@datagrok-libraries/utils 0.0.7 → 0.0.8

package/package.json

@@ -4,7 +4,7 @@
 		"access": "public"
 	},
 	"fullName": "Utils",
-	"version": "0.0.7",
+	"version": "0.0.8",
 	"description": "Common utilities",
 	"dependencies": {
 		"@keckelt/tsne": "^1.0.2",

package/src/bit-array.d.ts

@@ -0,0 +1,82 @@
+export default class BitArray {
+    static _onBitCount: Int8Array;
+    static _firstOnBit: Int8Array;
+    static _lastOnBit: Int8Array;
+    private _data;
+    private _length;
+    private _version;
+    private _updateLevel;
+    private _selectedCount;
+    private _selectedCountVersion;
+    private _selectedIndexesVersion;
+    private _versionedName;
+    private _versionedNameVersion;
+    SHRINK_THRESHOLD: number;
+    constructor(data: Uint32Array, length: number);
+    constructor(length: number, defaultValue?: boolean);
+    getRawData(): Uint32Array;
+    assureGoez(num: number, argName: String): void;
+    assureInRange(value: number, min: number, max: number, argName: String): void;
+    copy(src: Uint32Array, dst: Uint32Array, count: number): void;
+    copyFrom(other: BitArray): void;
+    get length(): number;
+    get buffer(): Uint32Array;
+    set buffer(data: Uint32Array);
+    get version(): number;
+    set version(value: number);
+    incrementVersion(notify?: boolean): void;
+    get lengthInInts(): number;
+    get versionedName(): string;
+    set versionedName(name: string);
+    get self(): this;
+    setLength(value: number): void;
+    static fromAnd(set1: BitArray, set2: BitArray): BitArray;
+    private static _createBuffer;
+    static fromValues(values: Array<boolean>): BitArray;
+    static fromSeq(count: number, flag: Function): BitArray;
+    static fromString(s: string): BitArray;
+    static fromUint32Array(_length: number, _data: Uint32Array): BitArray;
+    static fromBytes(bytes: Uint8Array): BitArray;
+    toString(): string;
+    equals(other: BitArray): boolean;
+    /** Clones a bitset. */
+    clone(): BitArray;
+    /** Initializes a bitset. */
+    init(flag: Function, notify: boolean): BitArray;
+    invert(notify?: boolean): void;
+    setAll(value: boolean, notify?: boolean): void;
+    setIndexes(indexes: Array<number>, value?: boolean, clear?: boolean, notify?: boolean): void;
+    everyIndex(indexes: Array<number>, value?: boolean): boolean;
+    anyIndex(indexes: Array<number>, value?: boolean): boolean;
+    setWhere(check: Function, value?: boolean, clear?: boolean, notify?: boolean, allowClear?: boolean): void;
+    setRange(from: number, to: number, value: boolean, notify?: boolean): BitArray;
+    setRandom(n: number, value: boolean, notify?: boolean): void;
+    and(value: BitArray, notify?: boolean): BitArray;
+    andNot(value: BitArray, notify?: boolean): BitArray;
+    notAnd(value: BitArray, notify?: boolean): BitArray;
+    not(notify?: boolean): BitArray;
+    or(value: BitArray, notify?: boolean): this;
+    xor(value: BitArray, notify?: boolean): this;
+    insertAt(pos: number, n: number, flag?: boolean): void;
+    removeAt(pos: number, n?: number): void;
+    removeByMask(mask: BitArray, flag?: boolean): BitArray;
+    getBit(pos: number): boolean;
+    setBit(pos: number, bit: boolean, notify?: boolean): void;
+    setFast(i: number, value: boolean): void;
+    setTrue(pos: number): void;
+    setFalse(pos: number): void;
+    trueCount(): number;
+    falseCount(): number;
+    countBits(value: boolean): number;
+    countWhere(check: Function): number;
+    andWithCountBits(second: BitArray, value: boolean): number;
+    clear(): void;
+    contains(value: boolean): boolean;
+    get allTrue(): boolean;
+    get allFalse(): boolean;
+    get anyTrue(): boolean;
+    get anyFalse(): boolean;
+    findNext(index: number, value?: boolean): number;
+    findPrev(index: number, value?: boolean): number;
+}
+//# sourceMappingURL=bit-array.d.ts.map

package/src/bit-array.d.ts.map

@@ -0,0 +1 @@
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package/src/operations.d.ts

