@datagrok-libraries/utils 0.0.7 → 0.0.11

package/src/reduce-dimensionality.js

@@ -1,233 +1,233 @@
-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';\r\nimport {TSNE} from '@keckelt/tsne';\r\n\r\nimport {Options, DistanceMetric, Coordinates, Vector, Vectors, Matrix} from './type_declarations';\r\nimport {calcDistanceMatrix, transposeMatrix} from './operations';\r\nimport {SPEBase, PSPEBase} from './spe';\r\nimport {Measurer} from './string-measure';\r\nimport {AlignedSequenceEncoder} from './sequence-encoder';\r\nimport {assert} from './operations';\r\n\r\n/**\r\n * Abstract dimensionality reducer.\r\n *\r\n * @abstract\r\n * @class Reducer\r\n */\r\nabstract class Reducer {\r\n  protected data: Vectors;\r\n\r\n  /**\r\n   * Creates an instance of Reducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof Reducer\r\n   */\r\n  constructor(options: Options) {\r\n    this.data = options.data;\r\n  }\r\n\r\n  /**\r\n   * Is to embed the data given into the two-dimensional space.\r\n   *\r\n   * @abstract\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   * @memberof Reducer\r\n   */\r\n  abstract transform(): Coordinates;\r\n}\r\n\r\n/**\r\n * Implements t-SNE dimensionality reduction.\r\n *\r\n * @class TSNEReducer\r\n * @extends {Reducer}\r\n */\r\nclass TSNEReducer extends Reducer {\r\n  protected reducer: TSNE;\r\n  protected iterations: number;\r\n  protected distance: DistanceMetric;\r\n\r\n  /**\r\n   * Creates an instance of TSNEReducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof TSNEReducer\r\n   */\r\n  constructor(options: Options) {\r\n    super(options);\r\n    this.reducer = new TSNE(options);\r\n    this.iterations = options?.iterations ?? 100;\r\n    this.distance = options.distance;\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using t-SNE method.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   */\r\n  public transform(): Coordinates {\r\n    this.reducer.initDataDist(calcDistanceMatrix(this.data, this.distance));\r\n\r\n    for (let i = 0; i < this.iterations; ++i) {\r\n      this.reducer.step(); // every time you call this, solution gets better\r\n    }\r\n    return this.reducer.getSolution();\r\n  }\r\n}\r\n\r\n/**\r\n * Implements UMAP dimensionality reduction.\r\n *\r\n * @class UMAPReducer\r\n * @extends {Reducer}\r\n */\r\nclass UMAPReducer extends Reducer {\r\n  protected reducer: umj.UMAP;\r\n  protected encoder: AlignedSequenceEncoder;\r\n  protected distanceFn: Function;\r\n  protected vectors: number[][];\r\n\r\n  /**\r\n   * Creates an instance of UMAPReducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof UMAPReducer\r\n   */\r\n  constructor(options: Options) {\r\n    super(options);\r\n\r\n    assert('distanceFn' in options);\r\n\r\n    this.encoder = new AlignedSequenceEncoder();\r\n    this.distanceFn = options.distanceFn;\r\n    this.vectors = [];\r\n    options.distanceFn = this._encodedDistance.bind(this);\r\n    this.reducer = new umj.UMAP(options);\r\n  }\r\n\r\n  /**\r\n   * Custom distance wrapper to have numeric inputs instead of string ones.\r\n   *\r\n   * @protected\r\n   * @param {number[]} a The first item.\r\n   * @param {number[]} b The first item.\r\n   * @return {number} Distance metric.\r\n   * @memberof UMAPReducer\r\n   */\r\n  protected _encodedDistance(a: number[], b: number[]): number {\r\n    return this.distanceFn(this.data[a[0]], this.data[b[0]]);\r\n  }\r\n\r\n  /**\r\n   * Encodes the input data as a vector of indices.\r\n   *\r\n   * @protected\r\n   * @memberof UMAPReducer\r\n   */\r\n  protected _encode() {\r\n    for (let i = 0; i < this.data.length; ++i) {\r\n      this.vectors.push([i]);\r\n    }\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using UMAP method.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   */\r\n  public transform(): Coordinates {\r\n    this._encode();\r\n\r\n    const embedding = this.reducer.fit(this.vectors);\r\n\r\n    function arrayCast2Coordinates(data: number[][]): Coordinates {\r\n      return new Array(data.length).fill(0).map((_, i) => (Vector.from(data[i])));\r\n    }\r\n\r\n    return arrayCast2Coordinates(embedding);\r\n  }\r\n}\r\n\r\n/**\r\n * Implements original SPE dimensionality reduction.