react-mutation-mapper 0.8.121 → 0.9.2

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Files changed (73) hide show
  1. package/dist/component/clinvar/ClinvarSummary.d.ts +1 -1
  2. package/dist/component/column/Annotation.d.ts +2 -2
  3. package/dist/component/column/ClinvarInterpretation.d.ts +1 -1
  4. package/dist/component/column/ColumnHeader.d.ts +1 -1
  5. package/dist/component/column/Hgvsc.d.ts +1 -1
  6. package/dist/component/column/Hgvsg.d.ts +1 -1
  7. package/dist/component/column/MutationStatus.d.ts +1 -1
  8. package/dist/component/column/MutationType.d.ts +2 -2
  9. package/dist/component/column/MyVariantInfoHelper.d.ts +1 -1
  10. package/dist/component/column/ProteinChange.d.ts +1 -1
  11. package/dist/component/column/Signal.d.ts +2 -2
  12. package/dist/component/dataTable/ColumnSelector.d.ts +2 -2
  13. package/dist/component/dataTable/DataTable.d.ts +4 -4
  14. package/dist/component/dataTable/DataTableToolbar.d.ts +1 -1
  15. package/dist/component/dbsnp/DbsnpId.d.ts +1 -1
  16. package/dist/component/filter/BadgeLabel.d.ts +1 -1
  17. package/dist/component/filter/BadgeSelector.d.ts +2 -2
  18. package/dist/component/filter/DropdownSelector.d.ts +1 -1
  19. package/dist/component/filter/MutationStatusBadgeSelector.d.ts +1 -1
  20. package/dist/component/filter/ProteinImpactTypeBadgeSelector.d.ts +1 -1
  21. package/dist/component/filter/ProteinImpactTypeDropdownSelector.d.ts +1 -1
  22. package/dist/component/gnomad/GnomadFrequency.d.ts +1 -1
  23. package/dist/component/hotspot/HotspotInfo.d.ts +1 -1
  24. package/dist/component/lollipopMutationPlot/DefaultLollipopPlotLegend.d.ts +1 -1
  25. package/dist/component/lollipopMutationPlot/LollipopMutationPlot.d.ts +1 -1
  26. package/dist/component/lollipopMutationPlot/LollipopMutationPlotControls.d.ts +1 -1
  27. package/dist/component/lollipopPlot/Domain.d.ts +1 -1
  28. package/dist/component/lollipopPlot/Lollipop.d.ts +1 -1
  29. package/dist/component/lollipopPlot/LollipopPlot.d.ts +1 -1
  30. package/dist/component/lollipopPlot/LollipopPlotNoTooltip.d.ts +1 -1
  31. package/dist/component/lollipopPlot/Sequence.d.ts +1 -1
  32. package/dist/component/mutationMapper/DefaultMutationRateSummary.d.ts +2 -2
  33. package/dist/component/mutationMapper/FilterResetPanel.d.ts +1 -1
  34. package/dist/component/mutationMapper/GeneSummary.d.ts +1 -1
  35. package/dist/component/mutationMapper/MutationMapper.d.ts +1 -1
  36. package/dist/component/mutationMapper/TranscriptDropdown.d.ts +1 -1
  37. package/dist/component/mutationTable/DefaultMutationTable.d.ts +2 -2
  38. package/dist/component/ptm/PtmAnnotationTable.d.ts +1 -1
  39. package/dist/component/ptm/PtmReferenceList.d.ts +1 -1
  40. package/dist/component/track/ExonTrack.d.ts +1 -1
  41. package/dist/component/track/HotspotTrack.d.ts +1 -1
  42. package/dist/component/track/OncoKbTrack.d.ts +1 -1
  43. package/dist/component/track/OncoKbTrackTooltip.d.ts +1 -1
  44. package/dist/component/track/PtmTrack.d.ts +1 -1
  45. package/dist/component/track/Track.d.ts +1 -1
  46. package/dist/component/track/TrackCircle.d.ts +2 -2
  47. package/dist/component/track/TrackItem.d.ts +2 -2
  48. package/dist/component/track/TrackPanel.d.ts +1 -1
  49. package/dist/component/track/TrackRect.d.ts +2 -2
  50. package/dist/component/track/TrackSelector.d.ts +3 -3
  51. package/dist/component/track/UniprotTopologyTrack.d.ts +1 -1
  52. package/dist/filter/CancerTypeFilter.d.ts +1 -1
  53. package/dist/filter/CategoricalFilter.d.ts +2 -2
  54. package/dist/filter/HotspotFilter.d.ts +1 -1
  55. package/dist/filter/MutationFilter.d.ts +2 -2
  56. package/dist/filter/MutationStatusFilter.d.ts +1 -1
  57. package/dist/filter/NumericalFilter.d.ts +2 -2
