@datagrok-libraries/utils 0.0.10 → 0.0.16

package/src/reduce-dimensionality.js

@@ -1,233 +0,0 @@
-import * as umj from 'umap-js';
-import { TSNE } from '@keckelt/tsne';
-import { Vector } from './type_declarations';
-import { calcDistanceMatrix, transposeMatrix } from './operations';
-import { SPEBase, PSPEBase } from './spe';
-import { Measurer } from './string-measure';
-import { AlignedSequenceEncoder } from './sequence-encoder';
-import { assert } from './operations';
-/**
- * Abstract dimensionality reducer.
- *
- * @abstract
- * @class Reducer
- */
-class Reducer {
-    /**
-     * Creates an instance of Reducer.
-     * @param {Options} options Options to pass to the constructor.
-     * @memberof Reducer
-     */
-    constructor(options) {
-        this.data = options.data;
-    }
-}
-/**
- * Implements t-SNE dimensionality reduction.
- *
- * @class TSNEReducer
- * @extends {Reducer}
- */
-class TSNEReducer extends Reducer {
-    /**
-     * Creates an instance of TSNEReducer.
-     * @param {Options} options Options to pass to the constructor.
-     * @memberof TSNEReducer
-     */
-    constructor(options) {
-        var _a;
-        super(options);
-        this.reducer = new TSNE(options);
-        this.iterations = (_a = options === null || options === void 0 ? void 0 : options.iterations) !== null && _a !== void 0 ? _a : 100;
-        this.distance = options.distance;
-    }
-    /**
-     * Embeds the data given into the two-dimensional space using t-SNE method.
-     * @return {Coordinates} Cartesian coordinate of this embedding.
-     */
-    transform() {
-        this.reducer.initDataDist(calcDistanceMatrix(this.data, this.distance));
-        for (let i = 0; i < this.iterations; ++i) {
-            this.reducer.step(); // every time you call this, solution gets better
-        }
-        return this.reducer.getSolution();
-    }
-}
-/**
- * Implements UMAP dimensionality reduction.
- *
- * @class UMAPReducer
- * @extends {Reducer}
- */
-class UMAPReducer extends Reducer {
-    /**
-     * Creates an instance of UMAPReducer.
-     * @param {Options} options Options to pass to the constructor.
-     * @memberof UMAPReducer
-     */
-    constructor(options) {
-        super(options);
-        assert('distanceFn' in options);
-        this.encoder = new AlignedSequenceEncoder();
-        this.distanceFn = options.distanceFn;
-        this.vectors = [];
-        options.distanceFn = this._encodedDistance.bind(this);
-        this.reducer = new umj.UMAP(options);
-    }
-    /**
-     * Custom distance wrapper to have numeric inputs instead of string ones.
-     *
-     * @protected
-     * @param {number[]} a The first item.
-     * @param {number[]} b The first item.
-     * @return {number} Distance metric.
-     * @memberof UMAPReducer
-     */
-    _encodedDistance(a, b) {
-        return this.distanceFn(this.data[a[0]], this.data[b[0]]);
-    }
-    /**
-     * Encodes the input data as a vector of indices.
-     *
-     * @protected
-     * @memberof UMAPReducer
-     */
-    _encode() {
-        for (let i = 0; i < this.data.length; ++i) {
-            this.vectors.push([i]);
-        }
-    }
-    /**
-     * Embeds the data given into the two-dimensional space using UMAP method.
-     * @return {Coordinates} Cartesian coordinate of this embedding.
-     */
-    transform() {
-        this._encode();
-        const embedding = this.reducer.fit(this.vectors);
-        function arrayCast2Coordinates(data) {
-            return new Array(data.length).fill(0).map((_, i) => (Vector.from(data[i])));
-        }
-        return arrayCast2Coordinates(embedding);
-    }
-}
-/**
- * Implements original SPE dimensionality reduction.
- *
- * @class SPEReducer
- * @extends {Reducer}
- */
-class SPEReducer extends Reducer {
-    /**
-     * Creates an instance of SPEReducer.
-     * @param {Options} options Options to pass to the constructor.
-     * @memberof SPEReducer
-     */
-    constructor(options) {
-        super(options);
-        this.reducer = new SPEBase(options);
-    }
-    /**
-     * Embeds the data given into the two-dimensional space using the original SPE method.
-     * @return {Coordinates} Cartesian coordinate of this embedding.
-     */
-    transform() {
-        return this.reducer.embed(this.data);
-    }
-}
-/**
- * Implements modified SPE dimensionality reduction.
- *
- * @class PSPEReducer
- * @extends {Reducer}
- */
-class PSPEReducer extends Reducer {
-    /**
-     * Creates an instance of PSPEReducer.
