molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-util/color/scale.js

@@ -1,84 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.ColorScale = exports.DefaultColorScaleProps = void 0;
-var tslib_1 = require("tslib");
-var color_1 = require("./color");
-var lists_1 = require("./lists");
-var mol_util_1 = require("../../mol-util");
-var legend_1 = require("../legend");
-var int_1 = require("../../mol-data/int");
-var interpolate_1 = require("../../mol-math/interpolate");
-exports.DefaultColorScaleProps = {
-    domain: [0, 1],
-    reverse: false,
-    listOrName: 'red-yellow-blue',
-    minLabel: '',
-    maxLabel: '',
-};
-var ColorScale;
-(function (ColorScale) {
-    function create(props) {
-        var _a = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultColorScaleProps), props), domain = _a.domain, reverse = _a.reverse, listOrName = _a.listOrName;
-        var list = typeof listOrName === 'string' ? (0, lists_1.getColorListFromName)(listOrName).list : listOrName;
-        var colors = reverse ? list.slice().reverse() : list;
-        var count1 = colors.length - 1;
-        var diff = 0, min = 0, max = 0;
-        function setDomain(_min, _max) {
-            min = _min;
-            max = _max;
-            diff = (max - min) || 1;
-        }
-        setDomain(domain[0], domain[1]);
-        var minLabel = (0, mol_util_1.defaults)(props.minLabel, min.toString());
-        var maxLabel = (0, mol_util_1.defaults)(props.maxLabel, max.toString());
-        var color;
-        var hasOffsets = colors.every(function (c) { return Array.isArray(c); });
-        if (hasOffsets) {
-            var sorted = (0, tslib_1.__spreadArray)([], colors, true);
-            sorted.sort(function (a, b) { return a[1] - b[1]; });
-            var src_1 = sorted.map(function (c) { return c[0]; });
-            var off_1 = int_1.SortedArray.ofSortedArray(sorted.map(function (c) { return c[1]; }));
-            var max_1 = src_1.length - 1;
-            color = function (v) {
-                var t = (0, interpolate_1.clamp)((v - min) / diff, 0, 1);
-                var i = int_1.SortedArray.findPredecessorIndex(off_1, t);
-                if (i === 0) {
-                    return src_1[min];
-                }
-                else if (i > max_1) {
-                    return src_1[max_1];
-                }
-                var o1 = off_1[i - 1], o2 = off_1[i];
-                var t1 = (0, interpolate_1.clamp)((t - o1) / (o2 - o1), 0, 1); // TODO: cache the deltas?
-                return color_1.Color.interpolate(src_1[i - 1], src_1[i], t1);
-            };
-        }
-        else {
-            color = function (value) {
-                var t = Math.min(colors.length - 1, Math.max(0, ((value - min) / diff) * count1));
-                var tf = Math.floor(t);
-                var c1 = colors[tf];
-                var c2 = colors[Math.ceil(t)];
-                return color_1.Color.interpolate(c1, c2, t - tf);
-            };
-        }
-        return {
-            color: color,
-            colorToArray: function (value, array, offset) {
-                color_1.Color.toArray(color(value), array, offset);
-            },
-            normalizedColorToArray: function (value, array, offset) {
-                color_1.Color.toArrayNormalized(color(value), array, offset);
-            },
-            setDomain: setDomain,
-            get legend() { return (0, legend_1.ScaleLegend)(minLabel, maxLabel, colors); }
-        };
-    }
-    ColorScale.create = create;
-})(ColorScale = exports.ColorScale || (exports.ColorScale = {}));
-//# sourceMappingURL=scale.js.map