  58. package/dist/filter/OncoKbFilter.d.ts +1 -1
  59. package/dist/filter/PositionFilter.d.ts +1 -1
  60. package/dist/filter/ProteinChangeFilter.d.ts +1 -1
  61. package/dist/filter/ProteinImpactTypeFilter.d.ts +1 -1
  62. package/dist/index.es.js +97 -79
  63. package/dist/index.es.js.map +1 -1
  64. package/dist/index.js +95 -77
  65. package/dist/index.js.map +1 -1
  66. package/dist/model/DataFilter.d.ts +1 -1
  67. package/dist/model/DomainSpec.d.ts +1 -1
  68. package/dist/model/FilterApplier.d.ts +1 -1
  69. package/dist/model/GnomadSummary.d.ts +1 -1
  70. package/dist/model/LollipopSpec.d.ts +2 -2
  71. package/dist/model/SequenceSpec.d.ts +1 -1
  72. package/dist/store/DefaultMutationMapperDataStore.d.ts +1 -1
  73. package/package.json +9 -9
package/dist/index.es.js CHANGED
@@ -1,4 +1,4 @@
1
- import { __extends, __decorate, __awaiter, __generator, __assign, __spreadArrays } from 'tslib';
1
+ import { __extends, __decorate, __awaiter, __generator, __assign, __spreadArray } from 'tslib';
2
2
  import * as _ from 'lodash';
3
3
  import ___default from 'lodash';
4
4
  import { makeObservable, observable, computed, action, reaction } from 'mobx';
@@ -8,7 +8,7 @@ import React__default from 'react';
8
8
  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';
9
9
  import classNames from 'classnames';
10
10
  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';
11
- import { getIndicatorData, calculateOncoKbAvailableDataType, oncoKbAnnotationSortValue, OncoKB, OncoKbSummaryTable, LEVELS, getTumorTypeNameWithExclusionInfo, ReferenceList, generateProteinChangeQuery, StructuralVariantType, generateAnnotateStructuralVariantQuery, defaultOncoKbFilter, groupOncoKbIndicatorDataByMutations, defaultOncoKbIndicatorFilter } from 'oncokb-frontend-commons';
11
+ import { getIndicatorData, calculateOncoKbAvailableDataType, oncoKbAnnotationSortValue, OncoKB, OncoKbSummaryTable, getTumorTypeNameWithExclusionInfo, LEVELS, ReferenceList, generateProteinChangeQuery, StructuralVariantType, generateAnnotateStructuralVariantQuery, defaultOncoKbFilter, groupOncoKbIndicatorDataByMutations, defaultOncoKbIndicatorFilter } from 'oncokb-frontend-commons';
12
12
  import { GenomeNexusAPI, GenomeNexusAPIInternal } from 'genome-nexus-ts-api-client';
13
13
  import { OncoKbAPI } from 'oncokb-ts-api-client';
14
14
  import autobind from 'autobind-decorator';
@@ -29,12 +29,12 @@ import memoize from 'memoize-weak-decorator';
29
29
  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"};
30
30
 
31
31
  function loaderIcon(className) {
32
- return (React.createElement("span", { className: classNames("" + annotationStyles['annotation-item'], "" + annotationStyles['annotation-item-load'], className) },
32
+ return (React.createElement("span", { className: classNames("".concat(annotationStyles['annotation-item']), "".concat(annotationStyles['annotation-item-load']), className) },
33
33
  React.createElement("i", { className: "fa fa-spinner fa-pulse" })));
34
34
  }
35
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  function errorIcon(errorMessage) {
36
36
  return (React.createElement(DefaultTooltip, { overlay: React.createElement("span", null, errorMessage), placement: "right", trigger: ['hover', 'focus'], destroyTooltipOnHide: true },
37
- React.createElement("span", { className: "" + annotationStyles['annotation-item-error'] },
37
+ React.createElement("span", { className: "".concat(annotationStyles['annotation-item-error']) },
38
38
  React.createElement("i", { className: "fa fa-exclamation-triangle text-danger" }))));
39
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  }
40
40
 
@@ -69,7 +69,7 @@ var CivicCard = /** @class */ (function (_super) {
69
69
  })
70
70
  .map(function (_a) {
71
71
  var key = _a[0], value = _a[1];
