src/hg/hgTracks/cds.h 1.22
1.22 2009/05/20 20:50:52 mikep
display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL)
Index: src/hg/hgTracks/cds.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/cds.h,v
retrieving revision 1.21
retrieving revision 1.22
diff -b -B -U 1000000 -r1.21 -r1.22
--- src/hg/hgTracks/cds.h 1 Apr 2009 01:33:18 -0000 1.21
+++ src/hg/hgTracks/cds.h 20 May 2009 20:50:52 -0000 1.22
@@ -1,177 +1,177 @@
/* 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(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. */
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. Assumes tg->items is linkedFeatures. */
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 psl *psl,
+ 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 */