-     * @param {Options} options Options to pass to the constructor.
-     * @memberof PSPEReducer
-     */
-    constructor(options) {
-        super(options);
-        this.reducer = new PSPEBase(options);
-    }
-    /**
-     * Embeds the data given into the two-dimensional space using the modified SPE method.
-     * @return {Coordinates} Cartesian coordinate of this embedding.
-     */
-    transform() {
-        return this.reducer.embed(this.data);
-    }
-}
-/**
- * Unified class implementing different dimensionality reduction methods.
- *
- * @export
- * @class DimensionalityReducer
- */
-export class DimensionalityReducer {
-    /**
-     * 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, method, metric, options) {
-        var _a;
-        assert(DimensionalityReducer.availableMethods.includes(method), `The method '${method}' is not supported`);
-        this.measurer = new Measurer(metric);
-        const measure = this.measurer.getMeasure();
-        if (method == 'UMAP') {
-            this.reducer = new UMAPReducer({
-                ...{ data: data },
-                ...{ distanceFn: measure },
-                ...{ nEpochs: options === null || options === void 0 ? void 0 : options.cycles },
-                ...options
-            });
-        }
-        else if (method == 't-SNE') {
-            this.reducer = new TSNEReducer({
-                ...{ data: data },
-                ...{ distance: measure },
-                ...{ iterations: (_a = options === null || options === void 0 ? void 0 : options.cycles) !== null && _a !== void 0 ? _a : undefined },
-                ...options,
-            });
-        }
-        else if (method == 'SPE') {
-            this.reducer = new SPEReducer({ ...{ data: data }, ...{ distance: measure }, ...options });
-        }
-        else {
-            this.reducer = new PSPEReducer({ ...{ data: data }, ...{ distance: measure }, ...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 = false) {
-        if (this.reducer == undefined) {
-            throw new Error('Reducer was not defined.');
-        }
-        let embedding = this.reducer.transform();
-        if (transpose) {
-            embedding = transposeMatrix(embedding);
-        }
-        return embedding;
-    }
-    /**
-     * Returns dimensionality reduction methods available.
-     *
-     * @readonly
-     * @memberof DimensionalityReducer
-     */
-    static get availableMethods() {
-        return DimensionalityReducer.methods;
-    }
-}
-DimensionalityReducer.methods = ['UMAP', 't-SNE', 'SPE', 'pSPE'];
-//# sourceMappingURL=data:application/json;base64,{"version":3,"file":"reduce-dimensionality.js","sourceRoot":"","sources":["reduce-dimensionality.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,GAAG,MAAM,SAAS,CAAC;AAC/B,OAAO,EAAC,IAAI,EAAC,MAAM,eAAe,CAAC;AAEnC,OAAO,EAAuC,MAAM,EAAkB,MAAM,qBAAqB,CAAC;AAClG,OAAO,EAAC,kBAAkB,EAAE,eAAe,EAAC,MAAM,cAAc,CAAC;AACjE,OAAO,EAAC,OAAO,EAAE,QAAQ,EAAC,MAAM,OAAO,CAAC;AACxC,OAAO,EAAC,QAAQ,EAAC,MAAM,kBAAkB,CAAC;AAC1C,OAAO,EAAC,sBAAsB,EAAC,MAAM,oBAAoB,CAAC;AAC1D,OAAO,EAAC,MAAM,EAAC,MAAM,cAAc,CAAC;AAEpC;;;;;GAKG;AACH,MAAe,OAAO;IAGpB;;;;OAIG;IACH,YAAY,OAAgB;QAC1B,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC;IAC3B,CAAC;CAUF;AAED;;;;;GAKG;AACH,MAAM,WAAY,SAAQ,OAAO;IAK/B;;;;OAIG;IACH,YAAY,OAAgB;;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,OAAO,GAAG,IAAI,IAAI,CAAC,OAAO,CAAC,CAAC;QACjC,IAAI,CAAC,UAAU,GAAG,MAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,UAAU,mCAAI,GAAG,CAAC;QAC7C,IAAI,CAAC,QAAQ,GAAG,OAAO,CAAC,QAAQ,CAAC;IACnC,CAAC;IAED;;;OAGG;IACI,SAAS;QACd,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,kBAAkB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC;QAExE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,UAAU,EAAE,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,CAAC,iDAAiD;SACvE;QACD,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC;IACpC,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,WAAY,SAAQ,OAAO;IAM/B;;;;OAIG;IACH,YAAY,OAAgB;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QAEf,MAAM,CAAC,YAAY,IAAI,OAAO,CAAC,CAAC;QAEhC,IAAI,CAAC,OAAO,GAAG,IAAI,sBAAsB,EAAE,CAAC;QAC5C,IAAI,CAAC,UAAU,GAAG,OAAO,CAAC,UAAU,CAAC;QACrC,IAAI,CAAC,OAAO,GAAG,EAAE,CAAC;QAClB,OAAO,CAAC,UAAU,GAAG,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACtD,IAAI,CAAC,OAAO,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACvC,CAAC;IAED;;;;;;;;OAQG;IACO,gBAAgB,CAAC,CAAW,EAAE,CAAW;QACjD,OAAO,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC3D,CAAC;IAED;;;;;OAKG;IACO,OAAO;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;YACzC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;SACxB;IACH,CAAC;IAED;;;OAGG;IACI,SAAS;QACd,IAAI,CAAC,OAAO,EAAE,CAAC;QAEf,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;QAEjD,SAAS,qBAAqB,CAAC,IAAgB;YAC7C,OAAO,IAAI,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAC9E,CAAC;QAED,OAAO,qBAAqB,CAAC,SAAS,CAAC,CAAC;IAC1C,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,UAAW,SAAQ,OAAO;IAG9B;;;;OAIG;IACH,YAAY,OAAgB;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,OAAO,GAAG,IAAI,OAAO,CAAC,OAAO,CAAC,CAAC;IACtC,CAAC;IAED;;;OAGG;IACI,SAAS;QACd,OAAO,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACvC,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,WAAY,SAAQ,OAAO;IAG/B;;;;OAIG;IACH,YAAY,OAAgB;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,OAAO,GAAG,IAAI,QAAQ,CAAC,OAAO,CAAC,CAAC;IACvC,CAAC;IAED;;;OAGG;IACI,SAAS;QACd,OAAO,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACvC,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,OAAO,qBAAqB;IAKhC;;;;;;;OAOG;IACH,YAAY,IAAW,EAAE,MAAc,EAAE,MAAc,EAAE,OAAiB;;QACxE,MAAM,CAAC,qBAAqB,CAAC,gBAAgB,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,eAAe,MAAM,oBAAoB,CAAC,CAAC;QAE3G,IAAI,CAAC,QAAQ,GAAG,IAAI,QAAQ,CAAC,MAAM,CAAC,CAAC;QACrC,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,UAAU,EAAE,CAAA;QAE1C,IAAI,MAAM,IAAI,MAAM,EAAE;YACpB,IAAI,CAAC,OAAO,GAAG,IAAI,WAAW,CAAC;gBAC7B,GAAG,EAAC,IAAI,EAAE,IAAI,EAAC;gBACf,GAAG,EAAC,UAAU,EAAE,OAAO,EAAC;gBACxB,GAAG,EAAC,OAAO,EAAE,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,MAAM,EAAC;gBAC7B,GAAG,OAAO;aACX,CAAC,CAAC;SACJ;aAAM,IAAI,MAAM,IAAI,OAAO,EAAE;YAC5B,IAAI,CAAC,OAAO,GAAG,IAAI,WAAW,CAAC;gBAC7B,GAAG,EAAC,IAAI,EAAE,IAAI,EAAC;gBACf,GAAG,EAAC,QAAQ,EAAE,OAAO,EAAC;gBACtB,GAAG,EAAC,UAAU,EAAE,MAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,MAAM,mCAAI,SAAS,EAAC;gBAC7C,GAAG,OAAO;aACX,CAAC,CAAC;SACJ;aAAM,IAAI,MAAM,IAAI,KAAK,EAAE;YAC1B,IAAI,CAAC,OAAO,GAAG,IAAI,UAAU,CAAC,EAAC,GAAG,EAAC,IAAI,EAAE,IAAI,EAAC,EAAE,GAAG,EAAC,QAAQ,EAAE,OAAO,EAAC,EAAE,GAAG,OAAO,EAAC,CAAC,CAAC;SACtF;aAAM;YACL,IAAI,CAAC,OAAO,GAAG,IAAI,WAAW,CAAC,EAAC,GAAG,EAAC,IAAI,EAAE,IAAI,EAAC,EAAE,GAAG,EAAC,QAAQ,EAAE,OAAO,EAAC,EAAE,GAAG,OAAO,EAAC,CAAC,CAAC;SACvF;IACH,CAAC;IAED;;;;;;;OAOG;IACI,SAAS,CAAC,YAAqB,KAAK;QACzC,IAAI,IAAI,CAAC,OAAO,IAAI,SAAS,EAAE;YAC7B,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAC;SAC7C;QACD,IAAI,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,CAAC;QAEzC,IAAI,SAAS,EAAE;YACb,SAAS,GAAG,eAAe,CAAC,SAAS,CAAC,CAAC;SACxC;QACD,OAAO,SAAS,CAAC;IACnB,CAAC;IAED;;;;;OAKG;IACH,MAAM,KAAK,gBAAgB;QACzB,OAAO,qBAAqB,CAAC,OAAO,CAAC;IACvC,CAAC;;AAlEa,6BAAO,GAAa,CAAC,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC","sourcesContent":["import * as umj from 'umap-js';\nimport {TSNE} from '@keckelt/tsne';\n\nimport {Options, DistanceMetric, Coordinates, Vector, Vectors, Matrix} from './type_declarations';\nimport {calcDistanceMatrix, transposeMatrix} from './operations';\nimport {SPEBase, PSPEBase} from './spe';\nimport {Measurer} from './string-measure';\nimport {AlignedSequenceEncoder} from './sequence-encoder';\nimport {assert} from './operations';\n\n/**\n * Abstract dimensionality reducer.\n *\n * @abstract\n * @class Reducer\n */\nabstract class Reducer {\n  protected data: Vectors;\n\n  /**\n   * Creates an instance of Reducer.\n   * @param {Options} options Options to pass to the constructor.\n   * @memberof Reducer\n   */\n  constructor(options: Options) {\n    this.data = options.data;\n  }\n\n  /**\n   * Is to embed the data given into the two-dimensional space.