72
- return key.slice(0, -5) + ": " + value;
72
+ return "".concat(key.slice(0, -5), ": ").concat(value);
73
73
  }) // Remove "Count" substring from key
74
74
  .join(', ');
75
75
  list.push(this.variantItem(name_1, variant.url, variant.name, entryTypes, variant.description));
@@ -166,7 +166,7 @@ function download$5(civicEntry) {
166
166
  var values = [];
167
167
  if (variants && variants.length > 0 && variants[0].evidenceCounts) {
168
168
  ___default.forEach(variants[0].evidenceCounts, function (value, key) {
169
- values.push(key + ": " + value);
169
+ values.push("".concat(key, ": ").concat(value));
170
170
  });
171
171
  }
172
172
  // this indicates that we have an entry but the evidence is empty
@@ -194,7 +194,7 @@ var Civic = /** @class */ (function (_super) {
194
194
  configurable: true,
195
195
  writable: true,
196
196
  value: function () {
197
- var civicContent = (React.createElement("span", { className: "" + annotationStyles['annotation-item'] }));
197
+ var civicContent = (React.createElement("span", { className: "".concat(annotationStyles['annotation-item']) }));
198
198
  var civicImgWidth = 14;
199
199
  var civicImgHeight = 14;
200
200
  var civicImgSrc = !this.props.hasCivicVariants
@@ -206,7 +206,7 @@ var Civic = /** @class */ (function (_super) {
206
206
  else if (this.props.civicEntry !== undefined) {
207
207
  if (this.props.civicEntry !== null &&
208
208
  this.props.civicStatus == 'complete') {
209
- civicContent = (React.createElement("span", { className: "" + annotationStyles['annotation-item'] },
209
+ civicContent = (React.createElement("span", { className: "".concat(annotationStyles['annotation-item']) },
210
210
  React.createElement("img", { width: civicImgWidth, height: civicImgHeight, src: civicImgSrc, alt: "Civic Variant Entry" })));
211
211
  civicContent = (React.createElement(DefaultTooltip, { overlay: this.cardContent.bind(this, this.props.civicEntry), placement: "right", trigger: ['hover', 'focus'], onPopupAlign: hideArrow, destroyTooltipOnHide: false }, civicContent));
212
212
  }
@@ -250,7 +250,7 @@ var ClinvarSummary = function (props) {
250
250
  }
251
251
  else {
252
252
  var clinvarId = props.clinvar.clinvarId;
253
- var clinvarLink = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + clinvarId + "/";
253
+ var clinvarLink = "https://www.ncbi.nlm.nih.gov/clinvar/variation/".concat(clinvarId, "/");
254
254
  var clinicalSignificance = props.clinvar.clinicalSignificance;
255
255
  var conflictingClinicalSignificance = props.clinvar.conflictingClinicalSignificance;
256
256
  return (React.createElement(TruncatedText, { maxLength: 30, text: clinicalSignificance, addTooltip: "always", tooltip: React.createElement("div", { style: { maxWidth: 300 } },
@@ -369,7 +369,7 @@ var HotspotAnnotation = /** @class */ (function (_super) {
369
369
  writable: true,
370
370
  value: function () {
371
371
  var _a = this.props, isHotspot = _a.isHotspot, is3dHotspot = _a.is3dHotspot;
372
- var hotspotContent = (React.createElement("span", { className: "" + annotationStyles['annotation-item'] }));
372
+ var hotspotContent = (React.createElement("span", { className: "".concat(annotationStyles['annotation-item']) }));
373
373
  if (this.props.status === 'pending') {
374
374
  hotspotContent = loaderIcon('pull-left');
375
375
  }
@@ -385,7 +385,7 @@ var HotspotAnnotation = /** @class */ (function (_super) {
385
385
  var arrowContent = React.createElement("div", { className: "rc-tooltip-arrow-inner" });
386
386
  var tooltipContent = (React.createElement(HotspotInfo, { isHotspot: isHotspot, is3dHotspot: is3dHotspot }));
387
387
  hotspotContent = (React.createElement(DefaultTooltip, { overlay: tooltipContent, placement: "topLeft", trigger: ['hover', 'focus'], arrowContent: arrowContent, onPopupAlign: placeArrow },
