gosling.js 1.0.5 → 2.0.0-alpha.2

package/dist/src/core/init.d.ts

@@ -1,5 +0,0 @@
-/**
- * Register plugin tracks and data fetchers to HiGlass. This is necessary for the first time before using Gosling.js.
- */
-export declare function init(): void;
-//# sourceMappingURL=init.d.ts.map

package/dist/src/core/init.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../src/core/init.ts"],"names":[],"mappings":"AAYA;;GAEG;AACH,wBAAgB,IAAI,SAsEnB"}

package/dist/src/core/utils/higlass-zoom-config.d.ts

@@ -1,6 +0,0 @@
-import type { HiGlassSpec } from '@gosling-lang/higlass-schema';
-/**
- * This makes sure that all the current zooming status is preserved when new tracks are added
- */
-export declare const preverseZoomStatus: (newSpec: HiGlassSpec, prevSpec: HiGlassSpec) => void;
-//# sourceMappingURL=higlass-zoom-config.d.ts.map

package/dist/src/core/utils/higlass-zoom-config.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"higlass-zoom-config.d.ts","sourceRoot":"","sources":["../../../../src/core/utils/higlass-zoom-config.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,8BAA8B,CAAC;AAEhE;;GAEG;AACH,eAAO,MAAM,kBAAkB,YAAa,WAAW,YAAY,WAAW,SAmB7E,CAAC"}

package/dist/src/core/utils/linking.d.ts

@@ -1,12 +0,0 @@
-import type { HiGlassModel } from '../../compiler/higlass-model';
-/**
- *
- */
-export declare function getLinkingInfo(hgModel: HiGlassModel): {
-    layout: 'circular' | 'linear';
-    hgViewId: string;
-    linkId: string;
-    isBrush: boolean;
-    style: any;
-}[];
-//# sourceMappingURL=linking.d.ts.map

package/dist/src/core/utils/linking.d.ts.map

@@ -1 +0,0 @@
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package/dist/src/exported-compiler.d.ts

@@ -1,2 +0,0 @@
-export { compile as _compile } from './compiler/compile';
-//# sourceMappingURL=exported-compiler.d.ts.map

package/dist/src/exported-compiler.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"exported-compiler.d.ts","sourceRoot":"","sources":["../../src/exported-compiler.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,QAAQ,EAAE,MAAM,oBAAoB,CAAC"}

