dd92daf267465a6323f9645576f1b9f42e7e95d0
fanhsu
  Tue May 17 16:06:21 2011 -0700
Updated new OMIM related track processing, using the omimPhenotype tale instead of omimDisoroderPhenotype.
diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index c43a49a..3374655 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -10735,49 +10735,49 @@
 
 if (dy == NULL)
     dy = dyStringNew(0);
 dyStringClear(dy);
 
 // get gene symbol(s) first
 conn = hAllocConn(database);
 safef(query,sizeof(query),
         "select geneSymbol from omimGeneMap where omimId =%s", name);
 char buf[256];
 char *ret = sqlQuickQuery(conn, query, buf, sizeof(buf));
 if (isNotEmpty(ret))
     dyStringAppend(dy, ret);
 
 safef(query,sizeof(query),
-        "select distinct disorder from omimDisorderMap, omimGene2 where name='%s' and name=cast(omimId as char) order by disorder", name);
+        "select distinct description from omimPhenotype, omimGene2 where name='%s' and name=cast(omimId as char) order by description", name);
 char *disorders = collapseRowsFromQuery(query, "; ", 20);
 if (isNotEmpty(disorders))
     {
     dyStringAppend(dy, "; disorder(s): ");
     dyStringAppend(dy, disorders);
     }
 hFreeConn(&conn);
 return(dy->string);
 }
 
 char *getDisorderClass(char *omimId)
 /* Look up phenotypeClass for omimId, for filtering items.  Don't free result! */
 {
 static char answer[256];
 struct sqlConnection *conn = hAllocConn(database);
 char query[256];
 safef(query,sizeof(query),
-      "select phenotypeClass from omimDisorderPhenotype where omimId =%s", omimId);
+      "select phenotypeClass from omimPhenotype where omimId =%s", omimId);
 char *ret = sqlQuickQuery(conn, query, answer, sizeof(answer));
 if (ret == NULL)
     safecpy(answer, sizeof(answer), "0");
 hFreeConn(&conn);
 return(answer);
 }
 
 boolean doThisOmimEntry(struct track *tg, char *omimId)
 /* check if the specific class of this OMIM entry is selected by the user */
 {
 char *disorderClass = NULL;
 boolean doIt;
 
 char labelName[255];
 boolean doClass1 = FALSE;
@@ -10854,31 +10854,31 @@
 }
 
 Color omimGene2Color(struct track *tg, void *item, struct hvGfx *hvg)
 /* set the color for omimLocation track items */
 {
 struct bed *el = item;
 char *omimId;
 char *phenClass;
 char query[256];
 struct sqlResult *sr;
 char **row;
 
 struct sqlConnection *conn = hAllocConn(database);
 
 safef(query, sizeof(query),
-      "select omimId, phenotypeClass from omimDisorderPhenotype where omimId=%s", el->name);
+      "select omimId, phenotypeClass from omimPhenotype where omimId=%s", el->name);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 
 hFreeConn(&conn);
 
 if (row == NULL)
     {
     // set to gray if this entry does not have any disorder info
     sqlFreeResult(&sr);
     return hvGfxFindColorIx(hvg, 200, 200, 200);
     }
 else
     {
     omimId    = row[0];
     phenClass = row[1];
@@ -10983,31 +10983,31 @@
 }
 
 Color omimLocationColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* set the color for omimLocation track items */
 {
 struct bed *el = item;
 char *omimId;
 char *phenClass;
 char query[256];
 struct sqlResult *sr;
 char **row;
 
 struct sqlConnection *conn = hAllocConn(database);
 
 safef(query, sizeof(query),
-      "select omimId, phenotypeClass from omimDisorderPhenotype where omimId=%s", el->name);
+      "select omimId, phenotypeClass from omimPhenotype where omimId=%s", el->name);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 
 hFreeConn(&conn);
 
 if (row == NULL)
     {
     // set to gray if this entry does not have any disorder info
     sqlFreeResult(&sr);
     return hvGfxFindColorIx(hvg, 200, 200, 200);
     }
 else
     {
     omimId    = row[0];
     phenClass = row[1];