@jbrowse/core 3.7.0 → 4.0.0

package/util/color/cssColorsLevel4.js

@@ -1,160 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.namedColorToHex = namedColorToHex;
-exports.isNamedColor = isNamedColor;
-const colors = {
-    aliceblue: '#F0F8FF',
-    antiquewhite: '#FAEBD7',
-    aqua: '#00FFFF',
-    aquamarine: '#7FFFD4',
-    azure: '#F0FFFF',
-    beige: '#F5F5DC',
-    bisque: '#FFE4C4',
-    black: '#000000',
-    blanchedalmond: '#FFEBCD',
-    blue: '#0000FF',
-    blueviolet: '#8A2BE2',
-    brown: '#A52A2A',
-    burlywood: '#DEB887',
-    cadetblue: '#5F9EA0',
-    chartreuse: '#7FFF00',
-    chocolate: '#D2691E',
-    coral: '#FF7F50',
-    cornflowerblue: '#6495ED',
-    cornsilk: '#FFF8DC',
-    crimson: '#DC143C',
-    cyan: '#00FFFF',
-    darkblue: '#00008B',
-    darkcyan: '#008B8B',
-    darkgoldenrod: '#B8860B',
-    darkgray: '#A9A9A9',
-    darkgreen: '#006400',
-    darkgrey: '#A9A9A9',
-    darkkhaki: '#BDB76B',
-    darkmagenta: '#8B008B',
-    darkolivegreen: '#556B2F',
-    darkorange: '#FF8C00',
-    darkorchid: '#9932CC',
-    darkred: '#8B0000',
-    darksalmon: '#E9967A',
-    darkseagreen: '#8FBC8F',
-    darkslateblue: '#483D8B',
-    darkslategray: '#2F4F4F',
-    darkslategrey: '#2F4F4F',
-    darkturquoise: '#00CED1',
-    darkviolet: '#9400D3',
-    deeppink: '#FF1493',
-    deepskyblue: '#00BFFF',
-    dimgray: '#696969',
-    dimgrey: '#696969',
-    dodgerblue: '#1E90FF',
-    firebrick: '#B22222',
-    floralwhite: '#FFFAF0',
-    forestgreen: '#228B22',
-    fuchsia: '#FF00FF',
-    gainsboro: '#DCDCDC',
-    ghostwhite: '#F8F8FF',
-    gold: '#FFD700',
-    goldenrod: '#DAA520',
-    gray: '#808080',
-    green: '#008000',
-    greenyellow: '#ADFF2F',
-    grey: '#808080',
-    honeydew: '#F0FFF0',
-    hotpink: '#FF69B4',
-    indianred: '#CD5C5C',
-    indigo: '#4B0082',
-    ivory: '#FFFFF0',
-    khaki: '#F0E68C',
-    lavender: '#E6E6FA',
-    lavenderblush: '#FFF0F5',
-    lawngreen: '#7CFC00',
-    lemonchiffon: '#FFFACD',
-    lightblue: '#ADD8E6',
-    lightcoral: '#F08080',
-    lightcyan: '#E0FFFF',
-    lightgoldenrodyellow: '#FAFAD2',
-    lightgray: '#D3D3D3',
-    lightgreen: '#90EE90',
-    lightgrey: '#D3D3D3',
-    lightpink: '#FFB6C1',
-    lightsalmon: '#FFA07A',
-    lightseagreen: '#20B2AA',
-    lightskyblue: '#87CEFA',
-    lightslategray: '#778899',
-    lightslategrey: '#778899',
-    lightsteelblue: '#B0C4DE',
-    lightyellow: '#FFFFE0',
-    lime: '#00FF00',
-    limegreen: '#32CD32',
-    linen: '#FAF0E6',
-    magenta: '#FF00FF',
-    maroon: '#800000',
-    mediumaquamarine: '#66CDAA',
-    mediumblue: '#0000CD',
-    mediumorchid: '#BA55D3',
-    mediumpurple: '#9370DB',
-    mediumseagreen: '#3CB371',
-    mediumslateblue: '#7B68EE',
-    mediumspringgreen: '#00FA9A',
-    mediumturquoise: '#48D1CC',
-    mediumvioletred: '#C71585',
-    midnightblue: '#191970',
-    mintcream: '#F5FFFA',
-    mistyrose: '#FFE4E1',
-    moccasin: '#FFE4B5',
-    navajowhite: '#FFDEAD',
-    navy: '#000080',
-    oldlace: '#FDF5E6',
-    olive: '#808000',
-    olivedrab: '#6B8E23',
-    orange: '#FFA500',
-    orangered: '#FF4500',
-    orchid: '#DA70D6',
-    palegoldenrod: '#EEE8AA',
-    palegreen: '#98FB98',
-    paleturquoise: '#AFEEEE',
-    palevioletred: '#DB7093',
-    papayawhip: '#FFEFD5',
-    peachpuff: '#FFDAB9',
-    peru: '#CD853F',
-    pink: '#FFC0CB',
-    plum: '#DDA0DD',
-    powderblue: '#B0E0E6',
-    purple: '#800080',
-    rebeccapurple: '#663399',
-    red: '#FF0000',
-    rosybrown: '#BC8F8F',
-    royalblue: '#4169E1',
-    saddlebrown: '#8B4513',
-    salmon: '#FA8072',
-    sandybrown: '#F4A460',
-    seagreen: '#2E8B57',
-    seashell: '#FFF5EE',
-    sienna: '#A0522D',
-    silver: '#C0C0C0',
-    skyblue: '#87CEEB',
-    slateblue: '#6A5ACD',
-    slategray: '#708090',
-    slategrey: '#708090',
-    snow: '#FFFAFA',
-    springgreen: '#00FF7F',
-    steelblue: '#4682B4',
-    tan: '#D2B48C',
-    teal: '#008080',
-    thistle: '#D8BFD8',
-    tomato: '#FF6347',
-    turquoise: '#40E0D0',
-    violet: '#EE82EE',
-    wheat: '#F5DEB3',
-    white: '#FFFFFF',
-    whitesmoke: '#F5F5F5',
-    yellow: '#FFFF00',
-    yellowgreen: '#9ACD32',
-};
-function namedColorToHex(name) {
-    return colors[name];
-}
-function isNamedColor(name) {
-    return !!colors[name];
-}

