react-mutation-mapper 0.8.29 → 0.8.34

package/dist/component/column/Annotation.d.ts

@@ -12,6 +12,7 @@ export declare type AnnotationProps = {
     oncoKbCancerGenes?: RemoteData<CancerGene[] | Error | undefined>;
     usingPublicOncoKbInstance: boolean;
     mergeOncoKbIcons?: boolean;
+    oncoKbContentPadding?: number;
     pubMedCache?: MobxCache;
     resolveEntrezGeneId?: (mutation: Mutation) => number;
     resolveTumorType?: (mutation: Mutation) => string;
@@ -27,6 +28,7 @@ export declare type GenericAnnotationProps = {
     enableMyCancerGenome: boolean;
     enableOncoKb: boolean;
     mergeOncoKbIcons?: boolean;
+    oncoKbContentPadding?: number;
     pubMedCache?: MobxCache;
     userEmailAddress?: string;
 };

package/dist/component/column/Signal.d.ts

@@ -1,23 +1,24 @@
 import * as React from 'react';
 import 'rc-tooltip/assets/bootstrap_white.css';
-import { IExtendedSignalMutation, Mutation, RemoteData } from 'cbioportal-utils';
+import { IExtendedSignalMutation, Mutation, RemoteData, Pathogenicity } from 'cbioportal-utils';
 import { VariantAnnotation } from 'genome-nexus-ts-api-client';
 declare type SignalProps = {
     mutation: Mutation;
     indexedVariantAnnotations?: RemoteData<{
         [genomicLocation: string]: VariantAnnotation;
     } | undefined>;
+    mutationType?: Pathogenicity;
 };
 declare type SignalValueProps = SignalProps & {
     significantDigits?: number;
 };
 export declare function getSignalData(mutation: Mutation, indexedVariantAnnotations?: RemoteData<{
     [genomicLocation: string]: VariantAnnotation;
-} | undefined>): IExtendedSignalMutation;
+} | undefined>, mutationType?: Pathogenicity): IExtendedSignalMutation[];
 export declare function signalSortMethod(a: IExtendedSignalMutation, b: IExtendedSignalMutation): number;
 export declare function getSortValue(signalData: IExtendedSignalMutation): number | null;
-export declare function download(signalData: IExtendedSignalMutation): string;
-export declare function getSignalValue(mutation: Mutation, indexedVariantAnnotations?: RemoteData<{
+export declare function download(signalData: IExtendedSignalMutation, mutationType?: Pathogenicity): string;
+export declare function getSingleSignalValue(mutation: Mutation, mutationType: Pathogenicity, indexedVariantAnnotations?: RemoteData<{
     [genomicLocation: string]: VariantAnnotation;
 } | undefined>, significantDigits?: number): number | null;
 export declare const SignalTable: React.FunctionComponent<SignalValueProps>;

package/dist/component/oncokb/OncoKB.d.ts

@@ -15,11 +15,12 @@ export interface IOncoKbProps {
     hugoGeneSymbol: string;
     userEmailAddress?: string;
     disableFeedback?: boolean;
+    contentPadding?: number;
 }
 export declare function sortValue(indicator?: IndicatorQueryResp | undefined | null): number[];
 export declare function download(indicator?: IndicatorQueryResp | undefined | null): string;
 export default class OncoKB extends React.Component<IOncoKbProps, {}> {
-    constructor(props: any);
+    constructor(props: IOncoKbProps);
     showFeedback: boolean;
     tooltipDataLoadComplete: boolean;
     render(): JSX.Element;

package/dist/component/track/ExonTrack.d.ts

@@ -11,6 +11,8 @@ export default class ExonTrack extends React.Component<ExonTrackProps, {}> {
     constructor(props: any);
     get transcriptId(): string | undefined;
     get transcript(): EnsemblTranscript | undefined;
+    get chromosome(): string;
+    get genomeBuild(): string;
     get exonSpecs(): TrackItemSpec[];
     get trackTitle(): JSX.Element;
     render(): JSX.Element;

package/dist/index.d.ts

@@ -14,7 +14,7 @@ export { default as Hgvsg } from './component/column/Hgvsg';
 export * from './component/column/HgvsHelper';
 export { default as MutationStatus } from './component/column/MutationStatus';
 export { default as ProteinChange, proteinChangeSortMethod, } from './component/column/ProteinChange';
-export { default as Signal, getSignalData, getSortValue as signalSortValue, download as signalDownload, getSignalValue, SignalTable, } from './component/column/Signal';
+export { default as Signal, getSignalData, getSortValue as signalSortValue, download as signalDownload, getSingleSignalValue, SignalTable, } from './component/column/Signal';
 export { default as DropdownSelector, DropdownSelectorProps, } from './component/filter/DropdownSelector';
 export { default as BadgeLabel } from './component/filter/BadgeLabel';
 export { default as BadgeSelector, BadgeSelectorOption, BadgeSelectorProps, } from './component/filter/BadgeSelector';

