react-mutation-mapper/dist/store/DefaultMutationMapperStore.d.ts

Generic Mutation Mapper

import { AggregatedHotspots, ICivicGeneIndex, ICivicVariantIndex, IHotspotIndex, IMyCancerGenomeData, IOncoKbData, PostTranslationalModification, UniprotFeature, UniprotTopology } from 'cbioportal-utils';
import { Gene, Mutation, IMyVariantInfoIndex } from 'cbioportal-utils';
import { CancerGene, IndicatorQueryResp, OncoKBInfo } from 'oncokb-ts-api-client';
import { EnsemblTranscript, Hotspot, PfamDomain, PostTranslationalModification as DbPtm, VariantAnnotation } from 'genome-nexus-ts-api-client';
import MobxPromise from 'mobxpromise';
import { DataFilter } from '../model/DataFilter';
import DataStore from '../model/DataStore';
import { ApplyFilterFn, FilterApplier } from '../model/FilterApplier';
import { MutationMapperDataFetcher } from '../model/MutationMapperDataFetcher';
import { MutationMapperStore } from '../model/MutationMapperStore';
interface DefaultMutationMapperStoreConfig {
    annotationFields?: string[];
    isoformOverrideSource?: string;
    ptmSources?: string[];
    filterMutationsBySelectedTranscript?: boolean;
    genomeNexusUrl?: string;
    oncoKbUrl?: string;
    enableCivic?: boolean;
    enableOncoKb?: boolean;
    enableRevue?: boolean;
    cachePostMethodsOnClients?: boolean;
    apiCacheLimit?: number;
    getMutationCount?: (mutation: Partial<Mutation>) => number;
    getTumorType?: (mutation: Partial<Mutation>) => string;
    filterApplier?: FilterApplier;
    filterAppliersOverride?: {
        [filterType: string]: ApplyFilterFn;
    };
    dataFetcher?: MutationMapperDataFetcher;
    dataFilters?: DataFilter[];
    selectionFilters?: DataFilter[];
    highlightFilters?: DataFilter[];
    groupFilters?: {
        group: string;
        filter: DataFilter;
    }[];
    genomeBuild?: string;
}
declare class DefaultMutationMapperStore<T extends Mutation> implements MutationMapperStore<T> {
    gene: Gene;
    protected config: DefaultMutationMapperStoreConfig;
    protected getMutations: () => T[];
    getTranscriptId?: (() => string | undefined) | undefined;
    protected getDataFetcher?: () => MutationMapperDataFetcher;
    private _selectedTranscript;
    get selectedTranscript(): string | undefined;
    constructor(gene: Gene, config: DefaultMutationMapperStoreConfig, getMutations: () => T[], getTranscriptId?: (() => string | undefined) | undefined);
    readonly activeTranscript: MobxPromise<string | undefined>;
    setSelectedTranscript(transcript: string | undefined): void;
    get isoformOverrideSource(): string;
    get ptmSources(): string[];
    get annotationFields(): string[];
    protected getDataStore?: () => DataStore;
    get dataStore(): DataStore;
    readonly myCancerGenomeData: IMyCancerGenomeData;
    get mutations(): T[];
    protected getAnnotatedMutationsByTranscriptId(mutations: T[], transcriptId: string, indexedVariantAnnotations: {
        [genomicLocation: string]: VariantAnnotation;
    }): T[];
    getAnnotatedMutations(transcriptId: string): T[];
    get filterApplier(): FilterApplier;
    get dataFetcher(): MutationMapperDataFetcher;
    get mutationsByPosition(): {
        [pos: number]: T[];
    };
    get groupedMutationsByPosition(): {
        group: string;
        mutations: {
            [pos: number]: T[];
        };
    }[];
    protected getMutationsGroupedByProteinImpactType?: () => {
        [type: string]: {
            group: string;
            data: any[];
        };
    };
    protected get mutationsGroupedByProteinImpactType(): {
