react-mutation-mapper 0.8.74 → 0.8.76

package/dist/component/filter/BadgeLabel.d.ts

@@ -7,6 +7,8 @@ export declare type BadgeLabelProps = {
     badgeClassName?: string;
     badgeFirst?: boolean;
     value?: string;
+    isDriverAnnotated?: boolean;
+    badgeLabelFormat?: (label: JSX.Element | string, badgeFirst?: boolean, value?: string, badge?: JSX.Element | null) => JSX.Element;
 };
 export declare const DEFAULT_BADGE_STYLE: {
     color: string;
@@ -16,7 +18,9 @@ export declare const DEFAULT_BADGE_STYLE: {
 };
 export declare class BadgeLabel extends React.Component<BadgeLabelProps, {}> {
     static defaultProps: Partial<BadgeLabelProps>;
-    protected get badge(): JSX.Element;
+    protected isDriverVusBadge(value: string): boolean;
+    protected isNotDriverVusProteinBadge(value: string): boolean;
+    protected get badge(): JSX.Element | null;
     protected get badgeFirst(): JSX.Element;
     protected get badgeLast(): JSX.Element;
     render(): JSX.Element;

package/dist/component/filter/BadgeSelector.d.ts

@@ -1,7 +1,7 @@
-import { CheckBoxType, Option } from 'cbioportal-frontend-commons';
 import * as React from 'react';
 import { CSSProperties } from 'react';
 import { DataFilter } from '../../model/DataFilter';
+import { CheckBoxType, Option } from 'cbioportal-frontend-commons';
 export declare type BadgeSelectorOption = {
     value: string;
     label?: string | JSX.Element;
@@ -13,7 +13,6 @@ export declare type BadgeSelectorProps = {
     name?: string;
     placeholder?: string;
     isDisabled?: boolean;
-    unselectOthersWhenAllSelected?: boolean;
     numberOfColumnsPerRow?: number;
     alignColumns?: boolean;
     uniformBadgeWidth?: boolean;
@@ -27,12 +26,27 @@ export declare type BadgeSelectorProps = {
     }, checkBoxType?: CheckBoxType) => JSX.Element;
     getBadgeLabel?: (option: BadgeSelectorOption, selectedValues: {
         [optionValue: string]: any;
-    }, badgeClassName?: string, badgeAlignmentStyle?: CSSProperties) => JSX.Element;
+    }, badgeClassName?: string, badgeAlignmentStyle?: CSSProperties, isDriverAnnotated?: boolean, badgeLabelFormat?: (label: JSX.Element | string, badgeFirst?: boolean, value?: string, badge?: JSX.Element | null) => JSX.Element) => JSX.Element;
     filter?: DataFilter<string>;
     options?: BadgeSelectorOption[];
     badgeClassName?: string;
     badgeContentPadding?: number;
     badgeCharWidth?: number;
+    isDriverAnnotated?: boolean;
+    onOnlyDriverVsVusSelect?: (selectedOption: string[], allValuesSelected: boolean) => void;
+    driverAnnotationIcon?: JSX.Element;
+    onBadgeSelect?: (value: string, selectedValues: {
+        value: string;
+    }[], onChange: (values: {
+        value: string;
+    }[]) => void) => void;
+    onOnlySelect?: (value: string, onChange: (values: {
+        value: string;
+    }[]) => void, onOnlyDriverVsVusChange: (values: {
+        value: string;
+    }[]) => void) => void;
+    badgeLabelFormat?: (label: JSX.Element | string, badgeFirst?: boolean, value?: string, badge?: JSX.Element | null) => JSX.Element;
+    useOnlyFeature?: boolean;
 };
 export declare const DEFAULT_BADGE_CHAR_WIDTH = 10;
 export declare const DEFAULT_BADGE_CONTENT_PADDING = 7;
@@ -53,10 +67,11 @@ export declare class BadgeSelector extends React.Component<BadgeSelectorProps, {
     };
     getBadgeLabel(option: BadgeSelectorOption, selectedValues: {
         [optionValue: string]: any;
-    }, badgeClassName?: string, badgeAlignmentStyle?: CSSProperties): JSX.Element;
+    }, badgeClassName?: string, badgeAlignmentStyle?: CSSProperties, isDriverAnnotated?: boolean, badgeLabelFormat?: (label: JSX.Element | string, badgeFirst?: boolean, value?: string, badge?: JSX.Element | null) => JSX.Element): JSX.Element;
     get badgeAlignmentStyles(): CSSProperties[] | undefined;
     get options(): Option[];
     render(): JSX.Element;
     private onChange;
+    private onOnlyDriverVsVusChange;
 }
 export default BadgeSelector;