package/dist/index.es.js

@@ -3,7 +3,7 @@ import { makeObservable, observable, action, computed, reaction } from 'mobx';
 import { observer } from 'mobx-react';
 import React__default, { createElement, Component, useState, Fragment } from 'react';
 import { DefaultTooltip, TruncatedText, getNCBIlink, trimOffHtmlTagEntities, cachePostMethodsOnClient, CanonicalMutationType, MutationTumorTypeFrequencyTable, FREQUENCY_COLUMNS_DEFINITION, FrequencyTableColumnEnum, CheckedSelect, getSelectedValuesMap, Checklist, MUT_COLOR_MISSENSE, MUT_COLOR_MISSENSE_PASSENGER, MUT_COLOR_INFRAME, MUT_COLOR_INFRAME_PASSENGER, MUT_COLOR_TRUNC, MUT_COLOR_TRUNC_PASSENGER, MUT_COLOR_SPLICE, MUT_COLOR_SPLICE_PASSENGER, STRUCTURAL_VARIANT_COLOR, STRUCTURAL_VARIANT_PASSENGER_COLOR, MUT_COLOR_OTHER, getCanonicalMutationType, getProteinImpactTypeFromCanonical, ProteinImpactType, getProteinImpactType, resolveColumnVisibility, resolveColumnVisibilityByColumnDefinition, longestCommonStartingSubstring, getTextWidth, unhoverAllComponents, SVGAxis, getComponentIndex, initHitZoneFromConfig, defaultHitzoneConfig, EditableSpan, DownloadControls, EllipsisTextTooltip, remoteData, WindowWrapper } from 'cbioportal-frontend-commons';
-import { CIVIC_NA_VALUE, generateQueryVariantId, OncoKbCardDataType, parseMyCancerGenomeLink, defaultArraySortMethod, defaultSortMethod, LEVELS, uniqueGenomicLocations, indexAnnotationsByGenomicLocation, getCivicEntry, getRemoteDataGroupStatus, getMyCancerGenomeLinks, isLinearClusterHotspot, is3dHotspot, calculateOncoKbAvailableDataType, getVariantAnnotation, getDbsnpRsId, getMyVariantInfoAnnotation, generateHgvsgByMutation, calcProteinChangeSortValue, extendMutations, formatNumberValueInSignificantDigits, generateTumorTypeDecomposition, formatPercentValue, countMutationsByProteinChange, numberOfLeadingDecimalZeros, filterLinearClusterHotspotsByMutations, filter3dHotspotsByMutations, isHotspot, defaultHotspotFilter, defaultStringArraySortMethod, extractExonInformation, formatExonLocation, compareByPtmTypePriority, ptmColor, UniprotTopologyTypeToTitle, UniprotTopologyTrackToColor, PtmSource, PTM_SOURCE_URL, getMyVariantInfoAnnotationsFromIndexedVariantAnnotations, generateProteinChangeQuery, StructuralVariantType, generateAnnotateStructuralVariantQuery, getMutationsByTranscriptId, groupMutationsByProteinStartPos, groupHotspotsByMutations, getMyCancerGenomeData, convertUniprotFeatureToPtm, convertDbPtmToPtm, indexHotspotsData, genomicLocationString, UniprotCategory, convertUniprotFeatureToUniprotTopology, groupPtmDataByPosition, groupPtmDataByTypeAndPosition, groupCancerHotspotDataByPosition, fetchCivicGenes, fetchCivicVariants } from 'cbioportal-utils';
+import { CIVIC_NA_VALUE, generateQueryVariantId, OncoKbCardDataType, parseMyCancerGenomeLink, defaultArraySortMethod, defaultSortMethod, LEVELS, uniqueGenomicLocations, indexAnnotationsByGenomicLocation, getCivicEntry, getRemoteDataGroupStatus, getMyCancerGenomeLinks, isLinearClusterHotspot, is3dHotspot, calculateOncoKbAvailableDataType, getVariantAnnotation, getDbsnpRsId, getMyVariantInfoAnnotation, generateHgvsgByMutation, calcProteinChangeSortValue, Pathogenicity, extendMutations, formatNumberValueInSignificantDigits, generateTumorTypeDecomposition, formatPercentValue, countMutationsByProteinChange, numberOfLeadingDecimalZeros, filterLinearClusterHotspotsByMutations, filter3dHotspotsByMutations, isHotspot, defaultHotspotFilter, defaultStringArraySortMethod, extractExonInformation, formatExonLocation, formatExonLength, compareByPtmTypePriority, ptmColor, UniprotTopologyTypeToTitle, UniprotTopologyTrackToColor, PtmSource, PTM_SOURCE_URL, getMyVariantInfoAnnotationsFromIndexedVariantAnnotations, generateProteinChangeQuery, StructuralVariantType, generateAnnotateStructuralVariantQuery, getMutationsByTranscriptId, groupMutationsByProteinStartPos, groupHotspotsByMutations, getMyCancerGenomeData, convertUniprotFeatureToPtm, convertDbPtmToPtm, indexHotspotsData, genomicLocationString, UniprotCategory, convertUniprotFeatureToUniprotTopology, groupPtmDataByPosition, groupPtmDataByTypeAndPosition, groupCancerHotspotDataByPosition, fetchCivicGenes, fetchCivicVariants } from 'cbioportal-utils';
 import classnames from 'classnames';
 import autobind from 'autobind-decorator';
 import { Tabs, Tab, Modal } from 'react-bootstrap';
@@ -15,7 +15,7 @@ import { OncoKbAPI } from 'oncokb-ts-api-client';
 import Select, { components } from 'react-select';
 import $ from 'jquery';
 import Slider from 'react-rangeslider';
-import request from 'superagent';
+import request, { get } from 'superagent';
 import memoize from 'memoize-weak-decorator';
 import { cached } from 'mobxpromise';
 