\n   *\n   * @abstract\n   * @return {Coordinates} Cartesian coordinate of this embedding.\n   * @memberof Reducer\n   */\n  abstract transform(): Coordinates;\n}\n\n/**\n * Implements t-SNE dimensionality reduction.\n *\n * @class TSNEReducer\n * @extends {Reducer}\n */\nclass TSNEReducer extends Reducer {\n  protected reducer: TSNE;\n  protected iterations: number;\n  protected distance: DistanceMetric;\n\n  /**\n   * Creates an instance of TSNEReducer.\n   * @param {Options} options Options to pass to the constructor.\n   * @memberof TSNEReducer\n   */\n  constructor(options: Options) {\n    super(options);\n    this.reducer = new TSNE(options);\n    this.iterations = options?.iterations ?? 100;\n    this.distance = options.distance;\n  }\n\n  /**\n   * Embeds the data given into the two-dimensional space using t-SNE method.\n   * @return {Coordinates} Cartesian coordinate of this embedding.\n   */\n  public transform(): Coordinates {\n    this.reducer.initDataDist(calcDistanceMatrix(this.data, this.distance));\n\n    for (let i = 0; i < this.iterations; ++i) {\n      this.reducer.step(); // every time you call this, solution gets better\n    }\n    return this.reducer.getSolution();\n  }\n}\n\n/**\n * Implements UMAP dimensionality reduction.\n *\n * @class UMAPReducer\n * @extends {Reducer}\n */\nclass UMAPReducer extends Reducer {\n  protected reducer: umj.UMAP;\n  protected encoder: AlignedSequenceEncoder;\n  protected distanceFn: Function;\n  protected vectors: number[][];\n\n  /**\n   * Creates an instance of UMAPReducer.\n   * @param {Options} options Options to pass to the constructor.\n   * @memberof UMAPReducer\n   */\n  constructor(options: Options) {\n    super(options);\n\n    assert('distanceFn' in options);\n\n    this.encoder = new AlignedSequenceEncoder();\n    this.distanceFn = options.distanceFn;\n    this.vectors = [];\n    options.distanceFn = this._encodedDistance.bind(this);\n    this.reducer = new umj.UMAP(options);\n  }\n\n  /**\n   * Custom distance wrapper to have numeric inputs instead of string ones.\n   *\n   * @protected\n   * @param {number[]} a The first item.\n   * @param {number[]} b The first item.\n   * @return {number} Distance metric.\n   * @memberof UMAPReducer\n   */\n  protected _encodedDistance(a: number[], b: number[]): number {\n    return this.distanceFn(this.data[a[0]], this.data[b[0]]);\n  }\n\n  /**\n   * Encodes the input data as a vector of indices.\n   *\n   * @protected\n   * @memberof UMAPReducer\n   */\n  protected _encode() {\n    for (let i = 0; i < this.data.length; ++i) {\n      this.vectors.push([i]);\n    }\n  }\n\n  /**\n   * Embeds the data given into the two-dimensional space using UMAP method.\n   * @return {Coordinates} Cartesian coordinate of this embedding.\n   */\n  public transform(): Coordinates {\n    this._encode();\n\n    const embedding = this.reducer.fit(this.vectors);\n\n    function arrayCast2Coordinates(data: number[][]): Coordinates {\n      return new Array(data.length).fill(0).map((_, i) => (Vector.from(data[i])));\n    }\n\n    return arrayCast2Coordinates(embedding);\n  }\n}\n\n/**\n * Implements original SPE dimensionality reduction.\n *\n * @class SPEReducer\n * @extends {Reducer}\n */\nclass SPEReducer extends Reducer {\n  protected reducer: SPEBase;\n\n  /**\n   * Creates an instance of SPEReducer.\n   * @param {Options} options Options to pass to the constructor.\n   * @memberof SPEReducer\n   */\n  constructor(options: Options) {\n    super(options);\n    this.reducer = new SPEBase(options);\n  }\n\n  /**\n   * Embeds the data given into the two-dimensional space using the original SPE method.\n   * @return {Coordinates} Cartesian coordinate of this embedding.\n   */\n  public transform(): Coordinates {\n    return this.reducer.embed(this.data);\n  }\n}\n\n/**\n * Implements modified SPE dimensionality reduction.\n *\n * @class PSPEReducer\n * @extends {Reducer}\n */\nclass PSPEReducer extends Reducer {\n  protected reducer: PSPEBase;\n\n  /**\n   * Creates an instance of PSPEReducer.\n   * @param {Options} options Options to pass to the constructor.