5a3cd681e0bebecf7acff2888b4aee6f2b5a0904 braney Fri Nov 8 11:08:32 2013 -0800 fix bug when the sequence is null from HAL snakes diff --git src/hg/hgTracks/snakeTrack.c src/hg/hgTracks/snakeTrack.c index ed7ac8d..452790e 100644 --- src/hg/hgTracks/snakeTrack.c +++ src/hg/hgTracks/snakeTrack.c @@ -1,1530 +1,1532 @@ #ifdef USE_HAL /* snakeTrack - stuff to load and display snake type tracks in browser. */ #include "common.h" #include "hash.h" #include "localmem.h" #include "linefile.h" #include "jksql.h" #include "hdb.h" #include "hgTracks.h" #include "chainBlock.h" #include "chainLink.h" #include "chainDb.h" #include "chainCart.h" #include "errCatch.h" #include "twoBit.h" #include "bigWarn.h" #include <pthread.h> #include "trackHub.h" #include "limits.h" #include "snakeUi.h" #include "halBlockViz.h" // this is the number of pixels used by the target self-align bar #define DUP_LINE_HEIGHT 4 struct snakeFeature { struct snakeFeature *next; int start, end; /* Start/end in browser coordinates. */ int qStart, qEnd; /* query start/end */ int level; /* level in snake */ int orientation; /* strand... -1 is '-', 1 is '+' */ boolean drawn; /* did we draw this feature? */ char *qSequence; /* may have sequence, or NULL */ char *tSequence; /* may have sequence, or NULL */ char *qName; /* chrom name on other species */ }; static int snakeFeatureCmpTStart(const void *va, const void *vb) /* sort by start position on the target sequence */ { const struct snakeFeature *a = *((struct snakeFeature **)va); const struct snakeFeature *b = *((struct snakeFeature **)vb); int diff = a->start - b->start; return diff; } static int snakeFeatureCmpQStart(const void *va, const void *vb) /* sort by start position on the query sequence */ { const struct snakeFeature *a = *((struct snakeFeature **)va); const struct snakeFeature *b = *((struct snakeFeature **)vb); int diff = a->qStart - b->qStart; if (diff == 0) { diff = a->start - b->start; } return diff; } // static machinery to calculate full and pack snake struct level { boolean init; /* has this level been initialized */ int orientation; /* strand.. see above */ unsigned long edge; /* the leading edge of this level */ int adjustLevel; /* used to compress out the unused levels */ boolean hasBlock; /* are there any blocks in this level */ }; static struct level Levels[10000]; /* for packing the snake, not re-entrant! */ static int maxLevel = 0; /* deepest level */ /* blocks that make it through the min size filter */ static struct snakeFeature *newList = NULL; static void clearLevels() /* clear out the data structure that we use to calculate full snakes */ { int ii; for(ii=0; ii < sizeof(Levels) / sizeof(Levels[0]); ii++) Levels[ii].init = FALSE; maxLevel = 0; } static void calcFullSnakeHelper(struct snakeFeature *list, int level) // calculate a full snake // updates global newList with unsorted blocks that pass the min // size filter. { struct snakeFeature *cb = list; struct snakeFeature *proposedList = NULL; if (level > maxLevel) maxLevel = level; if (level > ArraySize(Levels)) errAbort("too many levels"); if (Levels[level].init == FALSE) { // initialize the level if this is the first time we've seen it Levels[level].init = TRUE; Levels[level].orientation = list->orientation; if (list->orientation == -1) Levels[level].edge = LONG_MAX; // bigger than the biggest chrom else Levels[level].edge = 0; } // now we step through the blocks and assign them to levels struct snakeFeature *next; struct snakeFeature *insertHead = NULL; for(; cb; cb = next) { // we're going to add this block to a different list // so keep track of the next pointer next = cb->next; // if this block can't fit on this level add to the insert // list and move on to the next block if ((Levels[level].orientation != cb->orientation) || ((cb->orientation == 1) && (Levels[level].edge > cb->start)) || ((cb->orientation == -1) && (Levels[level].edge < cb->end))) { // add this to the list of an insert slAddHead(&insertHead, cb); continue; } // the current block will fit on this level // go ahead and deal with the blocks that wouldn't if (insertHead) { // we had an insert, go ahead and calculate where that goes slReverse(&insertHead); calcFullSnakeHelper(insertHead, level + 1); insertHead = NULL; } // assign the current block to this level cb->level = level; if (cb->orientation == 1) Levels[level].edge = cb->end; else Levels[level].edge = cb->start; // add this block to the list of proposed blocks for this level slAddHead(&proposedList, cb); } // we're at the end of the list. Deal with any blocks // that didn't fit on this level if (insertHead) { slReverse(&insertHead); int nextLevel = level + 1; calcFullSnakeHelper(insertHead, nextLevel); insertHead = NULL; } // do we have any proposed blocks if (proposedList == NULL) return; // we parsed all the blocks in the list to see if they fit in our level // now let's see if the list of blocks for this level is big enough // to actually add struct snakeFeature *temp; double scale = scaleForWindow(insideWidth, winStart, winEnd); int start, end; // order the blocks so lowest start position is first if (Levels[level].orientation == 1) slReverse(&proposedList); start=proposedList->start; for(temp=proposedList; temp->next; temp = temp->next) ; end=temp->end; // calculate how big the string of blocks is in screen coordinates double apparentSize = scale * (end - start); if (apparentSize < 0) errAbort("size of a list of blocks should not be less than zero"); // check to see if the apparent size is big enough if (apparentSize < 1) return; // transfer proposedList to new block list for(temp=proposedList; temp; temp = next) { next = temp->next; temp->next = NULL; slAddHead(&newList, temp); } } struct snakeInfo { int maxLevel; } snakeInfo; static void calcFullSnake(struct track *tg, void *item) { struct linkedFeatures *lf = (struct linkedFeatures *)item; if (lf->components == NULL) return; // we use the codons field to keep track of whether we already // calculated the height of this snake if (lf->codons == NULL) { clearLevels(); struct snakeFeature *sf; // this will destroy lf->components, and add to newList calcFullSnakeHelper((struct snakeFeature *)lf->components, 0); lf->components = (struct simpleFeature *)newList; newList = NULL; slSort(&lf->components, snakeFeatureCmpQStart); // now we're going to compress the levels that aren't used // to do that, we need to see which blocks are on the screen, // or connected to something on the screen int oldMax = maxLevel; clearLevels(); struct snakeFeature *prev = NULL; for(sf=(struct snakeFeature *)lf->components; sf; prev = sf, sf = sf->next) { if (Levels[sf->level].init == FALSE) { Levels[sf->level].init = TRUE; Levels[sf->level].orientation = sf->orientation; Levels[sf->level].hasBlock = FALSE; } else { if (Levels[sf->level].orientation != sf->orientation) errAbort("found snakeFeature with wrong orientation"); if ((sf->orientation == 1) && (Levels[sf->level].edge > sf->start)) errAbort("found snakeFeature that violates edge"); if ((sf->orientation == -1) && (Levels[sf->level].edge < sf->end)) errAbort("found snakeFeature that violates edge"); } if (sf->orientation == 1) Levels[sf->level].edge = sf->end; else Levels[sf->level].edge = sf->start; if (sf->level > maxLevel) maxLevel = sf->level; if(positiveRangeIntersection(winStart, winEnd, sf->start, sf->end)) { Levels[sf->level].hasBlock = TRUE; if (sf->next != NULL) Levels[sf->next->level].hasBlock = TRUE; if (prev != NULL) Levels[prev->level].hasBlock = TRUE; } } // now figure out how to remap the blocks int ii; int count = 0; for(ii=0; ii < oldMax + 1; ii++) { Levels[ii].adjustLevel = count; if ((Levels[ii].init) && (Levels[ii].hasBlock)) count++; } maxLevel = count - 1; // remap blocks for(sf=(struct snakeFeature *)lf->components; sf; sf = sf->next) sf->level = Levels[sf->level].adjustLevel; struct snakeInfo *si; AllocVar(si); si->maxLevel = maxLevel; lf->codons = (struct simpleFeature *)si; } } static void calcPackSnakeHelper(struct snakeFeature *list, int level) // calculate a packed snake // updates global newList with unsorted blocks that pass the min // size filter. { struct snakeFeature *cb = list; struct snakeFeature *proposedList = NULL; if (level > maxLevel) maxLevel = level; if (level > ArraySize(Levels)) errAbort("too many levels"); if (Levels[level].init == FALSE) { // initialize the level if this is the first time we've seen it Levels[level].init = TRUE; Levels[level].edge = 0; } // now we step through the