loom-browser 0.0.1 → 0.0.2

package/dist/igv.d.ts

@@ -1,667 +0,0 @@
-// either uppercase or lowercase
-type AnyCase<T extends string> = Uppercase<T> | Lowercase<T>;
-
-// any action that can be deferred as a promise
-type Deferrable<T> = T | Promise<T> | (() => T | Promise<T>);
-
-// simply prevents the type from being inferred
-declare class Opaque<N extends string> {
-    private readonly __opaque_brand: N;
-}
-
-export type TrackType =
-    "annotation" | "wig" | "alignment" | "variant" | "mut" | "seg" |
-    "gwas" | "interact" | 'interaction' | "qtl" | "junction" | "cnvpytor" | "merged" | "arc" | "longrange" |
-    /* undocumented options */
-    "snp" | "eqtl";
-
-// converts a track type into the options needed to create it
-export type TrackLoad<T extends TrackType> =
-    Tracks.TrackCommonOptions &
-    (T extends "annotation" ? Tracks.AnnotationTrackOptions & TypeFormatPair<'annotation'> :
-        T extends "wig" ? Tracks.WigTrackOptions & TypeFormatPair<'wig'> :
-            T extends "alignment" ? Tracks.AlignmentTrackOptions & TypeFormatPair<'alignment'> :
-                T extends "variant" ? Tracks.VariantTrackOptions & TypeFormatPair<'variant'> :
-                    T extends "mut" ? Tracks.MutationTrackOptions & TypeFormatPair<'mut'> :
-                        T extends "seg" ? Tracks.SegTrackOptions & TypeFormatPair<'seg'> :
-                            T extends "gwas" ? Tracks.GWASTrackOptions<Tracks.GWASFormat> & TypeFormatPair<'gwas'> :
-                                T extends "interact" | "interaction" ? Tracks.InteractTrackOptions & TypeFormatPair<'interact' | 'interaction'> :
-                                    T extends "qtl" ? Tracks.QTLTrackOptions & TypeFormatPair<'qtl'> :
-                                        T extends "junction" ? Tracks.JunctionTrackOptions & TypeFormatPair<'junction'> :
-                                            T extends "cnvpytor" ? Tracks.CnvPyTorTrackOptions & TypeFormatPair<'cnvpytor'> :
-                                                T extends "merged" ? Tracks.WigMergedTrackOptions & { type: 'merged' } :
-                                                    T extends "arc" ? Tracks.ArcTrackOptions & TypeFormatPair<'arc'> :
-                                                        /* undocumented options */
-                                                        T extends "snp" ? Tracks.SNPTrackOptions & TypeFormatPair<'snp'> :
-                                                            T extends "eqtl" ? Tracks.EQTLTrackOptions & TypeFormatPair<'eqtl'> :
-                                                                never);
-
-export type TypeFormatPair<T extends TrackType> = {
-    type?: T;
-    // if we know the format, type is not required
-    format: TrackFormatOf<T>;
-    // in this case URL can be anything
-    url: Deferrable<string>;
-} | ({
-    // an explicit type and manual reader is allowed, however format and url will not make sense in this context
-    type: T;
-    format?: never;
-    url?: never;
-} & (CustomReaderOf<T> | FeatureOf<T>));
-
-// converts a track type into the file formats that it can accept
-export type TrackFormatOf<T extends TrackType> =
-    T extends "annotation" ? Tracks.AnnotationFormat :
-        T extends "wig" ? Tracks.WigFormat :
-            T extends "alignment" ? Tracks.AlignmentFormat :
-                T extends "variant" ? Tracks.VariantFormat :
-                    T extends "mut" ? Tracks.MutationFormat :
-                        T extends "seg" ? Tracks.SegFormat :
-                            T extends "gwas" ? Tracks.GWASFormat :
-                                T extends "interact" | 'interaction' ? Tracks.InteractFormat :
-                                    T extends "qtl" ? Tracks.QTLFormat :
-                                        T extends "junction" ? Tracks.JunctionFormat :
-                                            T extends "cnvpytor" ? Tracks.CnvPyTorFormat :
-                                                T extends "arc" ? Tracks.ArcFormat :
-                                                    /* undocumented options */
