b01267e746a100118ca7045113d78b5fa588e685 braney Fri May 30 17:10:30 2025 -0700 when a composite has dense tracks the way we deal with center labels the draw routine leaves grek in the track when the decenders of the center label have been drawn even though the center label is not actually drawn, but hidden via CSS. Now in this condition we're drawing slightly smaller fonts for the center labels so they don't exceed the drawing box. refs #29500 diff --git src/hg/hgTracks/hgTracks.h src/hg/hgTracks/hgTracks.h index d2d4e1b0d81..67e42c3a8f0 100644 --- src/hg/hgTracks/hgTracks.h +++ src/hg/hgTracks/hgTracks.h @@ -1,1867 +1,1870 @@ /* hgTracks.h - stuff private to hgTracks, but shared with * individual tracks. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef HGTRACKS_H #define HGTRACKS_H #ifndef HVGFX_H #include "hvGfx.h" #endif #ifndef HUI_H #include "hui.h" #endif #include "jsHelper.h" #include "imageV2.h" #ifndef CART_H #include "cart.h" #endif #ifndef PSL_H #include "psl.h" #endif #ifndef BED_H #include "bed.h" #endif #ifndef TRACKLAYOUT_H #include "trackLayout.h" #endif /* TRACKLAYOUT_H */ #ifndef HPRINT_H #include "hPrint.h" #endif /* HPRINT_H */ #ifndef GBROWSE #ifndef ITEMATTR_H #include "itemAttr.h" #endif /* ITEMATTR_H */ #endif /* GBROWSE */ #include "soTerm.h" /* A few hgGenome cart constant defaults copied from */ #define hggPrefix "hgGenome_" #define hggGraphPrefix hggPrefix "graph" /* trackDb setting for expRatio tracks */ #define EXP_COLOR_DENSE "expColorDense" #ifdef LOWELAB #define MAXPIXELS 60000 #else #define MAXPIXELS 14000 #endif #define BIGBEDMAXIMUMITEMS 1000000 #define MULTI_REGION_VIRTUAL_CHROM_NAME "multi" // original name was 'virt' #define MULTI_REGION_CFG_BUTTON_TOP "multiRegionButtonTop" /* for botDelay call, 10 second for warning, 20 second for immediate exit */ #define delayFraction 0.25 extern long enteredMainTime; #include "lolly.h" #include "spaceSaver.h" struct track /* Structure that displays of tracks. The central data structure * of the graphical genome browser. */ { struct track *next; /* Next on list. */ char *track; /* Track symbolic name. Name on image map etc. Same as tdb->track. */ char *table; /* Table symbolic name. Name of database table. Same as tdb->table.*/ enum trackVisibility visibility; /* How much of this want to see. */ enum trackVisibility limitedVis; /* How much of this actually see. */ boolean limitedVisSet; /* Is limited visibility set? */ char *longLabel; /* Long label to put in center. */ char *shortLabel; /* Short label to put on side. */ bool mapsSelf; /* True if system doesn't need to do map box. */ bool drawName; /* True if BED wants name drawn in box. */ Color *colorShades; /* Color scale (if any) to use. */ struct rgbColor color; /* Main color. */ Color ixColor; /* Index of main color. */ Color *altColorShades; /* optional alternate color scale */ struct rgbColor altColor; /* Secondary color. */ Color ixAltColor; void (*loadItems)(struct track *tg); /* loadItems loads up items for the chromosome range indicated. */ void *items; /* Some type of slList of items. */ struct decoratorGroup *decoratorGroup; /* Some type of slList of decoration sets for items. */ char *(*itemName)(struct track *tg, void *item); /* Return name of one of an item to display on left side. */ char *(*mapItemName)(struct track *tg, void *item); /* Return name to associate on map. */ int (*totalHeight)(struct track *tg, enum trackVisibility vis); /* Return total height. Called before and after drawItems. * Must set the following variables. */ int height; /* Total height - must be set by above call. */ int lineHeight; /* Height per item line including border. */ int heightPer; /* Height per item line minus border. */ int (*itemHeight)(struct track *tg, void *item); /* Return height of one item in pixels. */ int (*itemHeightRowsForPack)(struct track *tg, void *item); /* If set, allows items to claim they a particular number of rows while being packed. * Useful for tracks with variable-height items. */ int (*itemRightPixels)(struct track *tg, void *item); /* Return number of pixels needed to right of item for additional labeling. (Optional) */ void (*preDrawMultiRegion)(struct track *tg); /* Handle multi-region issues after predraw and before draw such as autoScale for wigs. */ void (*preDrawItems)(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Do PreDraw item list, one per track. */ void (*drawItems)(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw item list, one per track. */ void (*drawItemAt)(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int yOff, double scale, MgFont *font, Color color, enum trackVisibility vis); /* Draw a single item. This is optional, but if it's here * then you can plug in genericDrawItems into the drawItems, * which takes care of all sorts of things including packing. */ void (*drawItemLabel)(struct track *tg, struct spaceNode *sn, struct hvGfx *hvg, int xOff, int y, int width, MgFont *font, Color color, Color labelColor, enum trackVisibility vis, double scale, boolean withLeftLabels); /* Draw the label for an item */ void (*doItemMapAndArrows)(struct track *tg, struct spaceNode *sn, struct hvGfx *hvg, int xOff, int y, int width, MgFont *font, Color color, Color labelColor, enum trackVisibility vis, double scale, boolean withLeftLabels); /* Handle item map and exon arrows for an item */ int (*itemStart)(struct track *tg, void *item); /* Return start of item in base pairs. */ int (*itemEnd)(struct track *tg, void *item); /* Return end of item in base pairs. */ void (*freeItems)(struct track *tg); /* Free item list. */ struct hash *attrTable; /* Persistent table to speed up lookup of attributes in secondary tables (optional). */ Color (*itemColor)(struct track *tg, void *item, struct hvGfx *hvg); /* Get color of item (optional). */ Color (*itemNameColor)(struct track *tg, void *item, struct hvGfx *hvg); /* Get color for the item's name (optional). */ Color (*itemLabelColor)(struct track *tg, void *item, struct hvGfx *hvg); /* Get color for the item's label (optional). */ void (*mapItem)(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height); /* Write out image mapping for a given item */ boolean hasUi; /* True if has an extended UI page. */ void *wigCartData; /* pointer to wigCart */ void *extraUiData; /* Pointer for track specific filter etc. data. */ void (*trackFilter)(struct track *tg); /* Stuff to handle user interface parts. */ void *customPt; /* Misc pointer variable unique to track. */ int customInt; /* Misc int variable unique to track. */ int subType; /* Variable to say what subtype this is for similar tracks * to share code. */ /* Stuff for the various wig incarnations - sample, wig, bigWig */ float minRange, maxRange; /*min and max range for sample tracks 0.0 to 1000.0*/ float scaleRange; /* What to scale samples by to get logical 0-1 */ double graphUpperLimit, graphLowerLimit; /* Limits of actual data in window for wigs. */ struct preDrawContainer *preDrawContainer; /* Numbers to graph in wig, one per pixel */ struct preDrawContainer *(*loadPreDraw)(struct track *tg, int seqStart, int seqEnd, int width); struct wigGraphOutput *wigGraphOutput; /* Where to draw wig - different for transparency */ /* Do bits that load the predraw buffer. Called to set preDrawContainer */ struct bbiFile *bbiFile; /* Associated bbiFile for bigWig or bigBed. */ int bedSize; /* Number of fields if a bed file. */ boolean isBigBed; /* If a bed, is it a bigBed? */ boolean isRemoteSql; /* Is using a remote mySQL connection. */ char *remoteSqlHost; /* Host machine name for remote DB. */ char *remoteSqlUser; /* User name for remote DB. */ char *remoteSqlPassword; /* Password for remote DB. */ char *remoteSqlDatabase; /* Database in remote DB. */ char *remoteSqlTable; /* Table name in remote DB. */ char *otherDb; /* Other database for an axt track. */ unsigned short private; /* True(1) if private, false(0) otherwise. */ float priority; /* Tracks are drawn in priority order. */ float defaultPriority; /* Tracks are drawn in priority order. */ char *groupName; /* Name of group if any. */ struct group *group; /* Group this track is associated with. */ char *defaultGroupName; /* default Group this track is associated with. */ boolean canPack; /* Can we pack the display for this track? */ struct spaceSaver *ss; /* Layout when packed. */ struct trackDb *tdb; /*todo:change visibility, etc. to use this */ float expScale; /* What to scale expression tracks by. */ char *expTable; /* Expression table in hgFixed. */ long sourceCount; /* Number of sources for factorSource tracks. */ struct expRecord **sources; /* Array of sources */ int sourceRightPixels; /* Number of pixels to right we'll need. */ boolean exonArrows; /* Draw