0440cfd6ef79932ae3d3d1934d9665b2848e8952 kate Mon Oct 7 14:54:50 2019 -0700 Add filter activated notice to bigNarrowPeak. refs #24271 diff --git src/hg/hgTracks/bigBedTrack.c src/hg/hgTracks/bigBedTrack.c index 00fe37c..e5dd9fe 100644 --- src/hg/hgTracks/bigBedTrack.c +++ src/hg/hgTracks/bigBedTrack.c @@ -1,577 +1,572 @@ /* bigBed - stuff to handle loading and display of bigBed type tracks in browser. * Mostly just links to bed code, but handles a few things itself, like the dense * drawing code. */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "jksql.h" #include "hdb.h" #include "bedCart.h" #include "hgTracks.h" #include "hmmstats.h" #include "localmem.h" #include "wigCommon.h" #include "bbiFile.h" #include "obscure.h" #include "bigWig.h" #include "bigBed.h" #include "bigWarn.h" #include "errCatch.h" #include "trackHub.h" #include "net.h" #include "bigPsl.h" #include "bigBedFilter.h" #include "bigBedLabel.h" static unsigned getFieldNum(struct bbiFile *bbi, char *field) // get field number for field name in bigBed. errAbort if field not found. { int fieldNum = bbFieldIndex(bbi, field); if (fieldNum < 0) errAbort("error building filter with field %s. Field not found.", field); return fieldNum; } struct bigBedFilter *bigBedMakeNumberFilter(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *filter, char *defaultLimits, char *field) /* Make a filter on this column if the trackDb or cart wants us to. */ { struct bigBedFilter *ret = NULL; char *setting = trackDbSettingClosestToHome(tdb, filter); int fieldNum = getFieldNum(bbi, field); if (setting) { struct asObject *as = bigBedAsOrDefault(bbi); // All this isFloat conditional code is here because the cart // variables used for floats are different than those used for ints // in ../lib/hui.c so we have to use the correct getScore*() routine // to access them.. We're doomed. boolean isFloat = FALSE; struct asColumn *asCol = asColumnFind(as, field); if (asCol != NULL) isFloat = asTypesIsFloating(asCol->lowType->type); boolean invalid = FALSE; double minValueTdb = 0,maxValueTdb = NO_VALUE; double minLimit=NO_VALUE,maxLimit=NO_VALUE,min = minValueTdb,max = maxValueTdb; if (!isFloat) { int minValueTdbInt = 0,maxValueTdbInt = NO_VALUE; colonPairToInts(setting,&minValueTdbInt,&maxValueTdbInt); int minLimitInt=NO_VALUE,maxLimitInt=NO_VALUE,minInt=minValueTdbInt,maxInt=maxValueTdbInt; colonPairToInts(defaultLimits,&minLimitInt,&maxLimitInt); getScoreIntRangeFromCart(cart,tdb,FALSE,filter,&minLimitInt,&maxLimitInt,&minInt,&maxInt); // copy all the ints over to the doubles (sigh) min = minInt; max = maxInt; minLimit = minLimitInt; maxLimit = maxLimitInt; minValueTdb = minValueTdbInt; maxValueTdb = maxValueTdbInt; } else { colonPairToDoubles(setting,&minValueTdb,&maxValueTdb); colonPairToDoubles(defaultLimits,&minLimit,&maxLimit); getScoreFloatRangeFromCart(cart,tdb,FALSE,filter,&minLimit,&maxLimit,&min,&max); } if ((int)minLimit != NO_VALUE || (int)maxLimit != NO_VALUE) { // assume tdb default values within range! // (don't give user errors that have no consequence) if ((min != minValueTdb && (((int)minLimit != NO_VALUE && min < minLimit) || ((int)maxLimit != NO_VALUE && min > maxLimit))) || (max != maxValueTdb && (((int)minLimit != NO_VALUE && max < minLimit) || ((int)maxLimit != NO_VALUE && max > maxLimit)))) { invalid = TRUE; char value[64]; if ((int)max == NO_VALUE) // min only is allowed, but max only is not safef(value, sizeof(value), "entered minimum (%g)", min); else safef(value, sizeof(value), "entered range (min:%g and max:%g)", min, max); char limits[64]; if ((int)minLimit != NO_VALUE && (int)maxLimit != NO_VALUE) safef(limits, sizeof(limits), "violates limits (%g to %g)", minLimit, maxLimit); else if ((int)minLimit != NO_VALUE) safef(limits, sizeof(limits), "violates lower limit (%g)", minLimit); else //if ((int)maxLimit != NO_VALUE) safef(limits, sizeof(limits), "violates uppper limit (%g)", maxLimit); warn("invalid filter by %s: %s %s for track %s", field, value, limits, tdb->track); } } if (invalid) { char filterLimitName[64]; safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, _MIN); cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, _MAX); cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); } else