archaeopteryx 1.8.1 → 2.3.2

package/forester.js

@@ -1,1944 +1,1749 @@
-/**
- *  Copyright (C) 2019 Christian M. Zmasek
- *  Copyright (C) 2019 Yun Zhang
- *  Copyright (C) 2019 J. Craig Venter Institute
- *  All rights reserved
- *
- *  This library is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public
- *  License as published by the Free Software Foundation; either
- *  version 2.1 of the License, or (at your option) any later version.
- *
- *  This library is distributed in the hope that it will be useful,
- *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this library; if not, write to the Free Software
- *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- *
- */
-
-// v 1.8.1
-// 2019-05-16
-//
-// forester.js is a general suite for dealing with phylogenetic trees.
-// 
-// forester.js is used by Archaeopteryx.js:
-//   https://github.com/cmzmasek/archaeopteryx-js
-//   https://www.npmjs.com/package/archaeopteryx
-//
-// Availability:
-//   https://github.com/cmzmasek/archaeopteryx-js
-//   https://www.npmjs.com/package/archaeopteryx
-//
-// Dependencies: none
-//
-//
-// In the following is a basic example shows how to parse a New Hampshire formatted String
-// into to a object representing a phylogenetic tree.
-// Followed by pre- and post-order traversal,
-// and writing back to a New Hampshire formatted String.
-//
-// Change './forester' to 'forester' if you use this code outside of this package
-//
-// var forester = require('./forester').forester;
-//
-// var newHampshireFormattedString = "(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;";
-// var phylogeneticTree = forester.parseNewHampshire(newHampshireFormattedString);
-//
-// console.log('Pre-order traversal:');
-// forester.preOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
-//     console.log(n.name + ':' + n.branch_length);
-// });
-//
-// console.log('Post-order traversal:');
-// forester.postOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
-//     console.log(n.name + ':' + n.branch_length);
-// });
-//
-// console.log('In New Hampshire format:');
-// var nh = forester.toNewHampshire(phylogeneticTree);
-// console.log(nh);
-
-(function forester() {
-
-    "use strict";
-
-    var BRANCH_EVENT_REF = 'aptx:branch_event';
-    var BRANCH_EVENT_DATATYPE = 'xsd:string';
-    var BRANCH_EVENT_APPLIES_TO = 'parent_branch';
-    var NH_FORMAT_ERR = 'New Hampshire (Newick) format error: ';
-
-    var NUMBERS_ONLY_PATTERN = /^[-+]?[0-9\\.]+$/;
-
-    var MSA_RESIDUE_SORT_MAP = new Map();
-    MSA_RESIDUE_SORT_MAP.set('A', 0);
-    MSA_RESIDUE_SORT_MAP.set('C', 1);
-    MSA_RESIDUE_SORT_MAP.set('D', 2);
-    MSA_RESIDUE_SORT_MAP.set('E', 3);
-    MSA_RESIDUE_SORT_MAP.set('F', 4);
-    MSA_RESIDUE_SORT_MAP.set('G', 5);
-    MSA_RESIDUE_SORT_MAP.set('H', 6);
-    MSA_RESIDUE_SORT_MAP.set('I', 7);
-    MSA_RESIDUE_SORT_MAP.set('K', 8);
-    MSA_RESIDUE_SORT_MAP.set('L', 9);
-    MSA_RESIDUE_SORT_MAP.set('M', 10);
-    MSA_RESIDUE_SORT_MAP.set('N', 11);
-    MSA_RESIDUE_SORT_MAP.set('P', 12);
-    MSA_RESIDUE_SORT_MAP.set('Q', 13);
-    MSA_RESIDUE_SORT_MAP.set('R', 14);
-    MSA_RESIDUE_SORT_MAP.set('S', 15);
-    MSA_RESIDUE_SORT_MAP.set('T', 16);
-    MSA_RESIDUE_SORT_MAP.set('U', 17);// Uracil
-    MSA_RESIDUE_SORT_MAP.set('V', 18);
-    MSA_RESIDUE_SORT_MAP.set('W', 19);
-    MSA_RESIDUE_SORT_MAP.set('Y', 20);
-    MSA_RESIDUE_SORT_MAP.set('B', 21);// Asparagine or aspartic acid
-    MSA_RESIDUE_SORT_MAP.set('Z', 22);// Glutamine or glutamic acid
-    MSA_RESIDUE_SORT_MAP.set('X', 23);
-    MSA_RESIDUE_SORT_MAP.set('?', 24);
-    MSA_RESIDUE_SORT_MAP.set('-', 25);
-    MSA_RESIDUE_SORT_MAP.set('.', 26);
-
-
-    /**
-     * Sets links to parent nodes for all nodes in a
-     * phyloXML-based tree object
-     *
-     * @param phy - A phyloXML-based tree object.
-     */
-    forester.addParents = function (phy) {
-        if (phy.children) {
-            for (var i = phy.children.length - 1; i >= 0; --i) {
-                var c = phy.children[i];
-                c.parent = phy;
-                forester.addParents(c);
-            }
-        }
-    };
-
-    /**
-     * Returns the real root node of a
-     * phyloXML-based tree object.
-     * Precondition: needs to have parents set.
-     *
-     * @param phy - A phyloXML-based tree object or node.
-     * @returns {*} - The real tree root node.
-     */
-    forester.getTreeRoot = function (phy) {
-        var root = phy;
-        if (!root.parent && root.children && root.children.length === 1) {
-            root = root.children[0];
-        }
-        while (root.parent && root.parent.parent) {
-            root = root.parent;
-        }
-        return root;
-    };
-
-    /**
-     * Visits all non-collapsed child nodes of a node
-     * while applying a function in pre-order.
-     *
-     * @param node - The root of the subtree to traverse.
-     * @param fn - The function to apply.
-     */
-    forester.preOrderTraversal = function (node, fn) {
-        fn(node);
-        if (node.children) {
-            for (var i = node.children.length - 1; i >= 0; --i) {
-                forester.preOrderTraversal(node.children[i], fn);
-            }
-        }
-    };
-
-    /**
-     * Visits all child nodes of a node
-     * while applying a function in pre-order.
-     *
-     * @param node - The root of the subtree to traverse.
-     * @param fn - The function to apply.
-     */
-    forester.preOrderTraversalAll = function (node, fn) {
-        fn(node);
-        if (node.children) {
-            for (var i = node.children.length - 1; i >= 0; --i) {
-                forester.preOrderTraversalAll(node.children[i], fn);
-            }
-        }
-        else if (node._children) {
-            for (var ii = node._children.length - 1; ii >= 0; --ii) {
-                forester.preOrderTraversalAll(node._children[ii], fn);
-            }
-        }
-    };
-
-    forester.postOrderTraversalAll = function (node, fn) {
-        if (node.children) {
-            var l = node.children.length;
-            for (var i = 0; i < l; ++i) {
-                forester.postOrderTraversalAll(node.children[i], fn);
-            }
-        }
-        else if (node._children) {
-            var ll = node._children.length;
-            for (var ii = 0; ii < ll; ++ii) {
-                forester.postOrderTraversalAll(node._children[ii], fn);
-            }
-        }
-        fn(node);
-    };
-
-
-    forester.findByNodeName = function (node, name) {
-        var found = [];
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n.name === name) {
-                found.push(n);
-            }
-        });
-        return found;
-    };
-
-    forester.findByTaxonomyCode = function (node, code) {
-        var found = [];
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n.taxonomies && n.taxonomies.length > 0 && n.taxonomies[0].code === code) {
-                found.push(n);
-            }
-        });
-        return found;
-    };
-
-    forester.findByTaxonomyScientificName = function (node, scientificName) {
-        var found = [];
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n.taxonomies && n.taxonomies.length > 0 && n.taxonomies[0].scientific_name === scientificName) {
-                found.push(n);
-            }
-        });
-        return found;
-    };
-
-    /**
-     * To delete a sub-tree or external node.
-     *
-     * @param phy
-     * @param nodeToDelete
-     */
-    forester.deleteSubtree = function (phy, nodeToDelete) {
-        if (!phy) {
-            throw ( "cannot delete null tree" );
-        }
-        if (!nodeToDelete) {
-            throw ( "cannot delete null node" );
-        }
-        if (!nodeToDelete.parent || !nodeToDelete.parent.parent) {
-            throw ( "cannot delete root" );
-        }
-        if (!nodeToDelete.parent.parent.parent) {
-            throw ( "cannot delete direct child of root" );
-        }
-
-        var p = nodeToDelete.parent;
-
-        if ((p.children) && (p.children.length > 1)) {
-            var i = p.children.indexOf(nodeToDelete);
-            if (i !== -1) {
-                p.children.splice(i, 1);
-            }
-        }
-        if ((p._children) && (p._children.length > 1)) {
-            var ii = p._children.indexOf(nodeToDelete);
-            if (ii !== -1) {
-                p._children.splice(ii, 1);
-            }
-        }
-
-        if (p.children.length === 1) {
-            var pp = p.parent;
-            var cni = forester.getChildNodeIndex(pp, p);
-            if ((cni < 0) || (cni > ( pp.children.length - 1 ) )) {
-                throw ( "this should never have happened, child node index = " + cni );
-            }
-            var x = p.children[0];
-            var nbl = undefined;
-            if (x.branch_length || p.branch_length) {
-                nbl = ( x.branch_length > 0 ? x.branch_length : 0 ) + ( p.branch_length > 0 ? p.branch_length : 0  );
-            }
-            x.parent = pp;
-            pp.children[cni] = x;
-            x.branch_length = nbl;
-        }
-
-    };
-
-
-    /**
-     * To re-root a tree object.
-     *
-     * @param phy - The tree to be re-rooted.
-     * @param node - The node on where to place the new root (on its parent branch).
-     * @param branchLength - The branch length to use if new root is not placed in the middle (if
-     * non-negative).