@@ -1859,17 +1859,11 @@ var OncoKB = /** @class */ (function (_super) {
                 ].map(function (dataType) { return (createElement(AnnotationIcon, { type: dataType, tooltipOverlay: _this.tooltipContent(dataType), indicator: _this.props.indicator, availableDataTypes: _this.props.availableDataTypes })); })));
             }
             else {
-                // TODO This doesn't always work, in some cases it adds unnecessary empty icons, we need a better solution.
-                // we still need to draw empty icons even if there is no indicator data.
-                // this is to keep the icon alignment consistent with the rest of the column
-                // return (
-                //     <>
-                //         {this.props.availableDataTypes?.map(() => (
-                //             <AnnotationIconWithTooltip icon={<i />} />
-                //         ))}
-                //     </>
-                // );
-                return null;
+                // workaround: use content padding value to draw an empty icon when there is no indicator data.
+                // this is to keep the icon alignment consistent with the rest of the column.
+                // ideally we should implement grouped columns to avoid these kind of workarounds
+                // (see https://github.com/cBioPortal/cbioportal/issues/8723)
+                return createElement("i", { style: { paddingRight: this.props.contentPadding } });
             }
         }
     });
@@ -2297,9 +2291,9 @@ function sortValue$4(annotation) {
     ]);
 }
 function GenericAnnotation(props) {
-    var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb, pubMedCache = props.pubMedCache, userEmailAddress = props.userEmailAddress, mergeOncoKbIcons = props.mergeOncoKbIcons;
+    var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb, pubMedCache = props.pubMedCache, userEmailAddress = props.userEmailAddress, mergeOncoKbIcons = props.mergeOncoKbIcons, oncoKbContentPadding = props.oncoKbContentPadding;
     return (createElement("span", { style: { display: 'flex', minWidth: 100 } },
-        enableOncoKb && (createElement(OncoKB, { usingPublicOncoKbInstance: annotation.usingPublicOncoKbInstance, hugoGeneSymbol: annotation.hugoGeneSymbol, geneNotExist: !annotation.oncoKbGeneExist, isCancerGene: annotation.isOncoKbCancerGene, status: annotation.oncoKbStatus, indicator: annotation.oncoKbIndicator, availableDataTypes: annotation.oncoKbAvailableDataTypes, mergeAnnotationIcons: mergeOncoKbIcons, pubMedCache: pubMedCache, userEmailAddress: userEmailAddress })),
+        enableOncoKb && (createElement(OncoKB, { usingPublicOncoKbInstance: annotation.usingPublicOncoKbInstance, hugoGeneSymbol: annotation.hugoGeneSymbol, geneNotExist: !annotation.oncoKbGeneExist, isCancerGene: annotation.isOncoKbCancerGene, status: annotation.oncoKbStatus, indicator: annotation.oncoKbIndicator, availableDataTypes: annotation.oncoKbAvailableDataTypes, mergeAnnotationIcons: mergeOncoKbIcons, pubMedCache: pubMedCache, userEmailAddress: userEmailAddress, contentPadding: oncoKbContentPadding })),
         enableCivic && (createElement(Civic, { civicEntry: annotation.civicEntry, civicStatus: annotation.civicStatus, hasCivicVariants: annotation.hasCivicVariants })),
         enableMyCancerGenome && (createElement(MyCancerGenome, { linksHTML: annotation.myCancerGenomeLinks })),
         enableHotspot && (createElement(HotspotAnnotation, { isHotspot: annotation.isHotspot, is3dHotspot: annotation.is3dHotspot, status: annotation.hotspotStatus }))));
@@ -3158,8 +3152,9 @@ var ProteinChange = /** @class */ (function (_super) {
     return ProteinChange;
 }(Component));
 