if (((int)min != NO_VALUE && ((int)minLimit == NO_VALUE || minLimit != min)) || ((int)max != NO_VALUE && ((int)maxLimit == NO_VALUE || maxLimit != max))) // Assumes min==NO_VALUE or min==minLimit is no filter // Assumes max==NO_VALUE or max==maxLimit is no filter! { AllocVar(ret); ret->fieldNum = fieldNum; if ((int)max == NO_VALUE || ((int)maxLimit != NO_VALUE && maxLimit == max)) { ret->comparisonType = COMPARE_MORE; ret->value1 = min; } else if ((int)min == NO_VALUE || ((int)minLimit != NO_VALUE && minLimit == min)) { ret->comparisonType = COMPARE_LESS; ret->value1 = max; } else { ret->comparisonType = COMPARE_BETWEEN; ret->value1 = min; ret->value2 = max; } } } return ret; } struct bigBedFilter *bigBedMakeFilterText(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *filterName, char *field) /* Add a bigBed filter using a trackDb filterText statement. */ { struct bigBedFilter *filter; char *setting = trackDbSettingClosestToHome(tdb, filterName); char *value = cartUsualStringClosestToHome(cart, tdb, FALSE, filterName, setting); if (isEmpty(value)) return NULL; char filterType[4096]; safef(filterType, sizeof filterType, "%s%s", field, FILTER_TYPE_NAME); char *typeValue = cartOrTdbString(cart, tdb, filterType, FILTERTEXT_WILDCARD); AllocVar(filter); filter->fieldNum = getFieldNum(bbi, field); if (sameString(typeValue, FILTERTEXT_REGEXP) ) { filter->comparisonType = COMPARE_REGEXP; regcomp(&filter->regEx, value, REG_NOSUB); } else { filter->comparisonType = COMPARE_WILDCARD; filter->wildCardString = cloneString(value); } return filter; } struct bigBedFilter *bigBedMakeFilterBy(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *field, struct slName *choices) /* Add a bigBed filter using a trackDb filterBy statement. */ { struct bigBedFilter *filter; char filterType[4096]; safef(filterType, sizeof filterType, "%s%s", field, FILTER_TYPE_NAME); char *setting = cartOrTdbString(cart, tdb, filterType, FILTERBY_SINGLE); AllocVar(filter); filter->fieldNum = getFieldNum(bbi, field); if (setting && (sameString(setting, FILTERBY_SINGLE_LIST) || sameString(setting, FILTERBY_MULTIPLE_LIST_OR))) filter->comparisonType = COMPARE_HASH_LIST_OR; else if (setting && sameString(setting, FILTERBY_MULTIPLE_LIST_AND)) filter->comparisonType = COMPARE_HASH_LIST_AND; else filter->comparisonType = COMPARE_HASH; filter->valueHash = newHash(5); filter->numValuesInHash = slCount(choices); for(; choices; choices = choices->next) hashStore(filter->valueHash, choices->name); return filter; } struct bigBedFilter *bigBedBuildFilters(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb) /* Build all the numeric and filterBy filters for a bigBed */ { struct bigBedFilter *filters = NULL, *filter; struct slName *filterSettings = trackDbSettingsWildMatch(tdb, FILTER_NUMBER_WILDCARD); if ((filterSettings == NULL) && !trackDbSettingOn(tdb, "noScoreFilter")) { AllocVar(filter); slAddHead(&filters, filter); filter->fieldNum = 4; filter->comparisonType = COMPARE_MORE; char buffer[2048]; safef(buffer, sizeof buffer, "%s.scoreFilter", tdb->track); filter->value1 = cartUsualDouble(cart, buffer, 0.0); } for(; filterSettings; filterSettings = filterSettings->next) { char *fieldName = extractFieldName(filterSettings->name, FILTER_NUMBER_NAME); if (sameString(fieldName, "noScore")) continue; if ((filter = bigBedMakeNumberFilter(cart, bbi, tdb, filterSettings->name, NULL, fieldName)) != NULL) slAddHead(&filters, filter); } filterSettings = trackDbSettingsWildMatch(tdb, FILTER_TEXT_WILDCARD); for(; filterSettings; filterSettings = filterSettings->next) { char *fieldName = extractFieldName(filterSettings->name, FILTER_TEXT_NAME); if ((filter = bigBedMakeFilterText(cart, bbi, tdb, filterSettings->name, fieldName)) != NULL) slAddHead(&filters, filter); } filterBy_t *filterBySet = filterBySetGet(tdb, cart,NULL); filterBy_t *filterBy = filterBySet; for (;filterBy != NULL; filterBy = filterBy->next) { if (filterBy->slChoices && differentString(filterBy->slChoices->name, "All")) { if ((filter = bigBedMakeFilterBy(cart, bbi, tdb, filterBy->column, filterBy->slChoices)) != NULL) slAddHead(&filters, filter); } } return