react-mutation-mapper 0.8.20 → 0.8.24

package/dist/index.js

@@ -4,7 +4,8 @@ Object.defineProperty(exports, '__esModule', { value: true });
 
 function _interopDefault (ex) { return (ex && (typeof ex === 'object') && 'default' in ex) ? ex['default'] : ex; }
 
-var _ = _interopDefault(require('lodash'));
+var _ = require('lodash');
+var ___default = _interopDefault(_);
 var mobx = require('mobx');
 var mobxReact = require('mobx-react');
 var React = require('react');
@@ -150,7 +151,7 @@ var CivicCard = /** @class */ (function (_super) {
         writable: true,
         value: function (variantMap) {
             var list = [];
-            if (_.isEmpty(variantMap)) {
+            if (___default.isEmpty(variantMap)) {
                 list.push(this.variantItem('_naVariant_'));
             }
             else {
@@ -255,10 +256,10 @@ function download(civicEntry) {
     if (!civicEntry) {
         return cbioportalUtils.CIVIC_NA_VALUE;
     }
-    var variants = _.values(civicEntry.variants);
+    var variants = ___default.values(civicEntry.variants);
     var values = [];
     if (variants && variants.length > 0 && variants[0].evidenceCounts) {
-        _.forEach(variants[0].evidenceCounts, function (value, key) {
+        ___default.forEach(variants[0].evidenceCounts, function (value, key) {
             values.push(key + ": " + value);
         });
     }
@@ -453,12 +454,12 @@ function mergeAlterations(alterations) {
     var positions = {};
     var regular = [];
     var regExp = new RegExp('^([A-Z])([0-9]+)([A-Z]$)');
-    if (_.isString(alterations)) {
+    if (___default.isString(alterations)) {
         return alterations;
     }
-    _.each(alterations, function (alteration) {
+    ___default.each(alterations, function (alteration) {
         var result = regExp.exec(alteration);
-        if (_.isArray(result) && result.length === 4) {
+        if (___default.isArray(result) && result.length === 4) {
             if (!positions.hasOwnProperty(result[2])) {
                 positions[result[2]] = {};
             }
@@ -472,15 +473,15 @@ function mergeAlterations(alterations) {
             regular.push(alteration);
         }
     });
-    _.each(_.keys(positions)
+    ___default.each(___default.keys(positions)
         .map(function (e) {
         return Number(e);
     })
         .sort(), function (position) {
-        _.each(_.keys(positions[position]).sort(), function (aa) {
+        ___default.each(___default.keys(positions[position]).sort(), function (aa) {
             regular.push(aa +
                 position +
-                _.keys(positions[position][aa])
+                ___default.keys(positions[position][aa])
                     .sort()
                     .join('/'));
         });
@@ -499,7 +500,7 @@ function getPositionalVariant(alteration) {
     // result[1]: reference alleles (there could be multiple reference alleles, we only return the first allele)
     // result[2]: position(protein start/end)
     // result[3]: variant alleles (empty if the alteration is positional variant already)
-    if (_.isArray(result) &&
+    if (___default.isArray(result) &&
         result.length === 4 &&
         (!result[3] || result[1].length === result[3].length)) {
         return "" + result[1][0] + result[2];
@@ -522,7 +523,7 @@ function getTumorTypeName(tumorType) {
 }
 function groupOncoKbIndicatorDataByMutations(mutationsByPosition, oncoKbData, getTumorType, getEntrezGeneId, filter) {
     var indicatorMap = {};
-    _.keys(mutationsByPosition).forEach(function (key) {
+    ___default.keys(mutationsByPosition).forEach(function (key) {
         var position = Number(key);
         var indicators = mutationsByPosition[position]
             .map(function (mutation) {
@@ -577,7 +578,7 @@ function download$1(links) {
 }
 function myCancerGenomeLinks(linksHTML) {
     var links = [];
-    _.each(linksHTML, function (link, index) {
+    ___default.each(linksHTML, function (link, index) {
         // TODO this is a workaround, ideally we should fix the data itself
         // parse the data as an HTML dom element, since it is formatted as an HTML link.
         var myCancerGenomeLink = cbioportalUtils.parseMyCancerGenomeLink(link);
@@ -788,11 +789,11 @@ var OncoKbHelper = /** @class */ (function () {
             switch (dataType) {
                 case cbioportalUtils.OncoKbCardDataType.TXS:
                 case cbioportalUtils.OncoKbCardDataType.TXR:
-                    return _.pick(this.LEVEL_DESC, this.TX_LEVELS);
+                    return ___default.pick(this.LEVEL_DESC, this.TX_LEVELS);
                 case cbioportalUtils.OncoKbCardDataType.DX:
-                    return _.pick(this.LEVEL_DESC, this.DX_LEVELS);
+                    return ___default.pick(this.LEVEL_DESC, this.DX_LEVELS);
                 case cbioportalUtils.OncoKbCardDataType.PX:
-                    return _.pick(this.LEVEL_DESC, this.PX_LEVELS);
+                    return ___default.pick(this.LEVEL_DESC, this.PX_LEVELS);
                 default:
                     return {};
             }
@@ -934,7 +935,7 @@ var OncoKbHelper = /** @class */ (function () {
             var content = React.createElement("span", null, mergedAlteration);
             if (alterations.length > 5) {
                 var lowerCasedQueryVariant_1 = variant.toLowerCase();
-                var matchedAlteration = _.find(alterations, function (alteration) {
+                var matchedAlteration = ___default.find(alterations, function (alteration) {
                     return alteration.toLocaleLowerCase() === lowerCasedQueryVariant_1;
                 });
                 if (!matchedAlteration) {
@@ -1019,7 +1020,7 @@ var ReferenceList = /** @class */ (function (_super) {
         get: function () {
             var _this = this;
             if (this.props.pmidData && this.props.pmids) {
-                var loadingItems = _.filter(this.props.pmids, function (uid) {
+                var loadingItems = ___default.filter(this.props.pmids, function (uid) {
                     var cacheData = _this.props.pmidData[uid.toString()];
                     // when the cacheData is undefined, the pmidData will fetch the uid info later which eventually results to an object with a status
                     return !cacheData || cacheData.status === 'pending';
@@ -1048,7 +1049,7 @@ var ReferenceList = /** @class */ (function (_super) {
                     var cacheData = _this.props.pmidData[uid.toString()];
                     var articleContent = cacheData ? cacheData.data : null;
                     if (articleContent) {
-                        list.push(React.createElement(PmidItem, { title: articleContent.title, author: _.isArray(articleContent.authors) &&
+                        list.push(React.createElement(PmidItem, { title: articleContent.title, author: ___default.isArray(articleContent.authors) &&
                                 articleContent.authors.length > 0
                                 ? articleContent.authors[0].name + ' et al.'
