36710988224ab9373893a97a6edc95e033b0d646 braney Fri Oct 18 08:52:28 2024 -0700 density mode on vcf tracks was crashing. Refs #34659 diff --git src/hg/hgTracks/wigCommon.h src/hg/hgTracks/wigCommon.h index c11b741..f23a2b1 100644 --- src/hg/hgTracks/wigCommon.h +++ src/hg/hgTracks/wigCommon.h @@ -1,201 +1,206 @@ /* wigCommon.h - common items to the two graphing types of tracks * type wig and type bedGraph */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef WIGCOMMON_H #define WIGCOMMON_H /* wigCartOptions structure - to carry cart options from wigMethods * to all the other methods via the track->extraUiData pointer */ struct wigCartOptions { enum wiggleGridOptEnum horizontalGrid; /* grid lines, ON/OFF */ enum wiggleGraphOptEnum lineBar; /* Line or Bar chart */ enum wiggleScaleOptEnum autoScale; /* autoScale on */ enum wiggleWindowingEnum windowingFunction; /* max,mean,min,sum */ enum wiggleSmoothingEnum smoothingWindow; /* N: [1:15] */ enum wiggleYLineMarkEnum yLineOnOff; /* OFF/ON */ enum wiggleAlwaysZeroEnum alwaysZero; /* OFF/ON */ enum wiggleTransformFuncEnum transformFunc; /* NONE/LOG */ double minY; /* from trackDb.ra words, the absolute minimum */ double maxY; /* from trackDb.ra words, the absolute maximum */ int maxHeight; /* maximum pixels height from trackDb */ int defaultHeight; /* requested height from cart */ int minHeight; /* minimum pixels height from trackDb */ double yLineMark; /* user requested line at y = */ char *colorTrack; /* Track to use for coloring wiggle track. */ int graphColumn; /* column to be graphing (bedGraph tracks) */ boolean bedGraph; /* is this a bedGraph track ? */ boolean isMultiWig; /* If true it's a multi-wig. */ enum wiggleAggregateFunctionEnum aggregateFunction; /* NONE/TRANSPARENT/STACKED */ boolean doNegative; /* should we negate the values */ struct mafBaseProbs *baseProbs; /* if we're in logoMaf mode, this will hold the base probabilities. */ boolean doSequenceLogo; /* should we draw a sequence logo when near baselevel? */ }; struct wigCartOptions *wigCartOptionsNew(struct cart *cart, struct trackDb *tdb, int wordCount, char *words[]); /* Create a wigCartOptions from cart contents and tdb. */ struct preDrawContainer /* A preDraw array with a little bit of extra info */ { struct preDrawContainer *nextPlaceholder; /* Refactoring code so not in list really. */ struct preDrawElement *preDraw; /* Array of values. */ int preDrawSize; /* Size of preDraw */ int preDrawZero; /* Offset from start of predraw array to data requested. We * get more because of smoothing */ int width; /* Passed in width, number of pixels to display without smooth */ double graphUpperLimit, graphLowerLimit; /* limits to the smoothed value */ boolean skipAutoscale; /* multiWig does its own autoscale */ }; struct preDrawElement { double max; /* maximum value seen for this point */ double min; /* minimum value seen for this point */ unsigned long long count; /* number of datum at this point */ double sumData; /* sum of all values at this point */ double sumSquares; /* sum of (values squared) at this point */ double plotValue; /* raw data to plot */ double smooth; /* smooth data values */ }; struct bedGraphItem /* A bedGraph track item. */ { struct bedGraphItem *next; int start, end; /* Start/end in chrom coordinates. */ char *name; /* Common name */ float dataValue; /* data value from bed table graphColumn */ double graphUpperLimit; /* filled in by DrawItems */ double graphLowerLimit; /* filled in by DrawItems */ }; typedef void (*WigVerticalLineVirtual)(void *image, int x, int y, int height, Color color); /* Draw a vertical line somewhere, maybe a regular image, maybe a transparent one. */ struct pixelCountBin /* A structure used to keep track of how many pixels are drawn in a set of bins. */ { unsigned binCount; unsigned binSize; unsigned long *bins; }; struct wigGraphOutput /* Info on where to draw a wig - may be pretty indirect in transparent case. */ { WigVerticalLineVirtual vLine; void *image; /* Some type in reality that goes with vLine. */ int xOff, yOff; /* Where to offset output within image. */ double *yOffsets; /* if not NULL, points to yOffsets for stacked bars */ int numTrack; /* the index of this track */ struct pixelCountBin *pixelBins; }; struct wigGraphOutput *wigGraphOutputStack(int