react-mutation-mapper 0.8.25 → 0.8.29
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/column/Annotation.d.ts +2 -0
- package/dist/component/oncokb/AnnotationIcon.d.ts +4 -1
- package/dist/component/oncokb/CompactAnnotationIcon.d.ts +8 -0
- package/dist/component/oncokb/OncoKB.d.ts +4 -0
- package/dist/component/oncokb/OncoKbCard.d.ts +1 -0
- package/dist/component/oncokb/OncoKbCardBody.d.ts +1 -0
- package/dist/index.es.js +322 -130
- package/dist/index.es.js.map +1 -1
- package/dist/index.js +321 -129
- package/dist/index.js.map +1 -1
- package/dist/util/OncoKbUtils.d.ts +4 -1
- package/package.json +6 -6
package/dist/index.es.js
CHANGED
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@@ -3,13 +3,13 @@ import { makeObservable, observable, action, computed, reaction } from 'mobx';
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import { observer } from 'mobx-react';
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import React__default, { createElement, Component, useState, Fragment } from 'react';
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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';
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import { CIVIC_NA_VALUE, generateQueryVariantId,
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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';
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import classnames from 'classnames';
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import autobind from 'autobind-decorator';
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import { Collapse } from 'react-collapse';
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import { Tabs, Tab, Modal } from 'react-bootstrap';
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import {
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import { Collapse } from 'react-collapse';
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import ReactTable from 'react-table';
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import { If, Then, Else } from 'react-if';
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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 Select, { components } from 'react-select';
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@@ -404,6 +404,12 @@ function normalizeLevel(level) {
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return null;
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}
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}
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function normalizeOncogenicity(oncogenicity) {
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return (oncogenicity || 'unknown')
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.trim()
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.toLowerCase()
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.replace(/\s/, '-');
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}
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function levelIconClassNames(level) {
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if (level) {
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return "oncokb icon level-" + level;
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@@ -411,13 +417,32 @@ function levelIconClassNames(level) {
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return '';
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}
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function oncogenicityIconClassNames(oncogenicity) {
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return "oncokb icon " + normalizeOncogenicity(oncogenicity);
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}
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function annotationIconClassNames(type, highestLevel, indicator) {
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return type === OncoKbCardDataType.BIOLOGICAL
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? oncogenicityIconClassNames((indicator === null || indicator === void 0 ? void 0 : indicator.oncogenic) || '')
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: levelIconClassNames(normalizeLevel(highestLevel) || '');
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}
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function calcHighestIndicatorLevel(type, indicator) {
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var highestLevel = '';
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if (indicator) {
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switch (type) {
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case OncoKbCardDataType.TXS:
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highestLevel = indicator.highestSensitiveLevel;
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break;
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case OncoKbCardDataType.TXR:
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highestLevel = indicator.highestResistanceLevel;
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break;
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case OncoKbCardDataType.DX:
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highestLevel = indicator.highestDiagnosticImplicationLevel;
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break;
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case OncoKbCardDataType.PX:
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highestLevel = indicator.highestPrognosticImplicationLevel;
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break;
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}
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}
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return
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.trim()
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.toLowerCase()
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.replace(/\s/, '-');
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return highestLevel;
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}
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function calcOncogenicScore(oncogenic) {
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return ONCOGENIC_SCORE[oncogenic] || 0;
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@@ -607,6 +632,125 @@ var MyCancerGenome = /** @class */ (function (_super) {
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return MyCancerGenome;
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}(Component));
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function hideArrow$1(tooltipEl) {
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var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
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arrowEl.style.display = 'none';
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}
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var AnnotationIcon = function (props) {
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if (props.availableDataTypes !== undefined &&
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!props.availableDataTypes.includes(props.type)) {
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return null;
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}
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var highestLevel = calcHighestIndicatorLevel(props.type, props.indicator);
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return (React__default.createElement(AnnotationIconWithTooltip, { tooltipOverlay: props.tooltipOverlay, icon: React__default.createElement("i", { className: annotationIconClassNames(props.type, highestLevel, props.indicator), "data-test": "oncogenic-icon-image" }) }));