-     */
-    forester.reRoot = function (phy, node, branchLength) {
-        if (!phy) {
-            throw ( "cannot re-root null tree" );
-        }
-        if (!node) {
-            throw ( "cannot re-root on null node" );
-        }
-        if (!branchLength) {
-            branchLength = -1;
-        }
-        if (forester.isString(node)) {
-            var nodes = forester.findByNodeName(phy, node);
-            if (nodes.length > 1) {
-                throw ("node name '" + node + "' is not unique");
-            }
-            else if (nodes.length < 1) {
-                throw ("node name '" + node + "' is not found");
-            }
-            node = nodes[0];
-        }
-
-        phy.rooted = true;
-        var root = forester.getTreeRoot(phy);
-
-        if (!node.parent || !node.parent.parent) {
-            //do noting
-        }
-        else if (!node.parent.parent.parent) {
-            if (( node.parent.children.length === 2 ) && ( branchLength >= 0 )) {
-                var d = node.parent.children[0].branch_length
-                    + node.parent.children[1].branch_length;
-                var other;
-                if (node.parent.children[0] === node) {
-                    other = node.parent.children[1];
-                }
-                else {
-                    other = node.parent.children[0];
-                }
-                node.branch_length = branchLength;
-                var dm = d - branchLength;
-                if (dm >= 0) {
-                    other.branch_length = dm;
-                }
-                else {
-                    other.branch_length = 0;
-                }
-            }
-            if (node.parent.children.length > 2) {
-                var index = forester.getChildNodeIndex(node.parent, node);
-                var dn = node.branch_length;
-                var prev_root = root;
-                prev_root.children.splice(index, 1);
-                var nr = {};
-                nr.children = [];
-                forester.setChildNode(nr, 0, node);
-                forester.setChildNode(nr, 1, prev_root);
-
-                forester.copyBranchData(node, prev_root);
-
-                phy.children[0] = nr;
-                nr.parent = phy;
-                if (branchLength >= 0) {
-                    node.branch_length = branchLength;
-                    var dnmp = dn - branchLength;
-                    if (dnmp >= 0) {
-                        prev_root.branch_length = dnmp;
-                    }
-                    else {
-                        prev_root.branch_length = 0;
-                    }
-                }
-                else {
-                    if (dn >= 0) {
-                        var dn2 = dn / 2.0;
-                        node.branch_length = dn2;
-                        prev_root.branch_length = dn2;
-                    }
-                }
-            }
-        }
-        else {
-            var a = node;
-            var new_root = {};
-            var distance1;
-            var distance2 = 0.0;
-            var branch_data_1;
-            var branch_data_2 = null;
-            var b = a.parent;
-            var c = b.parent;
-
-            new_root.children = [];
-            forester.setChildNode(new_root, 0, a);
-            forester.setChildNode(new_root, 1, b);
-
-            distance1 = c.branch_length;
-
-            branch_data_1 = forester.getBranchData(c);
-
-            c.branch_length = b.branch_length;
-
-            forester.copyBranchData(b, c);
-            forester.copyBranchData(a, b);
-
-            // New root is always placed in the middle of the branch:
-            if (!a.branch_length) {
-                b.branch_length = undefined;
-            }
-            else {
-                if (branchLength >= 0.0) {
-                    var diff = a.branch_length - branchLength;
-                    a.branch_length = branchLength;
-                    b.branch_length = ( diff >= 0.0 ? diff : 0.0 );
-                }
-                else {
-                    var d2 = a.branch_length / 2.0;
-                    a.branch_length = d2;
-                    b.branch_length = d2;
-                }
-            }
-            setChildNodeOnly(b, forester.getChildNodeIndex(b, a), c);
-            // moving to the old root, swapping references:
-            while (c.parent.parent) {
-                a = b;
-                b = c;
-                c = c.parent;
-                setChildNodeOnly(b, forester.getChildNodeIndex(b, a), c);
-                b.parent = a;
-                distance2 = c.branch_length;
-                branch_data_2 = forester.getBranchData(c);
-                c.branch_length = distance1;
-                forester.setBranchData(c, branch_data_1);
-                distance1 = distance2;
-                branch_data_1 = branch_data_2;
-            }
-            // removing the old root:
-            if (c.children.length == 2) {
-                var node2 = c.children[1 - forester.getChildNodeIndex(c, b)];
-                node2.parent = b;
-                if (( !c.branch_length  )
-                    && ( !node2.branch_length  )) {
-                    node2.branch_length = undefined;
-                }
-                else {
-                    node2.branch_length = ( c.branch_length >= 0.0 ? c.branch_length : 0.0 )
-                        + ( node2.branch_length >= 0.0 ? node2.branch_length : 0.0 );
-                }
-                var cbd = forester.getBranchData(c);
-                if (cbd) {
-                    forester.setBranchData(node2, cbd);
-                }
-                var l = b.children.length;
-                for (var i = 0; i < l; ++i) {
-                    if (b.children[i] === c) {
-                        setChildNodeOnly(b, i, node2);
-                        break;
-                    }
-                }
-            }
-            else {
-                c.parent = b;
-                forester.removeChildNode(c, forester.getChildNodeIndex(c, b));
-            }
-            phy.children[0] = new_root;
-            new_root.parent = phy;
-            forester.addParents(phy);
-        }
-
-        function setChildNodeOnly(parentNode, i, node) {
-            if (parentNode.children.length <= i) {
-                parentNode.children.push(node);
-            }
-            else {
-                parentNode.children[i] = node;
-            }
-        }
-    };
-
-    forester.midpointRoot = function (phy) {
-        var root = forester.getTreeRoot(phy);
-        var extNodes = forester.getAllExternalNodes(root);
-        if (( extNodes.length < 2 ) || ( forester.calcMaxBranchLength(root) <= 0 )) {
-            return;
-        }
-        var counter = 0;
-        var totalNodes = forester.getAllNodes(phy).length;
-        while (true) {
-            if (++counter > (totalNodes + 1)) {
-                throw( 'this should not have happened: midpoint rooting does not converge' );
-            }
-            var a = null;
-            var da = 0;
-            var db = 0;
-            var cl = forester.getTreeRoot(phy).children.length;
-            for (var i = 0; i < cl; ++i) {
-                var f = forester.getFurthestDescendant(forester.getTreeRoot(phy).children[i]);
-                var df = forester.getDistance(f, forester.getTreeRoot(phy));
-                if (df > 0) {
-                    if (df > da) {
-                        db = da;
-                        da = df;
-                        a = f;
-                    }
-                    else if (df > db) {
-                        db = df;
-                    }
-                }
-            }
-            var diff = da - db;
-            if (diff < 0.0001) {
-                break;
-            }
-            var x = da - ( diff / 2.0 );
-            while (( x > a.branch_length ) && a.parent) {
-                x -= ( a.branch_length > 0 ? a.branch_length : 0 );
-                a = a.parent;
-            }
-            forester.reRoot(phy, a, x);
-        }
-    };
-
-    forester.getFurthestDescendant = function (node) {
-        var children = forester.getAllExternalNodes(node);
-        var farthest = null;
-        var longest = -1000000;
-        var l = children.length;
-        for (var i = 0; i < l; ++i) {
-            var dist = forester.getDistance(children[i], node);
-            if (dist > longest) {
-                farthest = children[i];
-                longest = dist;
-            }
-        }
-        return farthest;
-    };
-
-    /**
-     * Calculates the distance between PhylogenyNodes n1 and n2.
-     * PRECONDITION: n1 is a descendant of n2.
-     *
-     * @param n1 a descendant of n2
-     * @param n2
-     * @returns {number} distance between n1 and n2
-     */
-    forester.getDistance = function (n1, n2) {
-        var d = 0.0;
-        while (n1 !== n2) {
-            if (n1.branch_length > 0.0) {
-                d += n1.branch_length;
-            }
-            n1 = n1.parent;
-        }
-        return d;
-    };
-
-    forester.removeChildNode = function (parentNode, i) {
-        if (!parentNode.children) {
-            throw ( "cannot remove the child node for a external node" );
-        }
-        if (( i >= parentNode.children.length ) || ( i < 0 )) {
-            throw ( "attempt to get child node " + i + " of a node with "
-            + parentNode.children.length + " child nodes." );
-        }
-        parentNode.children[i].parent = undefined;
-        parentNode.children.splice(i, 1);
-    };
-
-
-    /**
-     * Inserts node node at the specified position i into the list of
-     * child nodes of parentNode. This does not allow null slots in the list of child nodes:
-     * If i is larger than the number of child nodes, node is just added to the
-     * list, not placed at index i.
-     */
-    forester.setChildNode = function (parentNode, i, node) {
-        node.parent = parentNode;
-        if (parentNode.children.length <= i) {
-            parentNode.children.push(node);
-        }
-        else {
-            parentNode.children[i] = node;
-        }
-    };
-
-
-    forester.getBranchData = function (node) {
-        var branchData = null;
-        if (node.width || node.color || node.confidences) {
-            branchData = {};
-            branchData.width = node.width;
-            branchData.color = node.color;
-            branchData.confidences = node.confidences;
-        }
-        return branchData;
-    };
-
-
-    forester.setBranchData = function (node, branchData) {
-        if (branchData) {
-            node.width = branchData.width;
-            node.color = branchData.color;
-            node.confidences = branchData.confidences;
-        }
-    };
-
-    forester.unCollapseAll = function (node) {
-        forester.preOrderTraversal(node, function (d) {
-            if (d._children) {
-                d.children = d._children;
-                d._children = null;
-            }
-        });
-    };
-
-    forester.copyBranchData = function (nodeFrom, nodeTo) {
-        nodeTo.width = nodeFrom.width;
-        nodeTo.color = nodeFrom.color;
-        nodeTo.confidences = nodeFrom.confidences;
-    };
-
-
-    forester.getChildNodeIndex = function (parentNode, childNode) {
-        if (!parentNode) {
-            throw ( "cannot get the child index for a root node" );
-        }
-        var c = parentNode.children.length;
-        for (var i = 0; i < c; ++i) {
-            if (parentNode.children[i] === childNode) {
-                return i;
-            }
-        }
-        throw ( "unexpected exception: Could not determine the child index for a node" );
-    };
-
-
-    forester.getChildren = function (node) {
-        return node._children ? node._children : (node.children ? node.children : []);
-    };
-
-
-    forester.calcAverageTreeHeight = function (node, externalDescendants) {
-        var c = externalDescendants ? externalDescendants : forester.getAllExternalNodes(node);
-        var l = c.length;
-        var s = 0;
-        for (var i = 0; i < l; ++i) {
-            var cc = c[i];
-            while (cc != node) {
-                if (cc.branch_length > 0) {
-                    s += cc.branch_length;
-                }
-                cc = cc.parent;
-            }
-        }
-        return s / l;
-    };
-
-    forester.setToArray = function (set) {
-        var array = [];
-        if (set) {
-            set.forEach(function (e) {
-                array.push(e);
-            });
-        }
-        return array;
-    };
-
-    forester.setToSortedArray = function (set) {
-        var array = [];
-        if (set) {
-            set.forEach(function (e) {
-                array.push(e);
-            });
-        }
-        return array.sort();
-    };
-
-    forester.calcMinMaxInSet = function (set) {
-        var array = [];
-        var first = true;
-        var min = 0;
-        var max = 0;
-        if (set) {
-            set.forEach(function (e) {
-                e = parseFloat(e);
-                if (first) {
-                    first = false;
-                    min = e;
-                    max = e;
-                }
-                else {
-                    if (e < min) {
-                        min = e;
-                    }
-                    if (e > max) {
-                        max = e;
-                    }
-                }
-            });
-        }
-        array[0] = min;
-        array[1] = max;
-        return array;
-    };
-
-    forester.calcMinMeanMaxInSet = function (set) {
-        var array = [];
-        var first = true;
-        var min = 0;
-        var max = 0;
-        var mean = 0;
-        var sum = 0;
-        var n = 0;
-        if (set) {
-            set.forEach(function (e) {
-                e = parseFloat(e);
-                ++n;
-                sum += e;
-                if (first) {
-                    first = false;
-                    min = e;
-                    max = e;
-                }
-                else {
-                    if (e < min) {
-                        min = e;
-                    }
-                    if (e > max) {
-                        max = e;
-                    }
-                }
-            });
-        }
-        if (n > 0) {
-            mean = sum / n;
-        }
-        array[0] = min;
-        array[1] = mean;
-        array[2] = max;
-        return array;
-    };
-
-
-    /**
-     * This collects all properties in a tree
-     * and returns them as dictionary of Sets mapping
-     * keys to values.
-     * It only collects properly formed properties
-     * (as per phyloXML standard), which means
-     * that 'applies_to' and 'datatype' have to be present.
-     *
-     *
-     * @param phy - A phyloXML-based tree object or node.
-     * @param appliesTo - 'phylogeny', 'clade', 'node', 'annotation', 'parent_branch', or 'other'.
-     * @param externalOnly - To collect from external nodes only.
