src/hg/hgTracks/cds.h 1.20
1.20 2009/03/19 22:21:05 angie
Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
Index: src/hg/hgTracks/cds.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/cds.h,v
retrieving revision 1.19
retrieving revision 1.20
diff -b -B -U 1000000 -r1.19 -r1.20
--- src/hg/hgTracks/cds.h 20 Sep 2008 09:35:15 -0000 1.19
+++ src/hg/hgTracks/cds.h 19 Mar 2009 22:21:05 -0000 1.20
@@ -1,173 +1,172 @@
/* 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 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(char *chrom,
- struct linkedFeatures *lf, struct genePred *gp, unsigned *gaps,
- boolean useExonFrames, boolean colorStopStart);
+struct simpleFeature *baseColorCodonsFromGenePred(struct linkedFeatures *lf,
+ struct genePred *gp, boolean useExonFrames, 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. If useExonFrames is true,
* use the frames portion of gp (which should be from a genePredExt);
* otherwise determine frame from genomic sequence. */
-void baseColorCodonsFromPsl(char *chromName, struct linkedFeatures *lf,
+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,
- * set lf->codons to a list of simpleFeature elements, one per codon (or partial
+ * 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. */
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. */
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 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 */