cmpstr/dist/cjs/metric/SmithWaterman.cjs

CmpStr is a lightweight, fast and well performing package for calculating string similarity

// CmpStr v3.2.2 build-bb61120-260311 by Paul Köhler @komed3 / MIT License
'use strict';

var Pool = require('../utils/Pool.cjs');
var Metric = require('./Metric.cjs');

class SmithWatermanDistance extends Metric.Metric {
  constructor(a, b, opt = {}) {
    super('smithWaterman', a, b, opt, true);
  }
  compute(a, b, m, n) {
    const { match = 2, mismatch = -1, gap = -2 } = this.options;
    const len = m + 1;
    const [prev, curr] = Pool.Pool.acquireMany('int32', [len, len]);
    let maxScore = 0;
    try {
      for (let i = 0; i <= m; i++) prev[i] = 0;
      for (let j = 1; j <= n; j++) {
        curr[0] = 0;
        const cb = b.charCodeAt(j - 1);
        for (let i = 1; i <= m; i++) {
          const score = a.charCodeAt(i - 1) === cb ? match : mismatch;
          curr[i] = Math.max(
            0,
            prev[i - 1] + score,
            prev[i] + gap,
            curr[i - 1] + gap
          );
          if (curr[i] > maxScore) maxScore = curr[i];
        }
        prev.set(curr);
      }
      const denum = Math.min(m * match, n * match);
      return {
        res: denum === 0 ? 0 : Metric.Metric.clamp(maxScore / denum),
        raw: { score: maxScore, denum }
      };
    } finally {
      Pool.Pool.release('int32', prev, len);
      Pool.Pool.release('int32', curr, len);
    }
  }
}
Metric.MetricRegistry.add('smithWaterman', SmithWatermanDistance);

exports.SmithWatermanDistance = SmithWatermanDistance;