-     * @returns {{}}
-     */
-    forester.collectProperties = function (phy, appliesTo, externalOnly) {
-        var props = {};
-        forester.preOrderTraversalAll(phy, function (n) {
-
-            if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
-                if (n.properties && n.properties.length > 0) {
-                    var propertiesLength = n.properties.length;
-                    for (var i = 0; i < propertiesLength; ++i) {
-                        var property = n.properties[i];
-                        if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
-                            var ref = property.ref;
-                            if (!props[ref]) {
-                                props[ref] = new Set();
-                            }
-                            props[ref].add(property.value);
-                        }
-                    }
-                }
-            }
-        });
-        return props;
-    };
-
-    forester.collectPropertyRefs = function (phy, appliesTo, externalOnly) {
-        var propertyRefs = new Set();
-        forester.preOrderTraversalAll(phy, function (n) {
-
-            if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
-                if (n.properties && n.properties.length > 0) {
-                    var propertiesLength = n.properties.length;
-                    for (var i = 0; i < propertiesLength; ++i) {
-                        var property = n.properties[i];
-                        if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
-                            propertyRefs.add(property.ref);
-                        }
-                    }
-                }
-            }
-        });
-        return propertyRefs;
-    };
-
-
-    forester.shortenProperties = function (phy, appliesTo, externalOnly, sourceRef, targetRef) {
-        forester.preOrderTraversalAll(phy, function (n) {
-            if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
-                if (n.properties && n.properties.length > 0) {
-                    var propertiesLength = n.properties.length;
-                    for (var i = 0; i < propertiesLength; ++i) {
-                        var property = n.properties[i];
-                        if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
-                            if (property.ref === sourceRef) {
-                                var s = property.value.trim().split(/\s+/);
-                                if (s && s.length > 1) {
-                                    var newProp = {};
-                                    newProp.ref = targetRef;
-                                    if (s.length == 2) {
-                                        newProp.value = s[0];
-                                    }
-                                    else {
-                                        newProp.value = s[0] + ' ' + s[1];
-                                    }
-                                    newProp.datatype = property.datatype;
-                                    newProp.applies_to = property.applies_to;
-                                    n.properties.push(newProp);
-                                }
-                            }
-                        }
-                    }
-                }
-            }
-        });
-    };
-
-    forester.collectBasicTreeProperties = function (tree) {
-        var properties = {};
-        properties.internalNodeData = false;
-        properties.nodeNames = false;
-        properties.longestNodeName = 0;
-        properties.branchLengths = false;
-        properties.confidences = false;
-        properties.nodeEvents = false;
-        properties.sequences = false;
-        properties.taxonomies = false;
-        properties.alignedMolSeqs = true;
-        properties.maxMolSeqLength = 0;
-        properties.externalNodesCount = 0;
-        properties.molSeqResiduesPerPosition = null;
-        var molSeqs = [];
-        forester.preOrderTraversalAll(tree, function (n) {
-            if (n.name && n.name.length > 0) {
-                properties.nodeNames = true;
-                if (n.name.length > properties.longestNodeName) {
-                    properties.longestNodeName = n.name.length;
-                }
-                if ((n.children || n._children) && ( n.parent )) {
-                    properties.internalNodeData = true;
-                }
-            }
-            if (!(n.children || n._children)) {
-                properties.externalNodesCount += 1;
-            }
-            if (n.branch_length && n.branch_length > 0) {
-                properties.branchLengths = true;
-            }
-            if (n.events) {
-                properties.nodeEvents = true;
-            }
-            if (n.sequences && n.sequences.length > 0) {
-                properties.sequences = true;
-
-                if (n.children || n._children) {
-                    properties.internalNodeData = true;
-                }
-                else {
-                    var s = n.sequences[0];
-                    if (s.mol_seq && s.mol_seq.value) {
-                        if (s.mol_seq.value.length > properties.maxMolSeqLength) {
-                            properties.maxMolSeqLength = s.mol_seq.value.length;
-                        }
-                        if (!s.mol_seq.is_aligned) {
-                            properties.alignedMolSeqs = false;
-                        }
-                        else {
-                            molSeqs.push(s.mol_seq.value);
-                        }
-                    }
-                }
-            }
-            if (n.taxonomies && n.taxonomies.length > 0) {
-                properties.taxonomies = true;
-                if (n.children || n._children) {
-                    properties.internalNodeData = true;
-                }
-            }
-            if (n.confidences && n.confidences.length > 0) {
-                properties.confidences = true;
-            }
-            if (n.properties && n.properties.length > 0) {
-                var l = n.properties.length;
-                for (var p = 0; p < l; ++p) {
-                    if (n.properties[p].ref === BRANCH_EVENT_REF
-                        && n.properties[p].datatype === BRANCH_EVENT_DATATYPE
-                        && n.properties[p].applies_to === BRANCH_EVENT_APPLIES_TO) {
-                        properties.branchEvents = true;
-                    }
-                }
-            }
-
-        });
-
-        if (properties.alignedMolSeqs) {
-            properties.molSeqResiduesPerPosition = [];
-            for (var p = 0, maxLen = properties.maxMolSeqLength; p < maxLen; ++p) {
-                var mySet = new Set();
-                for (var i = 0, seqsLen = molSeqs.length; i < seqsLen; ++i) {
-                    var molSeq = molSeqs[i];
-                    var c = molSeq[p];
-                    if (c) {
-                        c = c.toUpperCase();
-                        mySet.add(c);
-                        if (!MSA_RESIDUE_SORT_MAP.has(c)) {
-                            throw ( "Unknown MSA residue '" + c + "'" );
-                        }
-                    }
-
-                }
-                var myArray = forester.setToArray(mySet);
-                myArray.sort(function (a, b) {
-                    return MSA_RESIDUE_SORT_MAP.get(a) - MSA_RESIDUE_SORT_MAP.get(b);
-                });
-                properties.molSeqResiduesPerPosition.push(myArray);
-            }
-        }
-        return properties;
-    };
-
-
-    forester.searchData = function (query,
-                                    phy,
-                                    caseSensitive,
-                                    partial,
-                                    regex) {
-        var nodes = new Set();
-        if (!phy || !query || query.length < 1) {
-            return nodes;
-        }
-        var my_query = query.trim();
-        if (my_query.length < 1) {
-            return nodes;
-        }
-        my_query = my_query.replace(/\s\s+/g, ' ');
-
-        if (!regex) {
-            my_query = my_query.replace(/\+\++/g, '+');
-        }
-
-        var queries = [];
-
-        if (!regex && ( my_query.indexOf(",") >= 0 )) {
-            queries = my_query.split(",");
-        }
-        else {
-            queries.push(my_query);
-        }
-        var queriesLength = queries.length;
-
-        for (var i = 0; i < queriesLength; ++i) {
-            var q = queries[i];
-            if (q) {
-                q = q.trim();
-                if (q.length > 0) {
-                    forester.preOrderTraversalAll(phy, matcher);
-                }
-            }
-        }
-
-        return nodes;
-
-
-        function matcher(node) {
-            var mqueries = [];
-            if (!regex && ( q.indexOf("+") >= 0 )) {
-                mqueries = q.split("+");
-            }
-            else {
-                mqueries.push(q);
-            }
-            var mqueriesLength = mqueries.length;
-            var match = true;
-            for (var i = 0; i < mqueriesLength; ++i) {
-                var mq = mqueries[i];
-                if (mq) {
-                    mq = mq.trim();
-                    if (mq.length > 0) {
-                        var ndf = null;
-                        if (( mq.length > 3 ) && ( mq.indexOf(":") === 2 )) {
-                            ndf = makeNDF(mq);
-                            if (ndf) {
-                                mq = mq.substring(3);
-                            }
-                        }
-                        var lmatch = false;
-                        if (( ( ndf === null ) || ( ndf === "NN" ) )
-                            && matchme(node.name, mq, caseSensitive, partial, regex)) {
-                            lmatch = true;
-                        }
-                        else if (( ( ndf === null ) || ( ndf === "TC" ) ) && node.taxonomies
-                            && node.taxonomies.length > 0
-                            && matchme(node.taxonomies[0].code,
-                                mq,
-                                caseSensitive,
-                                partial,
-                                regex)) {
-                            lmatch = true;
-                        }
-                        else if (( ( ndf === null ) || ( ndf === "TS" ) ) && node.taxonomies
-                            && node.taxonomies.length > 0
-                            && matchme(node.taxonomies[0].scientific_name,
-                                mq,
-                                caseSensitive,
-                                partial,
-                                regex)) {
-                            lmatch = true;
-                        }
-                        else if (( ( ndf === null ) || ( ndf === "TN" ) ) && node.taxonomies
-                            && node.taxonomies.length > 0
-                            && matchme(node.taxonomies[0].common_name,
-                                mq,
-                                caseSensitive,
-                                partial,
-                                regex)) {
-                            lmatch = true;
-                        }
-                        else if (( ( ndf === null ) || ( ndf === "SY" ) ) && node.taxonomies
-                            && node.taxonomies.length > 0
-                            && matchme(node.taxonomies[0].synonym,
-                                mq,
-                                caseSensitive,
-                                partial,
-                                regex)) {
-                            lmatch = true;
-                        }
-                        else if (( ( ndf === null ) || ( ndf === "TI" ) ) && node.taxonomies
-                            && node.taxonomies.length > 0 && node.taxonomies[0].id
-                            && matchme(node.taxonomies[0].id.value,
-                                mq,
-                                caseSensitive,
-                                partial,
-                                regex)) {
-                            lmatch = true;
-                        }
-                        else if (( ( ndf === null ) || ( ndf === "SN" ) ) && node.sequences
-                            && node.sequences.length > 0
-                            && matchme(node.sequences[0].name,
-                                mq,
-                                caseSensitive,
-                                partial,
-                                regex)) {
-                            lmatch = true;
-                        }
-                        else if (( ( ndf === null ) || ( ndf === "GN" ) ) && node.sequences
-                            && node.sequences.length > 0
-                            && matchme(node.sequences[0].gene_name,
-                                mq,
-                                caseSensitive,
-                                partial,
-                                regex)) {
-                            lmatch = true;
-                        }
-                        else if (( ( ndf === null ) || ( ndf === "SS" ) ) && node.sequences
-                            && node.sequences.length > 0
-                            && matchme(node.sequences[0].symbol,
-                                mq,
-                                caseSensitive,
-                                partial,
-                                regex)) {
-                            lmatch = true;
-                        }
-                        else if (( ( ndf === null ) || ( ndf === "SA" ) ) && node.sequences
-                            && node.sequences.length > 0 && node.sequences[0].accession
-                            && matchme(node.sequences[0].accession.value,
-                                mq,
-                                caseSensitive,
-                                partial,
-                                regex)) {
-                            lmatch = true;
-                        }
-                        if (!lmatch) {
-                            match = false;
-                            break;
-                        }
-
-                    } // if (mq.length > 0)
-                    else {
-                        match = false;
-                    }
-                } // if (mq)
-                else {
-                    match = false;
-                }
-            } //  for (var i = 0; i < mqueriesLength; ++i)
-            if (match) {
-                nodes.add(node);
-            }
-        }
-
-        function matchme(s,
-                         query,
-                         caseSensitive,
-                         partial,
-                         regex) {
-            if (!s || !query) {
-                return false;
-            }
-            var my_s = s.trim();
-            var my_query = query.trim();
-            if (!caseSensitive && !regex) {
-                my_s = my_s.toLowerCase();
-                my_query = my_query.toLowerCase();
-            }
-            if (regex) {
-                var re = null;
-                try {
-                    if (caseSensitive) {
-                        re = new RegExp(my_query);
-                    }
-                    else {
-                        re = new RegExp(my_query, 'i');
-                    }
-                }
-                catch (err) {
-                    return false;
-                }
-                if (re) {
-                    return ( my_s.search(re) > -1 );
-                }
-                else {
-                    return false;
-                }
-            }
-            else if (partial) {
-                return ( my_s.indexOf(my_query) > -1 );
-            }
-            else {
-                var np = new RegExp("(\\b|_)" + escapeRegExp(my_query) + "(\\b|_)");
-                if (np) {
-                    return ( my_s.search(np) > -1 );
-                }
-                else {
-                    return false;
-                }
-            }
-        }
-
-        function escapeRegExp(str) {
-            return str.replace(/[.*+?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
-        }
-
-        function makeNDF(query) {
-            var str = query.substring(0, 2);
-            if (str === "NN"
-                || str === "TC"
-                || str === "TN"
-                || str === "TS"
-                || str === "TI"
-                || str === "SY"
-                || str === "SN"
-                || str === "GN"
-                || str === "SS"
-                || str === "SA"
-                || str === "AN"
-                || str === "XR"
-                || str === "MS") {
-                return str;
-            }
-            else {
-                return null;
-            }
-        }
-    };
-
-
-    /**
-     * This calculates the sum of the external
-     * descendants of a node. It does not count descendants
-     * of collapsed nodes.
-     *
-     * @param node - A node.
-     * @returns {number} - The sum of external descendants.
-     */
-    forester.calcSumOfExternalDescendants = function (node) {
-        var nodes = 0;
-        forester.preOrderTraversal(node, function (n) {
-            if (!n.children) {
-                ++nodes;
-            }
-        });
-        return nodes;
-    };
-
-    /**
-     * This calculates the sum of all the external
-     * descendants of a node. It does count descendants
-     * of collapsed nodes.
-     *
-     * @param node - A node.
-     * @returns {number} - The sum of all external descendants.