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};
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var AnnotationIconWithTooltip = function (props) {
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if (props.icon) {
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return (React__default.createElement(DefaultTooltip, { overlayClassName: "oncokb-tooltip", overlay: function () {
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return props.tooltipOverlay ? props.tooltipOverlay : null;
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}, placement: "right", trigger: ['hover', 'focus'], onPopupAlign: hideArrow$1, destroyTooltipOnHide: true },
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React__default.createElement("span", { className: "" + annotationStyles['annotation-item'] }, props.icon)));
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}
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else {
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return null;
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}
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};
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var BIOLOGICAL_COLOR_MAP = {
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oncogenic: '#0968C3',
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'likely-oncogenic': '#0968C3',
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'predicted-oncogenic': '#0968C3',
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resistance: '#0968C3',
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neutral: '#696969',
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'likely-neutral': '#696969',
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inconclusive: '#AAAAAA',
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vus: '#696969',
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unknown: '#CCCCCC',
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};
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var LEVEL_COLOR_MAP = {
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'1': '#33A02C',
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'2': '#1F78B4',
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'3': '#984EA3',
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'3A': '#984EA3',
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'3B': '#BE98CE',
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'4': '#424242',
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R1: '#EE3424',
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R2: '#F79A92',
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R3: '#FCD6D3',
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Dx1: '#33A02C',
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Dx2: '#1F78B4',
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Dx3: '#984EA3',
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Px1: '#33A02C',
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Px2: '#1F78B4',
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Px3: '#984EA3',
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};
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function getLevelColor(highestLevel, defaultColor) {
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if (defaultColor === void 0) { defaultColor = '#CCCCCC'; }
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var level = normalizeLevel(highestLevel || null) || '';
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return LEVEL_COLOR_MAP[level] || defaultColor;
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}
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function shouldDrawShape(type, level, availableDataTypes) {
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return (level &&
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availableDataTypes !== undefined &&
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availableDataTypes.includes(type));
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}
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function getOncogenicShape(indicator) {
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var oncogenicity = normalizeOncogenicity((indicator === null || indicator === void 0 ? void 0 : indicator.oncogenic) || '');
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var color = BIOLOGICAL_COLOR_MAP[oncogenicity] || '#CCCCCC';
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return (React__default.createElement("g", { transform: "translate(9, 9)" },
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React__default.createElement("circle", { r: "6", fill: "none", strokeWidth: "2", stroke: color }),
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oncogenicity !== 'vus' && oncogenicity !== 'unknown' && (React__default.createElement("g", null,
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React__default.createElement("circle", { r: "3", fill: "none", strokeWidth: "2", stroke: color }),
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React__default.createElement("circle", { r: "1.5", fill: color, stroke: "none" })))));
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}
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function getTherapeuticSensitivityShape(indicator, availableDataTypes) {
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var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestSensitiveLevel;
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if (!shouldDrawShape(OncoKbCardDataType.TXS, highestLevel, availableDataTypes)) {
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return null;
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}
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var fillColor = getLevelColor(highestLevel, '#33A02C');
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return (React__default.createElement("g", { transform: "translate(14.5, 3.5)" },
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React__default.createElement("circle", { r: "4", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
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}
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function getTherapeuticResistanceShape(indicator, availableDataTypes) {
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var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestResistanceLevel;
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if (!shouldDrawShape(OncoKbCardDataType.TXR, highestLevel, availableDataTypes)) {
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return null;
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}
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var fillColor = getLevelColor(highestLevel, '#EE3424');
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return (React__default.createElement("g", { transform: "translate(14.5, 14.5)" },
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React__default.createElement("circle", { r: "4", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
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}
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function getDiagnosticShape(indicator, availableDataTypes) {
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var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestDiagnosticImplicationLevel;
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if (!shouldDrawShape(OncoKbCardDataType.DX, highestLevel, availableDataTypes)) {
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return null;
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}
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var fillColor = getLevelColor(highestLevel, '#33A02C');