-                                                    T extends "snp" ? Tracks.SNPFormat :
-                                                        T extends "eqtl" ? Tracks.EQTLFormat :
-                                                            never;
-
-// converts a track type into the manual features that it can accept
-export type FeatureOf<T extends TrackType> =
-    T extends "annotation" ? {
-            features: Record<string, any>[];
-        } :
-        T extends "wig" ? {
-                features: Tracks.WigTrackFeatures;
-            } :
-            T extends "seg" ? {
-                features: {
-                    chr: string;
-                    start: number;
-                    end: number;
-                    value: number;
-                    sample: string;
-                }[];
-            } : never;
-
-// some tracks can support a custom reader that polls data based on options
-export type CustomReaderOf<T extends TrackType> =
-    T extends "annotation" ? { reader: Tracks.AnnotationCustomReader } |
-        {
-            source: {
-                url: string;
-                method?: "GET" | "POST";
-                contentType?: string;
-                body?: string;
-            }
-        } :
-        T extends "seg" ? {
-                source: {
-                    url: (options: { chr: string }) => string;
-                    method?: "GET" | "POST";
-                    contentType?: string;
-                    body?: string;
-                    mappings: Record<string, string>;
-                }
-            } :
-            never;
-
-// converts a track type into the actual track class
-export type TrackOf<T extends TrackType> =
-    T extends "annotation" ? Tracks.Track :
-        T extends "wig" ? Tracks.Track :
-            T extends "alignment" ? Tracks.AlignmentTrack :
-                T extends "variant" ? Tracks.Track :
-                    T extends "mut" ? Tracks.Track :
-                        T extends "seg" ? Tracks.Track :
-                            T extends "gwas" ? Tracks.Track :
-                                T extends "interact" | 'interaction' ? Tracks.Track :
-                                    T extends "qtl" ? Tracks.Track :
-                                        T extends "junction" ? Tracks.Track :
-                                            T extends "cnvpytor" ? Tracks.Track :
-                                                T extends "merged" ? Tracks.Track :
-                                                    T extends "arc" ? Tracks.Track :
-                                                        /* undocumented options */
-                                                        T extends "snp" ? Tracks.Track :
-                                                            T extends "eqtl" ? Tracks.Track :
-                                                                never;
-
-
-export type StaticFeatureConfig<T extends Record<string, any>> = {
-    url(options: T): string;
-    method?: "GET" | "POST";
-    contentType?: string;
-    body?: string;
-    mappings: Record<keyof T, string>;
-}
-
-
-export namespace Tracks {
-    export class Track {
-        public readonly id: string;
-        public readonly type: string;
-        public readonly name?: string;
-    }
-
-
-    export interface TrackCommonOptions {
-        name?: string;
-        indexURL?: string | Promise<string>;
-        indexed?: false;
-        order?: number;
-        height?: number;
-        autoHeight?: boolean;
-        minHeight?: number;
-        maxHeight?: number;
-        visibilityWindow?: number | string;
-        removable?: boolean;
-        headers?: Record<string, string>;
-        oauthToken?: string | (() => string | Promise<string>);
-        sourceType?: string;
-        filename?: string;
-        roi?: DefineROI[];
-    }
-
-    export class AnnotationCustomReader {
-        constructor(config: TrackCommonOptions & AnnotationTrackOptions);
-        readFeatures(chr: string, start: number, end: number): Promise<Record<string, any>[]>;
-    }
-