package/lib/commonjs/mol-util/color/spaces/hcl.d.ts

@@ -1,46 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- *
- * Color conversion code adapted from chroma.js (https://github.com/gka/chroma.js)
- * Copyright (c) 2011-2018, Gregor Aisch, BSD license
- */
-import { Color } from '../color';
-import { Lab } from './lab';
-export { Hcl };
-interface Hcl extends Array<number> {
-    [d: number]: number;
-    '@type': 'hcl';
-    length: 3;
-}
-/**
- * CIE HCL (Hue-Chroma-Luminance) color
- *
- * - H [0..360]
- * - C [0..100]
- * - L [0..100]
- *
- * Cylindrical representation of CIELUV (see https://en.wikipedia.org/wiki/CIELUV)
- */
-declare function Hcl(): Hcl;
-declare namespace Hcl {
-    function zero(): Hcl;
-    function create(h: number, c: number, l: number): Hcl;
-    function fromColor(out: Hcl, color: Color): Hcl;
-    function fromLab(hcl: Hcl, lab: Lab): Hcl;
-    function toColor(hcl: Hcl): Color;
-    /**
-     * Convert from a qualitative parameter h and a quantitative parameter l to a 24-bit pixel.
-     *
-     * These formulas were invented by David Dalrymple to obtain maximum contrast without going
-     * out of gamut if the parameters are in the range 0-1.
-     * A saturation multiplier was added by Gregor Aisch
-     */
-    function toLab(out: Lab, hcl: Hcl): Lab;
-    function copy(out: Hcl, c: Hcl): Hcl;
-    function saturate(out: Hcl, c: Hcl, amount: number): Hcl;
-    function desaturate(out: Hcl, c: Hcl, amount: number): Hcl;
-    function darken(out: Hcl, c: Hcl, amount: number): Hcl;
-    function lighten(out: Hcl, c: Hcl, amount: number): Hcl;
-}

package/lib/commonjs/mol-util/color/spaces/hcl.js

@@ -1,106 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- *
- * Color conversion code adapted from chroma.js (https://github.com/gka/chroma.js)
- * Copyright (c) 2011-2018, Gregor Aisch, BSD license
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.Hcl = void 0;
-var misc_1 = require("../../../mol-math/misc");
-var lab_1 = require("./lab");
-/**
- * CIE HCL (Hue-Chroma-Luminance) color
- *
- * - H [0..360]
- * - C [0..100]
- * - L [0..100]
- *
- * Cylindrical representation of CIELUV (see https://en.wikipedia.org/wiki/CIELUV)
- */
-function Hcl() {
-    return Hcl.zero();
-}
-exports.Hcl = Hcl;
-(function (Hcl) {
-    function zero() {
-        var out = [0.1, 0.0, 0.0];
-        out[0] = 0;
-        return out;
-    }
-    Hcl.zero = zero;
-    function create(h, c, l) {
-        var out = zero();
-        out[0] = h;
-        out[1] = c;
-        out[2] = l;
-        return out;
-    }
-    Hcl.create = create;
-    var tmpFromColorLab = [0, 0, 0];
-    function fromColor(out, color) {
-        return lab_1.Lab.toHcl(out, lab_1.Lab.fromColor(tmpFromColorLab, color));
-    }
-    Hcl.fromColor = fromColor;
-    function fromLab(hcl, lab) {
-        return lab_1.Lab.toHcl(hcl, lab);
-    }
-    Hcl.fromLab = fromLab;
-    var tmpToColorLab = [0, 0, 0];
-    function toColor(hcl) {
-        return lab_1.Lab.toColor(toLab(tmpToColorLab, hcl));
-    }
-    Hcl.toColor = toColor;
-    /**
-     * Convert from a qualitative parameter h and a quantitative parameter l to a 24-bit pixel.
-     *
-     * These formulas were invented by David Dalrymple to obtain maximum contrast without going
-     * out of gamut if the parameters are in the range 0-1.
-     * A saturation multiplier was added by Gregor Aisch
-     */
-    function toLab(out, hcl) {
-        var h = hcl[0], c = hcl[1], l = hcl[2];
-        if (isNaN(h))
-            h = 0;
-        h = (0, misc_1.degToRad)(h);
-        out[0] = l;
-        out[1] = Math.cos(h) * c;
-        out[2] = Math.sin(h) * c;
-        return out;
-    }
-    Hcl.toLab = toLab;
-    function copy(out, c) {
-        out[0] = c[0];
-        out[1] = c[1];
-        out[2] = c[2];
-        return out;
-    }
-    Hcl.copy = copy;
-    function saturate(out, c, amount) {
-        out[0] = c[0];
-        out[1] = Math.max(0, c[1] + Kn * amount);
-        out[2] = c[2];
-        return out;
-    }
-    Hcl.saturate = saturate;
-    function desaturate(out, c, amount) {
-        return saturate(out, c, -amount);
-    }
-    Hcl.desaturate = desaturate;
-    var tmpDarkenLab = [0, 0, 0];
-    function darken(out, c, amount) {
-        toLab(tmpDarkenLab, c);
-        return lab_1.Lab.toHcl(out, lab_1.Lab.darken(tmpDarkenLab, tmpDarkenLab, amount));
-    }
-    Hcl.darken = darken;
-    function lighten(out, c, amount) {
-        return darken(out, c, -amount);
-    }
-    Hcl.lighten = lighten;
-    // Corresponds roughly to RGB brighter/darker
-    var Kn = 18;
-})(Hcl || (Hcl = {}));
-exports.Hcl = Hcl;
-//# sourceMappingURL=hcl.js.map

