react-mutation-mapper 0.8.121 → 0.9.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/component/clinvar/ClinvarSummary.d.ts +1 -1
- package/dist/component/column/Annotation.d.ts +2 -2
- package/dist/component/column/ClinvarInterpretation.d.ts +1 -1
- package/dist/component/column/ColumnHeader.d.ts +1 -1
- package/dist/component/column/Hgvsc.d.ts +1 -1
- package/dist/component/column/Hgvsg.d.ts +1 -1
- package/dist/component/column/MutationStatus.d.ts +1 -1
- package/dist/component/column/MutationType.d.ts +2 -2
- package/dist/component/column/MyVariantInfoHelper.d.ts +1 -1
- package/dist/component/column/ProteinChange.d.ts +1 -1
- package/dist/component/column/Signal.d.ts +2 -2
- package/dist/component/dataTable/ColumnSelector.d.ts +2 -2
- package/dist/component/dataTable/DataTable.d.ts +4 -4
- package/dist/component/dataTable/DataTableToolbar.d.ts +1 -1
- package/dist/component/dbsnp/DbsnpId.d.ts +1 -1
- package/dist/component/filter/BadgeLabel.d.ts +1 -1
- package/dist/component/filter/BadgeSelector.d.ts +2 -2
- package/dist/component/filter/DropdownSelector.d.ts +1 -1
- package/dist/component/filter/MutationStatusBadgeSelector.d.ts +1 -1
- package/dist/component/filter/ProteinImpactTypeBadgeSelector.d.ts +1 -1
- package/dist/component/filter/ProteinImpactTypeDropdownSelector.d.ts +1 -1
- package/dist/component/gnomad/GnomadFrequency.d.ts +1 -1
- package/dist/component/hotspot/HotspotInfo.d.ts +1 -1
- package/dist/component/lollipopMutationPlot/DefaultLollipopPlotLegend.d.ts +1 -1
- package/dist/component/lollipopMutationPlot/LollipopMutationPlot.d.ts +1 -1
- package/dist/component/lollipopMutationPlot/LollipopMutationPlotControls.d.ts +1 -1
- package/dist/component/lollipopPlot/Domain.d.ts +1 -1
- package/dist/component/lollipopPlot/Lollipop.d.ts +1 -1
- package/dist/component/lollipopPlot/LollipopPlot.d.ts +1 -1
- package/dist/component/lollipopPlot/LollipopPlotNoTooltip.d.ts +1 -1
- package/dist/component/lollipopPlot/Sequence.d.ts +1 -1
- package/dist/component/mutationMapper/DefaultMutationRateSummary.d.ts +2 -2
- package/dist/component/mutationMapper/FilterResetPanel.d.ts +1 -1
- package/dist/component/mutationMapper/GeneSummary.d.ts +1 -1
- package/dist/component/mutationMapper/MutationMapper.d.ts +1 -1
- package/dist/component/mutationMapper/TranscriptDropdown.d.ts +1 -1
- package/dist/component/mutationTable/DefaultMutationTable.d.ts +2 -2
- package/dist/component/ptm/PtmAnnotationTable.d.ts +1 -1
- package/dist/component/ptm/PtmReferenceList.d.ts +1 -1
- package/dist/component/track/ExonTrack.d.ts +1 -1
- package/dist/component/track/HotspotTrack.d.ts +1 -1
- package/dist/component/track/OncoKbTrack.d.ts +1 -1
- package/dist/component/track/OncoKbTrackTooltip.d.ts +1 -1
- package/dist/component/track/PtmTrack.d.ts +1 -1
- package/dist/component/track/Track.d.ts +1 -1
- package/dist/component/track/TrackCircle.d.ts +2 -2
- package/dist/component/track/TrackItem.d.ts +2 -2
- package/dist/component/track/TrackPanel.d.ts +1 -1
- package/dist/component/track/TrackRect.d.ts +2 -2
- package/dist/component/track/TrackSelector.d.ts +3 -3
- package/dist/component/track/UniprotTopologyTrack.d.ts +1 -1
- package/dist/filter/CancerTypeFilter.d.ts +1 -1
- package/dist/filter/CategoricalFilter.d.ts +2 -2
- package/dist/filter/HotspotFilter.d.ts +1 -1
- package/dist/filter/MutationFilter.d.ts +2 -2
- package/dist/filter/MutationStatusFilter.d.ts +1 -1
- package/dist/filter/NumericalFilter.d.ts +2 -2
- package/dist/filter/OncoKbFilter.d.ts +1 -1
- package/dist/filter/PositionFilter.d.ts +1 -1
- package/dist/filter/ProteinChangeFilter.d.ts +1 -1
- package/dist/filter/ProteinImpactTypeFilter.d.ts +1 -1
- package/dist/index.es.js +97 -79
- package/dist/index.es.js.map +1 -1
- package/dist/index.js +95 -77
- package/dist/index.js.map +1 -1
- package/dist/model/DataFilter.d.ts +1 -1
- package/dist/model/DomainSpec.d.ts +1 -1
- package/dist/model/FilterApplier.d.ts +1 -1
- package/dist/model/GnomadSummary.d.ts +1 -1
- package/dist/model/LollipopSpec.d.ts +2 -2
- package/dist/model/SequenceSpec.d.ts +1 -1
- package/dist/store/DefaultMutationMapperDataStore.d.ts +1 -1
- package/package.json +9 -9
package/dist/index.es.js
CHANGED
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@@ -1,4 +1,4 @@
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-
import { __extends, __decorate, __awaiter, __generator, __assign,
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import { __extends, __decorate, __awaiter, __generator, __assign, __spreadArray } from 'tslib';
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import * as _ from 'lodash';
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import ___default from 'lodash';
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import { makeObservable, observable, computed, action, reaction } from 'mobx';
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@@ -8,7 +8,7 @@ import React__default from 'react';
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import { DefaultTooltip, TruncatedText, getNCBIlink, cachePostMethodsOnClient, CanonicalMutationType, MutationTumorTypeFrequencyTable, FREQUENCY_COLUMNS_DEFINITION, FrequencyTableColumnEnum, CheckedSelect, getSelectedValuesMap, BadgeListSelector, 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, MUT_COLOR_OTHER_PASSENGER, getCanonicalMutationType, getProteinImpactTypeFromCanonical, ProteinImpactType, getProteinImpactType, resolveColumnVisibility, resolveColumnVisibilityByColumnDefinition, longestCommonStartingSubstring, getTextWidth, unhoverAllComponents, SVGAxis, getComponentIndex, defaultHitzoneConfig, initHitZoneFromConfig, EditableSpan, DownloadControls, EllipsisTextTooltip, cached, remoteData, WindowWrapper } from 'cbioportal-frontend-commons';
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import classNames from 'classnames';
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import { CIVIC_NA_VALUE, uniqueGenomicLocations, indexAnnotationsByGenomicLocation, getCivicEntry, getRemoteDataGroupStatus, isLinearClusterHotspot, is3dHotspot, getVariantAnnotation, OncoKbCardDataType, defaultArraySortMethod, defaultSortMethod, getDbsnpRsId, getMyVariantInfoAnnotation, generateHgvsgByMutation, calcProteinChangeSortValue, Pathogenicity, extendMutations, formatNumberValueInSignificantDigits, generateTumorTypeDecomposition, formatPercentValue, countMutationsByProteinChange, numberOfLeadingDecimalZeros, filterLinearClusterHotspotsByMutations, filter3dHotspotsByMutations, isHotspot, defaultHotspotFilter, extractExonInformation, formatExonLocation, formatExonLength, ptmColor, compareByPtmTypePriority, UniprotTopologyTrackToColor, UniprotTopologyTypeToTitle, PtmSource, PTM_SOURCE_URL, getMyVariantInfoAnnotationsFromIndexedVariantAnnotations, genomicLocationString, convertUniprotFeatureToPtm, convertDbPtmToPtm, UniprotCategory, convertUniprotFeatureToUniprotTopology, groupPtmDataByPosition, groupPtmDataByTypeAndPosition, groupCancerHotspotDataByPosition, indexHotspotsData, fetchCivicGenes, fetchCivicVariants, getMutationsByTranscriptId, groupMutationsByProteinStartPos, groupHotspotsByMutations } from 'cbioportal-utils';
