phylotree/src/formats/nexml.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 { XMLParser } from "fast-xml-parser";

var nexml_parser = function(xml_string, options) {
  const parser = new XMLParser({
    ignoreAttributes: false,
    attributeNamePrefix: "",
    parseAttributeValue: true
  });
  
  const xml = parser.parse(xml_string);
  var trees = xml["nex:nexml"].trees.tree.map(function(nexml_tree) {
      var node_list = nexml_tree.node.map(d => d),
        node_hash = node_list.reduce(function(a, b) {
          b.edges = [];
          b.name = b.id;
          a[b.id] = b;
          return a;
        }, {}),
        roots = node_list.filter(d => d.root),
        root_id = roots > 0 ? roots[0].id : node_list[0].id;
      node_hash[root_id].name = "root";

      nexml_tree.edge.map(d => d).forEach(function(edge) {
        node_hash[edge.source].edges.push(edge);
      });

      function parseNexml(node, index) {
        if (node.edges) {
          var targets = _.pluck(node.edges, "target");
          node.children = _.values(_.pick(node_hash, targets));
          node.children.forEach(function(child, i) {
            child.attribute = node.edges[i].length || "";
          });
          node.children.forEach(parseNexml);
          node.annotation = "";
        }
      }

      parseNexml(node_hash[root_id]);
      return node_hash[root_id];
    });
  return trees;
};

export default nexml_parser;