aba8125cb532df17beb7c7c9bc8467a43d09e3d6
braney
  Wed Feb 10 13:39:27 2016 -0800
changes to allow for GenBank metadata to be held in a common table.  #16809

diff --git src/hg/hgTracks/retroGene.c src/hg/hgTracks/retroGene.c
index 1b5ca94..cb35d13 100644
--- src/hg/hgTracks/retroGene.c
+++ src/hg/hgTracks/retroGene.c
@@ -1,20 +1,21 @@
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 
 #include "retroGene.h"
+#include "genbank.h"
 
 /* bit set of labels to use */
 enum {useOrgCommon = 0x01,
       useOrgAbbrv  = 0x02,
       useOrgDb     = 0x04,
       useGene      = 0x08,
       useAcc       = 0x10};
 
 struct linkedFeatures *lfFromRetroGene(struct ucscRetroInfo *pg)
 /* Return a linked feature from a retroGene. */
 {
 struct linkedFeatures *lf;
 struct simpleFeature *sf, *sfList = NULL;
 int grayIx = grayInRange(pg->score, 0, 1000);
 int *starts = pg->chromStarts, start;
@@ -80,34 +81,34 @@
 }
 
 char *getRetroParentSymbol(struct ucscRetroInfo *r, char *parentName)
 {
 struct sqlConnection *conn = hAllocConn(database);
 char cond_str[512];
 char *geneSymbol = NULL;
 if (r != NULL)
     {
     if (hTableExists(database, "kgXref") )
         {
         sqlSafefFrag(cond_str, sizeof(cond_str), "kgID='%s'", parentName);
         geneSymbol = sqlGetField(database, "kgXref", "geneSymbol", cond_str);
         }
 
-    if (hTableExists(database, "refLink") )
+    if (sqlTableExists(conn, refLinkTable) )
         {
         sqlSafefFrag(cond_str, sizeof(cond_str), "mrnaAcc = '%s'", r->refSeq);
-        geneSymbol = sqlGetField(database, "refLink", "name", cond_str);
+        geneSymbol = sqlGetField(database, refLinkTable, "name", cond_str);
         }
     }
 hFreeConn(&conn);
 return geneSymbol;
 }
 
 static unsigned getLabelTypes(struct track *tg)
 /* get set of labels to use */
 {
 unsigned labelSet = 0;
 
 // label setting are on parent track
 char prefix[128];
 safef(prefix, sizeof(prefix), "%s.label", tg->tdb->track);
 struct hashEl *labels = cartFindPrefix(cart, prefix);