254686140b97de7d7f85906dcf70f78a9601d7d0 braney Mon Sep 8 15:10:10 2025 -0700 ongoing work on quickLift diff --git src/hg/hgTracks/quickLift.c src/hg/hgTracks/quickLift.c index 6bd27e445d6..cff266216c5 100644 --- src/hg/hgTracks/quickLift.c +++ src/hg/hgTracks/quickLift.c @@ -1,178 +1,219 @@ #include "common.h" #include "hgTracks.h" #include "chromAlias.h" #include "hgConfig.h" #include "bigChain.h" #include "bigLink.h" #include "trackHub.h" #include "quickLift.h" #include "chainCart.h" +#include "bigChain.h" static Color *highlightColors; //static unsigned lengthLimit; struct cartOptions { enum chainColorEnum chainColor; /* ChromColors, ScoreColors, NoColors */ int scoreFilter ; /* filter chains by score if > 0 */ }; static Color getColor(char *confVariable, char *defaultRgba) { Color color = 0xff0000ff; char *str = cloneString(cfgOptionDefault(confVariable, defaultRgba)); char *words[10]; if (chopCommas(str, words) != 4) errAbort("conf variable '%s' is expected to have a string like r,g,b,a ", confVariable); color = MAKECOLOR_32_A(atoi(words[0]),atoi(words[1]),atoi(words[2]),atoi(words[3])); return color; } static void initializeHighlightColors() { if (highlightColors == NULL) { highlightColors = needMem(sizeof(Color) * 5); //lengthLimit = atoi(cfgOptionDefault("quickLift.lengthLimit", "10000")); highlightColors[QUICKTYPE_INSERT] = getColor("quickLift.insColor","255,0,0,255"); highlightColors[QUICKTYPE_DEL] = getColor("quickLift.delColor","0,255,0,255"); highlightColors[QUICKTYPE_DOUBLE] = getColor("quickLift.doubleColor","0,0,255,255"); highlightColors[QUICKTYPE_MISMATCH] = getColor("quickLift.mismatchColor","255,0,0,255"); } } static void drawTri(struct hvGfx *hvg, int x1, int x2, int y, Color color) /* Draw traingle. */ { struct gfxPoly *poly = gfxPolyNew(); int half = (x2 - x1) / 2; gfxPolyAddPoint(poly, x1, y); gfxPolyAddPoint(poly, x1+half, y+2*half); gfxPolyAddPoint(poly, x2, y); hvGfxDrawPoly(hvg, poly, color, TRUE); gfxPolyFree(&poly); } +static int snakePalette2[] = +{ +0x1f77b4, 0xaec7e8, 0xff7f0e, 0xffbb78, 0x2ca02c, 0x98df8a, 0xd62728, 0xff9896, 0x9467bd, 0xc5b0d5, 0x8c564b, 0xc49c94, 0xe377c2, 0xf7b6d2, 0x7f7f7f, 0xc7c7c7, 0xbcbd22, 0xdbdb8d, 0x17becf, 0x9edae5 +}; + +static void drawDenseChain(struct track *tg, struct hvGfx *hvg, char *fileName, int start, int end, int xOff, int yOff, int width, MgFont *font, Color color) +// draw a dense version of a chain that users can use to click through to the other species +{ +struct lm *lm = lmInit(0); +struct bbiFile *bbi = bigBedFileOpenAlias(fileName, chromAliasFindAliases); +struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chromName, start, end, 0, lm); +char *bedRow[12]; +char startBuf[16], endBuf[16]; +double scale = scaleForWindow(width, start, end); + +unsigned colorIndex = 0; +for(bb=bbList; bb; bb = bb->next, colorIndex++) + { + colorIndex %= sizeof(snakePalette2) / sizeof(int); + + bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow)); + struct bigChain *chain = bigChainLoad(bedRow); + if (chain->chromStart < start) + chain->chromStart = start; + if (chain->chromEnd > end) + chain->chromEnd = end; + int x1 = xOff + scale * (chain->chromStart - start); + int w = scale * (chain->chromEnd - chain->chromStart); + unsigned colorHex = snakePalette2[colorIndex]; + unsigned colorVal = MAKECOLOR_32(((colorHex >> 16) & 0xff),((colorHex >> 8) & 0xff),((colorHex >> 0) & 0xff)); + hvGfxBox(hvg, x1, yOff, w, tg->height, colorVal); + char otherChrom[1024]; + safef(otherChrom, sizeof otherChrom, "%s:%d-%d", chain->qName, chain->qStart, chain->qEnd); + mapBoxHc(hvg, chain->chromStart, chain->chromEnd, x1, yOff, w, tg->height, tg->track, chain->name, otherChrom); + } +} + 