src/hg/hgc/retroClick.c 1.16
1.16 2010/05/24 20:19:22 kent
Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
Index: src/hg/hgc/retroClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/retroClick.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 4 -r1.15 -r1.16
--- src/hg/hgc/retroClick.c 11 May 2010 01:43:29 -0000 1.15
+++ src/hg/hgc/retroClick.c 24 May 2010 20:19:22 -0000 1.16
@@ -632,31 +632,33 @@
}
printf("</TBODY></TABLE>\n");
}
-void printRetroAlignments(struct psl *pslList, int startFirst, char *hgcCommand,
- char *typeName, char *itemIn)
+static void printRetroAlignments(struct psl *pslList, int startFirst, char *hgcCommand,
+ char *aliTable, char *itemIn)
/* Print list of mRNA alignments. */
{
-if (pslList == NULL || typeName == NULL)
+if (pslList == NULL || aliTable == NULL)
return;
-printAlignmentsSimple(pslList, startFirst, hgcCommand, typeName, itemIn);
+printAlignmentsSimple(pslList, startFirst, hgcCommand, aliTable, itemIn);
+#ifdef UNUSED /* Does nothing in face in the end except trim the psls that nobody looks at. */
struct psl *psl = pslList;
for (psl = pslList; psl != NULL; psl = psl->next)
{
if ( pslTrimToTargetRange(psl, winStart, winEnd) != NULL
&&
- !startsWith("xeno", typeName)
- && !(startsWith("user", typeName) && pslIsProtein(psl))
+ !startsWith("xeno", aliTable)
+ && !(startsWith("user", aliTable) && pslIsProtein(psl))
&& psl->tStart == startFirst
)
{
char otherString[512];
- safef(otherString, sizeof(otherString), "%d&aliTrack=%s",
- psl->tStart, typeName);
+ safef(otherString, sizeof(otherString), "%d&aliTable=%s",
+ psl->tStart, aliTable);
}
}
+#endif /* DOES_NOTHING */
}
static void displayAligns(struct sqlConnection *conn, struct mappingInfo *mi)
@@ -770,9 +772,9 @@
void retroShowCdnaAli(char *mappedId)
/* Show alignment for accession, mostly ripped off from htcCdnaAli */
{
-char *track = cartString(cart, "aliTrack");
+char *track = cartString(cart, "aliTable");
struct trackDb *tdb = hashMustFindVal(trackHash, track);
char *table = cartString(cart, "table");
int start = cartInt(cart, "o");
struct sqlConnection *conn = hAllocConn(database);
@@ -807,10 +809,10 @@
char *extTable = words[2];
rnaSeq = hDnaSeqGet(database, acc, seqTable, extTable);
if (rnaSeq == NULL)
{
- safef(acc, sizeof(acc), "%s.%d",mi->seqId, mi->gbCurVer);
- rnaSeq = hDnaSeqGet(database, acc, "seq", "extFile");
+ char *acc = mi->seqId;
+ rnaSeq = hExtSeq(database, acc);
if (rnaSeq == NULL)
errAbort("can't get mRNA sequence from %s prefix %s for %s from %s mappedId %s",
database, mi->geneSet, acc, track, mappedId);
}