-     */
-    forester.calcSumOfAllExternalDescendants = function (node) {
-        var nodes = 0;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (!(n.children || n._children)) {
-                ++nodes;
-            }
-        });
-        return nodes;
-    };
-
-    /**
-     * Returns true if at least one of the child nodes
-     * of node is collapsed.
-     *
-     * @param node - A node.
-     * @returns {boolean} - true if at least one of the child nodes is
-     * collapsed
-     */
-    forester.isHasCollapsedNodes = function (node) {
-        var collapsed = false;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n._children) {
-                collapsed = true;
-
-            }
-        });
-        return collapsed;
-    };
-
-    forester.getAllExternalNodes = function (node) {
-        var nodes = [];
-        forester.preOrderTraversalAll(node, function (n) {
-            if (!n.children && !n._children) {
-                nodes.push(n);
-            }
-        });
-        return nodes;
-    };
-
-    forester.getAllNodes = function (phy) {
-        var nodes = [];
-        forester.preOrderTraversalAll(forester.getTreeRoot(phy), function (n) {
-            nodes.push(n);
-        });
-        return nodes;
-    };
-
-    forester.calcMaxDepth = function (node) {
-        var max = 0;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (!n.children && !n._children) {
-                var steps = forester.calcDepth(n);
-                if (steps > max) {
-                    max = steps;
-                }
-            }
-        });
-        return max;
-    };
-
-    forester.calcDepth = function (node) {
-
-        var steps = 0;
-        while (node.parent && node.parent.parent) {
-            steps++;
-            node = node.parent;
-        }
-        return steps;
-    };
-
-
-    forester.calcBranchLengthSimpleStatistics = function (node) {
-        var stats = {};
-        stats.mean = 0;
-        stats.min = Number.MAX_VALUE;
-        stats.max = 0;
-        stats.n = 0;
-        var sum = 0;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n !== node && n.branch_length && n.branch_length >= 0) {
-                ++stats.n;
-                sum += n.branch_length;
-                if (n.branch_length < stats.min) {
-                    stats.min = n.branch_length;
-                }
-                if (n.branch_length > stats.max) {
-                    stats.max = n.branch_length;
-                }
-            }
-        });
-        if (stats.n > 0) {
-            stats.mean = sum / stats.n;
-        }
-        return stats;
-    };
-
-    forester.calcMaxBranchLength = function (node) {
-        var max = 0;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n !== node && n.branch_length && (n.branch_length > max)) {
-                max = n.branch_length;
-            }
-        });
-        return max;
-    };
-
-
-    forester.isHasNodeData = function (node) {
-        return ( (node.name && node.name.length > 0 ) ||
-        (node.taxonomies && node.taxonomies.length > 0) ||
-        (node.sequences && node.sequences.length > 0) ||
-        (node.properties && node.properties.length > 0) );
-    };
-
-
-    forester.removeMaxBranchLength = function (node) {
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n.max) {
-                n.max = undefined;
-            }
-        });
-    };
-
-
-    forester.collapseToBranchLength = function (root, branchLength) {
-        if (root.children && root.children.length === 1) {
-            collapseToBranchLengthHelper(root.children[0], branchLength);
-        }
-
-        function collapseToBranchLengthHelper(n, branchLength) {
-            if (!(n.children || n._children)) {
-                return;
-            }
-
-            if (!n.max) {
-                n.max = forester.calcMaxBranchLength(n);
-            }
-            var max = n.max;
-            if (max < branchLength) {
-                forester.collapse(n);
-            }
-            else {
-                forester.unCollapse(n);
-                for (var i = n.children.length - 1; i >= 0; i--) {
-                    collapseToBranchLengthHelper(n.children[i], branchLength);
-                }
-            }
-        }
-    };
-
-    forester.collapseToDepth = function (root, depth) {
-        if (root.children && root.children.length === 1) {
-            collapseToDepthHelper(root.children[0], 0, depth);
-        }
-
-        function collapseToDepthHelper(n, d, depth) {
-            if (!n.children && !n._children) {
-                return;
-            }
-            if (d >= depth) {
-                forester.collapse(n);
-            }
-            else {
-                forester.unCollapse(n);
-                ++d;
-                for (var i = n.children.length - 1; i >= 0; i--) {
-                    collapseToDepthHelper(n.children[i], d, depth);
-                }
-            }
-        }
-    };
-
-    forester.collapse = function (node) {
-        if (node.children) {
-            node._children = node.children;
-            node.children = null;
-        }
-    };
-
-    forester.unCollapse = function (node) {
-        if (node._children) {
-            node.children = node._children;
-            node._children = null;
-        }
-    };
-
-    /**
-     * To parse a New Hampshire (Newick) formatted tree.
-     *
-     * @param nhStr - A New Hampshire (Newick) formatted string.
-     * @param confidenceValuesInBrackets - Set to true if confidence values are in brackets (default: true)
-     *                                     Format is: name:distance[confidence]
-     *                                     Example: "bcl2:0.000393[95]"
-     * @param confidenceValuesAsInternalNames - Set to true if confidence values are represented by internal names (default: false).
-     * @returns {{}} - A phylogenetic tree object.
-     */
-    forester.parseNewHampshire = function (nhStr, confidenceValuesInBrackets, confidenceValuesAsInternalNames) {
-
-        var NH_FORMAT_ERR_OPEN_PARENS = NH_FORMAT_ERR + 'likely cause: number of open parentheses is larger than number of close parentheses';
-        var NH_FORMAT_ERR_CLOSE_PARENS = NH_FORMAT_ERR + 'likely cause: number of close parentheses is larger than number of open parentheses';
-
-        if (confidenceValuesInBrackets == undefined) {
-            confidenceValuesInBrackets = true;
-        }
-        if (confidenceValuesAsInternalNames == undefined) {
-            confidenceValuesAsInternalNames = false;
-        }
-        if ((confidenceValuesInBrackets === true ) && (confidenceValuesAsInternalNames === true)) {
-            throw ( "confidence values cannot be both in brackets and as internal node names" );
-        }
-
-        var ancs = [];
-        var x = {};
-        var ss = nhStr.split(/(;|\(|\)|,|:|"|')/);
-        var ssl = ss.length;
-        var in_double_q = false;
-        var in_single_q = false;
-        var buffer = '';
-        for (var i = 0; i < ssl; ++i) {
-            var element = ss[i].replace(/\s+/g, '');
-
-            if (element === '"' && !in_single_q) {
-                if (!in_double_q) {
-                    in_double_q = true;
-                }
-                else {
-                    in_double_q = false;
-                    if (x.name && x.name.length > 0) {
-                        x.name = x.name + buffer;
-                    }
-                    else {
-                        x.name = buffer;
-                    }
-                    buffer = '';
-                }
-            }
-            else if (element === "'" && !in_double_q) {
-                if (!in_single_q) {
-                    in_single_q = true;
-                }
-                else {
-                    in_single_q = false;
-                    if (x.name && x.name.length > 0) {
-                        x.name = x.name + buffer;
-                    }
-                    else {
-                        x.name = buffer;
-                    }
-                    buffer = '';
-                }
-            }
-            else {
-                if (in_double_q || in_single_q) {
-                    buffer += ss[i].replace(/\s+/g, ' ');
-                }
-                else {
-                    if (element === '(') {
-                        if (!x) {
-                            throw ( NH_FORMAT_ERR_CLOSE_PARENS );
-                        }
-                        var subtree1 = {};
-                        x.children = [subtree1];
-                        ancs.push(x);
-                        x = subtree1;
-                    }
-                    else if (element === ',') {
-                        if (ancs.length === 0) {
-                            throw (NH_FORMAT_ERR_CLOSE_PARENS);
-                        }
-                        var subtree2 = {};
-                        ancs[ancs.length - 1].children.push(subtree2);
-                        x = subtree2;
-                    }
-                    else if (element === ')') {
-                        x = ancs.pop();
-                    }
-                    else if (element === ':') {
-                    }
-                    else {
-                        var e = ss[i - 1];
-                        if (e) {
-                            e = e.trim();
-                            if (( e === ')' ) || ( e === '(' ) || ( e === ',')) {
-                                if (element && element.length > 0) {
-                                    if (element.charAt(element.length - 1) === "]") {
-                                        var o = element.indexOf('[');
-                                        if (o > -1) {
-                                            if (confidenceValuesInBrackets === true) {
-                                                addConfidence(x, element);
-                                            }
-                                            x.name = element.substring(0, o);
-                                        }
-                                        else {
-                                            x.name = element;
-                                        }
-                                    }
-                                    else {
-                                        x.name = element;
-                                        var op = x.name.indexOf('[');
-                                        if (op > -1) {
-                                            var cl = x.name.indexOf(']');
-                                            if (cl > op) {
-                                                x.name = x.name.substring(0, op) + x.name.substring(cl + 1, x.name.length);
-                                            }
-                                        }
-                                    }
-                                }
-                            }
-                            else if (e === ':') {
-                                if (element && element.length > 0) {
-                                    if (element.charAt(element.length - 1) === ']') {
-                                        var o1 = element.indexOf('[');
-                                        if (o1 > -1) {
-                                            if (confidenceValuesInBrackets === true) {
-                                                addConfidence(x, element);
-                                            }
-                                            var bl = parseFloat(element.substring(0, o1));
-                                            if (forester.isNumber(bl)) {
-                                                x.branch_length = bl;
-                                            }
-                                        }
-                                    }
-                                    else {
-                                        var b = parseFloat(parseFloat(element));
-                                        if (forester.isNumber(b)) {
-                                            x.branch_length = b;
-                                        }
-                                        else {
-                                            throw ( NH_FORMAT_ERR + 'could not parse branch-length from "' + element + '"' );
-                                        }
-                                    }
-                                }
-                            }
-                            else if (e === '"' || e === "'") {
-                                if ((element && element.length > 0) && (x.name && x.name.length > 0 )) {
-                                    if (element.charAt(element.length - 1) === "]") {
-                                        var opp = element.indexOf('[');
-                                        if (opp > -1) {
-                                            if (confidenceValuesInBrackets === true) {
-                                                addConfidence(x, element);
-                                            }
-                                            x.name = x.name + element.substring(0, opp);
-                                        }
-                                        else {
-                                            x.name = x.name + element;
-                                        }
-                                    }
-                                    else {
-                                        x.name = x.name + element;
-                                    }
-                                }
-                            }
-                        }
-                    }
-                }
-            }
-        }
-        if (ancs.length !== 0) {
-            throw ( NH_FORMAT_ERR_OPEN_PARENS );
-        }
-        if (!x) {
-            throw ( NH_FORMAT_ERR_CLOSE_PARENS );
-        }
-
-        var phy = {};
-        phy.children = [x];
-
-        forester.addParents(phy);
-
-        if (confidenceValuesAsInternalNames === true) {
-            moveInternalNodeNamesToConfidenceValues(phy);
-        }
-
-        return phy;
-
-        function addConfidence(x, element) {
-            var confValue = parseConfidence(element);
-            if (confValue != null) {
-                x.confidences = [];
-                var conf = {};
-                conf.value = confValue;
-                conf.type = 'unknown';
-                x.confidences.push(conf);
-            }
-        }
-
-        function parseConfidence(str) {
-            var o = str.indexOf('[');
-            if (o > -1) {
-                var s = str.substring(o + 1, element.length - 1);
-                if (NUMBERS_ONLY_PATTERN.test(s)) {
-                    var confValue = parseFloat(s);
-                    if (forester.isNumber(confValue)) {
-                        return confValue;
-                    }
-                    else {
-                        throw ( NH_FORMAT_ERR + 'could not parse confidence value from "' + str + '"' );
-                    }
-                }
-            }
-            return null;
-        }
-
-        function moveInternalNodeNamesToConfidenceValues(node) {
-            forester.preOrderTraversalAll(node, function (n) {
-                if (n.children || n._children) {
-                    if (n.name) {
-                        var s = n.name;
-                        if (NUMBERS_ONLY_PATTERN.test(s)) {
-                            var confValue = parseFloat(s);
-                            if ((confValue != null) && (forester.isNumber(confValue))) {
-                                n.confidences = [];
-                                var conf1 = {};
-                                conf1.value = confValue;
-                                conf1.type = 'unknown';
-                                n.confidences.push(conf1);
-                                n.name = undefined;
-                            }
-                        }
-                    }
-                }
-            });
-        }
-    };
-
-    forester.isNumber = function (v) {
-        if (v === undefined || v === null) {
-            return false;
-        }
-        if (v !== v) {
-            // This can only be true if the v is NaN
-            return false;
-        }
-        return true;
-    };
-
-    forester.getOneDistinctTaxonomy = function (node) {
-        var id = null;
-        var code = null;
-        var sn = null;
-        var cn = null;
-        var result = true;
-        var sawTax = false;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n.taxonomies && n.taxonomies.length === 1) {
-                var tax = n.taxonomies[0];
-                if (tax.code && tax.code.length > 0) {
-                    sawTax = true;
-                    if (code === null) {
-                        code = tax.code;
-                    }
-                    else if (code != tax.code) {
-                        result = false;
-                        return;
-                    }
-                }
-                if (tax.scientific_name && tax.scientific_name.length > 0) {
-                    sawTax = true;
-                    if (sn === null) {
-                        sn = tax.scientific_name;
-                    }
-                    else if (sn != tax.scientific_name) {
-                        result = false;
-                        return;
-                    }
-                }
-                if (tax.common_name && tax.common_name.length > 0) {
-                    sawTax = true;
-                    if (cn === null) {
-                        cn = tax.common_name;
-                    }
-                    else if (cn != tax.common_name) {
-                        result = false;
-                        return;
-                    }
-                }
-                if (tax.id && tax.id.value && tax.id.value.length > 0) {
-                    sawTax = true;
-                    var myid;
-                    if (tax.id.provider && tax.id.provider.length > 0) {
-                        myid = tax.id.provider + ':' + tax.id.value;
-                    }
-                    else {
-                        myid = tax.id.value;
-                    }
-                    if (id === null) {
-                        id = myid;
-                    }
-                    else if (id != myid) {
-                        result = false;
-
-                    }
-                }
-            }
-            else if (!n.children && !n._children) {
-                // If an external node lacks taxonomy, return false.
