@datagrok-libraries/bio 0.0.3 → 0.0.4

package/package.json

@@ -5,7 +5,7 @@
   },
   "beta": true,
   "friendlyName": "Datagrok bio library",
-  "version": "0.0.3",
+  "version": "0.0.4",
   "description": "",
   "dependencies": {
     "datagrok-api": ">=0.108.0",

package/src/sequence-encoder.js

@@ -0,0 +1,155 @@
+import { assert } from '@datagrok-libraries/utils/src/operations';
+class SideChainScales {
+    static getAvailableScales() {
+        return Object.entries(this.scales).map(([k, _]) => k);
+    }
+    static getScale(name) {
+        assert(!(this.scales[name] === undefined), `Scale '${name}' was not found.`);
+        return this.scales[name];
+    }
+}
+SideChainScales.scales = {
+    // Wimley-White interfacial hydrophobicity scale
+    'WimleyWhite': {
+        '-': 0,
+        'A': 0.17,
+        'C': -0.24,
+        'D': -0.07,
+        'E': -0.01,
+        'F': -1.13,
+        'G': 0.01,
+        'H': 0.17,
+        'I': -0.31,
+        'K': 0.99,
+        'L': -0.56,
+        'M': -0.23,
+        'N': 0.42,
+        'P': 0.45,
+        'Q': 0.58,
+        'R': 0.81,
+        'S': 0.13,
+        'T': 0.14,
+        'V': 0.07,
+        'W': -1.85,
+        'Y': -0.94,
+    },
+    'categorial': {
+        '-': 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,
+    },
+};
+/**
+ * Class to categorial encode/decode aligned amino acid residues sequence.
+ *
+ * @export
+ * @class AlignedSequenceEncoder
+ */
+export class AlignedSequenceEncoder {
+    constructor(scale = 'categorial') {
+        this.aa2num = SideChainScales.getScale(scale);
+        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, '$2');
+    }
+    /**
+       * Performs truncation and cutting auxiliary defises.
+       *
+       * @static
+       * @param {string} sequence The sequence work under process.
+       * @return {string} Result of cleaning.
+       * @memberof AlignedSequenceEncoder
+       */
+    static clean(sequence) {
+        return AlignedSequenceEncoder._dropDefises(AlignedSequenceEncoder._truncateSequence(sequence));
+    }
+    /**
+       * Categorial encode of the sequence provided.
+       *
+       * @param {string} sequence The sequence.
+       * @return {number[]} Encoded vector.
+       * @memberof AlignedSequenceEncoder
+       */
+    encode(sequence) {
+        const nItems = sequence.length;
+        const values = new Array(nItems).fill(0);
+        for (let i = 0; i < nItems; ++i) {
+            const char = sequence[i];
+            assert(char in this.aa2num, `Unknown char '${char}' found in sequence '${sequence}'`);
+            values[i] = this.encodeLettter(char);
+        }
+        return values;
+    }
+    encodeLettter(letter) {
+        return this.aa2num[letter];
+    }
+    /**
+       * Decode the encoded vector into the sequence back.
+       *
+       * @param {number[]} value The vector encoded.
+       * @return {string} Decoded sequence.