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return (React__default.createElement("g", { transform: "translate(-0.5, -0.5)" },
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React__default.createElement("rect", { width: "7", height: "7", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
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}
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function getPrognosticShape(indicator, availableDataTypes) {
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var highestLevel = indicator === null || indicator === void 0 ? void 0 : indicator.highestPrognosticImplicationLevel;
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if (!shouldDrawShape(OncoKbCardDataType.PX, highestLevel, availableDataTypes)) {
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return null;
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}
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var fillColor = getLevelColor(highestLevel, '#33A02C');
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return (React__default.createElement("g", { transform: "translate(0, 10.5)" },
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React__default.createElement("polygon", { points: "3.5 0, 8 8, -1 8", fill: fillColor, stroke: "#ffffff", strokeWidth: "1" })));
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}
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var CompactAnnotationIcon = function (props) {
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var indicatorForLevelIcons = props.usingPublicOncoKbInstance
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? undefined
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: props.indicator;
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return (React__default.createElement("svg", { version: "1.1", width: "18", height: "18", "data-test": "oncogenic-icon-image" },
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getOncogenicShape(props.indicator),
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getTherapeuticSensitivityShape(indicatorForLevelIcons, props.availableDataTypes),
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getTherapeuticResistanceShape(indicatorForLevelIcons, props.availableDataTypes),
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getDiagnosticShape(indicatorForLevelIcons, props.availableDataTypes),
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getPrognosticShape(indicatorForLevelIcons, props.availableDataTypes)));
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};
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var oncoKbLogoImgSrc = "data:image/svg+xml,%3Csvg%20width%3D%22138%22%20height%3D%2226%22%20viewBox%3D%220%200%20138%2026%22%20fill%3D%22none%22%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%3E%20%20%3Cpath%20d%3D%22M13.3232%2026C21.0801%2026%2026.7182%2020.1464%2026.7182%2013V12.9282C26.7182%205.78177%2021.1519%200%2013.395%200C5.63812%200%200%205.85359%200%2013V13.0718C0%2020.2182%205.5663%2026%2013.3232%2026ZM13.395%2020.9006C8.94199%2020.9006%205.78177%2017.3094%205.78177%2013V12.9282C5.78177%208.61878%208.87016%205.09945%2013.3232%205.09945C17.7762%205.09945%2020.9365%208.69061%2020.9365%2013V13.0718C20.9365%2017.3812%2017.8481%2020.9006%2013.395%2020.9006Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20d%3D%22M29.9722%2025.5691H35.4307V14.8315C35.4307%2012.2459%2036.7594%2010.9171%2038.8423%2010.9171C40.9252%2010.9171%2042.1462%2012.2459%2042.1462%2014.8315V25.5691H47.6048V13.1077C47.6048%208.69061%2045.1987%205.96133%2041.0688%205.96133C38.3036%205.96133%2036.6876%207.4337%2035.4307%209.04972V6.32044H29.9722V25.5691Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20d%3D%22M60.3551%2026C64.1976%2026%2066.3523%2024.5276%2068.2197%2022.4807L65.0236%2019.2486C63.6948%2020.5055%2062.4379%2021.2956%2060.6064%2021.2956C57.6258%2021.2956%2055.7225%2018.9254%2055.7225%2015.9807V15.9088C55.7225%2013.0718%2057.6617%2010.6657%2060.391%2010.6657C62.3302%2010.6657%2063.5512%2011.4917%2064.7722%2012.7845L68.112%209.19337C66.3164%207.18232%2064.054%205.96133%2060.4269%205.96133C54.5374%205.96133%2050.3357%2010.4862%2050.3357%2015.9807V16.0525C50.3357%2021.547%2054.5733%2026%2060.3551%2026Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20d%3D%22M91.3584%2025.5691H96.8888V17.884L99.7977%2014.8674L107.59%2025.5691H114.234L103.532%2011.0967L113.803%200.430938H107.016L96.8888%2011.4199V0.430938H91.3584V25.5691Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20d%3D%22M116.182%2025.5691H128.14C133.814%2025.5691%20137.549%2023.2707%20137.549%2018.674V18.6022C137.549%2015.2265%20135.754%2013.5387%20132.845%2012.4254C134.64%2011.4199%20136.149%209.83978%20136.149%207.00276V6.93094C136.149%205.20718%20135.574%203.80663%20134.425%202.65746C132.989%201.22099%20130.726%200.430938%20127.853%200.430938H116.182V25.5691ZM130.654%207.93646C130.654%209.80387%20129.11%2010.5939%20126.668%2010.5939H121.569V5.27901H127.027C129.361%205.27901%20130.654%206.21271%20130.654%207.86464V7.93646ZM132.055%2017.9199V17.9917C132.055%2019.8591%20130.582%2020.721%20128.14%2020.721H121.569V15.1906H127.961C130.798%2015.1906%20132.055%2016.232%20132.055%2017.9199Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20fill-rule%3D%22evenodd%22%20clip-rule%3D%22evenodd%22%20d%3D%22M78.8032%2023.5C82.9454%2023.5%2086.3032%2020.1421%2086.3032%2016C86.3032%2011.8579%2082.9454%208.5%2078.8032%208.5C74.6611%208.5%2071.3032%2011.8579%2071.3032%2016C71.3032%2020.1421%2074.6611%2023.5%2078.8032%2023.5ZM78.8032%2026C84.3261%2026%2088.8032%2021.5228%2088.8032%2016C88.8032%2010.4772%2084.3261%206%2078.8032%206C73.2804%206%2068.8032%2010.4772%2068.8032%2016C68.8032%2021.5228%2073.2804%2026%2078.8032%2026Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20fill-rule%3D%22evenodd%22%20clip-rule%3D%22evenodd%22%20d%3D%22M78.8032%2019.5C80.7362%2019.5%2082.3032%2017.933%2082.3032%2016C82.3032%2014.067%2080.7362%2012.5%2078.8032%2012.5C76.8702%2012.5%2075.3032%2014.067%2075.3032%2016C75.3032%2017.933%2076.8702%2019.5%2078.8032%2019.5ZM78.8032%2022C82.1169%2022%2084.8032%2019.3137%2084.8032%2016C84.8032%2012.6863%2082.1169%2010%2078.8032%2010C75.4895%2010%2072.8032%2012.6863%2072.8032%2016C72.8032%2019.3137%2075.4895%2022%2078.8032%2022Z%22%20fill%3D%22%230968C3%22%2F%3E%20%20%3Cpath%20fill-rule%3D%22evenodd%22%20clip-rule%3D%22evenodd%22%20d%3D%22M78.8032%2018C79.9078%2018%2080.8032%2017.1046%2080.8032%2016C80.8032%2014.8954%2079.9078%2014%2078.8032%2014C77.6987%2014%2076.8032%2014.8954%2076.8032%2016C76.8032%2017.1046%2077.6987%2018%2078.8032%2018Z%22%20fill%3D%22%230968C3%22%2F%3E%3C%2Fsvg%3E";
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var mainStyles = {"oncokb-card":"main-module_oncokb-card__32DzD","tab-content":"main-module_tab-content__8nUyf","tooltip-refs":"main-module_tooltip-refs__SpA4W","disclaimer":"main-module_disclaimer__3CLlM","blue-icon":"main-module_blue-icon__2Hs-v","footer":"main-module_footer__2dc-8","oncokb-logo":"main-module_oncokb-logo__3RVg7","title":"main-module_title__2kT-n","additional-info":"main-module_additional-info__1nXTm","biological-info":"main-module_biological-info__2efDC","ellipsis-text-wrapper":"main-module_ellipsis-text-wrapper__18dny"};
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@@ -1171,35 +1315,6 @@ var EvidenceReferenceContent = function (props) {
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: 'Information is not available.')))));
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};
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var BiologicalContent = function (props) {
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return (React__default.createElement(EvidenceReferenceContent, { description: props.biologicalSummary, citations: props.mutationEffectCitations, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }));