-function getSignalData(mutation, indexedVariantAnnotations) {
-    var signalData = {};
+function getSignalData(mutation, indexedVariantAnnotations, mutationType // mutationType could be "germline", "somatic", or "undefined" which means both
+) {
+    var signalData = [];
     var variantAnnotation = indexedVariantAnnotations
         ? getVariantAnnotation(mutation, indexedVariantAnnotations.result)
         : undefined;
@@ -3167,12 +3162,37 @@ function getSignalData(mutation, indexedVariantAnnotations) {
         variantAnnotation.signalAnnotation &&
         variantAnnotation.signalAnnotation.annotation &&
         variantAnnotation.signalAnnotation.annotation.length > 0) {
-        variantAnnotation.signalAnnotation.annotation.forEach(function (annotation) {
-            // only have one germline annotation
-            if (annotation.mutationStatus.includes('germline')) {
-                signalData = extendMutations([annotation])[0];
+        // if mutation is somatic OR germline, get annotation depending on mutationType
+        if (variantAnnotation.signalAnnotation.annotation.length === 1) {
+            if ((mutationType === Pathogenicity.GERMLINE &&
+                variantAnnotation.signalAnnotation.annotation[0].mutationStatus.includes('germline')) ||
+                (mutationType === Pathogenicity.SOMATIC &&
+                    variantAnnotation.signalAnnotation.annotation[0].mutationStatus.includes('somatic'))) {
+                signalData = extendMutations([
+                    variantAnnotation.signalAnnotation.annotation[0],
+                ]);
+            }
+        }
+        // if mutation is both somatic AND germline, get annotation for both or get one of them depending on mutationType
+        else {
+            // if mutationType is undefined, get annotation for both somatic and germline
+            if (mutationType === undefined) {
+                signalData = extendMutations(variantAnnotation.signalAnnotation.annotation);
             }
-        });
+            // if mutationType is defined, get annotation depending on mutationType
+            else {
+                variantAnnotation.signalAnnotation.annotation.forEach(function (annotation) {
+                    if (mutationType === Pathogenicity.GERMLINE &&
+                        annotation.mutationStatus.includes('germline')) {
+                        signalData = extendMutations([annotation]);
+                    }
+                    else if (mutationType === Pathogenicity.SOMATIC &&
+                        annotation.mutationStatus.includes('somatic')) {
+                        signalData = extendMutations([annotation]);
+                    }
+                });
+            }
+        }
     }
     return signalData;
 }
@@ -3180,25 +3200,29 @@ function signalSortMethod(a, b) {
     return defaultSortMethod(getSortValue(a), getSortValue(b));
 }
 function getSortValue(signalData) {
-    return signalData.germlineFrequency || null;
+    return signalData ? signalData.germlineFrequency || null : null;
 }
-function download$7(signalData) {
-    return signalData.germlineFrequency != null
+function download$7(signalData, mutationType) {
+    return signalData && signalData.germlineFrequency !== null
         ? "" + formatNumberValueInSignificantDigits(signalData.germlineFrequency, 2)
         : '';
 }
-function getSignalValue(mutation, indexedVariantAnnotations, significantDigits) {
-    var signalData = getSignalData(mutation, indexedVariantAnnotations);
-    if (signalData.tumorTypeDecomposition) {
-        return formatNumberValueInSignificantDigits(signalData.germlineFrequency, significantDigits || 2);
+// Get germline OR somatic frequency value
+function getSingleSignalValue(mutation, mutationType, indexedVariantAnnotations, significantDigits) {
+    var signalData = getSignalData(mutation, indexedVariantAnnotations, mutationType);
+    if (signalData &&
+        signalData.length === 1 &&
+        signalData[0].tumorTypeDecomposition) {
+        return formatNumberValueInSignificantDigits(signalData[0].germlineFrequency || signalData[0].somaticFrequency, significantDigits || 2);
     }
     else {
         return null;
     }
 }
 var SignalTable = function (props) {
-    var signalData = getSignalData(props.mutation, props.indexedVariantAnnotations);
-    if (getSignalValue(props.mutation, props.indexedVariantAnnotations) !== null) {
+    // signal data should be either germline or somatic, so should be only one element
+    var signalData = getSignalData(props.mutation, props.indexedVariantAnnotations, props.mutationType)[0];
+    if (getSingleSignalValue(props.mutation, props.mutationType || Pathogenicity.GERMLINE, props.indexedVariantAnnotations) !== null) {
         return (createElement(MutationTumorTypeFrequencyTable, { data: generateTumorTypeDecomposition(signalData, signalData.countsByTumorType, signalData.biallelicCountsByTumorType, signalData.qcPassCountsByTumorType, signalData.statsByTumorType), columns: [
                 FREQUENCY_COLUMNS_DEFINITION[FrequencyTableColumnEnum.TUMOR_TYPE],