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import { getIndicatorData, calculateOncoKbAvailableDataType, oncoKbAnnotationSortValue, OncoKB, OncoKbSummaryTable,
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import { getIndicatorData, calculateOncoKbAvailableDataType, oncoKbAnnotationSortValue, OncoKB, OncoKbSummaryTable, getTumorTypeNameWithExclusionInfo, LEVELS, ReferenceList, generateProteinChangeQuery, StructuralVariantType, generateAnnotateStructuralVariantQuery, defaultOncoKbFilter, groupOncoKbIndicatorDataByMutations, defaultOncoKbIndicatorFilter } from 'oncokb-frontend-commons';
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import { GenomeNexusAPI, GenomeNexusAPIInternal } from 'genome-nexus-ts-api-client';
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import { OncoKbAPI } from 'oncokb-ts-api-client';
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import autobind from 'autobind-decorator';
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@@ -29,12 +29,12 @@ import memoize from 'memoize-weak-decorator';
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var annotationStyles = {"annotation-item-load":"annotation-module_annotation-item-load__1pDN0","annotation-item-text":"annotation-module_annotation-item-text__Gy_Jv","annotation-item-error":"annotation-module_annotation-item-error__5BhTo","annotation-item":"annotation-module_annotation-item__2EgnB"};
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function loaderIcon(className) {
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return (React.createElement("span", { className: classNames(""
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return (React.createElement("span", { className: classNames("".concat(annotationStyles['annotation-item']), "".concat(annotationStyles['annotation-item-load']), className) },
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React.createElement("i", { className: "fa fa-spinner fa-pulse" })));
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}
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function errorIcon(errorMessage) {
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return (React.createElement(DefaultTooltip, { overlay: React.createElement("span", null, errorMessage), placement: "right", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
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React.createElement("span", { className: ""
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React.createElement("span", { className: "".concat(annotationStyles['annotation-item-error']) },
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React.createElement("i", { className: "fa fa-exclamation-triangle text-danger" }))));
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}
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@@ -69,7 +69,7 @@ var CivicCard = /** @class */ (function (_super) {
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})
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.map(function (_a) {
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var key = _a[0], value = _a[1];
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return key.slice(0, -5)
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return "".concat(key.slice(0, -5), ": ").concat(value);
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}) // Remove "Count" substring from key
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.join(', ');
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list.push(this.variantItem(name_1, variant.url, variant.name, entryTypes, variant.description));
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@@ -166,7 +166,7 @@ function download$5(civicEntry) {
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var values = [];
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if (variants && variants.length > 0 && variants[0].evidenceCounts) {
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___default.forEach(variants[0].evidenceCounts, function (value, key) {
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values.push(key
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values.push("".concat(key, ": ").concat(value));
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});
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}
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// this indicates that we have an entry but the evidence is empty
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@@ -194,7 +194,7 @@ var Civic = /** @class */ (function (_super) {
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configurable: true,
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writable: true,
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value: function () {
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var civicContent = (React.createElement("span", { className: ""
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var civicContent = (React.createElement("span", { className: "".concat(annotationStyles['annotation-item']) }));
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var civicImgWidth = 14;
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var civicImgHeight = 14;
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var civicImgSrc = !this.props.hasCivicVariants
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@@ -206,7 +206,7 @@ var Civic = /** @class */ (function (_super) {
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else if (this.props.civicEntry !== undefined) {
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if (this.props.civicEntry !== null &&
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this.props.civicStatus == 'complete') {
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civicContent = (React.createElement("span", { className: ""
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civicContent = (React.createElement("span", { className: "".concat(annotationStyles['annotation-item']) },
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React.createElement("img", { width: civicImgWidth, height: civicImgHeight, src: civicImgSrc, alt: "Civic Variant Entry" })));
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civicContent = (React.createElement(DefaultTooltip, { overlay: this.cardContent.bind(this, this.props.civicEntry), placement: "right", trigger: ['hover', 'focus'], onPopupAlign: hideArrow, destroyTooltipOnHide: false }, civicContent));
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}
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@@ -250,7 +250,7 @@ var ClinvarSummary = function (props) {
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}
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else {
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var clinvarId = props.clinvar.clinvarId;
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var clinvarLink = "https://www.ncbi.nlm.nih.gov/clinvar/variation/"
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var clinvarLink = "https://www.ncbi.nlm.nih.gov/clinvar/variation/".concat(clinvarId, "/");