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};
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var ImplicationContent = function (props) {
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var columns = [
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__assign(__assign({}, OncoKbHelper.getDefaultColumnDefinition('level')), { accessor: 'levelOfEvidence', maxWidth: 100 }),
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__assign(__assign({}, OncoKbHelper.getDefaultColumnDefinition('alterations')), { Cell: function (cellProps) {
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return OncoKbHelper.getAlterationsColumnCell(cellProps.value, props.variant);
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} }),
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{
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id: 'referenceList',
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Header: createElement("span", null),
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sortable: false,
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maxWidth: 50,
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Cell: function (cellProps) { return (createElement(DefaultTooltip, { overlay: function () { return (createElement("div", { className: mainStyles['tooltip-refs'] },
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createElement(EvidenceReferenceContent, { description: cellProps.original.description, citations: {
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pmids: cellProps.original.pmids,
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abstracts: cellProps.original.abstracts,
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}, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }))); }, placement: "right", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
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createElement("i", { className: "fa fa-book" }))); },
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},
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];
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return (createElement("div", null,
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createElement("p", null, props.summary),
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createElement("div", null,
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createElement(ReactTable, { data: props.implications, columns: columns, showPagination: false, pageSize: props.implications.length, className: "-striped -highlight" }))));
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};
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var OncoKbTreatmentTable = /** @class */ (function (_super) {
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__extends(OncoKbTreatmentTable, _super);
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function OncoKbTreatmentTable() {
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@@ -1281,8 +1396,38 @@ var OncoKbTreatmentTable = /** @class */ (function (_super) {
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return OncoKbTreatmentTable;
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}(Component));
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var BiologicalContent = function (props) {
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return (React__default.createElement(EvidenceReferenceContent, { description: props.biologicalSummary, citations: props.mutationEffectCitations, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }));
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};
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+
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var ImplicationContent = function (props) {
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var columns = [
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__assign(__assign({}, OncoKbHelper.getDefaultColumnDefinition('level')), { accessor: 'levelOfEvidence', maxWidth: 100 }),
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__assign(__assign({}, OncoKbHelper.getDefaultColumnDefinition('alterations')), { Cell: function (cellProps) {
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return OncoKbHelper.getAlterationsColumnCell(cellProps.value, props.variant);
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} }),
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{
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id: 'referenceList',
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Header: createElement("span", null),
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sortable: false,
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maxWidth: 50,
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Cell: function (cellProps) { return (createElement(DefaultTooltip, { overlay: function () { return (createElement("div", { className: mainStyles['tooltip-refs'] },
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createElement(EvidenceReferenceContent, { description: cellProps.original.description, citations: {
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pmids: cellProps.original.pmids,
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abstracts: cellProps.original.abstracts,
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}, pmidData: props.pmidData, noInfoDisclaimer: 'Mutation effect information is not available.' }))); }, placement: "right", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
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+
createElement("i", { className: "fa fa-book" }))); },
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},
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];
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return (createElement("div", null,
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createElement("p", null, props.summary),
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createElement("div", null,
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createElement(ReactTable, { data: props.implications, columns: columns, showPagination: false, pageSize: props.implications.length, className: "-striped -highlight" }))));
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};
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var tabsStyles = {"tabs-wrapper":"tabs-module_tabs-wrapper__XKjzo","tabs":"tabs-module_tabs__2I3mz","tab":"tabs-module_tab__3MoDA","tab-pane":"tabs-module_tab-pane__sGd85","tab-title-a":"tabs-module_tab-title-a__2WTNA","tab-title":"tabs-module_tab-title__2z9-D","tab-subtitle":"tabs-module_tab-subtitle__1P8B_"};
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var _a$1;
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var OncoKbMedicalDisclaimer = (React__default.createElement("p", { className: mainStyles.disclaimer }, "The information above is intended for research purposes only and should not be used as a substitute for professional diagnosis and treatment."));
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var ONCOKB_DATA_ACCESS_PAGE_LINK = 'https://docs.cbioportal.org/2.4-integration-with-other-webservices/oncokb-data-access';
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var publicInstanceDisclaimerOverLay = (React__default.createElement("div", null,
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@@ -1292,9 +1437,24 @@ var publicInstanceDisclaimerOverLay = (React__default.createElement("div", null,
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React__default.createElement("a", { href: ONCOKB_DATA_ACCESS_PAGE_LINK, target: '_blank' }, "these instructions"),
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"."),