blocks and assign them to levels struct snakeFeature *next; struct snakeFeature *insertHead = NULL; for(; cb; cb = next) { // we're going to add this block to a different list // so keep track of the next pointer next = cb->next; // if this block can't fit on this level add to the insert // list and move on to the next block if ( Levels[level].edge > cb->start) { // add this to the list of an insert slAddHead(&insertHead, cb); continue; } // the current block will fit on this level // go ahead and deal with the blocks that wouldn't if (insertHead) { // we had an insert, go ahead and calculate where that goes slReverse(&insertHead); calcPackSnakeHelper(insertHead, level + 1); insertHead = NULL; } // assign the current block to this level cb->level = level; Levels[level].edge = cb->end; // add this block to the list of proposed blocks for this level slAddHead(&proposedList, cb); } // we're at the end of the list. Deal with any blocks // that didn't fit on this level if (insertHead) { slReverse(&insertHead); calcPackSnakeHelper(insertHead, level + 1); insertHead = NULL; } // do we have any proposed blocks if (proposedList == NULL) return; // we parsed all the blocks in the list to see if they fit in our level // now let's see if the list of blocks for this level is big enough // to actually add struct snakeFeature *temp; double scale = scaleForWindow(insideWidth, winStart, winEnd); int start, end; // order the blocks so lowest start position is first slReverse(&proposedList); start=proposedList->start; for(temp=proposedList; temp->next; temp = temp->next) ; end=temp->end; // calculate how big the string of blocks is in screen coordinates double apparentSize = scale * (end - start); if (apparentSize < 0) errAbort("size of a list of blocks should not be less than zero"); // check to see if the apparent size is big enough if (apparentSize < 1) return; // transfer proposedList to new block list for(temp=proposedList; temp; temp = next) { next = temp->next; temp->next = NULL; slAddHead(&newList, temp); } } static void calcPackSnake(struct track *tg, void *item) { struct linkedFeatures *lf = (struct linkedFeatures *)item; if (lf->components == NULL) return; // we use the codons field to keep track of whether we already // calculated the height of this snake if (lf->codons == NULL) { clearLevels(); // this will destroy lf->components, and add to newList calcPackSnakeHelper((struct snakeFeature *)lf->components, 0); lf->components = (struct simpleFeature *)newList; newList = NULL; //slSort(&lf->components, snakeFeatureCmpQStart); struct snakeInfo *si; AllocVar(si); si->maxLevel = maxLevel; lf->codons = (struct simpleFeature *)si; } } static int snakeItemHeight(struct track *tg, void *item) // return height of a single packed snake { 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 ; 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) /* calculate height of all the snakes being displayed */ { if (tg->networkErrMsg != NULL) { // we had a parallel load failure tg->drawItems = bigDrawWarning; tg->totalHeight = bigWarnTotalHeight; return bigWarnTotalHeight(tg, vis); } if (vis == tvDense) return tg->lineHeight; if (vis == tvSquish) return tg->lineHeight/2; int height = DUP_LINE_HEIGHT; struct slList *item = tg->items; item = tg->items; for (item=tg->items;item; item = item->next) { height += tg->itemHeight(tg, item); } return height; } static void snakeDraw(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. */ { struct slList *item; int y; struct linkedFeatures *lf; double scale = scaleForWindow(width, seqStart, seqEnd); int height = snakeHeight(tg, vis); hvGfxSetClip(hvg, xOff, yOff, width, height); if ((tg->visibility == tvFull) || (tg->visibility == tvPack)) { // score snakes by how many bases they cover for (item = tg->items; item != NULL; item = item->next) { lf = (struct linkedFeatures *)item; struct snakeFeature *sf; lf->score = 0; for (sf = (struct snakeFeature *)lf->components; sf != NULL; sf = sf->next) { lf->score += sf->end - sf->start; } } slSort(&tg->items, linkedFeaturesCmpScore); } 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 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); if (lf->components == NULL) return; boolean isHalSnake = lf->isHalSnake; struct snakeFeature *sf = (struct snakeFeature *)lf->components, *prevSf = NULL; int s = tg->itemStart(tg, item); int sClp = (s < winStart) ? winStart : s; int x1 = round((sClp - winStart)*scale) + xOff; int textX = x1; int yOff = y; boolean withLabels = (withLeftLabels && (vis == tvFull) && !tg->drawName); unsigned labelColor = MG_BLACK; // draw the labels if (withLabels) { char *name = tg->itemName(tg, item); int nameWidth = mgFontStringWidth(font, name); int dotWidth = tl.nWidth/2; boolean snapLeft = FALSE; boolean drawNameInverted = FALSE; textX -= nameWidth + dotWidth; snapLeft = (textX < insideX); /* Special tweak for expRatio in pack mode: force all labels * left to prevent only a subset from being placed right: */ snapLeft |= (startsWith("expRatio", tg->tdb->type)); #ifdef IMAGEv2_NO_LEFTLABEL_ON_FULL if (theImgBox == NULL && snapLeft) #else///ifndef IMAGEv2_NO_LEFTLABEL_ON_FULL if (snapLeft) /* Snap label to the left. */ #endif ///ndef IMAGEv2_NO_LEFTLABEL_ON_FULL { textX = leftLabelX; assert(hvgSide != NULL); hvGfxUnclip(hvgSide); hvGfxSetClip(hvgSide, leftLabelX, yOff, insideWidth, tg->height); if(drawNameInverted) { int boxStart = leftLabelX + leftLabelWidth - 2 - nameWidth; hvGfxBox(hvgSide, boxStart, y, nameWidth+1, tg->heightPer - 1, color); hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, tg->heightPer, MG_WHITE, font, name); } else hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, tg->heightPer, labelColor, font, name); hvGfxUnclip(hvgSide); hvGfxSetClip(hvgSide, insideX, yOff, insideWidth, tg->height); } else { if(drawNameInverted) { hvGfxBox(hvg, textX - 1, y, nameWidth+1, tg->heightPer-1, color); hvGfxTextRight(hvg, textX, y, nameWidth, tg->heightPer, MG_WHITE, font, name); } else hvGfxTextRight(hvg, textX, y, nameWidth, tg->heightPer, labelColor, font, name); } } // let's draw some blue bars for the duplications struct hal_target_dupe_list_t* dupeList = lf->dupeList; int count = 0; if ((tg->visibility == tvFull) || (tg->visibility == tvPack)) { for(; dupeList ; dupeList = dupeList->next, count++) { struct hal_target_range_t *range = dupeList->tRange; unsigned int colorInt = snakePalette[count % (sizeof(snakePalette)/sizeof(Color))]; Color color = MAKECOLOR_32(((colorInt >> 16) & 0xff),((colorInt >> 8) & 0xff),((colorInt >> 0) & 0xff)); for(; range; range = range->next) { int s = range->tStart; int e = range->tStart + range->size; int sClp = (s < winStart) ? winStart : s; int eClp = (e > winEnd) ? winEnd : e; int x1 = round((sClp - winStart)*scale) + xOff; int x2 = round((eClp - winStart)*scale) + xOff; hvGfxBox(hvg, x1, y , x2-x1, DUP_LINE_HEIGHT - 1 , color); } } y+=DUP_LINE_HEIGHT; } // now we're going to draw the boxes s = sf->start; int lastE = -1; int lastS = -1; int offY = y; 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 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 = hashColor(sf->qName); else color = darkBlueColor; int w = ex - sx; if (w == 0) w = 1; assert(w > 0); char buffer[1024]; 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); // now draw the mismatches if we're at high enough resolution if ((winBaseCount < showSnpWidth) && ((vis == tvFull) || (vis == tvPack))) { char *twoBitString = trackDbSetting(tg->tdb, "twoBit"); static struct twoBitFile *tbf = NULL; static char *lastTwoBitString = NULL; static struct dnaSeq *seq = NULL; static char *lastQName = NULL; // sequence for chain snakes is in 2bit files which we cache if (!isHalSnake) { if (twoBitString == NULL) twoBitString = "/gbdb/hg19/hg19.2bit"; if ((lastTwoBitString == NULL) || differentString(lastTwoBitString, twoBitString)) { if (tbf != NULL) { lastQName = NULL; twoBitClose(&tbf); } tbf = twoBitOpen(twoBitString); } // we're reading in the whole chrom if ((lastQName == NULL) || differentString(sf->qName, lastQName)) seq = twoBitReadSeqFrag(tbf, sf->qName, 0, 0); lastQName = sf->qName; lastTwoBitString = twoBitString; } char *ourDna; if (isHalSnake) ourDna = sf->qSequence; else ourDna = &seq->dna[sf->qStart]; int seqLen = sf->qEnd - sf->qStart; toUpperN(ourDna, seqLen); if (!isHalSnake && (sf->orientation == -1)) reverseComplement(ourDna,seqLen); // get the reference sequence char *refDna; if (isHalSnake) { refDna = sf->tSequence; } else { struct dnaSeq *extraSeq = hDnaFromSeq(database, chromName, sf->start, sf->end, dnaUpper); refDna = extraSeq->dna; } int si = s; char *ptr1 = refDna; char *ptr2 = ourDna; for(; si < e; si++,ptr1++,ptr2++) { if (*ptr1 != *ptr2) { int misX1 = round((double)((int)si-winStart)*scale) + xOff; int misX2 = round((double)((int)(si+1)-winStart)*scale) + xOff; int w1 = misX2 - misX1; if (w1 < 1) w1 = 1; // mismatch! hvGfxBox(hvg, misX1, y, w1, heightPer, MG_RED); } } // if we're zoomed to base level, draw sequence of mismatch if (zoomedToBaseLevel) { int mysx = round((double)((int)s-winStart)*scale) + xOff; int myex = round((double)((int)e-winStart)*scale) + xOff; int myw = myex - mysx; spreadAlignString(hvg, mysx, y, myw, heightPer, MG_WHITE, font, ourDna, refDna, seqLen, TRUE, FALSE); } } sf->drawn = TRUE; tEnd = e; tStart = s; qStart = sf->qStart; lastY = y; lastLevel = sf->level; //lastX = x; } if (vis != tvFull) return; // now we're going to draw the lines between the blocks lastX = -1,lastY = y; lastQEnd = 0; lastLevel = 0; qe = lastQEnd = 0; prevSf = NULL; for (sf = (struct snakeFeature *)lf->components; sf != NULL; lastQEnd = qe, prevSf = sf, sf = sf->next) { int y1, y2; int sx, ex; qs = sf->qStart; qe = sf->qEnd; if (lastLevel == sf->level) { y1 = offY + (lastLevel * 2) * lineHeight + lineHeight/2; y2 = offY + (sf->level * 2) * lineHeight + lineHeight/2; } else if (lastLevel > sf->level) { y1 = offY + (lastLevel * 2 ) * lineHeight; y2 = offY + (sf->level * 2 + 1) * lineHeight + lineHeight/3; } else { y1 = offY + (lastLevel * 2 + 1) * lineHeight - 1; y2 = offY + (sf->level * 2 ) * lineHeight - lineHeight/3;; } s = sf->start; e = sf->end; sx = round((double)((int)s-winStart)*scale) + xOff; ex = round((double)((int)e-winStart)*scale) + xOff; color = (sf->orientation == -1) ? MG_RED : MG_BLUE; if (lastX != -1) { char buffer[1024]; #define MG_ORANGE 0xff0082E6 int color = MG_GRAY; if (lastQEnd != qs) color = MG_ORANGE; // draw the vertical orange bars if there is an insert in the other sequence if ((winBaseCount < showSnpWidth) ) { if ((sf->orientation == 1) && (qs != lastQEnd) && (lastE == s)) { hvGfxLine(hvg, sx, y2 - lineHeight/2 , sx, y2 + lineHeight/2, MG_ORANGE); safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); mapBoxHgcOrHgGene(hvg, s, e, sx, y2 - lineHeight/2, 1, lineHeight, tg->track, "foo", buffer, NULL, TRUE, NULL); } else if ((sf->orientation == -1) && (qs != lastQEnd) && (lastS == e)) { hvGfxLine(hvg, ex, y2 - lineHeight/2 , ex, y2 + lineHeight/2, MG_ORANGE); safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); mapBoxHgcOrHgGene(hvg, s, e, ex, y2 - lineHeight/2, 1, lineHeight, tg->track, "foo", buffer, NULL, TRUE, NULL); } } // now draw the lines between blocks if ((!((lastX == sx) && (y1 == y2))) && (sf->drawn || ((prevSf != NULL) && (prevSf->drawn))) && (((lastE > winStart) && (lastE < winEnd)) || ((s > winStart) && (s < winEnd)))) { if (lastLevel == sf->level) { safef(buffer, sizeof buffer, "%dbp", qs - lastQEnd); if (sf->orientation == -1) { if (lastX != ex) { hvGfxLine(hvg, ex, y1, lastX, y2, color); mapBoxHgcOrHgGene(hvg, s, e, ex, y1, lastX-ex, 1, tg->track, "", buffer, NULL, TRUE, NULL); } } else { if (lastX != sx) { hvGfxLine(hvg, lastX, y1, sx, y2, color); mapBoxHgcOrHgGene(hvg, s, e, lastX, y1, sx-lastX, 1, tg->track, "", buffer, NULL, TRUE, NULL); } } } else if (lastLevel > sf->level) { hvGfxLine(hvg, lastX, y1, sx, y2, color); hvGfxLine(hvg, sx, y2, sx, y2 - lineHeight - lineHeight/3, color); char buffer[1024]; safef(buffer, sizeof buffer, "%d-%d %dbp gap",prevSf->qStart,prevSf->qEnd, qs - lastQEnd); mapBoxHgcOrHgGene(hvg, s, e, sx, y2 - lineHeight - lineHeight/3, 2, lineHeight + lineHeight/3, tg->track, "", buffer, NULL, TRUE, NULL); } else { char buffer[1024]; safef(buffer, sizeof buffer, "%d-%d %dbp gap",prevSf->qStart,prevSf->qEnd, qs - lastQEnd); if (sf->orientation == -1) { hvGfxLine(hvg, lastX-1, y1, ex, y2, color); hvGfxLine(hvg, ex, y2, ex, y2 + lineHeight , color); mapBoxHgcOrHgGene(hvg, s, e, ex-1, y2, 2, lineHeight , tg->track, "", buffer, NULL, TRUE, NULL); } else { hvGfxLine(hvg, lastX-1, y1, sx, y2, color); hvGfxLine(hvg, sx, y2, sx, y2 + lineHeight , color); mapBoxHgcOrHgGene(hvg, s, e, sx-1, y2, 2, lineHeight , tg->track, "", buffer, NULL, TRUE, NULL); } } } } tEnd = e; tStart = s; qStart = sf->qStart; if (sf->orientation == -1) lastX = sx; else lastX = ex; lastS = s; lastE = e; lastLevel = sf->level; lastQEnd = qe; } } void halSnakeLoadItems(struct track *tg) // load up a snake from a HAL file. This code is called in threads // so *no* use of globals please. All but full snakes are read into a single // linked feature. { unsigned showSnpWidth = cartOrTdbInt(cart, tg->tdb, SNAKE_SHOW_SNP_WIDTH, SNAKE_DEFAULT_SHOW_SNP_WIDTH); // if we have a network error we want to put out a message about it struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { char *fileName = trackDbSetting(tg->tdb, "bigDataUrl"); char *otherSpecies = trackDbSetting(tg->tdb, "otherSpecies"); int handle = halOpenLOD(fileName); boolean isPackOrFull = (tg->visibility == tvFull) || (tg->visibility == tvPack); hal_dup_type_t dupMode = (isPackOrFull) ? HAL_QUERY_AND_TARGET_DUPS : HAL_QUERY_DUPS; int needSeq = isPackOrFull && (winBaseCount < showSnpWidth) ? 1 : 0; int mapBackAdjacencies = (tg->visibility == tvFull); struct hal_block_results_t *head = halGetBlocksInTargetRange(handle, otherSpecies, trackHubSkipHubName(database), chromName, winStart, winEnd, 0, needSeq, dupMode,mapBackAdjacencies); // did we get any blocks from HAL if (head == NULL) { errCatchEnd(errCatch); return; } struct hal_block_t* cur = head->mappedBlocks; struct linkedFeatures *lf = NULL; struct hash *qChromHash = newHash(5); struct linkedFeatures *lfList = NULL; char buffer[4096]; #ifdef NOTNOW struct hal_target_dupe_list_t* targetDupeBlocks = head->targetDupeBlocks; 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; 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 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 } } } else { lf = hel->val; } struct snakeFeature *sf; AllocVar(sf); slAddHead(&lf->components, sf); sf->start = cur->tStart; sf->end = cur->tStart + cur->size; sf->qStart = cur->qStart; sf->qEnd = cur->qStart + cur->size; sf->orientation = (cur->strand == '+') ? 1 : -1; sf->tSequence = cloneString(cur->tSequence); sf->qSequence = cloneString(cur->qSequence); + if (sf->tSequence != NULL) toUpperN(sf->tSequence, strlen(sf->tSequence)); + if (sf->qSequence != NULL) toUpperN(sf->qSequence, strlen(sf->qSequence)); sf->qName = cur->qChrom; cur = cur->next; } if (tg->visibility == tvFull) { for(lf=lfList; lf ; lf = lf->next) { slSort(&lf->components, snakeFeatureCmpQStart); } } else if ((tg->visibility == tvPack) && (lfList != NULL)) { assert(lfList->next == NULL); slSort(&lfList->components, snakeFeatureCmpTStart); } //halFreeBlocks(head); //halClose(handle, myThread); tg->items = lfList; } errCatchEnd(errCatch); if (errCatch->gotError) { tg->networkErrMsg = cloneString(errCatch->message->string); tg->drawItems = bigDrawWarning; tg->totalHeight = bigWarnTotalHeight; } errCatchFree(&errCatch); } void halSnakeDrawLeftLabels(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 halSnakeMethods(struct track *tg, struct trackDb *tdb, int wordCount, char *words[]) { linkedFeaturesMethods(tg); tg->canPack = tdb->canPack = TRUE; tg->loadItems = halSnakeLoadItems; tg->drawItems = snakeDraw; tg->mapItemName = lfMapNameFromExtra; tg->subType = lfSubChain; //tg->extraUiData = (void *) chainCart; tg->totalHeight = snakeHeight; tg->drawLeftLabels = halSnakeDrawLeftLabels; tg->drawItemAt = snakeDrawAt; tg->itemHeight = snakeItemHeight; } #endif // USE_HAL #ifdef NOTNOW // from here down are routines to support the visualization of chains as snakes // this code is currently BROKEN, and may be removed completely in the future struct cartOptions { enum chainColorEnum chainColor; /* ChromColors, ScoreColors, NoColors */ int scoreFilter ; /* filter chains by score if > 0 */ }; // mySQL code to read in chains static void doQuery(struct sqlConnection *conn, char *fullName, struct lm *lm, struct hash *hash, int start, int end, boolean isSplit, int chainId) /* doQuery- check the database for chain elements between * start and end. Use the passed hash to resolve chain * id's and place the elements into the right * linkedFeatures structure */ { struct sqlResult *sr = NULL; char **row; struct linkedFeatures *lf; struct snakeFeature *sf; struct dyString *query = newDyString(1024); char *force = ""; if (isSplit) force = "force index (bin)"; if (chainId == -1) sqlDyStringPrintf(query, "select chainId,tStart,tEnd,qStart from %sLink %-s where ", fullName, force); else sqlDyStringPrintf(query, "select chainId, tStart,tEnd,qStart from %sLink where chainId=%d and ", fullName, chainId); if (!isSplit) sqlDyStringPrintf(query, "tName='%s' and ", chromName); hAddBinToQuery(start, end, query); dyStringPrintf(query, "tStart<%u and tEnd>%u", end, start); sr = sqlGetResult(conn, query->string); /* Loop through making up simple features and adding them * to the corresponding linkedFeature. */ while ((row = sqlNextRow(sr)) != NULL) { lf = hashFindVal(hash, row[0]); if (lf != NULL) { struct chain *pChain = lf->extra; lmAllocVar(lm, sf); sf->start = sqlUnsigned(row[1]); sf->end = sqlUnsigned(row[2]); sf->qStart = sqlUnsigned(row[3]); sf->qEnd = sf->qStart + (sf->end - sf->start); if ((pChain) && pChain->qStrand == '-') { int temp; temp = sf->qStart; sf->qStart = pChain->qSize - sf->qEnd; sf->qEnd = pChain->qSize - temp; } sf->orientation = lf->orientation; slAddHead(&lf->components, sf); } } sqlFreeResult(&sr); dyStringFree(&query); } static void fixItems(struct linkedFeatures *lf) // put all chain blocks from a single query chromosome into one // linkedFeatures structure { struct linkedFeatures *firstLf, *next; struct snakeFeature *sf, *nextSf; firstLf = lf; for (;lf; lf = next) { next = lf->next; if (!sameString(firstLf->name, lf->name) && (lf->components != NULL)) { slSort(&firstLf->components, snakeFeatureCmpQStart); firstLf = lf; } for (sf = (struct snakeFeature *)lf->components; sf != NULL; sf = nextSf) { sf->qName = lf->name; sf->orientation = lf->orientation; nextSf = sf->next; if (firstLf != lf) { lf->components = NULL; slAddHead(&firstLf->components, sf); } } } if (firstLf != NULL) { slSort(&firstLf->components, snakeFeatureCmpQStart); firstLf->next = 0; } } static void loadLinks(struct track *tg, int seqStart, int seqEnd, enum trackVisibility vis) // load up the chain elements into linkedFeatures { int start, end, extra; char fullName[64]; int maxOverLeft = 0, maxOverRight = 0; int overLeft, overRight; struct linkedFeatures *lf; struct lm *lm; struct hash *hash; /* Hash of chain ids. */ struct sqlConnection *conn; lm = lmInit(1024*4); hash = newHash(0); conn = hAllocConn(database); /* Make up a hash of all linked features keyed by * id, which is held in the extras field. */ for (lf = tg->items; lf != NULL; lf = lf->next) { char buf[256]; struct chain *pChain = lf->extra; safef(buf, sizeof(buf), "%d", pChain->id); hashAdd(hash, buf, lf); overRight = lf->end - seqEnd; if (overRight > maxOverRight) maxOverRight = overRight; overLeft = seqStart - lf->start ; if (overLeft > maxOverLeft) maxOverLeft = overLeft; } if (hash->size) { boolean isSplit = TRUE; /* Make up range query. */ safef(fullName, sizeof fullName, "%s_%s", chromName, tg->table); if (!hTableExists(database, fullName)) { strcpy(fullName, tg->table); isSplit = FALSE; } /* in dense mode we don't draw the lines * so we don't need items off the screen */ if (vis == tvDense) doQuery(conn, fullName, lm, hash, seqStart, seqEnd, isSplit, -1); else { /* if chains extend beyond edge of window we need to get * elements that are off the screen * in both directions so we know whether to draw * one or two lines to the edge of the screen. */ #define STARTSLOP 0 #define MULTIPLIER 10 #define MAXLOOK 100000 extra = (STARTSLOP < maxOverLeft) ? STARTSLOP : maxOverLeft; start = seqStart - extra; extra = (STARTSLOP < maxOverRight) ? STARTSLOP : maxOverRight; end = seqEnd + extra; doQuery(conn, fullName, lm, hash, start, end, isSplit, -1); } } hFreeConn(&conn); } void snakeLoadItems(struct track *tg) // Load chains from a mySQL database { char *track = tg->table; struct chain chain; int rowOffset; char **row; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; struct linkedFeatures *list = NULL, *lf; int qs; char optionChr[128]; /* Option - chromosome filter */ char *optionChrStr; char extraWhere[128] ; struct cartOptions *chainCart; struct chain *pChain; chainCart = (struct cartOptions *) tg->extraUiData; safef( optionChr, sizeof(optionChr), "%s.chromFilter", tg->table); optionChrStr = cartUsualString(cart, optionChr, "All"); int ourStart = winStart; int ourEnd = winEnd; // we're grabbing everything now.. we really should be // doing this as a preprocessing stage, rather than at run-time ourStart = 0; ourEnd = 500000000; //ourStart = winStart; //ourEnd = winEnd; if (startsWith("chr",optionChrStr)) { safef(extraWhere, sizeof(extraWhere), "qName = \"%s\" and score > %d",optionChrStr, chainCart->scoreFilter); sr = hRangeQuery(conn, track, chromName, ourStart, ourEnd, extraWhere, &rowOffset); } else { if (chainCart->scoreFilter > 0) { safef(extraWhere, sizeof(extraWhere), "score > \"%d\"",chainCart->scoreFilter); sr = hRangeQuery(conn, track, chromName, ourStart, ourEnd, extraWhere, &rowOffset); } else { safef(extraWhere, sizeof(extraWhere), " "); sr = hRangeQuery(conn, track, chromName, ourStart, ourEnd, NULL, &rowOffset); } } while ((row = sqlNextRow(sr)) != NULL) { chainHeadStaticLoad(row + rowOffset, &chain); AllocVar(pChain); *pChain = chain; AllocVar(lf); lf->start = lf->tallStart = chain.tStart; lf->end = lf->tallEnd = chain.tEnd; lf->grayIx = maxShade; if (chainCart->chainColor == chainColorScoreColors) { float normScore = sqlFloat((row+rowOffset)[11]); lf->grayIx = (int) ((float)maxShade * (normScore/100.0)); if (lf->grayIx > (maxShade+1)) lf->grayIx = maxShade+1; lf->score = normScore; } else lf->score = chain.score; lf->filterColor = -1; if (chain.qStrand == '-') { lf->orientation = -1; qs = chain.qSize - chain.qEnd; } else { lf->orientation = 1; qs = chain.qStart; } char buffer[1024]; safef(buffer, sizeof(buffer), "%s", chain.qName); lf->name = cloneString(buffer); lf->extra = pChain; slAddHead(&list, lf); } /* Make sure this is sorted if in full mode. Sort by score when * coloring by score and in dense */ if (tg->visibility != tvDense) slSort(&list, linkedFeaturesCmpStart); else if ((tg->visibility == tvDense) && (chainCart->chainColor == chainColorScoreColors)) slSort(&list, chainCmpScore); else slReverse(&list); tg->items = list; /* Clean up. */ sqlFreeResult(&sr); hFreeConn(&conn); /* now load the items */ loadLinks(tg, ourStart, ourEnd, tg->visibility); lf=tg->items; fixItems(lf); } /* chainLoadItems() */ void snakeMethods(struct track *tg, struct trackDb *tdb, int wordCount, char *words[]) /* Fill in custom parts of alignment chains. */ { struct cartOptions *chainCart; AllocVar(chainCart); boolean normScoreAvailable = chainDbNormScoreAvailable(tdb); /* what does the cart say about coloring option */ chainCart->chainColor = chainFetchColorOption(cart, tdb, FALSE); chainCart->scoreFilter = cartUsualIntClosestToHome(cart, tdb, FALSE, SCORE_FILTER, 0); linkedFeaturesMethods(tg); tg->itemColor = lfChromColor; /* default coloring option */ /* if normScore column is available, then allow coloring */ if (normScoreAvailable) { switch (chainCart->chainColor) { case (chainColorScoreColors): tg->itemColor = chainScoreColor; tg->colorShades = shadesOfGray; break; case (chainColorNoColors): setNoColor(tg); break; default: case (chainColorChromColors): break; } } else { char option[128]; /* Option - rainbow chromosome color */ char *optionStr; /* this old option was broken before */ safef(option, sizeof(option), "%s.color", tg->table); optionStr = cartUsualString(cart, option, "on"); if (differentWord("on",optionStr)) { setNoColor(tg); chainCart->chainColor = chainColorNoColors; } else chainCart->chainColor = chainColorChromColors; } tg->canPack = FALSE; tg->loadItems = snakeLoadItems; tg->drawItems = snakeDraw; tg->mapItemName = lfMapNameFromExtra; tg->subType = lfSubChain; tg->extraUiData = (void *) chainCart; tg->totalHeight = snakeHeight; tg->drawItemAt = snakeDrawAt; tg->itemHeight = snakeItemHeight; } static Color chainScoreColor(struct track *tg, void *item, struct hvGfx *hvg) { struct linkedFeatures *lf = (struct linkedFeatures *)item; return(tg->colorShades[lf->grayIx]); } static Color chainNoColor(struct track *tg, void *item, struct hvGfx *hvg) { return(tg->ixColor); } static void setNoColor(struct track *tg) { tg->itemColor = chainNoColor; tg->color.r = 0; tg->color.g = 0; tg->color.b = 0; tg->altColor.r = 127; tg->altColor.g = 127; tg->altColor.b = 127; tg->ixColor = MG_BLACK; tg->ixAltColor = MG_GRAY; } #endif