\n   * @memberof PSPEReducer\n   */\n  constructor(options: Options) {\n    super(options);\n    this.reducer = new PSPEBase(options);\n  }\n\n  /**\n   * Embeds the data given into the two-dimensional space using the modified SPE method.\n   * @return {Coordinates} Cartesian coordinate of this embedding.\n   */\n  public transform(): Coordinates {\n    return this.reducer.embed(this.data);\n  }\n}\n\n/**\n * Unified class implementing different dimensionality reduction methods.\n *\n * @export\n * @class DimensionalityReducer\n */\nexport class DimensionalityReducer {\n  private reducer: Reducer | undefined;\n  public static methods: string[] = ['UMAP', 't-SNE', 'SPE', 'pSPE'];\n  private measurer: Measurer;\n\n  /**\n   * Creates an instance of DimensionalityReducer.\n   * @param {any[]} data Vectors to embed.\n   * @param {string} method Embedding method to be applied\n   * @param {string} metric Distance metric to be computed between each of the vectors.\n   * @param {Options} [options] Options to pass to the implementing embedders.\n   * @memberof DimensionalityReducer\n   */\n  constructor(data: any[], method: string, metric: string, options?: Options) {\n    assert(DimensionalityReducer.availableMethods.includes(method), `The method '${method}' is not supported`);\n\n    this.measurer = new Measurer(metric);\n    const measure = this.measurer.getMeasure()\n\n    if (method == 'UMAP') {\n      this.reducer = new UMAPReducer({\n        ...{data: data}, \n        ...{distanceFn: measure}, \n        ...{nEpochs: options?.cycles},\n        ...options\n      });\n    } else if (method == 't-SNE') {\n      this.reducer = new TSNEReducer({\n        ...{data: data},\n        ...{distance: measure},\n        ...{iterations: options?.cycles ?? undefined},\n        ...options,\n      });\n    } else if (method == 'SPE') {\n      this.reducer = new SPEReducer({...{data: data}, ...{distance: measure}, ...options});\n    } else {\n      this.reducer = new PSPEReducer({...{data: data}, ...{distance: measure}, ...options});\n    }\n  }\n\n  /**\n   * Embeds the data given into the two-dimensional space using the chosen method.\n   *\n   * @param {boolean} transpose Whether to transform coordinates to have columns-first orientation.\n   * @throws {Error} If the embedding method was not found.\n   * @return {Coordinates} Cartesian coordinate of this embedding.\n   * @memberof DimensionalityReducer\n   */\n  public transform(transpose: boolean = false): Coordinates {\n    if (this.reducer == undefined) {\n      throw new Error('Reducer was not defined.');\n    }\n    let embedding = this.reducer.transform();\n\n    if (transpose) {\n      embedding = transposeMatrix(embedding);\n    }\n    return embedding;\n  }\n\n  /**\n   * Returns dimensionality reduction methods available.\n   *\n   * @readonly\n   * @memberof DimensionalityReducer\n   */\n  static get availableMethods() {\n    return DimensionalityReducer.methods;\n  }\n}\n"]}

package/src/sequence-encoder.d.ts

@@ -1,59 +0,0 @@
-/**
- * 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

package/src/sequence-encoder.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"sequence-encoder.d.ts","sourceRoot":"","sources":["sequence-encoder.ts"],"names":[],"mappings":"AAEA;;;;;GAKG;AACH,qBAAa,sBAAsB;IAC/B,SAAS,CAAC,MAAM,EAAE;QAAC,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAAA;KAAC,CAAC;IAC3C,SAAS,CAAC,MAAM,EAAE;QAAC,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAAA;KAAC,CAAC;;IA8B3C;;;;;;;OAOG;IACH,MAAM,CAAC,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM;IAkB7C;;;;;;;OAOG;IACH,MAAM,CAAC,YAAY,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM;IAIxC;;;;;;;OAOG;IACH,MAAM,CAAC,KAAK,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM;IAItC;;;;;;OAMG;IACI,MAAM,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE;IAczC;;;;;;OAMG;IACI,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,MAAM;CAYzC"}

package/src/sequence-encoder.js

@@ -1,116 +0,0 @@
-import { assert } from './operations';
-/**
- * Class to categorial encode/decode aligned amino acid residues sequence.