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var clinicalSignificance = props.clinvar.clinicalSignificance;
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var conflictingClinicalSignificance = props.clinvar.conflictingClinicalSignificance;
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return (React.createElement(TruncatedText, { maxLength: 30, text: clinicalSignificance, addTooltip: "always", tooltip: React.createElement("div", { style: { maxWidth: 300 } },
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writable: true,
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value: function () {
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var _a = this.props, isHotspot = _a.isHotspot, is3dHotspot = _a.is3dHotspot;
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var hotspotContent = (React.createElement("span", { className: ""
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var hotspotContent = (React.createElement("span", { className: "".concat(annotationStyles['annotation-item']) }));
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if (this.props.status === 'pending') {
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hotspotContent = loaderIcon('pull-left');
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}
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var arrowContent = React.createElement("div", { className: "rc-tooltip-arrow-inner" });
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var tooltipContent = (React.createElement(HotspotInfo, { isHotspot: isHotspot, is3dHotspot: is3dHotspot }));
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hotspotContent = (React.createElement(DefaultTooltip, { overlay: tooltipContent, placement: "topLeft", trigger: ['hover', 'focus'], arrowContent: arrowContent, onPopupAlign: placeArrow },
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React.createElement("span", { className: annotationStyles['annotation-item']
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React.createElement("span", { className: "".concat(annotationStyles['annotation-item'], " chang_hotspot") },
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React.createElement("img", { width: hotspotsImgWidth, height: hotspotsImgHeight, src: hotspotsImgSrc, alt: "Recurrent Hotspot Symbol" }))));
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}
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return hotspotContent;
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version: 'v2.0',
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date: '12/19/2019',
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},
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genomeNexus: {
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grch37: {
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genomeNexusVepVersion: '',
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genomeNexusVersion: '',
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vepVersion: '',
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},
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grch38: {
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genomeNexusVepVersion: '',
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genomeNexusVersion: '',
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vepVersion: '',
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},
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},
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levels: [],
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ncitVersion: '19.03d',
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oncoTreeVersion: 'oncotree_2019_12_01',
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@@ -518,7 +530,7 @@ var RevueTooltipContent = function (props) {
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"Revised Protein Effect by", " ",
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React__default.createElement("a", { href: "https://cancerrevue.org", target: "_blank", rel: "noopener noreferrer" }, "reVUE"), " (",
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props.vue.references.map(function (reference, index) { return (React__default.createElement("span", { key: index },
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React__default.createElement("a", { href: "https://pubmed.ncbi.nlm.nih.gov/"
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React__default.createElement("a", { href: "https://pubmed.ncbi.nlm.nih.gov/".concat(reference.pubmedId, "/"), rel: "noopener noreferrer", target: "_blank" }, reference.referenceText),
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index < props.vue.references.length - 1 && ';')); }), "): ",
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React__default.createElement("strong", null, props.vue.revisedProteinEffect))));
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};
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}
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var RevueCell = function (props) {
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return (React__default.createElement(DefaultTooltip, { placement: "bottom", overlay: React__default.createElement(RevueTooltipContent, { vue: props.vue }) },
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React__default.createElement("span", { className: ""
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React__default.createElement("span", { className: "".concat(annotationStyles['annotation-item']), style: { display: 'inline-flex' } },
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React__default.createElement("img", { src: img, alt: "reVUE logo", width: 14, height: 14 }))));
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};
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var value;
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if (mutation) {
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var key = '';
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var memoize = (oncoKbCancerGenes === null || oncoKbCancerGenes === void 0 ? void 0 : oncoKbCancerGenes.isComplete) &&
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var memoize = (oncoKbCancerGenes === null || oncoKbCancerGenes === void 0 ? void 0 : oncoKbCancerGenes.isComplete) &&
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(hotspotData === null || hotspotData === void 0 ? void 0 : hotspotData.isComplete) &&
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(oncoKbData === null || oncoKbData === void 0 ? void 0 : oncoKbData.isComplete) &&
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(civicGenes === null || civicGenes === void 0 ? void 0 : civicGenes.isComplete) &&
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(civicVariants === null || civicVariants === void 0 ? void 0 : civicVariants.isComplete) &&
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(indexedVariantAnnotations === null || indexedVariantAnnotations === void 0 ? void 0 : indexedVariantAnnotations.isComplete);
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if (memoize) {