-                result = false;
-            }
-        });
-        if (!sawTax) {
-            return null;
-        }
-        if (result === true) {
-
-            if (sn) {
-                return sn;
-            }
-            else if (code) {
-                return code;
-            }
-            else if (cn) {
-                return cn;
-            }
-            else if (id) {
-                return id;
-            }
-        }
-        return null;
-    };
-
-    forester.getOneDistinctNodePropertyValue = function (node, propertyRef) {
-        var propValue = null;
-        var result = true;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n.properties && n.properties.length > 0) {
-                var propertiesLength = n.properties.length;
-                var gotIt = false;
-                for (var i = 0; i < propertiesLength; ++i) {
-                    var property = n.properties[i];
-                    if (property.ref && property.value && (property.applies_to === 'node') && ( property.ref === propertyRef) && ( property.value.length > 0)) {
-                        if (propValue === null) {
-                            propValue = property.value;
-                        }
-                        else if (propValue != property.value) {
-                            result = false;
-                            return;
-                        }
-                        gotIt = true;
-                    }
-                }
-                if (!gotIt && !n.children && !n._children) {
-                    // If an external node lacks propertyRef, return false.
-                    result = false;
-
-                }
-            }
-        });
-        if (propValue === null) {
-            return null;
-        }
-        if (result === true) {
-            return propValue;
-        }
-        else {
-            return null;
-        }
-    };
-
-    /**
-     * To be deprecated!
-     *
-     * @param phy
-     * @returns {{}}
-     */
-    forester.moveSimpleCharacteristicsToProperties = function (phy) {
-        var apptype;
-        if (phy.desc) {
-            apptype = 'ird:'
-        }
-        else {
-            apptype = 'vipr:'
-        }
-
-        var HOST = apptype + 'Host';
-        var COUNTRY = apptype + 'Country';
-        var YEAR = apptype + 'Year';
-        var HA = apptype + 'HA';
-        var NA = apptype + 'NA';
-        var NODE = 'node';
-        var STRING = 'xsd:string';
-        var INT = 'xsd:integer';
-
-        forester.preOrderTraversalAll(phy, function (n) {
-            if (n.simple_characteristics) {
-                var sc = n.simple_characteristics;
-                var props;
-                if (sc.country && sc.country.length > 0) {
-                    props = {};
-                    props.ref = COUNTRY;
-                    props.datatype = STRING;
-                    props.applies_to = NODE;
-                    props.value = sc.country;
-                    addProperties(n, props);
-                }
-                if (sc.host && sc.host.length > 0) {
-                    props = {};
-                    props.ref = HOST;
-                    props.datatype = STRING;
-                    props.applies_to = NODE;
-                    props.value = sc.host;
-                    addProperties(n, props);
-                }
-                if (sc.year && sc.year.length > 0) {
-                    props = {};
-                    props.ref = YEAR;
-                    props.datatype = INT;
-                    props.applies_to = NODE;
-                    props.value = parseInt(sc.year);
-                    addProperties(n, props);
-                }
-                if (sc.ha && sc.ha.length > 0) {
-                    props = {};
-                    props.ref = HA;
-                    props.datatype = INT;
-                    props.applies_to = NODE;
-                    props.value = parseInt(sc.ha);
-                    addProperties(n, props);
-                }
-                if (sc.na && sc.na.length > 0) {
-                    props = {};
-                    props.ref = NA;
-                    props.datatype = INT;
-                    props.applies_to = NODE;
-                    props.value = parseInt(sc.na);
-                    addProperties(n, props);
-                }
-                n.simple_characteristics = undefined;
-            }
-        });
-        function addProperties(n, props) {
-            if (props) {
-                if (!n.properties) {
-                    n.properties = [];
-                }
-                var alreadyHave = false;
-                var l = n.properties.length;
-                for (var i = 0; i < l; ++i) {
-                    if (n.properties[i].ref === props.ref) {
-                        alreadyHave = true;
-                        break;
-                    }
-                }
-                if (!alreadyHave) {
-                    n.properties.push(props);
-                }
-            }
-        }
-    };
-
-
-    /**
-     * To convert a phylogentic tree object to a New Hampshire (Newick) formatted string.
-     *
-     * @param phy - A phylogentic tree object.
-     * @param decPointsMax - Maximal number of decimal points for branch lengths (optional)
-     * @param replaceChars - To replace illegal characters (),:;"' instead of surrounding with quotation marks
-     * @param writeConfidences - to write confidence values in brackets
-     * @returns {*} - a New Hampshire (Newick) formatted string.
-     */
-    forester.toNewHampshire = function (phy, decPointsMax, replaceChars, writeConfidences) {
-        var nh = "";
-        if (phy.children && phy.children.length === 1) {
-            toNewHampshireHelper(phy.children[0], true);
-        }
-        if (nh.length > 0) {
-            return nh + ";";
-        }
-        return nh;
-
-        function toNewHampshireHelper(node, last) {
-            if (node.children) {
-                var l = node.children.length;
-                nh += "(";
-                for (var i = 0; i < l; ++i) {
-                    toNewHampshireHelper(node.children[i], i === l - 1);
-                }
-                nh += ")";
-            }
-            else if (node._children) {
-                var ll = node._children.length;
-                nh += "(";
-                for (var ii = 0; ii < ll; ++ii) {
-                    toNewHampshireHelper(node._children[ii], ii === ll - 1);
-                }
-                nh += ")";
-            }
-            if (node.name && node.name.length > 0) {
-                if (replaceChars === true) {
-                    nh += replaceUnsafeChars(node.name);
-                }
-                else {
-                    var myName = node.name.replace(/\s+/g, ' ');
-                    if (/[\s,():;'"\[\]]/.test(myName)) {
-                        if ((myName.indexOf('"') > -1) && (myName.indexOf("'") > -1 )) {
-                            nh += '"' + myName.replace(/"/g, "'") + '"';
-                        }
-                        else if (myName.indexOf('"') > -1) {
-                            nh += "'" + myName + "'";
-                        }
-                        else {
-                            nh += '"' + myName + '"';
-                        }
-                    }
-                    else {
-                        nh += myName;
-                    }
-                }
-            }
-            if (node.branch_length !== undefined && node.branch_length !== null) {
-                if (decPointsMax && decPointsMax > 0) {
-                    nh += ":" + forester.roundNumber(node.branch_length, decPointsMax);
-                }
-                else {
-                    nh += ":" + node.branch_length;
-                }
-            }
-            if (writeConfidences && node.confidences && node.confidences.length === 1 && node.confidences[0].value !== undefined && node.confidences[0].value !== null) {
-                if (decPointsMax && decPointsMax > 0) {
-                    nh += "[" + forester.roundNumber(node.confidences[0].value, decPointsMax) + "]";
-                }
-                else {
-                    nh += "[" + node.confidences[0].value + "]";
-                }
-            }
-            if (!last) {
-                nh += ",";
-            }
-        }
-
-        function replaceUnsafeChars(str) {
-            return str.replace(/[\s,():;'"\[\]]+/g, '_');
-        }
-    };
-
-    forester.roundNumber = function (num, dec) {
-        return Math.round(num * Math.pow(10, dec)) / Math.pow(10, dec);
-    };
-
-    forester.isString = function (s) {
-        return (typeof s === 'string' || s instanceof String);
-    };
-
-
-    // --------------------------------------------------------------
-    // For exporting
-    // --------------------------------------------------------------
-    if (typeof module !== 'undefined' && module.exports && !global.xmldocAssumeBrowser)
-        module.exports.forester = forester;
-    else if (typeof window !== "undefined")
-        window.forester = forester;
-    else
-        this.forester = forester;
-})();
+/**
+ *  Copyright (C) 2026 Christian M. Zmasek
+ *  Copyright (C) 2026 Yun Zhang
+ *  Copyright (C) 2026 J. Craig Venter Institute
+ *  All rights reserved
+ *
+ *  This library is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU Lesser General Public
+ *  License as published by the Free Software Foundation; either
+ *  version 2.1 of the License, or (at your option) any later version.
+ *
+ *  This library is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *  Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public
+ *  License along with this library; if not, write to the Free Software
+ *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ *
+ */
+
+// v 2.3.2
+// 2026-04-22
+//
+// forester.js is a general suite for dealing with phylogenetic trees.
+// 
+// forester.js is used by Archaeopteryx.js:
+//   https://github.com/cmzmasek/archaeopteryx-js
+//   https://www.npmjs.com/package/archaeopteryx
+//
+// Availability:
+//   https://github.com/cmzmasek/archaeopteryx-js
+//   https://www.npmjs.com/package/archaeopteryx
+//
+// Dependencies: none
+//
+//
+// In the following is a basic example shows how to parse a New Hampshire formatted String
+// into to a object representing a phylogenetic tree.
+// Followed by pre- and post-order traversal,
+// and writing back to a New Hampshire formatted String.