-    export type AnnotationFormat = "bed" | "gff3" | "gtf" |
-        "genePred" | "genePredExt" | "peaks" |
-        "narrowPeak" | "broadPeak" | "bigBed" | "rmsk" | "vcf" |
-        "gtexgwas";
-
-    export type AnnotationTrackDisplay = {
-        displayMode: AnyCase<"EXPANDED">
-        expandedRowHeight?: number,
-    } | {
-        displayMode: AnyCase<"SQUISHED">
-        squishedRowHeight: number,
-    } | {
-        displayMode?: AnyCase<"COLLAPSED">
-    }
-
-    export type AnnotationTrackSearch = {
-        searchable: true,
-        searchableFields: string[],
-    } | {
-        searchable?: false,
-    }
-
-    export interface AnnotationTrackCommonOptions {
-        nameField?: string;
-        maxRows?: number;
-        filterTypes?: string[];
-        color?: string | ((feature: {
-            chr: string;
-            getAttributeValue: (name: string) => string;
-        }) => string);
-        colorBy?: string;
-        altColor?: string, rBy?: string,
-        colorTable?: Record<string, string>,
-    }
-
-    export type AnnotationTrackOptions = AnnotationTrackDisplay & AnnotationTrackSearch & AnnotationTrackCommonOptions;
-
-    export type WigFormat = AnyCase<"wig"> | "bigWig" | AnyCase<'bigWig'> | AnyCase<'tdf'> | AnyCase<'bw'>;
-
-    export interface WigTrackOptions {
-        autoscale?: boolean;
-        autoscaleGroup?: string;
-        min?: number;
-        max?: number;
-        color?: string,
-        altColor?: string,
-        guidelines?: { color: string, y: number, dotted: boolean }[];
-        graphType?: "points" | "bar" | "line" | "heatmap" | "dynseq"
-        flipAxis?: boolean;
-        windowFunction?: "mean" | "max" | "min";
-
-        height?: number;
-
-        displayMode?: AnyCase<"EXPANDED" | "SQUISHED" | "COLLAPSED">;
-    }
-
-    export type WigTrackFeatures = {
-        chr: string;
-        start: number;
-        end: number;
-        value: number;
-    }[];
-
-    export type WigMergedTrackOptions = {
-        tracks: (Partial<TrackCommonOptions> & ((TypeFormatPair<'wig'> & WigTrackOptions) | (TypeFormatPair<'junction'> & JunctionTrackOptions)))[];
-    };
-
-    export type VariantFormat = "vcf";
-
-    export type VCFItem = {
-        chrom: string;
-        pos: number;
-        id: string;
-        ref: string;
-        alt: string;
-        qual: number;
-        filter: string;
-        info: Record<string, string>;
-    }
-
-    export type VariantTrackOptions = {
-        displayMode?: AnyCase<"EXPANDED" | "SQUISHED" | "COLLAPSED">;
-        squishedCallHeight?: number;
-        expandedCallHeight?: number;
-        color?: string | ((variant: VCFItem) => string);
-        colorBy?: string;
-        colorTable?: Record<string, string>;
-        noCallColor?: string;
-        homvarColor?: string;
-        hetvarColor?: string;
-        homrefColor?: string;
-        supportsWholeGenome?: boolean;
-        showGenotypes?: boolean;
-        strokecolor?: (variant: VCFItem) => string | void;
-        context_hook?: unknown;
-    };
-
-    export type CnvPyTorFormat = "pytor" | "vcf";
-
-    export type CnvPyTorTrackOptions = {
-        signal_name?: string;
-        cnv_caller?: "ReadDepth" | "2D";
-        bin_size?: number;
-        colors?: string[];
-    }
-
-    export type AlignmentFormat = "bam" | "cram";
-
-    type AlignmentBy = (string & {}) // tag:tagName and base:position
-
-    export type AlignmentSortOptions = {
-        chr: string;
-        position: number;
-        direction?: "ASC" | "DESC";
-    } & ({
-        option: "BASE" | "STRAND" | "INSERT_SIZE" | "MATR_CHR" | "MQ";
-    } | {
-        option: "TAG";
-        tag: string;
-    });
-
-    export type AlignmentTrackOptions = {
-        showCoverage?: boolean;
-        showAlignments?: boolean;
-        viewAsPairs?: boolean;
-        pairsSupported?: boolean;
-        coverageColor?: string;
-        color?: string;
-        deletionColor?: string;
-        displayMode?: AnyCase<"FULL" | "EXPANDED" | "SQUISHED">;
-        groupBy?:
-            "strand" | "firstOfPairStrand" | "pairOrientation" | "mateChr" | "chimeric" | "supplementary" | "readOrder" | AlignmentBy;