                                 : 'Unknown', source: articleContent.source, date: new Date(articleContent.pubdate)
@@ -1517,7 +1518,7 @@ var OncoKbTooltip = /** @class */ (function (_super) {
                         allPmids_1 = allPmids_1.concat(implication.pmids);
                     });
                 }
-                for (var _i = 0, _a = _.uniq(allPmids_1).map(function (pmid) { return Number(pmid); }); _i < _a.length; _i++) {
+                for (var _i = 0, _a = ___default.uniq(allPmids_1).map(function (pmid) { return Number(pmid); }); _i < _a.length; _i++) {
                     var ref = _a[_i];
                     this.props.pubMedCache.get(ref);
                 }
@@ -1635,14 +1636,14 @@ function sortValue$2(indicator) {
     return values;
 }
 function download$2(indicator) {
+    var _a, _b;
     if (!indicator) {
         return 'NA';
     }
     var oncogenic = indicator.oncogenic ? indicator.oncogenic : 'Unknown';
-    var level = indicator.highestSensitiveLevel
-        ? indicator.highestSensitiveLevel.toLowerCase()
-        : 'level NA';
-    return oncogenic + ", " + level;
+    var sensitivityLevel = ((_a = indicator.highestSensitiveLevel) === null || _a === void 0 ? void 0 : _a.toLowerCase()) || 'level NA';
+    var resistanceLevel = ((_b = indicator.highestResistanceLevel) === null || _b === void 0 ? void 0 : _b.toLowerCase()) || 'resistance NA';
+    return oncogenic + ", " + sensitivityLevel + ", " + resistanceLevel;
 }
 var OncoKB = /** @class */ (function (_super) {
     __extends(OncoKB, _super);
@@ -1900,7 +1901,7 @@ var ONCOKB_DEFAULT_INFO = {
 };
 var DEFAULT_GENOME_NEXUS_CLIENT = initGenomeNexusClient();
 function getUrl(urlTemplate, templateVariables) {
-    return _.template(urlTemplate)(templateVariables);
+    return ___default.template(urlTemplate)(templateVariables);
 }
 function fetchVariantAnnotationsByMutation(mutations, fields, isoformOverrideSource, client) {
     if (fields === void 0) { fields = ['annotation_summary']; }
@@ -2017,7 +2018,7 @@ function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGen
         var isOncoKbCancerGene = false;
         if (oncoKbCancerGenes && !(oncoKbCancerGenes.result instanceof Error)) {
             oncoKbGeneExist =
-                _.find(oncoKbCancerGenes.result, function (gene) {
+                ___default.find(oncoKbCancerGenes.result, function (gene) {
                     return (mutation.mutationType &&
                         mutation.mutationType.toLowerCase() ===
                             cbioportalFrontendCommons.CanonicalMutationType.FUSION) ||
@@ -2025,7 +2026,7 @@ function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGen
                             gene.entrezGeneId === entrezGeneId_1);
                 }) !== undefined;
             isOncoKbCancerGene =
-                _.find(oncoKbCancerGenes.result, function (gene) { return gene.entrezGeneId === entrezGeneId_1; }) !== undefined;
+                ___default.find(oncoKbCancerGenes.result, function (gene) { return gene.entrezGeneId === entrezGeneId_1; }) !== undefined;
         }
         value = {
             hugoGeneSymbol: hugoGeneSymbol,
@@ -2079,7 +2080,7 @@ function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, myCancerGen
                 !(oncoKbData.result instanceof Error) &&
                 oncoKbData.status === 'complete') {
                 oncoKbIndicator = getIndicatorData(mutation, oncoKbData.result, resolveTumorType, resolveEntrezGeneId);
-                oncoKbAvailableDataTypes = _.uniq(__spreadArrays(oncoKbAvailableDataTypes, cbioportalUtils.calculateOncoKbAvailableDataType(_.values(oncoKbData.result.indicatorMap))));
+                oncoKbAvailableDataTypes = ___default.uniq(__spreadArrays(oncoKbAvailableDataTypes, cbioportalUtils.calculateOncoKbAvailableDataType(___default.values(oncoKbData.result.indicatorMap))));
             }
             value = __assign(__assign({}, value), { oncoKbStatus: oncoKbData ? oncoKbData.status : 'pending', oncoKbIndicator: oncoKbIndicator,
                 oncoKbAvailableDataTypes: oncoKbAvailableDataTypes });
@@ -2103,7 +2104,7 @@ function annotationSortMethod(a, b) {
     return cbioportalUtils.defaultArraySortMethod(sortValue$4(a), sortValue$4(b));
 }
 function sortValue$4(annotation) {
-    return _.flatten([
+    return ___default.flatten([
         sortValue$2(annotation.oncoKbIndicator),
         sortValue(annotation.civicEntry),
         sortValue$1(annotation.myCancerGenomeLinks),
@@ -2409,7 +2410,7 @@ function getGnomadDataSortedByFrequency(myVariantInfo) {
 }
 function sortGnomadDataByFrequency(gnomadData) {
     // sort by frequency
-    var sorted = _.sortBy(Object.values(gnomadData).slice(0, 8), [
+    var sorted = ___default.sortBy(Object.values(gnomadData).slice(0, 8), [
         'alleleFrequency',
     ]).reverse();
     // add the total row at the bottom
@@ -3336,10 +3337,10 @@ function calculateBadgeAlignmentStyles(options, numberOfColumnsPerRow, uniformBa
         var iterationCount = options.length;
         var maxLength = Math.max.apply(Math, getOptionContentLengths(options));
         var badgeWidth_1 = calculateBadgeAlignmentStyle(maxLength, maxLength, badgeCharWidth, badgeContentPadding, true);
-        return _.times(iterationCount, function () { return badgeWidth_1; });
+        return ___default.times(iterationCount, function () { return badgeWidth_1; });
     }
     else if (numberOfColumnsPerRow > 0) {
-        var groupedByCol_1 = _.groupBy(options, function (option) { return options.indexOf(option) % numberOfColumnsPerRow; });
+        var groupedByCol_1 = ___default.groupBy(options, function (option) { return options.indexOf(option) % numberOfColumnsPerRow; });
         return options.map(function (option, index) {
             // define a max badge length for each column
             var maxLengthInCol = Math.max.apply(Math, getOptionContentLengths(groupedByCol_1[index % numberOfColumnsPerRow]));
@@ -3519,7 +3520,7 @@ function getColorForProteinImpactType(mutations, colors, getMutationCount, isPut
         };
         counts[key].count += pMut.count;
     }
-    var sortedMutations = _.sortBy(_.values(counts), [
+    var sortedMutations = ___default.sortBy(___default.values(counts), [
         function (pMut) { return (pMut.isPutativeDriver ? 0 : 1); },
         function (// putative driver preferred non putative driver
         pMut) { return -pMut.count; },
@@ -3924,7 +3925,7 @@ function updatePositionSelectionFilters(dataStore, position, isMultiSelect, defa
         selectedPositions = findAllUniquePositions(dataStore.selectionFilters);
         // remove current position if already selected
         if (currentlySelected) {
-            selectedPositions = _.without(selectedPositions, position);
+            selectedPositions = ___default.without(selectedPositions, position);
         }
     }
     // add current position into list if not selected
@@ -3961,7 +3962,7 @@ function updatePositionRangeHighlightFilters(dataStore, startPosition, endPositi
     updatePositionHighlightFilters(dataStore, positions, defaultFilters);
 }
 function findAllUniquePositions(filters) {
-    return _.uniq(_.flatten(filters
+    return ___default.uniq(___default.flatten(filters
         // pick only position filters
         .filter(function (f) { return f.type === exports.DataFilterType.POSITION; })
         // we need to spread f.values, since it might be an observable mobx array
@@ -3969,7 +3970,7 @@ function findAllUniquePositions(filters) {
         .map(function (f) { return __spreadArrays(f.values); })));
 }
 function indexPositions(filters) {
-    return _.keyBy(findAllUniquePositions(filters).map(function (p) { return ({ position: p }); }), 'position');
+    return ___default.keyBy(findAllUniquePositions(filters).map(function (p) { return ({ position: p }); }), 'position');
 }
 function includesSearchTextIgnoreCase(value, searchText) {
     return (searchText &&
@@ -3982,7 +3983,7 @@ function findNonTextInputFilters(dataFilters) {
     return dataFilters.filter(function (f) { return f.id !== TEXT_INPUT_FILTER_ID; });
 }
 function findOneMutationFilterValue(filter) {
-    return filter.values.length > 0 ? _.values(filter.values[0])[0] : undefined;
+    return filter.values.length > 0 ? ___default.values(filter.values[0])[0] : undefined;
 }
 function applyDefaultPositionFilter(filter, mutation) {
     // const positions: {[position: string]: {position: number}} = indexPositions([filter]);
@@ -3994,7 +3995,7 @@ function applyDefaultProteinImpactTypeFilter(filter, mutation) {
 }
 function applyDefaultMutationStatusFilter(filter, mutation) {
     return (mutation.mutationStatus !== undefined &&
-        _.some(filter.values, function (value) {