\r\n *\r\n * @class SPEReducer\r\n * @extends {Reducer}\r\n */\r\nclass SPEReducer extends Reducer {\r\n  protected reducer: SPEBase;\r\n\r\n  /**\r\n   * Creates an instance of SPEReducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof SPEReducer\r\n   */\r\n  constructor(options: Options) {\r\n    super(options);\r\n    this.reducer = new SPEBase(options);\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using the original SPE method.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   */\r\n  public transform(): Coordinates {\r\n    return this.reducer.embed(this.data);\r\n  }\r\n}\r\n\r\n/**\r\n * Implements modified SPE dimensionality reduction.\r\n *\r\n * @class PSPEReducer\r\n * @extends {Reducer}\r\n */\r\nclass PSPEReducer extends Reducer {\r\n  protected reducer: PSPEBase;\r\n\r\n  /**\r\n   * Creates an instance of PSPEReducer.\r\n   * @param {Options} options Options to pass to the constructor.\r\n   * @memberof PSPEReducer\r\n   */\r\n  constructor(options: Options) {\r\n    super(options);\r\n    this.reducer = new PSPEBase(options);\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using the modified SPE method.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   */\r\n  public transform(): Coordinates {\r\n    return this.reducer.embed(this.data);\r\n  }\r\n}\r\n\r\n/**\r\n * Unified class implementing different dimensionality reduction methods.\r\n *\r\n * @export\r\n * @class DimensionalityReducer\r\n */\r\nexport class DimensionalityReducer {\r\n  private reducer: Reducer | undefined;\r\n  public static methods: string[] = ['UMAP', 't-SNE', 'SPE', 'pSPE'];\r\n  private measurer: Measurer;\r\n\r\n  /**\r\n   * Creates an instance of DimensionalityReducer.\r\n   * @param {any[]} data Vectors to embed.\r\n   * @param {string} method Embedding method to be applied\r\n   * @param {string} metric Distance metric to be computed between each of the vectors.\r\n   * @param {Options} [options] Options to pass to the implementing embedders.\r\n   * @memberof DimensionalityReducer\r\n   */\r\n  constructor(data: any[], method: string, metric: string, options?: Options) {\r\n    assert(DimensionalityReducer.availableMethods.includes(method), `The method '${method}' is not supported`);\r\n\r\n    this.measurer = new Measurer(metric);\r\n    const measure = this.measurer.getMeasure()\r\n\r\n    if (method == 'UMAP') {\r\n      this.reducer = new UMAPReducer({\r\n        ...{data: data}, \r\n        ...{distanceFn: measure}, \r\n        ...{nEpochs: options?.cycles},\r\n        ...options\r\n      });\r\n    } else if (method == 't-SNE') {\r\n      this.reducer = new TSNEReducer({\r\n        ...{data: data},\r\n        ...{distance: measure},\r\n        ...{iterations: options?.cycles ?? undefined},\r\n        ...options,\r\n      });\r\n    } else if (method == 'SPE') {\r\n      this.reducer = new SPEReducer({...{data: data}, ...{distance: measure}, ...options});\r\n    } else {\r\n      this.reducer = new PSPEReducer({...{data: data}, ...{distance: measure}, ...options});\r\n    }\r\n  }\r\n\r\n  /**\r\n   * Embeds the data given into the two-dimensional space using the chosen method.\r\n   *\r\n   * @param {boolean} transpose Whether to transform coordinates to have columns-first orientation.\r\n   * @throws {Error} If the embedding method was not found.\r\n   * @return {Coordinates} Cartesian coordinate of this embedding.\r\n   * @memberof DimensionalityReducer\r\n   */\r\n  public transform(transpose: boolean = false): Coordinates {\r\n    if (this.reducer == undefined) {\r\n      throw new Error('Reducer was not defined.');\r\n    }\r\n    let embedding = this.reducer.transform();\r\n\r\n    if (transpose) {\r\n      embedding = transposeMatrix(embedding);\r\n    }\r\n    return embedding;\r\n  }\r\n\r\n  /**\r\n   * Returns dimensionality reduction methods available.\r\n   *\r\n   * @readonly\r\n   * @memberof DimensionalityReducer\r\n   */\r\n  static get availableMethods() {\r\n    return DimensionalityReducer.methods;\r\n  }\r\n}\r\n"]}
+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

@@ -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

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

@@ -0,0 +1 @@
+{"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"}