-        samplingWindowSize?: number;
-        samplingDepth?: number;
-        readGroup?: string;
-        sort?: AlignmentSortOptions;
-        filter?: {
-            vendorFailed?: boolean;
-            duplicates?: boolean;
-            secondary?: boolean;
-            supplementary?: boolean;
-            mq?: number;
-            readGroups?: string[];
-        };
-        showSoftClips?: boolean;
-        showMismatches?: boolean;
-        showAllBases?: boolean;
-        showInsertionText?: boolean;
-        insertionTextColor?: string;
-        alignmentRowHeight?: number;
-        squishedRowHeight?: number;
-    } & (
-        {
-            colorBy: "strand" | "firstOfPairStrand";
-            insertionColor?: string;
-            negStrandColor?: string;
-        } |
-        {
-            colorBy: "pairOrientation" | "tlen"
-                | "unexpectedPair"
-                | "basemod" | "basemod2"
-                | AlignmentBy;
-        } |
-        {
-            colorBy?: "fragmentLength";
-        });
-
-
-    class AlignmentTrack extends Track {
-        setHighlightedReads(readNames: string[], color: string): void;
-        sort(options: AlignmentSortOptions): void;
-    }
-
-    export type GWASFormat = "gwas" | "bed";
-
-    export type GWASTrackOptions<F extends GWASFormat> = {
-        min?: number;
-        max?: number;
-        posteriorProbability?: boolean;
-        dotSize?: number;
-        colorTable?: Record<string, string>;
-        columns?: F extends "gwas" ? {
-            chromosome: number;
-            position: number;
-            value: number;
-        } : never;
-    }
-
-    export type MutationFormat = "maf" | "mut";
-
-    export type MutationTrackOptions = {
-        displayMode?: AnyCase<"EXPANDED" | "SQUISHED" | "COLLAPSED">;
-    }
-
-    export type SegFormat = "seg";
-
-    export type SegTrackOptions = {
-        displayMode?: AnyCase<"EXPANDED" | "SQUISHED" | "FILL">;
-        sort?: ({
-            option: "value" | "VALUE";
-        } | {
-            option: "attribute" | "ATTRIBUTE";
-            attribute: string;
-        });
-        samples?: string[];
-    } & (
-        {
-            isLog?: boolean;
-            log?: never;
-        } | {
-        log?: boolean;
-        isLog?: never;
-    });
-
-
-    export type InteractFormat = "interact" | "bedpe" | "bigInteract" | "bb" | "hic" | "longrange";
-
-    export type InteractTrackOptions = {
-        arcType?: "nested" | "proportional" | "inView" | "partialInView";
-        arcOrientation?: "UP" | "DOWN" | boolean;
-        color?: string;
-        alpha?: number | string;
-        logScale?: boolean;
-        showBlocks?: boolean;
-        thickness?: number;
-        useScore?: boolean;
-        max?: number;
-    }
-
-    export type QTLFormat = "qtl";
-
-    export type QTLTrackOptions = {
-        min?: number;
-        max?: number;
-        autoscalePercentile?: number;
-    }
-
-    export type JunctionFormat = "bed";
-
-    export type JunctionTrackFilteringOptions = {
-        minUniquelyMappedReads?: number;
-        minTotalReads?: number;
-        maxFractionMultiMappedReads?: number;
-        minSplicedAlignmentOverhang?: number;
-        hideStrand?: "+" | "-";
-        hideAnnotatedJunctions?: boolean;
-        hideUnannotatedJunctions?: boolean;
-        hideMotifs?: string[];
-    }
-
-    export type JunctionTrackOptions = ({
-        colorBy?: "numUniqueReads" | "numReads";
-        colorByNumReadsThreshold: number;
-    } | {
-        colorBy: "isAnnotatedJunction" | "strand" | "motif";
-        colorByNumReadsThreshold?: never;
-    }) & {
-        displayMode?: AnyCase<"COLLAPSED" | "EXPANDED" | "SQUISHED">;
-        thicknessBasedOn?: "numUniqueReads" | "numReads" | "isAnnotatedJunction";
-        bounceHeightBasedOn?: "random" | "distance" | "thickness";
-        labelUniqueReadCount?: boolean;
-        labelMultiMappedReadCount?: boolean;
-        labelTotalReadCount?: boolean;
-        labelMotif?: boolean;
-        // TODO: documented but not implemented?
