phylotree/src/max-parsimony.js

A JavaScript library for developing applications and interactive visualizations involving [phylogenetic trees](https://en.wikipedia.org/wiki/Phylogenetic_tree), written as an extension of the [D3](http://d3js.org) [hierarchy layout](https://github.com/d3/

import * as _ from "underscore";
import { isLeafNode } from "./nodes";

export default function maxParsimony(respect_existing, attr_name) {

  function populateMpMatrix(attr_name, d) {

    d.mp = [
      [0, 0], // score for parent selected / not selected
      [false, false]
    ]; // selected or not

    if (isLeafNode(d)) {

      d.mp[1][0] = d.mp[1][1] = d[attr_name] || false;
      d.mp[0][0] = d.mp[1][0] ? 1 : 0;
      d.mp[0][1] = 1 - d.mp[0][0];

    } else {

      d.children.forEach(pop_mp_mat);

      var s0 = d.children.reduce(function(p, n) {
        return n.mp[0][0] + p;
      }, 0);

      // cumulative children score if this node is 0
      var s1 = d.children.reduce(function(p, n) {
        return n.mp[0][1] + p;
      }, 0);

      // cumulative children score if this node is 1
      // parent = 0

      if (d[attr_name]) {
        // respect selected
        d.mp[0][0] = s1 + 1;
        d.mp[1][0] = true;
        d.mp[0][1] = s1;
        d.mp[1][1] = true;
      } else {
        if (s0 < s1 + 1) {
          d.mp[0][0] = s0;
          d.mp[1][0] = false;
        } else {
          d.mp[0][0] = s1 + 1;
          d.mp[1][0] = true;
        }

        // parent = 1

        if (s1 < s0 + 1) {
          d.mp[0][1] = s1;
          d.mp[1][1] = true;
        } else {
          d.mp[0][1] = s0 + 1;
          d.mp[1][1] = false;
        }
      }
    }
  }

  const pop_mp_mat = _.partial(populateMpMatrix, attr_name);
  pop_mp_mat(this.nodes);

  this.nodes.each(d => {
    if (d.parent) {
      d.mp = d.mp[1][d.parent.mp ? 1 : 0];
    } else {
      d.mp = d.mp[1][d.mp[0][0] < d.mp[0][1] ? 0 : 1];
    }
  });

  this.display.modifySelection((d, callback) => {
    if (isLeafNode(d.target)) {
      return d.target[attr_name];
    }
    return d.target.mp;
  });

}