package/lib/commonjs/mol-util/color/spaces/lab.d.ts

@@ -1,39 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- *
- * Color conversion code adapted from chroma.js (https://github.com/gka/chroma.js)
- * Copyright (c) 2011-2018, Gregor Aisch, BSD license
- */
-import { Color } from '../color';
-import { Hcl } from './hcl';
-export { Lab };
-interface Lab extends Array<number> {
-    [d: number]: number;
-    '@type': 'lab';
-    length: 3;
-}
-/**
- * CIE LAB color
- *
- * - L* [0..100] - lightness from black to white
- * - a [-100..100] - green (-) to red (+)
- * - b [-100..100] - blue (-) to yellow (+)
- *
- * see https://en.wikipedia.org/wiki/CIELAB_color_space
- */
-declare function Lab(): Lab;
-declare namespace Lab {
-    function zero(): Lab;
-    function create(l: number, a: number, b: number): Lab;
-    function fromColor(out: Lab, color: Color): Lab;
-    function fromHcl(out: Lab, hcl: Hcl): Lab;
-    function toColor(lab: Lab): Color;
-    function toHcl(out: Hcl, lab: Lab): Hcl;
-    function copy(out: Lab, c: Lab): Lab;
-    function darken(out: Lab, c: Lab, amount: number): Lab;
-    function lighten(out: Lab, c: Lab, amount: number): Lab;
-    function saturate(out: Lab, c: Lab, amount: number): Lab;
-    function desaturate(out: Lab, c: Lab, amount: number): Lab;
-}

