molstar/lib/commonjs/mol-model/sequence/alignment/alignment.js

A comprehensive macromolecular library.

"use strict";
/**
 * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
Object.defineProperty(exports, "__esModule", { value: true });
exports.align = align;
const substitution_matrix_1 = require("./substitution-matrix");
const DefaultAlignmentOptions = {
    gapPenalty: -11,
    gapExtensionPenalty: -1,
    substMatrix: 'default'
};
function align(seqA, seqB, options = {}) {
    const o = { ...DefaultAlignmentOptions, ...options };
    const alignment = new Alignment(seqA, seqB, o);
    alignment.calculate();
    return alignment.trace();
}
class Alignment {
    constructor(seqA, seqB, options) {
        this.seqA = seqA;
        this.seqB = seqB;
        this.S = [];
        this.V = [];
        this.H = [];
        this.gapPenalty = options.gapPenalty;
        this.gapExtensionPenalty = options.gapExtensionPenalty;
        this.substMatrix = options.substMatrix === 'default' ? undefined : substitution_matrix_1.SubstitutionMatrices[options.substMatrix];
        this.n = this.seqA.length;
        this.m = this.seqB.length;
    }
    initMatrices() {
        const { n, m, gapPenalty, S, V, H } = this;
        for (let i = 0; i <= n; ++i) {
            S[i] = [], V[i] = [], H[i] = [];
            for (let j = 0; j <= m; ++j) {
                S[i][j] = 0, V[i][j] = 0, H[i][j] = 0;
            }
        }
        for (let i = 0; i <= n; ++i) {
            S[i][0] = gapPenalty;
            H[i][0] = -Infinity;
        }
        for (let j = 0; j <= m; ++j) {
            S[0][j] = gapPenalty;
            V[0][j] = -Infinity;
        }
        S[0][0] = 0;
    }
    makeScoreFn() {
        const { seqA, seqB, substMatrix } = this;
        if (substMatrix) {
            return function score(i, j) {
                var _a, _b;
                const cA = seqA[i];
                const cB = seqB[j];
                return (_b = (_a = substMatrix[cA]) === null || _a === void 0 ? void 0 : _a[cB]) !== null && _b !== void 0 ? _b : -4;
            };
        }
        else {
            return function scoreNoSubstMat(i, j) {
                const cA = seqA[i];
                const cB = seqB[j];
                return cA === cB ? 5 : -3;
            };
        }
    }
    calculate() {
        this.initMatrices();
        const scoreFn = this.makeScoreFn();
        const { V, H, S, n, m, gapExtensionPenalty, gapPenalty } = this;
        let Vi1, Si1, Vi, Hi, Si;
        for (let i = 1; i <= n; ++i) {
            Si1 = S[i - 1], Vi1 = V[i - 1];
            Vi = V[i], Hi = H[i], Si = S[i];
            for (let j = 1; j <= m; ++j) {
                Vi[j] = Math.max(Si1[j] + gapPenalty, Vi1[j] + gapExtensionPenalty);
                Hi[j] = Math.max(Si[j - 1] + gapPenalty, Hi[j - 1] + gapExtensionPenalty);
                Si[j] = Math.max(Si1[j - 1] + scoreFn(i - 1, j - 1), // match
                Vi[j], // del
                Hi[j] // ins
                );
            }
        }
    }
    trace() {
        const scoreFn = this.makeScoreFn();
        const { V, H, S, seqA, seqB, gapExtensionPenalty, gapPenalty } = this;
        let i = this.n;
        let j = this.m;
        let mat;
        let score;
        let aliA = '';
        let aliB = '';
        if (S[i][j] >= V[i][j]) {
            mat = 'S';
            score = S[i][j];
        }
        else if (V[i][j] >= H[i][j]) {
            mat = 'V';
            score = V[i][j];
        }
        else {
            mat = 'H';
            score = H[i][j];
        }
        while (i > 0 && j > 0) {
            if (mat === 'S') {
                if (S[i][j] === S[i - 1][j - 1] + scoreFn(i - 1, j - 1)) {
                    aliA = seqA[i - 1] + aliA;
                    aliB = seqB[j - 1] + aliB;
                    --i;
                    --j;
                    mat = 'S';
                }
                else if (S[i][j] === V[i][j]) {
                    mat = 'V';
                }
                else if (S[i][j] === H[i][j]) {
                    mat = 'H';
                }
                else {
                    --i;
                    --j;
                }
            }
            else if (mat === 'V') {
                if (V[i][j] === V[i - 1][j] + gapExtensionPenalty) {
                    aliA = seqA[i - 1] + aliA;
                    aliB = '-' + aliB;
                    --i;
                    mat = 'V';
                }
                else if (V[i][j] === S[i - 1][j] + gapPenalty) {
                    aliA = seqA[i - 1] + aliA;
                    aliB = '-' + aliB;
                    --i;
                    mat = 'S';
                }
                else {
                    --i;
                }
            }
            else if (mat === 'H') {
                if (H[i][j] === H[i][j - 1] + gapExtensionPenalty) {
                    aliA = '-' + aliA;
                    aliB = seqB[j - 1] + aliB;
                    --j;
                    mat = 'H';
                }
                else if (H[i][j] === S[i][j - 1] + gapPenalty) {
                    aliA = '-' + aliA;
                    aliB = seqB[j - 1] + aliB;
                    --j;
                    mat = 'S';
                }
                else {
                    --j;
                }
            }
        }
        while (i > 0) {
            aliA = seqA[i - 1] + aliA;
            aliB = '-' + aliB;
            --i;
        }
        while (j > 0) {
            aliA = '-' + aliA;
            aliB = seqB[j - 1] + aliB;
            --j;
        }
        return { aliA, aliB, score };
    }
}