package/dist/component/filter/ProteinImpactTypeBadgeSelector.d.ts

@@ -12,7 +12,7 @@ export declare type ProteinImpactTypeBadgeSelectorProps = BadgeSelectorProps & {
 export declare function getProteinImpactTypeOptionLabel(option: Option): JSX.Element;
 export declare function getProteinImpactTypeBadgeLabel(option: BadgeSelectorOption, selectedValues: {
     [optionValue: string]: any;
-}, badgeClassName?: string, badgeAlignmentStyle?: CSSProperties): JSX.Element;
+}, badgeClassName?: string, badgeAlignmentStyle?: CSSProperties, isDriverAnnotated?: boolean, badgeLabelFormat?: (label: JSX.Element | string, badgeFirst?: boolean, value?: string, badge?: JSX.Element | null) => JSX.Element): JSX.Element;
 export declare class ProteinImpactTypeBadgeSelector<P extends ProteinImpactTypeBadgeSelectorProps = ProteinImpactTypeBadgeSelectorProps> extends React.Component<P, {}> {
     constructor(props: any);
     static defaultProps: Partial<ProteinImpactTypeBadgeSelectorProps>;

package/dist/index.es.js

@@ -4,7 +4,7 @@ import ___default from 'lodash';
 import { makeObservable, observable, computed, action, reaction } from 'mobx';
 import { observer } from 'mobx-react';
 import * as React from 'react';
-import { DefaultTooltip, TruncatedText, getNCBIlink, 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, defaultHitzoneConfig, initHitZoneFromConfig, EditableSpan, DownloadControls, EllipsisTextTooltip, remoteData, WindowWrapper } from 'cbioportal-frontend-commons';
+import { DefaultTooltip, TruncatedText, getNCBIlink, cachePostMethodsOnClient, CanonicalMutationType, MutationTumorTypeFrequencyTable, FREQUENCY_COLUMNS_DEFINITION, FrequencyTableColumnEnum, CheckedSelect, DriverVsVusType, 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, getCanonicalMutationType, getProteinImpactTypeFromCanonical, ProteinImpactType, getProteinImpactType, resolveColumnVisibility, resolveColumnVisibilityByColumnDefinition, longestCommonStartingSubstring, getTextWidth, unhoverAllComponents, SVGAxis, getComponentIndex, defaultHitzoneConfig, initHitZoneFromConfig, EditableSpan, DownloadControls, EllipsisTextTooltip, remoteData, WindowWrapper } from 'cbioportal-frontend-commons';
 import classNames from 'classnames';
 import { CIVIC_NA_VALUE, parseMyCancerGenomeLink, uniqueGenomicLocations, indexAnnotationsByGenomicLocation, getCivicEntry, getRemoteDataGroupStatus, getMyCancerGenomeLinks, isLinearClusterHotspot, is3dHotspot, OncoKbCardDataType, defaultArraySortMethod, getVariantAnnotation, 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, getMyCancerGenomeData, genomicLocationString, convertUniprotFeatureToPtm, convertDbPtmToPtm, UniprotCategory, convertUniprotFeatureToUniprotTopology, groupPtmDataByPosition, groupPtmDataByTypeAndPosition, groupCancerHotspotDataByPosition, indexHotspotsData, fetchCivicGenes, fetchCivicVariants, getMutationsByTranscriptId, groupMutationsByProteinStartPos, groupHotspotsByMutations } from 'cbioportal-utils';
 import { getIndicatorData, calculateOncoKbAvailableDataType, oncoKbAnnotationSortValue, OncoKB, OncoKbSummaryTable, LEVELS, getTumorTypeNameWithExclusionInfo, ReferenceList, generateProteinChangeQuery, StructuralVariantType, generateAnnotateStructuralVariantQuery, defaultOncoKbFilter, groupOncoKbIndicatorDataByMutations, defaultOncoKbIndicatorFilter } from 'oncokb-frontend-commons';
@@ -1851,30 +1851,62 @@ var BadgeLabel = /** @class */ (function (_super) {
     function BadgeLabel() {
         return _super !== null && _super.apply(this, arguments) || this;
     }
+    Object.defineProperty(BadgeLabel.prototype, "isDriverVusBadge", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function (value) {
+            return (!!value &&
+                Object.values(DriverVsVusType).includes(value));
+        }
+    });
+    Object.defineProperty(BadgeLabel.prototype, "isNotDriverVusProteinBadge", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function (value) {
+            return (!!value &&
+                Object.values(CanonicalMutationType).includes(value));
+        }
+    });
     Object.defineProperty(BadgeLabel.prototype, "badge", {
