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/hgGene/pseudoGene.c src/hg/hgGene/pseudoGene.c
index 79fe6fb..b9ce56a 100644
--- src/hg/hgGene/pseudoGene.c
+++ src/hg/hgGene/pseudoGene.c
@@ -1,30 +1,31 @@
 /* pseudoGene descriptions. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "spDb.h"
 #include "hdb.h"
 #include "web.h"
 #include "genePred.h"
 #include "bed.h"
 #include "hgGene.h"
+#include "genbank.h"
 
 
 static boolean pseudoGeneExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if mrna  on this one. */
 {
 boolean result;
 
 result = FALSE;
 if (hTableExists(sqlGetDatabase(conn), "ucscRetroInfo"))
     {
     struct sqlResult *sr;
     char **row;
     char query[255];
     sqlSafef(query, sizeof(query),
@@ -66,35 +67,35 @@
       "select distinct name, chrom, chromStart, chromEnd, refseq, type, score from ucscRetroInfo where name='%s' or kgName='%s' or refseq='%s'",
       geneId, geneId, geneId);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL) 
     {
     name 	= row[0];
     chrom	= row[1];
     chromStart  = row[2];
     chromEnd	= row[3];
     refseq	= row[4];
     rtype	= row[5];
     score	= sqlUnsigned(row[6]);
    
     desc = emptyStr;
     sqlSafefFrag(condStr, sizeof(condStr), "acc='%s'", refseq);
-    descID= sqlGetField(database, "gbCdnaInfo", "description", condStr);
+    descID= sqlGetField(database, gbCdnaInfoTable, "description", condStr);
     if (descID != NULL)
     	{
     	sqlSafefFrag(condStr, sizeof(condStr), "id=%s", descID);
-    	desc = sqlGetField(database, "description", "name", condStr);
+    	desc = sqlGetField(database, descriptionTable, "name", condStr);
 	if (desc == NULL) desc = emptyStr;
 	}
    	
     webPrintLinkCellStart();
     hPrintf("<A HREF=\"hgc?g=ucscRetroAli&i=%s\">%s</A>", name, name);
     webPrintLinkCellEnd();
     webPrintLinkCellStart();
     hPrintf("%s ", rtype);
     webPrintLinkCellEnd();
     webPrintLinkCellStart();
     hPrintf("%d ", score);
     webPrintLinkCellEnd();
     webPrintLinkCellStart();
     hPrintf("<A HREF=\"hgTracks?position=%s:%s-%s&ucscRetroAli=pack&hgFind.matches=%s,\">%s:%s-%s</A>",
            chrom, chromStart, chromEnd, name, chrom, chromStart, chromEnd);