+       * @memberof AlignedSequenceEncoder
+       */
+    decode(value) {
+        let s = '';
+        for (let i = 0; i < value.length; ++i) {
+            const code = value[i];
+            assert(code in this.num2aa, `Unknown code '${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,0CAA0C,CAAC;AAKhE,MAAM,eAAe;IAmDnB,MAAM,CAAC,kBAAkB;QACvB,OAAO,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;IACxD,CAAC;IAED,MAAM,CAAC,QAAQ,CAAC,IAAY;QAC1B,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,SAAS,CAAC,EAAE,UAAU,IAAI,kBAAkB,CAAC,CAAC;QAC7E,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IAC3B,CAAC;;AAzDM,sBAAM,GAA6B;IACxC,gDAAgD;IAChD,aAAa,EAAE;QACb,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,CAAC,IAAI;QACV,GAAG,EAAE,CAAC,IAAI;QACV,GAAG,EAAE,CAAC,IAAI;QACV,GAAG,EAAE,CAAC,IAAI;QACV,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,CAAC,IAAI;QACV,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,CAAC,IAAI;QACV,GAAG,EAAE,CAAC,IAAI;QACV,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,IAAI;QACT,GAAG,EAAE,CAAC,IAAI;QACV,GAAG,EAAE,CAAC,IAAI;KACX;IACD,YAAY,EAAE;QACZ,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,CAAC;QACN,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;QACP,GAAG,EAAE,EAAE;KACR;CACF,CAAC;AAYJ;;;;;GAKG;AACH,MAAM,OAAO,sBAAsB;IAIjC,YAAY,QAAgB,YAAY;QACtC,IAAI,CAAC,MAAM,GAAG,eAAe,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;QAC9C,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;IACxE,CAAC;IAED;;;;;;;SAOK;IACL,MAAM,CAAC,iBAAiB,CAAC,GAAW;QAClC,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;YAC9B,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,CAAC;YACjG,KAAK,GAAG,CAAC,CAAC;SACX;QACD,IAAI,GAAG,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE;YAC5B,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,CAAC;YACtG,GAAG,IAAI,CAAC,CAAC;SACV;QACD,OAAO,GAAG,CAAC,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IACnC,CAAC;IAED;;;;;;;SAOK;IACL,MAAM,CAAC,YAAY,CAAC,GAAW;QAC7B,OAAO,GAAG,CAAC,OAAO,CAAC,aAAa,EAAE,IAAI,CAAC,CAAC;IAC1C,CAAC;IAED;;;;;;;SAOK;IACL,MAAM,CAAC,KAAK,CAAC,QAAgB;QAC3B,OAAO,sBAAsB,CAAC,YAAY,CAAC,sBAAsB,CAAC,iBAAiB,CAAC,QAAQ,CAAC,CAAC,CAAC;IACjG,CAAC;IAED;;;;;;SAMK;IACE,MAAM,CAAC,QAAgB;QAC5B,MAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC;QAC/B,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAEzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,EAAE,CAAC,EAAE;YAC/B,MAAM,IAAI,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;YAEzB,MAAM,CAAC,IAAI,IAAI,IAAI,CAAC,MAAM,EAAE,iBAAiB,IAAI,wBAAwB,QAAQ,GAAG,CAAC,CAAC;YAEtF,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,IAAI,CAAC,CAAC;SACtC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC;IAEM,aAAa,CAAC,MAAc;QACjC,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IAC7B,CAAC;IAED;;;;;;SAMK;IACE,MAAM,CAAC,KAAe;QAC3B,IAAI,CAAC,GAAW,EAAE,CAAC;QAEnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;YACrC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;YAEtB,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;SACxB;QACD,OAAO,CAAC,CAAC;IACX,CAAC;CACF","sourcesContent":["import {assert} from '@datagrok-libraries/utils/src/operations';\r\n\r\ntype SideChainScale = {[name: string]: number};\r\ntype SideChainScaleCollection = {[name: string]: SideChainScale};\r\n\r\nclass SideChainScales {\r\n  static scales: SideChainScaleCollection = {\r\n    // Wimley-White interfacial hydrophobicity scale\r\n    'WimleyWhite': {\r\n      '-': 0,\r\n      'A': 0.17,\r\n      'C': -0.24,\r\n      'D': -0.07, // Asp-: 1.23\r\n      'E': -0.01, // Glu-: 2.02\r\n      'F': -1.13, //\r\n      'G': 0.01,\r\n      'H': 0.17, // His+: 0.96\r\n      'I': -0.31,\r\n      'K': 0.99, // Lys+\r\n      'L': -0.56,\r\n      'M': -0.23,\r\n      'N': 0.42,\r\n      'P': 0.45,\r\n      'Q': 0.58,\r\n      'R': 0.81, // Arg+\r\n      'S': 0.13,\r\n      'T': 