         get: function () {
             return (React.createElement("span", { style: this.props.badgeFirst
-                    ? { marginRight: 5 }
+                    ? this.props.isDriverAnnotated
+                        ? {}
+                        : { marginRight: 5 }
                     : { marginLeft: 5 } },
-                React.createElement("span", { className: this.props.badgeClassName, "data-test": "badge-" + this.props.value, style: __assign(__assign({}, DEFAULT_BADGE_STYLE), this.props.badgeStyleOverride) }, this.props.badgeContent)));
+                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
+                        ? { marginRight: 0, width: 'auto' }
+                        : {})) }, this.props.badgeContent)));
         },
         enumerable: false,
         configurable: true
     });
     Object.defineProperty(BadgeLabel.prototype, "badgeFirst", {
         get: function () {
-            return (React.createElement(React.Fragment, null,
-                this.badge,
-                this.props.label));
+            if (this.props.badgeLabelFormat) {
+                return this.props.badgeLabelFormat(this.props.label, true, this.props.value, this.badge);
+            }
+            else {
+                return (React.createElement(React.Fragment, null,
+                    this.badge,
+                    this.props.label));
+            }
         },
         enumerable: false,
         configurable: true
     });
     Object.defineProperty(BadgeLabel.prototype, "badgeLast", {
         get: function () {
-            return (React.createElement(React.Fragment, null,
-                this.props.label,
-                this.badge));
+            if (this.props.badgeLabelFormat) {
+                return this.props.badgeLabelFormat(this.props.label, false, this.props.value, this.badge);
+            }
+            else {
+                return (React.createElement(React.Fragment, null,
+                    this.props.label,
+                    this.badge));
+            }
         },
         enumerable: false,
         configurable: true
@@ -2005,8 +2037,8 @@ var BadgeSelector = /** @class */ (function (_super) {
         enumerable: false,
         configurable: true,
         writable: true,
-        value: function (option, selectedValues, badgeClassName, badgeAlignmentStyle) {
-            return this.props.getBadgeLabel ? (this.props.getBadgeLabel(option, selectedValues, badgeClassName, badgeAlignmentStyle)) : (React.createElement(BadgeLabel, { label: option.label || option.value, badgeContent: option.badgeContent, badgeStyleOverride: getBadgeStyleOverride(option, selectedValues, badgeAlignmentStyle), badgeClassName: this.props.badgeClassName }));
+        value: function (option, selectedValues, badgeClassName, badgeAlignmentStyle, isDriverAnnotated, badgeLabelFormat) {
+            return this.props.getBadgeLabel ? (this.props.getBadgeLabel(option, selectedValues, badgeClassName, badgeAlignmentStyle, isDriverAnnotated, badgeLabelFormat)) : (React.createElement(BadgeLabel, { label: option.label || option.value, badgeContent: option.badgeContent, badgeStyleOverride: getBadgeStyleOverride(option, selectedValues, badgeAlignmentStyle), badgeClassName: this.props.badgeClassName, isDriverAnnotated: this.props.isDriverAnnotated, badgeLabelFormat: this.props.badgeLabelFormat }));
         }
     });
     Object.defineProperty(BadgeSelector.prototype, "badgeAlignmentStyles", {
@@ -2024,7 +2056,7 @@ var BadgeSelector = /** @class */ (function (_super) {
             return (this.props.options || []).map(function (option, index) { return ({
                 label: _this.getBadgeLabel(option, _this.selectedValuesMap, _this.props.badgeClassName, _this.badgeAlignmentStyles && _this.props.numberOfColumnsPerRow
                     ? _this.badgeAlignmentStyles[index]
-                    : undefined),
+                    : undefined, _this.props.isDriverAnnotated, _this.props.badgeLabelFormat),
                 value: option.value,
             }); });
         },
@@ -2036,7 +2068,7 @@ var BadgeSelector = /** @class */ (function (_super) {