package/dist/src/higlass-schema/higlass.schema.d.ts

@@ -1,148 +0,0 @@
-import type { Assembly, FilterTransform } from '@gosling-lang/gosling-schema';
-export interface HiGlassSpec {
-    editable?: boolean;
-    zoomFixed?: boolean;
-    viewEditable?: boolean;
-    tracksEditable?: boolean;
-    compactLayout?: boolean;
-    trackSourceServers?: string[];
-    exportViewUrl?: string;
-    chromInfoPath?: string;
-    views: View[];
-    zoomLocks: GenericLocks;
-    locationLocks: GenericLocks;
-    valueScaleLocks?: ValueScaleLocks;
-}
-export interface View {
-    uid?: string;
-    initialXDomain?: number[];
-    initialYDomain?: number[];
-    zoomLimits?: [number | null, number | null];
-    autocompleteSource?: string;
-    genomePositionSearchBox?: GenomePositionSearchBox;
-    genomePositionSearchBoxVisible?: boolean;
-    chromInfoPath?: string;
-    tracks: Tracks;
-    layout: Layout;
-    overlays?: Overlay[];
-    selectionView?: boolean;
-    zoomFixed?: boolean;
-}
-export interface GenomePositionSearchBox {
-    chromInfoId: string;
-    chromInfoServer: string;
-    autocompleteId?: string;
-    autocompleteServer?: string;
-    visible?: boolean;
-}
-export interface Tracks {
-    top: Track[];
-    left: Track[];
-    center: Track[];
-    right: Track[];
-    bottom: Track[];
-    gallery: Track[];
-    whole: Track[];
-}
-export type Track = HeatmapTrack | CombinedTrack | IndependentViewportProjectionTrack | EnumTrack;
-export interface HeatmapTrack {
-    type: 'heatmap';
-    uid?: string;
-    data?: Data;
-    server?: string;
-    tilesetUid?: string;
-    position?: string;
-    width?: number;
-    height?: number;
-    options?: any;
-}
-export interface CombinedTrack {
-    type: 'combined';
-    contents: Track[];
-    uid?: string;
-    width?: number;
-    height?: number;
-    position?: string;
-    options?: any;
-}
-export interface IndependentViewportProjectionTrack {
-    type: 'viewport-projection-horizontal' | 'viewport-projection-vertical' | 'viewport-projection-center';
-    uid?: string;
-    fromViewUid?: null;
-    projectionXDomain?: number[];
-    projectionYDomain?: number[];
-    transforms?: any[];
-    width?: number;
-    x?: number;
-    y?: number;
-    options?: any;
-}
-export interface EnumTrack {
-    type: EnumTrackType;
-    uid?: string;
-    server?: string;
-    tilesetUid?: string;
-    chromInfoPath?: string;
-    data?: Data;
-    fromViewUid?: null | string;
-    width?: number;
-    height?: number;
-    x?: number;
-    y?: number;
-    options?: any;
-}
-export interface Data {
-    type?: string;
-    children?: any[];
-    tiles?: any;
-    tilesetInfo?: any;
-    url?: string;
-    assembly?: Assembly;
-    urlFetchOptions?: RequestInit;
-    indexUrl?: string;
-    indexUrlFetchOptions?: RequestInit;
-    filter?: FilterTransform[];
-}
-export interface RequestInit {
-    headers?: Record<string, any>;
-}
-export interface Overlay {
-    uid?: string;
-    type?: string;
-    chromInfoPath?: string;
-    includes?: any[];
-    options?: OverlayOptions;
-}
-export interface OverlayOptions {
-    extent?: any[];
-    fill?: string;
-    fillOpacity?: number;
-    minWidth?: number;
-    outline?: string;
-    outlineOpacity?: number;
-    outlinePos?: any[] | string;
-    outlineWidth?: number;
-    stroke?: string;
-    strokeOpacity?: number;
-    strokePos?: any[] | string;
-    strokeWidth?: number;
-}
-export interface Layout {
-    h: number;
-    w: number;
-    x: number;
-    y: number;
-}
-export interface GenericLocks {
-    locksByViewUid: LocksByViewUid;
-    locksDict: any;
-}
-export interface LocksByViewUid {
-    [k: string]: string;
-}
-export interface ValueScaleLocks {
-    locksByViewUid: LocksByViewUid;
-    locksDict?: any;
-}
-export type EnumTrackType = 'heatmap' | '2d-annotations' | '2d-chromosome-annotations' | '2d-chromosome-grid' | '2d-chromosome-labels' | '2d-rectangle-domains' | '2d-tiles' | 'arrowhead-domains' | 'bedlike' | 'cross-rule' | 'dummy' | 'horizontal-1d-annotations' | 'horizontal-1d-heatmap' | 'horizontal-1d-tiles' | 'horizontal-1d-value-interval' | 'horizontal-2d-rectangle-domains' | 'horizontal-bar' | 'horizontal-chromosome-grid' | 'horizontal-chromosome-labels' | 'horizontal-divergent-bar' | 'horizontal-gene-annotations' | 'horizontal-heatmap' | 'horizontal-line' | 'horizontal-multivec' | 'horizontal-point' | 'horizontal-rule' | 'horizontal-vector-heatmap' | 'image-tiles' | 'left-axis' | 'left-stacked-interval' | 'mapbox-tiles' | 'osm-2d-tile-ids' | 'osm-tiles' | 'raster-tiles' | 'simple-svg' | 'square-markers' | 'top-axis' | 'top-stacked-interval' | 'vertical-1d-annotations' | 'vertical-1d-heatmap' | 'vertical-1d-tiles' | 'vertical-1d-value-interval' | 'vertical-2d-rectangle-domains' | 'vertical-bar' | 'vertical-bedlike' | 'vertical-chromosome-grid' | 'vertical-chromosome-labels' | 'vertical-gene-annotations' | 'vertical-heatmap' | 'vertical-line' | 'vertical-multivec' | 'vertical-point' | 'vertical-rule' | 'vertical-vector-heatmap' | 'viewport-projection-center' | 'viewport-projection-horizontal' | 'viewport-projection-vertical' | 'gosling-track' | 'gosling-2d-track' | 'axis-track' | 'text' | 'dummy-track';
-//# sourceMappingURL=higlass.schema.d.ts.map

package/dist/src/higlass-schema/higlass.schema.d.ts.map

@@ -1 +0,0 @@
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package/dist/src/higlass-schema/index.d.ts