0.14,\r\n      'V': 0.07,\r\n      'W': -1.85,\r\n      'Y': -0.94,\r\n    },\r\n    'categorial': {\r\n      '-': 0,\r\n      'A': 1,\r\n      'C': 2,\r\n      'D': 3,\r\n      'E': 4,\r\n      'F': 5,\r\n      'G': 6,\r\n      'H': 7,\r\n      'I': 8,\r\n      'K': 9,\r\n      'L': 10,\r\n      'M': 11,\r\n      'N': 12,\r\n      'P': 13,\r\n      'Q': 14,\r\n      'R': 15,\r\n      'S': 16,\r\n      'T': 17,\r\n      'V': 18,\r\n      'W': 19,\r\n      'Y': 20,\r\n    },\r\n  };\r\n\r\n  static getAvailableScales(): string[] {\r\n    return Object.entries(this.scales).map(([k, _]) => k);\r\n  }\r\n\r\n  static getScale(name: string): SideChainScale {\r\n    assert(!(this.scales[name] === undefined), `Scale '${name}' was not found.`);\r\n    return this.scales[name];\r\n  }\r\n}\r\n\r\n/**\r\n * Class to categorial encode/decode aligned amino acid residues sequence.\r\n *\r\n * @export\r\n * @class AlignedSequenceEncoder\r\n */\r\nexport class AlignedSequenceEncoder {\r\n  protected aa2num: SideChainScale;\r\n  protected num2aa: {[code: number]: string};\r\n\r\n  constructor(scale: string = 'categorial') {\r\n    this.aa2num = SideChainScales.getScale(scale);\r\n    this.num2aa = {};\r\n    Object.entries(this.aa2num).forEach(([k, v]) => (this.num2aa[v] = k));\r\n  }\r\n\r\n  /**\r\n     * Truncate NH2 and -COOH terminals of the given sequence.\r\n     *\r\n     * @static\r\n     * @param {string} seq The sequence provided.\r\n     * @return {string} Truncated sequence.\r\n     * @memberof AlignedSequenceEncoder\r\n     */\r\n  static _truncateSequence(seq: string): string {\r\n    let start = 0;\r\n    let end = seq.length;\r\n    const termina = ['NH2', 'COOH'];\r\n\r\n    if (seq.startsWith(termina[0])) {\r\n      const l = termina[0].length; // Cut only 'NH2' without following '-'.\r\n      assert(seq[l] == '-', `Wrong sequence format: ${termina[0]} without following '-' in '${seq}'.`);\r\n      start = l;\r\n    }\r\n    if (seq.endsWith(termina[1])) {\r\n      const l = termina[1].length+1; // Cut both 'COOH' and precending '-'.\r\n      assert(seq[end-l] == '-', `Wrong sequence format: ${termina[1]} without '-' precending in '${seq}'.`);\r\n      end -= l;\r\n    }\r\n    return seq.substring(start, end);\r\n  }\r\n\r\n  /**\r\n     * Cuts auxiliary defises before a residue.\r\n     *\r\n     * @static\r\n     * @param {string} seq The sequence to process.\r\n     * @return {string} Processed sequence.\r\n     * @memberof AlignedSequenceEncoder\r\n     */\r\n  static _dropDefises(seq: string): string {\r\n    return seq.replace(/(-)([^-]+)/g, '$2');\r\n  }\r\n\r\n  /**\r\n     * Performs truncation and cutting auxiliary defises.\r\n     *\r\n     * @static\r\n     * @param {string} sequence The sequence work under process.\r\n     * @return {string} Result of cleaning.\r\n     * @memberof AlignedSequenceEncoder\r\n     */\r\n  static clean(sequence: string): string {\r\n    return AlignedSequenceEncoder._dropDefises(AlignedSequenceEncoder._truncateSequence(sequence));\r\n  }\r\n\r\n  /**\r\n     * Categorial encode of the sequence provided.\r\n     *\r\n     * @param {string} sequence The sequence.\r\n     * @return {number[]} Encoded vector.\r\n     * @memberof AlignedSequenceEncoder\r\n     */\r\n  public encode(sequence: string): number[] {\r\n    const nItems = sequence.length;\r\n    const values = new Array(nItems).fill(0);\r\n\r\n    for (let i = 0; i < nItems; ++i) {\r\n      const char = sequence[i];\r\n\r\n      assert(char in this.aa2num, `Unknown char '${char}' found in sequence '${sequence}'`);\r\n\r\n      values[i] = this.encodeLettter(char);\r\n    }\r\n    return values;\r\n  }\r\n\r\n  public encodeLettter(letter: string): number {\r\n    return this.aa2num[letter];\r\n  }\r\n\r\n  /**\r\n     * Decode the encoded vector into the sequence back.\r\n     *\r\n     * @param {number[]} value The vector encoded.\r\n     * @return {string} Decoded sequence.\r\n     * @memberof AlignedSequenceEncoder\r\n     */\r\n  public decode(value: number[]): string {\r\n    let s: string = '';\r\n\r\n    for (let i = 0; i < value.length; ++i) {\r\n      const code = value[i];\r\n\r\n      assert(code in this.num2aa, `Unknown code '${code}' found in vector '${value}'`);\r\n\r\n      s += this.num2aa[code];\r\n    }\r\n    return s;\r\n  }\r\n}\r\n"]}