+        ___default.some(filter.values, function (value) {
             return value.toLowerCase() === mutation.mutationStatus.toLowerCase();
         }));
 }
@@ -4018,7 +4019,7 @@ function groupDataByGroupFilters(groupFilters, sortedFilteredData, applyFilter)
         group: groupFilter.group,
         data: sortedFilteredData.filter(
         // TODO simplify array flatten if possible
-        function (m) { return applyFilter(groupFilter.filter, _.flatten([m])[0]); }),
+        function (m) { return applyFilter(groupFilter.filter, ___default.flatten([m])[0]); }),
     }); });
 }
 function groupDataByProteinImpactType(sortedFilteredData) {
@@ -4030,7 +4031,7 @@ function groupDataByProteinImpactType(sortedFilteredData) {
         },
     }); });
     var groupedData = groupDataByGroupFilters(filters, sortedFilteredData, applyDefaultProteinImpactTypeFilter);
-    return _.keyBy(groupedData, function (d) { return d.group; });
+    return ___default.keyBy(groupedData, function (d) { return d.group; });
 }
 function onFilterOptionSelect(selectedValues, allValuesSelected, dataStore, dataFilterType, dataFilterId) {
     // all other filters except the current filter with the given data filter id
@@ -4132,7 +4133,7 @@ var DataTableToolbar = /** @class */ (function (_super) {
                     React.createElement(ColumnSelector, __assign({ columnVisibility: this.props.columnVisibility, onColumnToggled: this.props.visibilityToggle }, this.props.columnSelectorProps)))),
                 this.props.showSearchBox && (React.createElement("div", { className: "small", style: { width: 200, marginLeft: this.searchBoxMargin } },
                     React.createElement(SearchBox, { placeholder: this.props.searchPlaceHolder, onChange: this.props.onSearch
-                            ? _.debounce(this.props.onSearch, this.props.searchDelay)
+                            ? ___default.debounce(this.props.onSearch, this.props.searchDelay)
                             : this.props.onSearch, filterInputRef: this.props.filterInputRef })))));
         }
     });
@@ -4158,7 +4159,7 @@ var DataTableToolbar = /** @class */ (function (_super) {
 })(exports.ColumnSortDirection || (exports.ColumnSortDirection = {}));
 function getInitialSortDataStatus(initialSortRemoteData) {
     return initialSortRemoteData
-        ? cbioportalUtils.getRemoteDataGroupStatus.apply(void 0, _.compact(initialSortRemoteData)) : 'complete';
+        ? cbioportalUtils.getRemoteDataGroupStatus.apply(void 0, ___default.compact(initialSortRemoteData)) : 'complete';
 }
 function getColumnVisibilityDef(columns, columnVisibility) {
     var colVisProp = [];
@@ -4894,7 +4895,7 @@ function mergeColumns(defaultColumns, customColumns) {
             overrides.push(colOverride);
         }
     });
-    return __spreadArrays(merged, _.difference(customColumns, overrides));
+    return __spreadArrays(merged, ___default.difference(customColumns, overrides));
 }
 
 var DefaultMutationTableComponent = /** @class */ (function (_super) {
@@ -4928,7 +4929,7 @@ var DefaultMutationTable = /** @class */ (function (_super) {
     });
     Object.defineProperty(DefaultMutationTable.prototype, "annotationColumnDataStatus", {
         get: function () {
-            return cbioportalUtils.getRemoteDataGroupStatus.apply(void 0, _.compact(this.annotationColumnData));
+            return cbioportalUtils.getRemoteDataGroupStatus.apply(void 0, ___default.compact(this.annotationColumnData));
         },
         enumerable: false,
         configurable: true
@@ -5674,6 +5675,7 @@ function generatePfamDomainColorMap(pfamDomains) {
     TrackName["dbPTM"] = "DB_PTM";
     TrackName["UniprotPTM"] = "UNIPROT_PTM";
     TrackName["Exon"] = "EXON";
+    TrackName["UniprotTopology"] = "UNIPROT_TOPOLOGY";
 })(exports.TrackName || (exports.TrackName = {}));
 var TrackSelector = /** @class */ (function (_super) {
     __extends(TrackSelector, _super);
@@ -5743,6 +5745,13 @@ var TrackSelector = /** @class */ (function (_super) {
                         this.isPending(exports.TrackName.Exon) && this.loaderIcon())),
                     value: exports.TrackName.Exon,
                 },
+                _a[exports.TrackName.UniprotTopology] = {
+                    label: (React.createElement("span", null,
+                        "Uniprot Topology",
+                        this.isPending(exports.TrackName.UniprotTopology) &&
+                            this.loaderIcon())),
+                    value: exports.TrackName.UniprotTopology,
+                },
                 _a;
         },
         enumerable: false,
@@ -5810,6 +5819,7 @@ var TrackSelector = /** @class */ (function (_super) {
                 exports.TrackName.dbPTM,
                 exports.TrackName.PDB,
                 exports.TrackName.Exon,
+                exports.TrackName.UniprotTopology,
             ],
         }
     });
@@ -5840,6 +5850,7 @@ function initDefaultTrackVisibility() {
         _a[exports.TrackName.UniprotPTM] = 'hidden',
         _a[exports.TrackName.PDB] = 'hidden',
         _a[exports.TrackName.Exon] = 'hidden',
+        _a[exports.TrackName.UniprotTopology] = 'hidden',
         _a;
 }
 
@@ -6560,7 +6571,7 @@ var LollipopPlotNoTooltip = /** @class */ (function (_super) {
             var _this = this;
             var sequenceComponents = [];
             var start = 0;
-            var segments = _.map(this.props.domains, function (domain) {
+            var segments = ___default.map(this.props.domains, function (domain) {
                 var segment = {
                     start: start,
                     end: _this.codonToX(domain.startCodon),
@@ -7100,7 +7111,7 @@ var LollipopMutationPlotControls = /** @class */ (function (_super) {
     Object.defineProperty(LollipopMutationPlotControls.prototype, "showBottomYAxisSlider", {
         get: function () {
             return (this.props.bottomCountRange &&
-                _.compact(this.props.bottomCountRange).length > 0 &&
+                ___default.compact(this.props.bottomCountRange).length > 0 &&
                 this.props.onBottomYAxisMaxSliderChange &&
                 this.props.onBottomYAxisMaxChange &&
                 this.props.bottomYMaxSlider &&
@@ -7474,7 +7485,7 @@ var TrackItem = /** @class */ (function (_super) {
                 return (React.createElement(TrackCircle, __assign({ isHovered: this.isHovered, radius: this.props.dim1, hoverRadius: this.props.hoverdim1 }, this.props)));
             }
             else {
-                return (React.createElement(TrackRect, __assign({ isHovered: this.isHovered, width: this.props.dim1 }, this.props)));
+                return (React.createElement(TrackRect, __assign({ isHovered: this.isHovered, width: this.props.dim1, height: this.props.dim2 }, this.props)));
             }
         }
     });
@@ -7493,6 +7504,7 @@ var TrackItem = /** @class */ (function (_super) {
 var styles$6 = {"trackTitle":"trackStyles-module_trackTitle__HOHY0"};
 
 var DEFAULT_ID_CLASS_PREFIX = 'track-circle-';
+var DEFAULT_HEIGHT = 15; // height of rectangle element
 var Track = /** @class */ (function (_super) {
     __extends(Track, _super);
     function Track(props) {
@@ -7681,7 +7693,7 @@ var Track = /** @class */ (function (_super) {
     });
     Object.defineProperty(Track.prototype, "svgHeight", {
         get: function () {
-            return 10;
+            return 10; // height of baseline element
         },
         enumerable: false,
         configurable: true
@@ -7700,8 +7712,8 @@ var Track = /** @class */ (function (_super) {
                         ((spec.endCodon - spec.startCodon) /
                             _this.props.proteinLength) *
                             _this.props.width;
-                    dim2 = 22;
-                    y = -_this.svgHeight / 2;
+                    dim2 = spec.height || DEFAULT_HEIGHT;
+                    y = (_this.svgHeight - dim2) / 2; // y is the vertical start position of rectangle, half of baseline element height = half of element height + y
                     specFeats = __assign(__assign({}, spec), { endCodon: spec.endCodon, itemType: TrackItemType.RECTANGLE });
                 }
                 else {
@@ -7875,7 +7887,7 @@ function hotspotTooltip(mutations, hotspotIndex, hotspots) {
         return cbioportalUtils.isHotspot(mutation, hotspotIndex, cbioportalUtils.defaultHotspotFilter);
     }).length;
     // generate custom info
-    var residues = _.uniq(hotspots.map(function (hotspot) { return hotspot.residue; }));
+    var residues = ___default.uniq(hotspots.map(function (hotspot) { return hotspot.residue; }));
     var residuesText = React.createElement("b", null, "" + residues.join(', '));
     var pluralSuffix = residues.length > 1 ? 's' : undefined;