         configurable: true,
         writable: true,
         value: function () {
-            return (React.createElement(Checklist, { onChange: this.onChange, options: this.options, getOptionLabel: this.props.getOptionLabel, value: this.selectedValues, isDisabled: this.props.isDisabled, numberOfColumnsPerRow: this.props.numberOfColumnsPerRow, unselectOthersWhenAllSelected: this.props.unselectOthersWhenAllSelected }));
+            return (React.createElement(BadgeListSelector, { onChange: this.onChange, options: this.options, getOptionLabel: this.props.getOptionLabel, selectedValue: this.selectedValues, isDisabled: this.props.isDisabled, numberOfColumnsPerRow: this.props.numberOfColumnsPerRow, isDriverAnnotated: this.props.isDriverAnnotated, onOnlyDriverVsVusChange: this.onOnlyDriverVsVusChange, driverAnnotationIcon: this.props.driverAnnotationIcon, onBadgeSelect: this.props.onBadgeSelect, onOnlySelect: this.props.onOnlySelect, useOnlyFeature: this.props.useOnlyFeature }));
         }
     });
     Object.defineProperty(BadgeSelector.prototype, "onChange", {
@@ -2047,6 +2079,14 @@ var BadgeSelector = /** @class */ (function (_super) {
             handleOptionSelect(values, this.allValues, this.props.onSelect);
         }
     });
+    Object.defineProperty(BadgeSelector.prototype, "onOnlyDriverVsVusChange", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function (values) {
+            handleOptionSelect(values, this.allValues, this.props.onOnlyDriverVsVusSelect);
+        }
+    });
     __decorate([
         computed
     ], BadgeSelector.prototype, "allValues", null);
@@ -2065,6 +2105,9 @@ var BadgeSelector = /** @class */ (function (_super) {
     __decorate([
         action.bound
     ], BadgeSelector.prototype, "onChange", null);
+    __decorate([
+        action.bound
+    ], BadgeSelector.prototype, "onOnlyDriverVsVusChange", null);
     BadgeSelector = __decorate([
         observer
     ], BadgeSelector);
@@ -2286,8 +2329,8 @@ var VALUES = [
 function getProteinImpactTypeOptionLabel(option) {
     return React.createElement("span", null, option.label || option.value);
 }
-function getProteinImpactTypeBadgeLabel(option, selectedValues, badgeClassName, badgeAlignmentStyle) {
-    return (React.createElement(BadgeLabel, { label: option.label || option.value, badgeContent: option.badgeContent, badgeStyleOverride: getBadgeStyleOverride(option, selectedValues, badgeAlignmentStyle), badgeClassName: badgeClassName, badgeFirst: true, value: option.value }));
+function getProteinImpactTypeBadgeLabel(option, selectedValues, badgeClassName, badgeAlignmentStyle, isDriverAnnotated, badgeLabelFormat) {
+    return (React.createElement(BadgeLabel, { label: option.label || option.value, badgeContent: option.badgeContent, badgeStyleOverride: getBadgeStyleOverride(option, selectedValues, badgeAlignmentStyle), badgeClassName: badgeClassName, badgeFirst: true, value: option.value, isDriverAnnotated: isDriverAnnotated, badgeLabelFormat: badgeLabelFormat }));
 }
 var ProteinImpactTypeBadgeSelector = /** @class */ (function (_super) {
     __extends(ProteinImpactTypeBadgeSelector, _super);
@@ -2334,7 +2377,7 @@ var ProteinImpactTypeBadgeSelector = /** @class */ (function (_super) {
         configurable: true,
         writable: true,
         value: function () {
-            return (React.createElement(BadgeSelector, __assign({ options: this.options, getOptionLabel: getProteinImpactTypeOptionLabel, getBadgeLabel: getProteinImpactTypeBadgeLabel }, this.props)));
+            return (React.createElement(BadgeSelector, __assign({ options: this.options, getOptionLabel: getProteinImpactTypeOptionLabel, getBadgeLabel: getProteinImpactTypeBadgeLabel, useOnlyFeature: true }, this.props)));
         }
     });
     Object.defineProperty(ProteinImpactTypeBadgeSelector, "defaultProps", {
@@ -2344,7 +2387,6 @@ var ProteinImpactTypeBadgeSelector = /** @class */ (function (_super) {
         value: {
             colors: DEFAULT_PROTEIN_IMPACT_TYPE_COLORS,
             alignColumns: true,
-            unselectOthersWhenAllSelected: false,
             numberOfColumnsPerRow: 2,
         }
     });