4586cbe789d7ff340473682da13625025263131d
larrym
  Mon Nov 15 10:52:07 2010 -0800
support codon numbering in genePred tracks
diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index 3eaf80a..f346988 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -2563,31 +2563,35 @@
 				drawOpt == baseColorDrawDiffCodons ||
 				drawOpt == baseColorDrawGenomicCodons);
 if (psl && baseColorNeedsCodons)
     {
     boolean isXeno = ((tg->subType == lfSubXeno) || (tg->subType == lfSubChain) ||
 		      startsWith("mrnaBla", tg->table));
     int sizeMul = pslIsProtein(psl) ? 3 : 1;
     lf->codons = baseColorCodonsFromPsl(lf, psl, sizeMul, isXeno, maxShade, drawOpt, tg);
     }
 else if (drawOpt > baseColorDrawOff)
     {
     struct genePred *gp = NULL;
     if (startsWith("genePred", tg->tdb->type))
 	gp = (struct genePred *)(lf->original);
     if (gp && gp->cdsStart != gp->cdsEnd)
-	lf->codons = baseColorCodonsFromGenePred(lf, gp, (drawOpt != baseColorDrawDiffCodons));
+        {
+        char var[256];
+        safef(var, sizeof(var), "%sCodonNumbering", tg->tdb->track);
+        lf->codons = baseColorCodonsFromGenePred(lf, gp, (drawOpt != baseColorDrawDiffCodons), cartUsualBoolean(cart, var, FALSE));
+        }
     }
 if (psl && drawOpt == baseColorDrawCds && !zoomedToCdsColorLevel)
     baseColorSetCdsBounds(lf, psl, tg);
 
 tallStart = lf->tallStart;
 tallEnd = lf->tallEnd;
 if ((tallStart == 0 && tallEnd == 0) && !sameWord(tg->table, "jaxQTL3"))
     {
     // sometimes a bed <8 will get passed off as a bed 8, tsk tsk
     tallStart = lf->start;
     tallEnd   = lf->end;
     }
 x1 = round((double)((int)lf->start-winStart)*scale) + xOff;
 x2 = round((double)((int)lf->end-winStart)*scale) + xOff;
 w = x2-x1;