     var residueInfo = (React.createElement("span", null,
@@ -7900,8 +7912,8 @@ var HotspotTrack = /** @class */ (function (_super) {
             var _this = this;
             var filteredHotspotsByProteinPosStart = this.props.store
                 .hotspotsByPosition;
-            if (!_.isEmpty(filteredHotspotsByProteinPosStart)) {
-                return _.keys(filteredHotspotsByProteinPosStart)
+            if (!___default.isEmpty(filteredHotspotsByProteinPosStart)) {
+                return ___default.keys(filteredHotspotsByProteinPosStart)
                     .filter(function (position) { return Number(position) >= 0; })
                     .map(function (position) { return ({
                     startCodon: Number(position),
@@ -8083,8 +8095,8 @@ function oncoKbTooltip(usingPublicOncoKbInstance, indicatorData) {
     var sampleCount = indicatorData.length;
     // generate info
     var pluralSuffix = sampleCount > 1 ? 's' : undefined;
-    var groupedByImplication = _.groupBy(indicatorData, 'oncogenic');
-    var oncogenicKeywords = _.keys(groupedByImplication).map(function (keyword) { return (React.createElement("b", null, keyword)); });
+    var groupedByImplication = ___default.groupBy(indicatorData, 'oncogenic');
+    var oncogenicKeywords = ___default.keys(groupedByImplication).map(function (keyword) { return (React.createElement("b", null, keyword)); });
     var oncogenicInfo = [];
     if (oncogenicKeywords.length > 1) {
         // join all except the last one with ','
@@ -8104,14 +8116,14 @@ function oncoKbTooltip(usingPublicOncoKbInstance, indicatorData) {
         // use oncogenic keywords array as is
         oncogenicInfo = oncogenicKeywords;
     }
-    var groupedByProteinChange = _.groupBy(indicatorData, function (d) { return d.query.alteration; });
-    var tableData = _.keys(groupedByProteinChange).map(function (proteinChange) { return ({
+    var groupedByProteinChange = ___default.groupBy(indicatorData, function (d) { return d.query.alteration; });
+    var tableData = ___default.keys(groupedByProteinChange).map(function (proteinChange) { return ({
         count: groupedByProteinChange[proteinChange].length,
         proteinChange: proteinChange,
-        clinicalImplication: _.uniq(groupedByProteinChange[proteinChange].map(function (indicator) {
+        clinicalImplication: ___default.uniq(groupedByProteinChange[proteinChange].map(function (indicator) {
             return indicator.oncogenic ? indicator.oncogenic : 'Unknown';
         })),
-        biologicalEffect: _.uniq(groupedByProteinChange[proteinChange].map(function (indicator) {
+        biologicalEffect: ___default.uniq(groupedByProteinChange[proteinChange].map(function (indicator) {
             return indicator.mutationEffect && indicator.mutationEffect.knownEffect
                 ? indicator.mutationEffect.knownEffect
                 : 'Unknown';
@@ -8139,11 +8151,11 @@ function generateLevelData(indicatorData) {
             levels[level].push(indicator.query.tumorType);
         });
     });
-    return _.keys(levels)
+    return ___default.keys(levels)
         .sort(function (a, b) {
         return cbioportalUtils.LEVELS.all.indexOf(a) > cbioportalUtils.LEVELS.all.indexOf(b) ? -1 : 1;
     })
-        .map(function (level) { return ({ level: level, tumorTypes: _.uniq(levels[level]) }); });
+        .map(function (level) { return ({ level: level, tumorTypes: ___default.uniq(levels[level]) }); });
 }
 var OncoKbTrackTooltip = function (props) {
     return props.indicatorData
@@ -8168,8 +8180,8 @@ var OncoKbTrack = /** @class */ (function (_super) {
             var _this = this;
             var filteredOncoKbDataByProteinPosStart = this.props.store
                 .oncoKbDataByPosition;
-            if (!_.isEmpty(filteredOncoKbDataByProteinPosStart)) {
-                return _.keys(filteredOncoKbDataByProteinPosStart)
+            if (!___default.isEmpty(filteredOncoKbDataByProteinPosStart)) {
+                return ___default.keys(filteredOncoKbDataByProteinPosStart)
                     .filter(function (position) { return Number(position) >= 0; })
                     .map(function (position) { return ({
                     startCodon: Number(position),
@@ -8445,14 +8457,14 @@ var PtmAnnotationTable = /** @class */ (function (_super) {
             if (!this.props.pubMedCache) {
                 cellRenderFn = function () { return null; };
             }
-            else if (!_.isEmpty(this.pmidData)) {
+            else if (!___default.isEmpty(this.pmidData)) {
                 cellRenderFn = function (props) {
-                    return !_.isEmpty(props.original.pubmedIds) ? (React.createElement(PtmReferenceList, { pmidData: _this.pmidData, pubmedIds: props.original.pubmedIds || [] })) : null;
+                    return !___default.isEmpty(props.original.pubmedIds) ? (React.createElement(PtmReferenceList, { pmidData: _this.pmidData, pubmedIds: props.original.pubmedIds || [] })) : null;
                 };
             }
             else {
                 cellRenderFn = function (props) {
-                    return !_.isEmpty(props.original.pubmedIds) ? (React.createElement("i", { className: "fa fa-spinner fa-pulse" })) : null;
+                    return !___default.isEmpty(props.original.pubmedIds) ? (React.createElement("i", { className: "fa fa-spinner fa-pulse" })) : null;
                 };
             }
             return cellRenderFn;
@@ -8569,7 +8581,7 @@ var PtmTrack = /** @class */ (function (_super) {
                 var ptms = Number(position) >= 0
                     ? filterPtmsBySource(ptmData, _this.props.dataSource)
                     : [];
-                if (!_.isEmpty(ptms)) {
+                if (!___default.isEmpty(ptms)) {
                     acc.push({
                         startCodon: Number(position),
                         color: cbioportalUtils.ptmColor(ptms),
@@ -8587,8 +8599,8 @@ var PtmTrack = /** @class */ (function (_super) {
         get: function () {
             var ptmDataByProteinPosStart = this.props.store
                 .ptmDataByProteinPosStart.result;
-            if (ptmDataByProteinPosStart && !_.isEmpty(ptmDataByProteinPosStart)) {
-                return _.reduce(ptmDataByProteinPosStart, this.ptmDataToTrackItemSpecsReducer, []);
+            if (ptmDataByProteinPosStart && !___default.isEmpty(ptmDataByProteinPosStart)) {
+                return ___default.reduce(ptmDataByProteinPosStart, this.ptmDataToTrackItemSpecsReducer, []);
             }
             else {
                 return [];
@@ -8603,14 +8615,14 @@ var PtmTrack = /** @class */ (function (_super) {
             var ptmDataByTypeAndProteinPosStart = this.props.store
                 .ptmDataByTypeAndProteinPosStart.result;
             if (ptmDataByTypeAndProteinPosStart &&
-                !_.isEmpty(ptmDataByTypeAndProteinPosStart)) {
-                return _.keys(ptmDataByTypeAndProteinPosStart)
+                !___default.isEmpty(ptmDataByTypeAndProteinPosStart)) {
+                return ___default.keys(ptmDataByTypeAndProteinPosStart)
                     .sort(cbioportalUtils.compareByPtmTypePriority)
                     .map(function (type) { return ({
                     title: type,
-                    specs: _.reduce(ptmDataByTypeAndProteinPosStart[type], _this.ptmDataToTrackItemSpecsReducer, []),
+                    specs: ___default.reduce(ptmDataByTypeAndProteinPosStart[type], _this.ptmDataToTrackItemSpecsReducer, []),
                 }); })
-                    .filter(function (s) { return !_.isEmpty(s.specs); });
+                    .filter(function (s) { return !___default.isEmpty(s.specs); });
             }
             else {
                 return [];
@@ -8770,6 +8782,255 @@ var PtmTrack = /** @class */ (function (_super) {
     return PtmTrack;
 }(React.Component));
 
+function topologyRectangleBlockSpec(color, title, uniprotData) {
+    return {
+        color: color,
+        startCodon: uniprotData.startPosition,
+        endCodon: uniprotData.endPosition,
+        tooltip: (React.createElement("span", null,
+            React.createElement("h5", null, title),
+            "Start: ",
+            uniprotData.startPosition,
+            React.createElement("br", null),
+            "End: ",
+            uniprotData.endPosition,
+            React.createElement("br", null),
+            "Length: ",
+            uniprotData.endPosition - uniprotData.startPosition,
+            React.createElement("br", null),
+            "Description: ",
+            uniprotData.description)),
+    };
+}
+var UniprotTopologyTrackDescriptionTooltip = function (props) {
+    var dataSourceDiv = props.uniprotId ? (React.createElement("div", null,
+        "Data Source:",