                 FREQUENCY_COLUMNS_DEFINITION[FrequencyTableColumnEnum.MUTATION_STATUS],
@@ -3239,11 +3263,11 @@ var Signal = /** @class */ (function (_super) {
                 }
                 else {
                     content = createElement("div", null);
-                    var signalValue = getSignalValue(this.props.mutation, this.props.indexedVariantAnnotations);
+                    var signalValue = getSingleSignalValue(this.props.mutation, this.props.mutationType || Pathogenicity.GERMLINE, this.props.indexedVariantAnnotations);
                     if (signalValue !== null) {
                         content = (createElement(DefaultTooltip, { placement: "top", overlayStyle: {
                                 width: 800,
-                            }, overlay: createElement(SignalTable, { mutation: this.props.mutation, indexedVariantAnnotations: this.props.indexedVariantAnnotations }) },
+                            }, overlay: createElement(SignalTable, { mutation: this.props.mutation, indexedVariantAnnotations: this.props.indexedVariantAnnotations, mutationType: this.props.mutationType }) },
                             createElement("span", null, signalValue)));
                     }
                 }
@@ -5191,7 +5215,7 @@ var DefaultMutationTable = /** @class */ (function (_super) {
             return this.indexedVariantAnnotationDataStatus === 'pending'
                 ? function () { return undefined; }
                 : function (mutation) {
-                    return getSignalData(mutation, _this.props.indexedVariantAnnotations);
+                    return getSignalData(mutation, _this.props.indexedVariantAnnotations, Pathogenicity.GERMLINE)[0];
                 };
         },
         enumerable: false,
@@ -5261,7 +5285,7 @@ var DefaultMutationTable = /** @class */ (function (_super) {
                 case MutationColumn.DBSNP:
                     return function (column) { return (createElement(Dbsnp, { mutation: column.original, indexedMyVariantInfoAnnotations: _this.props.indexedMyVariantInfoAnnotations })); };
                 case MutationColumn.SIGNAL:
-                    return function (column) { return (createElement(Signal, { mutation: column.original, indexedVariantAnnotations: _this.props.indexedVariantAnnotations })); };
+                    return function (column) { return (createElement(Signal, { mutation: column.original, indexedVariantAnnotations: _this.props.indexedVariantAnnotations, mutationType: Pathogenicity.GERMLINE })); };
                 default:
                     return undefined;
             }
@@ -8443,8 +8467,24 @@ var ExonTrack = /** @class */ (function (_super) {
         enumerable: false,
         configurable: true
     });
+    Object.defineProperty(ExonTrack.prototype, "chromosome", {
+        get: function () {
+            var _a, _b;
+            return (_b = (_a = this.props.store.ensemblTranscriptLookUp.result) === null || _a === void 0 ? void 0 : _a.body) === null || _b === void 0 ? void 0 : _b.seq_region_name;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(ExonTrack.prototype, "genomeBuild", {
+        get: function () {
+            return this.props.store.genomeBuild;
+        },
+        enumerable: false,
+        configurable: true
+    });
     Object.defineProperty(ExonTrack.prototype, "exonSpecs", {
         get: function () {
+            var _this = this;
             if (!this.transcriptId || !this.transcript) {
                 return [];
             }
@@ -8458,10 +8498,15 @@ var ExonTrack = /** @class */ (function (_super) {
                 ? exonInfo.map(function (exon, index) {
                     var startCodon = exon.start;
                     var endCodon = exon.start + exon.length;
-                    var exonLength = exon.length;
-                    var stringStart = formatExonLocation(startCodon);
-                    var stringEnd = formatExonLocation(endCodon);
-                    var stringLength = formatExonLocation(exonLength);
+                    var exonStartLocation = formatExonLocation(startCodon, index);
+                    var exonEndLocation = formatExonLocation(endCodon);
+                    var exonLength = formatExonLength(exon.length);
+                    var link = _this.chromosome
+                        ? "https://igv.org/app/?locus=chr" + _this.chromosome + ":" + exon.genomicLocationStart + "-" + exon.genomicLocationEnd + "&genome=" + _this.genomeBuild
+                        : 'https://igv.org';
+                    var linkText = _this.chromosome
+                        ? _this.genomeBuild + ":chr" + _this.chromosome + ":" + exon.genomicLocationStart + " - " + exon.genomicLocationEnd
+                        : exon.genomicLocationStart + " - " + exon.genomicLocationEnd;
                     return {
                         color: altColors[index % 2],
                         startCodon: startCodon,
@@ -8473,14 +8518,41 @@ var ExonTrack = /** @class */ (function (_super) {
                                 " Exon ",
                                 exon.rank,
