src/hg/hgGene/mrnaDescriptions.c 1.9

Index: src/hg/hgGene/mrnaDescriptions.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgGene/mrnaDescriptions.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 1000000 -r1.8 -r1.9
--- src/hg/hgGene/mrnaDescriptions.c	3 Sep 2008 19:18:50 -0000	1.8
+++ src/hg/hgGene/mrnaDescriptions.c	26 Jun 2009 21:28:23 -0000	1.9
@@ -1,98 +1,98 @@
 /* mRNA descriptions. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "spDb.h"
 #include "hdb.h"
 #include "genePred.h"
 #include "bed.h"
 #include "hgGene.h"
 
 static char const rcsid[] = "$Id$";
 
 static boolean mrnaDescriptionsExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if mrna  on this one. */
 {
 struct psl *list = NULL;
 if (hTableExists(sqlGetDatabase(conn), "all_mrna"))
     {
     struct sqlResult *sr;
     char **row;
     struct psl *psl;
     int rowOffset;
     char extra[64];
     safef(extra, sizeof(extra), "strand='%c'", curGenePred->strand[0]);
-    sr = hRangeQuery(conn, "mrna", curGeneChrom, curGeneStart, curGeneEnd,
+    sr = hRangeQuery(conn, "all_mrna", curGeneChrom, curGeneStart, curGeneEnd,
     	extra, &rowOffset);
     while ((row = sqlNextRow(sr)) != NULL)
          {
 	 psl = pslLoad(row+rowOffset);
 	 slAddHead(&list, psl);
 	 }
     slReverse(&list);
     section->items = list;
     }
 return slCount(list) > 0;
 }
 
 static int basesShared(struct genePred *gp, struct psl *psl)
 /* Return number of bases a&b share. */
 {
 int intersect = 0;
 int i, blockCount = psl->blockCount;
 int s,e;
 for (i=0; i<blockCount; ++i)
     {
     s = psl->tStarts[i];
     e = s + psl->blockSizes[i];
     if (psl->strand[1] == '-')
 	reverseIntRange(&s, &e, psl->tSize);
     intersect += gpRangeIntersection(gp, s, e);
     }
 return intersect;
 }
 
 static void mrnaDescriptionsPrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out mrna descriptions annotations. */
 {
 struct psl *psl, *pslList = section->items;
 for (psl = pslList; psl != NULL; psl = psl->next)
     {
     if (basesShared(curGenePred, psl) > 12)	/* Filter out possible little noisy flecks. */
         {
 	char query[512];
 	char *description;
 	safef(query, sizeof(query),
 	    "select description.name from gbCdnaInfo,description"
 	    " where gbCdnaInfo.acc='%s' and gbCdnaInfo.description = description.id"
 	    , psl->qName);
 	description = sqlQuickString(conn, query);
 	if (description != NULL)
 	    {
 	    char *url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
 	    		"?cmd=Search&db=Nucleotide&term=%s&doptcmdl=GenBank"
 			"&tool=genome.ucsc.edu";
 	    hPrintf("<A HREF=\"");
 	    hPrintf(url, psl->qName);
 	    hPrintf("\" TARGET=_blank>");
 	    hPrintf("%s</A> - ", psl->qName);
 	    hPrintf("%s<BR>", description);
 	    }
 	freeMem(description);
 	}
     }
 }
 
 struct section *mrnaDescriptionsSection(struct sqlConnection *conn, 
 	struct hash *sectionRa)
 /* Create mrnaDescriptions section. */
 {
 struct section *section = sectionNew(sectionRa, "mrnaDescriptions");
 section->exists = mrnaDescriptionsExists;
 section->print = mrnaDescriptionsPrint;
 return section;
 }