+        ' ',
+        React.createElement("a", { href: "https://www.uniprot.org/uniprot/" + props.uniprotId, target: "_blank" }, "UniProt"))) : (React.createElement("div", null,
+        "Data Source:",
+        ' ',
+        React.createElement("a", { href: 'https://www.uniprot.org/', target: "_blank" }, "UniProt")));
+    return (React.createElement("div", { style: { maxWidth: 400 } },
+        React.createElement("p", null, "Information of the subcellular location of the mature protein."),
+        props.displayList.length > 0 && (React.createElement("p", null,
+            "Domains and corresponding color codes are as follows:",
+            React.createElement("ul", null, _.map(props.displayList, function (type) { return (React.createElement("li", { style: {
+                    color: cbioportalUtils.UniprotTopologyTrackToColor[type],
+                } },
+                React.createElement("strong", null, cbioportalUtils.UniprotTopologyTypeToTitle[type]))); })))),
+        dataSourceDiv));
+};
+var UniprotTopologyTrack = /** @class */ (function (_super) {
+    __extends(UniprotTopologyTrack, _super);
+    function UniprotTopologyTrack(props) {
+        var _this = _super.call(this, props) || this;
+        Object.defineProperty(_this, "expanded", {
+            enumerable: true,
+            configurable: true,
+            writable: true,
+            value: !_this.props.collapsed
+        });
+        Object.defineProperty(_this, "uniprotDataToTrackItemSpecsReducer", {
+            enumerable: true,
+            configurable: true,
+            writable: true,
+            value: function (acc, uniprotData) {
+                var trackColor = cbioportalUtils.UniprotTopologyTrackToColor[uniprotData.type];
+                var trackTitle = cbioportalUtils.UniprotTopologyTypeToTitle[uniprotData.type];
+                if (trackTitle && trackColor) {
+                    acc.push(topologyRectangleBlockSpec(trackColor, trackTitle, uniprotData));
+                }
+                return acc;
+            }
+        });
+        mobx.makeObservable(_this);
+        return _this;
+    }
+    UniprotTopologyTrack_1 = UniprotTopologyTrack;
+    Object.defineProperty(UniprotTopologyTrack.prototype, "subTrackMargin", {
+        get: function () {
+            return (this.props.subTrackMargin ||
+                UniprotTopologyTrack_1.defaultProps.subTrackMargin);
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "subTrackTitleWidth", {
+        get: function () {
+            return this.props.xOffset
+                ? this.props.xOffset - this.subTrackMargin
+                : 0;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "uniprotTopologySpecs", {
+        get: function () {
+            var uniprotData = this.props.store.uniprotTopologyData.result;
+            if (uniprotData && !_.isEmpty(uniprotData)) {
+                return _.reduce(uniprotData, this.uniprotDataToTrackItemSpecsReducer, []);
+            }
+            else {
+                return [];
+            }
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "expander", {
+        get: function () {
+            var className = this.hasSubTracks
+                ? this.mainTrackHidden
+                    ? 'fa fa-caret-down'
+                    : 'fa fa-caret-right'
+                : null;
+            if (className) {
+                return (React.createElement("i", { className: className, style: { width: 10, marginLeft: 2 } }));
+            }
+            return null;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "mainTrackTitle", {
+        get: function () {
+            return (React.createElement("span", { style: { cursor: 'pointer' } },
+                React.createElement("span", { onClick: this.handleToggleExpand }, this.expander),
+                React.createElement(cbioportalFrontendCommons.DefaultTooltip, { placement: "right", overlay: React.createElement(UniprotTopologyTrackDescriptionTooltip, { displayList: this.uniprotTopologyTypes, uniprotId: this.props.store.uniprotId.result }), destroyTooltipOnHide: true },
+                    React.createElement("span", { style: { marginLeft: 4 }, onClick: this.handleToggleExpand },
+                        "Topology ",
+                        React.createElement("i", { className: "fa fa-info-circle" })))));
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "uniprotTopologyTypes", {
+        get: function () {
+            var uniprotData = this.props.store.uniprotTopologyData.result;
+            var uniprotDataByType = _.uniq(_.map(uniprotData, function (data) { return data.type; }));
+            return uniprotDataByType || [];
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "uniprotTopologySubSpecs", {
+        get: function () {
+            var _this = this;
+            var uniprotData = this.props.store.uniprotTopologyData.result;
+            var uniprotDataByType = _.groupBy(uniprotData, function (data) { return data.type; });
+            return _.keys(uniprotDataByType)
+                .map(function (type) { return ({
+                title: cbioportalUtils.UniprotTopologyTypeToTitle[type],
+                specs: _.reduce(uniprotDataByType[type], _this.uniprotDataToTrackItemSpecsReducer, []),
+            }); })
+                .filter(function (s) { return !_.isEmpty(s.specs); });
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "mainTrackHidden", {
+        get: function () {
+            return this.expanded && this.hasSubTracks;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "hasSubTracks", {
+        get: function () {
+            return this.uniprotTopologySubSpecs.length > 0;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "subTracks", {
+        get: function () {
+            var _this = this;
+            return this.hasSubTracks
+                ? this.uniprotTopologySubSpecs.map(function (item, index) { return (React.createElement(Track, { key: item.title, dataStore: _this.props.dataStore, xOffset: _this.props.xOffset, trackTitle: React.createElement("span", { style: {
+                            marginLeft: _this.subTrackMargin,
+                            width: _this.subTrackTitleWidth,
+                            display: 'flex',
+                        } },
+                        React.createElement(cbioportalFrontendCommons.EllipsisTextTooltip, { text: item.title, style: {
+                                overflow: 'hidden',
+                                whiteSpace: 'nowrap',
+                                textOverflow: 'ellipsis',
+                            } })), width: _this.props.width, proteinLength: _this.props.proteinLength, trackItems: item.specs, idClassPrefix: "uniprot-topology-" + index + "-", isSubTrack: true })); })
+                : null;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "render", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function () {
+            return (React.createElement("span", null,
+                React.createElement(Track, { dataStore: this.props.dataStore, width: this.props.width, xOffset: this.props.xOffset, proteinLength: this.props.proteinLength, trackTitle: this.mainTrackTitle, trackItems: this.mainTrackHidden ? [] : this.uniprotTopologySpecs, hideBaseline: this.mainTrackHidden, idClassPrefix: 'uniprot-topology-track-' }),
+                React.createElement(reactCollapse.Collapse, { isOpened: this.mainTrackHidden },
+                    React.createElement("span", null, this.subTracks))));
+        }
+    });
+    Object.defineProperty(UniprotTopologyTrack.prototype, "handleToggleExpand", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function () {
+            this.expanded = !this.expanded;
+        }
+    });
+    var UniprotTopologyTrack_1;
+    Object.defineProperty(UniprotTopologyTrack, "defaultProps", {
+        enumerable: true,
+        configurable: true,
+        writable: true,
+        value: {
+            subTrackMargin: 25,
+        }
+    });
+    __decorate([
+        mobx.observable
+    ], UniprotTopologyTrack.prototype, "expanded", void 0);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "subTrackMargin", null);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "subTrackTitleWidth", null);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "uniprotTopologySpecs", null);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "expander", null);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "mainTrackTitle", null);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "uniprotTopologyTypes", null);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "uniprotTopologySubSpecs", null);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "mainTrackHidden", null);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "hasSubTracks", null);