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key = JSON.stringify(mutation) + !!usingPublicOncoKbInstance;
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var val = memoized.get(key);
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hotspotStatus: hotspotData ? hotspotData.status : 'pending',
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vue: (indexedVariantAnnotations === null || indexedVariantAnnotations === void 0 ? void 0 : indexedVariantAnnotations.isComplete) &&
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indexedVariantAnnotations.result
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? (_b = (_a = getVariantAnnotation(mutation, indexedVariantAnnotations.result)) === null || _a === void 0 ? void 0 : _a.annotation_summary) === null || _b === void 0 ? void 0 : _b.vues
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? (_b = (_a = getVariantAnnotation(mutation, indexedVariantAnnotations.result)) === null || _a === void 0 ? void 0 : _a.annotation_summary) === null || _b === void 0 ? void 0 : _b.vues
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: undefined,
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};
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// oncoKbData may exist but it might be an instance of Error, in that case we flag the status as error
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if (oncoKbData && oncoKbData.result instanceof Error) {
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oncoKbData.status === 'complete') {
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oncoKbIndicator = getIndicatorData(mutation, oncoKbData.result, resolveTumorType, resolveEntrezGeneId);
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oncoKbAvailableDataTypes = ___default.uniq(
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oncoKbAvailableDataTypes = ___default.uniq(__spreadArray(__spreadArray([], oncoKbAvailableDataTypes, true), calculateOncoKbAvailableDataType(___default.values(oncoKbData.result.indicatorMap)), true));
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}
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value = __assign(__assign({}, value), { oncoKbStatus: oncoKbData ? oncoKbData.status : 'pending', oncoKbIndicator: oncoKbIndicator,
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oncoKbAvailableDataTypes: oncoKbAvailableDataTypes });
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value = __assign(__assign({}, value), { oncoKbStatus: oncoKbData ? oncoKbData.status : 'pending', oncoKbIndicator: oncoKbIndicator, oncoKbAvailableDataTypes: oncoKbAvailableDataTypes });
|
|
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|
}
|
|
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|
else if (oncoKbData && oncoKbData.isPending) {
|
|
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|
value = __assign(__assign({}, value), { oncoKbStatus: 'pending', oncoKbIndicator: undefined });
|
|
@@ -669,7 +686,7 @@ function GenericAnnotation(props) {
|
|
|
669
686
|
var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableOncoKb = props.enableOncoKb, enableRevue = props.enableRevue; props.pubMedCache; var userDisplayName = props.userDisplayName, mergeOncoKbIcons = props.mergeOncoKbIcons, oncoKbContentPadding = props.oncoKbContentPadding, hasMultipleCancerTypes = props.hasMultipleCancerTypes;
|
|
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|
return (React.createElement("span", { style: { display: 'flex', minWidth: 100 } },
|
|
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|
enableOncoKb && (React.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, userDisplayName: userDisplayName, contentPadding: oncoKbContentPadding, hasMultipleCancerTypes: hasMultipleCancerTypes })),
|
|
672
|
-
enableRevue ? (annotation.vue ? (React.createElement(RevueCell, { vue: annotation.vue })) : (React.createElement("span", { className: ""
|
|
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|
+
enableRevue ? (annotation.vue ? (React.createElement(RevueCell, { vue: annotation.vue })) : (React.createElement("span", { className: "".concat(annotationStyles['annotation-item']) }))) : (React.createElement(React.Fragment, null)),
|
|
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|
enableCivic && (React.createElement(Civic, { civicEntry: annotation.civicEntry, civicStatus: annotation.civicStatus, hasCivicVariants: annotation.hasCivicVariants })),
|
|
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|
enableHotspot && (React.createElement(HotspotAnnotation, { isHotspot: annotation.isHotspot, is3dHotspot: annotation.is3dHotspot, status: annotation.hotspotStatus }))));
|
|
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|
}
|
|
@@ -1043,7 +1060,7 @@ function getGnomadData(myVariantInfo) {
|
|
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|
}
|
|
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1061
|
function generateGnomadUrl(chromosome, position, reference, variant) {
|
|
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1062
|
if (chromosome && position && reference && variant) {
|
|
1046
|
-
return "https://gnomad.broadinstitute.org/variant/"
|
|
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|
+
return "https://gnomad.broadinstitute.org/variant/".concat(chromosome, "-").concat(position, "-").concat(reference, "-").concat(variant);
|
|
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1064
|
}
|
|
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|
else {
|
|
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|
return 'https://gnomad.broadinstitute.org/';
|
|
@@ -1402,7 +1419,7 @@ var Hgvsg = /** @class */ (function (_super) {
|
|
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|
configurable: true,
|
|
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|
writable: true,
|
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value: {
|
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|
-
constructLink: function (hgvsg, content, href) { return (React.createElement("a", { href: href || "https:/www.genomenexus.org/variant/"
|
|
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|
+
constructLink: function (hgvsg, content, href) { return (React.createElement("a", { href: href || "https:/www.genomenexus.org/variant/".concat(hgvsg), target: "_blank", rel: "noopener noreferrer" }, content)); },
|
|
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|
mainContent: function (hgvsg) { return (React.createElement(React.Fragment, null,
|
|
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1424
|
hgvsg,
|
|
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|
"\u00A0",
|
|
@@ -1579,7 +1596,7 @@ function getSortValue(signalData) {
|
|
|
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|
}
|
|
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1597
|
function download(signalData, mutationType) {
|
|
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1598
|
return signalData && signalData.germlineFrequency !== null
|
|
1582
|
-
? ""
|
|
1599
|
+
? "".concat(formatNumberValueInSignificantDigits(signalData.germlineFrequency, 2))
|
|
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1600
|
: '';