                                 " "),
-                            "Start: ",
-                            stringStart,
+                            "Start: Nucleotide",
+                            ' ',
+                            createElement("strong", null, exonStartLocation.nucleotideLocation),
+                            ' ',
+                            "of amino acid",
+                            ' ',
+                            createElement("strong", null, exonStartLocation.aminoAcidLocation),
                             createElement("br", null),
-                            "End: ",
-                            stringEnd,
+                            "End: Nucleotide",
+                            ' ',
+                            createElement("strong", null, exonEndLocation.nucleotideLocation),
+                            ' ',
+                            "of amino acid",
+                            ' ',
+                            createElement("strong", null, exonEndLocation.aminoAcidLocation),
+                            createElement("br", null),
+                            "Length:",
+                            ' ',
+                            createElement("strong", null, exonLength.aminoAcidLength),
+                            ' ',
+                            "amino acids",
+                            ' ',
+                            exonLength.nucleotideLength && (createElement(Fragment, null,
+                                ' ',
+                                "and",
+                                ' ',
+                                createElement("strong", null, exonLength.nucleotideLength),
+                                ' ',
+                                "nucleotides")),
                             createElement("br", null),
-                            "Length: ",
-                            stringLength)),
+                            "Genomic location:", " ",
+                            createElement("a", { target: "_blank", href: link, rel: "noopener noreferrer" },
+                                createElement(Fragment, null,
+                                    linkText, " ",
+                                    createElement("i", { className: "fa fa-external-link" }))))),
                     };
                 })
                 : [];
@@ -8511,6 +8583,12 @@ var ExonTrack = /** @class */ (function (_super) {
     __decorate([
         computed
     ], ExonTrack.prototype, "transcript", null);
+    __decorate([
+        computed
+    ], ExonTrack.prototype, "chromosome", null);
+    __decorate([
+        computed
+    ], ExonTrack.prototype, "genomeBuild", null);
     __decorate([
         computed
     ], ExonTrack.prototype, "exonSpecs", null);
@@ -11700,6 +11778,28 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                 },
             })
         });
+        Object.defineProperty(this, "ensemblTranscriptLookUp", {
+            enumerable: true,
+            configurable: true,
+            writable: true,
+            value: remoteData({
+                await: function () { return [_this.activeTranscript]; },
+                invoke: function () { return __awaiter(_this, void 0, void 0, function () {
+                    var ensemblTranscriptLookUpLink;
+                    return __generator(this, function (_a) {
+                        ensemblTranscriptLookUpLink = this.genomeBuild === 'hg19'
+                            ? "https://grch37.rest.ensembl.org/lookup/id/" + this.activeTranscript.result + "?content-type=application/json"
+                            : "https://rest.ensembl.org/lookup/id/" + this.activeTranscript.result + "?content-type=application/json";
+                        return [2 /*return*/, this.activeTranscript.result
+                                ? get(ensemblTranscriptLookUpLink)
+                                : undefined];
+                    });
+                }); },
+                onError: function () {
+                    // fail silently, leave the error handling responsibility to the data consumer
+                },
+            })
+        });
         makeObservable(this);
     }
     Object.defineProperty(DefaultMutationMapperStore.prototype, "selectedTranscript", {
@@ -12009,6 +12109,13 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                 0);
         }
     });
+    Object.defineProperty(DefaultMutationMapperStore.prototype, "genomeBuild", {
+        get: function () {
+            return this.config.genomeBuild || 'hg19';
+        },
+        enumerable: false,
+        configurable: true
+    });
     __decorate([
         observable
     ], DefaultMutationMapperStore.prototype, "_selectedTranscript", void 0);
@@ -12079,6 +12186,9 @@ var DefaultMutationMapperStore = /** @class */ (function () {
     __decorate([
         autobind
     ], DefaultMutationMapperStore.prototype, "getDefaultEntrezGeneId", null);
+    __decorate([
+        computed
+    ], DefaultMutationMapperStore.prototype, "genomeBuild", null);
     return DefaultMutationMapperStore;
 }());
 
