3b51318fe05fce338719b56a70d44f1436ff5311 kate Tue Dec 5 12:37:26 2017 -0800 Fix problems with computing centers and position starts (esp. noticeable for SNPs). Also some cleanup. refs #17512 diff --git src/hg/hgTracks/longRangeTrack.c src/hg/hgTracks/longRangeTrack.c index 383c7d0..99ff5ee 100644 --- src/hg/hgTracks/longRangeTrack.c +++ src/hg/hgTracks/longRangeTrack.c @@ -1,150 +1,154 @@ #include "common.h" #include "hgTracks.h" #include "longRange.h" static int longRangeHeight(struct track *tg, enum trackVisibility vis) /* calculate height of all the snakes being displayed */ { if ( tg->visibility == tvDense) return tl.fontHeight; int min, max, deflt, current; cartTdbFetchMinMaxPixels(cart, tg->tdb, LONG_MINHEIGHT, LONG_MAXHEIGHT, atoi(LONG_DEFHEIGHT), &min, &max, &deflt, ¤t); return tg->height = current; } static Color longRangeItemColor(struct track *tg, void *item, struct hvGfx *hvg) /* Return color to draw a long range item */ { struct longRange *lr = item; if (lr->hasColor) { struct rgbColor itemRgb; + // There must be a better way... itemRgb.r = (lr->rgb & 0xff0000) >> 16; itemRgb.g = (lr->rgb & 0xff00) >> 8; itemRgb.b = lr->rgb & 0xff; return hvGfxFindColorIx(hvg, itemRgb.r, itemRgb.g, itemRgb.b); } return tg->ixColor; } static void longRangeDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Draw a list of longTabix structures. */ { double scale = scaleForWindow(width, seqStart, seqEnd); struct bed *beds = tg->items; unsigned int maxWidth; struct longRange *longRange; char buffer[1024]; char itemBuf[2048]; -char statusBuf[2048]; - safef(buffer, sizeof buffer, "%s.%s", tg->tdb->track, LONG_MINSCORE); double minScore = sqlDouble(cartUsualString(cart, buffer, LONG_DEFMINSCORE)); struct longRange *longRangeList = parseLongTabix(beds, &maxWidth, minScore); for(longRange=longRangeList; longRange; longRange=longRange->next) { safef(itemBuf, sizeof itemBuf, "%d", longRange->id); - safef(statusBuf, sizeof statusBuf, "%g %s:%d %s:%d", longRange->score, longRange->sChrom, longRange->s, longRange->eChrom, longRange->e); + struct dyString *ds = dyStringNew(0); + if (!longRange->hasColor) + dyStringPrintf(ds, "%g ", longRange->score); + dyStringPrintf(ds, "%s:%d %s:%d", longRange->sChrom, longRange->s, longRange->eChrom, longRange->e); + char *statusBuf = dyStringCannibalize(&ds); + color = longRangeItemColor(tg, longRange, hvg); - boolean sOnScreen = (longRange->s >= seqStart) && (longRange->s < seqEnd); - unsigned sx = 0, ex = 0; - if (sOnScreen) - sx = (longRange->s - seqStart) * scale + xOff; + int sx = ((longRange->s - seqStart) + .5) * scale + xOff; // x coord of center (lower region) + int sFootWidth = scale * (double)longRange->sw / 2; // width in pixels of half foot (lower) + int ex = ((longRange->e - seqStart) + .5) * scale + xOff; + int eFootWidth = scale * (double)longRange->ew / 2; if (differentString(longRange->sChrom, longRange->eChrom)) { - if (!sOnScreen) - continue; + // different chromosomes + // FIXME: Most of this code should be shared with same chrom display // draw the foot - int footWidth = scale * (longRange->sw / 2); + int footWidth = sFootWidth; hvGfxLine(hvg, sx - footWidth, yOff, sx + footWidth, yOff, color); int height = tg->height/2; if (tg->visibility == tvDense) height = tg->height; unsigned yPos = yOff + height; hvGfxLine(hvg, sx, yOff, sx, yPos, color); if (tg->visibility == tvFull) { mapBoxHgcOrHgGene(hvg, longRange->s, longRange->s, sx - 2, yOff, 4, tg->height/2, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); safef(buffer, sizeof buffer, "%s:%d", longRange->eChrom, longRange->e); hvGfxTextCentered(hvg, sx, yPos + 2, 4, 4, MG_BLUE, font, buffer); int width = vgGetFontStringWidth(hvg->vg, font, buffer); int height = vgGetFontPixelHeight(hvg->vg, font); mapBoxHgcOrHgGene(hvg, longRange->s, longRange->s, sx - width/2, yPos, width, height, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); } + continue; } - else - { + + // same chromosome + boolean sOnScreen = (longRange->s >= seqStart) && (longRange->s < seqEnd); boolean eOnScreen = (longRange->e >= seqStart) && (longRange->e < seqEnd); if (!(sOnScreen || eOnScreen)) continue; - if (eOnScreen) - ex = (longRange->e - seqStart) * scale + xOff; - double longRangeWidth = longRange->e - longRange->s; int peak = (tg->height - 15) * ((double)longRangeWidth / maxWidth) + yOff + 10; if (tg->visibility == tvDense) peak = yOff + tg->height; if (sOnScreen) { - int footWidth = scale * (longRange->sw / 2); - hvGfxLine(hvg, sx - footWidth, yOff, sx + footWidth, yOff, color); + // draw foot of 'lower' region + hvGfxLine(hvg, sx - sFootWidth, yOff, sx + sFootWidth, yOff, color); + + // draw vertical hvGfxLine(hvg, sx, yOff, sx, peak, color); } if (eOnScreen) { - int footWidth = scale * (longRange->ew / 2); - hvGfxLine(hvg, ex - footWidth, yOff, ex + footWidth, yOff, color); - hvGfxLine(hvg, ex, yOff, ex, peak, color); + // draw foot of 'upper' region + hvGfxLine(hvg, ex - eFootWidth, yOff, ex + eFootWidth, yOff, color); + + // draw vertical + hvGfxLine(hvg, ex, yOff, ex, peak, color); //OLD } if (tg->visibility == tvFull) { - unsigned sPeak = sOnScreen ? sx : xOff; + // draw link between regions (dense mode just shows feet ??) unsigned ePeak = eOnScreen ? ex : xOff + width; - + unsigned sPeak = sOnScreen ? sx : xOff; hvGfxLine(hvg, sPeak, peak, ePeak, peak, color); - safef(statusBuf, sizeof statusBuf, "%g %s:%d %s:%d", longRange->score, longRange->sChrom, longRange->s, longRange->eChrom, longRange->e); if (sOnScreen) mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, sx - 2, yOff, 4, peak - yOff, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); if (eOnScreen) mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, ex - 2, yOff, 4, peak - yOff, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, sPeak, peak-2, ePeak - sPeak, 4, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL); - - } } } } void longRangeDrawLeftLabels(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) { } void longRangeMethods(struct track *tg, struct trackDb *tdb) { tg->drawLeftLabels = longRangeDrawLeftLabels; tg->drawItems = longRangeDraw; tg->totalHeight = longRangeHeight; tg->mapsSelf = TRUE; }