388
- React.createElement("span", { className: annotationStyles['annotation-item'] + " chang_hotspot" },
388
+ React.createElement("span", { className: "".concat(annotationStyles['annotation-item'], " chang_hotspot") },
389
389
  React.createElement("img", { width: hotspotsImgWidth, height: hotspotsImgHeight, src: hotspotsImgSrc, alt: "Recurrent Hotspot Symbol" }))));
390
390
  }
391
391
  return hotspotContent;
@@ -428,6 +428,18 @@ var ONCOKB_DEFAULT_INFO = {
428
428
  version: 'v2.0',
429
429
  date: '12/19/2019',
430
430
  },
431
+ genomeNexus: {
432
+ grch37: {
433
+ genomeNexusVepVersion: '',
434
+ genomeNexusVersion: '',
435
+ vepVersion: '',
436
+ },
437
+ grch38: {
438
+ genomeNexusVepVersion: '',
439
+ genomeNexusVersion: '',
440
+ vepVersion: '',
441
+ },
442
+ },
431
443
  levels: [],
432
444
  ncitVersion: '19.03d',
433
445
  oncoTreeVersion: 'oncotree_2019_12_01',
@@ -518,7 +530,7 @@ var RevueTooltipContent = function (props) {
518
530
  "Revised Protein Effect by", " ",
519
531
  React__default.createElement("a", { href: "https://cancerrevue.org", target: "_blank", rel: "noopener noreferrer" }, "reVUE"), " (",
520
532
  props.vue.references.map(function (reference, index) { return (React__default.createElement("span", { key: index },
521
- React__default.createElement("a", { href: "https://pubmed.ncbi.nlm.nih.gov/" + reference.pubmedId + "/", rel: "noopener noreferrer", target: "_blank" }, reference.referenceText),
533
+ React__default.createElement("a", { href: "https://pubmed.ncbi.nlm.nih.gov/".concat(reference.pubmedId, "/"), rel: "noopener noreferrer", target: "_blank" }, reference.referenceText),
522
534
  index < props.vue.references.length - 1 && ';')); }), "): ",
523
535
  React__default.createElement("strong", null, props.vue.revisedProteinEffect))));
524
536
  };
@@ -527,7 +539,7 @@ function sortValue$5(vue) {
527
539
  }
528
540
  var RevueCell = function (props) {
529
541
  return (React__default.createElement(DefaultTooltip, { placement: "bottom", overlay: React__default.createElement(RevueTooltipContent, { vue: props.vue }) },
530
- React__default.createElement("span", { className: "" + annotationStyles['annotation-item'], style: { display: 'inline-flex' } },
542
+ React__default.createElement("span", { className: "".concat(annotationStyles['annotation-item']), style: { display: 'inline-flex' } },
531
543
  React__default.createElement("img", { src: img, alt: "reVUE logo", width: 14, height: 14 }))));
532
544
  };
533
545
 
@@ -558,7 +570,12 @@ function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, oncoKbData,
558
570
  var value;
559
571
  if (mutation) {
560
572
  var key = '';
561
- var memoize = (oncoKbCancerGenes === null || oncoKbCancerGenes === void 0 ? void 0 : oncoKbCancerGenes.isComplete) && (hotspotData === null || hotspotData === void 0 ? void 0 : hotspotData.isComplete) && (oncoKbData === null || oncoKbData === void 0 ? void 0 : oncoKbData.isComplete) && (civicGenes === null || civicGenes === void 0 ? void 0 : civicGenes.isComplete) && (civicVariants === null || civicVariants === void 0 ? void 0 : civicVariants.isComplete) && (indexedVariantAnnotations === null || indexedVariantAnnotations === void 0 ? void 0 : indexedVariantAnnotations.isComplete);
573
+ var memoize = (oncoKbCancerGenes === null || oncoKbCancerGenes === void 0 ? void 0 : oncoKbCancerGenes.isComplete) &&
574
+ (hotspotData === null || hotspotData === void 0 ? void 0 : hotspotData.isComplete) &&
575
+ (oncoKbData === null || oncoKbData === void 0 ? void 0 : oncoKbData.isComplete) &&
576
+ (civicGenes === null || civicGenes === void 0 ? void 0 : civicGenes.isComplete) &&
577