package/util/color/index.d.ts

@@ -1,5 +0,0 @@
-export declare function contrastingTextColor(color: string): string;
-export declare function emphasize(color: string, coefficient?: number): string;
-export declare function makeContrasting(foreground: string, background?: string, minContrastRatio?: number): string;
-export { isNamedColor, namedColorToHex } from './cssColorsLevel4';
-export declare function randomColor(str: string): string;

package/util/color/index.js

@@ -1,48 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.namedColorToHex = exports.isNamedColor = void 0;
-exports.contrastingTextColor = contrastingTextColor;
-exports.emphasize = emphasize;
-exports.makeContrasting = makeContrasting;
-exports.randomColor = randomColor;
-const styles_1 = require("@mui/material/styles");
-const cssColorsLevel4_1 = require("./cssColorsLevel4");
-function contrastingTextColor(color) {
-    const luminance = getLuminance(color);
-    return luminance > 0.5 ? 'black' : 'white';
-}
-function getLuminance(color) {
-    const convertedColor = (0, cssColorsLevel4_1.namedColorToHex)(color);
-    return (0, styles_1.getLuminance)(convertedColor || color);
-}
-function emphasize(color, coefficient = 0.15) {
-    const convertedColor = (0, cssColorsLevel4_1.namedColorToHex)(color);
-    return (0, styles_1.emphasize)(convertedColor || color, coefficient);
-}
-function makeContrasting(foreground, background = 'white', minContrastRatio = 3) {
-    let convertedForeground = (0, cssColorsLevel4_1.namedColorToHex)(foreground) || foreground;
-    const convertedBackground = (0, cssColorsLevel4_1.namedColorToHex)(background) || background;
-    const backgroundLuminance = getLuminance(convertedBackground);
-    let contrastRatio = (0, styles_1.getContrastRatio)(convertedForeground, convertedBackground);
-    const originalColor = convertedForeground;
-    let coefficient = 0.05;
-    while (contrastRatio < minContrastRatio) {
-        convertedForeground =
-            backgroundLuminance > 0.5
-                ? (0, styles_1.darken)(originalColor, coefficient)
-                : (0, styles_1.lighten)(originalColor, coefficient);
-        coefficient += 0.05;
-        contrastRatio = (0, styles_1.getContrastRatio)(convertedForeground, convertedBackground);
-    }
-    return convertedForeground;
-}
-var cssColorsLevel4_2 = require("./cssColorsLevel4");
-Object.defineProperty(exports, "isNamedColor", { enumerable: true, get: function () { return cssColorsLevel4_2.isNamedColor; } });
-Object.defineProperty(exports, "namedColorToHex", { enumerable: true, get: function () { return cssColorsLevel4_2.namedColorToHex; } });
-function randomColor(str) {
-    let sum = 0;
-    for (let i = 0; i < str.length; i++) {
-        sum += str.charCodeAt(i);
-    }
-    return `hsl(${sum * 10}, 50%, 50%)`;
-}