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OncoKbMedicalDisclaimer));
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var DATA_TYPE_TO_TITLE = (_a$1 = {},
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_a$1[OncoKbCardDataType.BIOLOGICAL] = 'Biological Effect',
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_a$1[OncoKbCardDataType.TXS] = 'Therapeutic Implications',
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_a$1[OncoKbCardDataType.TXR] = 'Therapeutic Implications',
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_a$1[OncoKbCardDataType.DX] = 'Diagnostic Implications',
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_a$1[OncoKbCardDataType.PX] = 'Prognostic Implications',
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_a$1);
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var TabContentWrapper = function (props) {
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return React__default.createElement("div", { className: mainStyles['tab-content'] }, props.children);
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};
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var TabTitle = function (props) {
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var title = DATA_TYPE_TO_TITLE[props.type];
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var icon = props.displayHighestLevelInTabTitle ? (React__default.createElement("i", { className: annotationIconClassNames(props.type, calcHighestIndicatorLevel(props.type, props.indicator), props.indicator) })) : null;
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return icon ? (React__default.createElement("span", { style: { display: 'flex' } },
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icon,
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" ",
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title)) : (React__default.createElement("span", null, title));
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};
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var OncoKbCardBody = function (props) {
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var defaultTabActiveKey;
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// Do not assign a default key if the data type specified through the property does not have any content
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@@ -1338,13 +1498,13 @@ var OncoKbCardBody = function (props) {
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function getBody(type, indicator) {
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var tabs = [];
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if (dataTypeHasContent(OncoKbCardDataType.BIOLOGICAL)) {
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tabs.push(React__default.createElement(Tab, { eventKey: OncoKbCardDataType.BIOLOGICAL, title:
|
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tabs.push(React__default.createElement(Tab, { eventKey: OncoKbCardDataType.BIOLOGICAL, title: React__default.createElement(TabTitle, { type: OncoKbCardDataType.BIOLOGICAL, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
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React__default.createElement(TabContentWrapper, null,
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React__default.createElement(BiologicalContent, { mutationEffectCitations: indicator.mutationEffect.citations, biologicalSummary: indicator.mutationEffect.description, pmidData: props.pmidData }))));
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}
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if (!props.usingPublicOncoKbInstance &&
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dataTypeHasContent(OncoKbCardDataType.TXS)) {
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tabs.push(React__default.createElement(Tab, { eventKey: OncoKbCardDataType.TXS, title:
|
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tabs.push(React__default.createElement(Tab, { eventKey: OncoKbCardDataType.TXS, title: React__default.createElement(TabTitle, { type: OncoKbCardDataType.TXS, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
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React__default.createElement(TabContentWrapper, null,
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React__default.createElement("div", { style: {
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marginTop: 10,
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@@ -1353,13 +1513,13 @@ var OncoKbCardBody = function (props) {
|
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}
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if (!props.usingPublicOncoKbInstance &&
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dataTypeHasContent(OncoKbCardDataType.DX)) {
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tabs.push(React__default.createElement(Tab, { eventKey: OncoKbCardDataType.DX, title:
|
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+
tabs.push(React__default.createElement(Tab, { eventKey: OncoKbCardDataType.DX, title: React__default.createElement(TabTitle, { type: OncoKbCardDataType.DX, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
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React__default.createElement(TabContentWrapper, null,
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React__default.createElement(ImplicationContent, { variant: indicator.query.alteration, summary: indicator.diagnosticSummary, implications: indicator.diagnosticImplications, pmidData: props.pmidData }))));
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}
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if (!props.usingPublicOncoKbInstance &&
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dataTypeHasContent(OncoKbCardDataType.PX)) {
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tabs.push(React__default.createElement(Tab, { eventKey: OncoKbCardDataType.PX, title:
|
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+
tabs.push(React__default.createElement(Tab, { eventKey: OncoKbCardDataType.PX, title: React__default.createElement(TabTitle, { type: OncoKbCardDataType.PX, indicator: props.indicator, displayHighestLevelInTabTitle: props.displayHighestLevelInTabTitle }) },
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React__default.createElement(TabContentWrapper, null,
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React__default.createElement(ImplicationContent, { variant: indicator.query.alteration, summary: indicator.prognosticSummary, implications: indicator.prognosticImplications, pmidData: props.pmidData }))));
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}
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@@ -1456,7 +1616,6 @@ var OncoKbCard = /** @class */ (function (_super) {
|
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enumerable: false,
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configurable: true
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});
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-
// TODO we should replace the tabs with an actual ReactBootstrap Tab,
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|
Object.defineProperty(OncoKbCard.prototype, "render", {
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enumerable: false,
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configurable: true,
|
|
@@ -1468,7 +1627,7 @@ var OncoKbCard = /** @class */ (function (_super) {
|
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!this.props.geneNotExist && this.props.indicator && (createElement(OncoKbCardTitle, { hugoSymbol: this.props.indicator.query.hugoSymbol, variant: this.props.indicator.query.alteration, tumorType: this.props.indicator
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? this.props.indicator.query.tumorType