@@ -0,0 +1,66 @@
+import { Matrix, Vector, Vectors, DistanceMetric } from './type_declarations';
+/**
+ * Asserts a condition by throwing an Error.
+ *
+ * @export
+ * @param {boolean} [condition=false] Condition to assert.
+ * @param {string} [message='Assertion error.'] Message to output.
+ * @throws {Error}
+ */
+export declare function assert(condition?: boolean, message?: string): void;
+/**
+ * Generates single random integer from 0 to range.
+ *
+ * @export
+ * @param {number} range Max generating value.
+ * @return {number} A random integer generated.
+ */
+export declare function randomInt(range: number): number;
+/**
+ * Transpose matrix.
+ *
+ * @export
+ * @param {Matrix} matrix The matrix to be transposed.
+ * @return {Matrix} Transposed matrix.
+ * @todo Might be slow since used Array.map. Probably needs performance revision.
+ */
+export declare function transposeMatrix(matrix: Matrix): Matrix;
+/**
+ * Adds two vectors with the second one to be multiplied by the given ratio.
+ *
+ * @export
+ * @param {Vector} p The first vector to add.
+ * @param {Vector} q The second vector to add.
+ * @param {number} [multiplier=1] A multiplier to be used before the second vector is added.
+ * @return {Vector} New vector contained the result of operation p+multiplier*q.
+ */
+export declare function vectorAdd(p: Vector, q: Vector, multiplier?: number): Vector;
+/**
+ * Creates a matrix filled with random floating point values.
+ *
+ * @export
+ * @param {number} dimension1 The first dimension of the matrix.
+ * @param {number} dimension2 The second dimension of the matrix.
+ * @param {number} [scale=1.] Max value given by random generator.
+ * @return {Matrix} A new matrix filled with random floating point  values.
+ */
+export declare function fillRandomMatrix(dimension1: number, dimension2: number, scale?: number): Matrix;
+/**
+ * Calculates Euclidean distance between two vectors.
+ *
+ * @export
+ * @param {Vector} p The first vector.
+ * @param {Vector} q The second vector.
+ * @return {number} Euclidean distance between the given vectors.
+ */
+export declare function calculateEuclideanDistance(p: Vector, q: Vector): number;
+/**
+ * Creates a distance matrix using a custom distance function.
+ *
+ * @export
+ * @param {Vectors} data Input vectors to calculate distances.
+ * @param {DistanceMetric} distance Custom distance function.
+ * @return {Matrix} Calculated custom distance matrix.
+ */
+export declare function calcDistanceMatrix(data: Vectors, distance: DistanceMetric): Matrix;
+//# sourceMappingURL=operations.d.ts.map

package/src/operations.d.ts.map

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package/src/reduce-dimensionality.d.ts

@@ -0,0 +1,38 @@
+import { Options, Coordinates } from './type_declarations';
+/**
+ * Unified class implementing different dimensionality reduction methods.
+ *
+ * @export
+ * @class DimensionalityReducer
+ */
+export declare class DimensionalityReducer {
+    private reducer;
+    static methods: string[];
+    private measurer;
+    /**
+     * Creates an instance of DimensionalityReducer.
+     * @param {any[]} data Vectors to embed.
+     * @param {string} method Embedding method to be applied
+     * @param {string} metric Distance metric to be computed between each of the vectors.
+     * @param {Options} [options] Options to pass to the implementing embedders.
+     * @memberof DimensionalityReducer
+     */
+    constructor(data: any[], method: string, metric: string, options?: Options);
+    /**
+     * Embeds the data given into the two-dimensional space using the chosen method.
+     *
+     * @param {boolean} transpose Whether to transform coordinates to have columns-first orientation.
+     * @throws {Error} If the embedding method was not found.
+     * @return {Coordinates} Cartesian coordinate of this embedding.
+     * @memberof DimensionalityReducer
+     */
+    transform(transpose?: boolean): Coordinates;
+    /**
+     * Returns dimensionality reduction methods available.
+     *
+     * @readonly
+     * @memberof DimensionalityReducer
+     */
+    static get availableMethods(): string[];
+}
+//# sourceMappingURL=reduce-dimensionality.d.ts.map