arrows on exons? */ boolean exonArrowsAlways; /* Draw arrows on exons even with introns showing? */ boolean nextExonButtonable; /* Use the next-exon buttons? */ boolean nextItemButtonable; /* Use the next-gene buttons? */ struct itemAttrTbl *itemAttrTbl; /* relational attributes for specific items (color) */ /* fill in left label drawing area */ Color labelColor; /* Fixed color for the track label (optional) */ void (*drawLeftLabels)(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, int height, boolean withCenterLabels, MgFont *font, Color color, enum trackVisibility vis); struct track *subtracks; /* list of subsidiary tracks that are loaded and drawn by this track. This is used for "composite" tracks, such as "mafWiggle */ struct track *parent; /* Parent track if any */ struct track *prevTrack; // if not NULL, points to track immediately above in the image. // Needed by ConditionalCenterLabel logic boolean (*nextPrevExon)(struct track *tg, struct hvGfx *hvg, void *item, int x, int y, int w, int h, boolean next); /* Function will draw the button on a track item and assign a map */ /* box to it as well, so that a click will move the browser window */ /* to the next (or previous if next==FALSE) item. This is meant to */ /* jump to parts of an item already partially in the window but is */ /* hanging off the edge... e.g. the next exon in a gene. */ void (*nextPrevItem)(struct track *tg, boolean next); /* If this function is given, it can dictate where the browser loads */ /* up based on whether a next-item button on the longLabel line of */ /* the track was pressed (as opposed to the next-item buttons on the */ /* track items themselves... see nextPrevExon() ). This is meant for */ /* going to the next/previous item currently unseen in the browser, */ /* e.g. the next gene. */ char *(*itemDataName)(struct track *tg, char *itemName); /* If not NULL, function to translated an itemName into a data name. * This is can be used for looking up sequence, CDS, etc. It is used * to support item names that have uniqueness identifiers added to deal * with multiple alignments. The resulting value should *not* be freed, * and it should be assumed that it might only remain valid for a short * period of time.*/ int loadTime; /* Time it takes to load (for performance tuning) */ int drawTime; /* Time it takes to draw (for performance tuning) */ enum enumBool remoteDataSource; /* The data for this track is from a remote source */ /* Slow retrieval means image can be rendered via an AJAX callback. */ boolean customTrack; /* Need to explicitly declare this is a custom track */ boolean syncChildVisToSelf; /* If TRUE sync visibility to of children to self. */ char *networkErrMsg; /* Network layer error message */ boolean parallelLoading; /* If loading in parallel, usually network resources. */ struct bbiSummaryElement *summary; /* for bigBed */ struct bbiSummaryElement *sumAll; /* for bigBed */ boolean drawLabelInBox; /* draw labels into the features instead of next to them */ boolean drawLabelInBoxNotDense; /* don't draw labels in dense mode, (needed only when drawLabelInBox set */ struct track *nextWindow; /* Same track in next window's track list. */ struct track *prevWindow; /* Same track in prev window's track list. */ // Fixed-width non-proportional tracks void (*nonPropDrawItemAt)(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int yOff, double scale, MgFont *font, Color color, enum trackVisibility vis); /* Draw a single Non-proportional fixed-width item. Such as gtexGene. * This is method is optional, but if it's here * then you can plug in genericDrawItems into the drawItems, * which takes care of all sorts of things including packing. */ int (*nonPropPixelWidth)(struct track *tg, void *item); /* Return the width in pixels of the non-proportional part of track, e.g. gtexGene graphic */ struct slInt *labelColumns; /* The columns in a bigBed that can be used for labels. */ boolean subTrackVisSet; /* have we calculated visibility on this subtrack */ boolean subTrackVis; /* if we calculated it, what is it */ struct lollyCartOptions *lollyCart; double squishyPackPoint; /* the value at which we switch to squish mode. */ char * originalTrack; /* the name of the original track if this a pseduo-duplicate track used for squishyPack */ boolean limitWiggle; /* TRUE if this track is drawing in coverage mode because of limited visibility */ boolean isColorBigBed; /* True if this track is a fake track used for wiggle coloring. */ }; struct window // window in multiwindow image { struct window *next; // Next on list. // These two were experimental and will be removed soon: char *organism; /* Name of organism */ char *database; /* Name of database */ char *chromName; int winStart; // in bases int winEnd; int insideX; // in pixels int insideWidth; long virtStart; // in bases on virt chrom long virtEnd; boolean regionOdd; // window comes from odd region? or even? for window separator coloring struct track *trackList; // track list for window }; extern boolean forceWiggle; // we've run out of space so all tracks become coverage tracks typedef void (*TrackHandler)(struct track *tg); int trackPriCmp(const void *va, const void *vb); /* Compare for sort based on priority */ boolean trackIsCompositeWithSubtracks(struct track *track); /* Temporary function until all composite tracks point to their own children */ struct trackRef /* A reference to a track. */ { struct trackRef *next; /* Next in list. */ struct track *track; /* Underlying track. */ }; struct group /* A group of related tracks. */ { struct group *next; /* Next group in list. */ char *name; /* Symbolic name. */ char *label; /* User visible name. */ float priority; /* Display order, 0 is on top. */ float defaultPriority; /* original priority before reordering */ struct trackRef *trackList; /* List of tracks. */ boolean defaultIsClosed; /* close the track group by default. */ char *errMessage; /* any error messages that came up during trackDb parsing. */ }; struct simpleFeature /* Minimal feature - just stores position in browser coordinates. */ { struct simpleFeature *next; int start, end; /* Start/end in browser coordinates. */ int qStart, qEnd; /* query start/end */ int grayIx; /* Level of gray usually. */ int codonIndex; /* 1-based codon index (ignored if 0) */ }; /* Some details of how to draw linked features. */ enum {lfSubXeno = 1}; enum {lfSubSample = 2}; enum {lfWithBarbs = 3}; /* Turn on barbs to show direction based on * strand field */ enum {lfSubChain = 4}; enum {lfNoIntronLines = 5}; /* Draw no lines between exon blocks */ enum highlightMode { highlightNone=0, highlightBackground=1, highlightOutline=2 }; struct linkedFeatures /* A linked set of features - drawn as a bunch of boxes (often exons) * connected by horizontal lines (often introns). About 75% of * the browser tracks end up as linkedFeatures. */ { struct linkedFeatures *next; int start, end; /* Start/end in browser coordinates. */ int tallStart, tallEnd; /* Start/end of fat display. */ int grayIx; /* Average of components. */ int filterColor; /* Filter color (-1 for none) */ float score; /* score for this feature */ char *name; /* Accession of query seq. Usually also the label. */ int orientation; /* Orientation. */ struct simpleFeature *components; /* List of component simple features. Usually exons. */ struct simpleFeature *codons; /* If zoomed to CDS or codon level.*/ boolean useItemRgb; /* If true, use rgb from item. */ void *extra; /* Extra info that varies with type. */ void *original; /* The structure that was converted into this (when needed later). */ struct itemAttr *itemAttr; /* itemAttr object for this lf, or NULL */ unsigned highlightColor; /* highlight color,0 if no highlight */ enum highlightMode highlightMode; /* highlight mode,0 if no highlight */ char* mouseOver; /* mouse over text */ char* cds; /* CDS in NCBI format */ #ifdef USE_HAL boolean isHalSnake; struct hal_target_dupe_list_t *dupeList; #endif boolean isBigGenePred; char *label; /* Label for bigBeds. */ int qSize; /* Query size for chain/bigChain */ double squishyPackVal; /* the squishyPoint value for this item. */ struct snakeInfo *snakeInfo; /* if we're in snake mode, here's the deets */ }; struct linkedFeaturesSeries /* series of linked features that are comprised of multiple linked features */ { struct linkedFeaturesSeries *next; char *name; /* name for series of linked features */ int start, end; /* Start/end in browser coordinates. */ int orientation; /* Orientation. */ int grayIx; /* Gray index (average of features) */ boolean noLine; /* if true don't draw line connecting features */ struct linkedFeatures *features; /* linked features for a series */ }; struct knownGenesExtra /* need