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 in quickLifted tracks as a highlight. */ { char *quickLiftFile = cloneString(trackDbSetting(tg->tdb, "quickLiftUrl")); if (quickLiftFile == NULL) return; initializeHighlightColors(); boolean drawTriangle = FALSE; if (startsWith("bigQuickLiftChain", tg->tdb->type)) drawTriangle = TRUE; char *liftDb = trackDbSetting(tg->tdb, "quickLiftDb"); struct quickLiftRegions *regions = quickLiftGetRegions(database, liftDb, quickLiftFile, chromName, seqStart, seqEnd); struct quickLiftRegions *hr = regions; int fontHeight = mgFontLineHeight(tl.font); int height = tg->height; if (!drawTriangle && isCenterLabelIncluded(tg)) { height += fontHeight; yOff -= fontHeight; } -//if (drawTriangle && (hr == NULL)) // if there are no differences make a map for the whole track - //mapBoxHc(hvg, seqStart, seqEnd, xOff, yOff, width, tg->height, tg->track, hr->id, "identical"); +if (drawTriangle && (hr == NULL)) + { + drawDenseChain(tg, hvg, quickLiftFile, seqStart, seqEnd, xOff, yOff, width, font, color); + return; + } int pos = xOff; char * lastId = 0; for(; hr; hr = hr->next) { unsigned int hexColor = highlightColors[hr->type]; double scale = scaleForWindow(width, seqStart, seqEnd); int x1 = xOff + scale * (hr->chromStart - seqStart); int w = scale * (hr->chromEnd - hr->chromStart); if (w == 0) w = 1; hvGfxSetClip(hvg, xOff, yOff, width, height); // we're drawing in the center label at the moment int startX, endX; char mouseOver[4096]; if (drawTriangle) { startX = x1 + w/2 - fontHeight/2; endX = x1 + w/2 + fontHeight/2 ; drawTri(hvg, startX, endX , yOff, hexColor); if (drawTriangle && (x1 > pos)) mapBoxHc(hvg, seqStart, seqEnd, pos, yOff, startX - pos, tg->height, tg->track, hr->id, "identical"); pos = endX; } else { startX = x1; endX = x1 + w; hvGfxBox(hvg, startX, yOff, w, height, hexColor); continue; } if (hr->type == QUICKTYPE_MISMATCH) safef(mouseOver, sizeof mouseOver, "mismatch %c->%c", *hr->otherBases, *hr->bases); else if (hr->chromStart == hr->chromEnd) safef(mouseOver, sizeof mouseOver, "deletion %ldbp (%.*s)", hr->oChromEnd - hr->oChromStart, hr->otherBaseCount, hr->otherBases); else if (hr->oChromStart == hr->oChromEnd) safef(mouseOver, sizeof mouseOver, "insertion %ldbp (%.*s)", hr->chromEnd - hr->chromStart, hr->baseCount, hr->bases); else safef(mouseOver, sizeof mouseOver, "double %ldbp", hr->oChromEnd - hr->oChromStart); mapBoxHc(hvg, seqStart, seqEnd, startX, yOff, endX - startX, height, tg->track, hr->id, mouseOver); lastId = hr->id; } if (drawTriangle && (pos != xOff)) mapBoxHc(hvg, seqStart, seqEnd, pos, yOff, width - pos, tg->height, tg->track, lastId, "identical"); } void quickLiftDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) { //mapBoxHc(hvg, seqStart, seqEnd, xOff, yOff, width, tg->height, tg->track, "fart", "hallo"); maybeDrawQuickLiftLines( tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); } static int quickLiftTotalHeight(struct track *tg, enum trackVisibility vis) /* Return configured height of track. */ { return tg->lineHeight; } static void quickLiftDoLeftLabels(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) /* For now, draw no left labels. */ { return; } void quickLiftChainMethods(struct track *tg, struct trackDb *tdb, int wordCount, char *words[]) /* Fill in custom parts of quickLift chains */ { struct cartOptions *chainCart; AllocVar(chainCart); tg->extraUiData = (void *) chainCart; tg->isBigBed = TRUE; void bigChainLoadItems(struct track *tg); tg->loadItems = bigChainLoadItems; tg->drawItems = quickLiftDraw; tg->totalHeight = quickLiftTotalHeight; tg->drawLeftLabels = quickLiftDoLeftLabels; tg->mapsSelf = TRUE; }