wuepgg3-track 3.0.3 → 4.0.0

package/dist/getRemoteData/BigSourceWorker.d.ts

@@ -0,0 +1,47 @@
+/**
+ * Reads and gets data from bigwig or bigbed files hosted remotely.  Gets DASFeature records, which vary in schema
+ * depending on the file.
+ *
+ * @license MIT
+ */
+declare class BigSourceWorker {
+    url: any;
+    bigWigPromise: Promise<unknown>;
+    /**
+     * Prepares to fetch bigwig or bigbed data from a URL.
+     *
+     * @param {string} url - the URL from which to fetch data
+     */
+    constructor(url: any);
+    private loadBigWig;
+    /**
+     * Gets BigWig or BigBed features inside the requested locations.
+     *
+     * @param {ChromosomeInterval[]} loci - locations for which to fetch data
+     * @param {number} [basesPerPixel] - used to determine fetch resolution
+     * @return {Promise<DASFeature[]>} a Promise for the data
+     * @override
+     */
+    getData(loci: any, basesPerPixel: any, options: any): Promise<any[]>;
+    /**
+     * BigWig files contain zoom levels, where data across many bases is aggregated into bins.  This selects an
+     * appropriate zoom index from the BigWig file given the number of bases per pixel at which the data will be
+     * visualized.  This function may also return -1, which indicates base pair resolution (no aggregation) is
+     * appropriate.
+     *
+     * @param {BigWig} bigWigObj - BigWig object provided by bbi-js
+     * @param {number} [basesPerPixel] - bases per pixel to use to calculate an appropriate zoom level
+     * @return {number} a zoom level index inside the BigWig file, or -1 if base pair resolution is appropriate.
+     */
+    _getMatchingZoomLevel(bigWigObj: any, basesPerPixel: number): number;
+    /**
+     * Gets BigWig features stored in a single chromosome interval.
+     *
+     * @param {ChromosomeInterval} interval - coordinates
+     * @param {BigWig} bigWigObj - BigWig object provided by bbi-js
+     * @param {number} zoomLevel - a zoom level index inside the BigWig file.  If -1, gets data at base pair resolution.
+     * @return {Promise<DASFeature[]>} - a Promise for the data, an array of DASFeature provided by bbi-js
+     */
+    _getDataForChromosome(interval: any, bigWigObj: any, zoomLevel: number): Promise<any[]>;
+}
+export default BigSourceWorker;

package/dist/getRemoteData/BigSourceWorkerGmod.d.ts

@@ -1,20 +1,29 @@
-export declare function resolveUriLocation(location: any): any;
+import { BigWig } from "@gmod/bbi";
 declare class BigSourceWorkerGmod {
     url: any;
-    bw: any;
+    private chromNamingCache;
+    bw: BigWig;
+    useEnsemblStyle: null | boolean;
     /**
      *
      * @param {string} url - the URL from which to fetch data
      */
     constructor(url: any);
     /**
-     * Creates a new BigWig instance (no caching between requests)
+     * Recreates the BigWig instance to clear any cached data
      */
+    private recreateBigWigInstance;
     /**
-     * Detects if the BigWig file uses Ensembl chromosome naming convention
+     * Detects if the BigWig file uses Ensembl
      * @return {Promise<boolean>} True if Ensembl naming (1, 2, 3...), false if UCSC naming (chr1, chr2, chr3...)
      */
     detectChromosomeNaming(): Promise<boolean>;
+    /**
+     * Fetches features from BigWig/BigBed file for the given loci
+     * @param {ChromosomeInterval[]} loci - locations for which to fetch data
+     * @return {Promise<DASFeature[]>} a Promise for the data
+     */
+    private fetchSource;
     /**
      * Gets BigWig or BigBed features inside the requested locations.
      *
@@ -23,6 +32,6 @@ declare class BigSourceWorkerGmod {
      * @return {Promise<DASFeature[]>} a Promise for the data
      * @override
      */
-    getData(loci: any, basesPerPixel: any, options: any): Promise<any[]>;
+    getData: (loci: any, basesPerPixel: any, options: any) => Promise<any[]>;
 }
 export default BigSourceWorkerGmod;

package/dist/getRemoteData/VcfSource.d.ts

@@ -3,7 +3,16 @@ declare class VcfSource {
     header: any;
     vcf: TabixIndexedFile;
     parser: any;
+    url: any;
+    indexUrl: any;
     constructor(url: any, indexUrl?: null);
+    /**
+     * Fetches data from VCF file for the given regions
+     * @param {ChromosomeInterval[]} region - locations for which to fetch data
+     * @param {any} options - fetch options including ensemblStyle
+     * @return {Promise<any[]>} a Promise for the data
+     */
+    private fetchSource;
     getData(region: any, basesPerPixel: any, options: any): Promise<any[]>;
     _getDataInLocus(locus: any, options: any): Promise<any>;
 }