package/util/colord.d.ts

@@ -1 +0,0 @@
-export { Colord, colord } from 'colord';

package/util/colord.js

@@ -1,13 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.colord = exports.Colord = void 0;
-const colord_1 = require("colord");
-const mix_1 = __importDefault(require("colord/plugins/mix"));
-const names_1 = __importDefault(require("colord/plugins/names"));
-(0, colord_1.extend)([mix_1.default, names_1.default]);
-var colord_2 = require("colord");
-Object.defineProperty(exports, "Colord", { enumerable: true, get: function () { return colord_2.Colord; } });
-Object.defineProperty(exports, "colord", { enumerable: true, get: function () { return colord_2.colord; } });

package/util/compositeMap.js

@@ -1,61 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-class CompositeMap {
-    constructor(submaps) {
-        this.submaps = submaps;
-    }
-    has(id) {
-        for (const submap of this.submaps.values()) {
-            if (submap.has(id)) {
-                return true;
-            }
-        }
-        return false;
-    }
-    get(id) {
-        for (const submap of this.submaps.values()) {
-            if (submap.has(id)) {
-                return submap.get(id);
-            }
-        }
-        return undefined;
-    }
-    *values() {
-        for (const key of this.keys()) {
-            yield this.get(key);
-        }
-    }
-    *keys() {
-        const keys = new Set();
-        for (const submap of this.submaps.values()) {
-            for (const key of submap.keys()) {
-                keys.add(key);
-            }
-        }
-        for (const key of keys) {
-            yield key;
-        }
-    }
-    find(f) {
-        for (const submap of this.submaps.values()) {
-            for (const value of submap.values()) {
-                const found = f(value);
-                if (found) {
-                    return value;
-                }
-            }
-        }
-        return undefined;
-    }
-    *[Symbol.iterator]() {
-        for (const key of this.keys()) {
-            yield [key, this.get(key)];
-        }
-    }
-    *entries() {
-        for (const k of this.keys()) {
-            yield [k, this.get(k)];
-        }
-    }
-}
-exports.default = CompositeMap;

package/util/convertCodingSequenceToPeptides.d.ts

@@ -1,6 +0,0 @@
-import type { Feat } from '../BaseFeatureWidget/util';
-export declare function convertCodingSequenceToPeptides({ cds, sequence, codonTable, }: {
-    cds: Feat[];
-    sequence: string;
-    codonTable: Record<string, string>;
-}): string;

package/util/convertCodingSequenceToPeptides.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.convertCodingSequenceToPeptides = convertCodingSequenceToPeptides;
-const util_1 = require("../BaseFeatureWidget/util");
-function convertCodingSequenceToPeptides({ cds, sequence, codonTable, }) {
-    const str = (0, util_1.stitch)(cds, sequence);
-    let protein = '';
-    for (let i = 0; i < str.length; i += 3) {
-        protein += codonTable[str.slice(i, i + 3)] || '&';
-    }
-    return protein;
-}

