e35e2a3124664586de5f18b8950be23cc5dc170b braney Thu Feb 10 15:45:10 2011 -0800 works now. diff --git src/hg/hgTracks/snakeTrack.c src/hg/hgTracks/snakeTrack.c index de97348..d4cfc82 100644 --- src/hg/hgTracks/snakeTrack.c +++ src/hg/hgTracks/snakeTrack.c @@ -1,917 +1,918 @@ /* chainTrack - stuff to load and display chain type tracks in * browser. Chains are typically from cross-species genomic * alignments. */ #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" static char const rcsid[] = "$Id: chainTrack.c,v 1.27 2006/02/23 01:41:31 baertsch Exp $"; struct cartOptions { enum chainColorEnum chainColor; /* ChromColors, ScoreColors, NoColors */ int scoreFilter ; /* filter chains by score if > 0 */ }; 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 simpleFeature *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. */ //printf("read chain\n"); 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; } //printf("%d \n",sf->qStart); sf->grayIx = lf->orientation; slAddHead(&lf->components, sf); } } sqlFreeResult(&sr); dyStringFree(&query); } int snakeItemHeight(struct track *tg, void *item) { //printf("snakeItemHeight\n"); //return 40; struct linkedFeatures *lf = (struct linkedFeatures *)item; struct simpleFeature *sf; int s, e; int lineHeight = tg->lineHeight ; int oldOrient = 0; int tStart, tEnd; int size = lineHeight; //int count = 0; tStart = 0; tEnd = 0; for (sf = lf->components; sf ; sf = sf->next) { int orient = sf->grayIx; s = sf->start; e = sf->end; /* if ((e < winStart) || (s > winEnd)) continue; if (s < winStart) s = winStart; */ //printf("bounds %d %d\n",winStart, winEnd); if (((oldOrient) && (oldOrient != orient)) || ((oldOrient == 1) && (tEnd) && (s < tEnd)) || ((oldOrient == -1) && (tStart) && (e > tStart))) { //printf("plus \n"); size += lineHeight; } oldOrient = orient; tEnd = e; tStart = s; } //printf("snakeItemHieght %d\n",size); return size; } static int linkedFeaturesCmpScore(const void *va, const void *vb) /* Help sort linkedFeatures by starting pos. */ { 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 *lfStart = (struct linkedFeatures *)tg->items; struct linkedFeatures *lf; //int lineHeight = tg->lineHeight; double scale = scaleForWindow(width, seqStart, seqEnd); //printf("snakeDraw "); for(lf = lfStart; lf; lf = lf->next) { struct simpleFeature *sf; lf->score = 0; for (sf = 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); // break; } } 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 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. */ { //printf("snakeDrawAt %d %d %g \n",xOff, y, scale); //return; struct linkedFeatures *lf = (struct linkedFeatures *)item; struct simpleFeature *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; //int prevStart; //int count = 0; qStart = 0; tStart = xOff; tEnd = winEnd; prevSf = NULL; //printf("snakeDrawAt\n"); //prevStart = 0; //for (sf = lf->components; sf != NULL; prevStart = sf->qStart,prevSf = sf, sf = sf->next) //printf("%d \n",sf->qStart - prevStart); qe = lastQEnd = 0; for (sf = lf->components; sf != NULL; lastQEnd = qe, prevSf = sf, sf = sf->next) { int orient = sf->grayIx; 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; //printf("bounds %d %d\n",winStart, winEnd); if (((oldOrient) && (oldOrient != orient)) || ((oldOrient == 1) && (tEnd) && (s < tEnd)) || ((oldOrient == -1) && (tStart) && (e > tStart))) { //printf("one\n"); if ((qStart) && (sf->qStart - qStart) < 500000) { //printf("three\n"); if (oldOrient == 1) { //printf("four\n"); if ((orient == -1) && (tEnd < sf->start)) { int x1, x2, x3, w; //printf("five\n"); 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, y, x2, y, color); + //hvGfxLine(hvg, x1, y, x2, y, color); hvGfxLine(hvg, x1, midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight + midY, x2, midY, color); hvGfxLine(hvg, x2, lineHeight+midY, x3, lineHeight+midY, color); //innerLine(vg, x2, midY, 1, 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; //printf("siz\n"); 