@@ -1,3 +0,0 @@
-export * from './higlass.schema';
-export { default as HiGlassSchema } from './higlass.schema.json';
-//# sourceMappingURL=index.d.ts.map

package/dist/src/higlass-schema/index.d.ts.map

@@ -1 +0,0 @@
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package/dist/src/tracks/gosling-brush/brush-track.d.ts

@@ -1,26 +0,0 @@
-declare function BrushTrack(HGC: any, ...args: any[]): any;
-declare namespace BrushTrack {
-    var config: {
-        type: string;
-        datatype: string[];
-        local: boolean;
-        projection: boolean;
-        orientation: string;
-        thumbnail: HTMLElement;
-        availableOptions: string[];
-        defaultOptions: {
-            innerRadius: number;
-            outerRadius: number;
-            startAngle: number;
-            endAngle: number;
-            axisPositionHorizontal: string;
-            projectionFillColor: string;
-            projectionStrokeColor: string;
-            projectionFillOpacity: number;
-            projectionStrokeOpacity: number;
-            strokeWidth: number;
-        };
-    };
-}
-export default BrushTrack;
-//# sourceMappingURL=brush-track.d.ts.map

package/dist/src/tracks/gosling-brush/brush-track.d.ts.map

@@ -1 +0,0 @@
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package/dist/src/tracks/gosling-brush/index.d.ts

@@ -1,3 +0,0 @@
-export { default as BrushTrack } from './brush-track';
-export { LinearBrushModel } from './linear-brush-model';
-//# sourceMappingURL=index.d.ts.map

package/dist/src/tracks/gosling-brush/index.d.ts.map

@@ -1 +0,0 @@
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package/dist/src/tracks/gosling-brush/linear-brush-model.d.ts.map

@@ -1 +0,0 @@
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package/dist/src/tracks/gosling-genomic-axis/axis-track.d.ts

@@ -1,40 +0,0 @@
-/// <reference types="src/missing-types" />
-import type { TextStyle } from '../../core/utils/text-style';
-import type { Assembly } from '@gosling-lang/gosling-schema';
-type AxisTrackOptions = {
-    innerRadius: number;
-    outerRadius: number;
-    startAngle: number;
-    endAngle: number;
-    width: number;
-    height: number;
-    layout: 'linear' | 'circular';
-    labelMargin: number;
-    excludeChrPrefix: boolean;
-    labelPosition: string;
-    labelColor: string;
-    labelTextOpacity: number;
-    trackBorderWidth: number;
-    trackBorderColor: string;
-    tickPositions: 'even' | 'ends';
-    fontSize: number;
-    fontFamily: string;
-    fontWeight: NonNullable<TextStyle['fontWeight']>;
-    color: string;
-    stroke: string;
-    backgroundColor: string;
-    showMousePosition: boolean;
-    tickColor: number;
-    tickFormat?: string;
-    assembly?: Assembly;
-    reverseOrientation?: boolean;
-};
-declare const _default: (new (HGC: import("@higlass/types").HGC, context: import("@higlass/tracks").Context<never, AxisTrackOptions>, options: AxisTrackOptions) => import("@higlass/tracks").Track<AxisTrackOptions>) & {
-    config: import("@higlass/tracks").TrackConfig<AxisTrackOptions>;
-} & {
-    config: {
-        availableOptions: (keyof AxisTrackOptions)[];
-    };
-};
-export default _default;
-//# sourceMappingURL=axis-track.d.ts.map

package/dist/src/tracks/gosling-genomic-axis/axis-track.d.ts.map

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package/dist/src/tracks/gosling-genomic-axis/index.d.ts