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: '' })),
|
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|
-
createElement(OncoKbCardBody, { type: this.props.type, indicator: this.props.indicator, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, hugoSymbol: this.props.hugoSymbol, pmidData: this.props.pmidData, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance }),
|
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|
+
createElement(OncoKbCardBody, { type: this.props.type, indicator: this.props.indicator, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, hugoSymbol: this.props.hugoSymbol, pmidData: this.props.pmidData, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, displayHighestLevelInTabTitle: this.props.displayHighestLevelInTabTitle }),
|
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createElement("div", { className: mainStyles.footer },
|
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|
this.oncokbLinkOut === undefined ? ({ oncokbLogo: oncokbLogo }) : (createElement("a", { href: "" + this.oncokbLinkOut, target: "_blank", className: mainStyles['oncokb-logo'] }, oncokbLogo)),
|
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this.props.handleFeedbackOpen && (createElement("span", null,
|
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@@ -1527,14 +1686,14 @@ var OncoKbTooltip = /** @class */ (function (_super) {
|
|
|
1527
1686
|
value: function () {
|
|
1528
1687
|
var tooltipContent = createElement("span", null);
|
|
1529
1688
|
if (this.props.geneNotExist) {
|
|
1530
|
-
tooltipContent = (createElement(OncoKbCard, { type: this.props.type, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, hugoSymbol: this.props.hugoSymbol, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, pmidData: {}, handleFeedbackOpen: this.props.handleFeedbackOpen }));
|
|
1689
|
+
tooltipContent = (createElement(OncoKbCard, { type: this.props.type, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, hugoSymbol: this.props.hugoSymbol, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, pmidData: {}, handleFeedbackOpen: this.props.handleFeedbackOpen, displayHighestLevelInTabTitle: true }));
|
|
1531
1690
|
}
|
|
1532
1691
|
if (!this.props.indicator) {
|
|
1533
1692
|
return tooltipContent;
|
|
1534
1693
|
}
|
|
1535
1694
|
if (!this.props.geneNotExist) {
|
|
1536
1695
|
var pmidData = this.pmidData;
|
|
1537
|
-
tooltipContent = (createElement(OncoKbCard, { type: this.props.type, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, hugoSymbol: this.props.hugoSymbol, indicator: this.props.indicator, pmidData: pmidData, handleFeedbackOpen: this.props.handleFeedbackOpen }));
|
|
1696
|
+
tooltipContent = (createElement(OncoKbCard, { type: this.props.type, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance, geneNotExist: this.props.geneNotExist, isCancerGene: this.props.isCancerGene, hugoSymbol: this.props.hugoSymbol, indicator: this.props.indicator, pmidData: pmidData, handleFeedbackOpen: this.props.handleFeedbackOpen, displayHighestLevelInTabTitle: true }));
|
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1538
1697
|
}
|
|
1539
1698
|
return tooltipContent;
|
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1540
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|
}
|
|
@@ -1578,44 +1737,6 @@ var OncoKbFeedback = /** @class */ (function (_super) {
|
|
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1578
1737
|
return OncoKbFeedback;
|
|
1579
1738
|
}(Component));
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1580
1739
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|
|
1581
|
-
function hideArrow$1(tooltipEl) {
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1582
|
-
var arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
|
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1583
|
-
arrowEl.style.display = 'none';
|
|
1584
|
-
}
|
|
1585
|
-
var AnnotationIcon = function (props) {
|
|
1586
|
-
var _a;
|
|
1587
|
-
if (props.availableDataTypes !== undefined &&
|
|
1588
|
-
!props.availableDataTypes.includes(props.type)) {
|
|
1589
|
-
return null;
|
|
1590
|
-
}
|
|
1591
|
-
var highestLevel = '';
|
|
1592
|
-
if (props.indicator) {
|
|
1593
|
-
switch (props.type) {
|
|
1594
|
-
case OncoKbCardDataType.TXS:
|
|
1595
|
-
highestLevel = props.indicator.highestSensitiveLevel;
|
|
1596
|
-
break;
|
|
1597
|
-
case OncoKbCardDataType.TXR:
|
|
1598
|
-
highestLevel = props.indicator.highestResistanceLevel;
|
|
1599
|
-
break;
|
|
1600
|
-
case OncoKbCardDataType.DX:
|
|
1601
|
-
highestLevel =
|
|
1602
|
-
props.indicator.highestDiagnosticImplicationLevel;
|
|
1603
|
-
break;
|
|
1604
|
-
case OncoKbCardDataType.PX:
|
|
1605
|
-
highestLevel =
|
|
1606
|
-
props.indicator.highestPrognosticImplicationLevel;
|
|
1607
|
-
break;
|
|
1608
|
-
}
|
|
1609
|
-
}
|
|
1610
|
-
return (React__default.createElement("span", { className: "" + annotationStyles['annotation-item'] },
|
|
1611
|
-
React__default.createElement(DefaultTooltip, { overlayClassName: "oncokb-tooltip", overlay: function () {
|
|
1612
|
-
return props.tooltipOverlay ? props.tooltipOverlay : null;
|
|
1613
|
-
}, placement: "right", trigger: ['hover', 'focus'], onPopupAlign: hideArrow$1, destroyTooltipOnHide: true },
|
|
1614
|
-
React__default.createElement("i", { className: props.type === OncoKbCardDataType.BIOLOGICAL
|
|
1615
|
-
? oncogenicityIconClassNames(((_a = props.indicator) === null || _a === void 0 ? void 0 : _a.oncogenic) || '')
|
|
1616
|
-
: levelIconClassNames(normalizeLevel(highestLevel) || ''), "data-test": "oncogenic-icon-image" }))));
|
|
1617
|
-
};
|
|
1618
|
-
|
|
1619
1740
|
function sortValue$2(indicator) {
|
|
1620
1741
|
var values = [0, 0, 0];
|
|
1621
1742
|
if (indicator) {
|
|
@@ -1637,6 +1758,33 @@ function download$2(indicator) {
|
|
|
1637
1758
|
var resistanceLevel = ((_b = indicator.highestResistanceLevel) === null || _b === void 0 ? void 0 : _b.toLowerCase()) || 'resistance NA';
|
|
1638
1759
|
return oncogenic + ", " + sensitivityLevel + ", " + resistanceLevel;
|
|
1639
1760
|
}
|
|
1761
|
+
function findDefaultDataTypeForTooltip(usingPublicOncoKbInstance, indicator, availableDataTypes) {
|
|
1762
|
+
if (usingPublicOncoKbInstance || !indicator) {
|
|
1763
|
+
return OncoKbCardDataType.BIOLOGICAL;
|
|
1764
|
+
}
|
|
1765
|
+
// priority is in this order: Tx > Dx > Px > Biological
|
|
1766
|
+
if (indicator.highestSensitiveLevel &&
|
|
1767
|
+
availableDataTypes &&
|
|
1768
|
+
availableDataTypes.includes(OncoKbCardDataType.TXS)) {
|
|
1769
|
+
return OncoKbCardDataType.TXS;
|
|
1770
|
+
}
|
|
1771
|
+
else if (indicator.highestResistanceLevel &&
|
|
1772
|
+
availableDataTypes &&
|
|
1773
|
+
availableDataTypes.includes(OncoKbCardDataType.TXR)) {
|
|
1774
|
+
return OncoKbCardDataType.TXR;
|
|
1775
|
+
}
|
|
1776
|
+
else if (indicator.highestDiagnosticImplicationLevel &&
|
|
1777
|
+
availableDataTypes &&
|
|
1778
|
+
availableDataTypes.includes(OncoKbCardDataType.DX)) {
|
|
1779
|
+
return OncoKbCardDataType.DX;
|
|
1780
|
+
}
|
|
1781
|
+
else if (indicator.highestPrognosticImplicationLevel &&
|
|
1782
|
+
availableDataTypes &&
|
|
1783
|
+
availableDataTypes.includes(OncoKbCardDataType.PX)) {
|
|
1784
|
+
return OncoKbCardDataType.PX;
|
|
1785
|
+
}
|
|
1786
|
+
return OncoKbCardDataType.BIOLOGICAL;
|
|
1787
|
+
}
|
|
1640
1788
|
var OncoKB = /** @class */ (function (_super) {
|
|
1641
1789
|
__extends(OncoKB, _super);
|
|
1642
1790
|
function OncoKB(props) {
|
|
@@ -1661,8 +1809,7 @@ var OncoKB = /** @class */ (function (_super) {
|
|
|
1661
1809
|
configurable: true,
|
|
1662
1810
|
writable: true,
|
|
1663
1811
|
value: function () {
|
|
1664
|
-
var
|
|
1665
|
-
var oncoKbContent = (createElement("span", { className: "" + annotationStyles['annotation-item'] }));
