src/hg/hgc/hgc.c 1.1590

Index: src/hg/hgc/hgc.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/hgc.c,v
retrieving revision 1.1589
retrieving revision 1.1590
diff -b -B -U 4 -r1.1589 -r1.1590
--- src/hg/hgc/hgc.c	19 Jan 2010 23:13:17 -0000	1.1589
+++ src/hg/hgc/hgc.c	20 Jan 2010 00:29:53 -0000	1.1590
@@ -15365,8 +15365,33 @@
     printf("\"> HapMap SNP</A> </B><BR>\n");
     }
 }
 
+static void checkForGwasCatalog(struct sqlConnection *conn, struct trackDb *tdb, char *item)
+/* If item is in gwasCatalog, add link to make the track visible. */
+{
+char *gcTable = "gwasCatalog";
+if (sqlTableExists(conn, gcTable))
+    {
+    char query[512];
+    safef(query, sizeof(query), "select count(*) from %s where name = '%s'", gcTable, item);
+    if (sqlQuickNum(conn, query) > 0)
+	{
+	struct trackDb *gcTdb = hashFindVal(trackHash, gcTable);
+	if (gcTdb != NULL)
+	    {
+	    printf("<B><A HREF=\"%s", hgTracksPathAndSettings());
+	    // If gcTable is hidden, make it dense; otherwise, leave it alone.
+	    if (sameString("hide",
+			   cartUsualString(cart, gcTable,
+					   trackDbSettingOrDefault(gcTdb, "visibility", "hide"))))
+		printf("&%s=dense", gcTable);
+	    printf("\">%s SNP</A> </B><BR>\n", gcTdb->shortLabel);
+	    }
+	}
+    }
+}
+
 static void printLsSnpPdb(struct sqlConnection *conn, char *pdbId, char *snpId)
 /* generate LS-SNP and chimera links for a PDB id */
 {
 char *lsSnpUrl = lsSnpPdbGetUrlPdbSnp(pdbId, snpId);
@@ -15476,8 +15501,9 @@
 	printf("<BR>");
 	}
     }
 sqlFreeResult(&sr);
+checkForGwasCatalog(conn, tdb, itemName);
 checkForHgdpGeo(conn, tdb, itemName, start);
 checkForHapmap(conn, tdb, itemName);
 checkForLsSnpMappings(conn, itemName);
 printSnpAlignment(tdb, snpAlign);