package/src/reduce-dimensionality.d.ts.map

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package/src/sequence-encoder.d.ts

@@ -0,0 +1,59 @@
+/**
+ * Class to categorial encode/decode aligned amino acid residues sequence.
+ *
+ * @export
+ * @class AlignedSequenceEncoder
+ */
+export declare class AlignedSequenceEncoder {
+    protected aa2num: {
+        [name: string]: number;
+    };
+    protected num2aa: {
+        [code: number]: string;
+    };
+    constructor();
+    /**
+     * Truncate NH2 and -COOH terminals of the given sequence.
+     *
+     * @static
+     * @param {string} seq The sequence provided.
+     * @return {string} Truncated sequence.
+     * @memberof AlignedSequenceEncoder
+     */
+    static _truncateSequence(seq: string): string;
+    /**
+     * Cuts auxiliary defises before a residue.
+     *
+     * @static
+     * @param {string} seq The sequence to process.
+     * @return {string} Processed sequence.
+     * @memberof AlignedSequenceEncoder
+     */
+    static _dropDefises(seq: string): string;
+    /**
+     * Performs truncation and cutting auxiliary defises.
+     *
+     * @static
+     * @param {string} sequence The sequence work under process.
+     * @return {string} Result of cleaning.
+     * @memberof AlignedSequenceEncoder
+     */
+    static clean(sequence: string): string;
+    /**
+     * Categorial encode of the sequence provided.
+     *
+     * @param {string} sequence The sequence.
+     * @return {number[]} Encoded vector.
+     * @memberof AlignedSequenceEncoder
+     */
+    encode(sequence: string): number[];
+    /**
+     * Decode the encoded vector into the sequence back.
+     *
+     * @param {number[]} value The vector encoded.
+     * @return {string} Decoded sequence.
+     * @memberof AlignedSequenceEncoder
+     */
+    decode(value: number[]): string;
+}
+//# sourceMappingURL=sequence-encoder.d.ts.map

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package/src/spe.d.ts

@@ -0,0 +1,68 @@
+import { Options, Coordinates, Vectors, DistanceMetric } from './type_declarations';
+/**
+ * Implements stochastic proximity embedding.
+ *
+ * @export
+ * @class SPEBase
+ * @link doi:10.1016/S1093-3263(03)00155-4
+ */
+export declare class SPEBase {
+    protected static dimension: number;
+    protected steps: number;
+    protected cycles: number;
+    protected cutoff: number;
+    protected lambda: number;
+    protected dlambda: number;
+    protected lambda2: number;
+    protected dlambda2: number;
+    protected epsilon: number;
+    protected distanceFunction: DistanceMetric;
+    protected distance: Coordinates;
+    /**
+     * Creates an instance of SPEBase.
+     * @param {Options} [options] Options to pass to the constructor.
+     * @memberof SPEBase
+     */
+    constructor(options?: Options);
+    /**
+     * Initializes distance matrix.
+     *
+     * @protected
+     * @param {Vectors} vectors Input vectors to calculate distance between.
+     * @memberof SPEBase
+     */
+    protected initDistance(vectors: Vectors): void;
+    /**
+     * Calculates distance between the two vectors given.
+     *
+     * @param {Vectors} vectors Set of vectors to calculate distances between.
+     * @param {number} index1 Index of the first vector of the pair.
+     * @param {number} index2 Index of the second vector of the pair.
+     * @return {number} Distance between these two vectors.
+     */
+    protected calcDistance(vectors: Vectors, index1: number, index2: number): number;
+    /**
+     * Embeds the vectors given into a two-dimensional space.
+     *
+     * @param {Vectors} vectors D-dimensional coordinates.
+     * @return {Coordinates} SPE coordinates in D space.
+     */
+    embed(vectors: Vectors): Coordinates;
+}
+/**
+ * Implements modified stochastic proximity embedding.
+ *
+ * @export
+ * @class PSPEBase
+ * @link doi:10.1016/S1093-3263(03)00155-4
+ */
+export declare class PSPEBase extends SPEBase {
+    /**
+     * Embeds the vectors given into a two-dimensional space using a modified update rule.
+     *
+     * @param {Vectors} vectors D-dimensional coordinates.
+     * @return {Coordinates} SPE coordinates in D space.
+     */
+    embed(vectors: Vectors): Coordinates;
+}
+//# sourceMappingURL=spe.d.ts.map