@@ -12785,5 +12895,5 @@ var MutationMapper = /** @class */ (function (_super) {
     return MutationMapper;
 }(Component));
 
-export { Annotation, BadgeLabel, BadgeSelector, Civic, ClinvarInterpretation, ClinvarSummary, ColumnHeader, ColumnSelector, ColumnSortDirection, DEFAULT_ANNOTATION_DATA, DEFAULT_GENOME_NEXUS_URL, DEFAULT_MUTATION_ALIGNER_PROXY_URL_TEMPLATE, DEFAULT_MUTATION_ALIGNER_URL_TEMPLATE, DEFAULT_MUTATION_COLUMNS, DEFAULT_MY_GENE_URL_TEMPLATE, DEFAULT_ONCO_KB_URL, DEFAULT_PROTEIN_IMPACT_TYPE_COLORS, DEFAULT_UNIPROT_ID_URL_TEMPLATE, DataFilterType, DataTable, Dbsnp, DbsnpId, DefaultMutationMapperDataFetcher, DefaultMutationMapperDataStore, DefaultMutationMapperFilterApplier, DefaultMutationMapperStore, DefaultMutationTable, Domain, DropdownSelector, FilterResetPanel, GenericAnnotation, Gnomad, GnomadFrequency, GnomadFrequencyBreakdown, GnomadFrequencyTable, GnomadFrequencyValue, Hgvsc, Hgvsg, HotspotAnnotation, HotspotInfo, Lollipop, LollipopMutationPlot, LollipopPlot, LollipopPlotNoTooltip, MSI_H_NAME, MUTATION_COLUMNS_DEFINITION, MUTATION_COLUMN_HEADERS, MUTATION_STATUS_BADGE_STYLE_OVERRIDE, MUTATION_TYPE_PRIORITY, MutationColumn, MutationColumnName, MutationMapper, MutationStatus, MutationStatusBadgeSelector, MyCancerGenome, ONCOKB_DEFAULT_DATA, ONCOKB_DEFAULT_INFO, OTHER_BIOMARKER_HUGO_SYMBOL, OTHER_BIOMARKER_NAME, OncoKB, OncoKBSuggestAnnotationLinkout, OncoKbFeedback, OncoKbHelper, OncoKbTooltip, OncoKbTreatmentTable, OtherBiomarkersQueryType, ProteinChange, ProteinImpactTypeBadgeSelector, ProteinImpactTypeDropdownSelector, RefComponent, ReferenceList, LollipopPlot as Sequence, Signal, SignalTable, SummaryWithRefs, TEXT_INPUT_FILTER_ID, TMB_H_NAME, TrackName, TrackSelector, USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB, sortValue$4 as annotationSortValue, applyDataFilters, applyDataFiltersOnDatum, applyDefaultMutationFilter, applyDefaultMutationStatusFilter, applyDefaultPositionFilter, applyDefaultProteinImpactTypeFilter, calculateGnomadAlleleFrequency, download as civicDownload, sortValue as civicSortValue, download$3 as clinvarDownload, sortValue$5 as clinvarSortValue, download$4 as dbsnpDownload, sortValue$6 as dbsnpSortValue, defaultOncoKbFilter, errorIcon, fetchVariantAnnotationsByMutation, fetchVariantAnnotationsIndexedByGenomicLocation, findAllUniquePositions, findNonTextInputFilters, findOneMutationFilterValue, findTextInputFilter, getAllOptionValues, getAnnotationData, getClinvarData, getColorForProteinImpactType, getGnomadData, getHgvscColumnData, getHgvsgColumnData, getProteinImpactTypeBadgeLabel, getProteinImpactTypeOptionLabel, getSelectedOptionValues, getSignalData, getSignalValue, getUrl, download$5 as gnomadDownload, sortValue$7 as gnomadSortValue, groupDataByGroupFilters, groupDataByProteinImpactType, groupOncoKbIndicatorDataByMutations, handleOptionSelect, download$6 as hgvscDownload, sortValue$8 as hgvscSortValue, sortValue$3 as hotspotAnnotationSortValue, includesSearchTextIgnoreCase, indexPositions, initDefaultMutationMapperStore, initDefaultTrackVisibility, initGenomeNexusClient, initGenomeNexusInternalClient, initOncoKbClient, levelIconClassNames, loaderIcon, mergeColumns, mutationTypeSort, download$1 as myCancerGenomeDownload, sortValue$1 as myCancerGenomeSortValue, normalizeLevel, onFilterOptionSelect, download$2 as oncoKbAnnotationDownload, sortValue$2 as oncoKbAnnotationSortValue, oncogenicityIconClassNames, proteinChangeSortMethod, rightAlignedCell, download$7 as signalDownload, getSortValue as signalSortValue, updatePositionHighlightFilters, updatePositionRangeHighlightFilters, updatePositionSelectionFilters };