-        // labelAnnotatedJunction?: string | null;
-        minSplicedAlignmentOverhang?: number;
-    } & JunctionTrackFilteringOptions;
-
-    export type ArcFormat = "bp";
-
-    export type ArcTrackOptions = {
-        arcOrientation?: "UP" | "DOWN";
-    }
-
-    // TODO: undocumented
-    export type SNPFormat = "snp";
-
-    export interface SNPTrackOptions {
-    }
-
-    export type EQTLFormat = "eqtl";
-
-    export interface EQTLTrackOptions {
-        sourceType: "gtex-ws";
-        tissueSiteDetailId: string;
-    }
-}
-
-type Nucleotide = 'A' | 'C' | 'G' | 'T' | 'N';
-
-type SuggestedGenomeIDs = "hs1" | "chm13v1.1" | "hg38" | "hg38_1kg" | "hg19" |
-    "hg18" | "mm39" | "mm10" | "mm9" | "rn7" |
-    "rn6" | "gorGor6" | "gorGor4" | "panTro6" | "panTro5" |
-    "panTro4" | "macFas5" | "GCA_011100615.1" | "panPan2" | "canFam3" |
-    "canFam4" | "canFam5" | "bosTau9" | "bosTau8" | "susScr11" |
-    "galGal6" | "danRer11" | "danRer10" | "ce11" |
-    "dm6" | "dm3" | "dmel_r5.9" | "sacCer3" | "ASM294v2" |
-    "ASM985889v3" | "tair10"
-
-export type GenomeDef = SuggestedGenomeIDs | (string & {}) | ReferenceGenome;
-
-export type GenomeOpt = { reference: GenomeDef, genome?: never } | { genome: GenomeDef, reference?: never };
-
-/**
- * To define or customize a reference genome the reference property can be used.
- */
-export interface ReferenceGenome {
-    id?: string;
-    name?: string;
-    fastaURL: string;
-    indexURL?: string;
-    cytobandURL?: string;
-    aliasURL?: string;
-    /**
-     * @deprecated
-     */
-    indexed?: true;
-    chromosomeOrder?: string[];
-    headers?: Record<string, string>;
-    wholeGenomeView?: boolean;
-}
-
-interface CreateOptExtras {
-    supportQueryParameters?: boolean;
-    queryParametersSupported?: boolean;
-
-    showNavigation?: boolean;
-
-    showSampleNames?: boolean;
-    sampleNameViewportWidth?: number;
-    locus?: string | string[];
-    nucleotideColors?: Partial<Record<Nucleotide, string>>;
-
-    roi?: DefineROI[];
-    tracks?: TrackLoad<TrackType>[];
-
-    search?: {
-        url: string;
-        chromosomeField: string;
-        displayName: string;
-    };
-}
-
-export namespace BrowserEvents {
-    export type EventType = "trackremoved" | "trackdrag" | "trackdragend" | "locuschange" | "trackclick" | "trackorderchanged" | "zoom";
-
-    // returns the type of the event handler based on the event type
-    export type EventHandler<T extends EventType> =
-        T extends "trackremoved" ? (tracks: Tracks.Track[]) => EventReturn<T> :
-            T extends "locusChange" ? (loci: {
-                    chr: string;
-                    start: number;
-                    end: number;
-                    getLocusString: () => string;
-                }[]) => EventReturn<T> :
-                T extends "trackclick" ? (
-                        track: Tracks.Track,
-                        popoverData?: Record<string, string>,
-                        genomicLocation?: number
-                    ) => EventReturn<T> :
-                    T extends "trackorderchanged" ? (trackNames: string[]) => EventReturn<T> :
-                        T extends "roiadded" ? (roi: { chr: string; start: number; end: number; name?: string }) => EventReturn<T> :
-                            T extends "roiremoved" ? (roi: { chr: string; start: number; end: number; name?: string }) => EventReturn<T> :
-                                (payload: any) => EventReturn<T>;
-
-    export type EventReturn<T extends EventType> =
-        T extends "trackclick" ? string | boolean | undefined :
-            void;
-}
-
-export type CreateOpt = (GenomeOpt & CreateOptExtras) | (
-    // if a session URL is provided, we do not need a complete definition, additionally we should not allow a different genome