- *
- * @export
- * @class AlignedSequenceEncoder
- */
-export class AlignedSequenceEncoder {
-    constructor() {
-        this.aa2num = {
-            '-': 0,
-            'A': 1,
-            'C': 2,
-            'D': 3,
-            'E': 4,
-            'F': 5,
-            'G': 6,
-            'H': 7,
-            'I': 8,
-            'K': 9,
-            'L': 10,
-            'M': 11,
-            'N': 12,
-            'P': 13,
-            'Q': 14,
-            'R': 15,
-            'S': 16,
-            'T': 17,
-            'V': 18,
-            'W': 19,
-            'Y': 20,
-        };
-        this.num2aa = {};
-        Object.entries(this.aa2num).forEach(([k, v]) => (this.num2aa[v] = k));
-    }
-    /**
-     * 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) {
-        let start = 0;
-        let end = seq.length;
-        const termina = ['NH2', 'COOH'];
-        if (seq.startsWith(termina[0])) {
-            const l = termina[0].length; // Cut only 'NH2' without following '-'.
-            assert(seq[l] == '-', `Wrong sequence format: ${termina[0]} without following '-' in '${seq}'.`);
-            start = l;
-        }
-        if (seq.endsWith(termina[1])) {
-            const l = termina[1].length + 1; // Cut both 'COOH' and precending '-'.
-            assert(seq[end - l] == '-', `Wrong sequence format: ${termina[1]} without '-' precending in '${seq}'.`);
-            end -= l;
-        }
-        return seq.substring(start, end);
-    }
-    /**
-     * Cuts auxiliary defises before a residue.
-     *
-     * @static
-     * @param {string} seq The sequence to process.
-     * @return {string} Processed sequence.
-     * @memberof AlignedSequenceEncoder
-     */
-    static _dropDefises(seq) {
-        return seq.replace(/(-)([^-]+)/g, '$2');
-    }
-    /**
-     * Performs truncation and cutting auxiliary defises.
-     *
-     * @static
-     * @param {string} sequence The sequence work under process.
-     * @return {string} Result of cleaning.
-     * @memberof AlignedSequenceEncoder
-     */
-    static clean(sequence) {
-        return AlignedSequenceEncoder._dropDefises(AlignedSequenceEncoder._truncateSequence(sequence));
-    }
-    /**
-     * Categorial encode of the sequence provided.
-     *
-     * @param {string} sequence The sequence.
-     * @return {number[]} Encoded vector.
-     * @memberof AlignedSequenceEncoder
-     */
-    encode(sequence) {
-        const nItems = sequence.length;
-        let values = new Array(nItems).fill(0);
-        for (let i = 0; i < nItems; ++i) {
-            let char = sequence[i];
-            assert(char in this.aa2num, `Unknown char '${char}' found in sequence '${sequence}'`);
-            values[i] = this.aa2num[char];
-        }
-        return values;
-    }
-    /**
-     * Decode the encoded vector into the sequence back.
-     *
-     * @param {number[]} value The vector encoded.
-     * @return {string} Decoded sequence.
