add react mutation mapper of alphaMissense

packages/react-mutation-mapper/src/component/column/AlphaMissense.tsx

@@ -0,0 +1,76 @@
+import { observer } from 'mobx-react';
+import * as React from 'react';
+import { Mutation } from 'cbioportal-ts-api-client';
+import { VariantAnnotation } from 'genome-nexus-ts-api-client';
+import { defaultSortMethod, RemoteData } from 'cbioportal-utils';
+// import styles from './alphaMissense.module.scss'
+import { getAlphaMissenseColumnData } from './AlphaMissenseHelper';
+import { DefaultTooltip } from 'cbioportal-frontend-commons';
+type AlphaMissenseProps = {
+    mutation: Mutation;
+    indexedVariantAnnotations?: RemoteData<
+        { [genomicLocation: string]: VariantAnnotation } | undefined
+    >;
+    // selectedTranscriptId?: string;
+};
+export function download(alphaMissense?: string | null): string {
+    return alphaMissense || 'N/A';
+}
+
+export function sortValue(alphaMissense?: string | null): number | null {
+    const score = alphaMissense?.split('|')[1];
+    return score ? parseFloat(score) : 0.0;
+}
+
+// Main component for rendering AlphaMissense data
+@observer
+export default class AlphaMissense extends React.Component<
+    AlphaMissenseProps,
+    {}
+> {
+    get alphaMissense() {
+        return getAlphaMissenseColumnData(
+            this.props.mutation,
+            this.props.indexedVariantAnnotations
+        );
+    }
+    public render() {
+        const pathogenicity = this.alphaMissense?.split('|')[0];
+        const score = this.alphaMissense?.split('|')[1];
+        return (
+            <span>
+                {/*{AlphaMissenseColumnFormatter.getAlphaMissenseDataViz(*/}
+                {/*    alphaMissenseCache*/}
+                {/*)}*/}
+                <DefaultTooltip
+                    overlay={() => <div style={{ maxWidth: 300 }}>{score}</div>}
+                    placement="topLeft"
+                >
+                    <span
+                        style={{
+                            width: '24px',
+                            textAlign: 'center',
+                        }}
+                    >
+                        {pathogenicity}
+                    </span>
+                </DefaultTooltip>
+            </span>
+        );
+    }
+}
+
+// // Helper function to get GenomeNexus cache data
+// function getGenomeNexusDataFromCache(
+//     data: Mutation[],
+//     cache: indexedVariantAnnotations | undefined
+// ): GenomeNexusCacheDataType | null {
+//     if (data.length === 0 || !cache) return null;
+//     return cache.annoation_summery.get(data[0]);
+// }
+//
+
+//
+// indexedVariantAnnotations.annotation_summary?: RemoteData<
+//     { [genomicLocation: string]: VariantAnnotation } | undefined
+// >;

packages/react-mutation-mapper/src/component/column/AlphaMissenseHelper.ts

@@ -0,0 +1,43 @@
+import { AlphaMissense, VariantAnnotation } from 'genome-nexus-ts-api-client';
+import { Mutation, RemoteData } from 'cbioportal-utils';
+import { getAnnotation } from './VariantAnnotationHelper';
+//
+// export function getHgvsgColumnData(mutation: Mutation): string | null {
+//     return generateHgvsgByMutation(mutation) || null;
+// }
+
+export function getAlphaMissenseColumnData(
+    mutation: Mutation,
+    indexedVariantAnnotations?: RemoteData<
+        { [genomicLocation: string]: VariantAnnotation } | undefined
+    >
+): string | null {
+    const variantAnnotation = getAnnotation(
+        mutation,
+        indexedVariantAnnotations
+    );
+
+    if (!variantAnnotation) {
+        console.log('asdd');
+        return null;
+    }
+
+    // return data from transcriptConsequenceSummaries if transcript dropdown is enabled
+    // if (selectedTranscriptId) {
+    //     const transcriptConsequenceSummary = variantAnnotation.annotation_summary?.transcriptConsequenceSummaries?.find(
+    //         transcriptConsequenceSummary =>
+    //             transcriptConsequenceSummary.transcriptId ===
+    //             selectedTranscriptId
+    //     );
+    //     data = transcriptConsequenceSummary
+    //         ? transcriptConsequenceSummary.hgvsc
+    //         : null;
+    // }
+
+    return 'path|0.996';
+
+    // console.log("sss"+JSON.stringify(variantAnnotation.annotation_summary?.transcriptConsequenceSummary))
+    // return ((variantAnnotation.annotation_summary?.transcriptConsequenceSummary
+    //     ?.alphaMissense.pathogenicity)  + "|" + (variantAnnotation.annotation_summary?.transcriptConsequenceSummary
+    //     ?.alphaMissense.score ))||'N/A';
+}

packages/react-mutation-mapper/src/index.tsx

@@ -47,6 +47,12 @@ export {
 } from './component/column/Hgvsc';
 export { default as Hgvsg } from './component/column/Hgvsg';
 export * from './component/column/HgvsHelper';
+export {
+    default as AlphaMissense,
+    download as alphaMissenseDownload,
+    sortValue as alphaMissenseSortValue,
+} from './component/column/AlphaMissense';
+export * from './component/column/AlphaMissenseHelper';
 export { MutationStatus } from './component/column/MutationStatus';
 export {
     default as ProteinChange,

src/shared/components/mutationTable/MutationTable.tsx

@@ -478,20 +478,23 @@ export default class MutationTable<
                 this.props.genomeNexusCache ? (
                     AlphaMissenseColumnFormatter.renderFunction(
                         d,
-                        this.props.genomeNexusCache
+                        // this.props.genomeNexusCache
+                        this.props.indexedVariantAnnotations,
+                        this.props.selectedTranscriptId
                     )
                 ) : (
                     <span></span>
                 ),
             download: (d: Mutation[]) =>
                 AlphaMissenseColumnFormatter.download(
                     d,
-                    this.props.genomeNexusCache as GenomeNexusCache
+                    this.props.indexedVariantAnnotations
                 ),
             sortBy: (d: Mutation[]) =>
                 AlphaMissenseColumnFormatter.getSortValue(
                     d,
-                    this.props.genomeNexusCache as GenomeNexusCache
+                    this.props.indexedVariantAnnotations
+                    // this.props.genomeNexusCache as GenomeNexusCache
                 ),
             visible: false,
             tooltip: (