|
|
1812
|
+
var oncoKbContent;
|
|
1666
1813
|
if (this.props.status === 'error') {
|
|
1667
1814
|
oncoKbContent = errorIcon('Error fetching OncoKB data');
|
|
1668
1815
|
}
|
|
@@ -1670,15 +1817,9 @@ var OncoKB = /** @class */ (function (_super) {
|
|
|
1670
1817
|
oncoKbContent = loaderIcon('pull-left');
|
|
1671
1818
|
}
|
|
1672
1819
|
else {
|
|
1673
|
-
oncoKbContent =
|
|
1674
|
-
|
|
1675
|
-
|
|
1676
|
-
this.props.indicator && (createElement(Fragment, null, [
|
|
1677
|
-
OncoKbCardDataType.TXS,
|
|
1678
|
-
OncoKbCardDataType.TXR,
|
|
1679
|
-
OncoKbCardDataType.DX,
|
|
1680
|
-
OncoKbCardDataType.PX,
|
|
1681
|
-
].map(function (dataType) { return (createElement(AnnotationIcon, { type: dataType, tooltipOverlay: _this.tooltipContent(dataType), indicator: _this.props.indicator, availableDataTypes: _this.props.availableDataTypes })); })))));
|
|
1820
|
+
oncoKbContent = this.props.mergeAnnotationIcons
|
|
1821
|
+
? this.singleAnnotationIcon()
|
|
1822
|
+
: this.multiAnnotationIcon();
|
|
1682
1823
|
if (!this.props.disableFeedback && this.showFeedback) {
|
|
1683
1824
|
oncoKbContent = (createElement("span", null,
|
|
1684
1825
|
oncoKbContent,
|
|
@@ -1690,6 +1831,57 @@ var OncoKB = /** @class */ (function (_super) {
|
|
|
1690
1831
|
return oncoKbContent;
|
|
1691
1832
|
}
|
|
1692
1833
|
});
|
|
1834
|
+
Object.defineProperty(OncoKB.prototype, "multiAnnotationIcon", {
|
|
1835
|
+
enumerable: false,
|
|
1836
|
+
configurable: true,
|
|
1837
|
+
writable: true,
|
|
1838
|
+
value: function () {
|
|
1839
|
+
return (createElement("span", { className: "oncokb-content", style: { display: 'inline-flex' } },
|
|
1840
|
+
createElement(AnnotationIcon, { type: OncoKbCardDataType.BIOLOGICAL, tooltipOverlay: this.tooltipContent(OncoKbCardDataType.BIOLOGICAL), indicator: this.props.indicator, availableDataTypes: this.props.availableDataTypes }),
|
|
1841
|
+
this.levelIcons()));
|
|
1842
|
+
}
|
|
1843
|
+
});
|
|
1844
|
+
Object.defineProperty(OncoKB.prototype, "levelIcons", {
|
|
1845
|
+
enumerable: false,
|
|
1846
|
+
configurable: true,
|
|
1847
|
+
writable: true,
|
|
1848
|
+
value: function () {
|
|
1849
|
+
var _this = this;
|
|
1850
|
+
if (this.props.usingPublicOncoKbInstance) {
|
|
1851
|
+
return null;
|
|
1852
|
+
}
|
|
1853
|
+
if (this.props.indicator) {
|
|
1854
|
+
return (createElement(Fragment, null, [
|
|
1855
|
+
OncoKbCardDataType.TXS,
|
|
1856
|
+
OncoKbCardDataType.TXR,
|
|
1857
|
+
OncoKbCardDataType.DX,
|
|
1858
|
+
OncoKbCardDataType.PX,
|
|
1859
|
+
].map(function (dataType) { return (createElement(AnnotationIcon, { type: dataType, tooltipOverlay: _this.tooltipContent(dataType), indicator: _this.props.indicator, availableDataTypes: _this.props.availableDataTypes })); })));
|
|
1860
|
+
}
|
|
1861
|
+
else {
|
|
1862
|
+
// TODO This doesn't always work, in some cases it adds unnecessary empty icons, we need a better solution.
|
|
1863
|
+
// we still need to draw empty icons even if there is no indicator data.
|
|
1864
|
+
// this is to keep the icon alignment consistent with the rest of the column
|
|
1865
|
+
// return (
|
|
1866
|
+
// <>
|
|
1867
|
+
// {this.props.availableDataTypes?.map(() => (
|
|
1868
|
+
// <AnnotationIconWithTooltip icon={<i />} />
|
|
1869
|
+
// ))}
|
|
1870
|
+
// </>
|
|
1871
|
+
// );
|
|
1872
|
+
return null;
|
|
1873
|
+
}
|
|
1874
|
+
}
|
|
1875
|
+
});
|
|
1876
|
+
Object.defineProperty(OncoKB.prototype, "singleAnnotationIcon", {
|
|
1877
|
+
enumerable: false,
|
|
1878
|
+
configurable: true,
|
|
1879
|
+
writable: true,
|
|
1880
|
+
value: function () {
|
|
1881
|
+
return (createElement("span", { className: "oncokb-content", style: { display: 'inline-flex' } },
|
|
1882
|
+
createElement(AnnotationIconWithTooltip, { tooltipOverlay: this.tooltipContent(findDefaultDataTypeForTooltip(this.props.usingPublicOncoKbInstance, this.props.indicator, this.props.availableDataTypes)), icon: createElement(CompactAnnotationIcon, { indicator: this.props.indicator, availableDataTypes: this.props.availableDataTypes, usingPublicOncoKbInstance: this.props.usingPublicOncoKbInstance }) })));
|
|
1883
|
+
}
|
|
1884
|
+
});
|
|
1693
1885
|
Object.defineProperty(OncoKB.prototype, "tooltipContent", {
|
|
1694
1886
|
enumerable: false,
|
|
1695
1887
|
configurable: true,
|
|
@@ -2105,9 +2297,9 @@ function sortValue$4(annotation) {
|
|
|
2105
2297
|
]);
|
|
2106
2298
|
}
|
|
2107
2299
|
function GenericAnnotation(props) {
|
|
2108
|
-
var annotation = props.annotation, enableCivic = props.enableCivic, enableHotspot = props.enableHotspot, enableMyCancerGenome = props.enableMyCancerGenome, enableOncoKb = props.enableOncoKb, pubMedCache = props.pubMedCache, userEmailAddress = props.userEmailAddress;
|
|
2300
|
+
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;
|
|
2109
2301
|
return (createElement("span", { style: { display: 'flex', minWidth: 100 } },
|
|
2110
|
-
enableOncoKb && (createElement(OncoKB, { usingPublicOncoKbInstance: annotation.usingPublicOncoKbInstance, hugoGeneSymbol: annotation.hugoGeneSymbol, geneNotExist: !annotation.oncoKbGeneExist, isCancerGene: annotation.isOncoKbCancerGene, status: annotation.oncoKbStatus, indicator: annotation.oncoKbIndicator, availableDataTypes: annotation.oncoKbAvailableDataTypes, pubMedCache: pubMedCache, userEmailAddress: userEmailAddress })),
|
|
2302
|
+
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 })),
|
|
2111
2303
|
enableCivic && (createElement(Civic, { civicEntry: annotation.civicEntry, civicStatus: annotation.civicStatus, hasCivicVariants: annotation.hasCivicVariants })),
|
|
2112
2304
|
enableMyCancerGenome && (createElement(MyCancerGenome, { linksHTML: annotation.myCancerGenomeLinks })),
|
|
2113
2305
|
enableHotspot && (createElement(HotspotAnnotation, { isHotspot: annotation.isHotspot, is3dHotspot: annotation.is3dHotspot, status: annotation.hotspotStatus }))));
|
|
@@ -2489,7 +2681,7 @@ function generateGnomadUrl(chromosome, position, reference, variant) {
|
|
|
2489
2681
|
}
|
|
2490
2682
|
}
|
|
2491
2683
|
|
|
2492
|
-
var _a$
|
|
2684
|
+
var _a$2;
|
|
2493
2685
|
function frequencyOutput(frequency) {
|
|
2494
2686
|
if (frequency === 0) {
|
|
2495
2687
|
return createElement("span", null, "0");
|
|
@@ -2503,13 +2695,13 @@ function frequencyOutput(frequency) {
|
|
|
2503
2695
|
}
|
|
2504
2696
|
}
|
|
2505
2697
|
var headerClassName = 'text-wrap font-weight-bold';
|
|
2506
|
-
var HEADERS = (_a$
|
|
2507
|
-
_a$
|
|
2508
|
-
_a$
|
|
2509
|
-
_a$
|
|
2510
|
-
_a$
|
|
2511
|
-
_a$
|
|
2512
|
-
_a$
|
|
2698
|
+
var HEADERS = (_a$2 = {},
|
|
2699
|
+
_a$2[GnomadTableColumnName.population] = (createElement(ColumnHeader, { className: headerClassName, headerContent: createElement("span", null, "Population") })),
|
|
2700
|
+
_a$2[GnomadTableColumnName.alleleCount] = (createElement(ColumnHeader, { className: headerClassName, headerContent: createElement("span", null, "Allele Count"), overlay: createElement("span", null, "Number of individuals with this allele") })),
|
|
2701
|
+
_a$2[GnomadTableColumnName.alleleNumber] = (createElement(ColumnHeader, { className: headerClassName, headerContent: createElement("span", null, "Allele Number"), overlay: createElement("span", null, "Number of times any allele has been observed at this position in the population") })),
|
|
2702
|
+
_a$2[GnomadTableColumnName.homozygotes] = (createElement(ColumnHeader, { className: headerClassName, headerContent: createElement("span", null, "Number of Homozygotes"), overlay: createElement("span", null, "Number of individuals carrying this allele in both copies") })),
|
|
2703
|
+