package/lib/commonjs/mol-util/color/spaces/lab.js

@@ -1,152 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- *
- * Color conversion code adapted from chroma.js (https://github.com/gka/chroma.js)
- * Copyright (c) 2011-2018, Gregor Aisch, BSD license
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.Lab = void 0;
-var color_1 = require("../color");
-var hcl_1 = require("./hcl");
-var misc_1 = require("../../../mol-math/misc");
-var interpolate_1 = require("../../../mol-math/interpolate");
-/**
- * CIE LAB color
- *
- * - L* [0..100] - lightness from black to white
- * - a [-100..100] - green (-) to red (+)
- * - b [-100..100] - blue (-) to yellow (+)
- *
- * see https://en.wikipedia.org/wiki/CIELAB_color_space
- */
-function Lab() {
-    return Lab.zero();
-}
-exports.Lab = Lab;
-(function (Lab) {
-    function zero() {
-        var out = [0.1, 0.0, 0.0];
-        out[0] = 0;
-        return out;
-    }
-    Lab.zero = zero;
-    function create(l, a, b) {
-        var out = zero();
-        out[0] = l;
-        out[1] = a;
-        out[2] = b;
-        return out;
-    }
-    Lab.create = create;
-    function fromColor(out, color) {
-        var _a = color_1.Color.toRgb(color), r = _a[0], g = _a[1], b = _a[2];
-        var _b = rgbToXyz(r, g, b), x = _b[0], y = _b[1], z = _b[2];
-        var l = 116 * y - 16;
-        out[0] = l < 0 ? 0 : l;
-        out[1] = 500 * (x - y);
-        out[2] = 200 * (y - z);
-        return out;
-    }
-    Lab.fromColor = fromColor;
-    function fromHcl(out, hcl) {
-        return hcl_1.Hcl.toLab(out, hcl);
-    }
-    Lab.fromHcl = fromHcl;
-    function toColor(lab) {
-        var y = (lab[0] + 16) / 116;
-        var x = isNaN(lab[1]) ? y : y + lab[1] / 500;
-        var z = isNaN(lab[2]) ? y : y - lab[2] / 200;
-        y = Yn * lab_xyz(y);
-        x = Xn * lab_xyz(x);
-        z = Zn * lab_xyz(z);
-        var r = xyz_rgb(3.2404542 * x - 1.5371385 * y - 0.4985314 * z); // D65 -> sRGB
-        var g = xyz_rgb(-0.9692660 * x + 1.8760108 * y + 0.0415560 * z);
-        var b = xyz_rgb(0.0556434 * x - 0.2040259 * y + 1.0572252 * z);
-        return color_1.Color.fromRgb(Math.round((0, interpolate_1.clamp)(r, 0, 255)), Math.round((0, interpolate_1.clamp)(g, 0, 255)), Math.round((0, interpolate_1.clamp)(b, 0, 255)));
-    }
-    Lab.toColor = toColor;
-    function toHcl(out, lab) {
-        var l = lab[0], a = lab[1], b = lab[2];
-        var c = Math.sqrt(a * a + b * b);
-        var h = ((0, misc_1.radToDeg)(Math.atan2(b, a)) + 360) % 360;
-        if (Math.round(c * 10000) === 0)
-            h = Number.NaN;
-        out[0] = h;
-        out[1] = c;
-        out[2] = l;
-        return out;
-    }
-    Lab.toHcl = toHcl;
-    function copy(out, c) {
-        out[0] = c[0];
-        out[1] = c[1];
-        out[2] = c[2];
-        return out;
-    }
-    Lab.copy = copy;
-    function darken(out, c, amount) {
-        out[0] = c[0] - Kn * amount;
-        out[1] = c[1];
-        out[2] = c[2];
-        return out;
-    }
-    Lab.darken = darken;
-    function lighten(out, c, amount) {
-        return darken(out, c, -amount);
-    }
-    Lab.lighten = lighten;
-    var tmpSaturateHcl = [0, 0, 0];
-    function saturate(out, c, amount) {
-        toHcl(tmpSaturateHcl, c);
-        return hcl_1.Hcl.toLab(out, hcl_1.Hcl.saturate(tmpSaturateHcl, tmpSaturateHcl, amount));
-    }
-    Lab.saturate = saturate;
-    function desaturate(out, c, amount) {
-        return saturate(out, c, -amount);
-    }
-    Lab.desaturate = desaturate;
-    // Corresponds roughly to RGB brighter/darker
-    var Kn = 18;
-    /** D65 standard referent */
-    var Xn = 0.950470;
-    var Yn = 1;
-    var Zn = 1.088830;
-    var T0 = 0.137931034; // 4 / 29
-    var T1 = 0.206896552; // 6 / 29
-    var T2 = 0.12841855; // 3 * t1 * t1
-    var T3 = 0.008856452; // t1 * t1 * t1
-    /** convert component from xyz to rgb */
-    function xyz_rgb(c) {
-        return 255 * (c <= 0.00304 ? 12.92 * c : 1.055 * Math.pow(c, 1 / 2.4) - 0.055);
-    }
-    /** convert component from lab to xyz */
-    function lab_xyz(t) {
-        return t > T1 ? t * t * t : T2 * (t - T0);
-    }
-    /** convert component from rgb to xyz */
-    function rgb_xyz(c) {
-        if ((c /= 255) <= 0.04045)
-            return c / 12.92;
-        return Math.pow((c + 0.055) / 1.055, 2.4);
-    }
-    /** convert component from xyz to lab */
-    function xyz_lab(t) {
-        if (t > T3)
-            return Math.pow(t, 1 / 3);
-        return t / T2 + T0;
-    }
-    function rgbToXyz(r, g, b) {
-        r = rgb_xyz(r);
-        g = rgb_xyz(g);
-        b = rgb_xyz(b);
-        var x = xyz_lab((0.4124564 * r + 0.3575761 * g + 0.1804375 * b) / Xn);
-        var y = xyz_lab((0.2126729 * r + 0.7151522 * g + 0.0721750 * b) / Yn);
-        var z = xyz_lab((0.0193339 * r + 0.1191920 * g + 0.9503041 * b) / Zn);
-        return [x, y, z];
-    }
-})(Lab || (Lab = {}));
-exports.Lab = Lab;
-//# sourceMappingURL=lab.js.map

package/lib/commonjs/mol-util/color/swatches.d.ts

@@ -1,8 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import { ColorSwatch } from './color';
-export declare const DefaultColorSwatch: ColorSwatch;

package/lib/commonjs/mol-util/color/swatches.js

@@ -1,25 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.DefaultColorSwatch = void 0;
-var color_1 = require("./color");
-exports.DefaultColorSwatch = (0, color_1.ColorSwatch)([
-    ['black', 0x000000],
-    ['gray', 0x808080],
-    ['white', 0xFFFFFF],
-    ['red', 0xD33115],
-    ['orange', 0xE27300],
-    ['yellow', 0xFCC400],
-    ['green', 0x68BC00],
-    ['cyan', 0x16A5A5],
-    ['blue', 0x009CE0],
-    ['purple', 0x7B64FF],
-    ['magenta', 0xFA28FF],
-    ['violet', 0x7D2187]
-]);
-//# sourceMappingURL=swatches.js.map