package/src/sequence-encoder.ts

@@ -1,177 +0,0 @@
-import {assert} from '@datagrok-libraries/utils/src/operations';
-
-type SideChainScale = {[name: string]: number};
-type SideChainScaleCollection = {[name: string]: SideChainScale};
-
-class SideChainScales {
-  static scales: SideChainScaleCollection = {
-    // Wimley-White interfacial hydrophobicity scale
-    'WimleyWhite': {
-      '-': 0,
-      'A': 0.17,
-      'C': -0.24,
-      'D': -0.07, // Asp-: 1.23
-      'E': -0.01, // Glu-: 2.02
-      'F': -1.13, //
-      'G': 0.01,
-      'H': 0.17, // His+: 0.96
-      'I': -0.31,
-      'K': 0.99, // Lys+
-      'L': -0.56,
-      'M': -0.23,
-      'N': 0.42,
-      'P': 0.45,
-      'Q': 0.58,
-      'R': 0.81, // Arg+
-      'S': 0.13,
-      'T': 0.14,
-      'V': 0.07,
-      'W': -1.85,
-      'Y': -0.94,
-    },
-    'categorial': {
-      '-': 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,
-    },
-  };
-
-  static getAvailableScales(): string[] {
-    return Object.entries(this.scales).map(([k, _]) => k);
-  }
-
-  static getScale(name: string): SideChainScale {
-    assert(!(this.scales[name] === undefined), `Scale '${name}' was not found.`);
-    return this.scales[name];
-  }
-}
-
-/**
- * Class to categorial encode/decode aligned amino acid residues sequence.
- *
- * @export
- * @class AlignedSequenceEncoder
- */
-export class AlignedSequenceEncoder {
-  protected aa2num: SideChainScale;
-  protected num2aa: {[code: number]: string};
-
-  constructor(scale: string = 'categorial') {
-    this.aa2num = SideChainScales.getScale(scale);
-    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: string): string {
-    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: string): string {
-    return seq.replace(/(-)([^-]+)/g, '$2');
-  }
-
-  /**
-     * Performs truncation and cutting auxiliary defises.
-     *
-     * @static
-     * @param {string} sequence The sequence work under process.
-     * @return {string} Result of cleaning.
-     * @memberof AlignedSequenceEncoder
-     */
-  static clean(sequence: string): string {
-    return AlignedSequenceEncoder._dropDefises(AlignedSequenceEncoder._truncateSequence(sequence));
-  }
-
-  /**
-     * Categorial encode of the sequence provided.
-     *
-     * @param {string} sequence The sequence.
-     * @return {number[]} Encoded vector.
-     * @memberof AlignedSequenceEncoder
-     */
-  public encode(sequence: string): number[] {
-    const nItems = sequence.length;
-    const values = new Array(nItems).fill(0);
-
-    for (let i = 0; i < nItems; ++i) {
-      const char = sequence[i];
-
-      assert(char in this.aa2num, `Unknown char '${char}' found in sequence '${sequence}'`);
-
-      values[i] = this.encodeLettter(char);
-    }
-    return values;
-  }
-
-  public encodeLettter(letter: string): number {
-    return this.aa2num[letter];
-  }
-
-  /**
-     * Decode the encoded vector into the sequence back.
-     *
-     * @param {number[]} value The vector encoded.
-     * @return {string} Decoded sequence.
-     * @memberof AlignedSequenceEncoder
-     */
-  public decode(value: number[]): string {
-    let s: string = '';
-
-    for (let i = 0; i < value.length; ++i) {
-      const code = value[i];
-
-      assert(code in this.num2aa, `Unknown code '${code}' found in vector '${value}'`);
-
-      s += this.num2aa[code];
-    }
-    return s;
-  }
-}