-    {
-        sessionURL: string;
-    } & Partial<CreateOptExtras>
-    )
-
-export interface ROISet {
-    url: string;
-    name: string;
-    indexed: boolean;
-    isUserDefined: boolean;
-    color: string;
-    headerColor: string;
-    isvisible: boolean;
-    chr: string;
-    start: number;
-    end: number;
-}
-
-export type DefineROI = {
-    name?: string;
-    color: string;
-} & ({
-    url: string;
-    indexed?: boolean;
-    format?: string;
-} | {
-    features: {
-        chr: string;
-        start: number;
-        end: number;
-    }[]
-});
-
-
-declare class _Browser {
-    currentLoci(): string[] | string;
-    loadGenome(genome: string | ReferenceGenome): Promise<void>;
-    loadSessionObject(session: Opaque<'igv.js session JSON'>): void;
-    loadSession(session: string): void;
-    loadTrack<T extends TrackType>(track: TrackLoad<T>): Promise<TrackOf<T>>;
-    loadSampleInfo({ url: string }): void;
-    findTracks(func: (track: Tracks.Track) => boolean): Tracks.Track[];
-    findTracks(property: string, value: any): Tracks.Track[];
-    removeTrack(track: Tracks.Track): void;
-    removeTrackByName(trackName: string): void;
-    loadROI(roi: DefineROI | DefineROI[]): void;
-    clearROIs(): void;
-    getUserDefinedROIs(): Promise<ROISet[]>;
-    search(query: string): void;
-    zoomIn(): void;
-    zoomOut(): void;
-    visibilityChange(): void;
-    toJSON(): Opaque<'igv.js session JSON'>;
-    compressedSession(): string;
-    toSVG(): string;
-    setCustomCursorGuideMouseHandler(handler: (state: {
-        bp: number,
-        start: number,
-        end: number,
-        interpolant: number,
-    }) => void): void;
-
-    sessionURL(): string;
-
-    on<T extends BrowserEvents.EventType>(event: T, handler: BrowserEvents.EventHandler<T>): void;
-    off(event: BrowserEvents.EventType): void;
-}
-
-export type Browser = _Browser;
-
-type CreateBrowser = (div: HTMLElement, options: CreateOpt) => Promise<Browser>;
-
-export type GlobalConfig = {
-    minimumBases: number;
-    showIdeogram: boolean;
-    showCircularView: boolean;
-    showCircularViewButton: boolean;
-    showTrackLabelButton: boolean;
-    showTrackLabels: boolean;
-    doShowROITableButton: boolean;
-    showROITable: boolean;
-    showCursorTrackingGuideButton: boolean;
-    showCursorTrackingGuide: boolean;
-    showCenterGuideButton: boolean;
-    showCenterGuide: boolean;
-    showSampleNames: boolean;
-    showSVGButton: boolean;
-    showControls: boolean;
-    showNavigation: boolean;
-    showRuler: boolean;
-    flanking: number;
-    pairsSupported: boolean;
-    tracks: TrackLoad<TrackType>[];
-}
-
-
-export type IGV = {
-    readonly setDefaults: (config: Partial<GlobalConfig>) => void;
-    /**
-     * Create an igv.browser instance.  This object defines the public API for interacting with the genome browser.
-     *
-     * @param parentDiv - DOM tree root
-     * @param config - configuration options.
-     *
-     */
-    readonly createBrowser: CreateBrowser;
-    readonly removeBrowser: (browser: Browser) => void;
-    readonly removeAllBrowsers: () => void;
-    readonly setApiKey: (apiKey: string) => void;
-    readonly setGoogleOauthToken: (token: string) => void;
-    readonly setOauthToken: (token: string, host: string) => void;
-    readonly getAllBrowsers: () => Browser[];
-    /**
-     * This function provided so clients can inform igv of a visibility change, typically when an igv instance is
-     * made visible from a tab, accordion, or similar widget.
-     */
-    readonly visibilityChange: () => Promise<void>;
-    readonly version: () => string;
-}
-
-declare const igv: IGV;
-
-export default igv;