react-mutation-mapper/dist/model/MutationMapperDataFetcher.d.ts

Generic Mutation Mapper

import { AggregatedHotspots, EvidenceType, IOncoKbData, Mutation, UniprotFeature } from 'cbioportal-utils';
import { EnsemblFilter, EnsemblTranscript, GenomeNexusAPI, GenomeNexusAPIInternal, Hotspot, MyVariantInfo, PfamDomain, PostTranslationalModification, VariantAnnotation } from 'genome-nexus-ts-api-client';
import { CancerGene, OncoKbAPI, OncoKBInfo } from 'oncokb-ts-api-client';
export interface MutationMapperDataFetcher {
    fetchSwissProtAccession(entrezGeneId: number): Promise<any>;
    fetchUniprotId(swissProtAccession: string): Promise<string>;
    fetchPfamDomainData(pfamAccessions: string[], client?: GenomeNexusAPI): Promise<PfamDomain[]>;
    fetchVariantAnnotationsIndexedByGenomicLocation(mutations: Partial<Mutation>[], fields: string[], isoformOverrideSource: string, client?: GenomeNexusAPI): Promise<{
        [genomicLocation: string]: VariantAnnotation;
    }>;
    fetchMyVariantInfoAnnotationsIndexedByGenomicLocation(mutations: Partial<Mutation>[], isoformOverrideSource: string, client?: GenomeNexusAPI): Promise<{
        [genomicLocation: string]: MyVariantInfo;
    }>;
    fetchCanonicalTranscriptWithFallback(hugoSymbol: string, isoformOverrideSource: string, allTranscripts: EnsemblTranscript[] | undefined, client?: GenomeNexusAPI): Promise<EnsemblTranscript | undefined>;
    fetchCanonicalTranscript(hugoSymbol: string, isoformOverrideSource: string, client?: GenomeNexusAPI): Promise<EnsemblTranscript>;
    fetchEnsemblTranscriptsByEnsemblFilter(ensemblFilter: Partial<EnsemblFilter>, client?: GenomeNexusAPI): Promise<EnsemblTranscript[] | undefined>;
    fetchPtmData(ensemblId: string, client?: GenomeNexusAPI): Promise<PostTranslationalModification[]>;
    fetchUniprotFeatures(swissProtId: string, category: string[], client?: GenomeNexusAPI): Promise<UniprotFeature[]>;
    fetchCancerHotspotData(ensemblId: string, client?: GenomeNexusAPIInternal): Promise<Hotspot[]>;
    fetchAggregatedHotspotsData(mutations: Mutation[], client?: GenomeNexusAPIInternal): Promise<AggregatedHotspots[]>;
    fetchOncoKbCancerGenes(client?: OncoKbAPI): Promise<CancerGene[]>;
    fetchOncoKbInfo(client?: OncoKbAPI): Promise<OncoKBInfo>;
    fetchOncoKbData(mutations: Mutation[], annotatedGenes: {
        [entrezGeneId: number]: boolean;
    } | Error, getTumorType: (mutation: Mutation) => string, getEntrezGeneId: (mutation: Mutation) => number, evidenceTypes?: EvidenceType[], client?: OncoKbAPI): Promise<IOncoKbData | Error>;
}
export default MutationMapperDataFetcher;