+ (civicVariants === null || civicVariants === void 0 ? void 0 : civicVariants.isComplete) &&
578
+ (indexedVariantAnnotations === null || indexedVariantAnnotations === void 0 ? void 0 : indexedVariantAnnotations.isComplete);
562
579
  if (memoize) {
563
580
  key = JSON.stringify(mutation) + !!usingPublicOncoKbInstance;
564
581
  var val = memoized.get(key);
@@ -614,7 +631,8 @@ function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, oncoKbData,
614
631
  hotspotStatus: hotspotData ? hotspotData.status : 'pending',
615
632
  vue: (indexedVariantAnnotations === null || indexedVariantAnnotations === void 0 ? void 0 : indexedVariantAnnotations.isComplete) &&
616
633
  indexedVariantAnnotations.result
617
- ? (_b = (_a = getVariantAnnotation(mutation, indexedVariantAnnotations.result)) === null || _a === void 0 ? void 0 : _a.annotation_summary) === null || _b === void 0 ? void 0 : _b.vues : undefined,
634
+ ? (_b = (_a = getVariantAnnotation(mutation, indexedVariantAnnotations.result)) === null || _a === void 0 ? void 0 : _a.annotation_summary) === null || _b === void 0 ? void 0 : _b.vues
635
+ : undefined,
618
636
  };
619
637
  // oncoKbData may exist but it might be an instance of Error, in that case we flag the status as error
620
638
  if (oncoKbData && oncoKbData.result instanceof Error) {
@@ -633,10 +651,9 @@ function getAnnotationData(mutation, oncoKbCancerGenes, hotspotData, oncoKbData,
633
651
  !(oncoKbData.result instanceof Error) &&
634
652
  oncoKbData.status === 'complete') {
635
653
  oncoKbIndicator = getIndicatorData(mutation, oncoKbData.result, resolveTumorType, resolveEntrezGeneId);
636
- oncoKbAvailableDataTypes = ___default.uniq(__spreadArrays(oncoKbAvailableDataTypes, calculateOncoKbAvailableDataType(___default.values(oncoKbData.result.indicatorMap))));
654
+ oncoKbAvailableDataTypes = ___default.uniq(__spreadArray(__spreadArray([], oncoKbAvailableDataTypes, true), calculateOncoKbAvailableDataType(___default.values(oncoKbData.result.indicatorMap)), true));
637
655
  }
638
- value = __assign(__assign({}, value), { oncoKbStatus: oncoKbData ? oncoKbData.status : 'pending', oncoKbIndicator: oncoKbIndicator,
639
- oncoKbAvailableDataTypes: oncoKbAvailableDataTypes });
656
+ value = __assign(__assign({}, value), { oncoKbStatus: oncoKbData ? oncoKbData.status : 'pending', oncoKbIndicator: oncoKbIndicator, oncoKbAvailableDataTypes: oncoKbAvailableDataTypes });
640
657
  }
641
658
  else if (oncoKbData && oncoKbData.isPending) {
642
659
  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;
670
687
  return (React.createElement("span", { style: { display: 'flex', minWidth: 100 } },
671
688
  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: "" + annotationStyles['annotation-item'] }))) : (React.createElement(React.Fragment, null)),
689
+ enableRevue ? (annotation.vue ? (React.createElement(RevueCell, { vue: annotation.vue })) : (React.createElement("span", { className: "".concat(annotationStyles['annotation-item']) }))) : (React.createElement(React.Fragment, null)),
673
690
  enableCivic && (React.createElement(Civic, { civicEntry: annotation.civicEntry, civicStatus: annotation.civicStatus, hasCivicVariants: annotation.hasCivicVariants })),
674
691
  enableHotspot && (React.createElement(HotspotAnnotation, { isHotspot: annotation.isHotspot, is3dHotspot: annotation.is3dHotspot, status: annotation.hotspotStatus }))));
675
692
  }
@@ -1043,7 +1060,7 @@ function getGnomadData(myVariantInfo) {
1043
1060
  }
1044
1061
  function generateGnomadUrl(chromosome, position, reference, variant) {
1045
1062
  if (chromosome && position && reference && variant) {
1046
- return "https://gnomad.broadinstitute.org/variant/" + chromosome + "-" + position + "-" + reference + "-" + variant;
1063