filters; } boolean bigBedFilterInterval(char **bedRow, struct bigBedFilter *filters) /* Go through a row and filter based on filters. Return TRUE if all filters are passed. */ { struct bigBedFilter *filter; for(filter = filters; filter; filter = filter->next) { double val = atof(bedRow[filter->fieldNum]); switch(filter->comparisonType) { case COMPARE_WILDCARD: if ( !wildMatch(filter->wildCardString, bedRow[filter->fieldNum])) return FALSE; break; case COMPARE_REGEXP: if (regexec(&filter->regEx,bedRow[filter->fieldNum], 0, NULL,0 ) != 0) return FALSE; break; case COMPARE_HASH_LIST_AND: case COMPARE_HASH_LIST_OR: { struct slName *values = commaSepToSlNames(bedRow[filter->fieldNum]); unsigned found = 0; struct hash *seenHash = newHash(3); for(; values; values = values->next) { if (hashLookup(seenHash, values->name)) continue; hashStore(seenHash, values->name); if (hashLookup(filter->valueHash, values->name)) { found++; if (filter->comparisonType == COMPARE_HASH_LIST_OR) break; } } if (filter->comparisonType == COMPARE_HASH_LIST_AND) { if (found < filter->numValuesInHash) return FALSE; } else if (!found) return FALSE; } break; case COMPARE_HASH: if (!hashLookup(filter->valueHash, bedRow[filter->fieldNum])) return FALSE; break; case COMPARE_LESS: if (!(val <= filter->value1)) return FALSE; break; case COMPARE_MORE: if (!(val >= filter->value1)) return FALSE; break; case COMPARE_BETWEEN: if (!((val >= filter->value1) && (val <= filter->value2))) return FALSE; break; } } return TRUE; } struct bbiFile *fetchBbiForTrack(struct track *track) /* Fetch bbiFile from track, opening it if it is not already open. */ { struct bbiFile *bbi = track->bbiFile; if (bbi == NULL) { char *fileName = NULL; if (track->parallelLoading) // do not use mysql during parallel fetch { fileName = cloneString(trackDbSetting(track->tdb, "bigDataUrl")); if (fileName == NULL) fileName = cloneString(trackDbSetting(track->tdb, "bigGeneDataUrl")); } else { struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = hAllocConnTrack(database, track->tdb); fileName = bbiNameFromSettingOrTable(track->tdb, conn, track->table); hFreeConn(&conn); } #ifdef USE_GBIB_PWD #include "gbib.c" #endif bbi = track->bbiFile = bigBedFileOpen(fileName); } return bbi; } struct bigBedInterval *bigBedSelectRangeExt(struct track *track, char *chrom, int start, int end, struct lm *lm, int maxItems) /* Return list of intervals in range. */ { struct bigBedInterval *result = NULL; /* protect against temporary network error */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { struct bbiFile *bbi = fetchBbiForTrack(track); result = bigBedIntervalQuery(bbi, chrom, start, end, maxItems + 1, lm); if (slCount(result) > maxItems) { track->limitedVis = tvDense; track->limitedVisSet = TRUE; result = NULL; AllocArray(track->summary, insideWidth); if (bigBedSummaryArrayExtended(bbi, chrom, start, end, insideWidth, track->summary)) { char *denseCoverage = trackDbSettingClosestToHome(track->tdb, "denseCoverage"); if (denseCoverage != NULL) { double endVal = atof(denseCoverage); if (endVal <= 0) { AllocVar(track->sumAll); *track->sumAll = bbiTotalSummary(bbi); } } } else freez(&track->summary); } bbiFileClose(&bbi); track->bbiFile = NULL; } errCatchEnd(errCatch); if (errCatch->gotError) { track->networkErrMsg = cloneString(errCatch->message->string); track->drawItems = bigDrawWarning; track->totalHeight = bigWarnTotalHeight; result = NULL; } errCatchFree(&errCatch); return result; } char* restField(struct bigBedInterval *bb, int fieldIdx) /* return a given field from the bb->rest field, NULL on error */ { if (fieldIdx==0) // we don't return the first(=name) field of bigBed return NULL; char *rest = cloneString(bb->rest); char *restFields[1024]; int restCount = chopTabs(rest, restFields); char *field = NULL; if (fieldIdx < restCount) field = cloneString(restFields[fieldIdx]); freeMem(rest); return field; } void bigBedAddLinkedFeaturesFromExt(struct track *track, char *chrom, int start, int end, int scoreMin, int scoreMax, boolean useItemRgb, int fieldCount, struct linkedFeatures **pLfList, int maxItems) /* Read in items in chrom:start-end from bigBed file named in