Index: src/hg/hgTracks/cds.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/cds.h,v
retrieving revision 1.24
retrieving revision 1.25
diff -b -B -U 1000000 -r1.24 -r1.25
--- src/hg/hgTracks/cds.h	5 Apr 2010 21:04:43 -0000	1.24
+++ src/hg/hgTracks/cds.h	7 Apr 2010 23:07:31 -0000	1.25
@@ -1,190 +1,190 @@
 /* cds.h - code for coloring of bases, codons, or alignment differences. */
 
 #ifndef CDS_H
 #define CDS_H
 
 #ifndef HVGFX_H
 #include "hvGfx.h"
 #endif
 
 #ifndef PSL_H
 #include "psl.h"
 #endif
 
 #ifndef GENEPRED_H
 #include "genePred.h"
 #endif
 
 #ifndef HGTRACKS_H
 #include "hgTracks.h"
 #endif
 
 /* Definitions of cds colors for coding coloring display */
 #define CDS_ERROR   0
 
 #define CDS_ODD     1
 #define	CDS_ODD_R	0x00
 #define	CDS_ODD_G	0x00
 #define	CDS_ODD_B	0x9e
 
 #define CDS_EVEN    2
 #define	CDS_EVEN_R	0x00
 #define	CDS_EVEN_G	0x00
 #define	CDS_EVEN_B	0xdc
 
 #define CDS_START   3
 #define	CDS_START_R	0x00
 #define	CDS_START_G	0xf0
 #define	CDS_START_B	0x00
 
 #define CDS_STOP    4
 #define	CDS_STOP_R	0xe1
 #define	CDS_STOP_G	0x00
 #define	CDS_STOP_B	0x00
 
 #define CDS_SPLICE      5
 #define	CDS_SPLICE_R	0xa0
 #define	CDS_SPLICE_G	0xa0
 #define	CDS_SPLICE_B	0xd9
 
 #define CDS_PARTIAL_CODON	6
 #define CDS_PARTIAL_CODON_R	0x0
 #define CDS_PARTIAL_CODON_G 0xc0
 #define CDS_PARTIAL_CODON_B	0xc0
 
 #define CDS_QUERY_INSERTION   7
 #define CDS_QUERY_INSERTION_R 220
 #define CDS_QUERY_INSERTION_G 128
 #define CDS_QUERY_INSERTION_B 0
 
 #define CDS_QUERY_INSERTION_AT_END 8
-#define CDS_QUERY_INSERTION_AT_END_R 30
-#define CDS_QUERY_INSERTION_AT_END_G 60
-#define CDS_QUERY_INSERTION_AT_END_B 240
+#define CDS_QUERY_INSERTION_AT_END_R 90
+#define CDS_QUERY_INSERTION_AT_END_G 210
+#define CDS_QUERY_INSERTION_AT_END_B 255
 
 #define CDS_POLY_A 9
 #define CDS_POLY_A_R 0
 #define CDS_POLY_A_G 210
 #define CDS_POLY_A_B 0
 
 #define CDS_ALT_START    10
 #define CDS_ALT_START_R  0 
 #define CDS_ALT_START_G  0 
 #define CDS_ALT_START_B  128
 
 #define CDS_SYN_PROT    11   /* yellow, protein seq change "synonymous" ie I->V , R->K etc */
 #define CDS_SYN_PROT_R  255 
 #define CDS_SYN_PROT_G  215 
 #define CDS_SYN_PROT_B  0
 
 #define CDS_SYN_BLEND    12  /* brown, protein seq part syn and part non-syn */
 #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);
 /* 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 
  * linkedFeatures or linkedFeaturesSeries.  Return TRUE if tg->drawItems
  * implies that tg->items is linkedFeatures or linkedFeaturesSeries, and from
  * a subtype supported by the baseColor code. */
 {
 return (tg->drawItems == linkedFeaturesDraw || tg->drawItems == linkedFeaturesAverageDense ||
 	tg->drawItems == linkedFeaturesAverageDenseOrientEst ||
 	tg->drawItems == linkedFeaturesSeriesDraw);
 