+//
+// Change './forester' to 'forester' if you use this code outside of this package
+//
+// let forester = require('./forester').forester;
+//
+// let newHampshireFormattedString = "(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;";
+// let phylogeneticTree = forester.parseNewHampshire(newHampshireFormattedString);
+//
+// console.log('Pre-order traversal:');
+// forester.preOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
+//     console.log(n.name + ':' + n.branch_length);
+// });
+//
+// console.log('Post-order traversal:');
+// forester.postOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
+//     console.log(n.name + ':' + n.branch_length);
+// });
+//
+// console.log('In New Hampshire format:');
+// let nh = forester.toNewHampshire(phylogeneticTree);
+// console.log(nh);
+
+
+(function forester() {
+
+    "use strict";
+
+    const BRANCH_EVENT_REF = 'aptx:branch_event';
+    const BRANCH_EVENT_DATATYPE = 'xsd:string';
+    const BRANCH_EVENT_APPLIES_TO = 'parent_branch';
+    const NH_FORMAT_ERR = 'New Hampshire (Newick) format error: ';
+
+    const NUMBERS_ONLY_PATTERN = /^[-+]?[0-9\\.]+$/;
+
+    const MSA_RESIDUE_SORT_MAP = new Map();
+    MSA_RESIDUE_SORT_MAP.set('A', 0);
+    MSA_RESIDUE_SORT_MAP.set('C', 1);
+    MSA_RESIDUE_SORT_MAP.set('D', 2);
+    MSA_RESIDUE_SORT_MAP.set('E', 3);
+    MSA_RESIDUE_SORT_MAP.set('F', 4);
+    MSA_RESIDUE_SORT_MAP.set('G', 5);
+    MSA_RESIDUE_SORT_MAP.set('H', 6);
+    MSA_RESIDUE_SORT_MAP.set('I', 7);
+    MSA_RESIDUE_SORT_MAP.set('K', 8);
+    MSA_RESIDUE_SORT_MAP.set('L', 9);
+    MSA_RESIDUE_SORT_MAP.set('M', 10);
+    MSA_RESIDUE_SORT_MAP.set('N', 11);
+    MSA_RESIDUE_SORT_MAP.set('P', 12);
+    MSA_RESIDUE_SORT_MAP.set('Q', 13);
+    MSA_RESIDUE_SORT_MAP.set('R', 14);
+    MSA_RESIDUE_SORT_MAP.set('S', 15);
+    MSA_RESIDUE_SORT_MAP.set('T', 16);
+    MSA_RESIDUE_SORT_MAP.set('U', 17);// Uracil
+    MSA_RESIDUE_SORT_MAP.set('V', 18);
+    MSA_RESIDUE_SORT_MAP.set('W', 19);
+    MSA_RESIDUE_SORT_MAP.set('Y', 20);
+    MSA_RESIDUE_SORT_MAP.set('B', 21);// Asparagine or aspartic acid
+    MSA_RESIDUE_SORT_MAP.set('Z', 22);// Glutamine or glutamic acid
+    MSA_RESIDUE_SORT_MAP.set('X', 23);
+    MSA_RESIDUE_SORT_MAP.set('?', 24);
+    MSA_RESIDUE_SORT_MAP.set('-', 25);
+    MSA_RESIDUE_SORT_MAP.set('.', 26);
+
+
+    /**
+     * Sets links to parent nodes for all nodes in a
+     * phyloXML-based tree object
+     *
+     * @param phy - A phyloXML-based tree object.
+     */
+    forester.addParents = function (phy) {
+        if (phy.children) {
+            for (let i = phy.children.length - 1; i >= 0; --i) {
+                let c = phy.children[i];
+                c.parent = phy;
+                forester.addParents(c);
+            }
+        }
+    };
+
+    /**
+     * Returns the real root node of a
+     * phyloXML-based tree object.
+     * Precondition: needs to have parents set.
+     *
+     * @param phy - A phyloXML-based tree object or node.
+     * @returns {*} - The real tree root node.
+     */
+    forester.getTreeRoot = function (phy) {
+        let root = phy;
+        if (!root.parent && root.children && root.children.length === 1) {
+            root = root.children[0];
+        }
+        while (root.parent && root.parent.parent) {
+            root = root.parent;
+        }
+        return root;
+    };
+
+    /**
+     * Visits all non-collapsed child nodes of a node
+     * while applying a function in pre-order.
+     *
+     * @param node - The root of the subtree to traverse.
+     * @param fn - The function to apply.
+     */
+    forester.preOrderTraversal = function (node, fn) {
+        fn(node);
+        if (node.children) {
+            for (let i = node.children.length - 1; i >= 0; --i) {
+                forester.preOrderTraversal(node.children[i], fn);
+            }
+        }
+    };
+
+    /**
+     * Visits all child nodes of a node
+     * while applying a function in pre-order.
+     *
+     * @param node - The root of the subtree to traverse.
+     * @param fn - The function to apply.
+     */
+    forester.preOrderTraversalAll = function (node, fn) {
+        fn(node);
+        if (node.children) {
+            for (let i = node.children.length - 1; i >= 0; --i) {
+                forester.preOrderTraversalAll(node.children[i], fn);
+            }
+        } else if (node._children) {
+            for (let ii = node._children.length - 1; ii >= 0; --ii) {
+                forester.preOrderTraversalAll(node._children[ii], fn);
+            }
+        }
+    };
+
+    forester.postOrderTraversalAll = function (node, fn) {
+        if (node.children) {
+            let l = node.children.length;
+            for (let i = 0; i < l; ++i) {
+                forester.postOrderTraversalAll(node.children[i], fn);
+            }
+        } else if (node._children) {
+            let ll = node._children.length;
+            for (let ii = 0; ii < ll; ++ii) {
+                forester.postOrderTraversalAll(node._children[ii], fn);
+            }
+        }
+        fn(node);
+    };
+
+
+    forester.findByNodeName = function (node, name) {
+        let found = [];
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n.name === name) {
+                found.push(n);
+            }
+        });
+        return found;
+    };
+
+    forester.findByTaxonomyCode = function (node, code) {
+        let found = [];
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n.taxonomies && n.taxonomies.length > 0 && n.taxonomies[0].code === code) {
+                found.push(n);
+            }
+        });
+        return found;
+    };
+
+    forester.findByTaxonomyScientificName = function (node, scientificName) {
+        let found = [];
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n.taxonomies && n.taxonomies.length > 0 && n.taxonomies[0].scientific_name === scientificName) {
+                found.push(n);
+            }
+        });
+        return found;
+    };
+
+
+    forester.filterByNodeProperty = function (positive, phy, propertyMap) {
+        if (!phy) {
+            throw ("cannot delete null tree");
+        }
+        if (!propertyMap) {
+            throw ("property list is null");
+        }
+        const toDelete = [];
+        forester.preOrderTraversalAll(phy, function (n) {
+            if (!n.children && !n._children) {
+                if (n.properties && n.properties.length > 0) {
+                    const propertiesLength = n.properties.length;
+                    for (let i = 0; i < propertiesLength; ++i) {
+                        const property = n.properties[i];
+                        if (property.ref && property.value && property.applies_to === 'node') {
+                            if (positive) {
+                                if (property.ref in propertyMap && !propertyMap[property.ref].includes(property.value)) {
+                                    toDelete.push(n);
+                                }
+                            } else {
+                                if (property.ref in propertyMap && propertyMap[property.ref].includes(property.value)) {
+                                    toDelete.push(n);
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        });
+        const l = toDelete.length;
+        console.log(toDelete);
+        for (let i = 0; i < l; ++i) {
+            forester.deleteSubtree(phy, toDelete[i]);
+        }
+    };
+
+
+    /**
+     * To delete a sub-tree or external node.
+     *
+     * @param phy
+     * @param nodeToDelete
+     */
+    forester.deleteSubtree = function (phy, nodeToDelete) {
+        if (!phy) {
+            throw ("cannot delete null tree");
+        }
+        if (!nodeToDelete) {
+            throw ("cannot delete null node");
+        }
+        if (!nodeToDelete.parent || !nodeToDelete.parent.parent) {
+            throw ("cannot delete root");
+        }
+        if (!nodeToDelete.parent.parent.parent) {
+            throw ("cannot delete direct child of root");
+        }
+
+        let p = nodeToDelete.parent;
+
+        if ((p.children) && (p.children.length > 1)) {
+            let i = p.children.indexOf(nodeToDelete);
+            if (i !== -1) {
+                p.children.splice(i, 1);
+            }
+        }
+        if ((p._children) && (p._children.length > 1)) {
+            let ii = p._children.indexOf(nodeToDelete);
+            if (ii !== -1) {
+                p._children.splice(ii, 1);
+            }
+        }
+
+        if (p.children.length === 1) {
+            let pp = p.parent;
+            let cni = forester.getChildNodeIndex(pp, p);
+            if ((cni < 0) || (cni > (pp.children.length - 1))) {
+                throw ("this should never have happened, child node index = " + cni);
+            }
+            let x = p.children[0];
+            let nbl = undefined;
+            if (x.branch_length || p.branch_length) {
+                nbl = (x.branch_length > 0 ? x.branch_length : 0) + (p.branch_length > 0 ? p.branch_length : 0);
+            }
+            x.parent = pp;
+            pp.children[cni] = x;
+            x.branch_length = nbl;
+        }
+
+    };
+
+
+    /**
+     * To re-root a tree object.
+     *
+     * @param phy - The tree to be re-rooted.
+     * @param node - The node on where to place the new root (on its parent branch).
+     * @param branchLength - The branch length to use if new root is not placed in the middle (if
+     * non-negative).
+     */
+    forester.reRoot = function (phy, node, branchLength) {
+        if (!phy) {
+            throw ("cannot re-root null tree");
+        }
+        if (!node) {
+            throw ("cannot re-root on null node");
+        }
+        if (!branchLength) {
+            branchLength = -1;
+        }
+        if (forester.isString(node)) {
+            let nodes = forester.findByNodeName(phy, node);
+            if (nodes.length > 1) {
+                throw ("node name '" + node + "' is not unique");
+            } else if (nodes.length < 1) {
+                throw ("node name '" + node + "' is not found");
+            }
+            node = nodes[0];
+        }
+
+        phy.rooted = true;
+        let root = forester.getTreeRoot(phy);
+
+        if (!node.parent || !node.parent.parent) {
+            //do noting
+        } else if (!node.parent.parent.parent) {
+            if ((node.parent.children.length === 2) && (branchLength >= 0)) {
+                let d = node.parent.children[0].branch_length + node.parent.children[1].branch_length;
+                let other;
+                if (node.parent.children[0] === node) {
+                    other = node.parent.children[1];
+                } else {
+                    other = node.parent.children[0];
+                }
+                node.branch_length = branchLength;
+                let dm = d - branchLength;
+                if (dm >= 0) {
+                    other.branch_length = dm;
+                } else {
+                    other.branch_length = 0;
+                }
+            }
+            if (node.parent.children.length > 2) {
+                let index = forester.getChildNodeIndex(node.parent, node);
+                let dn = node.branch_length;
+                let prev_root = root;
+                prev_root.children.splice(index, 1);
+                let nr = {};
+                nr.children = [];
+                forester.setChildNode(nr, 0, node);
+                forester.setChildNode(nr, 1, prev_root);
+
+                forester.copyBranchData(node, prev_root);
+
+                phy.children[0] = nr;
+                nr.parent = phy;
+                if (branchLength >= 0) {
+                    node.branch_length = branchLength;
+                    let dnmp = dn - branchLength;
+                    if (dnmp >= 0) {
+                        prev_root.branch_length = dnmp;
+                    } else {
+                        prev_root.branch_length = 0;
+                    }
+                } else {
+                    if (dn >= 0) {
+                        let dn2 = dn / 2.0;
+                        node.branch_length = dn2;
+                        prev_root.branch_length = dn2;
+                    }
+                }
+            }
+        } else {
+            let a = node;
+            let new_root = {};
+            let distance1;
+            let distance2 = 0.0;
+            let branch_data_1;
+            let branch_data_2 = null;
+            let b = a.parent;
+            let c = b.parent;
+
+            new_root.children = [];
+            forester.setChildNode(new_root, 0, a);
+            forester.setChildNode(new_root, 1, b);
+
+            distance1 = c.branch_length;
+
+            branch_data_1 = forester.getBranchData(c);
+
+            c.branch_length = b.branch_length;
+
+            forester.copyBranchData(b, c);
+            forester.copyBranchData(a, b);
+
+            // New root is always placed in the middle of the branch:
+            if (!a.branch_length) {
+                b.branch_length = undefined;
+            } else {
+                if (branchLength >= 0.0) {
+                    let diff = a.branch_length - branchLength;
+                    a.branch_length = branchLength;
+                    b.branch_length = (diff >= 0.0 ? diff : 0.0);
+                } else {
+                    let d2 = a.branch_length / 2.0;
+                    a.branch_length = d2;
+                    b.branch_length = d2;
+                }
+            }
+            setChildNodeOnly(b, forester.getChildNodeIndex(b, a), c);
+            // moving to the old root, swapping references:
+            while (c.parent.parent) {
+                a = b;
+                b = c;
+                c = c.parent;
+                setChildNodeOnly(b, forester.getChildNodeIndex(b, a), c);
+                b.parent = a;
+                distance2 = c.branch_length;
+                branch_data_2 = forester.getBranchData(c);
+                c.branch_length = distance1;
+                forester.setBranchData(c, branch_data_1);
+                distance1 = distance2;
+                branch_data_1 = branch_data_2;
+            }
+            // removing the old root:
+            if (c.children.length === 2) {
+                let node2 = c.children[1 - forester.getChildNodeIndex(c, b)];
+                node2.parent = b;
+                if ((!c.branch_length) && (!node2.branch_length)) {
+                    node2.branch_length = undefined;
+                } else {
+                    node2.branch_length = (c.branch_length >= 0.0 ? c.branch_length : 0.0) + (node2.branch_length >= 0.0 ? node2.branch_length : 0.0);
+                }
+                let cbd = forester.getBranchData(c);
+                if (cbd) {
+                    forester.setBranchData(node2, cbd);
+                }
+                let l = b.children.length;
+                for (let i = 0; i < l; ++i) {
+                    if (b.children[i] === c) {
+                        setChildNodeOnly(b, i, node2);
+                        break;
+                    }
+                }
+            } else {
+                c.parent = b;
+                forester.removeChildNode(c, forester.getChildNodeIndex(c, b));
+            }
+            phy.children[0] = new_root;
+            new_root.parent = phy;
+            forester.addParents(phy);
+        }
+
+        function setChildNodeOnly(parentNode, i, node) {
+            if (parentNode.children.length <= i) {
+                parentNode.children.push(node);
+            } else {
+                parentNode.children[i] = node;
+            }
+        }
+    };
+
+    forester.midpointRoot = function (phy) {
+        let root = forester.getTreeRoot(phy);
+        let extNodes = forester.getAllExternalNodes(root);
+        if ((extNodes.length < 2) || (forester.calcMaxBranchLength(root) <= 0)) {
+            return;
+        }
+        let counter = 0;
+        let totalNodes = forester.getAllNodes(phy).length;
+        while (true) {
+            if (++counter > (totalNodes + 1)) {
+                throw('this should not have happened: midpoint rooting does not converge');
+            }
+            let a = null;
+            let da = 0;
+            let db = 0;
+            let cl = forester.getTreeRoot(phy).children.length;
+            for (let i = 0; i < cl; ++i) {
+                let f = forester.getFurthestDescendant(forester.getTreeRoot(phy).children[i]);
+                let df = forester.getDistance(f, forester.getTreeRoot(phy));
+                if (df > 0) {
+                    if (df > da) {
+                        db = da;
+                        da = df;
+                        a = f;
+                    } else if (df > db) {
+                        db = df;
+                    }
+                }
+            }
+            let diff = da - db;
+            if (diff < 0.0001) {
+                break;
+            }
+            let x = da - (diff / 2.0);
+            while ((x > a.branch_length) && a.parent) {
+                x -= (a.branch_length > 0 ? a.branch_length : 0);
+                a = a.parent;
+            }
+            forester.reRoot(phy, a, x);
+        }
+    };
+
+    forester.getFurthestDescendant = function (node) {
+        let children = forester.getAllExternalNodes(node);
+        let farthest = null;
+        let longest = -1000000;
+        let l = children.length;
+        for (let i = 0; i < l; ++i) {
+            let dist = forester.getDistance(children[i], node);
+            if (dist > longest) {
+                farthest = children[i];
+                longest = dist;
+            }
+        }
+        return farthest;
+    };
+
+    /**
+     * Calculates the distance between PhylogenyNodes n1 and n2.