        [type: string]: {
            group: string;
            data: any[];
        };
    };
    get mutationCountsByProteinImpactType(): {
        [proteinImpactType: string]: number;
    };
    get uniqueMutationCountsByPosition(): {
        [pos: number]: number;
    };
    get uniqueGroupedMutationCountsByPosition(): {
        group: string;
        counts: {
            [pos: number]: number;
        };
    }[];
    get transcriptsByTranscriptId(): {
        [transcriptId: string]: EnsemblTranscript;
    };
    countUniqueMutationsByPosition(mutationsByPosition: {
        [pos: number]: T[];
    }, group?: string): {
        [pos: number]: number;
    };
    countUniqueMutations(mutations: T[], group?: string): number;
    protected getMutationCount(mutations: T[], getMutationCount: (mutation: Partial<T>) => number): number;
    readonly mutationData: MobxPromise<Partial<T>[] | undefined>;
    readonly swissProtId: MobxPromise<string>;
    readonly uniprotId: MobxPromise<string | undefined>;
    readonly pfamDomainData: MobxPromise<PfamDomain[] | undefined>;
    readonly canonicalTranscript: MobxPromise<EnsemblTranscript | undefined>;
    readonly allTranscripts: MobxPromise<EnsemblTranscript[] | undefined>;
    readonly transcriptsByHugoSymbol: MobxPromise<EnsemblTranscript[] | undefined>;
    readonly transcriptsWithProteinLength: MobxPromise<string[] | undefined>;
    readonly transcriptsWithAnnotations: MobxPromise<string[] | undefined>;
    readonly ptmData: MobxPromise<PostTranslationalModification[]>;
    readonly uniprotPtmData: MobxPromise<UniprotFeature[]>;
    readonly uniprotTopologyData: MobxPromise<UniprotTopology[]>;
    readonly dbPtmData: MobxPromise<DbPtm[]>;
    readonly ptmDataByProteinPosStart: MobxPromise<{
        [pos: number]: PostTranslationalModification[];
    } | undefined>;
    readonly ptmDataByTypeAndProteinPosStart: MobxPromise<{
        [type: string]: {
            [position: number]: PostTranslationalModification[];
        };
    } | undefined>;
    readonly cancerHotspotsData: MobxPromise<Hotspot[]>;
    readonly cancerHotspotsDataByProteinPosStart: MobxPromise<{
        [pos: number]: Hotspot[];
    }>;
    readonly hotspotData: MobxPromise<AggregatedHotspots[]>;
    readonly indexedHotspotData: MobxPromise<IHotspotIndex | undefined>;
    get hotspotsByPosition(): {
        [pos: number]: Hotspot[];
    };
    readonly oncoKbCancerGenes: MobxPromise<CancerGene[] | Error>;
    readonly oncoKbInfo: MobxPromise<OncoKBInfo>;
    get usingPublicOncoKbInstance(): boolean;
    readonly oncoKbAnnotatedGenes: MobxPromise<{
        [entrezGeneId: number]: boolean;
    }>;
    readonly oncoKbData: MobxPromise<IOncoKbData | Error>;
    get oncoKbDataByPosition(): {
        [pos: number]: IndicatorQueryResp[];
    };
    readonly civicGenes: MobxPromise<ICivicGeneIndex | undefined>;
    readonly civicVariants: import("mobxpromise").MobxPromiseUnionType<ICivicVariantIndex | undefined>;
    readonly indexedVariantAnnotations: MobxPromise<{
        [genomicLocation: string]: VariantAnnotation;
    } | undefined>;
    readonly indexedMyVariantInfoAnnotations: MobxPromise<IMyVariantInfoIndex | undefined>;
    get mutationsByTranscriptId(): {
        [transcriptId: string]: T[];
    };
    protected getDefaultTumorType(mutation: T): string;
    protected getDefaultEntrezGeneId(mutation: T): number;
    readonly ensemblTranscriptLookUp: MobxPromise<any | undefined>;
    get genomeBuild(): string;
}
export default DefaultMutationMapperStore;