329 lines
7.4 KiB
JavaScript
329 lines
7.4 KiB
JavaScript
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class WavefrontComponent {
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constructor () {
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this.lo = [0]; // lo for each wavefront
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this.hi = [0]; // hi for each wavefront
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this.W = []; // wavefront diag distance for each wavefront
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this.A = []; // compact CIGAR for backtrace
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}
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// get value for wavefront=score, diag=k
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get_val (score, k) {
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if (this.W[score] !== undefined && this.W[score][k] !== undefined) {
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return this.W[score][k];
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}
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else {
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return NaN;
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}
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}
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// set value for wavefront=score, diag=k
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set_val (score, k, val) {
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if (this.W[score]) {
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this.W[score][k] = val;
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}
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else {
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this.W[score] = [];
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this.W[score][k] = val;
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}
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}
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// get alignment traceback
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get_traceback (score, k) {
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if (this.A[score] !== undefined && this.A[score][k] !== undefined) {
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return this.A[score][k];
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}
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else {
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return undefined;
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}
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}
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// set alignment traceback
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set_traceback (score, k, traceback) {
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if (this.A[score]) {
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this.A[score][k] = traceback;
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}
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else {
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this.A[score] = [];
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this.A[score][k] = traceback;
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}
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}
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// get hi for wavefront=score
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get_hi (score) {
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const hi = this.hi[score];
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return isNaN(hi) ? 0 : hi;
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}
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// set hi for wavefront=score
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set_hi (score, hi) {
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this.hi[score] = hi;
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}
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// get lo for wavefront=score
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get_lo (score) {
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const lo = this.lo[score];
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return isNaN(lo) ? 0 : lo;
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}
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// set lo for wavefront=score
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set_lo (score, lo) {
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this.lo[score] = lo;
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}
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// string representation of all wavefronts
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toString () {
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const traceback_str = ["OI", "EI", "OD", "ED", "SB", "IN", "DL", "EN"];
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let s = "<";
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let min_lo = Infinity;
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let max_hi = -Infinity;
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// get the min lo and max hi values across all wavefronts
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for (let i = 0; i < this.W.length; i++) {
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const lo = this.lo[i];
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const hi = this.hi[i];
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if (lo < min_lo) {
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min_lo = lo;
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}
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if (hi > max_hi) {
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max_hi = hi;
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}
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}
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// print out two headers, one for wavefront and one for traceback
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for (let k = min_lo; k <= max_hi; k++) {
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s += FormatNumberLength(k, 2);
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if (k < max_hi) {
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s += "|";
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}
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}
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s += ">\t<";
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for (let k = min_lo; k <= max_hi; k++) {
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s += FormatNumberLength(k, 2);
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if (k < max_hi) {
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s += "|";
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}
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}
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s += ">\n";
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// for each wavefront
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for (let i = 0; i < this.W.length; i++) {
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s += "[";
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const lo = this.lo[i];
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const hi = this.hi[i];
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// print out the wavefront matrix
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for (let k = min_lo; k <= max_hi; k++) {
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if (this.W[i] !== undefined && this.W[i][k] !== undefined && !isNaN(this.W[i][k])) {
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s += FormatNumberLength(this.W[i][k], 2);
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}
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else if (k < lo || k > hi) {
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s += "--";
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}
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else {
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s += " ";
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}
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if (k < max_hi) {
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s += "|";
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}
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}
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s += "]\t[";
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// print out the traceback matrix
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for (let k = min_lo; k <= max_hi; k++) {
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if (this.A[i] !== undefined && this.A[i][k] !== undefined) {
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s += traceback_str[this.A[i][k].toString()];
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}
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else if (k < lo || k > hi) {
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s += "--";
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}
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else {
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s += " ";
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}
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if (k < max_hi) {
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s += "|";
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}
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}
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s += "]\n";
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}
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return s;
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}
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}
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const traceback = {
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OpenIns: 0,
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ExtdIns: 1,
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OpenDel: 2,
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ExtdDel: 3,
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Sub: 4,
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Ins: 5,
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Del: 6,
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End: 7
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};
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function FormatNumberLength (num, length) {
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let r = "" + num;
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while (r.length < length) {
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r = " " + r;
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}
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return r;
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}
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function min (args) {
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args.forEach((el, idx, arr) => {
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arr[idx] = isNaN(el) ? Infinity : el;
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});
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const min = Math.min.apply(Math, args);
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return min === Infinity ? NaN : min;
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}
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function max (args) {
