7aae72b0cc4cbb6e590d2c061b32df43eb9688cc
fanhsu
  Tue Feb 1 06:17:42 2011 -0800
Updated for OMIM related tracks.
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 21dc8d8..8f8f02c 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -9032,32 +9032,34 @@
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 char *strand={"+"};
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 char *chrom = cartString(cart, "c");
 
 printf("<H3>Patient %s </H3>", itemName);
 
 /* print phenotypes */
 safef(query, sizeof(query),
       "select distinct phenotype from decipherRaw where id ='%s' order by phenotype", itemName);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
-if (row != NULL)
+//if (row != NULL)
+if ((row != NULL) && strlen(row[0]) >= 1)
     {
+    printf("<br>---%s---\n", row[0]);fflush(stdout);
     printf("<B>Phenotype: </B><UL>");
     while (row != NULL)
     	{
 	printf("<LI>");
 	printf("%s\n", row[0]);
 	row = sqlNextRow(sr);
         }
     printf("</UL>");
     }
 sqlFreeResult(&sr);
 
 /* link to Ensembl DECIPHER Patient View page */
 printf("<B>Patient View: </B>\n");
 printf("More details on patient %s at ", itemName);
 printf("<A HREF=\"%s%s\" target=_blank>",
@@ -9307,43 +9309,43 @@
 char *url = tdb->url;
 char *kgId= NULL;
 char *title1 = NULL;
 char *title2 = NULL;
 char *geneSymbol = NULL;
 char *chrom, *chromStart, *chromEnd;
 char *kgDescription = NULL;
 char *refSeq;
 
 chrom      = cartOptionalString(cart, "c");
 chromStart = cartOptionalString(cart, "o");
 chromEnd   = cartOptionalString(cart, "t");
 
 if (url != NULL && url[0] != 0)
     {
-    printf("<B>OMIM Gene ");fflush(stdout);
+    printf("<B>OMIM Gene: ");fflush(stdout);
     printf("<A HREF=\"%s%s\" target=_blank>", url, itemName);
     printf("%s</A></B>", itemName);
     safef(query, sizeof(query),
     	  "select title1, title2 from omimGeneMap where omimId=%s;", itemName);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
     	{
 	if (row[0] != NULL)
 	    {
 	    title1 = cloneString(row[0]);
-    	    printf(": %s", title1);
+    	    printf(" %s", title1);
 	    }
 	if (row[1] != NULL)
 	    {
 	    title2 = cloneString(row[1]);
     	    printf(" %s ", title2);
 	    }
 	}
     sqlFreeResult(&sr);
 
     printf("<BR>\n");
     
     safef(query, sizeof(query),
     	  "select geneSymbol from omimGeneMap where omimId=%s;", itemName);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
@@ -9481,30 +9483,33 @@
 		    printf(", ");
     	    	printf("<A HREF=\"%s%s&hgg_chrom=none\" target=_blank>", "../cgi-bin/hgGene?hgg_gene=", row[0]);
     	    	printf("%s</A></B>", row[0]);
 	    	printedCnt++;
 		}
             if (printedCnt >= 1) printf("<BR>\n");
 	    }
 	sqlFreeResult(&sr);
 	}
     }
 
 printf("<HR>");
 printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName);
 }
 
+
+#include "jl.c"
+#include "js.c"
 void doOmimGeneClass3(struct trackDb *tdb, char *item)
 /* Put up OmimGene track info. */
 {
 genericHeader(tdb, item);
 printOmimGeneClass3Details(tdb, item, FALSE);
 printTrackHtml(tdb);
 }
 
 void doOmimGene(struct trackDb *tdb, char *item)
 /* Put up OmimGene track info. */
 {
 genericHeader(tdb, item);
 printOmimGeneDetails(tdb, item, FALSE);
 printTrackHtml(tdb);
 }
@@ -23420,33 +23425,37 @@
     {
     doCpgIsland(tdb, item);
     }
 else if (sameWord(table, "illuminaProbes"))
     {
     doIlluminaProbes(tdb, item);
     }
 else if (sameWord(table, "htcIlluminaProbesAlign"))
     {
     htcIlluminaProbesAlign(item);
     }
 else if (sameWord(table, "switchDbTss"))
     {
     doSwitchDbTss(tdb, item);
     }
-else if (sameWord(table, "omimLocationClass2"))
+else if (sameWord(table, "omimLocation"))
     {
-    doOmimGeneClass3(tdb, item);
+    doOmimLocation(tdb, item);
+    }
+else if (sameWord(table, "omimAvSnp"))
+    {
+    doOmimAvSnp(tdb, item);
     }
 else if (sameWord(table, "omimGeneClass2"))
     {
     doOmimGeneClass3(tdb, item);
     }
 else if (sameWord(table, "omimGeneClass3"))
     {
     doOmimGeneClass3(tdb, item);
     }
 else if (sameWord(table, "omimAv"))
     {
     doOmimAv(tdb, item);
     }
 else if (sameWord(table, "rgdGene"))
     {