void loadGappedBed(struct track *tg) /* Convert bed info in window to linked feature. */ { struct sqlResult *sr; char **row; int rowOffset; struct bed *bed; struct linkedFeatures *lfList = NULL, *lf; struct trackDb *tdb = tg->tdb; int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0")); int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000")); boolean useItemRgb = FALSE; useItemRgb = bedItemRgb(tdb); if (tg->isBigBed) { // avoid opening an unneeded db connection for bigBed; required not to use mysql for parallel fetch tracks bigBedAddLinkedFeaturesFrom(tg, chromName, winStart, winEnd, scoreMin, scoreMax, useItemRgb, 12, &lfList); } else { /* Use tg->tdb->track because subtracks inherit composite track's tdb * by default, and the variable is named after the composite track. */ struct sqlConnection *conn = hAllocConn(database); char *scoreFilterClause = getScoreFilterClause(cart, tg->tdb,NULL); if (scoreFilterClause != NULL) { sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd,scoreFilterClause, &rowOffset); freeMem(scoreFilterClause); } else { sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); } while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoad12(row+rowOffset); adjustBedScoreGrayLevel(tdb, bed, scoreMin, scoreMax); lf = lfFromBedExtra(bed, scoreMin, scoreMax); if (useItemRgb) { lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ lf->filterColor=bed->itemRgb; } slAddHead(&lfList, lf); bedFree(&bed); } sqlFreeResult(&sr); hFreeConn(&conn); } slReverse(&lfList); if(tg->extraUiData) filterBed(tg, &lfList); slSort(&lfList, linkedFeaturesCmp); tg->items = lfList; }
struct linkedFeatures *bedMungToLinkedFeatures(struct bed **pBed, struct trackDb *tdb, int fieldCount, int scoreMin, int scoreMax, boolean useItemRgb) /* Convert bed to a linkedFeature, destroying bed in the process. */ { struct bed *bed = *pBed; if (fieldCount < 12) bed8To12(bed); adjustBedScoreGrayLevel(tdb, bed, scoreMin, scoreMax); struct linkedFeatures *lf = lfFromBedExtra(bed, scoreMin, scoreMax); if (useItemRgb) { lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ lf->filterColor=bed->itemRgb; } bedFree(pBed); return lf; }
static struct linkedFeatures *lfFromEncodePeak(struct slList *item, struct trackDb *tdb, int scoreMin, int scoreMax) /* Translate an {encode,narrow,broad,gapped}Peak item into a linkedFeatures. */ { struct encodePeak *peak = (struct encodePeak *)item; struct linkedFeatures *lf; struct simpleFeature *sfList = NULL; if (!peak) return NULL; AllocVar(lf); lf->start = peak->chromStart; lf->end = peak->chromEnd; if (peak->peak > -1) { lf->tallStart = peak->chromStart + peak->peak; lf->tallEnd = lf->tallStart + 1; } lf->filterColor = -1; lf->orientation = orientFromChar(peak->strand[0]); adjustBedScoreGrayLevel(tdb, (struct bed *)peak, scoreMin, scoreMax); lf->grayIx = grayInRange((int)peak->score, scoreMin, scoreMax); lf->name = cloneString(peak->name); if (peak->blockCount > 0) { int i; for (i = 0; i < peak->blockCount; i++) { struct simpleFeature *sf; AllocVar(sf); sf->start = lf->start + peak->blockStarts[i]; sf->end = lf->start + peak->blockStarts[i] + peak->blockSizes[i]; sf->grayIx = lf->grayIx; slAddHead(&sfList, sf); } slReverse(&sfList); } else { AllocVar(sfList); sfList->start = lf->start; sfList->end = lf->end; sfList->grayIx = lf->grayIx; } lf->components = sfList; return lf; }
void bedDrawSimpleAt(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 bed *bed = item; int heightPer = tg->heightPer; int s = max(bed->chromStart, winStart), e = min(bed->chromEnd, winEnd); if (s > e) return; int x1 = round((s-winStart)*scale) + xOff; int x2 = round((e-winStart)*scale) + xOff; int w = x2 - x1; if (w < 1) w = 1; struct trackDb *tdb = tg->tdb; int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0")); int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000")); char *directUrl = trackDbSetting(tdb, "directUrl"); boolean withHgsid = (trackDbSetting(tdb, "hgsid") != NULL); boolean thickDrawItem = (trackDbSetting(tdb, "thickDrawItem") != NULL); if (tg->itemColor != NULL) { color = tg->itemColor(tg, bed, hvg); } else if (tg->colorShades) { adjustBedScoreGrayLevel(tdb, bed, scoreMin, scoreMax); color = tg->colorShades[grayInRange(bed->score, scoreMin, scoreMax)]; } /* Keep the item at least 4 pixels wide at all viewpoints */ if (thickDrawItem && (w < 4)) { x1 -= ((5-w) >> 1); w = 4; x2 = x1 + w; }