+    __decorate([
+        mobx.computed
+    ], UniprotTopologyTrack.prototype, "subTracks", null);
+    __decorate([
+        mobx.action.bound
+    ], UniprotTopologyTrack.prototype, "handleToggleExpand", null);
+    UniprotTopologyTrack = UniprotTopologyTrack_1 = __decorate([
+        mobxReact.observer
+    ], UniprotTopologyTrack);
+    return UniprotTopologyTrack;
+}(React.Component));
+
 var TrackPanel = /** @class */ (function (_super) {
     __extends(TrackPanel, _super);
     function TrackPanel(props) {
@@ -8798,6 +9059,9 @@ var TrackPanel = /** @class */ (function (_super) {
                 _a[exports.TrackName.UniprotPTM] = this.getPtmTrack(exports.TrackName.UniprotPTM, cbioportalUtils.PtmSource.Uniprot),
                 _a[exports.TrackName.Exon] = !this.props.trackVisibility ||
                     this.props.trackVisibility[exports.TrackName.Exon] === 'visible' ? (React.createElement(ExonTrack, { store: this.props.store, dataStore: this.props.store.dataStore, width: this.props.geneWidth, xOffset: this.props.geneXOffset, proteinLength: this.proteinLength })) : null,
+                _a[exports.TrackName.UniprotTopology] = !this.props.trackVisibility ||
+                    this.props.trackVisibility[exports.TrackName.UniprotTopology] ===
+                        'visible' ? (React.createElement(UniprotTopologyTrack, { store: this.props.store, dataStore: this.props.store.dataStore, width: this.props.geneWidth, xOffset: this.props.geneXOffset, proteinLength: this.proteinLength, collapsed: this.props.collapseUniprotTopologyTrack })) : null,
                 _a;
         },
         enumerable: false,
@@ -8857,6 +9121,7 @@ var TrackPanel = /** @class */ (function (_super) {
                 exports.TrackName.OncoKB,
                 exports.TrackName.dbPTM,
                 exports.TrackName.Exon,
+                exports.TrackName.UniprotTopology,
             ],
         }
     });
@@ -9098,7 +9363,7 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
                     : -1;
             });
             var specs = this.createInitialSpecs(positionMutations, countsByPosition, group, placement);
-            var noLabelsAreShown = !_.isEmpty(specs) && specs.every(function (spec) { return !spec.label.show; });
+            var noLabelsAreShown = !___default.isEmpty(specs) && specs.every(function (spec) { return !spec.label.show; });
             if (noLabelsAreShown) {
                 this.labelOneLollipopByDefault(this.getRemainingDomains(positionMutations), specs);
             }
@@ -9309,7 +9574,7 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
             if (!this.props.store.pfamDomainData.isPending &&
                 this.props.store.pfamDomainData.result &&
                 this.props.store.pfamDomainData.result.length > 0) {
-                return _.keyBy(this.props.store.pfamDomainData.result, 'pfamAccession');
+                return ___default.keyBy(this.props.store.pfamDomainData.result, 'pfamAccession');
             }
             else {
                 return {};
@@ -9509,7 +9774,7 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
                     React.createElement(LollipopPlot, { sequence: this.sequence, lollipops: this.lollipops, domains: this.domains, dataStore: this.props.store.dataStore, vizWidth: this.props.geneWidth, vizHeight: this.props.vizHeight, hugoGeneSymbol: this.hugoGeneSymbol, xMax: this.proteinLength, yMax: this.yMaxInput, yMaxFractionDigits: this.yMaxSliderStep < 1
                             ? this.props.yMaxFractionDigits
                             : undefined, yMaxLabelPostfix: this.props.yMaxLabelPostfix, yAxisLabelPadding: this.props.yAxisLabelPadding, showYAxis: this.props.showYAxis, bottomYMax: this.bottomYMaxInput, onXAxisOffset: this.onXAxisOffset, topYAxisSymbol: this.props.topYAxisSymbol, bottomYAxisSymbol: this.props.bottomYAxisSymbol, groups: this.groups }),
-                    React.createElement(TrackPanel, { store: this.props.store, geneWidth: this.props.geneWidth, tracks: this.props.tracks, trackVisibility: this.trackVisibility, pubMedCache: this.props.pubMedCache, proteinLength: this.proteinLength, geneXOffset: this.geneXOffset, collapsePtmTrack: this.props.collapsePtmTrack })));
+                    React.createElement(TrackPanel, { store: this.props.store, geneWidth: this.props.geneWidth, tracks: this.props.tracks, trackVisibility: this.trackVisibility, pubMedCache: this.props.pubMedCache, proteinLength: this.proteinLength, geneXOffset: this.geneXOffset, collapsePtmTrack: this.props.collapsePtmTrack, collapseUniprotTopologyTrack: this.props.collapseUniprotTopologyTrack })));
             }
             else if (this.props.store.canonicalTranscript.isComplete &&
                 this.props.store.canonicalTranscript.result === undefined) {
@@ -9646,7 +9911,7 @@ var DefaultStringQueryCache = /** @class */ (function () {
     });
     Object.defineProperty(DefaultStringQueryCache.prototype, "cache", {
         get: function () {
-            return _.fromPairs(this._cache.toJSON());
+            return ___default.fromPairs(this._cache.toJSON());
         },
         enumerable: false,
         configurable: true
@@ -9793,7 +10058,7 @@ var DefaultMutationMapperDataStore = /** @class */ (function () {
     }
     Object.defineProperty(DefaultMutationMapperDataStore.prototype, "groupFiltersKeyedByGroup", {
         get: function () {
-            return _.keyBy(this.groupFilters, 'group');
+            return ___default.keyBy(this.groupFilters, 'group');
         },
         enumerable: false,
         configurable: true
@@ -9810,7 +10075,7 @@ var DefaultMutationMapperDataStore = /** @class */ (function () {
             var _this = this;
             return this.dataFilters.length > 0
                 ? // TODO simplify array flatten if possible
-                    this.data.filter(function (m) { return _this.dataMainFilter(_.flatten([m])[0]); })
+                    this.data.filter(function (m) { return _this.dataMainFilter(___default.flatten([m])[0]); })
                 : this.data;
         },
         enumerable: false,
@@ -9836,7 +10101,7 @@ var DefaultMutationMapperDataStore = /** @class */ (function () {
             return this.selectionFilters.length > 0
                 ? // TODO simplify array flatten if possible
                     this.sortedFilteredData.filter(function (m) {
-                        return _this.dataSelectFilter(_.flatten([m])[0]);
+                        return _this.dataSelectFilter(___default.flatten([m])[0]);
                     })
                 : [];
         },
@@ -10180,7 +10445,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
                 return __generator(this, function (_a) {
                     return [2 /*return*/, this.fetchCanonicalTranscript(hugoSymbol, isoformOverrideSource, client).catch(function () {
                             // get transcript with max protein length in given list of all transcripts
-                            var transcript = _.maxBy(allTranscripts, function (t) { return t.proteinLength; });
+                            var transcript = ___default.maxBy(allTranscripts, function (t) { return t.proteinLength; });
                             return transcript ? transcript : undefined;
                         })];
                 });
@@ -10251,7 +10516,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
         enumerable: false,
         configurable: true,
         writable: true,
-        value: function (swissProtId, client) {
+        value: function (swissProtId, category, client) {
             if (client === void 0) { client = this.genomeNexusClient; }
             return __awaiter(this, void 0, void 0, function () {
                 var uniprotData, featureList;
@@ -10259,7 +10524,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
                     switch (_a.label) {
                         case 0:
                             if (!swissProtId) return [3 /*break*/, 2];
-                            return [4 /*yield*/, request.get(getUrl("https://www.ebi.ac.uk/proteins/api/features/<%= uniprotAccession %>?categories=PTM", { uniprotAccession: swissProtId }))];
+                            return [4 /*yield*/, request.get(getUrl("https://www.ebi.ac.uk/proteins/api/features/<%= uniprotAccession %>?categories=" + category.join(','), { uniprotAccession: swissProtId }))];
                         case 1:
                             uniprotData = _a.sent();
                             featureList = JSON.parse(uniprotData.text);
@@ -10335,7 +10600,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
                     else if (mutations.length === 0) {
                         return [2 /*return*/, ONCOKB_DEFAULT_DATA];