+     * PRECONDITION: n1 is a descendant of n2.
+     *
+     * @param n1 a descendant of n2
+     * @param n2
+     * @returns {number} distance between n1 and n2
+     */
+    forester.getDistance = function (n1, n2) {
+        let d = 0.0;
+        while (n1 !== n2) {
+            if (n1.branch_length > 0.0) {
+                d += n1.branch_length;
+            }
+            n1 = n1.parent;
+        }
+        return d;
+    };
+
+    forester.removeChildNode = function (parentNode, i) {
+        if (!parentNode.children) {
+            throw ("cannot remove the child node for a external node");
+        }
+        if ((i >= parentNode.children.length) || (i < 0)) {
+            throw ("attempt to get child node " + i + " of a node with " + parentNode.children.length + " child nodes.");
+        }
+        parentNode.children[i].parent = undefined;
+        parentNode.children.splice(i, 1);
+    };
+
+
+    /**
+     * Inserts node node at the specified position i into the list of
+     * child nodes of parentNode. This does not allow null slots in the list of child nodes:
+     * If i is larger than the number of child nodes, node is just added to the
+     * list, not placed at index i.
+     */
+    forester.setChildNode = function (parentNode, i, node) {
+        node.parent = parentNode;
+        if (parentNode.children.length <= i) {
+            parentNode.children.push(node);
+        } else {
+            parentNode.children[i] = node;
+        }
+    };
+
+
+    forester.getBranchData = function (node) {
+        let branchData = null;
+        if (node.width || node.color || node.confidences) {
+            branchData = {};
+            branchData.width = node.width;
+            branchData.color = node.color;
+            branchData.confidences = node.confidences;
+        }
+        return branchData;
+    };
+
+
+    forester.setBranchData = function (node, branchData) {
+        if (branchData) {
+            node.width = branchData.width;
+            node.color = branchData.color;
+            node.confidences = branchData.confidences;
+        }
+    };
+
+    forester.unCollapseAll = function (node) {
+        forester.preOrderTraversal(node, function (d) {
+            if (d._children) {
+                d.children = d._children;
+                d._children = null;
+            }
+        });
+    };
+
+    forester.copyBranchData = function (nodeFrom, nodeTo) {
+        nodeTo.width = nodeFrom.width;
+        nodeTo.color = nodeFrom.color;
+        nodeTo.confidences = nodeFrom.confidences;
+    };
+
+
+    forester.getChildNodeIndex = function (parentNode, childNode) {
+        if (!parentNode) {
+            throw ("cannot get the child index for a root node");
+        }
+        let c = parentNode.children.length;
+        for (let i = 0; i < c; ++i) {
+            if (parentNode.children[i] === childNode) {
+                return i;
+            }
+        }
+        throw ("unexpected exception: Could not determine the child index for a node");
+    };
+
+
+    forester.getChildren = function (node) {
+        return node._children ? node._children : (node.children ? node.children : []);
+    };
+
+
+    forester.calcAverageTreeHeight = function (node, externalDescendants) {
+        let c = externalDescendants ? externalDescendants : forester.getAllExternalNodes(node);
+        let l = c.length;
+        let s = 0;
+        for (let i = 0; i < l; ++i) {
+            let cc = c[i];
+            while (cc !== node) {
+                if (cc.branch_length > 0) {
+                    s += cc.branch_length;
+                }
+                cc = cc.parent;
+            }
+        }
+        return s / l;
+    };
+
+    forester.setToArray = function (set) {
+        let array = [];
+        if (set) {
+            set.forEach(function (e) {
+                array.push(e);
+            });
+        }
+        return array;
+    };
+
+    forester.setToSortedArray = function (set) {
+        let array = [];
+        if (set) {
+            set.forEach(function (e) {
+                array.push(e);
+            });
+        }
+        return array.sort();
+    };
+
+    forester.calcMinMaxInSet = function (set) {
+        let array = [];
+        let first = true;
+        let min = 0;
+        let max = 0;
+        if (set) {
+            set.forEach(function (e) {
+                e = parseFloat(e);
+                if (first) {
+                    first = false;
+                    min = e;
+                    max = e;
+                } else {
+                    if (e < min) {
+                        min = e;
+                    }
+                    if (e > max) {
+                        max = e;
+                    }
+                }
+            });
+        }
+        array[0] = min;
+        array[1] = max;
+        return array;
+    };
+
+    forester.calcMinMeanMaxInSet = function (set) {
+        let array = [];
+        let first = true;
+        let min = 0;
+        let max = 0;
+        let mean = 0;
+        let sum = 0;
+        let n = 0;
+        if (set) {
+            set.forEach(function (e) {
+                e = parseFloat(e);
+                ++n;
+                sum += e;
+                if (first) {
+                    first = false;
+                    min = e;
+                    max = e;
+                } else {
+                    if (e < min) {
+                        min = e;
+                    }
+                    if (e > max) {
+                        max = e;
+                    }
+                }
+            });
+        }
+        if (n > 0) {
+            mean = sum / n;
+        }
+        array[0] = min;
+        array[1] = mean;
+        array[2] = max;
+        return array;
+    };
+
+
+    /**
+     * This collects all properties in a tree
+     * and returns them as dictionary of Sets mapping
+     * keys to values.
+     * It only collects properly formed properties
+     * (as per phyloXML standard), which means
+     * that 'applies_to' and 'datatype' have to be present.
+     *
+     *
+     * @param phy - A phyloXML-based tree object or node.
+     * @param appliesTo - 'phylogeny', 'clade', 'node', 'annotation', 'parent_branch', or 'other'.
+     * @param externalOnly - To collect from external nodes only.
+     * @returns {{}}
+     */
+    forester.collectProperties = function (phy, appliesTo, externalOnly) {
+        let props = {};
+        forester.preOrderTraversalAll(phy, function (n) {
+
+            if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
+                if (n.properties && n.properties.length > 0) {
+                    let propertiesLength = n.properties.length;
+                    for (let i = 0; i < propertiesLength; ++i) {
+                        let property = n.properties[i];
+                        if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
+                            let ref = property.ref;
+                            if (!props[ref]) {
+                                props[ref] = new Set();
+                            }
+                            props[ref].add(property.value);
+                        }
+                    }
+                }
+            }
+        });
+        return props;
+    };
+
+
+    /**
+     *
+     * Special method for IRD database.