track->bbiFileName, convert * them to linkedFeatures, and add to head of list. */ { struct lm *lm = lmInit(0); struct trackDb *tdb = track->tdb; struct bigBedInterval *bb, *bbList = bigBedSelectRangeExt(track, chrom, start, end, lm, maxItems); char *scoreFilter = cartOrTdbString(cart, track->tdb, "scoreFilter", NULL); char *mouseOverField = cartOrTdbString(cart, track->tdb, "mouseOverField", NULL); int minScore = 0; if (scoreFilter) minScore = atoi(scoreFilter); struct bbiFile *bbi = fetchBbiForTrack(track); int seqTypeField = 0; if (sameString(track->tdb->type, "bigPsl")) { seqTypeField = bbExtraFieldIndex(bbi, "seqType"); } int mouseOverIdx = bbExtraFieldIndex(bbi, mouseOverField); track->bbiFile = NULL; struct bigBedFilter *filters = bigBedBuildFilters(cart, bbi, track->tdb) ; -if (filters) +if (filters || compositeHideEmptySubtracks(cart, track->tdb, NULL, NULL)) labelTrackAsFiltered(track); -// also label parent composite track filtered -struct trackDb *parentTdb = tdbGetComposite(track->tdb); -if (parentTdb && (filters || compositeHideEmptySubtracks(cart, parentTdb, NULL, NULL))) - parentTdb->longLabel = labelAsFiltered(parentTdb->longLabel); - for (bb = bbList; bb != NULL; bb = bb->next) { struct linkedFeatures *lf = NULL; if (sameString(track->tdb->type, "bigPsl")) { char *seq, *cds; struct psl *psl = pslFromBigPsl(chromName, bb, seqTypeField, &seq, &cds); int sizeMul = pslIsProtein(psl) ? 3 : 1; boolean isXeno = 0; // just affects grayIx boolean nameGetsPos = FALSE; // we want the name to stay the name lf = lfFromPslx(psl, sizeMul, isXeno, nameGetsPos, track); lf->original = psl; if ((seq != NULL) && (lf->orientation == -1)) reverseComplement(seq, strlen(seq)); lf->extra = seq; lf->cds = cds; } else { char startBuf[16], endBuf[16]; char *bedRow[bbi->fieldCount]; bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow)); if (bigBedFilterInterval(bedRow, filters)) { struct bed *bed = bedLoadN(bedRow, fieldCount); lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount, scoreMin, scoreMax, useItemRgb); } } if (lf == NULL) continue; lf->label = bigBedMakeLabel(track->tdb, track->labelColumns, bb, chromName); if (sameString(track->tdb->type, "bigGenePred") || startsWith("genePred", track->tdb->type)) { lf->original = genePredFromBigGenePred(chromName, bb); } char* mouseOver = restField(bb, mouseOverIdx); lf->mouseOver = mouseOver; // leaks some memory, cloneString handles NULL ifself if (scoreFilter == NULL || lf->score >= minScore) slAddHead(pLfList, lf); } lmCleanup(&lm); if (!trackDbSettingClosestToHomeOn(track->tdb, "linkIdInName")) track->itemName = bigLfItemName; bbiFileClose(&bbi); } boolean canDrawBigBedDense(struct track *tg) /* Return TRUE if conditions are such that can do the fast bigBed dense data fetch and * draw. */ { return tg->isBigBed; } void bigBedDrawDense(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color) /* Use big-bed summary data to quickly draw bigBed. */ { struct bbiSummaryElement *summary = tg->summary; if (summary) { char *denseCoverage = trackDbSettingClosestToHome(tg->tdb, "denseCoverage"); if (denseCoverage != NULL) { double startVal = 0, endVal = atof(denseCoverage); if (endVal <= 0) { struct bbiSummaryElement sumAll = *tg->sumAll; double mean = sumAll.sumData/sumAll.validCount; double std = calcStdFromSums(sumAll.sumData, sumAll.sumSquares, sumAll.validCount); rangeFromMinMaxMeanStd(0, sumAll.maxVal, mean, std, &startVal, &endVal); } int x; for (x=0; x 0) { Color color = shadesOfGray[grayInRange(summary[x].maxVal, startVal, endVal)]; hvGfxBox(hvg, x+xOff, yOff, 1, tg->heightPer, color); } } } else { int x; for (x=0; x 0) { hvGfxBox(hvg, x+xOff, yOff, 1, tg->heightPer, color); } } } } freez(&tg->summary); } char *bigBedItemName(struct track *tg, void *item) // return label for simple beds { struct bed *bed = (struct bed *)item; return bed->label; } char *bigLfItemName(struct track *tg, void *item) // return label for linked features { struct linkedFeatures *lf = (struct linkedFeatures *)item; return lf->label; } void bigBedMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]) /* Set up bigBed methods. */ { complexBedMethods(track, tdb, TRUE, wordCount, words); }