-     * @memberof AlignedSequenceEncoder
-     */
-    decode(value) {
-        let s = '';
-        for (let i = 0; i < value.length; ++i) {
-            let code = value[i];
-            assert(code in this.num2aa, `Unknown code '${code}' found in vector '${value}'`);
-            s += this.num2aa[code];
-        }
-        return s;
-    }
-}
-//# sourceMappingURL=data:application/json;base64,{"version":3,"file":"sequence-encoder.js","sourceRoot":"","sources":["sequence-encoder.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,MAAM,EAAC,MAAM,cAAc,CAAC;AAEpC;;;;;GAKG;AACH,MAAM,OAAO,sBAAsB;IAI/B;QACI,IAAI,CAAC,MAAM,GAAG;YACV,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;YACP,GAAG,EAAE,EAAE;SACV,CAAC;QACF,IAAI,CAAC,MAAM,GAAG,EAAE,CAAC;QACjB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;IAC1E,CAAC;IAED;;;;;;;OAOG;IACH,MAAM,CAAC,iBAAiB,CAAC,GAAW;QAChC,IAAI,KAAK,GAAG,CAAC,CAAC;QACd,IAAI,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC;QACrB,MAAM,OAAO,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;QAEhC,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE;YAC5B,MAAM,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,wCAAwC;YACrE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,0BAA0B,OAAO,CAAC,CAAC,CAAC,8BAA8B,GAAG,IAAI,CAAC,CAAA;YAChG,KAAK,GAAG,CAAC,CAAC;SACb;QACD,IAAI,GAAG,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE;YAC1B,MAAM,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,GAAC,CAAC,CAAC,CAAC,sCAAsC;YACrE,MAAM,CAAC,GAAG,CAAC,GAAG,GAAC,CAAC,CAAC,IAAI,GAAG,EAAE,0BAA0B,OAAO,CAAC,CAAC,CAAC,+BAA+B,GAAG,IAAI,CAAC,CAAA;YACrG,GAAG,IAAI,CAAC,CAAC;SACZ;QACD,OAAO,GAAG,CAAC,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IACrC,CAAC;IAED;;;;;;;OAOG;IACH,MAAM,CAAC,YAAY,CAAC,GAAW;QAC3B,OAAO,GAAG,CAAC,OAAO,CAAC,aAAa,EAAE,IAAI,CAAC,CAAA;IAC3C,CAAC;IAED;;;;;;;OAOG;IACH,MAAM,CAAC,KAAK,CAAC,QAAgB;QACzB,OAAO,sBAAsB,CAAC,YAAY,CAAC,sBAAsB,CAAC,iBAAiB,CAAC,QAAQ,CAAC,CAAC,CAAC;IACnG,CAAC;IAED;;;;;;OAMG;IACI,MAAM,CAAC,QAAgB;QAC1B,MAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC;QAC/B,IAAI,MAAM,GAAG,IAAI,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAEvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,EAAE,CAAC,EAAE;YAC7B,IAAI,IAAI,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;YAEvB,MAAM,CAAC,IAAI,IAAI,IAAI,CAAC,MAAM,EAAE,iBAAiB,IAAI,wBAAwB,QAAQ,GAAG,CAAC,CAAC;YAEtF,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;SACjC;QACD,OAAO,MAAM,CAAC;IAClB,CAAC;IAED;;;;;;OAMG;IACI,MAAM,CAAC,KAAe;QACzB,IAAI,CAAC,GAAW,EAAE,CAAC;QAEnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;YACnC,IAAI,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;YAEpB,MAAM,CAAC,IAAI,IAAI,IAAI,CAAC,MAAM,EAAE,iBAAiB,IAAI,sBAAsB,KAAK,GAAG,CAAC,CAAC;YAEjF,CAAC,IAAI,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;SAC1B;QACD,OAAO,CAAC,CAAC;IACb,CAAC;CACJ","sourcesContent":["import {assert} from './operations';\n\n/**\n * Class to categorial encode/decode aligned amino acid residues sequence.\n *\n * @export\n * @class AlignedSequenceEncoder\n */\nexport class AlignedSequenceEncoder {\n    protected aa2num: {[name: string]: number};\n    protected num2aa: {[code: number]: string};\n\n    constructor () {\n        this.aa2num = {\n            '-': 0,\n            'A': 1,\n            'C': 2,\n            'D': 3,\n            'E': 4,\n            'F': 5,\n            'G': 6,\n            'H': 7,\n            'I': 8,\n            'K': 9,\n            'L': 10,\n            'M': 11,\n            'N': 12,\n            'P': 13,\n            'Q': 14,\n            'R': 15,\n            'S': 16,\n            'T': 17,\n            'V': 18,\n            'W': 19,\n            'Y': 20,\n        };\n        this.num2aa = {};\n        Object.entries(this.aa2num).forEach(([k, v]) => (this.num2aa[v] = k));\n    }\n\n    /**\n     * Truncate NH2 and -COOH terminals of the given sequence.