src/hg/hgc/hgc.c 1.1561

Index: src/hg/hgc/hgc.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/hgc.c,v
retrieving revision 1.1560
retrieving revision 1.1561
diff -b -B -U 4 -r1.1560 -r1.1561
--- src/hg/hgc/hgc.c	15 Jul 2009 18:22:37 -0000	1.1560
+++ src/hg/hgc/hgc.c	24 Jul 2009 04:20:10 -0000	1.1561
@@ -6310,9 +6310,9 @@
 trashDirFile(&bodyTn, "body", "body", ".html");
 
 /* Writing body of alignment. */
 body = mustOpen(bodyTn.forCgi, "w");
-htmStart(body, psl->qName);
+htmStartDirDepth(body, psl->qName, 2);
 if (qType == gftRna || qType == gftDna)
     blockCount = showPartialDnaAlignment(psl, oSeq, body, cdsS, cdsE, FALSE);
 else
     blockCount = showGfAlignment(psl, oSeq, body, qType, qStart, qEnd, qName);
@@ -6323,9 +6323,9 @@
 /* Write index. */
 index = mustOpen(indexTn.forCgi, "w");
 if (qName == NULL)
     qName = psl->qName;
-htmStart(index, qName);
+htmStartDirDepth(index, qName, 2);
 fprintf(index, "<H3>Alignment of %s</H3>", qName);
 fprintf(index, "<A HREF=\"../%s#cDNA\" TARGET=\"body\">%s</A><BR>\n", bodyTn.forCgi, qName);
 fprintf(index, "<A HREF=\"../%s#genomic\" TARGET=\"body\">%s.%s</A><BR>\n", bodyTn.forCgi, hOrganism(database), psl->tName);
 for (i=1; i<=blockCount; ++i)
@@ -6360,9 +6360,9 @@
 trashDirFile(&bodyTn, "body", "body", ".html");
 
 /* Writing body of alignment. */
 body = mustOpen(bodyTn.forCgi, "w");
-htmStart(body, partPsl->qName);
+htmStartDirDepth(body, partPsl->qName, 2);
 blockCount = showPartialDnaAlignment(wholePsl, oSeq, body, cdsS, cdsE, TRUE);
 htmEnd(body);
 fclose(body);
 chmod(bodyTn.forCgi, 0666);
@@ -6370,9 +6370,9 @@
 /* Write index. */
 index = mustOpen(indexTn.forCgi, "w");
 if (qName == NULL)
     qName = partPsl->qName;
-htmStart(index, qName);
+htmStartDirDepth(index, qName, 2);
 fprintf(index, "<H3>Alignment of %s</H3>", qName);
 fprintf(index, "<A HREF=\"../%s#cDNA\" TARGET=\"body\">%s</A><BR>\n", bodyTn.forCgi, qName);
 if (partPsl != wholePsl)
     fprintf(index, "<A HREF=\"../%s#cDNAStart\" TARGET=\"body\">%s in browser window</A><BR>\n", bodyTn.forCgi, qName);
@@ -19511,9 +19511,9 @@
 genePredFree(&gene);
 
 /* Writing body of alignment. */
 body = mustOpen(bodyTn.forCgi, "w");
-htmStart(body, psl->qName);
+htmStartDirDepth(body, psl->qName, 2);
 
 /* protein psl's have a tEnd that isn't quite right */
 if ((psl->strand[1] == '+') && (qType == gftProt))
     tEnd = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1] * 3;
@@ -19548,9 +19548,9 @@
 /* Write index. */
 index = mustOpen(indexTn.forCgi, "w");
 if (entryName == NULL)
     entryName = psl->qName;
-htmStart(index, entryName);
+htmStartDirDepth(index, entryName, 2);
 fprintf(index, "<H3>Alignment of %s</H3>", entryName);
 fprintf(index, "<A HREF=\"../%s#cDNA\" TARGET=\"body\">%s</A><BR>\n", bodyTn.forCgi, entryName);
 fprintf(index, "<A HREF=\"../%s#genomic\" TARGET=\"body\">%s.%s</A><BR>\n", bodyTn.forCgi, hOrganism(database), psl->tName);
 for (i=1; i<=blockCount; ++i)