+ return "https://gnomad.broadinstitute.org/variant/".concat(chromosome, "-").concat(position, "-").concat(reference, "-").concat(variant);
1047
1064
  }
1048
1065
  else {
1049
1066
  return 'https://gnomad.broadinstitute.org/';
@@ -1402,7 +1419,7 @@ var Hgvsg = /** @class */ (function (_super) {
1402
1419
  configurable: true,
1403
1420
  writable: true,
1404
1421
  value: {
1405
- constructLink: function (hgvsg, content, href) { return (React.createElement("a", { href: href || "https:/www.genomenexus.org/variant/" + hgvsg, target: "_blank", rel: "noopener noreferrer" }, content)); },
1422
+ constructLink: function (hgvsg, content, href) { return (React.createElement("a", { href: href || "https:/www.genomenexus.org/variant/".concat(hgvsg), target: "_blank", rel: "noopener noreferrer" }, content)); },
1406
1423
  mainContent: function (hgvsg) { return (React.createElement(React.Fragment, null,
1407
1424
  hgvsg,
1408
1425
  "\u00A0",
@@ -1579,7 +1596,7 @@ function getSortValue(signalData) {
1579
1596
  }
1580
1597
  function download(signalData, mutationType) {
1581
1598
  return signalData && signalData.germlineFrequency !== null
1582
- ? "" + formatNumberValueInSignificantDigits(signalData.germlineFrequency, 2)
1599
+ ? "".concat(formatNumberValueInSignificantDigits(signalData.germlineFrequency, 2))
1583
1600
  : '';
1584
1601
  }
1585
1602
  // Get germline OR somatic frequency value
@@ -1824,7 +1841,7 @@ var BadgeLabel = /** @class */ (function (_super) {
1824
1841
  ? {}
1825
1842
  : { marginRight: 5 }
1826
1843
  : { marginLeft: 5 } },
1827
- React.createElement("span", { className: this.props.badgeClassName, "data-test": "badge-" + this.props.value, style: __assign(__assign(__assign({}, DEFAULT_BADGE_STYLE), this.props.badgeStyleOverride), (this.props.isDriverAnnotated
1844
+ 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' }
1829
1846
  : {})) }, this.props.badgeContent)));
1830
1847
  },
@@ -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 + "_" + pMut.isPutativeDriver;
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(__spreadArrays([
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(__spreadArrays(defaultFilters, [positionFilter]));
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 __spreadArrays(f.values); })));
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(__spreadArrays(otherFilters, [dataFilter]));
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 __spreadArrays(merged, ___default.difference(customColumns, overrides));
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(__spreadArrays(otherFilters, [
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 + " and " + (mutationCountsByProteinChange.length -
4168
- proteinChanges.length) + " more";
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 + "px");
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 + "_" + (lollipop.placement === LollipopPlacement.BOTTOM
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 + " " + (this.props.hugoGeneSymbol ||
5328
- '') + " " + groupName + " Mutations"
5329
- : symbol + " " + (this.props.hugoGeneSymbol || '') + " Mutations";
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_" + (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 }));
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_" + (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 }));
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 "" + DOMAIN_ID_CLASS_PREFIX + index;
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 "" + LOLLIPOP_ID_CLASS_PREFIX + index;
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 "" + SEQUENCE_ID_CLASS_PREFIX + index;
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" + scale, style: {
