0bdb46a5dcc479a127fa7eb33f24e2f600887414 angie Tue Jun 28 11:34:12 2011 -0700 safef sticklerism. diff --git src/hg/hgTracks/snakeTrack.c src/hg/hgTracks/snakeTrack.c index 81a7359..52e9f7e 100644 --- src/hg/hgTracks/snakeTrack.c +++ src/hg/hgTracks/snakeTrack.c @@ -1,1168 +1,1168 @@ /* snakeTrack - stuff to load and display snake type tracks in browser. */ /* uses standard chains from the database */ #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" struct snakeFeature { struct snakeFeature *next; int start, end; /* Start/end in browser coordinates. */ int qStart, qEnd; /* query start/end */ int level; /* level in packed snake */ int orientation; /* strand... -1 is '-', 1 is '+' */ boolean drawn; /* did we draw this feature? */ }; struct level { boolean init; /* has this level been initialized */ int orientation; /* strand.. see above */ int 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[1000000]; /* for packing the snake */ static int maxLevel = 0; /* deepest level */ /* blocks that make it through the min size filter */ static struct snakeFeature *newList = NULL; 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; } void clearLevels() /* clear out the data structure that we use to pack the snake */ { int ii; for(ii=0; ii < sizeof(Levels) / sizeof(Levels[0]); ii++) Levels[ii].init = FALSE; maxLevel = 0; } void calcSnake(struct snakeFeature *list, int level) // calculate the 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].orientation = list->orientation; if (list->orientation == -1) Levels[level].edge = 1000000000; // 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); calcSnake(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; calcSnake(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 cartOptions { enum chainColorEnum chainColor; /* ChromColors, ScoreColors, NoColors */ int scoreFilter ; /* filter chains by score if > 0 */ }; int snakeHeight(struct track *tg, enum trackVisibility vis) /* calculate height of all the snakes being displayed */ { int height = 0; 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 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) dyStringPrintf(query, "select chainId,tStart,tEnd,qStart from %sLink %s where ", fullName, force); else dyStringPrintf(query, "select chainId, tStart,tEnd,qStart from %sLink where chainId=%d and ", fullName, chainId); if (!isSplit) dyStringPrintf(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); } struct snakeInfo { int maxLevel; } snakeInfo; 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(); struct snakeFeature *sf; // this will destroy lf->components, and add to newList calcSnake((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; } } int packSnakeItemHeight(struct track *tg, void *item) // return height of a single packed snake { if (item == NULL) return 0; struct linkedFeatures *lf = (struct linkedFeatures *)item; if (lf->components == NULL) return 0; calcPackSnake(tg, item); struct snakeInfo *si = (struct snakeInfo *)lf->codons; int lineHeight = tg->lineHeight ; return (si->maxLevel + 1) * (2 * lineHeight); } int fullSnakeItemHeight(struct track *tg, void *item) // return height of full snake { struct linkedFeatures *lf = (struct linkedFeatures *)item; struct snakeFeature *sf; int s, e; int lineHeight = tg->lineHeight ; int oldOrient = 0; int tStart, tEnd; int size = 0; //int count = 0; tStart = 0; tEnd = 0; if (lf->components) size = lineHeight; for (sf = (struct snakeFeature *)lf->components; sf ; sf = sf->next) { int orient = sf->orientation; s = sf->start; e = sf->end; /* if ((e < winStart) || (s > winEnd)) continue; if (s < winStart) s = winStart; */ if (((oldOrient) && (oldOrient != orient)) || ((oldOrient == 1) && (tEnd) && (s < tEnd)) || ((oldOrient == -1) && (tStart) && (e > tStart))) { size += lineHeight; } oldOrient = orient; tEnd = e; tStart = s; } return size; } int snakeItemHeight(struct track *tg, void *item) { if (tg->visibility == tvFull) return fullSnakeItemHeight(tg, item); else if (tg->visibility == tvPack) return packSnakeItemHeight(tg, item); return 0; } 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; } 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); // 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); y += tg->itemHeight(tg, item); } } void snakeLeftLabels(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 packSnakeDrawAt(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. */ { struct linkedFeatures *lf = (struct linkedFeatures *)item; calcPackSnake(tg, item); int lastE = -1; int offY = y; struct snakeFeature *sf, *prevSf; int lineHeight = tg->lineHeight ; int tStart, tEnd, qStart; int qs, qe; int s, e; int heightPer = tg->heightPer; int lastX = -1,lastY = y; int lastQEnd = 0; int lastLevel = -1; qe = lastQEnd = 0; for (sf = (struct snakeFeature *)lf->components; sf != NULL; lastQEnd = qe, prevSf = sf, sf = sf->next) { qs = sf->qStart; qe = sf->qEnd; y = offY + (sf->level * 2) * lineHeight; s = sf->start; e = sf->end; tEnd = sf->end; int sx, ex; if (!positiveRangeIntersection(winStart, winEnd, s, e)) continue; sx = round((double)((int)s-winStart)*scale) + xOff; ex = round((double)((int)e-winStart)*scale) + xOff; // color by strand color = (sf->orientation == -1) ? MG_RED : MG_BLUE; 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 (sx < insideX) { int olap = insideX - sx; sx = insideX; w -= olap; } mapBoxHgcOrHgGene(hvg, s, e, sx+1, y, w-2, heightPer, tg->track, "blockAlign", buffer, NULL, TRUE, "boxAlignExtra=on"); hvGfxBox(hvg, sx, y, w, heightPer, color); sf->drawn = TRUE; tEnd = e; tStart = s; qStart = sf->qStart; lastY = y; lastLevel = sf->level; //lastX = x; } 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; #ifdef NOTNOW // insert in query if (sf->orientation == -1) { if ((lastE == e) && (qs != lastQEnd)) { printf("%d ",qs-lastQEnd); hvGfxLine(hvg, ex, y2, ex, y2 + lineHeight, MG_ORANGE); } } else { if ((lastE == s )) // && (qs != lastQEnd)) printf("%d ",qs-lastQEnd); if ((lastE == s ) && (qs != lastQEnd)) { printf("%d ",qs-lastQEnd); hvGfxLine(hvg, sx, y2, sx, y2 + lineHeight, MG_ORANGE); printf("%d %d |",lastE,s); } } #endif 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, "foo", buffer, NULL, TRUE, NULL); } } else { if (lastX != sx - 1) { hvGfxLine(hvg, lastX, y1, sx, y2, color); mapBoxHgcOrHgGene(hvg, s, e, lastX, y1, sx-lastX, 1, tg->track, "foo", 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, "foo", buffer, NULL, TRUE, NULL); } else { hvGfxLine(hvg, lastX-1, y1, sx, y2, color); hvGfxLine(hvg, sx, y2, sx, y2 + lineHeight , color); char buffer[1024]; safef(buffer, sizeof buffer, "%d-%d %dbp gap",prevSf->qStart,prevSf->qEnd, qs - lastQEnd); mapBoxHgcOrHgGene(hvg, s, e, sx-1, y2, 2, lineHeight , tg->track, "foo", buffer, NULL, TRUE, NULL); } } } tEnd = e; tStart = s; qStart = sf->qStart; if (sf->orientation == -1) lastX = sx; else lastX = ex; lastE = e; lastLevel = sf->level; lastQEnd = qe; } } void fullSnakeDrawAt(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. */ { struct linkedFeatures *lf = (struct linkedFeatures *)item; struct snakeFeature *sf, *prevSf; int s, e; int heightPer = tg->heightPer; int lineHeight = tg->lineHeight ; int oldOrient = 0; int tStart, tEnd, qStart; int lastQEnd = 0; int midY; int qs, qe; qStart = 0; tStart = xOff; tEnd = winEnd; prevSf = NULL; qe = lastQEnd = 0; for (sf = (struct snakeFeature *)lf->components; sf != NULL; lastQEnd = qe, prevSf = sf, sf = sf->next) { int orient = sf->orientation; midY = y + heightPer/2; qs = sf->qStart; s = sf->start; e = sf->end; /* if (qs < lastQEnd ) continue; */ qe = sf->qEnd; /* if ((e < winStart) || (s > winEnd)) continue; */ //if (s < winStart) s = winStart; if (((oldOrient) && (oldOrient != orient)) || ((oldOrient == 1) && (tEnd) && (s < tEnd)) || ((oldOrient == -1) && (tStart) && (e > tStart))) { if ((qStart) && (sf->qStart - qStart) < 500000) { if (oldOrient == 1) { if ((orient == -1) && (tEnd < sf->start)) { int x1, x2, x3, w; x1 = round((double)((int)tEnd-winStart)*scale) + xOff; x2 = round((double)((int)e-winStart)*scale) + xOff + 8; x3 = round((double)((int)sf->end-winStart)*scale) + xOff; w = x2-x1; hvGfxLine(hvg, x1, midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight + midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight+midY, x3, lineHeight+midY, color); clippedBarbs(hvg, x1, midY, w, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); clippedBarbs(hvg, x3, midY + lineHeight, x2-x3, tl.barbHeight, tl.barbSpacing, orient, color, FALSE); } else if ((orient == -1) && (tEnd > sf->start)) { int x1, x2, x3, w; x1 = round((double)((int)tEnd-winStart)*scale) + xOff; x2 = round((double)((int)tEnd-winStart)*scale) + xOff + 8; x3 = round((double)((int)sf->end-winStart)*scale) + xOff; w = x2-x1; hvGfxLine(hvg, x1, midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight + midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight+midY, x3, lineHeight+midY, color); clippedBarbs(hvg, x1, midY, w+1, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); clippedBarbs(hvg, x3, midY + lineHeight, x2-x3+1, tl.barbHeight, tl.barbSpacing, orient, color, FALSE); } else if ((orient == 1) && (s < tEnd)) { int x1, x2, x3,x4, w; x1 = round((double)((int)tEnd-winStart)*scale) + xOff; x2 = round((double)((int)tEnd-winStart)*scale) + xOff + 8; x3 = round((double)((int)s-winStart)*scale) + xOff - 8; x4 = round((double)((int)s-winStart)*scale) + xOff; w = x2-x1; hvGfxLine(hvg, x1, midY, x2, midY, color); hvGfxBox(hvg, x2, midY-2, 4, 4, color); hvGfxBox(hvg, x3 - 4, midY-2 + lineHeight, 4, 4, color); hvGfxLine(hvg, x3, lineHeight + midY, x4, lineHeight+midY, color); clippedBarbs(hvg, x1, midY, w+1, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); if (x3 > x4) printf("oops\n"); clippedBarbs(hvg, x3, midY + lineHeight, x4-x3+1, tl.barbHeight, tl.barbSpacing, orient , color, FALSE); } } else if (oldOrient == -1) { if ((orient == 1) && (tStart >= sf->start)) { int x1, x2, x3, w; x1 = round((double)((int)tStart-winStart)*scale) + xOff; x2 = round((double)((int)sf->start-winStart)*scale) + xOff - 8; x3 = round((double)((int)sf->start-winStart)*scale) + xOff; w = x1 - x2; hvGfxLine(hvg, x1, midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight + midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight+midY, x3, lineHeight+midY, color); clippedBarbs(hvg, x2, midY, w, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); clippedBarbs(hvg, x2, lineHeight+midY, x3-x2+1, tl.barbHeight, tl.barbSpacing, orient, color, FALSE); } else if ((orient == 1) && (tStart < sf->start)) { int x1, x2, x3, w; x1 = round((double)((int)tStart-winStart)*scale) + xOff; x2 = round((double)((int)tStart-winStart)*scale) + xOff - 8; x3 = round((double)((int)sf->start-winStart)*scale) + xOff; w = x1-x2; hvGfxLine(hvg, x1, midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight + midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight+midY, x3, lineHeight+midY, color); clippedBarbs(hvg, x2, midY, w, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); if (x3 < x2) printf("oops\n"); clippedBarbs(hvg, x2, midY + lineHeight, x3-x2, tl.barbHeight, tl.barbSpacing, orient, color, FALSE); } else if ((orient == -1) && (e > sf->start)) { int x1, x2, x3,x4, w; x1 = round((double)((int)tStart-winStart)*scale) + xOff; x2 = round((double)((int)tStart-winStart)*scale) + xOff - 8; x3 = round((double)((int)e-winStart)*scale) + xOff + 8; x4 = round((double)((int)e-winStart)*scale) + xOff; w = x1-x2; hvGfxLine(hvg, x1, midY, x2, midY, color); hvGfxBox(hvg, x2, midY-2, 4, 4, color); hvGfxLine(hvg, x3, lineHeight + midY, x4, lineHeight+midY, color); hvGfxBox(hvg, x3, lineHeight + midY-2, 4, 4, color); clippedBarbs(hvg, x2, midY, w+1, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); if (x4 > x3) printf("oops\n"); clippedBarbs(hvg, x4, midY + lineHeight, x3-x4+1, tl.barbHeight, tl.barbSpacing, oldOrient , color, FALSE); } } } y += lineHeight; } else if ((oldOrient) && ((qStart) && (sf->qStart - qStart) < 500000)) { int x1, x2, w; x1 = round((double)((int)tEnd-winStart)*scale) + xOff; x2 = round((double)((int)sf->start -winStart)*scale) + xOff; hvGfxLine(hvg, x1, midY, x2, midY, color); if (x2 > x1) { w = x2-x1; clippedBarbs(hvg, x1, midY, w+1, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); } else { w = x1-x2; clippedBarbs(hvg, x2, midY, w+1, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); } } color = lfChromColor(tg, item, hvg); color = (sf->orientation == -1) ? MG_RED : MG_BLUE; drawScaledBoxSample(hvg, s, e, scale, xOff, y, heightPer, color, lf->score ); tEnd = e; tStart = s; qStart = sf->qStart; oldOrient = orient; } } 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. */ { if (tg->visibility == tvFull) fullSnakeDrawAt(tg, item, hvg, xOff, y, scale, font, color, vis); else if (tg->visibility == tvPack) packSnakeDrawAt(tg, item, hvg, xOff, y, scale, font, color, vis); } void fixItems(struct linkedFeatures *lf) // put all 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->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) { 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; -snprintf( optionChr, sizeof(optionChr), "%s.chromFilter", tg->table); +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; if (startsWith("chr",optionChrStr)) { - snprintf(extraWhere, sizeof(extraWhere), + 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) { - snprintf(extraWhere, sizeof(extraWhere), + safef(extraWhere, sizeof(extraWhere), "score > \"%d\"",chainCart->scoreFilter); sr = hRangeQuery(conn, track, chromName, ourStart, ourEnd, extraWhere, &rowOffset); } else { - snprintf(extraWhere, sizeof(extraWhere), " "); + 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]; - snprintf(buffer, sizeof(buffer), "%s", chain.qName); + 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() */ 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; } 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 */ - snprintf(option, sizeof(option), "%s.color", tg->table); + 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 = TRUE; 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; }