|
|
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|
}
|
|
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|
// Get germline OR somatic frequency value
|
|
@@ -1824,7 +1841,7 @@ var BadgeLabel = /** @class */ (function (_super) {
|
|
|
1824
1841
|
? {}
|
|
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|
: { marginRight: 5 }
|
|
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: { marginLeft: 5 } },
|
|
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React.createElement("span", { className: this.props.badgeClassName, "data-test": "badge-"
|
|
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|
+
React.createElement("span", { className: this.props.badgeClassName, "data-test": "badge-".concat(this.props.value), style: __assign(__assign(__assign({}, DEFAULT_BADGE_STYLE), this.props.badgeStyleOverride), (this.props.isDriverAnnotated
|
|
1828
1845
|
? { marginRight: 0, width: 'auto' }
|
|
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1846
|
: {})) }, this.props.badgeContent)));
|
|
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|
},
|
|
@@ -2121,7 +2138,7 @@ function getColorForProteinImpactType(mutations, colors, getMutationCount, isPut
|
|
|
2121
2138
|
var counts = {};
|
|
2122
2139
|
for (var _i = 0, processedMutations_1 = processedMutations; _i < processedMutations_1.length; _i++) {
|
|
2123
2140
|
var pMut = processedMutations_1[_i];
|
|
2124
|
-
var key = pMut.canonicalType
|
|
2141
|
+
var key = "".concat(pMut.canonicalType, "_").concat(pMut.isPutativeDriver);
|
|
2125
2142
|
counts[key] = counts[key] || {
|
|
2126
2143
|
count: 0,
|
|
2127
2144
|
isPutativeDriver: pMut.isPutativeDriver,
|
|
@@ -2393,7 +2410,7 @@ var MutationStatusBadgeSelector = /** @class */ (function (_super) {
|
|
|
2393
2410
|
get: function () {
|
|
2394
2411
|
var _this = this;
|
|
2395
2412
|
return this.props.badgeSelectorOptions.map(function (option) { return (__assign(__assign({}, option), { badgeContent: _this.props.rates
|
|
2396
|
-
? formatPercentValue(_this.props.rates[option.value])
|
|
2413
|
+
? "".concat(formatPercentValue(_this.props.rates[option.value]), "%")
|
|
2397
2414
|
: undefined })); });
|
|
2398
2415
|
},
|
|
2399
2416
|
enumerable: false,
|
|
@@ -2569,9 +2586,9 @@ function updatePositionSelectionFilters(dataStore, position, isMultiSelect, defa
|
|
|
2569
2586
|
var otherFilters = dataStore.selectionFilters.filter(function (f) { return f.type !== DataFilterType.POSITION; });
|
|
2570
2587
|
// reset filters
|
|
2571
2588
|
dataStore.clearSelectionFilters();
|
|
2572
|
-
dataStore.setSelectionFilters(
|
|
2589
|
+
dataStore.setSelectionFilters(__spreadArray(__spreadArray([
|
|
2573
2590
|
positionFilter
|
|
2574
|
-
], defaultFilters, otherFilters));
|
|
2591
|
+
], defaultFilters, true), otherFilters, true));
|
|
2575
2592
|
}
|
|
2576
2593
|
function updatePositionHighlightFilters(dataStore, positions, defaultFilters) {
|
|
2577
2594
|
if (defaultFilters === void 0) { defaultFilters = []; }
|
|
@@ -2580,7 +2597,7 @@ function updatePositionHighlightFilters(dataStore, positions, defaultFilters) {
|
|
|
2580
2597
|
type: DataFilterType.POSITION,
|
|
2581
2598
|
values: positions,
|
|
2582
2599
|
};
|
|
2583
|
-
dataStore.setHighlightFilters(
|
|
2600
|
+
dataStore.setHighlightFilters(__spreadArray(__spreadArray([], defaultFilters, true), [positionFilter], false));
|
|
2584
2601
|
}
|
|
2585
2602
|
function updatePositionRangeHighlightFilters(dataStore, startPosition, endPosition, defaultFilters) {
|
|
2586
2603
|
if (defaultFilters === void 0) { defaultFilters = []; }
|
|
@@ -2596,7 +2613,7 @@ function findAllUniquePositions(filters) {
|
|
|
2596
2613
|
.filter(function (f) { return f.type === DataFilterType.POSITION; })
|
|
2597
2614
|
// we need to spread f.values, since it might be an observable mobx array
|
|
2598
2615
|
// (mobx observable arrays does not play well with some array functions)
|
|
2599
|
-
.map(function (f) { return
|
|
2616
|
+
.map(function (f) { return __spreadArray([], f.values, true); })));
|
|
2600
2617
|
}
|
|
2601
2618
|
function indexPositions(filters) {
|
|
2602
2619
|
return ___default.keyBy(findAllUniquePositions(filters).map(function (p) { return ({ position: p }); }), 'position');
|
|
@@ -2683,7 +2700,7 @@ function onFilterOptionSelect(selectedValues, allValuesSelected, dataStore, data
|
|
|
2683
2700
|
values: selectedValues,
|
|
2684
2701
|
};
|
|
2685
2702
|
// replace the existing data filter wrt the current selection (other filters + new data filter)
|
|
2686
|
-
dataStore.setDataFilters(
|
|
2703
|
+
dataStore.setDataFilters(__spreadArray(__spreadArray([], otherFilters, true), [dataFilter], false));
|
|
2687
2704
|
}
|
|
2688
2705
|
}
|
|
2689
2706
|
function applyDataFiltersOnDatum(datum, dataFilters, applyFilter) {
|
|
@@ -2902,7 +2919,7 @@ var DataTable = /** @class */ (function (_super) {
|
|
|
2902
2919
|
else {
|
|
2903
2920
|
return this.props.initialSort.map(function (s) { return ({
|
|
2904
2921
|
id: s.column,
|
|
2905
|
-
desc: s.sortDirection !== ColumnSortDirection.ASC,
|
|
2922
|
+
desc: s.sortDirection !== ColumnSortDirection.ASC, // default: DESC
|
|
2906
2923
|
}); });
|
|
2907
2924
|
}
|
|
2908
2925
|
},
|
|
@@ -3533,7 +3550,7 @@ function mergeColumns(defaultColumns, customColumns) {
|
|
|
3533
3550
|
overrides.push(colOverride);
|
|
3534
3551
|
}
|
|
3535
3552
|
});
|
|
3536
|
-
return
|
|
3553
|
+
return __spreadArray(__spreadArray([], merged, true), ___default.difference(customColumns, overrides), true);
|
|
3537
3554
|
}
|
|
3538
3555
|
|
|
3539
3556
|
var DefaultMutationTableComponent = /** @class */ (function (_super) {
|
|
@@ -3770,9 +3787,9 @@ var DefaultMutationTable = /** @class */ (function (_super) {
|
|
|
3770
3787
|
values: dataFilterValues,
|
|
3771
3788
|
};
|
|
3772
3789
|
// replace current text input filter with the new one
|
|
3773
|
-
this.props.dataStore.setDataFilters(
|
|
3790
|
+
this.props.dataStore.setDataFilters(__spreadArray(__spreadArray([], otherFilters, true), [
|
|
3774
3791
|
textInputFilter,
|
|
3775
|
-
]));
|
|
3792
|
+
], false));
|
|
3776
3793
|
}
|
|
3777
3794
|
else {
|
|
3778
3795
|
// if no text input remove text input filter (set data filters to all other filters except input)
|
|
@@ -4164,14 +4181,14 @@ function lollipopLabelText(mutationsAtPosition, size) {
|
|
|
4164
4181
|
// construct label (sorted by protein change count, not alphabetically)
|
|
4165
4182
|
var label = startStr + proteinChangesTrimmed.join('/');
|
|
4166
4183
|
if (proteinChanges.length < mutationCountsByProteinChange.length) {
|
|
4167
|
-
label = label
|
|
4168
|
-
proteinChanges.length
|
|
4184
|
+
label = "".concat(label, " and ").concat(mutationCountsByProteinChange.length -
|
|
4185
|
+
proteinChanges.length, " more");
|
|
4169
4186
|
}
|
|
4170
4187
|
return label;
|
|
4171
4188
|
}
|
|
4172
4189
|
function lollipopLabelTextAnchor(labelText, codon, fontFamily, fontSize, geneWidth, proteinLength) {
|
|
4173
4190
|
var anchor = 'middle';
|
|
4174
|
-
var approxLabelWidth = getTextWidth(labelText, fontFamily, fontSize
|
|
4191
|
+
var approxLabelWidth = getTextWidth(labelText, fontFamily, "".concat(fontSize, "px"));