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); //innerLine(vg, x2, midY, 1, 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; //printf("seven\n"); 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); //hvGfxLine(vg, x2, lineHeight + midY, x2, midY, color); //hvGfxLine(vg, x2, lineHeight + midY, x3, lineHeight+midY, color); //hvGfxLine(vg, x3, lineHeight + midY, x3, 2*lineHeight+midY, color); //hvGfxLine(vg, x2, midY, x3, lineHeight+midY, color); //hvGfxLine(vg, x3, 2*lineHeight + midY, x4, 2*lineHeight+midY, color); hvGfxBox(hvg, x3 - 4, midY-2 + lineHeight, 4, 4, color); hvGfxLine(hvg, x3, lineHeight + midY, x4, lineHeight+midY, color); //y += lineHeight; //innerLine(vg, x2, midY, 1, color); clippedBarbs(hvg, x1, midY, w+1, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); //clippedBarbs(vg, x3, midY + lineHeight, x2-x3+1, tl.barbHeight, tl.barbSpacing, //-1 , color, FALSE); if (x3 > x4) printf("oops\n"); clippedBarbs(hvg, x3, midY + lineHeight, x4-x3+1, tl.barbHeight, tl.barbSpacing, orient , color, FALSE); //clippedBarbs(vg, x3, midY + 2* 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; //printf("gook\n"); 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); //innerLine(vg, x2, midY, 1, 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; //printf("grook\n"); 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); //innerLine(vg, x2, midY, 1, 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; //printf("tStart %d e %d sf %d %d\n",tStart,e,sf->start,sf->end); //printf("loop\n"); 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(vg, x2, lineHeight + midY, x2, midY, color); //hvGfxLine(vg, x2, lineHeight + midY, x3, lineHeight+midY, color); //hvGfxLine(vg, x3, lineHeight + midY, x3, 2*lineHeight+midY, color); hvGfxLine(hvg, x3, lineHeight + midY, x4, lineHeight+midY, color); hvGfxBox(hvg, x3, lineHeight + midY-2, 4, 4, color); //y += lineHeight; //innerLine(vg, x2, midY, 1, color); clippedBarbs(hvg, x2, midY, w+1, tl.barbHeight, tl.barbSpacing, oldOrient, color, FALSE); //clippedBarbs(vg, x2, midY + lineHeight, x3-x2+1, tl.barbHeight, tl.barbSpacing, //1 , color, FALSE); if (x4 > x3) printf("oops\n"); clippedBarbs(hvg, x4, midY + lineHeight, x3-x4+1, tl.barbHeight, tl.barbSpacing, oldOrient , color, FALSE); } } else printf("eat me\n"); } //else //printf("sf %d qStart %d \n",sf->qStart,qStart); y += lineHeight; } else if ((oldOrient) && ((qStart) && (sf->qStart - qStart) < 500000)) { //printf("two\n"); 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); } } //printf("sf %d %d\n",s - tStart,e -tStart); //printf("sfq %d %d\n",sf->qStart, sf->qEnd); //if(tg->itemColor != NULL) color = lfChromColor(tg, item, hvg); drawScaledBoxSample(hvg, s, e, scale, xOff, y, heightPer, color, lf->score ); tEnd = e; tStart = s; qStart = sf->qStart; oldOrient = orient; //if (++count == 5) //break; } //linkedFeaturesDrawAt(tg, item, vg, xOff, y, scale, font, color, vis); } static int simpleFeatureCmpQStart(const void *va, const void *vb) { const struct simpleFeature *a = *((struct simpleFeature **)va); const struct simpleFeature *b = *((struct simpleFeature **)vb); int diff = a->qStart - b->qStart; if (diff == 0) { diff = a->start - b->start; } return diff; } static int linkedFeaturesCmpChrom(const void *va, const void *vb) /* Help sort linkedFeatures by starting pos. */ { const struct linkedFeatures *a = *((struct linkedFeatures **)va); const struct linkedFeatures *b = *((struct linkedFeatures **)vb); return strcmp(a->name, b->name); } int snakeHeight(struct track *tg, enum trackVisibility vis) /* set up size of sequence logo */ { //printf("snakeHeight\n"); //return 50; int height = 0; struct slList *item = tg->items, *nextItem; struct linkedFeatures *firstLf, *lf = (struct linkedFeatures *)tg->items; struct simpleFeature *sf, *nextSf; //tg->drawItems = snakeDraw; slSort(&tg->items, linkedFeaturesCmpChrom); item = tg->items; lf = (struct linkedFeatures *)tg->items; //item = NULL; if (item) { firstLf = lf; //printf("orient %d %c |\n",lf->orientation,lf->orientation); for (;item; item = nextItem) { struct linkedFeatures *lf = (struct linkedFeatures *)item; // slAddTail(&firstSf, lf->components); nextItem = item->next; //printf("orient %d %c |\n",lf->orientation,lf->orientation); if (!sameString(firstLf->name, lf->name)) { //printf("name %s %s\n",firstLf->name, lf->name); slSort(&firstLf->components, simpleFeatureCmpQStart); firstLf = lf; } for (sf = lf->components; sf != NULL; sf = nextSf) { sf->grayIx = lf->orientation; nextSf = sf->next; if (firstLf != lf) { lf->components = NULL; slAddHead(&firstLf->components, sf); } } height += tg->itemHeight(tg, item); } slSort(&firstLf->components, simpleFeatureCmpQStart); /* for (item=tg->items;item; item = item->next) { struct linkedFeatures *lf = (struct linkedFeatures *)item; int lastQ = 0; printf("begin\n"); slSort(&lf->components, simpleFeatureCmpQStart); for (sf = lf->components; sf != NULL; sf = sf->next) { if (sf == lf->components) printf("%d ",sf->qStart); else printf("%d ",sf->qStart - lastQ) ; lastQ = sf->qStart; } printf("end\n"); } */ } return 1800; } static void chainDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Draw chained features. This loads up the simple features from * the chainLink table, calls linkedFeaturesDraw, and then * frees the simple features again. */ { struct linkedFeatures *lf; struct simpleFeature *sf; struct lm *lm; struct hash *hash; /* Hash of chain ids. */ struct sqlConnection *conn; //double scale = ((double)(winEnd - winStart))/width; char fullName[64]; int start, end, extra; struct simpleFeature *lastSf = NULL; int maxOverLeft = 0, maxOverRight = 0; int overLeft, overRight; if (tg->items == NULL) /*Exit Early if nothing to do */ return; 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. To * avoid burning memory on full chromosome views * we'll just make a single simple feature and * exclude from hash chains less than three pixels wide, * since these would always appear solid. */ for (lf = tg->items; lf != NULL; lf = lf->next) { //double pixelWidth = (lf->end - lf->start) / scale; if (1)//pixelWidth >= 2.5) { char buf[256]; struct chain *pChain = lf->extra; safef(buf, sizeof(buf), "%d", pChain->id); //hashAdd(hash, lf->extra, lf); hashAdd(hash, buf, lf); overRight = lf->end - seqEnd; if (overRight > maxOverRight) maxOverRight = overRight; overLeft = seqStart - lf->start ; if (overLeft > maxOverLeft) maxOverLeft = overLeft; } else { lmAllocVar(lm, sf); sf->start = lf->start; sf->end = lf->end; sf->grayIx = lf->grayIx; lf->components = sf; } } /* if some chains are bigger than 3 pixels */ if (hash->size) { boolean isSplit = TRUE; /* Make up range query. */ sprintf(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 10000 #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); for (lf = tg->items; lf != NULL; lf = lf->next) { struct chain *pChain = lf->extra; int chainId = pChain->id; if (lf->components == NULL) continue; slSort(&lf->components, linkedFeaturesCmpStart); extra = (STARTSLOP < maxOverRight)?STARTSLOP:maxOverRight; end = seqEnd + extra; lastSf = NULL; while (lf->end > end ) { for(lastSf=sf=lf->components;sf;lastSf=sf,sf=sf->next) ; /* get out if we have an element off right side */ if (( (lastSf != NULL) &&(lastSf->end > seqEnd)) || (extra > MAXLOOK)) break; extra *= MULTIPLIER; start = end; end = start + extra; doQuery(conn, fullName, lm, hash, start, end, isSplit, chainId); slSort(&lf->components, linkedFeaturesCmpStart); } /* if we didn't find an element off to the right , add one */ if ((lf->end > seqEnd) && ((lastSf == NULL) ||(lastSf->end < seqEnd))) { lmAllocVar(lm, sf); sf->start = seqEnd; sf->end = seqEnd+1; sf->grayIx = lf->grayIx; sf->qStart = 0; sf->qEnd = sf->qStart + (sf->end - sf->start); sf->next = lf->components; lf->components = sf; slSort(&lf->components, linkedFeaturesCmpStart); } /* we know we have a least one component off right * now look for one off left */ extra = (STARTSLOP < maxOverLeft) ? STARTSLOP:maxOverLeft; start = seqStart - extra; while((extra < MAXLOOK) && (lf->start < seqStart) && (lf->components->start > seqStart)) { extra *= MULTIPLIER; end = start; start = end - extra; if (start < 0) start = 0; doQuery(conn, fullName, lm, hash, start, end, isSplit, chainId); slSort(&lf->components, linkedFeaturesCmpStart); } if ((lf->components->start > seqStart) && (lf->start < lf->components->start)) { lmAllocVar(lm, sf); sf->start = 0; sf->end = 1; sf->grayIx = lf->grayIx; sf->qStart = lf->components->qStart; sf->qEnd = sf->qStart + (sf->end - sf->start); sf->next = lf->components; lf->components = sf; slSort(&lf->components, linkedFeaturesCmpStart); } } } } if (1) { snakeHeight(tg, vis); snakeDraw(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); } else { linkedFeaturesDraw(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis); } /* Cleanup time. */ for (lf = tg->items; lf != NULL; lf = lf->next) lf->components = NULL; lmCleanup(&lm); freeHash(&hash); hFreeConn(&conn); } void snakeLoadItems(struct track *tg) /* Load up all of the chains from correct table into tg->items * item list. At this stage to conserve memory for other tracks * we don't load the links into the components list until draw time. */ { 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); optionChrStr = cartUsualString(cart, optionChr, "All"); if (startsWith("chr",optionChrStr)) { snprintf(extraWhere, sizeof(extraWhere), "qName = \"%s\" and score > %d",optionChrStr, chainCart->scoreFilter); sr = hRangeQuery(conn, track, chromName, winStart, winEnd, extraWhere, &rowOffset); } else { if (chainCart->scoreFilter > 0) { snprintf(extraWhere, sizeof(extraWhere), "score > \"%d\"",chainCart->scoreFilter); sr = hRangeQuery(conn, track, chromName, winStart, winEnd, extraWhere, &rowOffset); } else { snprintf(extraWhere, sizeof(extraWhere), " "); sr = hRangeQuery(conn, track, chromName, winStart, winEnd, NULL, &rowOffset); } } while ((row = sqlNextRow(sr)) != NULL) { //char buf[16]; 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 %c %dk", - chain.qName, chain.qStrand, qs/1000); + snprintf(buffer, sizeof(buffer), "%s", chain.qName); + //snprintf(buffer, sizeof(buffer), "%s %c %dk", + //chain.qName, chain.qStrand, qs/1000); lf->name = cloneString(buffer); //snprintf(lf->name, sizeof(lf->name), "%s %c %dk", // chain.qName, chain.qStrand, qs/1000); //snprintf(lf->name, sizeof(lf->name), "%s", // chain.qName); //snprintf(lf->popUp, sizeof(lf->name), "%s %c start %d size %d", // chain.qName, chain.qStrand, qs, chain.qEnd - chain.qStart); //snprintf(buf, sizeof(buf), "%d", chain.id); //lf->extra = cloneString(buf); lf->extra = pChain; //printf("setting extra to %llu\n",(long long) 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); } /* 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. */ { //boolean normScoreAvailable = FALSE; struct cartOptions *chainCart; //char scoreOption[256]; AllocVar(chainCart); boolean normScoreAvailable = chainDbNormScoreAvailable(tdb); //normScoreAvailable = chainDbNormScoreAvailable(chromName, tg->table, NULL); /* what does the cart say about coloring option */ chainCart->chainColor = chainFetchColorOption(cart, tdb, FALSE); //snprintf( scoreOption, sizeof(scoreOption), "%s.scoreFilter", tdb->tableName); chainCart->scoreFilter = cartUsualIntClosestToHome(cart, tdb, FALSE, SCORE_FILTER, 0); //chainCart->scoreFilter = cartUsualInt(cart, scoreOption, 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); optionStr = cartUsualString(cart, option, "on"); if (differentWord("on",optionStr)) { setNoColor(tg); chainCart->chainColor = chainColorNoColors; } else chainCart->chainColor = chainColorChromColors; } tg->loadItems = snakeLoadItems; tg->drawItems = chainDraw; tg->mapItemName = lfMapNameFromExtra; tg->subType = lfSubChain; tg->extraUiData = (void *) chainCart; // tg->drawItems = snakeDraw; tg->drawItemAt = snakeDrawAt; tg->totalHeight = snakeHeight; tg->itemHeight = snakeItemHeight; }