_a$2[GnomadTableColumnName.alleleFrequency] = (createElement(ColumnHeader, { className: headerClassName, headerContent: createElement("span", null, "Allele Frequency"), overlay: createElement("span", null, "Proportion of the population with this allele") })),
|
|
2704
|
+
_a$2);
|
|
2513
2705
|
function renderNumericalValue(column) {
|
|
2514
2706
|
return createElement("span", { className: "pull-right mr-1" }, column.value);
|
|
2515
2707
|
}
|
|
@@ -4663,7 +4855,7 @@ var MutationType = /** @class */ (function (_super) {
|
|
|
4663
4855
|
return MutationType;
|
|
4664
4856
|
}(Component));
|
|
4665
4857
|
|
|
4666
|
-
var _a$
|
|
4858
|
+
var _a$3, _b;
|
|
4667
4859
|
var MutationColumn;
|
|
4668
4860
|
(function (MutationColumn) {
|
|
4669
4861
|
MutationColumn["PROTEIN_CHANGE"] = "proteinChange";
|
|
@@ -4703,33 +4895,33 @@ var MutationColumnName;
|
|
|
4703
4895
|
function rightAlignedCell(cellProps) {
|
|
4704
4896
|
return createElement("span", { className: "pull-right mr-3" }, cellProps.value);
|
|
4705
4897
|
}
|
|
4706
|
-
var MUTATION_COLUMN_HEADERS = (_a$
|
|
4707
|
-
_a$
|
|
4708
|
-
_a$
|
|
4709
|
-
_a$
|
|
4710
|
-
_a$
|
|
4711
|
-
_a$
|
|
4712
|
-
_a$
|
|
4713
|
-
_a$
|
|
4714
|
-
_a$
|
|
4715
|
-
_a$
|
|
4716
|
-
_a$
|
|
4717
|
-
_a$
|
|
4718
|
-
_a$
|
|
4898
|
+
var MUTATION_COLUMN_HEADERS = (_a$3 = {},
|
|
4899
|
+
_a$3[MutationColumn.PROTEIN_CHANGE] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-left" }, MutationColumnName.PROTEIN_CHANGE) })),
|
|
4900
|
+
_a$3[MutationColumn.ANNOTATION] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-left" }, MutationColumnName.ANNOTATION) })),
|
|
4901
|
+
_a$3[MutationColumn.MUTATION_STATUS] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-left" }, MutationColumnName.MUTATION_STATUS) })),
|
|
4902
|
+
_a$3[MutationColumn.MUTATION_TYPE] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-left" }, MutationColumnName.MUTATION_TYPE) })),
|
|
4903
|
+
_a$3[MutationColumn.CHROMOSOME] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-right mr-3" }, MutationColumnName.CHROMOSOME) })),
|
|
4904
|
+
_a$3[MutationColumn.START_POSITION] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-right mr-3" }, MutationColumnName.START_POSITION) })),
|
|
4905
|
+
_a$3[MutationColumn.END_POSITION] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-right mr-3" }, MutationColumnName.END_POSITION) })),
|
|
4906
|
+
_a$3[MutationColumn.REFERENCE_ALLELE] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-left" }, MutationColumnName.REFERENCE_ALLELE), overlay: createElement("span", null, "Reference Allele") })),
|
|
4907
|
+
_a$3[MutationColumn.VARIANT_ALLELE] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-left" }, MutationColumnName.VARIANT_ALLELE), overlay: createElement("span", null, "Variant Allele") })),
|
|
4908
|
+
_a$3[MutationColumn.HGVSG] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-left" }, MutationColumnName.HGVSG) })),
|
|
4909
|
+
_a$3[MutationColumn.HGVSC] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-left" }, MutationColumnName.HGVSC) })),
|
|
4910
|
+
_a$3[MutationColumn.GNOMAD] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-right mr-3" },
|
|
4719
4911
|
MutationColumnName.GNOMAD,
|
|
4720
4912
|
' ',
|
|
4721
4913
|
createElement("i", { className: "fa fa-info-circle" })), overlay: createElement("span", null,
|
|
4722
4914
|
createElement("a", { href: "https://gnomad.broadinstitute.org/", target: "_blank" }, "gnomAD"),
|
|
4723
4915
|
' ',
|
|
4724
4916
|
"population allele frequencies. Overall population allele frequency is shown. Hover over a frequency to see the frequency for each specific population.") })),
|
|
4725
|
-
_a$
|
|
4917
|
+
_a$3[MutationColumn.CLINVAR] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-left" },
|
|
4726
4918
|
MutationColumnName.CLINVAR,
|
|
4727
4919
|
' ',
|
|
4728
4920
|
createElement("i", { className: "fa fa-info-circle" })), overlay: createElement("span", null,
|
|
4729
4921
|
createElement("a", { href: "https://www.ncbi.nlm.nih.gov/clinvar/", target: "_blank" }, "ClinVar"),
|
|
4730
4922
|
' ',
|
|
4731
4923
|
"aggregates information about genomic variation and its relationship to human health.") })),
|
|
4732
|
-
_a$
|
|
4924
|
+
_a$3[MutationColumn.DBSNP] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-right mr-3" },
|
|
4733
4925
|
MutationColumnName.DBSNP,
|
|
4734
4926
|
' ',
|
|
4735
4927
|
createElement("i", { className: "fa fa-info-circle" })), overlay: createElement("span", null,
|
|
@@ -4738,14 +4930,14 @@ var MUTATION_COLUMN_HEADERS = (_a$2 = {},
|
|
|
4738
4930
|
") is a free public archive for genetic variation within and across different species.",
|
|
4739
4931
|
createElement("br", null),
|
|
4740
4932
|
"NOTE: Currently only SNPs, single base deletions and insertions are supported.") })),
|
|
4741
|
-
_a$
|
|
4933
|
+
_a$3[MutationColumn.SIGNAL] = (createElement(ColumnHeader, { headerContent: createElement("span", { className: "pull-right mr-3" },
|
|
4742
4934
|
MutationColumnName.SIGNAL,
|
|
4743
4935
|
' ',
|
|
4744
4936
|
createElement("i", { className: "fa fa-info-circle" })), overlay: createElement("span", null,
|
|
4745
4937
|
"Prevalence of germline mutations in cancer patients from",
|
|
4746
4938
|
' ',
|
|
4747
4939
|
createElement("a", { href: "https://www.signaldb.org/", target: "_blank" }, "SIGNAL")) })),
|
|
4748
|
-
_a$
|
|
4940
|
+
_a$3);
|
|
4749
4941
|
/**
|
|
4750
4942
|
* These default columns only include static props.
|
|
4751
4943
|
* So, for some columns, like Annotation, no default accessor or Cell (render) properties included.
|
|
@@ -8368,7 +8560,7 @@ var PtmReferenceList = /** @class */ (function (_super) {
|
|
|
8368
8560
|
return PtmReferenceList;
|
|
8369
8561
|
}(Component));
|
|
8370
8562
|
|
|
8371
|
-
var _a$
|
|
8563
|
+
var _a$4;
|
|
8372
8564
|
var PtmAnnotationTableColumnId;
|
|
8373
8565
|
(function (PtmAnnotationTableColumnId) {
|
|
8374
8566
|
PtmAnnotationTableColumnId["POSITION"] = "position";
|
|
@@ -8376,33 +8568,33 @@ var PtmAnnotationTableColumnId;
|
|
|
8376
8568
|
PtmAnnotationTableColumnId["DESCRIPTION"] = "description";
|
|
8377
8569
|
PtmAnnotationTableColumnId["PUBMED_IDS"] = "pubmedIds";
|
|
8378
8570
|
})(PtmAnnotationTableColumnId || (PtmAnnotationTableColumnId = {}));
|
|
8379
|
-
var PTM_ANNOTATION_DEFAULT_COLUMNS = (_a$
|
|
8380
|
-
_a$
|
|
8571
|
+
var PTM_ANNOTATION_DEFAULT_COLUMNS = (_a$4 = {},
|
|
8572
|
+
_a$4[PtmAnnotationTableColumnId.POSITION] = {
|
|
8381
8573
|
id: PtmAnnotationTableColumnId.POSITION,
|
|
8382
8574
|
accessor: function (ptm) { return ptm.residue.start; },
|
|
8383
8575
|
Header: 'Residue',
|
|
8384
8576
|
Cell: function (props) { return (createElement("div", { style: { textAlign: 'right' } }, getResidue(props.original))); },
|
|
8385
8577
|
maxWidth: 64,
|
|
8386
8578
|
},
|
|
8387
|
-
_a$
|
|
8579
|
+
_a$4[PtmAnnotationTableColumnId.TYPE] = {
|
|
8388
8580
|
id: PtmAnnotationTableColumnId.TYPE,
|
|
8389
8581
|
accessor: function (ptm) { return ptm.type; },
|
|
8390
8582
|
Header: 'Type',
|
|
8391
8583
|
minWidth: 100,
|
|
8392
8584
|
},
|
|
8393
|
-
_a$
|
|
8585
|
+
_a$4[PtmAnnotationTableColumnId.DESCRIPTION] = {
|
|
8394
8586
|
id: PtmAnnotationTableColumnId.DESCRIPTION,
|
|
8395
8587
|
accessor: function (ptm) { return ptm.description; },
|
|
8396
8588
|
Header: 'Description',
|
|
8397
8589
|
minWidth: 180,
|
|
8398
8590
|
},
|
|
8399
|
-
_a$
|
|
8591
|
+
_a$4[PtmAnnotationTableColumnId.PUBMED_IDS] = {
|
|
8400
8592
|
id: PtmAnnotationTableColumnId.PUBMED_IDS,
|
|
8401
8593
|
Header: '',
|
|
8402
8594
|
sortable: false,
|
|
8403
8595
|
maxWidth: 32,
|
|
8404
8596
|
},
|
|
8405
|
-
_a$
|
|
8597
|
+
_a$4);
|
|
8406
8598
|
function getResidue(ptm) {
|
|
8407
8599
|
if (ptm.residue.end && ptm.residue.end > ptm.residue.start) {
|
|
8408
8600
|
return ptm.residue.start + "-" + ptm.residue.end;
|