733ba7b804e84d7b60ccad1f137398ecd52db983 chmalee Tue Apr 23 18:15:09 2024 -0700 Add a general highlight trackDb variable(s), working like trackDb filters, except put a color behind the item, refs #24507 diff --git src/hg/hgTracks/bigBedTrack.c src/hg/hgTracks/bigBedTrack.c index 5ea2890..2d16790 100644 --- src/hg/hgTracks/bigBedTrack.c +++ src/hg/hgTracks/bigBedTrack.c @@ -31,32 +31,32 @@ #include "quickLift.h" #include "hgConfig.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) fieldNum = defaultFieldLocation(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 *bigBedMakeNumberFilter(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *filter, char *defaultLimits, char *field, boolean isHighlight) +/* Make a filter/highlight 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) { boolean invalid = FALSE; double minValueTdb = 0,maxValueTdb = NO_VALUE; double minLimit=NO_VALUE,maxLimit=NO_VALUE,min = minValueTdb,max = maxValueTdb; 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! @@ -101,89 +101,121 @@ { 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; } + if (isHighlight) + ret->isHighlight = TRUE; } } return ret; } -struct bigBedFilter *bigBedMakeFilterText(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *filterName, char *field) +struct bigBedFilter *bigBedMakeFilterText(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *filterName, char *field, boolean isHighlight) /* 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 *typeValue = getFilterType(cart, tdb, field, 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); } +filter->isHighlight = isHighlight; + return filter; } -struct bigBedFilter *bigBedMakeFilterBy(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *field, struct slName *choices) +char *getHighlightType(struct cart *cart, struct trackDb *tdb, char *field, char *def) +{ +char settingString[4096]; +safef(settingString, sizeof settingString, "%s.%s", HIGHLIGHT_TYPE_NAME_LOW, field); +char *setting = cartOrTdbString(cart, tdb, settingString, NULL); +if (setting == NULL) + { + safef(settingString, sizeof settingString, "%s.%s", field, HIGHLIGHT_TYPE_NAME_CAP); + setting = cartOrTdbString(cart, tdb, settingString, NULL); + } +if (setting == NULL) + { + safef(settingString, sizeof settingString, "%s%s", field, HIGHLIGHT_TYPE_NAME_CAP); + setting = cartOrTdbString(cart, tdb, settingString, def); + } +return setting; +} + +struct bigBedFilter *bigBedMakeFilterBy(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *field, struct slName *choices, boolean isHighlight) /* Add a bigBed filter using a trackDb filterBy statement. */ { struct bigBedFilter *filter; -char *setting = getFilterType(cart, tdb, field, FILTERBY_DEFAULT); +char *setting = NULL; +if (isHighlight) + setting = getHighlightType(cart, tdb, field, HIGHLIGHTBY_DEFAULT); +else +setting = getFilterType(cart, tdb, field, FILTERBY_DEFAULT); AllocVar(filter); filter->fieldNum = getFieldNum(bbi, field); filter->comparisonType = COMPARE_HASH; if (setting) { if (sameString(setting, FILTERBY_SINGLE_LIST) || sameString(setting, FILTERBY_MULTIPLE_LIST_OR) - || sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_OR)) + || sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_OR) + || sameString(setting, HIGHLIGHTBY_SINGLE_LIST) + || sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_OR) + || sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_ONLY_OR)) filter->comparisonType = COMPARE_HASH_LIST_OR; else if (sameString(setting, FILTERBY_MULTIPLE_LIST_AND) - || sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_AND)) + || sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_AND) + || sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_AND) + || sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_ONLY_AND)) filter->comparisonType = COMPARE_HASH_LIST_AND; } filter->valueHash = newHash(5); filter->numValuesInHash = slCount(choices); for(; choices; choices = choices->next) hashStore(filter->valueHash, choices->name); +filter->isHighlight = isHighlight; return filter; } static void addGencodeFilters(struct cart *cart, struct trackDb *tdb, struct bigBedFilter **pFilters) /* Add GENCODE custom bigBed filters. */ { struct bigBedFilter *filter; char varName[64]; struct hash *hash; /* canonical */ safef(varName, sizeof(varName), "%s.show.spliceVariants", tdb->track); boolean option = cartUsualBoolean(cart, varName, TRUE); if (!option) { @@ -245,73 +277,103 @@ struct trackDbFilter *tdbFilters = tdbGetTrackNumFilters(tdb); if ((tdbFilters == NULL) && !trackDbSettingOn(tdb, "noScoreFilter") && (bbi->definedFieldCount >= 5)) { 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(; tdbFilters; tdbFilters = tdbFilters->next) { - if ((filter = bigBedMakeNumberFilter(cart, bbi, tdb, tdbFilters->name, NULL, tdbFilters->fieldName)) != NULL) + if ((filter = bigBedMakeNumberFilter(cart, bbi, tdb, tdbFilters->name, NULL, tdbFilters->fieldName, FALSE)) != NULL) slAddHead(&filters, filter); } tdbFilters = tdbGetTrackTextFilters(tdb); for(; tdbFilters; tdbFilters = tdbFilters->next) { - if ((filter = bigBedMakeFilterText(cart, bbi, tdb, tdbFilters->name, tdbFilters->fieldName)) != NULL) + if ((filter = bigBedMakeFilterText(cart, bbi, tdb, tdbFilters->name, tdbFilters->fieldName, FALSE)) != 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) + if ((filter = bigBedMakeFilterBy(cart, bbi, tdb, filterBy->column, filterBy->slChoices, FALSE)) != NULL) slAddHead(&filters, filter); } } /* custom gencode filters */ boolean isGencode3 = trackDbSettingOn(tdb, "isGencode3"); if (isGencode3) addGencodeFilters(cart, tdb, &filters); return filters; } +struct bigBedFilter *bigBedBuildHighlights(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb) +/* Build all the numeric and highlights for a bigBed */ +{ +struct bigBedFilter *highlights = NULL, *highlight; +struct trackDbFilter *tdbHighlights = tdbGetTrackNumHighlights(tdb); -boolean bigBedFilterInterval(struct bbiFile *bbi, char **bedRow, struct bigBedFilter *filters) -/* Go through a row and filter based on filters. Return TRUE if all filters are passed. */ +for(; tdbHighlights; tdbHighlights = tdbHighlights->next) + { + if ((highlight = bigBedMakeNumberFilter(cart, bbi, tdb, tdbHighlights->name, NULL, tdbHighlights->fieldName, TRUE)) != NULL) + slAddHead(&highlights, highlight); + } + +tdbHighlights = tdbGetTrackTextHighlights(tdb); + +for(; tdbHighlights; tdbHighlights = tdbHighlights->next) + { + if ((highlight = bigBedMakeFilterText(cart, bbi, tdb, tdbHighlights->name, tdbHighlights->fieldName, TRUE)) != NULL) + slAddHead(&highlights, highlight); + } + +filterBy_t *filterBySet = highlightBySetGet(tdb, cart,NULL); +filterBy_t *filterBy = filterBySet; +for (;filterBy != NULL; filterBy = filterBy->next) + { + if (filterBy->slChoices && differentString(filterBy->slChoices->name, "All")) + { + if ((highlight = bigBedMakeFilterBy(cart, bbi, tdb, filterBy->column, filterBy->slChoices, TRUE)) != NULL) + slAddHead(&highlights, highlight); + } + } + +return highlights; +} + +boolean bigBedFilterOne(struct bigBedFilter *filter, char **bedRow, struct bbiFile *bbi) +/* Return TRUE if a bedRow passes one filter or is in hgFindMatches */ { if ((bbi->definedFieldCount > 3) && (hgFindMatches != NULL) && (bedRow[3] != NULL) && hashLookup(hgFindMatches, bedRow[3]) != NULL) return TRUE; -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: { @@ -345,31 +407,45 @@ 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; } + + +boolean bigBedFilterInterval(struct bbiFile *bbi, char **bedRow, struct bigBedFilter *filters) +/* Go through a row and filter based on filters. Return TRUE if all filters are passed. */ +{ +if ((bbi->definedFieldCount > 3) && (hgFindMatches != NULL) && + (bedRow[3] != NULL) && hashLookup(hgFindMatches, bedRow[3]) != NULL) + return TRUE; + +struct bigBedFilter *filter; +for(filter = filters; filter; filter = filter->next) + if (!bigBedFilterOne(filter, bedRow, bbi)) + return FALSE; 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) @@ -477,30 +553,47 @@ 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 addHighlightToLinkedFeature(struct linkedFeatures *lf, struct bigBedFilter *highlights, struct bbiFile *bbi, char **bedRow, struct trackDb *tdb) +/* Fill out the lf->highlightColor if the cart says to highlight this item. The color will + * be the 'average' of all the highlight colors specified */ +{ +struct bigBedFilter *highlight; +char *cartHighlightColor = cartOrTdbString(cart, tdb, HIGHLIGHT_COLOR_CART_VAR, HIGHLIGHT_COLOR_DEFAULT); +for (highlight = highlights; highlight != NULL; highlight = highlight->next) + { + if (bigBedFilterOne(highlight, bedRow, bbi)) + { + unsigned rgb = bedParseColor(cartHighlightColor); + Color color = bedColorToGfxColor(rgb); + lf->highlightColor = color; + lf->highlightMode = highlightBackground; + } + } +} 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; char *mouseOverField = cartOrTdbString(cart, track->tdb, "mouseOverField", NULL); // check if this track can merge large items, this setting must be allowed in the trackDb // stanza for the track, but can be enabled/disabled via trackUi/right click menu so // we also need to check the cart for the current status int mergeCount = 0; @@ -541,30 +634,31 @@ char *squishField = cartOrTdbString(cart, track->tdb, "squishyPackField", NULL); int squishFieldIdx = bbExtraFieldIndex(bbi, squishField); 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) ; +struct bigBedFilter *highlights = bigBedBuildHighlights(cart, bbi, track->tdb) ; if (compositeChildHideEmptySubtracks(cart, track->tdb, NULL, NULL)) labelTrackAsHideEmpty(track); // mouseOvers can be built constructed via trackDb settings instead // of embedded directly in bigBed char *mouseOverPattern = NULL; char **fieldNames = NULL; if (!mouseOverIdx) { mouseOverPattern = cartOrTdbString(cart, track->tdb, "mouseOver", NULL); if (mouseOverPattern) { AllocArray(fieldNames, bbi->fieldCount); struct slName *field = NULL, *fields = bbFieldNames(bbi); @@ -622,30 +716,33 @@ { bedCopy = cloneBed(bed); lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount, scoreMin, scoreMax, useItemRgb); } } else { bed = bedLoadN(bedRow, fieldCount); bedCopy = cloneBed(bed); lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount, scoreMin, scoreMax, useItemRgb); } } + if (lf && highlights) + addHighlightToLinkedFeature(lf, highlights, bbi, bedRow, track->tdb); + if (lf && squishFieldIdx) lf->squishyPackVal = atof(restField(bb, squishFieldIdx)); if (track->visibility != tvDense && lf && doWindowSizeFilter && bb->start < winStart && bb->end > winEnd) { mergeCount++; struct bed *bed = bedLoadN(bedRow, fieldCount); struct linkedFeatures *tmp = bedMungToLinkedFeatures(&bed, tdb, fieldCount, scoreMin, scoreMax, useItemRgb); if (spannedLf) { if (tmp->start < spannedLf->start) spannedLf->start = tmp->start; if (tmp->end > spannedLf->end) spannedLf->end = tmp->end;