|
|
4175
4192
|
var lollipopDistanceToOrigin = codon * (geneWidth / proteinLength);
|
|
4176
4193
|
var lollipopDistanceToXMax = geneWidth - lollipopDistanceToOrigin;
|
|
4177
4194
|
// if lollipop is too close to the origin, in order to prevent label overlap set anchor to "start"
|
|
@@ -5225,7 +5242,7 @@ var LollipopPlotNoTooltip = /** @class */ (function (_super) {
|
|
|
5225
5242
|
var segments = ___default.map(this.props.domains, function (domain) {
|
|
5226
5243
|
var segment = {
|
|
5227
5244
|
start: start,
|
|
5228
|
-
end: _this.codonToX(domain.startCodon),
|
|
5245
|
+
end: _this.codonToX(domain.startCodon), // segment ends at the start of the current domain
|
|
5229
5246
|
};
|
|
5230
5247
|
// next segment starts at the end of the current domain
|
|
5231
5248
|
start = _this.codonToX(domain.endCodon);
|
|
@@ -5273,7 +5290,7 @@ var LollipopPlotNoTooltip = /** @class */ (function (_super) {
|
|
|
5273
5290
|
? -_this.countToHeight(lollipop.count, _this.bottomYMax, _this.zeroHeight)
|
|
5274
5291
|
: _this.countToHeight(lollipop.count, _this.yMax, _this.zeroHeight);
|
|
5275
5292
|
var stickBaseY = _this.calcStickBaseY(lollipop.placement);
|
|
5276
|
-
return (React.createElement(Lollipop, { key: lollipop.codon
|
|
5293
|
+
return (React.createElement(Lollipop, { key: "".concat(lollipop.codon, "_").concat(lollipop.placement === LollipopPlacement.BOTTOM
|
|
5277
5294
|
? 'bottom'
|
|
5278
5295
|
: 'top'), ref: function (lollipopComponent) {
|
|
5279
5296
|
if (lollipopComponent !== null) {
|
|
@@ -5324,12 +5341,12 @@ var LollipopPlotNoTooltip = /** @class */ (function (_super) {
|
|
|
5324
5341
|
}
|
|
5325
5342
|
else {
|
|
5326
5343
|
label = groupName
|
|
5327
|
-
? symbol
|
|
5328
|
-
''
|
|
5329
|
-
: symbol
|
|
5344
|
+
? "".concat(symbol, " ").concat(this.props.hugoGeneSymbol ||
|
|
5345
|
+
'', " ").concat(groupName, " Mutations")
|
|
5346
|
+
: "".concat(symbol, " ").concat(this.props.hugoGeneSymbol || '', " Mutations");
|
|
5330
5347
|
}
|
|
5331
5348
|
var placeOnBottom = placement === LollipopPlacement.BOTTOM;
|
|
5332
|
-
return (React.createElement(SVGAxis, { key: "lollipopPlotYAxis_"
|
|
5349
|
+
return (React.createElement(SVGAxis, { key: "lollipopPlotYAxis_".concat(placeOnBottom ? 'bottom' : 'top'), x: this.geneX - this.yAxisPadding, y: y, length: this.yAxisHeight, tickLength: 7, rangeLower: 0, rangeUpper: yMax, ticks: ticks, vertical: true, verticalLabelPadding: this.props.yAxisLabelPadding, reverse: placeOnBottom, label: label }));
|
|
5333
5350
|
}
|
|
5334
5351
|
});
|
|
5335
5352
|
Object.defineProperty(LollipopPlotNoTooltip.prototype, "xAxis", {
|
|
@@ -5338,7 +5355,7 @@ var LollipopPlotNoTooltip = /** @class */ (function (_super) {
|
|
|
5338
5355
|
writable: true,
|
|
5339
5356
|
value: function (y, placement) {
|
|
5340
5357
|
var placeOnTop = placement === LollipopPlacement.TOP;
|
|
5341
|
-
return (React.createElement(SVGAxis, { key: "lollipopPlotXAxis_"
|
|
5358
|
+
return (React.createElement(SVGAxis, { key: "lollipopPlotXAxis_".concat(placeOnTop ? 'top' : 'bottom'), x: this.geneX, y: y + (placeOnTop ? this.xAxisHeight : 0), length: this.props.vizWidth, tickLength: 7, rangeLower: 0, rangeUpper: this.props.xMax, ticks: this.xTicks, invertTicks: placeOnTop }));
|
|
5342
5359
|
}
|
|
5343
5360
|
});
|
|
5344
5361
|
Object.defineProperty(LollipopPlotNoTooltip.prototype, "axisTicks", {
|
|
@@ -5399,7 +5416,7 @@ var LollipopPlotNoTooltip = /** @class */ (function (_super) {
|
|
|
5399
5416
|
configurable: true,
|
|
5400
5417
|
writable: true,
|
|
5401
5418
|
value: function (index) {
|
|
5402
|
-
return ""
|
|
5419
|
+
return "".concat(DOMAIN_ID_CLASS_PREFIX).concat(index);
|
|
5403
5420
|
}
|
|
5404
5421
|
});
|
|
5405
5422
|
Object.defineProperty(LollipopPlotNoTooltip.prototype, "makeLollipopIndexClass", {
|
|
@@ -5407,7 +5424,7 @@ var LollipopPlotNoTooltip = /** @class */ (function (_super) {
|
|
|
5407
5424
|
configurable: true,
|
|
5408
5425
|
writable: true,
|
|
5409
5426
|
value: function (index) {
|
|
5410
|
-
return ""
|
|
5427
|
+
return "".concat(LOLLIPOP_ID_CLASS_PREFIX).concat(index);
|
|
5411
5428
|
}
|
|
5412
5429
|
});
|
|
5413
5430
|
Object.defineProperty(LollipopPlotNoTooltip.prototype, "makeSequenceIndexClass", {
|
|
@@ -5415,7 +5432,7 @@ var LollipopPlotNoTooltip = /** @class */ (function (_super) {
|
|
|
5415
5432
|
configurable: true,
|
|
5416
5433
|
writable: true,
|
|
5417
5434
|
value: function (index) {
|
|
5418
|
-
return ""
|
|
5435
|
+
return "".concat(SEQUENCE_ID_CLASS_PREFIX).concat(index);
|
|
5419
5436
|
}
|
|
5420
5437
|
});
|
|
5421
5438
|
Object.defineProperty(LollipopPlotNoTooltip.prototype, "getDomainIndex", {
|
|
@@ -5819,7 +5836,7 @@ var AxisScaleSwitch = /** @class */ (function (_super) {
|
|
|
5819
5836
|
return (React.createElement("button", { className: classNames({
|
|
5820
5837
|
'btn-secondary': this.props.selectedScale === scale,
|
|
5821
5838
|
'btn-outline-secondary': this.props.selectedScale !== scale,
|
|
5822
|
-
}, 'btn', 'btn-sm', 'btn-axis-switch'), "data-test": "AxisScaleSwitch"
|
|
5839
|
+
}, 'btn', 'btn-sm', 'btn-axis-switch'), "data-test": "AxisScaleSwitch".concat(scale), style: {
|
|
5823
5840
|
lineHeight: 1,
|
|
5824
5841
|
cursor: this.props.selectedScale === scale
|
|
5825
5842
|
? 'default'
|
|
@@ -5998,7 +6015,7 @@ var LollipopMutationPlotControls = /** @class */ (function (_super) {
|
|
|
5998
6015
|
});
|
|
5999
6016
|
Object.defineProperty(LollipopMutationPlotControls.prototype, "downloadControls", {
|
|
6000
6017
|
get: function () {
|
|
6001
|
-
return (React.createElement(DownloadControls, { getSvg: this.props.getSVG, filename: this.props.hugoGeneSymbol
|
|
6018
|
+
return (React.createElement(DownloadControls, { getSvg: this.props.getSVG, filename: "".concat(this.props.hugoGeneSymbol, "_lollipop"), dontFade: true, type: "button" }));
|
|
6002
6019
|
},
|
|
6003
6020
|
enumerable: false,
|
|
6004
6021
|
configurable: true
|
|
@@ -6555,7 +6572,7 @@ var Track = /** @class */ (function (_super) {
|
|
|
6555
6572
|
if (item !== null) {
|
|
6556
6573
|
_this.shapes[index] = item;
|
|
6557
6574
|
}
|
|
6558
|
-
}, key: spec.startCodon, hitZoneClassName: ""
|
|
6575
|
+
}, key: spec.startCodon, hitZoneClassName: "".concat(_this.props.idClassPrefix).concat(index), hitZoneXOffset: _this.props.xOffset, x: (spec.startCodon / _this.props.proteinLength) *
|
|
6559
6576
|
_this.props.width, y: y, dim1: dim1, dim2: dim2, spec: specFeats }));
|
|
6560
6577
|
});
|
|
6561
6578
|
},
|
|
@@ -6632,7 +6649,7 @@ var Track = /** @class */ (function (_super) {
|
|
|
6632
6649
|
position: 'relative',
|
|
6633
6650
|
display: 'flex',
|
|
6634
6651
|
} },
|
|
6635
|
-
React.createElement("span", { className: classNames(styles$4.trackTitle, 'small', (this.props.isSubTrack ? 'subtrack-' : ''
|
|
6652
|
+
React.createElement("span", { className: classNames(styles$4.trackTitle, 'small', "".concat(this.props.isSubTrack ? 'subtrack-' : '', "trackTitle")) }, this.props.trackTitle),
|
|
6636
6653
|
React.createElement("span", null,
|
|
6637
6654
|