@@ -1,3 +0,0 @@
-import AxisTrack from './axis-track';
-export { AxisTrack };
-//# sourceMappingURL=index.d.ts.map

package/dist/src/tracks/gosling-genomic-axis/index.d.ts.map

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package/dist/utils-DAef6RYs.js

@@ -1,85 +0,0 @@
-var __defProp = Object.defineProperty;
-var __defNormalProp = (obj, key, value) => key in obj ? __defProp(obj, key, { enumerable: true, configurable: true, writable: true, value }) : obj[key] = value;
-var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "symbol" ? key + "" : key, value);
-import { bisector } from "d3-array";
-import { RemoteFile as RemoteFile$1 } from "generic-filehandle";
-function filterUsingGenoPos(data, [minX, maxX], config) {
-  const { x, xe, x1, x1e } = config;
-  const definedXFields = [x, xe, x1, x1e].filter((f) => f);
-  return data.filter((d) => {
-    if (definedXFields.length === 0) {
-      return true;
-    } else if (definedXFields.length === 1) {
-      const value = +d[definedXFields[0]];
-      return typeof value === "number" && minX < value && value <= maxX;
-    } else {
-      const values = definedXFields.map((f) => +d[f]).filter((v) => !isNaN(v));
-      const minValue = Math.min(...values);
-      const maxValue = Math.max(...values);
-      return minX <= maxValue && minValue <= maxX;
-    }
-  });
-}
-bisector((d) => d.pos).left;
-function sanitizeChrName(chrName, assembly, chromosomePrefix) {
-  if (Array.isArray(assembly)) {
-    return chrName;
-  }
-  if (chromosomePrefix) {
-    chrName = chrName.replace(chromosomePrefix, "chr");
-  } else if (!chrName.includes("chr")) {
-    chrName = `chr${chrName}`;
-  }
-  return chrName;
-}
-class RemoteFile extends RemoteFile$1 {
-  constructor() {
-    super(...arguments);
-    // Overrides `read` to eagerly read 200 or 206 response
-    // from https://github.com/GMOD/generic-filehandle/blob/0e8209be25e3097307bd15e964edd8c017e808d7/src/remoteFile.ts#L100-L162
-    __publicField(this, "read", async (buffer, offset = 0, length, position = 0, opts = {}) => {
-      const { headers = {}, signal, overrides = {} } = opts;
-      if (length < Infinity) {
-        headers.range = `bytes=${position}-${position + length}`;
-      } else if (length === Infinity && position !== 0) {
-        headers.range = `bytes=${position}-`;
-      }
-      const args = {
-        // @ts-expect-error private property
-        ...this.baseOverrides,
-        ...overrides,
-        headers: {
-          ...headers,
-          ...overrides.headers,
-          // @ts-expect-error private property
-          ...this.baseOverrides.headers
-        },
-        method: "GET",
-        redirect: "follow",
-        mode: "cors",
-        signal
-      };
-      const response = await this.fetch(this.url, args);
-      if (!response.ok) {
-        throw new Error(`HTTP ${response.status} ${response.statusText} ${this.url}`);
-      }
-      if (response.status === 200 || response.status === 206) {
-        const responseData = await this.getBufferFromResponse(response);
-        const bytesCopied = responseData.copy(buffer, offset, 0, Math.min(length, responseData.length));
-        const res = response.headers.get("content-range");
-        const sizeMatch = /\/(\d+)$/.exec(res || "");
-        if (sizeMatch && sizeMatch[1]) {
-          this._stat = { size: parseInt(sizeMatch[1], 10) };
-        }
-        return { bytesRead: bytesCopied, buffer };
-      }
-      throw new Error(`HTTP ${response.status} fetching ${this.url}`);
-    });
-  }
-}
-export {
-  RemoteFile as R,
-  filterUsingGenoPos as f,
-  sanitizeChrName as s
-};
-//# sourceMappingURL=utils-DAef6RYs.js.map