more than 1 string in linkedFeatures extra field */ { char *hgg_prot; /* protein ID */ char *name; /* name to be used on label */ }; struct gsidSubj /* global GSID subject list */ { struct gsidSubj *next; char *subjId; }; struct gsidSeq /* global GSID sequence list */ { struct gsidSeq *next; char *seqId; char *subjId; }; struct virtRegion /* virtual chromosome structure */ { struct virtRegion *next; char *chrom; int start; int end; char strand[2]; /* + or - for strand */ }; struct virtChromRegionPos /* virtual chromosome region position*/ { long virtPos; struct virtRegion *virtRegion; }; struct positionMatch /* virtual chroom position that matches or overlaps search query chrom,start,end */ { struct positionMatch *next; long virtStart; long virtEnd; }; /* mouseOver business declared in hgTracks.c */ extern boolean enableMouseOver; extern struct tempName *mouseOverJsonFile; extern struct jsonWrite *mouseOverJson; struct wigMouseOver { struct wigMouseOver *next; int x1; /* beginning of a rectangle for this value */ int x2; /* end of the rectangle */ double value; /* data value for this region */ int valueCount; /* number of data values in this rectangle */ }; extern struct virtRegion *virtRegionList; extern struct virtChromRegionPos *virtChrom; // Array extern int virtRegionCount; extern long virtWinStart; // start of virtual window in bases extern long virtWinEnd; // end of virtual window in bases extern long defaultVirtWinStart; // default start of virtual window in bases extern long defaultVirtWinEnd; // default end of virtual window in bases extern long virtWinBaseCount; /* Number of bases in windows, also virtWinEnd - virtWinStart. */ extern long virtSeqBaseCount; // all bases in virt chrom //extern char *virtPosition; /* Name of virtual position. TODO Remove? */ extern char *virtChromName; /* Name of virtual chrom */ extern boolean virtMode; /* Are we in virtual chrom mode? */ extern boolean virtChromChanged; /* Has the virtChrom changed? */ extern boolean emAltHighlight; /* Highlight alternativing regions in virt view? */ extern int emPadding; /* # bases padding for exon-mostly regions */ extern int gmPadding; /* # bases padding for gene-mostly regions */ extern char *emGeneTable; /* Gene table to use for exon mostly */ extern struct track *emGeneTrack; /* Track for gene table for exon mostly */ extern struct rgbColor vertWindowSeparatorColor; /* color for vertical windows separator */ extern char *multiRegionsBedUrl; /* URL to bed regions list */ // is genome RNA? extern boolean genomeIsRna; // demo2 extern int demo2NumWindows; extern int demo2WindowSize; extern int demo2StepSize; // singleTrans (single transcript) extern char *singleTransId; // singleAltHaplos (one alternate haplotype) extern char *singleAltHaploId; extern char *virtModeType; /* virtual chrom mode type */ extern char *lastVirtModeType; extern char *virtModeShortDescr; /* short description of virt mode */ extern char *virtModeExtraState; /* Other settings that affect the virtMode state such as padding or some parameter */ extern char *lastVirtModeExtraState; extern struct cart *lastDbPosCart; /* store settings for use in lastDbPos and hgTracks.js setupHistory */ extern char *excludeVars[]; extern struct trackLayout tl; extern struct jsonElement *jsonForClient; /* multiple windows */ extern struct window *windows; // list of windows in image extern struct window *currentWindow; // current window extern bool trackLoadingInProgress; // flag to delay ss layout until all windows are ready. extern int fullInsideX; // full-image insideX extern int fullInsideWidth; // full-image insideWidth extern struct cart *cart; /* The cart where we keep persistent variables. */ extern struct hash *oldVars; /* List of vars from previous cart. */ extern struct track *trackList; /* List of all tracks. */ extern struct hash *trackHash; /* Hash of the tracks by their name. */ extern char *chromName; /* Name of chromosome sequence . */ extern char *displayChromName; /* Name of chromosome sequence to display . */ extern char *database; /* Name of database we're using. */ extern char *organism; /* Name of organism we're working on. */ extern char *browserName; /* Test or public browser */ extern char *organization; /* UCSC or MGC */ extern int winStart; /* Start of window in sequence. */ extern int winEnd; /* End of window in sequence. */ extern int maxItemsInFullTrack; /* Maximum number of items displayed in full */ extern char *position; /* Name of position. */ extern int gfxBorder; /* Width of graphics border. */ extern int insideWidth; /* Width of area to draw tracks in in pixels. */ extern int insideX; /* Start of area to draw track in in pixels. */ extern int leftLabelX; /* Start of area to draw left labels on. */ extern int leftLabelWidth; /* Width of area to draw left labels on. */ extern boolean withLeftLabels; /* Display left labels? */ extern boolean withCenterLabels; /* Display center labels? */ extern boolean withGuidelines; /* Display guidelines? */ extern boolean withNextExonArrows; /* Display next exon navigation buttons near center labels? */ extern boolean withExonNumbers; /* Display exon and intron numbers in mouseOver instead of item name */ extern struct hvGfx *hvgSide; // An extra pointer to side label image that can be built if needed extern int seqBaseCount; /* Number of bases in sequence. */ extern int winBaseCount; /* Number of bases in window. */ extern float basesPerPixel; /* bases covered by a pixel; a measure of zoom */ extern boolean zoomedToBaseLevel; /* TRUE if zoomed so we can draw bases. */ extern boolean zoomedToCodonLevel; /* TRUE if zoomed so we can print codon text in genePreds*/ extern boolean zoomedToCodonNumberLevel; /* TRUE if zoomed so we can print codons and exon number text in genePreds*/ extern boolean zoomedToCdsColorLevel; /* TRUE if zoomed so we cancolor each codon*/ extern char *ctFileName; /* Custom track file. */ extern struct customTrack *ctList; /* Custom tracks. */ extern struct slName *browserLines; /* Custom track "browser" lines. */ extern int rulerMode; /* on, off, full */ extern boolean withLeftLabels; /* Display left labels? */ extern boolean withCenterLabels; /* Display center labels? */ extern boolean withPriorityOverride; /* enable track reordering? */ extern boolean revCmplDisp; /* reverse-complement display */ extern boolean measureTiming; /* Flip this on to display timing * stats on each track at bottom of page. */ extern struct hash *hgFindMatches; /* The matches found by hgFind that should be highlighted. */ extern int maxShade; /* Highest shade in a color gradient. */ extern Color shadesOfGray[10+1]; /* 10 shades of gray from white to black * Red is put at end to alert overflow. */ extern Color shadesOfBrown[10+1]; /* 10 shades of brown from tan to tar. */ extern struct rgbColor guidelineColor; extern struct rgbColor multiRegionAltColor; extern struct rgbColor undefinedYellowColor; extern Color darkGreenColor; extern Color shadesOfSea[10+1]; /* Ten sea shades. */ /* 16 shades from black to fully saturated of red/green/blue for * expression data. */ #define EXPR_DATA_SHADES 16 extern Color shadesOfGreen[EXPR_DATA_SHADES]; extern Color shadesOfRed[EXPR_DATA_SHADES]; extern Color shadesOfBlue[EXPR_DATA_SHADES]; extern Color shadesOfYellow[EXPR_DATA_SHADES]; extern Color shadesOfGreenOnWhite[EXPR_DATA_SHADES]; extern Color shadesOfRedOnWhite[EXPR_DATA_SHADES]; extern Color shadesOfBlueOnWhite[EXPR_DATA_SHADES]; extern Color shadesOfYellowOnWhite[EXPR_DATA_SHADES]; extern Color shadesOfRedOnYellow[EXPR_DATA_SHADES]; extern Color shadesOfBlueOnYellow[EXPR_DATA_SHADES]; extern boolean chromosomeColorsMade; /* Have the 3 shades of 8 chromosome colors been allocated? */ extern boolean doPliColors; /* Put up the color legend for the gnomAD pLI track */ extern boolean exprBedColorsMade; /* Have the shades of Green, Red, and Blue been allocated? */ extern int maxRGBShade; extern int colorLookup[256]; /* Common to variation.c and rnaPLFoldtrack.c */ extern boolean trackImgOnly; /* caller wants just the track image and track table html */ /* used in MAF display */ #define UNALIGNED_SEQ 'o' #define MAF_DOUBLE_GAP '=' void abbr(char *s, char *fluff); /* Cut out fluff from s. */ struct track *getTrackList(struct group **pGroupList, int vis); /* Return list of all tracks, organizing by groups. * If vis is -1, restore default groups to tracks. * Shared by hgTracks and configure page. */ void groupTrackListAddSuper(struct cart *cart, struct group *group, struct hash *superHash); /* Construct a new track list that includes supertracks, sort by priority, * and determine if supertracks have visible members. * Replace the group track list with this new list. * Shared by hgTracks