@datagrok-libraries/utils 0.0.7 → 0.0.11

package/src/sequence-encoder.js

@@ -1,117 +1,116 @@
-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, '$2');
-    }
-    /**
-     * Performs truncation and cutting auxiliary defises.
-     *
-     * @static
-     * @param {string} sequence The sequence work under process.
-     * @return {string} Result of cleaning.
-     * @memberof AlignedSequenceEncoder
-     */
-    static clean(sequence) {
-        return AlignedSequenceEncoder._dropDefises(AlignedSequenceEncoder._truncateSequence(sequence));
-    }
-    /**
-     * Categorial encode of the sequence provided.
-     *
-     * @param {string} sequence The sequence.
-     * @return {number[]} Encoded vector.
-     * @memberof AlignedSequenceEncoder
-     */
-    encode(sequence) {
-        const seq = AlignedSequenceEncoder.clean(sequence);
-        const nItems = seq.length;
-        let values = new Array(nItems).fill(0);
-        for (let i = 0; i < nItems; ++i) {
-            let char = seq[i];
-            assert(char in this.aa2num, `Unknown char '${char}' found in sequence '${seq}'`);
-            values[i] = this.aa2num[char];
-        }
-        return values;
-    }
-    /**
-     * Decode the encoded vector into the sequence back.
-     *
-     * @param {number[]} value The vector encoded.
-     * @return {string} Decoded sequence.
-     * @memberof AlignedSequenceEncoder
-     */
-    decode(value) {
-        let s = '';
-        for (let i = 0; i < value.length; ++i) {
-            let code = value[i];
-            assert(code in this.num2aa, `Unknown code '${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,GAAG,GAAG,sBAAsB,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;QACnD,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,CAAC;QAC1B,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,GAAG,CAAC,CAAC,CAAC,CAAC;YAElB,MAAM,CAAC,IAAI,IAAI,IAAI,CAAC,MAAM,EAAE,iBAAiB,IAAI,wBAAwB,GAAG,GAAG,CAAC,CAAC;YAEjF,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';\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: {[name: string]: number};\r\n    protected num2aa: {[code: number]: string};\r\n\r\n    constructor () {\r\n        this.aa2num = {\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        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, '$2')\r\n    }\r\n\r\n    /**\r\n     * Performs truncation and cutting auxiliary defises.\r\n     *\r\n     * @static\r\n     * @param {string} sequence The sequence work under process.\r\n     * @return {string} Result of cleaning.\r\n     * @memberof AlignedSequenceEncoder\r\n     */\r\n    static clean(sequence: string): string {\r\n        return AlignedSequenceEncoder._dropDefises(AlignedSequenceEncoder._truncateSequence(sequence));\r\n    }\r\n\r\n    /**\r\n     * Categorial encode of the sequence provided.\r\n     *\r\n     * @param {string} sequence The sequence.\r\n     * @return {number[]} Encoded vector.\r\n     * @memberof AlignedSequenceEncoder\r\n     */\r\n    public encode(sequence: string): number[] {\r\n        const seq = AlignedSequenceEncoder.clean(sequence);\r\n        const nItems = seq.length;\r\n        let values = new Array(nItems).fill(0);\r\n    \r\n        for (let i = 0; i < nItems; ++i) {\r\n            let char = seq[i];\r\n    \r\n            assert(char in this.aa2num, `Unknown char '${char}' found in sequence '${seq}'`);\r\n    \r\n            values[i] = this.aa2num[char];\r\n        }\r\n        return values;\r\n    }\r\n\r\n    /**\r\n     * Decode the encoded vector into the sequence back.\r\n     *\r\n     * @param {number[]} value The vector encoded.\r\n     * @return {string} Decoded sequence.\r\n     * @memberof AlignedSequenceEncoder\r\n     */\r\n    public decode(value: number[]): string {\r\n        let s: string = '';\r\n    \r\n        for (let i = 0; i < value.length; ++i) {\r\n            let code = value[i];\r\n\r\n            assert(code in this.num2aa, `Unknown code '${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"]}
+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

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

package/src/spe.d.ts.map

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