package/src/spe.d.ts.map

@@ -0,0 +1 @@
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package/src/string-measure.d.ts

@@ -0,0 +1,33 @@
+import { DistanceMetric } from './type_declarations';
+/**
+ * Unified class implementing the different string measures.
+ *
+ * @export
+ * @class Measurer
+ */
+export declare class Measurer {
+    protected method: string;
+    static receipt: {
+        [name: string]: DistanceMetric;
+    };
+    /**
+     * Creates an instance of Measurer.
+     * @param {string} method Method to calculate distance between strings.
+     * @memberof Measurer
+     */
+    constructor(method: string);
+    /**
+     * Returns custom string distance function specified.
+     * @return {DistanceMetric} Callback of the measure chosen.
+     */
+    getMeasure(): DistanceMetric;
+    /**
+     * Returns available string distance metrics.
+     *
+     * @readonly
+     * @type {string[]}
+     * @memberof Measurer
+     */
+    static get availableMeasures(): string[];
+}
+//# sourceMappingURL=string-measure.d.ts.map

package/src/string-measure.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"string-measure.d.ts","sourceRoot":"","sources":["string-measure.ts"],"names":[],"mappings":"AAGA,OAAO,EAAC,cAAc,EAAC,MAAM,qBAAqB,CAAC;AAGnD;;;;;GAKG;AACH,qBAAa,QAAQ;IACjB,SAAS,CAAC,MAAM,EAAE,MAAM,CAAC;IACzB,OAAc,OAAO,EAAE;QAAC,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc,CAAA;KAAC,CAGrD;IAEF;;;;OAIG;gBACS,MAAM,EAAE,MAAM;IAK1B;;;OAGG;IACI,UAAU,IAAI,cAAc;IAInC;;;;;;OAMG;IACH,WAAkB,iBAAiB,IAAK,MAAM,EAAE,CAO/C;CAEJ"}

package/src/string-utils.d.ts

@@ -0,0 +1,2 @@
+export declare function tryParseJson(s: string): any;
+//# sourceMappingURL=string-utils.d.ts.map

package/src/string-utils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"string-utils.d.ts","sourceRoot":"","sources":["string-utils.ts"],"names":[],"mappings":"AAAA,wBAAgB,YAAY,CAAC,CAAC,EAAE,MAAM,GAAI,GAAG,CAO5C"}

package/src/table-validation.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=table-validation.d.ts.map

package/src/table-validation.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"table-validation.d.ts","sourceRoot":"","sources":["table-validation.ts"],"names":[],"mappings":""}

package/src/test-utils.d.ts

@@ -0,0 +1,11 @@
+export declare function getToken(url: string, key: string): Promise<any>;
+export declare function getWebUrl(url: string, token: string): Promise<any>;
+export declare function getDevKey(hostKey: string): {
+    url: string;
+    key: string;
+};
+export declare function getBrowserPage(puppeteer: any): Promise<{
+    browser: any;
+    page: any;
+}>;
+//# sourceMappingURL=test-utils.d.ts.map