                     }
-                    mutationsToQuery = _.filter(mutations, function (m) {
+                    mutationsToQuery = ___default.filter(mutations, function (m) {
                         return (m.mutationType &&
                             m.mutationType.toLowerCase() ===
                                 cbioportalFrontendCommons.CanonicalMutationType.FUSION) ||
@@ -10357,10 +10622,10 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
                 return __generator(this, function (_c) {
                     switch (_c.label) {
                         case 0:
-                            mutationQueryVariants = _.uniqBy(_.map(queryVariants.filter(function (mutation) { return mutation.mutationType !== 'Fusion'; }), function (mutation) {
+                            mutationQueryVariants = ___default.uniqBy(___default.map(queryVariants.filter(function (mutation) { return mutation.mutationType !== 'Fusion'; }), function (mutation) {
                                 return cbioportalUtils.generateProteinChangeQuery(getEntrezGeneId(mutation), getTumorType(mutation), mutation.proteinChange, mutation.mutationType, mutation.proteinPosStart, mutation.proteinPosEnd, evidenceTypes);
                             }), 'id');
-                            structuralQueryVariants = _.uniqBy(_.map(queryVariants.filter(function (mutation) {
+                            structuralQueryVariants = ___default.uniqBy(___default.map(queryVariants.filter(function (mutation) {
                                 var _a;
                                 return ((_a = mutation.mutationType) === null || _a === void 0 ? void 0 : _a.toUpperCase()) ===
                                     cbioportalUtils.StructuralVariantType.FUSION;
@@ -10391,7 +10656,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
                             structuralVariantQueryResult = _b;
                             return [2 /*return*/, {
                                     // generateIdToIndicatorMap(oncokbSearch)
-                                    indicatorMap: _.keyBy(mutationQueryResult.concat(structuralVariantQueryResult), function (indicator) { return indicator.query.id; }),
+                                    indicatorMap: ___default.keyBy(mutationQueryResult.concat(structuralVariantQueryResult), function (indicator) { return indicator.query.id; }),
                                 }];
                     }
                 });
@@ -10676,7 +10941,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                                 return [4 /*yield*/, this.dataFetcher.fetchSwissProtAccession(this.gene.entrezGeneId)];
                             case 1:
                                 accession = _a.sent();
-                                if (_.isArray(accession)) {
+                                if (___default.isArray(accession)) {
                                     return [2 /*return*/, accession[0]];
                                 }
                                 else {
@@ -10733,7 +10998,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                                 this.transcriptsWithProteinLength.result &&
                                 this.transcriptsWithProteinLength.result.length > 0) {
                                 // add domain ranges for all transcripts to this call
-                                domainRanges = [].concat.apply([domainRanges], _.compact(this.transcriptsWithProteinLength.result.map(function (transcriptId) {
+                                domainRanges = [].concat.apply([domainRanges], ___default.compact(this.transcriptsWithProteinLength.result.map(function (transcriptId) {
                                     return _this.transcriptsByTranscriptId[transcriptId].pfamDomains;
                                 })));
                             }
@@ -10778,7 +11043,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                 ]; },
                 invoke: function () { return __awaiter(_this, void 0, void 0, function () {
                     return __generator(this, function (_a) {
-                        return [2 /*return*/, _.compact(_.unionBy(this.transcriptsByHugoSymbol.result, [this.canonicalTranscript.result], function (t) { return t && t.transcriptId; }))];
+                        return [2 /*return*/, ___default.compact(___default.unionBy(this.transcriptsByHugoSymbol.result, [this.canonicalTranscript.result], function (t) { return t && t.transcriptId; }))];
                     });
                 }); },
                 onError: function () {
@@ -10818,7 +11083,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                             this.canonicalTranscript.result) {
                             // ignore transcripts without protein length
                             // TODO: better solution is to hide lollipop plot for those transcripts
-                            return [2 /*return*/, _.compact(this.allTranscripts.result.map(function (et) {
+                            return [2 /*return*/, ___default.compact(this.allTranscripts.result.map(function (et) {
                                     return et.proteinLength && et.transcriptId;
                                 }))];
                         }
@@ -10851,13 +11116,13 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                             this.allTranscripts.result &&
                             this.transcriptsWithProteinLength.result &&
                             this.transcriptsWithProteinLength.result.length > 0) {
-                            transcripts = _.uniq([].concat.apply([], cbioportalUtils.uniqueGenomicLocations(this.getMutations()).map(function (gl) {
+                            transcripts = ___default.uniq([].concat.apply([], cbioportalUtils.uniqueGenomicLocations(this.getMutations()).map(function (gl) {
                                 var variantAnnotation = _this
                                     .indexedVariantAnnotations.result
                                     ? _this.indexedVariantAnnotations.result[cbioportalUtils.genomicLocationString(gl)]
                                     : undefined;
                                 if (variantAnnotation &&
-                                    !_.isEmpty(variantAnnotation.transcript_consequences)) {
+                                    !___default.isEmpty(variantAnnotation.transcript_consequences)) {
                                     return variantAnnotation.transcript_consequences
                                         .map(function (tc) { return tc.transcript_id; })
                                         .filter(function (transcriptId) {
@@ -10936,7 +11201,9 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                             // return this.dataFetcher.fetchPtmData(
                             //     this.activeTranscript.result
                             // );
-                            return [2 /*return*/, this.dataFetcher.fetchUniprotFeatures(uniprotId)];
+                            return [2 /*return*/, this.dataFetcher.fetchUniprotFeatures(uniprotId, [
+                                    cbioportalUtils.UniprotCategory.PTM,
+                                ])];
                         }
                         else {
                             return [2 /*return*/, []];
@@ -10948,6 +11215,46 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                 },
             }, [])
         });
+        Object.defineProperty(this, "uniprotTopologyData", {
+            enumerable: true,
+            configurable: true,
+            writable: true,
+            value: cbioportalFrontendCommons.remoteData({
+                await: function () { return [
+                    _this.mutationData,
+                    _this.activeTranscript,
+                    _this.allTranscripts,
+                ]; },
+                invoke: function () { return __awaiter(_this, void 0, void 0, function () {
+                    var uniprotId, data, transcript, uniprotFeatures;
+                    return __generator(this, function (_a) {
+                        switch (_a.label) {
+                            case 0:
+                                data = [];
+                                if (this.activeTranscript.result) {
+                                    transcript = this.transcriptsByTranscriptId[this.activeTranscript.result];
+                                    uniprotId = transcript === null || transcript === void 0 ? void 0 : transcript.uniprotId;
+                                }
+                                if (!uniprotId) return [3 /*break*/, 2];
+                                return [4 /*yield*/, this.dataFetcher.fetchUniprotFeatures(uniprotId, [cbioportalUtils.UniprotCategory.TOPOLOGY])];