xOff, int yOff, int width, int numTracks, struct hvGfx *image); /* Get appropriate wigGraphOutput for non-transparent stacked rendering */ struct wigGraphOutput *wigGraphOutputSolid(int xOff, int yOff, struct hvGfx *image); /* Get appropriate wigGraphOutput for non-transparent rendering */ /* source to these routines is in wigTrack.c */ struct preDrawContainer *initPreDrawContainer(int width); /* initialize a preDraw array of size width */ void preDrawWindowFunction(struct preDrawElement *preDraw, int preDrawSize, enum wiggleWindowingEnum windowingFunction, enum wiggleTransformFuncEnum transformFunc, boolean doNegative); /* apply windowing function to the values in preDraw array */ void preDrawSmoothing(struct preDrawElement *preDraw, int preDrawSize, enum wiggleSmoothingEnum smoothingWindow); /* apply smoothing function to preDraw array */ double preDrawLimits(struct preDrawElement *preDraw, int preDrawZero, int width, double *overallUpperLimit, double *overallLowerLimit); /* scan preDraw array and determine graph limits */ double preDrawAutoScale(struct preDrawElement *preDraw, int preDrawZero, int width, enum wiggleScaleOptEnum autoScale, enum wiggleWindowingEnum windowingFunction, double *graphUpperLimit, double *graphLowerLimit, double *epsilon, int lineHeight, double maxY, double minY, enum wiggleAlwaysZeroEnum alwaysZero); /* if autoScaling, scan preDraw array and determine limits */ void drawZeroLine(enum trackVisibility vis, enum wiggleGridOptEnum horizontalGrid, double graphUpperLimit, double graphLowerLimit, struct hvGfx *hvg, int xOff, int yOff, int width, int lineHeight); /* draw a line at y=0 on the graph */ void drawArbitraryYLine(enum trackVisibility vis, enum wiggleGridOptEnum horizontalGrid, double graphUpperLimit, double graphLowerLimit, struct hvGfx *hvg, int xOff, int yOff, int width, int lineHeight, double yLineMark, double graphRange, enum wiggleYLineMarkEnum yLineOnOff); /* draw a line at y=yLineMark on the graph */ void wigMapSelf(struct track *tg, struct hvGfx *hvg, int seqStart, int seqEnd, int xOff, int yOff, int width); /* if self mapping, create the mapping box */ void wigLeftLabels(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); /* drawing left labels */ char *wigNameCallback(struct track *tg, void *item); /* Return name of wig level track. */ void wigFindItemLimits(void *items, double *graphUpperLimit, double *graphLowerLimit); /* find upper and lower limits of graphed items (wigItem) */ void wigMultiRegionGraphLimits(struct track *tg); /* Set common graphLimits across all windows */ void wigPreDrawPredraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis, struct preDrawContainer *preContainer, int preDrawZero, int preDrawSize, double *retGraphUpperLimit, double *retGraphLowerLimit); /* Figure out graph limits after running windowingFunction and smoothing if needed. */ void wigDrawPredraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis, struct preDrawContainer *preDrawContainer, int preDrawZero, int preDrawSize, double graphUpperLimit, double graphLowerLimit); /* Draw once we've figured out predraw. */ void wigLeftAxisLabels(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, char *shortLabel, double graphUpperLimit, double graphLowerLimit, boolean showNumbers); /* Draw labels on left for a wiggle-type track. */ double wiggleLogish(double x); /* Return log-like transform without singularity at 0. */ /****************** in source file bedGraph.c ************************/ void wigBedGraphFindItemLimits(void *items, double *graphUpperLimit, double *graphLowerLimit); /* find upper and lower limits of graphed items (bedGraphItem) */ int normalizeCount(struct preDrawElement *el, double countFactor, double minVal, double maxVal, double sumData, double sumSquares); /* Normalize statistics to be based on an integer number of valid bases. * Integer value is the smallest integer not less than countFactor. */ void wigLogoMafCheck(struct track *tg, int start, int end); /* Check to see if we should draw a sequence logo for the wiggle contents. */ + +int setupForWiggle(struct track *tg, enum trackVisibility vis); +/* Check to see if this track should show density coverage and if so + * make sure it has the cart data to support it. + */ #endif /* WIGCOMMON_H */