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args.forEach((el, idx, arr) => {
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arr[idx] = isNaN(el) ? -Infinity : el;
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});
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const max = Math.max.apply(Math, args);
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return max === -Infinity ? NaN : max;
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}
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function argmax (args) {
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const val = max(args);
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return args.indexOf(val);
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}
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export default function wf_align (s1, s2, penalties) {
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const n = s1.length;
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const m = s2.length;
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const A_k = m - n;
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const A_offset = m;
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let score = 0;
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const M = new WavefrontComponent();
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M.set_val(0, 0, 0);
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M.set_hi(0, 0);
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M.set_lo(0, 0);
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M.set_traceback(0, 0, traceback.End);
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const I = new WavefrontComponent();
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const D = new WavefrontComponent();
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while (true) {
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wf_extend(M, s1, n, s2, m, score);
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if (M.get_val(score, A_k) >= A_offset) {
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break;
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}
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score++;
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wf_next(M, I, D, score, penalties);
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}
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return wf_backtrace(M, I, D, score, penalties, A_k, A_offset);
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}
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function wf_extend (M, s1, n, s2, m, score) {
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const lo = M.get_lo(score);
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const hi = M.get_hi(score);
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for (let k = lo; k <= hi; k++) {
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let v = M.get_val(score, k) - k;
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let h = M.get_val(score, k);
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if (isNaN(v) || isNaN(h)) {
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continue;
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}
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while (s1[v] === s2[h]) {
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M.set_val(score, k, M.get_val(score, k) + 1);
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v++;
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h++;
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if (v > n || h > m) {
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break;
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}
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}
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}
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}
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function wf_next (M, I, D, score, penalties) {
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const x = penalties.x;
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const o = penalties.o;
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const e = penalties.e;
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const lo = min([M.get_lo(score - x), M.get_lo(score - o - e), I.get_lo(score - e), D.get_lo(score - e)]) - 1;
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const hi = max([M.get_hi(score - x), M.get_hi(score - o - e), I.get_hi(score - e), D.get_hi(score - e)]) + 1;
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M.set_hi(score, hi);
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I.set_hi(score, hi);
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D.set_hi(score, hi);
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M.set_lo(score, lo);
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I.set_lo(score, lo);
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D.set_lo(score, lo);
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for (let k = lo; k <= hi; k++) {
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I.set_val(score, k, max([
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M.get_val(score - o - e, k - 1),
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I.get_val(score - e, k - 1)
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]) + 1);
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I.set_traceback(score, k, [traceback.OpenIns, traceback.ExtdIns][argmax([
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M.get_val(score - o - e, k - 1),
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I.get_val(score - e, k - 1)
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])]);
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D.set_val(score, k, max([
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M.get_val(score - o - e, k + 1),
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D.get_val(score - e, k + 1)
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]));
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D.set_traceback(score, k, [traceback.OpenDel, traceback.ExtdDel][argmax([
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M.get_val(score - o - e, k + 1),
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D.get_val(score - e, k + 1)
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])]);
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M.set_val(score, k, max([
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M.get_val(score - x, k) + 1,
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I.get_val(score, k),
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D.get_val(score, k)
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]));
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M.set_traceback(score, k, [traceback.Sub, traceback.Ins, traceback.Del][argmax([
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M.get_val(score - x, k) + 1,
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I.get_val(score, k),
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D.get_val(score, k)
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])]);
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}
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}
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function wf_backtrace (M, I, D, score, penalties, A_k) {
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const traceback_CIGAR = ["I", "I", "D", "D", "X", "", "", ""];
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const x = penalties.x;
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const o = penalties.o;
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const e = penalties.e;
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let CIGAR_rev = ""; // reversed CIGAR
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let tb_s = score; // traceback score
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let tb_k = A_k; // traceback diag k
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let current_traceback = M.get_traceback(tb_s, tb_k);
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let done = false;
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while (!done) {
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CIGAR_rev += traceback_CIGAR[current_traceback];
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switch (current_traceback) {
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case traceback.OpenIns:
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tb_s = tb_s - o - e;
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tb_k = tb_k - 1;
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current_traceback = M.get_traceback(tb_s, tb_k);
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break;
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case traceback.ExtdIns:
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tb_s = tb_s - e;
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tb_k = tb_k - 1;
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current_traceback = I.get_traceback(tb_s, tb_k);
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break;
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case traceback.OpenDel:
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tb_s = tb_s - o - e;
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tb_k = tb_k + 1;
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current_traceback = M.get_traceback(tb_s, tb_k);
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break;
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case traceback.ExtdDel:
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tb_s = tb_s - e;
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tb_k = tb_k + 1;
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current_traceback = D.get_traceback(tb_s, tb_k);
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break;
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case traceback.Sub:
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tb_s = tb_s - x;
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// tb_k = tb_k;
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current_traceback = M.get_traceback(tb_s, tb_k);
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break;
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case traceback.Ins:
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// tb_s = tb_s;
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// tb_k = tb_k;
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current_traceback = I.get_traceback(tb_s, tb_k);
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break;
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case traceback.Del:
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// tb_s = tb_s;
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// tb_k = tb_k;
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current_traceback = D.get_traceback(tb_s, tb_k);
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break;
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case traceback.End:
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done = true;
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break;
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}
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}
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const CIGAR = Array.from(CIGAR_rev).reverse().join("");
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return { CIGAR, score };
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}
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