629bb6f183fd2102cec5fdb484aa8d3270fb4f6d braney Thu Oct 3 11:25:05 2013 -0700 add chromosome color mode to snakes that uses a hash of the chrom to geta color ffrom a fixed palette. Also make pack mode a little more dense diff --git src/hg/hgTracks/snakeTrack.c src/hg/hgTracks/snakeTrack.c index 7ad3cee..22ab830 100644 --- src/hg/hgTracks/snakeTrack.c +++ src/hg/hgTracks/snakeTrack.c @@ -425,31 +425,35 @@ { if ((item == NULL) || (tg->visibility == tvSquish) || (tg->visibility == tvDense)) return 0; struct linkedFeatures *lf = (struct linkedFeatures *)item; if (lf->components == NULL) return 0; if (tg->visibility == tvFull) calcFullSnake(tg, item); else if (tg->visibility == tvPack) calcPackSnake(tg, item); struct snakeInfo *si = (struct snakeInfo *)lf->codons; int lineHeight = tg->lineHeight ; -return (si->maxLevel + 1) * (2 * lineHeight); +int multiplier = 1; + +if (tg->visibility == tvFull) + multiplier = 2; +return (si->maxLevel + 1) * (multiplier * lineHeight); } static int linkedFeaturesCmpScore(const void *va, const void *vb) /* Help sort linkedFeatures by score */ { const struct linkedFeatures *a = *((struct linkedFeatures **)va); const struct linkedFeatures *b = *((struct linkedFeatures **)vb); if (a->score > b->score) return -1; else if (a->score < b->score) return 1; return 0; } static int snakeHeight(struct track *tg, enum trackVisibility vis) @@ -513,40 +517,48 @@ } y = yOff; for (item = tg->items; item != NULL; item = item->next) { if(tg->itemColor != NULL) color = tg->itemColor(tg, item, hvg); tg->drawItemAt(tg, item, hvg, xOff, y, scale, font, color, vis); if (vis == tvFull) y += tg->itemHeight(tg, item); } } // this is a 16 color palette with every other color being a lighter version of // the color before it -//static int snakePalette[] = -//{ -//0x1f77b4, 0xaec7e8, 0xff7f0e, 0xffbb78, 0x2ca02c, 0x98df8a, 0xd62728, 0xff9896, 0x9467bd, 0xc5b0d5, 0x8c564b, 0xc49c94, 0xe377c2, 0xf7b6d2, 0x7f7f7f, 0xc7c7c7, 0xbcbd22, 0xdbdb8d, 0x17becf, 0x9edae5 -//}; +static int snakePalette2[] = +{ +0x1f77b4, 0xaec7e8, 0xff7f0e, 0xffbb78, 0x2ca02c, 0x98df8a, 0xd62728, 0xff9896, 0x9467bd, 0xc5b0d5, 0x8c564b, 0xc49c94, 0xe377c2, 0xf7b6d2, 0x7f7f7f, 0xc7c7c7, 0xbcbd22, 0xdbdb8d, 0x17becf, 0x9edae5 +}; static int snakePalette[] = { 0x1f77b4, 0xff7f0e, 0x2ca02c, 0xd62728, 0x9467bd, 0x8c564b, 0xe377c2, 0x7f7f7f, 0xbcbd22, 0x17becf }; +static Color hashColor(char *name) +{ +bits32 hashVal = hashString(name); +unsigned int colorInt = snakePalette2[hashVal % (sizeof(snakePalette2)/sizeof(Color))]; + +return MAKECOLOR_32(((colorInt >> 16) & 0xff),((colorInt >> 8) & 0xff),((colorInt >> 0) & 0xff)); +} + static void snakeDrawAt(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. */ { unsigned showSnpWidth = cartOrTdbInt(cart, tg->tdb, SNAKE_SHOW_SNP_WIDTH, SNAKE_DEFAULT_SHOW_SNP_WIDTH); struct linkedFeatures *lf = (struct linkedFeatures *)item; if (tg->visibility == tvFull) calcFullSnake(tg, item); else if (tg->visibility == tvPack) calcPackSnake(tg, item); @@ -649,70 +661,76 @@ int lineHeight = tg->lineHeight ; int tStart, tEnd, qStart; int qs, qe; int heightPer = tg->heightPer; int lastX = -1,lastY = y; int lastQEnd = 0; int lastLevel = -1; int e; qe = lastQEnd = 0; for (sf = (struct snakeFeature *)lf->components; sf != NULL; lastQEnd = qe, prevSf = sf, sf = sf->next) { qs = sf->qStart; qe = sf->qEnd; if (vis == tvDense) y = offY; - else + else if ((vis == tvPack) || (vis == tvSquish)) + y = offY + (sf->level * 1) * lineHeight; + else if (vis == tvFull) y = offY + (sf->level * 2) * lineHeight; s = sf->start; e = sf->end; tEnd = sf->end; int osx; int sx, ex; if (!positiveRangeIntersection(winStart, winEnd, s, e)) continue; osx = sx = round((double)((int)s-winStart)*scale) + xOff; ex = round((double)((int)e-winStart)*scale) + xOff; // color by strand static Color darkBlueColor = 0; static Color darkRedColor = 0; if (darkRedColor == 0) { //the light blue: rgb(149, 204, 252) //the light red: rgb(232, 156, 156) darkRedColor = hvGfxFindColorIx(hvg, 232,156,156); darkBlueColor = hvGfxFindColorIx(hvg, 149,204,252); } char *colorBy = cartOrTdbString(cart, tg->tdb, SNAKE_COLOR_BY, SNAKE_DEFAULT_COLOR_BY); extern Color getChromColor(char *name, struct hvGfx *hvg); if (sameString(colorBy, SNAKE_COLOR_BY_STRAND_VALUE)) color = (sf->orientation == -1) ? darkRedColor : darkBlueColor; else if (sameString(colorBy, SNAKE_COLOR_BY_CHROM_VALUE)) - color = getChromColor(lf->name, hvg); + color = hashColor(sf->qName); else color = darkBlueColor; int w = ex - sx; if (w == 0) w = 1; assert(w > 0); char buffer[1024]; - safef(buffer, sizeof buffer, "%d %d",sf->qStart,sf->qEnd); + + if (vis == tvFull) + safef(buffer, sizeof buffer, "%d-%d",sf->qStart,sf->qEnd); + else + safef(buffer, sizeof buffer, "%s:%d-%d",sf->qName,sf->qStart,sf->qEnd); if (sx < insideX) { int olap = insideX - sx; sx = insideX; w -= olap; } char qAddress[4096]; if ((vis == tvFull) || (vis == tvPack) ) { safef(qAddress, sizeof qAddress, "qName=%s&qs=%d&qe=%d&qWidth=%d",sf->qName, qs, qe, winEnd - winStart); mapBoxHgcOrHgGene(hvg, s, e, sx+1, y, w-2, heightPer, tg->track, buffer, buffer, NULL, TRUE, qAddress); } hvGfxBox(hvg, sx, y, w, heightPer, color); @@ -975,58 +993,57 @@ for(;targetDupeBlocks; targetDupeBlocks = targetDupeBlocks->next) { printf("<br>id: %d qChrom %s\n", targetDupeBlocks->id, targetDupeBlocks->qChrom); struct hal_target_range_t *range = targetDupeBlocks->tRange; for(; range; range = range->next) { printf("<br> %ld : %ld\n", range->tStart, range->size); } } #endif while (cur) { struct hashEl* hel; - //safef(buffer, sizeof buffer, "%s.%c", cur->qChrom,cur->strand); if (tg->visibility == tvFull) safef(buffer, sizeof buffer, "%s", cur->qChrom); else { // make sure the block is on the screen if (!positiveRangeIntersection(winStart, winEnd, cur->tStart, cur->tStart + cur->size)) { cur = cur->next; continue; } safef(buffer, sizeof buffer, "allInOne"); } if ((hel = hashLookup(qChromHash, buffer)) == NULL) { AllocVar(lf); lf->isHalSnake = TRUE; slAddHead(&lfList, lf); lf->start = 0; lf->end = 1000000000; lf->grayIx = maxShade; lf->name = cloneString(buffer); lf->extra = cloneString(buffer); lf->orientation = (cur->strand == '+') ? 1 : -1; hashAdd(qChromHash, lf->name, lf); - // now figure out where the blue bars go + // now figure out where the duplication bars go struct hal_target_dupe_list_t* targetDupeBlocks = head->targetDupeBlocks; if ((tg->visibility == tvPack) || (tg->visibility == tvFull)) for(;targetDupeBlocks; targetDupeBlocks = targetDupeBlocks->next) { if ((tg->visibility == tvPack) || ((tg->visibility == tvFull) && (sameString(targetDupeBlocks->qChrom, cur->qChrom)))) { struct hal_target_dupe_list_t* dupeList; AllocVar(dupeList); *dupeList = *targetDupeBlocks; slAddHead(&lf->dupeList, dupeList); // TODO: should clone the target_range structures // rather than copying them