and configure page to expand track list, * in contexts where no track display functions (which don't understand * supertracks) are invoked. */ void removeTrackFromGroup(struct track *track); /* Remove track from group it is part of. */ struct sqlConnection *remoteTrackConnection(struct track *tg); /* Get a connection to remote database as specified in remoteSql settings... */ int orientFromChar(char c); /* Return 1 or -1 in place of + or - */ enum trackVisibility limitVisibility(struct track *tg); /* Return default visibility limited by number of items. */ char *hgcNameAndSettings(); /* Return path to hgc with variables to store UI settings. */ void mapBoxHc(struct hvGfx *hvg, int start, int end, int x, int y, int width, int height, char *group, char *item, char *statusLine); /* Print out image map rectangle that would invoke the htc (human track click) * program. */ void mapBoxReinvoke(struct hvGfx *hvg, int x, int y, int width, int height, struct track *track, boolean toggle, char *chrom, long start, long end, char *message, char *extra); /* Print out image map rectangle that would invoke this program again. * If track is non-NULL then put that track's id in the map item. * if toggle is true, then toggle track between full and dense. * If chrom is non-null then jump to chrom:start-end. * Add extra string to the URL if it's not NULL */ void mapBoxToggleVis(struct hvGfx *hvg, int x, int y, int width, int height, struct track *curGroup); /* Print out image map rectangle that would invoke this program again. * program with the current track expanded. */ void mapBoxJumpTo(struct hvGfx *hvg, int x, int y, int width, int height, struct track *toggleGroup, char *newChrom, long newStart, long newEnd, char *message); /* Print out image map rectangle that would invoke this program again * at a different window. */ void mapBoxHgcOrHgGene(struct hvGfx *hvg, int start, int end, int x, int y, int width, int height, char *track, char *item, char *statusLine, char *directUrl, boolean withHguid, char *extra); /* Print out image map rectangle that would invoke the hgc (human genome click) * program. */ void genericDrawItemLabel(struct track *tg, struct spaceNode *sn, struct hvGfx *hvg, int xOff, int y, int width, MgFont *font, Color color, Color labelColor, enum trackVisibility vis, double scale, boolean withLeftLabels); /* Generic function for writing out an item label */ void genericItemMapAndArrows(struct track *tg, struct spaceNode *sn, struct hvGfx *hvg, int xOff, int y, int width, MgFont *font, Color color, Color labelColor, enum trackVisibility vis, double scale, boolean withLeftLabels); /* Generic function for putting down a mapbox with a label and drawing exon arrows */ void genericMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height); /* This is meant to be used by genericDrawItems to set to tg->mapItem in */ /* case tg->mapItem isn't set to anything already. */ void mapStatusMessage(char *format, ...) /* Write out stuff that will cause a status message to * appear when the mouse is over this box. */ #if defined(__GNUC__) __attribute__((format(printf, 1, 2))) #endif ; double scaleForWindow(double width, int seqStart, int seqEnd); /* Return the scale for the window. */ double scaleForPixels(double pixelWidth); /* Return what you need to multiply bases by to * get to scale of pixel coordinates. */ boolean scaledBoxToPixelCoords(int chromStart, int chromEnd, double scale, int xOff, int *pX1, int *pX2); /* Convert chrom coordinates to pixels. Clip to window to prevent integer overflow. * For special case of a SNP insert location with width==0, set width=1. * Returns FALSE if it does not intersect the window, or if it would have a negative width. */ void drawScaledBox(struct hvGfx *hvg, int chromStart, int chromEnd, double scale, int xOff, int y, int height, Color color); /* Draw a box scaled from chromosome to window coordinates. * Get scale first with scaleForPixels. */ void drawScaledBoxLabel(struct hvGfx *hvg, int chromStart, int chromEnd, double scale, int xOff, int y, int height, Color color, MgFont *font, char *label); /* Draw a box scaled from chromosome to window coordinates and draw a label onto it. */ typedef enum { GLYPH_CIRCLE, GLYPH_TRIANGLE, GLYPH_INV_TRIANGLE, GLYPH_SQUARE, GLYPH_DIAMOND, GLYPH_OCTAGON, GLYPH_STAR, GLYPH_PENTAGRAM } glyphType; void drawScaledGlyph(struct hvGfx *hvg, int chromStart, int chromEnd, double scale, int xOff, int y, int heightPer, glyphType glyph, boolean filled, Color outlineColor, Color fillColor); /* Draw a glyph as a circle/polygon. If filled, draw as with fillColor, * which may have transparency. */ glyphType parseGlyphType(char *glyphStr); /* Return the enum glyph type for a string specifying a glyph. * Defaults to GLYPH_CIRCLE if the string is unrecognized. */ Color whiteIndex(); /* Return index of white. */ Color blackIndex(); /* Return index of black. */ Color grayIndex(); /* Return index of gray. */ Color lightGrayIndex(); /* Return index of light gray. */ Color veryLightGrayIndex(); /* Return index of very light gray. */ int grayInRange(int val, int minVal, int maxVal); /* Return gray shade corresponding to a number from minVal - maxVal */ int pslGrayIx(struct psl *psl, boolean isXeno, int maxShade); /* Figure out gray level for an RNA block. */ Color getSeqColor(char *name, struct hvGfx *hvg); /* Return color index corresponding to chromosome/scaffold name. */ Color darkerColor(struct hvGfx *hvg, Color color); /* Get darker shade of a color - half way between this color and black */ Color somewhatDarkerColor(struct hvGfx *hvg, Color color); /* Get a somewhat lighter shade of a color - 1/3 of the way towards black. */ Color slightlyDarkerColor(struct hvGfx *hvg, Color color); /* Get a slightly darker shade of a color - 1/4 of the way towards black. */ Color lighterColor(struct hvGfx *hvg, Color color); /* Get lighter shade of a color - half way between this color and white */ Color somewhatLighterColor(struct hvGfx *hvg, Color color); /* Get a somewhat lighter shade of a color - 1/3 of the way towards white. */ Color slightlyLighterColor(struct hvGfx *hvg, Color color); /* Get slightly lighter shade of a color - closer to gray actually */ void clippedBarbs(struct hvGfx *hvg, int x, int y, int width, int barbHeight, int barbSpacing, int barbDir, Color color, boolean needDrawMiddle); /* Draw barbed line. Clip it to fit the window first though since * some barbed lines will span almost the whole chromosome, and the * clipping at the lower level is not efficient since we added * PostScript output support. */ void innerLine(struct hvGfx *hvg, int x, int y, int w, Color color); /* Draw a horizontal line of given width minus a pixel on either * end. This pixel is needed for PostScript only, but doesn't * hurt elsewhere. */ void grayThreshold(UBYTE *pt, int count, Color *colors); /* Convert from 0-4 representation to gray scale rep. */ /* Some little functional stubs to fill in track group * function pointers with if we have nothing to do. */ void tgLoadNothing(struct track *tg); void tgDrawNothing(struct track *tg); void tgFreeNothing(struct track *tg); int tgItemNoStart(struct track *tg, void *item); int tgItemNoEnd(struct track *tg, void *item); int tgFixedItemHeight(struct track *tg, void *item); /* Return item height for fixed height track. */ int tgFixedTotalHeightOptionalOverflow(struct track *tg, enum trackVisibility vis, int lineHeight, int heightPer, boolean allowOverflow); /* Most fixed height track groups will use this to figure out the height * they use. */ int tgFixedTotalHeightNoOverflow(struct track *tg, enum trackVisibility vis); /* Most fixed height track groups will use this to figure out the height * they use. */ void changeTrackVis(struct group *groupList, char *groupTarget, int changeVis); /* Change track visibilities. If groupTarget is * NULL then set visibility for tracks in all groups. Otherwise, * just set it for the given group. If vis is -2, then visibility is * unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ void genericDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw generic item list. Features must be fixed height * and tg->drawItemAt has to be filled in. */ void bedDrawSimpleAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis); /* Draw a single simple bed item at position. */ void bedDrawSimple(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw simple Bed items. */ typedef struct slList *(*ItemLoader)(char **row); typedef struct bed *(*bedItemLoader)(char **row); void bedLoadItemByQuery(struct track *tg, char *table, char *query, ItemLoader loader); /* Generic tg->item loader. If query is NULL use generic hRangeQuery(). */ void bedLoadItemWhere(struct track *tg, char *table, char *extraWhere, ItemLoader loader); /* Generic tg->item loader, adding extra clause to hgRangeQuery. */ void bedLoadItem(struct track *tg, char *table, ItemLoader loader); /* Generic tg->item loader. */ boolean simpleBedNextPrevEdge(struct track *tg, struct hvGfx *hvg, void *item, int x, int y, int w, int h, boolean next); /* Like linkedFeaturesNextPrevItem, but for simple bed which has no block structure so * this simply zaps us to the right/left edge of the feature. Arrows have already been * drawn; here we figure out coords and draw a mapBox. */ void loadLinkedFeaturesWithLoaders(struct track *tg, struct slList *(*itemLoader)(char **row), struct linkedFeatures *(*lfFromWhatever)(struct slList *item), char *scoreColumn, char *moreWhere, boolean (*itemFilter)(struct slList *item)); /* Make a linkedFeatures loader by providing three functions: (1) a regular */ /* item loader found in all autoSql modules, (2) a custom myStruct->linkedFeatures */ /* translating function, and (3) a function to free the thing loaded in (1). */ struct linkedFeatures *linkedFeaturesFromGenePred(struct track *tg, struct genePred *gp, boolean extra); /* construct a linkedFeatures object from a genePred */ struct linkedFeatures *bedMungToLinkedFeatures(struct bed **pBed, struct trackDb *tdb, int fieldCount, int scoreMin, int scoreMax, boolean useItemRgb); /* Convert bed to a linkedFeature, destroying bed in the process. */ struct bigBedInterval *bigBedSelectRangeExt(struct track *track, char *chrom, int start, int end, struct lm *lm, int maxItems); /* Return list of intervals in range. */ #define bigBedSelectRange(track, chrom, start, end, lm) \ bigBedSelectRangeExt(track, chrom,start, end, lm, min(BIGBEDMAXIMUMITEMS, maximumTrackItems(track))) /* Return list of intervals in range. */ void bigBedAddLinkedFeaturesFromExt(struct track *track, char *chrom, int start, int end, int scoreMin, int scoreMax, boolean useItemRgb, int fieldCount, struct linkedFeatures **pLfList, int maxItems); /* Read in items in chrom:start-end from bigBed file named in track->bbiFileName, convert * them to linkedFeatures, and add to head of list. */ #define bigBedAddLinkedFeaturesFrom(track, chrom, start, end, scoreMin, scoreMax, useItemRgb, fieldCount, pLfList) \ bigBedAddLinkedFeaturesFromExt(track, chrom, start, end, scoreMin, scoreMax, useItemRgb, fieldCount, pLfList, min(BIGBEDMAXIMUMITEMS, maximumTrackItems(track))) char *bigBedItemName(struct track *tg, void *item) ; // return label for simple beds char *bigLfItemName(struct track *tg, void *item); // return label for linked features char *makeLabel(struct track *track, struct bigBedInterval *bb); // Build a label for a bigBedTrack from the requested label fields. // boolean canDrawBigBedDense(struct track *tg); /* Return TRUE if conditions are such that can do the fast bigBed dense data fetch and * draw. */ void bigBedDrawDense(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color); /* Use big-bed summary data to quickly draw bigBed. */ void adjustBedScoreGrayLevel(struct trackDb *tdb, struct bed *bed, int scoreMin, int scoreMax); /* For each distinct trackName passed in, check cart for trackName.minGrayLevel; if * that is different from the gray level implied by scoreMin's place in [0..scoreMax], * then linearly transform bed->score from the range of [scoreMin,scoreMax] to * [(cartMinGrayLevel*scoreMax)/maxShade,scoreMax]. * Note: this assumes that scoreMin and scoreMax are constant for each track. */ struct linkedFeatures *lfFromBedExtra(struct bed *bed, int scoreMin, int scoreMax); /* Return a linked feature from a (full) bed. */ struct linkedFeatures *lfFromBed(struct bed *bed); /* Return a linked feature from a (full) bed. */ void loadSimpleBedAsLinkedFeaturesPerBase(struct track *tg); /* bed list not freed as pointer to it is stored in 'original' field */ void loadSimpleBed(struct track *tg); /* Load the items in one track - just move beds in window... */ void loadSimpleBedWithLoader(struct track *tg, bedItemLoader loader); /* Load the items in one track using specified loader - just move beds in window... */ void loadBed8(struct track *tg); /* Convert bed 8 info in window to linked feature. */ void loadBed9(struct track *tg); /* Convert bed 9 info in window to linked feature. (to handle itemRgb)*/ void loadGappedBed(struct track *tg); /* Convert bed info in window to linked feature. */ void linkedFeaturesFreeList(struct linkedFeatures **pList); /* Free up a linked features list. */ void freeLinkedFeaturesSeries(struct linkedFeaturesSeries **pList); /* Free up a linked features series list. */ int simpleFeatureCmp(const void *va, const void *vb); /* Compare to sort based on start. */ int linkedFeaturesCmpScore(const void *va, const void *vb); /* Help sort linkedFeatures by score (descending), then by starting pos. */ int linkedFeaturesCmp(const void *va, const void *vb); /* Compare to sort based on chrom,chromStart. */ int linkedFeaturesCmpName(const void *va, const void *vb); /* Help sort linkedFeatures by name. */ int linkedFeaturesCmpStart(const void *va, const void *vb); /* Help sort linkedFeatures by starting pos. */ void linkedFeaturesBoundsAndGrays(struct linkedFeatures *lf); /* Calculate beginning and end of lf from components, etc. */ int lfCalcGrayIx(struct linkedFeatures *lf); /* Calculate gray level from components. */ void linkedFeaturesDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw linked features items. */ void linkedFeaturesAverageDense(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw dense linked features items. */ void linkedFeaturesAverageDenseOrientEst(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw dense linked features items. */ void linkedFeaturesMethods(struct track *tg); /* Fill in track group methods for linked features. * Many other methods routines will call this first * to get a reasonable set of defaults. */ Color lfChromColor(struct track *tg, void *item, struct hvGfx *hvg); /* Return color of chromosome for linked feature type items * where the chromosome is listed somewhere in the lf->name. */ char *lfMapNameFromExtra(struct track *tg, void *item); /* Return map name of item from extra field. */ char *linkedFeaturesName(struct track *tg, void *item); /* Return name of item. */ int getFilterColor(char *type, int colorIx); /* Get color corresponding to type - MG_RED for "red" etc. */ void spreadBasesString(struct hvGfx *hvg, int x, int y, int width, int height, Color color, MgFont *font, char *s, int count, bool isCodon); /* Draw evenly spaced base letters in string. */ void spreadAlignString(struct hvGfx *hvg, int x, int y, int width, int height, Color color, MgFont *font, char *s, char *match, int count, bool dots, bool isCodon); /* Draw evenly spaced letters in string. For multiple alignments, * supply a non-NULL match string, and then matching letters will be colored * with the main color, mismatched letters will have alt color. * Draw a vertical bar in light yellow where sequence lacks gaps that * are in reference sequence (possible insertion) -- this is indicated * by an escaped ('/') insert count in the sequence. * If "dots" is set, matching bases are displayed as a dot. */ void spreadAlignStringProt(struct hvGfx *hvg, int x, int y, int width, int height, Color color, MgFont *font, char *s, char *match, int count, bool dots, bool isCodon, int initialColorIndex, int mafOrigOffset); /* similar to spreadAlignString, but it is used for protein sequences. */ void contigMethods(struct track *tg); /* Make track for contig */ void goldMethods(struct track *tg); /* Make track for golden path (assembly track). */ void cgapSageMethods(struct track *tg); /* Make CGAP SAGE track. */ #define CGAP_SAGE_DENSE_GOVERNOR 3000000 /* Size of browser window to dense the CGAP SAGE track at. */ void coverageMethods(struct track *tg); /* Make track for golden path positions of all frags. */ void cytoBandIdeoMethods(struct track *tg); /* Draw ideogram of chromosome. */ void cytoBandMethods(struct track *tg); /* Make track for simple repeats. */ #ifdef USE_HAL void halSnakeMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Make track group for hal-based snake alignment. */ #endif void longRangeMethods(struct track *track, struct trackDb *tdb); /* Make track group for long range connections . */ void snakeMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Make track group for chain-based snake alignment. */ void chainMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Make track group for chain alignment. */ void netMethods(struct track *tg); /* Make track group for chain/net alignment. */ void mafMethods(struct track *tg); /* Make track group for maf multiple alignment. */ void bamMethods(struct track *track); /* Methods for BAM alignment files. */ void vcfPhasedMethods(struct track *track); /* Load items from a VCF of one individuals phased genotypes */ void vcfTabixMethods(struct track *track); /* Methods for Variant Call Format compressed & indexed by tabix. */ void vcfMethods(struct track *track); /* Methods for Variant Call Format. */ void altGraphXMethods(struct track *tg); /* setup special methods for altGraphX track */ void wabaMethods(struct track *tg); /* Return track with fields shared by waba-based * alignment tracks filled in. */ void axtMethods(struct track *tg, char *otherDb); /* Make track group for axt alignments. */ void repeatMethods(struct track *tg); /* Make track for repeats. */ void affyTransfragsMethods(struct track *tg); /* Substitute a new load method that filters based on score. Also add a new itemColor() method that draws transfrags that overlap dups and pseudoGenes in a different color. */ struct repeatItem /* A repeat track item. */ { struct repeatItem *next; char *class; char *className; int yOffset; Color color; }; void pslMethods(struct track *track, struct trackDb *tdb, int argc, char *argv[]); /* Load up psl type methods. */ void loadXenoPsl(struct track *tg); /* Load a xeno psl */ void loadProteinPsl(struct track *tg); /* Load a protein psl */ struct linkedFeatures *lfFromPslx(struct psl *psl, int sizeMul, boolean isXeno, boolean nameGetsPos, struct track *tg); /* Create a linked feature item from pslx. Pass in sizeMul=1 for DNA, * sizeMul=3 for protein. * Don't free psl afterwards! (may be used by baseColor code) */ struct simpleFeature *sfFromPslX(struct psl *psl,int grayIx, int sizeMul); struct linkedFeatures *lfFromPsl(struct psl *psl, boolean isXeno); /* Create a linked feature item from psl. * Don't free psl afterwards! (may be used by baseColor code) */ struct linkedFeatures *lfFromPslsWScoresInRange(char *table, int start, int end, char *chromName, boolean isXeno, float maxScore); /* Return linked features from range of table with the scores scaled appropriately */ void ctWigLoadItems(struct track *tg); /* load custom wiggle track data */ void wigLoadItems(struct track *tg); /* load wiggle track data from database */ void wigMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Set up wig pointers and do some other precalculations on a wig type track. */ void bedGraphMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); void bigWigMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Make track group for wig - wiggle tracks. */ void mathWigMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* mathWig load and draw methods. */ void bigRmskMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Set up bigRmsk methods. */ void commonBigBedMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Set up common bigBed methods used by several track types that depend on the bigBed format. */ void bigBedMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Set up bigBed methods for tracks that are type bigBed. */ void chromGraphMethods(struct track *tg); /* Fill in chromGraph methods for built in track. */ void chromGraphMethodsCt(struct track *tg); /* Fill in chromGraph methods for custom track. */ void factorSourceMethods(struct track *track); /* Set up special methods for factorSource type tracks. */ void makeItemsMethods(struct track *track); /* Set up special methods for makeItems type tracks. */ void makeItemsJsCommand(char *command, struct track *trackList, struct hash *trackHash); /* Execute some command sent to us from the javaScript. All we know for sure is that * the first word of the command is "makeItems." We expect it to be of format: * makeItems <trackName> <chrom> <chromStart> <chromEnd> * If it is indeed of this form then we'll create a new makeItemsItem that references this * location and stick it in the named track. */ void wigMafPMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); void wigMafMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); int wigTotalHeight(struct track *tg, enum trackVisibility vis); /* Wiggle track will use this to figure out the height they use as defined in the cart */ /* Make track for wig - wiggle tracks. */ /* Make track group for maf track with wiggle. */ void rnaSecStrMethods(struct track *tg); /* Make track which visualizes RNA secondary structure annotation. */ void sampleMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Load up methods for a generic sample type track. */ int sampleUpdateY( char *name, char *nextName, int lineHeight ); /* only increment height when name root (minus the period if * there is one) is different from previous one. *This assumes that the entries are sorted by name as they would *be if loaded by hgLoadSample*/ void samplePrintYAxisLabel( struct hvGfx *hvg, int y, struct track *track, char *labelString, double min0, double max0 ); /*print a label for a horizontal y-axis line*/ int whichSampleBin( double num, double thisMin, double thisMax, double binCount ); /* Get bin value from num. */ double whichSampleNum( double bin, double thisMin, double thisMax, double binCount ); /* gets range nums. from bin values*/ void humMusLMethods( struct track *tg ); /* Overide the humMusL load function to look for zoomed out tracks. */ void zooMethods( struct track *tg ); /* Overide the zoo sample type load function to look for zoomed out tracks. */ void expRatioMethods(struct track *tg); /* Set up methods for expRatio type tracks in general. */ void expRatioMethodsFromCt(struct track *tg); /* Set up methods for expRatio type tracks from custom track. */ void loweExpRatioMethods(struct track *tg); /* Set up methods for expRatio type tracks in general. */ void affyTranscriptomeMethods(struct track *tg); /* Overide the load function to look for zoomed out tracks. */ void rosettaMethods(struct track *tg); /* methods for Rosetta track using bed track */ void nci60Methods(struct track *tg); /* set up special methods for NCI60 track and tracks with multiple scores in general */ void affyMethods(struct track *tg); /* set up special methods for NCI60 track and tracks with multiple scores in general */ void expRatioMethodsFromDotRa(struct track *tg); /* Special methods for tracks using new microarrayGroups.ra files. */ void affyRatioMethods(struct track *tg); /* set up special methods for NCI60 track and tracks with multiple scores in general */ void affyUclaMethods(struct track *tg); /* set up special methods for affyUcla track and tracks with multiple scores in general */ void affyUclaNormMethods(struct track *tg); /* Set up special methods for the affyUcla normal tissue track scores in general */ void cghNci60Methods(struct track *tg); /* set up special methods for CGH NCI60 track */ char *getOrganism(struct sqlConnection *conn, char *acc); /* lookup the organism for an mrna, or NULL if not found. * WARNING: static return */ char *getOrganismShort(struct sqlConnection *conn, char *acc); /* lookup the organism for an mrna, or NULL if not found. This will * only return the genus, and only the first seven letters of that. * WARNING: static return */ char *getGeneName(struct sqlConnection *conn, char *acc); /* get geneName from refLink or NULL if not found. * WARNING: static return */ char *refGeneName(struct track *tg, void *item); /* Get name to use for refGene item. */ char *refGeneMapName(struct track *tg, void *item); /* Return un-abbreviated gene name. */ #define uglyh printHtmlComment /* Debugging aid. */ int linkedFeaturesSeriesCmp(const void *va, const void *vb); /* Compare to sort based on chrom,chromStart. */ void lfDrawSpecialGaps(struct linkedFeatures *lf, int intronGap, boolean chainLines, int gapFactor, struct track *tg, struct hvGfx *hvg, int xOff, int y, double scale, Color color, Color bColor, enum trackVisibility vis); /* If applicable, draw something special for the gap following this block. * If intronGap has been specified, draw exon arrows only if the target gap * length is at least intronGap. * If chainLines, draw a double-line gap if both target and query have a gap * (mismatching sequence). */ void bamWigMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Set up bamWig methods. */ void bamLinkedFeaturesDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw linked features items. */ void bamLinkedFeaturesSeriesDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw BAM linked features series items. */ void chainDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw chained features. This loads up the simple features from * the chainLink table, calls linkedFeaturesDraw, and then * frees the simple features again. */ void linkedFeaturesSeriesDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw linked features series items. */ struct linkedFeaturesSeries *lfsFromColoredExonBed(struct bed *bed); /* Convert a single BED 14 thing into a special linkedFeaturesSeries */ /* where each linkedFeatures is a colored block. */ void makeRedGreenShades(struct hvGfx *hvg); /* Makes some colors for the typical red/green microarray spectrum. */ void linkedFeaturesSeriesMethods(struct track *tg); void lfsMapItemName(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height); struct track *trackFromTrackDb(struct trackDb *tdb); /* Create a track based on the tdb */ int spreadStringCharWidth(int width, int count); Color getOrangeColor(); /* Return color used for insert indicators in multiple alignments */ Color getBlueColor(); Color getChromBreakBlueColor(); Color getChromBreakGreenColor(); void linkedFeaturesDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis); /* Draw a single simple bed item at position. */ Color lighterColor(struct hvGfx *hvg, Color color); /* Get lighter shade of a color */ struct track *chromIdeoTrack(struct track *trackList); /* Find chromosome ideogram track */ void setRulerMode(); /* Set the rulerMode variable from cart. */ #define configHideAll "hgt_doConfigHideAll" #define configShowAll "hgt_doConfigShowAll" #define configDefaultAll "hgt_doDefaultShowAll" #define configHideAllGroups "hgt_doConfigHideAllGroups" #define configShowAllGroups "hgt_doConfigShowAllGroups" #define configHideEncodeGroups "hgt_doConfigHideEncodeGroups" #define configShowEncodeGroups "hgt_doConfigShowEncodeGroups" #define configGroupTarget "hgt_configGroupTarget" #define configPriorityOverride "hgt_priorityOverride" #define hgtJsCommand "hgt_doJsCommand" void doMiddle(struct cart *theCart); /* Print the body of html file. */ void initTl(); /* Initialize layout around small font and a picture about 800 pixels * wide. */ void setLayoutGlobals(); /* Figure out basic dimensions of display. */ struct hash *makeGlobalTrackHash(struct track *trackList); /* Create a global track hash and returns a pointer to it. */ void makeActiveImage(struct track *trackList, char *psOutput); /* Make image and image map. */ void configPage(); /* Put up configuration page. */ void configPageSetTrackVis(int vis); /* Do config page after setting track visibility. If vis is -2, then visibility * is unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ void configMultiRegionPage(); /* Put up multi-region configuration page. */ struct track *trackNew(); /* Allocate track . */ void bedMethods(struct track *tg); /* Fill in methods for (simple) bed tracks. */ void bed9Methods(struct track *tg); /* Fill in methods for bed9 tracks. */ void complexBedMethods(struct track *track, struct trackDb *tdb, boolean isBigBed, int wordCount, char *words[]); /* Fill in methods for more complex bed tracks. */ void makeCompositeTrack(struct track *track, struct trackDb *tdb); /* Construct track subtrack list from trackDb entry. * Sets up color gradient in subtracks if requested */ void makeContainerTrack(struct track *track, struct trackDb *tdb); /* Construct track subtrack list from trackDb entry for container tracks. */ bool isSubtrackVisible(struct track *tg); /* Should this subtrack be displayed? */ void compositeTrackVis(struct track *track); /* set visibilities of subtracks */ boolean isWithCenterLabels(struct track *track); /* Special cases: inhibit center labels of subtracks in dense mode, and * of composite track in non-dense mode. * BUT if track->tdb has a centerLabelDense setting, let subtracks go with * the default and inhibit composite track center labels in all modes. * Otherwise use the global boolean withCenterLabels. */ boolean isCenterLabelConditional(struct track *track); /* Dense subtracks and pack subtracks (when centerLabelsPack off set) * show center labels depending on vis of previous track */ boolean isCenterLabelConditionallySeen(struct track *track); /* Returns FALSE if track and prevTrack have same parent, and are both conditional * i.e. dense subtrack or pack subtrack with centerLabelsPack off set */ boolean isCenterLabelsPackOff(struct track *track); /* Check for trackDb setting to suppress center labels of composite in pack mode */ boolean isCenterLabelIncluded(struct track *track); /* Center labels may be conditionally included */ boolean doHideEmptySubtracks(struct track *track, char **multiBedFile, char **subtrackIdFile); /* Suppress display of empty subtracks. Initial support only for bed's. */ Color maybeDarkerLabels(struct track *track, struct hvGfx *hvg, Color color); /* For tracks having light track display but needing a darker label */ void affyTxnPhase2Methods(struct track *track); /* Methods for dealing with a composite transcriptome tracks. */ void loadGenePred(struct track *tg); /* Convert gene pred in window to linked feature. */ void genePredAssignConfiguredName(struct track *tg); /* Set name on genePred in "extra" field to gene name, accession, or both, * depending, on UI on all items in track */ void loadGenePredWithConfiguredName(struct track *tg); /* Convert gene pred info in window to linked feature. Include name * in "extra" field (gene name, accession, or both, depending on UI) */ boolean highlightItem(struct track *tg, void *item); /* Should this item be highlighted? */ void linkedFeaturesSeriesDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis); /* Draw a linked features series item at position. */ #define NEXT_ITEM_ARROW_BUFFER 1 /* Space around "next item" arrow (in pixels). */ void addWikiTrack(struct track **pGroupList); /* Add wiki track and append to group list. */ void wikiTrackMethods(struct track *tg); /* establish loadItems function for wiki track */ struct bed *wikiTrackGetBedRange(char *mapName, char *chromName, int start, int end); /* fetch wiki track items as simple bed 3 list in given range */ void addVariomeWikiTrack(struct track **pGroupList); /* Add variome wiki track and append to group list. */ void bed8To12(struct bed *bed); /* Turn a bed 8 into a bed 12 by defining one block. */ char *collapseGroupVar(char *name); /* Construct cart variable name for collapsing group */ boolean isCollapsedGroup(struct group *grp); /* Determine if group is collapsed */ void collapseGroupGoodies(boolean isOpen, boolean wantSmallImage, char **img, char **indicator, char **otherState); /* Get image, char representation of image, and 'otherState' (1 or 0) * for a group, based on whether it is collapsed, and whether we want * larger or smaller image for collapse box */ void parseSs(char *ss, char **retPsl, char **retFa); /* Parse out ss variable into components. */ boolean ssFilesExist(char *ss); /* Return TRUE if both files in ss exist. */ int maximumTrackItems(struct track *tg); /* Return the maximum number of items allowed in track. */ int maximumTrackHeight(struct track *tg); /* Return the maximum track height allowed in pixels. */ struct dyString *uiStateUrlPart(struct track *toggleGroup); /* Return a string that contains all the UI state in CGI var * format. If toggleGroup is non-null the visibility of that * track will be toggled in the string. */ boolean nextItemCompatible(struct track *tg); /* Check to see if we draw nextPrev item buttons on a track. */ void linkedFeaturesLabelNextPrevItem(struct track *tg, boolean next); /* Default next-gene function for linkedFeatures. Changes winStart/winEnd * and updates position in cart. */ void createHgFindMatchHash(); /* Read from the cart the string assocated with matches and put the matching items into a hash for highlighting later. */ TrackHandler lookupTrackHandlerClosestToHome(struct trackDb *tdb); /* Lookup handler for track of give name. Try parents if * subtrack has a NULL handler. Return NULL if none. */ void registerTrackHandlers(); /* Register tracks that include some non-standard methods. */ void initColors(struct hvGfx *hvg); /* Initialize the shades of gray etc. */ void findTrackColors(struct hvGfx *hvg, struct track *trackList); /* Find colors to draw in. */ char *getItemDataName(struct track *tg, char *itemName); /* Translate an itemName to its itemDataName, using tg->itemDataName if is not * NULL. The resulting value should *not* be freed, and it should be assumed * that it will only remain valid until the next call of this function.