package/dist/getRemoteData/hicSource.d.ts

@@ -2,7 +2,7 @@ import { NormalizationMode } from "./HicDataModes";
 /**
  * Data source that fetches data from .hic files.
  *
- * @author Silas Hsu
+ * @author Chanrung(Chad) Seng, Silas Hsu
  */
 export declare class HicSource {
     currentBinSize: number;

package/dist/getRemoteData/io/remoteFile.d.ts

@@ -2,6 +2,6 @@ declare class RemoteFile {
     config: any;
     url: any;
     constructor(args: any);
-    read(position: any, length: any): Promise<any>;
+    read(position: any, length: any): Promise<ArrayBuffer>;
 }
 export default RemoteFile;

package/dist/getRemoteData/tabixSource.d.ts

@@ -10,6 +10,8 @@ declare class TabixSource {
     indexUrl?: any;
     dataLimit: number;
     tabix: TabixIndexedFile;
+    private chromNamingCache;
+    useEnsemblStyle: null | boolean;
     /**
      * Prepares to fetch data from a bed file located at the input url.  Assumes the index is located at the same url,
      * plus a file extension of ".tbi".  This method will request and store the tabix index from this url immediately.
@@ -17,6 +19,22 @@ declare class TabixSource {
      * @param {string} url - the url of the bed-like file to fetch.
      */
     constructor(url: any, indexUrl?: null, dataLimit?: number);
+    /**
+     * Recreates the Tabix instance to clear any cached data
+     */
+    private recreateTabixInstance;
+    /**
+     * Detects if the Tabix file uses Ensembl
+     * @return {Promise<boolean>} True if Ensembl naming (1, 2, 3...), false if UCSC naming (chr1, chr2, chr3...)
+     */
+    detectChromosomeNaming(): Promise<boolean>;
+    /**
+     * Fetches data from Tabix file for the given loci
+     * @param {ChromosomeInterval[]} loci - locations for which to fetch data
+     * @param {any} options - fetch options including ensemblStyle
+     * @return {Promise<BedRecord[]>} a Promise for the data
+     */
+    private fetchSource;
     /**
      * Gets data for a list of chromosome intervals.
      *

package/dist/getRemoteData/vendor/bbi-js/main/bigwig.d.ts

@@ -0,0 +1 @@
+export function makeBwg(data: any, callback: any, name: any): void;

package/dist/getRemoteData/vendor/bbi-js/utils/bin.d.ts

@@ -0,0 +1,20 @@
+export function BlobFetchable(b: any): void;
+export class BlobFetchable {
+    constructor(b: any);
+    blob: any;
+    slice(start: any, length: any): BlobFetchable;
+    salted(): BlobFetchable;
+    fetch(callback: any): void;
+}
+export function URLFetchable(url: any, start: any, end: any, opts: any): void;
+export class URLFetchable {
+    constructor(url: any, start: any, end: any, opts: any);
+    url: any;
+    start: any;
+    end: any;
+    opts: any;
+    slice(s: any, l: any): URLFetchable;
+    fetchAsText(callback: any): any;
+    salted(): URLFetchable;
+    fetch(callback: any, opts: any): any;
+}

package/dist/getRemoteData/vendor/bbi-js/utils/das.d.ts

@@ -0,0 +1,6 @@
+export function DASFeature(): void;
+export function DASGroup(id: any): void;
+export class DASGroup {
+    constructor(id: any);
+    id: any;
+}

package/dist/getRemoteData/vendor/bbi-js/utils/jszlib.d.ts

@@ -0,0 +1 @@
+export function jszlib_inflate_buffer(buffer: any, start: any, length: any, afterUncOffset: any): ArrayBufferLike;

package/dist/getRemoteData/vendor/bbi-js/utils/sha1.d.ts

@@ -0,0 +1 @@
+export function b64_sha1(s: any): string;

package/dist/getRemoteData/vendor/bbi-js/utils/spans.d.ts

@@ -0,0 +1,13 @@
+export function Range(min: any, max: any): void;
+export class Range {
+    constructor(min: any, max: any);
+    _min: number;
+    _max: number;
+    min(): number;
+    max(): number;
+    contains(pos: any): boolean;
+    isContiguous(): boolean;
+    ranges(): Range[];
+    _pushRanges(ranges: any): void;
+    toString(): string;
+}