9cc2351f465f585965408ff48fea2ad79a1aaa91
markd
  Mon Jun 6 17:40:11 2011 -0700
meger of GENCODE V7 tracks
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 07240bc..3e40da6 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -201,30 +201,31 @@
 #include "gv.h"
 #include "gvUi.h"
 #include "protVar.h"
 #include "oreganno.h"
 #include "oregannoUi.h"
 #include "pgSnp.h"
 #include "pgPhenoAssoc.h"
 #include "pgSiftPred.h"
 #include "pgPolyphenPred.h"
 #include "bedDetail.h"
 #include "ec.h"
 #include "transMapClick.h"
 #include "retroClick.h"
 #include "mgcClick.h"
 #include "ccdsClick.h"
+#include "gencodeClick.h"
 #include "memalloc.h"
 #include "trashDir.h"
 #include "kg1ToKg2.h"
 #include "wikiTrack.h"
 #include "grp.h"
 #include "omicia.h"
 #include "atomDb.h"
 #include "pcrResult.h"
 #include "twoBit.h"
 #include "itemConf.h"
 #include "chromInfo.h"
 #include "gbWarn.h"
 #include "lsSnpPdbChimera.h"
 #include "mammalPsg.h"
 #include "net.h"
@@ -370,39 +371,45 @@
 
 void printEntrezGeneUrl(FILE *f, int geneid)
 /* Print URL for Entrez browser on a gene details page. */
 {
 fprintf(f, entrezUidFormat, "gene", geneid, "Graphics");
 }
 
 static void printEntrezOMIMUrl(FILE *f, int id)
 /* Print URL for Entrez browser on an OMIM search. */
 {
 char buf[64];
 snprintf(buf, sizeof(buf), "%d", id);
 fprintf(f, entrezFormat, "OMIM", buf, "Detailed");
 }
 
+void printSwissProtAccUrl(FILE *f, char *accession)
+/* Print URL for Swiss-Prot protein accession. */
+{
+fprintf(f, uniprotFormat, accession);
+}
+
 static void printSwissProtProteinUrl(FILE *f, char *accession)
 /* Print URL for Swiss-Prot NiceProt on a protein. */
 {
 char *spAcc;
 /* make sure accession number is used (not display ID) when linking to Swiss-Prot */
 spAcc = uniProtFindPrimAcc(accession);
 if (spAcc != NULL)
     {
-    fprintf(f, uniprotFormat , spAcc);
+    printSwissProtAccUrl(f, accession);
     }
 else
     {
     fprintf(f, uniprotFormat, accession);
     }
 }
 
 static void printSwissProtVariationUrl(FILE *f, char *accession)
 /* Print URL for Swiss-Prot variation data on a protein. */
 {
 if (accession != NULL)
     {
     fprintf(f, "\"http://www.expasy.org/cgi-bin/get-sprot-variant.pl?%s\"", accession);
     }
 }
@@ -23931,30 +23938,34 @@
     {
     doRefGene(tdb, item);
     }
 else if (sameWord(table, "knownGene"))
     {
     doKnownGene(tdb, item);
     }
 else if (sameWord(table, "refGene"))
     {
     doRefGene(tdb, item);
     }
 else if (sameWord(table, "ccdsGene"))
     {
     doCcdsGene(tdb, item);
     }
+else if (isNewGencodeGene(tdb))
+    {
+    doGencodeGene(tdb, item);
+    }
 else if (sameWord(table, "mappedRefSeq"))
     /* human refseqs on chimp browser */
     {
     doRefGene(tdb, item);
     }
 else if (sameWord(table, "mgcGenes") || sameWord(table, "mgcFullMrna"))
     {
     doMgcGenes(tdb, item);
     }
 else if (sameWord(table, "orfeomeGenes") || sameWord(table, "orfeomeMrna"))
     {
     doOrfeomeGenes(tdb, item);
     }
 else if (startsWith("viralProt", table))
     {