 }
 
 void baseColorInitTrack(struct hvGfx *hvg, struct track *tg);
 /* Set up base coloring state (e.g. cache genomic sequence) for tg.
  * This must be called by tg->drawItems if baseColorDrawSetup is used 
  * in tg->drawItemAt, but note that this should be called only if
  * baseColorCanDraw(tg) (above). */
 
 enum baseColorDrawOpt baseColorDrawSetup(struct hvGfx *hvg, struct track *tg,
 			struct linkedFeatures *lf,
 			struct dnaSeq **retMrnaSeq, struct psl **retPsl);
 /* Returns the CDS coloring option, allocates colors if necessary, and 
  * returns the sequence and psl record for the given item if applicable. 
  * Note: even if base coloring is not enabled, this will return psl and 
  * mrna seq if query insert/polyA display is enabled.
  * baseColorInitTrack must be called before this (in tg->drawItems) --
  * this is meant to be called by tg->drawItemAt (i.e. linkedFeaturesDrawAt). */
 
 void baseColorDrawItem(struct track *tg,  struct linkedFeatures *lf,
         int grayIx, struct hvGfx *hvg, int xOff, int y,
         double scale, MgFont *font, int s, int e, int heightPer,
         boolean zoomedToCodonLevel, struct dnaSeq *mrnaSeq, struct simpleFeature *sf, struct psl *psl,
 	enum baseColorDrawOpt drawOpt,
         int maxPixels, int winStart, Color originalColor);
 /*draw a box that is colored by the bases inside it and its
  * orientation. Stop codons are red, start are green, otherwise they
  * alternate light/dark blue colors. */
 
 void baseColorOverdrawDiff(struct track *tg,  struct linkedFeatures *lf,
 			   struct hvGfx *hvg, int xOff,
 			   int y, double scale, int heightPer,
 			   struct dnaSeq *mrnaSeq, struct psl *psl,
 			   int winStart, enum baseColorDrawOpt drawOpt);
 /* If we're drawing different bases/codons, and zoomed out past base/codon 
  * level, draw 1-pixel wide red lines only where bases/codons differ from 
  * genomic.  This tests drawing mode and zoom level but assumes that lf itself 
  * has been drawn already and we're not in dense mode etc. */
 
 void baseColorOverdrawQInsert(struct track *tg,  struct linkedFeatures *lf,
 			      struct hvGfx *hvg, int xOff,
 			      int y, double scale, int heightPer,
 			      struct dnaSeq *mrnaSeq, struct psl *psl,
 			      int winStart, enum baseColorDrawOpt drawOpt,
 			      boolean indelShowQInsert, boolean indelShowPolyA);
 /* If applicable, draw 1-pixel wide orange lines for query insertions in the
  * middle of the query, 1-pixel wide blue lines for query insertions at the 
  * end of the query, and 1-pixel wide green (instead of blue) when a query 
  * insertion at the end is a valid poly-A tail. */
 
 void baseColorDrawCleanup(struct linkedFeatures *lf, struct dnaSeq **pMrnaSeq,
 			  struct psl **pPsl);
 /* Free structures allocated just for base/cds coloring. */
 
 
 struct simpleFeature *baseColorCodonsFromDna(int frame, int chromStart,
 					     int chromEnd, struct dnaSeq *seq,
 					     bool reverse);
 /* Create list of codons from a DNA sequence */
 
 void baseColorDrawRulerCodons(struct hvGfx *hvg, struct simpleFeature *sfList,
                 double scale, int xOff, int y, int height, MgFont *font, 
                 int winStart, int maxPixels, bool zoomedToText);
 /* Draw amino acid translation of genomic sequence based on a list
    of codons. Used for browser ruler in full mode*/
 
 void baseColorSetCdsBounds(struct linkedFeatures *lf, struct psl *psl,
                            struct track *tg);
 /* set CDS bounds in linked features for a PSL.  Used when zoomed out too far
  * for codon or base coloring, but still want to render CDS bounds */
 
 #endif /* CDS_H */