package/util/dedupe.js

@@ -1,15 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.dedupe = dedupe;
-function dedupe(list, hasher = JSON.stringify) {
-    const clone = [];
-    const lookup = new Set();
-    for (const entry of list) {
-        const hashed = hasher(entry);
-        if (!lookup.has(hashed)) {
-            clone.push(entry);
-            lookup.add(hashed);
-        }
-    }
-    return clone;
-}

package/util/fetchSeq.d.ts

@@ -1,8 +0,0 @@
-import type { AbstractSessionModel } from './types';
-export declare function fetchSeq({ start, end, refName, assemblyName, session, }: {
-    start: number;
-    end: number;
-    refName: string;
-    assemblyName: string;
-    session: AbstractSessionModel;
-}): Promise<string>;

package/util/fetchSeq.js

@@ -1,27 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fetchSeq = fetchSeq;
-const configuration_1 = require("../configuration");
-async function fetchSeq({ start, end, refName, assemblyName, session, }) {
-    const { rpcManager, assemblyManager } = session;
-    const assembly = await assemblyManager.waitForAssembly(assemblyName);
-    if (!assembly) {
-        throw new Error('assembly not found');
-    }
-    const sessionId = 'getSequence';
-    const canonicalRefName = assembly.getCanonicalRefName(refName);
-    const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
-        adapterConfig: (0, configuration_1.getConf)(assembly, ['sequence', 'adapter']),
-        sessionId,
-        regions: [
-            {
-                start,
-                end,
-                refName: canonicalRefName,
-                assemblyName,
-            },
-        ],
-    });
-    const [feat] = feats;
-    return (feat === null || feat === void 0 ? void 0 : feat.get('seq')) || '';
-}

package/util/flatbush/index.d.ts

@@ -1,25 +0,0 @@
-export default class Flatbush {
-    static from(data: ArrayBufferLike, byteOffset?: number): Flatbush;
-    constructor(numItems: number, nodeSize?: number, ArrayType?: TypedArrayConstructor, ArrayBufferType?: ArrayBufferConstructor | SharedArrayBufferConstructor, data?: ArrayBufferLike, byteOffset?: number);
-    numItems: number;
-    nodeSize: number;
-    byteOffset: number;
-    _levelBounds: number[];
-    ArrayType: TypedArrayConstructor;
-    IndexArrayType: Uint16ArrayConstructor | Uint32ArrayConstructor;
-    data: ArrayBufferLike;
-    _boxes: Int8Array<ArrayBuffer> | Float64Array<ArrayBuffer> | Uint8Array<ArrayBuffer> | Uint8ClampedArray<ArrayBuffer> | Int16Array<ArrayBuffer> | Uint16Array<ArrayBuffer> | Int32Array<ArrayBuffer> | Uint32Array<ArrayBuffer> | Float32Array<ArrayBuffer>;
-    _indices: Uint16Array<ArrayBuffer> | Uint32Array<ArrayBuffer>;
-    _pos: number;
-    minX: number | undefined;
-    minY: number | undefined;
-    maxX: number | undefined;
-    maxY: number | undefined;
-    _queue: FlatQueue<number>;
-    add(minX: number, minY: number, maxX?: number, maxY?: number): number;
-    finish(): void;
-    search(minX: number, minY: number, maxX: number, maxY: number, filterFn?: (index: number, x0: number, y0: number, x1: number, y1: number) => boolean): number[];
-    neighbors(x: number, y: number, maxResults?: number, maxDistance?: number, filterFn?: (index: number) => boolean): number[];
-}
-export type TypedArrayConstructor = Int8ArrayConstructor | Uint8ArrayConstructor | Uint8ClampedArrayConstructor | Int16ArrayConstructor | Uint16ArrayConstructor | Int32ArrayConstructor | Uint32ArrayConstructor | Float32ArrayConstructor | Float64ArrayConstructor;
-import FlatQueue from '../flatqueue';