4586cbe789d7ff340473682da13625025263131d
larrym
  Mon Nov 15 10:52:07 2010 -0800
support codon numbering in genePred tracks
diff --git src/hg/hgTracks/cds.h src/hg/hgTracks/cds.h
index 65049ff..8174b24 100644
--- src/hg/hgTracks/cds.h
+++ src/hg/hgTracks/cds.h
@@ -81,31 +81,31 @@
 #define CDS_SYN_BLEND_R  100 
 #define CDS_SYN_BLEND_G  50 
 #define CDS_SYN_BLEND_B  0
 
 #define CDS_NUM_COLORS 13
 
 Color getCdsColor(int index);
 /* return color from index of types of colors */
 
 enum baseColorDrawOpt baseColorGetDrawOpt(struct track *tg);
 /* Determine what base/codon coloring option (if any) has been selected 
  * in trackDb/cart, and gate with zoom level. */
 
 
 struct simpleFeature *baseColorCodonsFromGenePred(struct linkedFeatures *lf,
-	struct genePred *gp, boolean colorStopStart);
+        struct genePred *gp, boolean colorStopStart, boolean codonNumbering);
 /* Given an lf and the genePred from which the lf was constructed, 
  * return a list of simpleFeature elements, one per codon (or partial 
  * codon if the codon falls on a gap boundary. */
 
 struct simpleFeature *baseColorCodonsFromPsl(struct linkedFeatures *lf, 
         struct psl *psl, int sizeMul, boolean isXeno, int maxShade,
         enum baseColorDrawOpt drawOpt, struct track *tg);
 /* Given an lf and the psl from which the lf was constructed, 
  * return a list of simpleFeature elements, one per codon (or partial 
  * codon if the codon falls on a gap boundary.  sizeMul, isXeno and maxShade
  * are for defaulting to one-simpleFeature-per-exon if cds is not found. */
 
 
 INLINE boolean baseColorCanDraw(struct track *tg)
 /* baseColor uses tg->drawItems as a proxy for type of tg->items, which must be