/* cds.h - code for coloring of bases, codons, or alignment differences. */ /* Copyright (C) 2011 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #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 146 #define CDS_QUERY_INSERTION_AT_END_G 20 #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 // Ribosomal shift colors #define CDS_RIBO_SLIP1 13 /* purple */ #define CDS_RIBO_SLIP1_R 250 #define CDS_RIBO_SLIP1_G 50 #define CDS_RIBO_SLIP1_B 255 #define CDS_RIBO_SLIP2 14 /* cyan */ #define CDS_RIBO_SLIP2_R 50 #define CDS_RIBO_SLIP2_G 250 #define CDS_RIBO_SLIP2_B 255 #define CDS_NUM_COLORS 15 extern struct cacheTwoBitRanges *cdsQueryCache; /* Cache of querie sequences in alignments */ 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, 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 * 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 || tg->drawItems == bamLinkedFeaturesDraw || tg->drawItems == chainDraw || tg->drawItems == bamLinkedFeaturesSeriesDraw); } 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, int *retMrnaOffset, 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 *qSeq, int qOffset, 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 *qSeq, int qOffset, 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 *qSeq, int qOffset, struct psl *psl, MgFont *font, 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 purple lines for query insertions at the * end of the query, and 1-pixel wide green (instead of purple) when a query * insertion at the end is a valid poly-A tail. */ 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 */