package/dist/utils-DAef6RYs.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"utils-DAef6RYs.js","sources":["../src/data-fetchers/utils.ts"],"sourcesContent":["import { bisector } from 'd3-array';\nimport { RemoteFile as _RemoteFile } from 'generic-filehandle';\n\nimport type * as HiGlass from '@higlass/types';\nimport type { Assembly, ChromSizes, Datum } from '@gosling-lang/gosling-schema';\n\nexport type CommonDataConfig = {\n    assembly: Assembly;\n    x?: string;\n    xe?: string;\n    x1?: string;\n    x1e?: string;\n    urlFetchOptions?: RequestInit;\n};\n\nexport class DataSource<File, Options> {\n    chromInfo: ExtendedChromInfo;\n    tilesetInfo: ReturnType<typeof tilesetInfoFromChromInfo>;\n\n    constructor(public file: File, chromSizes: ChromSizes, public options: Options) {\n        this.chromInfo = sizesToChromInfo(chromSizes);\n        this.tilesetInfo = tilesetInfoFromChromInfo(this.chromInfo);\n    }\n}\n\n/**\n * Filter data before sending to a track considering the visible genomic area in the track.\n * TODO(2022-Jul-13): Consider genomic `y` channels as well.\n */\nexport function filterUsingGenoPos(\n    data: Datum[],\n    [minX, maxX]: [number, number],\n    config: Omit<CommonDataConfig, 'assembly'>\n) {\n    const { x, xe, x1, x1e } = config;\n    const definedXFields = [x, xe, x1, x1e].filter(f => f) as string[];\n    return data.filter((d: Datum) => {\n        if (definedXFields.length === 0) {\n            // no filter applies\n            return true;\n        } else if (definedXFields.length === 1) {\n            // filter based on one genomic position\n            const value = +d[definedXFields[0]];\n            return typeof value === 'number' && minX < value && value <= maxX;\n        } else {\n            // filter based on two genomic positions, i.e., check overlaps\n            const values = definedXFields.map(f => +d[f]).filter(v => !isNaN(v));\n            const minValue = Math.min(...values);\n            const maxValue = Math.max(...values);\n            return minX <= maxValue && minValue <= maxX;\n        }\n    });\n}\n\nconst chromInfoBisector = bisector((d: { pos: number }) => d.pos).left;\n\nconst chrToAbs = (chrom: string, chromPos: number, chromInfo: HiGlass.ChromInfo) =>\n    chromInfo.chrPositions[chrom].pos + chromPos;\n\nconst absToChr = (absPosition: number, chromInfo: HiGlass.ChromInfo) => {\n    if (!chromInfo || !chromInfo.cumPositions || !chromInfo.cumPositions.length) {\n        return null;\n    }\n\n    let insertPoint = chromInfoBisector(chromInfo.cumPositions, absPosition);\n    const lastChr = chromInfo.cumPositions[chromInfo.cumPositions.length - 1].chr;\n    const lastLength = chromInfo.chromLengths[lastChr];\n\n    // @ts-expect-error\n    insertPoint -= insertPoint > 0 && 1;\n\n    let chrPosition = Math.floor(absPosition - chromInfo.cumPositions[insertPoint].pos);\n    let offset = 0;\n\n    if (chrPosition < 0) {\n        // before the start of the genome\n        offset = chrPosition - 1;\n        chrPosition = 1;\n    }\n\n    if (insertPoint === chromInfo.cumPositions.length - 1 && chrPosition > lastLength) {\n        // beyond the last chromosome\n        offset = chrPosition - lastLength;\n        chrPosition = lastLength;\n    }\n\n    return [chromInfo.cumPositions[insertPoint].chr, chrPosition, offset, insertPoint] as const;\n};\n\n/**\n * Get a chromosome name for the consistentcy, e.g., `1` --> `chr1`.