React.createElement(DefaultTooltip, __assign({ placement: this.getOverlayPlacement(), overlay: this.getOverlay, onVisibleChange: this.onTooltipVisibleChange, destroyTooltipOnHide: true }, this.tooltipVisibleProps), this.hitZone),
|
|
6638
6655
|
React.createElement("span", { style: { marginLeft: this.props.xOffset }, onMouseOver: this.onMouseOver },
|
|
@@ -6713,7 +6730,7 @@ function hotspotTooltip(mutations, hotspotIndex, hotspots) {
|
|
|
6713
6730
|
}).length;
|
|
6714
6731
|
// generate custom info
|
|
6715
6732
|
var residues = ___default.uniq(hotspots.map(function (hotspot) { return hotspot.residue; }));
|
|
6716
|
-
var residuesText = React.createElement("b", null, ""
|
|
6733
|
+
var residuesText = React.createElement("b", null, "".concat(residues.join(', ')));
|
|
6717
6734
|
var pluralSuffix = residues.length > 1 ? 's' : undefined;
|
|
6718
6735
|
var residueInfo = (React.createElement("span", null,
|
|
6719
6736
|
"on residue",
|
|
@@ -6988,11 +7005,11 @@ var ExonTrack = /** @class */ (function (_super) {
|
|
|
6988
7005
|
var exonEndLocation = formatExonLocation(endCodon);
|
|
6989
7006
|
var exonLength = formatExonLength(exon.length);
|
|
6990
7007
|
var link = _this.chromosome
|
|
6991
|
-
? "https://igv.org/app/?locus=chr"
|
|
7008
|
+
? "https://igv.org/app/?locus=chr".concat(_this.chromosome, ":").concat(exon.genomicLocationStart, "-").concat(exon.genomicLocationEnd, "&genome=").concat(_this.genomeBuild)
|
|
6992
7009
|
: 'https://igv.org';
|
|
6993
7010
|
var linkText = _this.chromosome
|
|
6994
|
-
? _this.genomeBuild
|
|
6995
|
-
: exon.genomicLocationStart
|
|
7011
|
+
? "".concat(_this.genomeBuild, ":chr").concat(_this.chromosome, ":").concat(exon.genomicLocationStart, " - ").concat(exon.genomicLocationEnd)
|
|
7012
|
+
: "".concat(exon.genomicLocationStart, " - ").concat(exon.genomicLocationEnd);
|
|
6996
7013
|
return {
|
|
6997
7014
|
color: altColors[index % 2],
|
|
6998
7015
|
startCodon: startCodon,
|
|
@@ -7161,7 +7178,7 @@ var PTM_ANNOTATION_DEFAULT_COLUMNS = (_a = {},
|
|
|
7161
7178
|
_a);
|
|
7162
7179
|
function getResidue(ptm) {
|
|
7163
7180
|
if (ptm.residue.end && ptm.residue.end > ptm.residue.start) {
|
|
7164
|
-
return ptm.residue.start
|
|
7181
|
+
return "".concat(ptm.residue.start, "-").concat(ptm.residue.end);
|
|
7165
7182
|
}
|
|
7166
7183
|
else {
|
|
7167
7184
|
return ptm.residue.start.toString();
|
|
@@ -7400,7 +7417,7 @@ var PtmTrack = /** @class */ (function (_super) {
|
|
|
7400
7417
|
"PTM",
|
|
7401
7418
|
' ',
|
|
7402
7419
|
this.props.dataSource
|
|
7403
|
-
? "("
|
|
7420
|
+
? "(".concat(this.props.dataSource, ")")
|
|
7404
7421
|
: 'Sites',
|
|
7405
7422
|
' ',
|
|
7406
7423
|
React.createElement("i", { className: "fa fa-info-circle" })))));
|
|
@@ -7452,7 +7469,7 @@ var PtmTrack = /** @class */ (function (_super) {
|
|
|
7452
7469
|
overflow: 'hidden',
|
|
7453
7470
|
whiteSpace: 'nowrap',
|
|
7454
7471
|
textOverflow: 'ellipsis',
|
|
7455
|
-
} })), width: _this.props.width, proteinLength: _this.props.proteinLength, trackItems: item.specs, idClassPrefix: "ptm-"
|
|
7472
|
+
} })), width: _this.props.width, proteinLength: _this.props.proteinLength, trackItems: item.specs, idClassPrefix: "ptm-".concat(index, "-"), isSubTrack: true })); })
|
|
7456
7473
|
: null;
|
|
7457
7474
|
},
|
|
7458
7475
|
enumerable: false,
|
|
@@ -7563,7 +7580,7 @@ var UniprotTopologyTrackDescriptionTooltip = function (props) {
|
|
|
7563
7580
|
var dataSourceDiv = props.uniprotId ? (React.createElement("div", null,
|
|
7564
7581
|
"Data Source:",
|
|
7565
7582
|
' ',
|
|
7566
|
-
React.createElement("a", { href: "https://www.uniprot.org/uniprot/"
|
|
7583
|
+
React.createElement("a", { href: "https://www.uniprot.org/uniprot/".concat(props.uniprotId), target: "_blank" }, "UniProt"))) : (React.createElement("div", null,
|
|
7567
7584
|
"Data Source:",
|
|
7568
7585
|
' ',
|
|
7569
7586
|
React.createElement("a", { href: 'https://www.uniprot.org/', target: "_blank" }, "UniProt")));
|
|
@@ -7712,7 +7729,7 @@ var UniprotTopologyTrack = /** @class */ (function (_super) {
|
|
|
7712
7729
|
overflow: 'hidden',
|
|
7713
7730
|
whiteSpace: 'nowrap',
|
|
7714
7731
|
textOverflow: 'ellipsis',
|
|
7715
|
-
} })), width: _this.props.width, proteinLength: _this.props.proteinLength, trackItems: item.specs, idClassPrefix: "uniprot-topology-"
|
|
7732
|
+
} })), width: _this.props.width, proteinLength: _this.props.proteinLength, trackItems: item.specs, idClassPrefix: "uniprot-topology-".concat(index, "-"), isSubTrack: true })); })
|
|
7716
7733
|
: null;
|
|
7717
7734
|
},
|
|
7718
7735
|
enumerable: false,
|
|
@@ -7910,7 +7927,7 @@ var DomainTooltip = function (props) {
|
|
|
7910
7927
|
var pfamAccession = domain ? domain.pfamAccession : pfamDomainId;
|
|
7911
7928
|
// if no domain info, then just display the accession
|
|
7912
7929
|
var domainInfo = domain
|
|
7913
|
-
? domain.name
|
|
7930
|
+
? "".concat(domain.name, ": ").concat(domain.description)
|
|
7914
7931
|
: pfamAccession;
|
|
7915
7932
|
return (React.createElement("div", { style: { maxWidth: 200 } },
|
|
7916
7933
|
React.createElement("div", null,
|
|
@@ -7921,7 +7938,7 @@ var DomainTooltip = function (props) {
|
|
|
7921
7938
|
range.pfamDomainEnd,
|
|
7922
7939
|
")"),
|
|
7923
7940
|
React.createElement("div", null,
|
|
7924
|
-
React.createElement("a", { style: { marginRight: '5px' }, href: "http://pfam.xfam.org/family/"
|
|
7941
|
+
React.createElement("a", { style: { marginRight: '5px' }, href: "http://pfam.xfam.org/family/".concat(pfamAccession), target: "_blank" }, "PFAM"),
|
|
7925
7942
|
React.createElement(MutationAlignerLink, { mutationAlignerCache: props.mutationAlignerCache, pfamAccession: pfamAccession }))));
|
|
7926
7943
|
};
|
|
7927
7944
|
|
|
@@ -8054,9 +8071,9 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
|
|
|
8054
8071
|
var count = countsByPosition[codon];
|
|
8055
8072
|
var countInfo = this.props.lollipopTooltipCountInfo ? (this.props.lollipopTooltipCountInfo(count, mutationsAtPosition, this.props.axisMode, group)) : (React.createElement("strong", null,
|
|
8056
8073
|
count,
|
|
8057
|
-
" mutation", ""
|
|
8074
|
+
" mutation", "".concat(count !== 1 ? 's' : '')));
|
|
8058
8075
|
var label = lollipopLabelText(mutationsAtPosition);
|
|
8059
|
-
return (React.createElement("div", { "data-test": "tooltip-"
|
|
8076
|
+
return (React.createElement("div", { "data-test": "tooltip-".concat(codon).concat(group ? "-".concat(group) : '') },
|
|
8060
8077
|
countInfo,
|
|
8061
8078
|
React.createElement("br", null),
|
|
8062
8079
|
React.createElement("span", null,
|
|
@@ -8359,7 +8376,7 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
|
|
|
8359
8376
|
writable: true,
|
|
8360
8377
|
value: function () {
|
|
8361
8378
|
return (React.createElement("div", { style: { maxWidth: 200 } },
|
|
8362
|
-
React.createElement("a", { href: "https://www.uniprot.org/uniprot/"
|
|
8379
|
+
React.createElement("a", { href: "https://www.uniprot.org/uniprot/".concat(this.props.store.uniprotId.result), target: "_blank" }, this.props.store.uniprotId.result)));
|
|
8363
8380
|
}
|
|
8364
8381
|
});
|
|
8365
8382
|
Object.defineProperty(LollipopMutationPlot.prototype, "sequence", {