*/ void registerTrackHandler(char *name, TrackHandler handler); /* Register a track handling function. */ void doSearchTracks(struct group *groupList); boolean superTrackHasVisibleMembers(struct trackDb *tdb); enum trackVisibility limitedVisFromComposite(struct track *subtrack); /* returns the subtrack visibility which may be limited by composite with multi-view dropdowns. */ INLINE enum trackVisibility actualVisibility(struct track *track) // return actual visibility for this track (limited to limitedVis if appropriate) { return track->limitedVisSet ? track->limitedVis : track->visibility; } char *getScoreFilterClause(struct cart *cart,struct trackDb *tdb,char *scoreColumn); // Returns "score >= ..." extra where clause if one is needed /* useful for declaring small arrays */ #define SMALLBUF 128 #define LARGEBUF 256 /* and for dyStringNew */ #define SMALLDYBUF 64 char *trackUrl(char *mapName, char *chromName); /* Return hgTrackUi url; chromName is optional. */ void bedDetailCtMethods (struct track *tg, struct customTrack *ct); /* Load bedDetail track from custom tracks as bed or linked features */ void pgSnpMethods (struct track *tg); /* Personal Genome SNPs: show two alleles with stacked color bars for base alleles and * (if available) allele counts in mouseover. */ int pgSnpHeight(struct track *tg, enum trackVisibility vis); void pgSnpCtMethods (struct track *tg); /* Load pgSnp track from custom tracks */ void pgSnpMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height); /* create a special map box item with different pop-up statusLine with allele counts */ void gvfMethods(struct track *tg); /* Load GVF variant data. */ void gtexGeneMethods(struct track *tg); /* Gene-Tissue Expression (GTEX) gene track*/ void messageLineMethods(struct track *track); /* Methods for drawing a single-height message line instead of track items, * e.g. if source was compiled without a necessary library. */ void rmskJoinedMethods(struct track *track); /* construct track for detailed repeat visualization */ void lrgMethods(struct track *tg); /* Locus Reference Genomic (bigBed 12 +) handlers. */ void peptideAtlasMethods(struct track *tg); /* PeptideAtlas (bed 12+) handlers */ void barChartMethods(struct track *tg); /* Bar Chart track type: draw fixed width chart of colored bars over a BED item */ void barChartCtMethods(struct track *tg); /* Bar Chart track methods for custom track */ void gtexEqtlClusterMethods(struct track *tg); /* GTEx eQTL Cluster (bigBed 5 +) tracks */ void gtexEqtlTissueMethods(struct track *tg); /* Install handler for GTEx eQTL Tissues track */ void instaPortMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* instaPort track type methods */ void bigBaseViewMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* bigBaseView track type methods */ void lollyMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]); /* Lollipop track type methods */ void interactMethods(struct track *tg); /* Interact track type methods */ void interactCtMethods(struct track *tg); /* Interact track methods for custom track */ void hicMethods(struct track *tg); /* Methods for Hi-C interaction data */ void hicCtMethods(struct track *tg); /* Hi-C track methods for custom track */ void bedMethylCtMethods(struct track *tg); /* bedMethyl track methods for custom track */ void parentChildCartCleanup(struct track *trackList,struct cart *newCart,struct hash *oldVars); /* When composite/view settings changes, remove subtrack specific vis When superTrackChild is found and selected, shape superTrack to match. */ void dontLoadItems(struct track *tg); /* No-op loadItems when we aren't going to try. */ void filterItems(struct track *tg, boolean (*filter)(struct track *tg, void *item), char *filterType); /* Filter out items from track->itemList. */ void filterItemsOnNames(struct track *tg); /* Only keep items with a name in the .nameFilter cart var. * Not using filterItems(), because filterItems has no state at all. */ int gCmpPriority(const void *va, const void *vb); /* Compare groups based on priority. */ int tgCmpPriority(const void *va, const void *vb); /* Compare to sort based on priority; use shortLabel as secondary sort key. */ void printMenuBar(); /* Put up the menu bar. */ boolean winTooBigDoWiggle(struct cart *cart, struct track *tg); /* return true if we wiggle because the window size exceeds a certain threshold */ boolean checkIfWiggling(struct cart *cart, struct track *tg); /* Check to see if a track should be drawing as a wiggle. */ boolean isTypeBedLike(struct track *track); /* Check if track type is BED-like packable thing (but not rmsk or joinedRmsk) */ boolean isTypeUseItemNameAsKey(struct track *track); /* Check if track type is like expRatio and key is just item name. */ boolean isTypeUseMapItemNameAsKey(struct track *track); /* Check if track type is like interact and uses map item name to link across multi regions */ void setEMGeneTrack(); /* Find the track for the gene table to use for exonMostly and geneMostly. */ void findBestEMGeneTable(struct track *trackList); /* Find the best gene table to use for exonMostly */ struct window *makeWindowListFromVirtChrom(long virtWinStart, long virtWinEnd); /* make list of windows from virtual position on virtualChrom */ struct convertRange { struct convertRange *next; char *chrom; int start; int end; long vStart; long vEnd; boolean found; boolean skipIt; }; void linkedFeaturesNextPrevExonFind(struct track *tg, boolean next, struct convertRange *crList); /* Find next-exon function for linkedFeatures. Finds corresponding position on virtual chrom for new winStart/winEnd of exon non-virt position, * and returns it. This function was cloned from linkedFeaturesLabelNextPrevItem and modified. */ boolean virtualSingleChrom(); /* Return TRUE if using virtual single chromosome mode */ void parseVPosition(char *position, char **pChrom, long *pStart, long *pEnd); /* parse Virt position */ char *undisguisePosition(char *position); // UN-DISGUISE VMODE /* Find the virt position * position should be real chrom span. * Limitation: can only convert things in the current windows set. */ char *disguisePositionVirtSingleChrom(char *position); // DISGUISE VMODE /* Hide the virt position, convert to real single chrom span. * position should be virt chrom span. * Can handle anything in the virt single chrom. */ #define measureTime uglyTime #define SUPPORT_CONTENT_TYPE 1 struct bbiFile *fetchBbiForTrack(struct track *track); /* Fetch bbiFile from track, opening it if it is not already open. */ void genericDrawNextItem(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, Color color, enum trackVisibility vis); /* Draw next item buttons and map boxes */ struct spaceSaver *findSpaceSaver(struct track *tg, enum trackVisibility vis); /* Find SpaceSaver in list. Return spaceSaver found or NULL. */ void labelTrackAsFilteredNumber(struct track *tg, unsigned numOut); /* add text to track long label to indicate filter is active and how many items were deleted */ void labelTrackAsFiltered(struct track *tg); /* add text to track long label to indicate filter is active */ void labelTrackAsHideEmpty(struct track *tg); /* add text to track long label to indicate empty subtracks are hidden */ void labelTrackAsDensity(struct track *tg); /* Add text to track long label to indicate density mode */ void labelTrackAsDensityWindowSize(struct track *tg); /* Add text to track long label to indicate density mode because window size exceeds some threshold */ void setupHotkeys(boolean gotExtTools); /* setup keyboard shortcuts and a help dialog for it */ void calcWiggleOrdering(struct cart *cart, struct flatTracks *flatTracks); void bedPlusLabelDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis); /* Draw a single bed item at position. If vis is full, draw the associated label to the left * of the item. */ Color blackItemNameColor(struct track *tg, void *item, struct hvGfx *hvg); /* Force item name (label) color to black */ void linkedFeaturesMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height); boolean recTrackSetsEnabled(); /* Return TRUE if feature is available */ boolean recTrackSetsChangeDetectEnabled(); /* Return TRUE if feature is available, in hgConf */ int recTrackSetsForDb(); /* Return number of recommended track sets for this database */ boolean hasRecTrackSet(struct cart *cart); /* Check if currently loaded session is in the recommended track set */ void printRecTrackSets(); /* Create dialog with list of recommended track sets */ Color colorFromSoTerm(enum soTerm term); /* Assign a Color according to soTerm: red for non-synonymous, green for synonymous, blue for * UTR/noncoding, black otherwise. */ void maybeNewFonts(struct hvGfx *hvg); /* Check to see if we want to use the alternate font engine (FreeType2). */ Color colorFromCart(struct track *tg, Color color); /* Return the RGB color from the cart setting 'colorOverride' or just return color */ unsigned getParaLoadTimeout(); // get the parallel load timeout in seconds (defaults to 90) void maybeDrawQuickLiftLines( struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis); /* Draw the indel regions as a highlight. */ + +unsigned findBiggest(unsigned num); +/* find biggest font not bigger than num */ #endif /* HGTRACKS_H */