package/lib/commonjs/mol-util/console-logger.d.ts

@@ -1,13 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-export declare namespace ConsoleLogger {
-    function formatTime(t: number): string;
-    function log(tag: string, msg: string): void;
-    function logId(guid: string, tag: string, msg: string): void;
-    function error(ctx: string, e: any): void;
-    function warn(ctx: string, e: any): void;
-    function errorId(guid: string, e: any): void;
-}

package/lib/commonjs/mol-util/console-logger.js

@@ -1,52 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.ConsoleLogger = void 0;
-var ConsoleLogger;
-(function (ConsoleLogger) {
-    function formatTime(t) {
-        if (isNaN(t))
-            return 'n/a';
-        var h = Math.floor(t / (60 * 60 * 1000)), m = Math.floor(t / (60 * 1000) % 60), s = Math.floor(t / 1000 % 60);
-        var ms = Math.floor(t % 1000).toString();
-        while (ms.length < 3)
-            ms = '0' + ms;
-        if (h > 0)
-            return "".concat(h, "h").concat(m, "m").concat(s, ".").concat(ms, "s");
-        if (m > 0)
-            return "".concat(m, "m").concat(s, ".").concat(ms, "s");
-        if (s > 0)
-            return "".concat(s, ".").concat(ms, "s");
-        return "".concat(t.toFixed(0), "ms");
-    }
-    ConsoleLogger.formatTime = formatTime;
-    function log(tag, msg) {
-        console.log("[".concat(tag, "] ").concat(msg));
-    }
-    ConsoleLogger.log = log;
-    function logId(guid, tag, msg) {
-        console.log("[".concat(guid, "][").concat(tag, "] ").concat(msg));
-    }
-    ConsoleLogger.logId = logId;
-    function error(ctx, e) {
-        console.error("[Error] (".concat(ctx, ") ").concat(e));
-        if (e.stack)
-            console.error(e.stack);
-    }
-    ConsoleLogger.error = error;
-    function warn(ctx, e) {
-        console.error("[Warn] (".concat(ctx, ") ").concat(e));
-    }
-    ConsoleLogger.warn = warn;
-    function errorId(guid, e) {
-        console.error("[".concat(guid, "][Error] ").concat(e));
-        if (e.stack)
-            console.error(e.stack);
-    }
-    ConsoleLogger.errorId = errorId;
-})(ConsoleLogger = exports.ConsoleLogger || (exports.ConsoleLogger = {}));
-//# sourceMappingURL=console-logger.js.map

package/lib/commonjs/mol-util/data-source.d.ts

@@ -1,48 +0,0 @@
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- *
- * Adapted from LiteMol
- */
-import { Task, RuntimeContext } from '../mol-task';
-import { AssetManager, Asset } from './assets';
-export declare enum DataCompressionMethod {
-    None = 0,
-    Gzip = 1,
-    Zip = 2
-}
-export declare type DataType = 'json' | 'xml' | 'string' | 'binary' | 'zip';
-export declare type DataValue = 'string' | any | XMLDocument | Uint8Array;
-export declare type DataResponse<T extends DataType> = T extends 'json' ? any : T extends 'xml' ? XMLDocument : T extends 'string' ? string : T extends 'binary' ? Uint8Array : T extends 'zip' ? {
-    [k: string]: Uint8Array;
-} : never;
-export interface AjaxGetParams<T extends DataType = 'string'> {
-    url: string;
-    type?: T;
-    title?: string;
-    headers?: [string, string][];
-    body?: string;
-}
-export declare function readStringFromFile(file: File): Task<string>;
-export declare function readUint8ArrayFromFile(file: File): Task<Uint8Array>;
-export declare function readFromFile<T extends DataType>(file: File, type: T): Task<DataResponse<T>>;
-export declare function ajaxGet(url: string): Task<DataValue>;
-export declare function ajaxGet<T extends DataType>(params: AjaxGetParams<T>): Task<DataResponse<T>>;
-export declare type AjaxTask = typeof ajaxGet;
-export declare type AjaxGetManyEntry = {
-    kind: 'ok';
-    id: string;
-    result: Asset.Wrapper<'string' | 'binary'>;
-} | {
-    kind: 'error';
-    id: string;
-    error: any;
-};
-export declare function ajaxGetMany(ctx: RuntimeContext, assetManager: AssetManager, sources: {
-    id: string;
-    url: Asset.Url | string;
-    isBinary?: boolean;
-    canFail?: boolean;
-}[], maxConcurrency: number): Promise<AjaxGetManyEntry[]>;