\n     *\n     * @static\n     * @param {string} seq The sequence provided.\n     * @return {string} Truncated sequence.\n     * @memberof AlignedSequenceEncoder\n     */\n    static _truncateSequence(seq: string): string {\n        let start = 0;\n        let end = seq.length;\n        const termina = ['NH2', 'COOH'];\n    \n        if (seq.startsWith(termina[0])) {\n            const l = termina[0].length; // Cut only 'NH2' without following '-'.\n            assert(seq[l] == '-', `Wrong sequence format: ${termina[0]} without following '-' in '${seq}'.`)\n            start = l;\n        }\n        if (seq.endsWith(termina[1])) {\n            const l = termina[1].length+1; // Cut both 'COOH' and precending '-'.\n            assert(seq[end-l] == '-', `Wrong sequence format: ${termina[1]} without '-' precending in '${seq}'.`)\n            end -= l;\n        }\n        return seq.substring(start, end);\n    }\n\n    /**\n     * Cuts auxiliary defises before a residue.\n     *\n     * @static\n     * @param {string} seq The sequence to process.\n     * @return {string} Processed sequence.\n     * @memberof AlignedSequenceEncoder\n     */\n    static _dropDefises(seq: string): string {\n        return seq.replace(/(-)([^-]+)/g, '$2')\n    }\n\n    /**\n     * Performs truncation and cutting auxiliary defises.\n     *\n     * @static\n     * @param {string} sequence The sequence work under process.\n     * @return {string} Result of cleaning.\n     * @memberof AlignedSequenceEncoder\n     */\n    static clean(sequence: string): string {\n        return AlignedSequenceEncoder._dropDefises(AlignedSequenceEncoder._truncateSequence(sequence));\n    }\n\n    /**\n     * Categorial encode of the sequence provided.\n     *\n     * @param {string} sequence The sequence.\n     * @return {number[]} Encoded vector.\n     * @memberof AlignedSequenceEncoder\n     */\n    public encode(sequence: string): number[] {\n        const nItems = sequence.length;\n        let values = new Array(nItems).fill(0);\n    \n        for (let i = 0; i < nItems; ++i) {\n            let char = sequence[i];\n    \n            assert(char in this.aa2num, `Unknown char '${char}' found in sequence '${sequence}'`);\n    \n            values[i] = this.aa2num[char];\n        }\n        return values;\n    }\n\n    /**\n     * Decode the encoded vector into the sequence back.\n     *\n     * @param {number[]} value The vector encoded.\n     * @return {string} Decoded sequence.\n     * @memberof AlignedSequenceEncoder\n     */\n    public decode(value: number[]): string {\n        let s: string = '';\n    \n        for (let i = 0; i < value.length; ++i) {\n            let code = value[i];\n\n            assert(code in this.num2aa, `Unknown code '${code}' found in vector '${value}'`);\n\n            s += this.num2aa[code];\n        }\n        return s;\n    }\n}\n"]}

package/src/spe.d.ts

@@ -1,68 +0,0 @@
-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

@@ -1 +0,0 @@
-{"version":3,"file":"spe.d.ts","sourceRoot":"","sources":["spe.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,EAAC,MAAM,qBAAqB,CAAC;AAGlF;;;;;;GAMG;AACH,qBAAa,OAAO;IAClB,SAAS,CAAC,MAAM,CAAC,SAAS,SAAK;IAC/B,SAAS,CAAC,KAAK,EAAE,MAAM,CAAC;IACxB,SAAS,CAAC,MAAM,EAAE,MAAM,CAAC;IACzB,SAAS,CAAC,MAAM,EAAE,MAAM,CAAC;IACzB,SAAS,CAAC,MAAM,EAAE,MAAM,CAAC;IACzB,SAAS,CAAC,OAAO,EAAE,MAAM,CAAC;IAC1B,SAAS,CAAC,OAAO,EAAE,MAAM,CAAC;IAC1B,SAAS,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC3B,SAAS,CAAC,OAAO,EAAE,MAAM,CAAC;IAC1B,SAAS,CAAC,gBAAgB,EAAE,cAAc,CAAC;IAC3C,SAAS,CAAC,QAAQ,EAAE,WAAW,CAAC;IAEhC;;;;OAIG;gBACS,OAAO,CAAC,EAAE,OAAO;IAgB7B;;;;;;OAMG;IACH,SAAS,CAAC,YAAY,CAAC,OAAO,EAAE,OAAO;IAIvC;;;;;;;OAOG;IACH,SAAS,CAAC,YAAY,CAAC,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM;IAIhF;;;;;OAKG;IACI,KAAK,CAAC,OAAO,EAAE,OAAO,GAAG,WAAW;CA4C5C;AAED;;;;;;GAMG;AACF,qBAAa,QAAS,SAAQ,OAAO;IACpC;;;;;OAKG;IACI,KAAK,CAAC,OAAO,EAAE,OAAO,GAAG,WAAW;CAsC5C"}