options->expect_value *= EVALUE_EXPAND;
     }
-    
+
     /* SMITH_WATERMAN */
     
     if (WWWGetValueByName(theInfo->info, "SMITH_WATERMAN") != NULL)