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 + "_lollipop", dontFade: true, type: "button" }));
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: "" + _this.props.idClassPrefix + index, hitZoneXOffset: _this.props.xOffset, x: (spec.startCodon / _this.props.proteinLength) *
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-' : '') + "trackTitle") }, this.props.trackTitle),
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, "" + residues.join(', '));
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" + _this.chromosome + ":" + exon.genomicLocationStart + "-" + exon.genomicLocationEnd + "&genome=" + _this.genomeBuild
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 + ":chr" + _this.chromosome + ":" + exon.genomicLocationStart + " - " + exon.genomicLocationEnd
6995
- : exon.genomicLocationStart + " - " + exon.genomicLocationEnd;
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 + "-" + ptm.residue.end;
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
- ? "(" + this.props.dataSource + ")"
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-" + index + "-", isSubTrack: true })); })
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/" + props.uniprotId, target: "_blank" }, "UniProt"))) : (React.createElement("div", null,
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-" + index + "-", isSubTrack: true })); })
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 + ": " + domain.description
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/" + pfamAccession, target: "_blank" }, "PFAM"),
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", "" + (count !== 1 ? 's' : '')));
8074
+ " mutation", "".concat(count !== 1 ? 's' : '')));
8058
8075
  var label = lollipopLabelText(mutationsAtPosition);
8059
- return (React.createElement("div", { "data-test": "tooltip-" + codon + (group ? "-" + group : '') },
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/" + this.props.store.uniprotId.result, target: "_blank" }, this.props.store.uniprotId.result)));
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, " + LollipopPlot.defaultProps.vizHeight + ")");
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(" + _this.geneXOffset + "," + trackYShift + ")");
8418
+ var trackSvgGroup = createGroupTag("translate(".concat(_this.geneXOffset, ",").concat(trackYShift, ")"));
8402
8419
  trackSvgGroup.appendChild(track.cloneNode(true));
8403
- var trackNameGroup = createGroupTag("translate(0," + (trackYShift + 8) + ")");
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", "" + (count !== 1 ? 's' : '')));
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/" + pfamAccession);
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=" + category.join(','), { uniprotAccession: swissProtId }))];
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/" + this.activeTranscript.result + "?content-type=application/json"
10305
- : "https://rest.ensembl.org/lookup/id/" + this.activeTranscript.result + "?content-type=application/json";
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 = "" + (refseqMrnaId ? refseqMrnaId + " / " : '') + t + " " + (ccdsId ? "(" + ccdsId + ")" : '') + " " + (length ? "(" + length + " amino acids)" : '') + " " + (nrOfMutations
10815
- ? "(" + nrOfMutations + " mutations)"
10816
- : '') + " " + (t === canonicalTranscript ? ' (default)' : '');
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/" + refseqMrnaId), target: "_blank" }, refseqMrnaId)) : ('-');
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/" + uniprotId, target: "_blank" }, uniprotId)) : ('-');
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 " + tableData.length + " of " + allData.length + " mutations.", resetFilters: this.resetFilters }));
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