iham-parsers/src/tree_utils.js

orthoxml, phyloxml and newick parsers for the iHam widget

/**
 * Collection of functions operating on a tree
 *
 * Copyright (c) Adrian Altenhoff 2017
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 */

module.exports = {
    extractParentRelations : function(tree) {
        var uprels = {};
        var rec_trav = function(node){
            if (node !== undefined && node.children !== undefined) {
                node.children.forEach(function (child) {
                    uprels[child.name] = node.name;
                });
                node.children.map(rec_trav);
            }
        };
        rec_trav(tree);
        return uprels;
    },

    ladderize: function(tree){
        var rec_trav = function(node){
            var tot_children;
            if (node.children !== undefined){
                var rec_res = node.children.map(rec_trav);
                rec_res.sort(function(a,b){
                    if (a.cnts !== b.cnts) {
                        return a.cnts - b.cnts;
                    } else {
                        return a.data.name.localeCompare(b.data.name);
                    }
                });
                tot_children = rec_res.map(x => x.cnts).reduce((a, b) => a + b, 0);
                node.children = rec_res.map(x => x.data);
            } else {
                tot_children = 1;
            }
            return {cnts: tot_children, data: node};
        };
        return rec_trav(tree).data;
    },

    extractTree: function (xmltree) {
        if (xmltree && (xmltree.constructor === Array) && (xmltree[0].rooted !== undefined)){
            return xmltree[0].children[0];
        } else { return xmltree; }
    },

    add_nodenames_from_taxonomy_if_needed: function(tree){
        var rec_trav = function(node){
            if ((node.name === undefined) && (node.taxonomies !== undefined)){
                node.name = node.taxonomies[0].scientific_name;
            }
            if (node.children !== undefined){
                node.children.map(rec_trav);
            }
        };
        rec_trav(tree);
        return tree;
    },

    same_trees: function(t1, t2){
        var rec_trav = function(n1, n2){
            if (n1.name !== n2.name) return false;
            if (!n1.children && !n2.children) return true;  // identical leaves
            if ((!n1.children && n2.children) || (n1.children && !n2.children) ||
                (n1.children.length !== n2.children.length)) return false; // one leaf, the other not, or different nr children
            let sames = n1.children.map(function(e, i){
                return rec_trav(e, n2.children[i]);
            });
            return sames.every(x => x);
        };
        return rec_trav(t1, t2);
    }
};