package/src/test-utils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"test-utils.d.ts","sourceRoot":"","sources":["test-utils.ts"],"names":[],"mappings":"AAOA,wBAAsB,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,gBAOtD;AAED,wBAAsB,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,gBAIzD;AAaD,wBAAgB,SAAS,CAAC,OAAO,EAAE,MAAM,GAAG;IAAC,GAAG,EAAE,MAAM,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAC,CAkBrE;AAED,wBAAsB,cAAc,CAAC,SAAS,EAAE,GAAG,GAAG,OAAO,CAAC;IAAC,OAAO,EAAE,GAAG,CAAC;IAAC,IAAI,EAAE,GAAG,CAAA;CAAC,CAAC,CA8BvF"}

package/src/type_declarations.d.ts

@@ -0,0 +1,56 @@
+/**
+ * Denotes a vector of floating poit values.
+ *
+ * @export
+ * @class Vector
+ * @extends {Float32Array}
+ */
+export declare class Vector extends Float32Array {
+}
+/**
+ * Denotes a two-dimensional matrix.
+ *
+ * @export
+ * @class Matrix
+ * @extends {Array<Vector>}
+ */
+export declare class Matrix extends Array<Vector> {
+}
+/**
+ * Denotes cartesian coordinates.
+ *
+ * @export
+ * @class Coordinates
+ * @extends {Matrix}
+ */
+export declare class Coordinates extends Matrix {
+}
+/**
+ * Denotes an array of arbitrary-typed vectors.
+ *
+ * @export
+ * @class Vectors
+ * @extends {Array<any>}
+ */
+export declare class Vectors extends Array<any> {
+}
+/**
+ * Denotes a dictionary containing function options.
+ *
+ * @export
+ * @type Options
+ */
+export declare type Options = {
+    [name: string]: any;
+};
+/**
+ * Denotes custom distance metric between the two given vectors.
+ *
+ * @export
+ * @type DistanceMetric
+ * @param {any} v1 The first vector.
+ * @param {any} v2 The second vector.
+ * @return {number} Distance between these two vectors.
+ */
+export declare type DistanceMetric = (v1: any, v2: any) => (number);
+//# sourceMappingURL=type_declarations.d.ts.map

package/src/type_declarations.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"type_declarations.d.ts","sourceRoot":"","sources":["type_declarations.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AACH,qBAAa,MAAO,SAAQ,YAAY;CAAG;AAE3C;;;;;;GAMG;AACH,qBAAa,MAAO,SAAQ,KAAK,CAAC,MAAM,CAAC;CAAG;AAE5C;;;;;;GAMG;AACH,qBAAa,WAAY,SAAQ,MAAM;CAAG;AAE1C;;;;;;GAMG;AACH,qBAAa,OAAQ,SAAQ,KAAK,CAAC,GAAG,CAAC;CAAG;AAE1C;;;;;GAKG;AACH,oBAAY,OAAO,GAAG;IAAC,CAAC,IAAI,EAAE,MAAM,GAAG,GAAG,CAAA;CAAC,CAAC;AAE5C;;;;;;;;GAQG;AACF,oBAAY,cAAc,GAAG,CAAC,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC"}

package/tsconfig.json

@@ -10,8 +10,8 @@
     // "allowJs": true,                             /* Allow javascript files to be compiled. */
     // "checkJs": true,                             /* Report errors in .js files. */
     // "jsx": "preserve",                           /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */
-    // "declaration": true,                         /* Generates corresponding '.d.ts' file. */
-    // "declarationMap": true,                      /* Generates a sourcemap for each corresponding '.d.ts' file. */
+     "declaration": true,                         /* Generates corresponding '.d.ts' file. */
+     "declarationMap": true,                      /* Generates a sourcemap for each corresponding '.d.ts' file. */
     // "sourceMap": true,                           /* Generates corresponding '.map' file. */
     // "outFile": "./",                             /* Concatenate and emit output to single file. */
     // "outDir": "./",                              /* Redirect output structure to the directory. */