|
|
@@ -8392,15 +8409,15 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
|
|
|
8392
8409
|
//Add svg to the dom so getBBox can calculate dimensions
|
|
8393
8410
|
document.body.appendChild(outerSvg);
|
|
8394
8411
|
// Group the tracks and translate below the lollipop chart
|
|
8395
|
-
var allTracksG = createGroupTag("translate(0, "
|
|
8412
|
+
var allTracksG = createGroupTag("translate(0, ".concat(LollipopPlot.defaultProps.vizHeight, ")"));
|
|
8396
8413
|
outerSvg.append(allTracksG);
|
|
8397
8414
|
var trackSvgList = $(this.divContainer).find('.track-svgnode');
|
|
8398
8415
|
var trackTitles = $(this.divContainer).find('span[class*=trackTitle]');
|
|
8399
8416
|
var trackYShift = 0;
|
|
8400
8417
|
trackSvgList.each(function (idx, track) {
|
|
8401
|
-
var trackSvgGroup = createGroupTag("translate("
|
|
8418
|
+
var trackSvgGroup = createGroupTag("translate(".concat(_this.geneXOffset, ",").concat(trackYShift, ")"));
|
|
8402
8419
|
trackSvgGroup.appendChild(track.cloneNode(true));
|
|
8403
|
-
var trackNameGroup = createGroupTag("translate(0,"
|
|
8420
|
+
var trackNameGroup = createGroupTag("translate(0,".concat(trackYShift + 8, ")"));
|
|
8404
8421
|
var isSubTrack = trackTitles[idx].className.includes('subtrack-');
|
|
8405
8422
|
var trackName = createTextTag(document.createTextNode(trackTitles[idx].innerText), TEXT_STYLE, isSubTrack ? SUBTRACK_INDENT : TRACK_INDENT, 0);
|
|
8406
8423
|
trackNameGroup.append(trackName);
|
|
@@ -8648,7 +8665,7 @@ var LollipopTooltipCountInfo = function (_a) {
|
|
|
8648
8665
|
formatPercentValue(count, fractionDigits),
|
|
8649
8666
|
"% mutation rate")) : (React.createElement("strong", null,
|
|
8650
8667
|
count,
|
|
8651
|
-
" mutation", ""
|
|
8668
|
+
" mutation", "".concat(count !== 1 ? 's' : '')));
|
|
8652
8669
|
};
|
|
8653
8670
|
|
|
8654
8671
|
var DefaultStringQueryCache = /** @class */ (function () {
|
|
@@ -8771,7 +8788,7 @@ var MutationAlignerCache = /** @class */ (function (_super) {
|
|
|
8771
8788
|
// )
|
|
8772
8789
|
// )
|
|
8773
8790
|
// .catch(e => Promise.reject(e));
|
|
8774
|
-
return Promise.resolve("http://mutationaligner.org/domains/"
|
|
8791
|
+
return Promise.resolve("http://mutationaligner.org/domains/".concat(pfamAccession));
|
|
8775
8792
|
}
|
|
8776
8793
|
});
|
|
8777
8794
|
return MutationAlignerCache;
|
|
@@ -9298,7 +9315,7 @@ var DefaultMutationMapperDataFetcher = /** @class */ (function () {
|
|
|
9298
9315
|
switch (_a.label) {
|
|
9299
9316
|
case 0:
|
|
9300
9317
|
if (!swissProtId) return [3 /*break*/, 2];
|
|
9301
|
-
return [4 /*yield*/, request.get(getUrl("https://www.ebi.ac.uk/proteins/api/features/<%= uniprotAccession %>?categories="
|
|
9318
|
+
return [4 /*yield*/, request.get(getUrl("https://www.ebi.ac.uk/proteins/api/features/<%= uniprotAccession %>?categories=".concat(category.join(',')), { uniprotAccession: swissProtId }))];
|
|
9302
9319
|
case 1:
|
|
9303
9320
|
uniprotData = _a.sent();
|
|
9304
9321
|
featureList = JSON.parse(uniprotData.text);
|
|
@@ -10301,8 +10318,8 @@ var DefaultMutationMapperStore = /** @class */ (function () {
|
|
|
10301
10318
|
var ensemblTranscriptLookUpLink;
|
|
10302
10319
|
return __generator(this, function (_a) {
|
|
10303
10320
|
ensemblTranscriptLookUpLink = this.genomeBuild === 'hg19'
|
|
10304
|
-
? "https://grch37.rest.ensembl.org/lookup/id/"
|
|
10305
|
-
: "https://rest.ensembl.org/lookup/id/"
|
|
10321
|
+
? "https://grch37.rest.ensembl.org/lookup/id/".concat(this.activeTranscript.result, "?content-type=application/json")
|
|
10322
|
+
: "https://rest.ensembl.org/lookup/id/".concat(this.activeTranscript.result, "?content-type=application/json");
|
|
10306
10323
|
return [2 /*return*/, this.activeTranscript.result
|
|
10307
10324
|
? get(ensemblTranscriptLookUpLink)
|
|
10308
10325
|
: undefined];
|
|
@@ -10701,6 +10718,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
|
|
|
10701
10718
|
], DefaultMutationMapperStore.prototype, "getDefaultEntrezGeneId", null);
|
|
10702
10719
|
__decorate([
|
|
10703
10720
|
computed
|
|
10721
|
+
// Get genome build for exon track
|
|
10704
10722
|
], DefaultMutationMapperStore.prototype, "genomeBuild", null);
|
|
10705
10723
|
return DefaultMutationMapperStore;
|
|
10706
10724
|
}());
|
|
@@ -10811,9 +10829,9 @@ var TranscriptDropdown = /** @class */ (function (_super) {
|
|
|
10811
10829
|
var nrOfMutations = mutationsByTranscriptId &&
|
|
10812
10830
|
mutationsByTranscriptId[t] &&
|
|
10813
10831
|
mutationsByTranscriptId[t].length;
|
|
10814
|
-
var label = ""
|
|
10815
|
-
? "("
|
|
10816
|
-
: ''
|
|
10832
|
+
var label = "".concat(refseqMrnaId ? "".concat(refseqMrnaId, " / ") : '').concat(t, " ").concat(ccdsId ? "(".concat(ccdsId, ")") : '', " ").concat(length ? "(".concat(length, " amino acids)") : '', " ").concat(nrOfMutations
|
|
10833
|
+
? "(".concat(nrOfMutations, " mutations)")
|
|
10834
|
+
: '', " ").concat(t === canonicalTranscript ? ' (default)' : '');
|
|
10817
10835
|
return { label: label, value: t };
|
|
10818
10836
|
}), onChange: function (option) {
|
|
10819
10837
|
if (option.value) {
|
|
@@ -10873,7 +10891,7 @@ var GeneSummaryInfo = function (_a) {
|
|
|
10873
10891
|
: transcriptsByTranscriptId[activeTranscript];
|
|
10874
10892
|
var refseqMrnaId = transcript && transcript.refseqMrnaId;
|
|
10875
10893
|
var ccdsId = transcript && transcript.ccdsId;
|
|
10876
|
-
var refSeq = refseqMrnaId ? (React.createElement("a", { href: getNCBIlink("/nuccore/"
|
|
10894
|
+
var refSeq = refseqMrnaId ? (React.createElement("a", { href: getNCBIlink("/nuccore/".concat(refseqMrnaId)), target: "_blank" }, refseqMrnaId)) : ('-');
|
|
10877
10895
|
var ensembl = showDropDown
|
|
10878
10896
|
? activeTranscript && (React.createElement("a", { href: getUrl(transcriptSummaryUrlTemplate, {
|
|
10879
10897
|
transcriptId: activeTranscript,
|
|
@@ -10890,7 +10908,7 @@ var GeneSummaryInfo = function (_a) {
|
|
|
10890
10908
|
DATA: ccdsId,
|
|
10891
10909
|
},
|
|
10892
10910
|
}), target: "_blank" }, ccdsId)) : ('-');
|
|
10893
|
-
var uniprot = uniprotId ? (React.createElement("a", { href: "https://www.uniprot.org/uniprot/"
|
|
10911
|
+
var uniprot = uniprotId ? (React.createElement("a", { href: "https://www.uniprot.org/uniprot/".concat(uniprotId), target: "_blank" }, uniprotId)) : ('-');
|
|
10894
10912
|
var compactGeneSummaryInfo = (React.createElement("div", null,
|
|
10895
10913
|
React.createElement("span", { "data-test": "compactGeneSummaryRefSeq" }, refSeq), " | ",
|
|
10896
10914
|
ensembl,
|
|
@@ -11246,7 +11264,7 @@ var MutationMapper = /** @class */ (function (_super) {
|
|
|
11246
11264
|
? dataStore.sortedFilteredSelectedData
|
|
11247
11265
|
: dataStore.sortedFilteredData;
|
|
11248
11266
|
var allData = dataStore.allData;
|
|
11249
|
-
return (React.createElement(FilterResetPanel, { filterInfo: "Showing "
|
|
11267
|
+
return (React.createElement(FilterResetPanel, { filterInfo: "Showing ".concat(tableData.length, " of ").concat(allData.length, " mutations."), resetFilters: this.resetFilters }));
|
|
11250
11268
|
},
|
|
11251
11269
|
enumerable: false,
|
|
11252
11270
|
configurable: true
|