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/synonym.c src/hg/hgGene/synonym.c
index f217179..0a1249d 100644
--- src/hg/hgGene/synonym.c
+++ src/hg/hgGene/synonym.c
@@ -1,28 +1,29 @@
 /* Synonym - print out other names for this gene. */
 
 /* 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 "hdb.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "hgGene.h"
 #include "spDb.h"
 #include "ccdsGeneMap.h"
+#include "genbank.h"
 
 
 static void printOurMrnaUrl(FILE *f, char *accession)
 /* Print URL for Entrez browser on a nucleotide. */
 {
 fprintf(f, "../cgi-bin/hgc?%s&g=mrna&i=%s&c=%s&o=%d&t=%d&l=%d&r=%d&db=%s",
     cartSidUrlString(cart), accession, curGeneChrom, curGeneStart, curGeneEnd, curGeneStart,
     curGeneEnd, database);
 }
 
 static void printOurRefseqUrl(FILE *f, char *accession)
 /* Print URL for Entrez browser on a nucleotide. */
 {
 fprintf(f, "../cgi-bin/hgc?%s&g=refGene&i=%s&c=%s&o=%d&l=%d&r=%d&db=%s",
     cartSidUrlString(cart),  accession, curGeneChrom, curGeneStart, curGeneStart,
@@ -328,38 +329,38 @@
     if (sameWord(genome, "C. elegans"))
 	hPrintf("<B>WormBase ID:</B> %s<BR>", id);
     else
 	hPrintf("<B>UCSC ID:</B> %s<BR>", id);
     }
     
 if (refSeqAcc[0] != 0)
     {
     hPrintf("<B>RefSeq Accession: </B> <A HREF=\"");
     printOurRefseqUrl(stdout, refSeqAcc);
     hPrintf("\">%s</A><BR>\n", refSeqAcc);
     }
 else if (mrnaAcc[0] != 0)
     {
     sqlSafefFrag(condStr, sizeof(condStr), "acc = '%s'", mrnaAcc);
-    if (sqlGetField(database, "gbCdnaInfo", "acc", condStr) != NULL)
+    if (sqlGetField(database, gbCdnaInfoTable, "acc", condStr) != NULL)
         {
     	hPrintf("<B>Representative RNA: </B> <A HREF=\"");
     	printOurMrnaUrl(stdout, mrnaAcc);
     	hPrintf("\">%s</A><BR>\n", mrnaAcc);
     	}
     else
-    /* do not show URL link if it is not found in gbCdnaInfo */
+    /* do not show URL link if it is not found in gbCdnaInfoTable */
     	{
     	hPrintf("<B>Representative RNA: %s </B>", mrnaAcc);
     	}
     }
 if (protAcc != NULL)
     {
     kgProteinID = cloneString("");
     if (hTableExists(sqlGetDatabase(conn), "knownGene")
         && (isNotEmpty(curGeneChrom) &&
 	      differentWord(curGeneChrom,"none")))
     	{
     	sqlSafefFrag(condStr, sizeof(condStr), "name = '%s' and chrom = '%s' and txStart=%d and txEnd=%d", 
 	        id, curGeneChrom, curGeneStart, curGeneEnd);
     	kgProteinID = sqlGetField(database, "knownGene", "proteinID", condStr);
     	}