+                            case 1:
+                                uniprotFeatures = _a.sent();
+                                uniprotFeatures.forEach(function (uniprotFeature) {
+                                    var uniprotTopology = cbioportalUtils.convertUniprotFeatureToUniprotTopology(uniprotFeature);
+                                    if (uniprotTopology) {
+                                        data.push(uniprotTopology);
+                                    }
+                                });
+                                return [2 /*return*/, data];
+                            case 2: return [2 /*return*/, []];
+                        }
+                    });
+                }); },
+                onError: function () {
+                    // fail silently
+                },
+            }, [])
+        });
         Object.defineProperty(this, "dbPtmData", {
             enumerable: true,
             configurable: true,
@@ -11081,7 +11388,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
             value: cbioportalFrontendCommons.remoteData({
                 await: function () { return [_this.oncoKbCancerGenes]; },
                 invoke: function () {
-                    return Promise.resolve(_.reduce(_this.oncoKbCancerGenes.result, function (map, next) {
+                    return Promise.resolve(___default.reduce(_this.oncoKbCancerGenes.result, function (map, next) {
                         if (next.oncokbAnnotated) {
                             map[next.entrezGeneId] = true;
                         }
@@ -11155,7 +11462,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                     return __generator(this, function (_b) {
                         switch (_b.label) {
                             case 0:
-                                if (!!_.isEmpty(this.getMutations())) return [3 /*break*/, 2];
+                                if (!!___default.isEmpty(this.getMutations())) return [3 /*break*/, 2];
                                 return [4 /*yield*/, this.dataFetcher.fetchVariantAnnotationsIndexedByGenomicLocation(this.getMutations(), this.annotationFields, this.isoformOverrideSource)];
                             case 1:
                                 _a = _b.sent();
@@ -11183,7 +11490,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                     return __generator(this, function (_b) {
                         switch (_b.label) {
                             case 0:
-                                if (!!_.isEmpty(this.getMutations())) return [3 /*break*/, 2];
+                                if (!!___default.isEmpty(this.getMutations())) return [3 /*break*/, 2];
                                 return [4 /*yield*/, this.dataFetcher.fetchMyVariantInfoAnnotationsIndexedByGenomicLocation(this.getMutations(), this.isoformOverrideSource)];
                             case 1:
                                 _a = _b.sent();
@@ -11242,7 +11549,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
     });
     Object.defineProperty(DefaultMutationMapperStore.prototype, "annotationFields", {
         get: function () {
-            return _.uniq(['annotation_summary', 'hotspots'].concat(this.config.annotationFields || []));
+            return ___default.uniq(['annotation_summary', 'hotspots'].concat(this.config.annotationFields || []));
         },
         enumerable: false,
         configurable: true
@@ -11269,7 +11576,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
             else if (this.config.filterMutationsBySelectedTranscript &&
                 this.activeTranscript.result &&
                 this.indexedVariantAnnotations.result &&
-                !_.isEmpty(this.indexedVariantAnnotations.result)) {
+                !___default.isEmpty(this.indexedVariantAnnotations.result)) {
                 return this.getAnnotatedMutations(this.activeTranscript.result);
             }
             else {
@@ -11329,7 +11636,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
     });
     Object.defineProperty(DefaultMutationMapperStore.prototype, "mutationsByPosition", {
         get: function () {
-            return cbioportalUtils.groupMutationsByProteinStartPos(_.flatten(this.dataStore.sortedFilteredData));
+            return cbioportalUtils.groupMutationsByProteinStartPos(___default.flatten(this.dataStore.sortedFilteredData));
         },
         enumerable: false,
         configurable: true
@@ -11338,7 +11645,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
         get: function () {
             return this.dataStore.sortedFilteredGroupedData.map(function (groupedData) { return ({
                 group: groupedData.group,
-                mutations: cbioportalUtils.groupMutationsByProteinStartPos(_.flatten(groupedData.data)),
+                mutations: cbioportalUtils.groupMutationsByProteinStartPos(___default.flatten(groupedData.data)),
             }); });
         },
         enumerable: false,
@@ -11391,7 +11698,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
     });
     Object.defineProperty(DefaultMutationMapperStore.prototype, "transcriptsByTranscriptId", {
         get: function () {
-            return _.keyBy(this.allTranscripts.result, function (transcript) { return transcript.transcriptId; });
+            return ___default.keyBy(this.allTranscripts.result, function (transcript) { return transcript.transcriptId; });
         },
         enumerable: false,
         configurable: true
@@ -11476,7 +11783,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
             if (this.indexedVariantAnnotations.result &&
                 this.transcriptsWithAnnotations.result &&
                 this.canonicalTranscript.isComplete) {
-                return _.fromPairs(this.transcriptsWithAnnotations.result.map(function (t) { return [
+                return ___default.fromPairs(this.transcriptsWithAnnotations.result.map(function (t) { return [
                     t,
                     _this.getAnnotatedMutations(t),
                 ]; }));
@@ -11710,7 +12017,7 @@ var TranscriptDropdown = /** @class */ (function (_super) {
             // then ones with refseq id
             // then protein length
             // lastly the ensembl id
-            transcripts = _.orderBy(transcripts, [
+            transcripts = ___default.orderBy(transcripts, [
                 function (t) {
                     return canonicalTranscript.result &&
                         t === canonicalTranscript.result.transcriptId;
@@ -12058,7 +12365,7 @@ var MutationMapper = /** @class */ (function (_super) {
                     this.isFiltered &&
                     this.filterResetPanel
                     ? this.filterResetPanel
-                    : undefined, trackDataStatus: this.trackDataStatus, showTrackSelector: this.props.showTrackSelector, onXAxisOffset: this.onXAxisOffset, onTrackVisibilityChange: this.props.onTrackVisibilityChange, getMutationCount: this.props.getMutationCount, getLollipopColor: this.props.getLollipopColor, yMaxLabelPostfix: this.plotYMaxLabelPostfix, yMaxFractionDigits: this.props.plotYMaxFractionDigits, yAxisLabelPadding: this.props.plotYAxisLabelPadding, showYAxis: this.props.showPlotYAxis, topYAxisSymbol: this.plotTopYAxisSymbol, bottomYAxisSymbol: this.plotBottomYAxisSymbol, topYAxisDefaultMax: this.plotTopYAxisDefaultMax, topYAxisDefaultMin: this.plotBottomYAxisDefaultMin, bottomYAxisDefaultMax: this.plotBottomYAxisDefaultMax, bottomYAxisDefaultMin: this.plotBottomYAxisDefaultMin, lollipopTooltipCountInfo: this.props.plotLollipopTooltipCountInfo, collapsePtmTrack: this.props.collapsePtmTrack }));
+                    : undefined, trackDataStatus: this.trackDataStatus, showTrackSelector: this.props.showTrackSelector, onXAxisOffset: this.onXAxisOffset, onTrackVisibilityChange: this.props.onTrackVisibilityChange, getMutationCount: this.props.getMutationCount, getLollipopColor: this.props.getLollipopColor, yMaxLabelPostfix: this.plotYMaxLabelPostfix, yMaxFractionDigits: this.props.plotYMaxFractionDigits, yAxisLabelPadding: this.props.plotYAxisLabelPadding, showYAxis: this.props.showPlotYAxis, topYAxisSymbol: this.plotTopYAxisSymbol, bottomYAxisSymbol: this.plotBottomYAxisSymbol, topYAxisDefaultMax: this.plotTopYAxisDefaultMax, topYAxisDefaultMin: this.plotBottomYAxisDefaultMin, bottomYAxisDefaultMax: this.plotBottomYAxisDefaultMax, bottomYAxisDefaultMin: this.plotBottomYAxisDefaultMin, lollipopTooltipCountInfo: this.props.plotLollipopTooltipCountInfo, collapsePtmTrack: this.props.collapsePtmTrack, collapseUniprotTopologyTrack: this.props.collapseUniprotTopologyTrack }));
         },
         enumerable: false,
         configurable: true