\n * @param chrName A chromosome name to be sanitized\n * @param assembly A genome assembly of the data\n * @param chromosomePrefix A prefix string that can be replaced to 'chr'\n * @returns\n */\nexport function sanitizeChrName(chrName: string, assembly: Assembly, chromosomePrefix?: string) {\n    if (Array.isArray(assembly)) {\n        // this is a custom assembly, so use this as is\n        return chrName;\n    }\n\n    // For assemblies in Gosling, we use the `chr` prefix consistently\n    if (chromosomePrefix) {\n        // `hs1` --> `chr1`\n        chrName = chrName.replace(chromosomePrefix, 'chr');\n    } else if (!chrName.includes('chr')) {\n        // `1` --> `chr1`\n        chrName = `chr${chrName}`;\n    }\n    return chrName;\n}\n\nexport type ExtendedChromInfo = HiGlass.ChromInfo & {\n    absToChr(absPos: number): ReturnType<typeof absToChr> | null;\n    chrToAbs(chr: [name: string, pos: number]): number | null;\n};\n\nexport function tilesetInfoFromChromInfo(chromInfo: ExtendedChromInfo, tileSize = 1024) {\n    return {\n        tile_size: tileSize,\n        bins_per_dimension: tileSize,\n        max_zoom: Math.ceil(Math.log(chromInfo.totalLength / tileSize) / Math.log(2)),\n        max_width: chromInfo.totalLength,\n        min_pos: [0],\n        max_pos: [chromInfo.totalLength]\n    };\n}\n\nexport function sizesToChromInfo(sizes: [string, number][]): ExtendedChromInfo {\n    const info: HiGlass.ChromInfo = {\n        cumPositions: [],\n        chromLengths: {},\n        chrPositions: {},\n        totalLength: 0\n    };\n\n    sizes.forEach(([chr, length], i) => {\n        const chrPosition = { id: i, chr, pos: info.totalLength };\n        info.chrPositions[chr] = chrPosition;\n        info.chromLengths[chr] = length;\n        info.cumPositions.push(chrPosition);\n        info.totalLength += length;\n    });\n\n    return {\n        ...info,\n        absToChr: absPos => (info.chrPositions ? absToChr(absPos, info) : null),\n        chrToAbs: ([chrName, chrPos]) => (info.chrPositions ? chrToAbs(chrName, chrPos, info) : null)\n    };\n}\n\nexport class RemoteFile extends _RemoteFile {\n    // Overrides `read` to eagerly read 200 or 206 response\n    // from https://github.com/GMOD/generic-filehandle/blob/0e8209be25e3097307bd15e964edd8c017e808d7/src/remoteFile.ts#L100-L162\n    public read: _RemoteFile['read'] = async (\n        buffer,\n        offset = 0,\n        length,\n        position = 0,\n        opts = {}\n    ): Promise<{ bytesRead: number; buffer: Buffer }> => {\n        const { headers = {}, signal, overrides = {} } = opts;\n\n        if (length < Infinity) {\n            headers.range = `bytes=${position}-${position + length}`;\n        } else if (length === Infinity && position !== 0) {\n            headers.range = `bytes=${position}-`;\n        }\n        const args = {\n            // @ts-expect-error private property\n            ...this.baseOverrides,\n            ...overrides,\n            headers: {\n                ...headers,\n                ...overrides.headers,\n                // @ts-expect-error private property\n                ...this.baseOverrides.headers\n            },\n            method: 'GET',\n            redirect: 'follow',\n            mode: 'cors',\n            signal\n        };\n        const response = await this.fetch(this.url, args);\n\n        if (!response.ok) {\n            throw new Error(`HTTP ${response.status} ${response.statusText} ${this.url}`);\n        }\n\n        // Just read the response if it was successful.\n        if (response.status === 200 || response.status === 206) {\n            // @ts-expect-error private method\n            const responseData = await this.getBufferFromResponse(response);\n            const bytesCopied = responseData.copy(buffer, offset, 0, Math.min(length, responseData.length));\n\n            // try to parse out the size of the remote file\n            const res = response.headers.get('content-range');\n            const sizeMatch = /\\/(\\d+)$/.exec(res || '');\n            if (sizeMatch && sizeMatch[1]) {\n                // @ts-expect-error private property\n                this._stat = { size: parseInt(sizeMatch[1], 10) };\n            }\n\n            return { bytesRead: bytesCopied, buffer };\n        }\n\n        // TODO: try harder here to gather more information about what the problem is\n        throw new Error(`HTTP ${response.status} fetching ${this.url}`);\n    };\n}\n\nexport interface TabularDataFetcher<Tile> {\n    getTabularData(tileIds: string[]): 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