+export { Annotation, BadgeLabel, BadgeSelector, Civic, ClinvarInterpretation, ClinvarSummary, ColumnHeader, ColumnSelector, ColumnSortDirection, DEFAULT_ANNOTATION_DATA, DEFAULT_GENOME_NEXUS_URL, DEFAULT_MUTATION_ALIGNER_PROXY_URL_TEMPLATE, DEFAULT_MUTATION_ALIGNER_URL_TEMPLATE, DEFAULT_MUTATION_COLUMNS, DEFAULT_MY_GENE_URL_TEMPLATE, DEFAULT_ONCO_KB_URL, DEFAULT_PROTEIN_IMPACT_TYPE_COLORS, DEFAULT_UNIPROT_ID_URL_TEMPLATE, DataFilterType, DataTable, Dbsnp, DbsnpId, DefaultMutationMapperDataFetcher, DefaultMutationMapperDataStore, DefaultMutationMapperFilterApplier, DefaultMutationMapperStore, DefaultMutationTable, Domain, DropdownSelector, FilterResetPanel, GenericAnnotation, Gnomad, GnomadFrequency, GnomadFrequencyBreakdown, GnomadFrequencyTable, GnomadFrequencyValue, Hgvsc, Hgvsg, HotspotAnnotation, HotspotInfo, Lollipop, LollipopMutationPlot, LollipopPlot, LollipopPlotNoTooltip, MSI_H_NAME, MUTATION_COLUMNS_DEFINITION, MUTATION_COLUMN_HEADERS, MUTATION_STATUS_BADGE_STYLE_OVERRIDE, MUTATION_TYPE_PRIORITY, MutationColumn, MutationColumnName, MutationMapper, MutationStatus, MutationStatusBadgeSelector, MyCancerGenome, ONCOKB_DEFAULT_DATA, ONCOKB_DEFAULT_INFO, OTHER_BIOMARKER_HUGO_SYMBOL, OTHER_BIOMARKER_NAME, OncoKB, OncoKBSuggestAnnotationLinkout, OncoKbFeedback, OncoKbHelper, OncoKbTooltip, OncoKbTreatmentTable, OtherBiomarkersQueryType, ProteinChange, ProteinImpactTypeBadgeSelector, ProteinImpactTypeDropdownSelector, RefComponent, ReferenceList, LollipopPlot as Sequence, Signal, SignalTable, SummaryWithRefs, TEXT_INPUT_FILTER_ID, TMB_H_NAME, TrackName, TrackSelector, USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB, sortValue$4 as annotationSortValue, applyDataFilters, applyDataFiltersOnDatum, applyDefaultMutationFilter, applyDefaultMutationStatusFilter, applyDefaultPositionFilter, applyDefaultProteinImpactTypeFilter, calculateGnomadAlleleFrequency, download as civicDownload, sortValue as civicSortValue, download$3 as clinvarDownload, sortValue$5 as clinvarSortValue, download$4 as dbsnpDownload, sortValue$6 as dbsnpSortValue, defaultOncoKbFilter, errorIcon, fetchVariantAnnotationsByMutation, fetchVariantAnnotationsIndexedByGenomicLocation, findAllUniquePositions, findNonTextInputFilters, findOneMutationFilterValue, findTextInputFilter, getAllOptionValues, getAnnotationData, getClinvarData, getColorForProteinImpactType, getGnomadData, getHgvscColumnData, getHgvsgColumnData, getProteinImpactTypeBadgeLabel, getProteinImpactTypeOptionLabel, getSelectedOptionValues, getSignalData, getSingleSignalValue, getUrl, download$5 as gnomadDownload, sortValue$7 as gnomadSortValue, groupDataByGroupFilters, groupDataByProteinImpactType, groupOncoKbIndicatorDataByMutations, handleOptionSelect, download$6 as hgvscDownload, sortValue$8 as hgvscSortValue, sortValue$3 as hotspotAnnotationSortValue, includesSearchTextIgnoreCase, indexPositions, initDefaultMutationMapperStore, initDefaultTrackVisibility, initGenomeNexusClient, initGenomeNexusInternalClient, initOncoKbClient, levelIconClassNames, loaderIcon, mergeColumns, mutationTypeSort, download$1 as myCancerGenomeDownload, sortValue$1 as myCancerGenomeSortValue, normalizeLevel, onFilterOptionSelect, download$2 as oncoKbAnnotationDownload, sortValue$2 as oncoKbAnnotationSortValue, oncogenicityIconClassNames, proteinChangeSortMethod, rightAlignedCell, download$7 as signalDownload, getSortValue as signalSortValue, updatePositionHighlightFilters, updatePositionRangeHighlightFilters, updatePositionSelectionFilters };
 //# sourceMappingURL=index.es.js.map