+     * Returns true if at least one 'ird:Host' property with 'Avian' found
+     *
+     * @param phy
+     * @param targetValue
+     * @param fromRef
+     * @param toRef
+     * @returns {boolean}
+     */
+    forester.splitProperty = function (phy, targetValue, fromRef, toRef) {
+        let found = false;
+        let targetValue_ = targetValue + ' ';
+        forester.preOrderTraversalAll(phy, function (n) {
+            if (n.properties && n.properties.length > 0) {
+                let propertiesLength = n.properties.length;
+                for (let i = 0; i < propertiesLength; ++i) {
+                    let property = n.properties[i];
+                    if (property.ref === fromRef && property.value) {
+                        let newValue = '';
+                        if (property.value.startsWith(targetValue_)) {
+                            newValue = targetValue;
+                            found = true;
+                        } else {
+                            newValue = property.value;
+                        }
+                        let newproperty = {};
+                        newproperty.ref = toRef;
+                        newproperty.value = newValue;
+                        newproperty.datatype = 'xsd:string';
+                        newproperty.applies_to = 'node';
+                        n.properties.push(newproperty);
+                    }
+                }
+            }
+        });
+        return found;
+    };
+
+    forester.collectPropertyRefs = function (phy, appliesTo, externalOnly) {
+        let propertyRefs = new Set();
+        forester.preOrderTraversalAll(phy, function (n) {
+
+            if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
+                if (n.properties && n.properties.length > 0) {
+                    let propertiesLength = n.properties.length;
+                    for (let i = 0; i < propertiesLength; ++i) {
+                        let property = n.properties[i];
+                        if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
+                            propertyRefs.add(property.ref);
+                        }
+                    }
+                }
+            }
+        });
+        return propertyRefs;
+    };
+
+
+    forester.shortenProperties = function (phy, appliesTo, externalOnly, sourceRef, targetRef) {
+        forester.preOrderTraversalAll(phy, function (n) {
+            if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
+                if (n.properties && n.properties.length > 0) {
+                    let propertiesLength = n.properties.length;
+                    for (let i = 0; i < propertiesLength; ++i) {
+                        let property = n.properties[i];
+                        if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
+                            if (property.ref === sourceRef) {
+                                let s = property.value.trim().split(/\s+/);
+                                if (s && s.length > 1) {
+                                    let newProp = {};
+                                    newProp.ref = targetRef;
+                                    if (s.length === 2) {
+                                        newProp.value = s[0];
+                                    } else {
+                                        newProp.value = s[0] + ' ' + s[1];
+                                    }
+                                    newProp.datatype = property.datatype;
+                                    newProp.applies_to = property.applies_to;
+                                    n.properties.push(newProp);
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        });
+    };
+
+    forester.collectBasicTreeProperties = function (tree) {
+        let properties = {};
+        properties.internalNodeData = false;
+        properties.nodeNames = false;
+        properties.longestNodeName = 0;
+        properties.branchLengths = false;
+        properties.confidences = false;
+        properties.nodeEvents = false;
+        properties.sequences = false;
+        properties.taxonomies = false;
+        properties.alignedMolSeqs = true;
+        properties.maxMolSeqLength = 0;
+        properties.externalNodesCount = 0;
+        properties.molSeqResiduesPerPosition = null;
+        properties.averageBranchLength = 0;
+        let bl_counter = 0;
+        let bl_sum = 0;
+        let molSeqs = [];
+        forester.preOrderTraversalAll(tree, function (n) {
+            if (n.name && n.name.length > 0) {
+                properties.nodeNames = true;
+                if (n.name.length > properties.longestNodeName) {
+                    properties.longestNodeName = n.name.length;
+                }
+                if ((n.children || n._children) && (n.parent)) {
+                    properties.internalNodeData = true;
+                }
+            }
+            if (!(n.children || n._children)) {
+                properties.externalNodesCount += 1;
+            }
+            if (n.branch_length && n.branch_length > 0) {
+                properties.branchLengths = true;
+                bl_sum += n.branch_length;
+                bl_counter += 1;
+            }
+            if (n.events) {
+                properties.nodeEvents = true;
+            }
+            if (n.sequences && n.sequences.length > 0) {
+                properties.sequences = true;
+
+                if (n.children || n._children) {
+                    properties.internalNodeData = true;
+                } else {
+                    let s = n.sequences[0];
+                    if (s.mol_seq && s.mol_seq.value) {
+                        if (s.mol_seq.value.length > properties.maxMolSeqLength) {
+                            properties.maxMolSeqLength = s.mol_seq.value.length;
+                        }
+                        if (!s.mol_seq.is_aligned) {
+                            properties.alignedMolSeqs = false;
+                        } else {
+                            molSeqs.push(s.mol_seq.value);
+                        }
+                    }
+                }
+            }
+            if (n.taxonomies && n.taxonomies.length > 0) {
+                properties.taxonomies = true;
+                if (n.children || n._children) {
+                    properties.internalNodeData = true;
+                }
+            }
+            if (n.confidences && n.confidences.length > 0) {
+                properties.confidences = true;
+            }
+            if (n.properties && n.properties.length > 0) {
+                let l = n.properties.length;
+                for (let p = 0; p < l; ++p) {
+                    if (n.properties[p].ref === BRANCH_EVENT_REF && n.properties[p].datatype === BRANCH_EVENT_DATATYPE && n.properties[p].applies_to === BRANCH_EVENT_APPLIES_TO) {
+                        properties.branchEvents = true;
+                    }
+                }
+            }
+
+        });
+
+        if (properties.alignedMolSeqs) {
+            properties.molSeqResiduesPerPosition = [];
+            for (let p = 0, maxLen = properties.maxMolSeqLength; p < maxLen; ++p) {
+                let mySet = new Set();
+                for (let i = 0, seqsLen = molSeqs.length; i < seqsLen; ++i) {
+                    let molSeq = molSeqs[i];
+                    let c = molSeq[p];
+                    if (c) {
+                        c = c.toUpperCase();
+                        mySet.add(c);
+                        if (!MSA_RESIDUE_SORT_MAP.has(c)) {
+                            throw ("Unknown MSA residue '" + c + "'");
+                        }
+                    }
+
+                }
+                let myArray = forester.setToArray(mySet);
+                myArray.sort(function (a, b) {
+                    return MSA_RESIDUE_SORT_MAP.get(a) - MSA_RESIDUE_SORT_MAP.get(b);
+                });
+                properties.molSeqResiduesPerPosition.push(myArray);
+            }
+        }
+
+        if (bl_counter > 0) {
+            properties.averageBranchLength = bl_sum / bl_counter;
+        }
+
+
+        return properties;
+    };
+
+    /**
+     * This calculates the sum of the external
+     * descendants of a node. It does not count descendants
+     * of collapsed nodes.
+     *
+     * @param node - A node.
+     * @returns {number} - The sum of external descendants.
+     */
+    forester.calcSumOfExternalDescendants = function (node) {
+        let nodes = 0;
+        forester.preOrderTraversal(node, function (n) {
+            if (!n.children) {
+                ++nodes;
+            }
+        });
+        return nodes;
+    };
+
+    /**
+     * This calculates the sum of all the external
+     * descendants of a node. It does count descendants
+     * of collapsed nodes.
+     *
+     * @param node - A node.
+     * @returns {number} - The sum of all external descendants.
+     */
+    forester.calcSumOfAllExternalDescendants = function (node) {
+        let nodes = 0;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (!(n.children || n._children)) {
+                ++nodes;
+            }
+        });
+        return nodes;
+    };
+
+    /**
+     * Returns true if at least one of the child nodes
+     * of node is collapsed.
+     *
+     * @param node - A node.
+     * @returns {boolean} - true if at least one of the child nodes is
+     * collapsed
+     */
+    forester.isHasCollapsedNodes = function (node) {
+        let collapsed = false;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n._children) {
+                collapsed = true;
+
+            }
+        });
+        return collapsed;
+    };
+
+    forester.getAllExternalNodes = function (node) {
+        let nodes = [];
+        forester.preOrderTraversalAll(node, function (n) {
+            if (!n.children && !n._children) {
+                nodes.push(n);
+            }
+        });
+        return nodes;
+    };
+
+    forester.getAllNodes = function (phy) {
+        let nodes = [];
+        forester.preOrderTraversalAll(forester.getTreeRoot(phy), function (n) {
+            nodes.push(n);
+        });
+        return nodes;
+    };
+
+    forester.calcMaxDepth = function (node) {
+        let max = 0;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (!n.children && !n._children) {
+                let steps = forester.calcDepth(n);
+                if (steps > max) {
+                    max = steps;
+                }
+            }
+        });
+        return max;
+    };
+
+    forester.calcDepth = function (node) {
+
+        let steps = 0;
+        while (node.parent && node.parent.parent) {
+            steps++;
+            node = node.parent;
+        }
+        return steps;
+    };
+
+
+    forester.calcBranchLengthSimpleStatistics = function (node) {
+        let stats = {};
+        stats.mean = 0;
+        stats.min = Number.MAX_VALUE;
+        stats.max = 0;
+        stats.n = 0;
+        let sum = 0;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n !== node && n.branch_length && n.branch_length >= 0) {
+                ++stats.n;
+                sum += n.branch_length;
+                if (n.branch_length < stats.min) {
+                    stats.min = n.branch_length;
+                }
+                if (n.branch_length > stats.max) {
+                    stats.max = n.branch_length;
+                }
+            }
+        });
+        if (stats.n > 0) {
+            stats.mean = sum / stats.n;
+        }
+        return stats;
+    };
+
+    forester.calcMaxBranchLength = function (node) {
+        let max = 0;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n !== node && n.branch_length && (n.branch_length > max)) {
+                max = n.branch_length;
+            }
+        });
+        return max;
+    };
+
+
+    forester.isHasNodeData = function (node) {
+        return ((node.name && node.name.length > 0) || (node.taxonomies && node.taxonomies.length > 0) || (node.sequences && node.sequences.length > 0) || (node.properties && node.properties.length > 0));
+    };
+
+
+    forester.removeMaxBranchLength = function (node) {
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n.max) {
+                n.max = undefined;
+            }
+        });
+    };
+
+
+    forester.collapseToBranchLength = function (root, branchLength) {
+        if (root.children && root.children.length === 1) {
+            collapseToBranchLengthHelper(root.children[0], branchLength);
+        }
+
+        function collapseToBranchLengthHelper(n, branchLength) {
+            if (!(n.children || n._children)) {
+                return;
+            }
+
+            if (!n.max) {
+                n.max = forester.calcMaxBranchLength(n);
+            }
+            let max = n.max;
+            if (max < branchLength) {
+                forester.collapse(n);
+            } else {
+                forester.unCollapse(n);
+                for (let i = n.children.length - 1; i >= 0; i--) {
+                    collapseToBranchLengthHelper(n.children[i], branchLength);
+                }
+            }
+        }
+    };
+
+    forester.collapseToDepth = function (root, depth) {
+        if (root.children && root.children.length === 1) {
+            collapseToDepthHelper(root.children[0], 0, depth);
+        }
+
+        function collapseToDepthHelper(n, d, depth) {
+            if (!n.children && !n._children) {
+                return;
+            }
+            if (d >= depth) {
+                forester.collapse(n);
+            } else {
+                forester.unCollapse(n);
+                ++d;
+                for (let i = n.children.length - 1; i >= 0; i--) {
+                    collapseToDepthHelper(n.children[i], d, depth);
+                }
+            }
+        }
+    };
+
+    forester.collapse = function (node) {
+        if (node.children) {
+            node._children = node.children;
+            node.children = null;
+        }
+    };
+
+    forester.unCollapse = function (node) {
+        if (node._children) {
+            node.children = node._children;
+            node._children = null;
+        }
+    };
+
+    /**
+     * To parse a New Hampshire (Newick) formatted tree.
+     *
+     * @param nhStr - A New Hampshire (Newick) formatted string.
+     * @param confidenceValuesInBrackets - Set to true if confidence values are in brackets (default: true)
+     *                                     Format is: name:distance[confidence]
+     *                                     Example: "bcl2:0.000393[95]"
+     * @param confidenceValuesAsInternalNames - Set to true if confidence values are represented by internal names (default: false).
+     * @returns {{}} - A phylogenetic tree object.
+     */
+    forester.parseNewHampshire = function (nhStr, confidenceValuesInBrackets, confidenceValuesAsInternalNames) {
+
+        let NH_FORMAT_ERR_OPEN_PARENS = NH_FORMAT_ERR + 'likely cause: number of open parentheses is larger than number of close parentheses';
+        let NH_FORMAT_ERR_CLOSE_PARENS = NH_FORMAT_ERR + 'likely cause: number of close parentheses is larger than number of open parentheses';
+
+        if (confidenceValuesInBrackets === undefined) {
+            confidenceValuesInBrackets = true;
+        }
+        if (confidenceValuesAsInternalNames === undefined) {
+            confidenceValuesAsInternalNames = false;
+        }
+        if ((confidenceValuesInBrackets === true) && (confidenceValuesAsInternalNames === true)) {
+            throw ("confidence values cannot be both in brackets and as internal node names");
+        }
+
+        let ancs = [];
+        let x = {};
+
+        let sss = nhStr.replace(/\[\s*&.+?\]/g, '');
+
+        let ss = sss.split(/(;|\(|\)|,|:|"|')/);
+        let ssl = ss.length;
+        let in_double_q = false;
+        let in_single_q = false;
+        let buffer = '';
+        for (let i = 0; i < ssl; ++i) {
+            let element = ss[i].replace(/\s+/g, '');
+
+            if (element === '"' && !in_single_q) {
+                if (!in_double_q) {
+                    in_double_q = true;
+                } else {
+                    in_double_q = false;
+                    if (x.name && x.name.length > 0) {
+                        x.name = x.name + buffer;
+                    } else {
+                        x.name = buffer;
+                    }
+                    buffer = '';
+                }
+            } else if (element === "'" && !in_double_q) {
+                if (!in_single_q) {
+                    in_single_q = true;
+                } else {
+                    in_single_q = false;
+                    if (x.name && x.name.length > 0) {
+                        x.name = x.name + buffer;
+                    } else {
+                        x.name = buffer;
+                    }
+                    buffer = '';
+                }
+            } else {
+                if (in_double_q || in_single_q) {
+                    buffer += ss[i].replace(/\s+/g, ' ');
+                } else {
+                    if (element === '(') {
+                        if (!x) {
+                            throw (NH_FORMAT_ERR_CLOSE_PARENS);
+                        }
+                        let subtree1 = {};
+                        x.children = [subtree1];
+                        ancs.push(x);
+                        x = subtree1;
+                    } else if (element === ',') {
+                        if (ancs.length === 0) {
+                            throw (NH_FORMAT_ERR_CLOSE_PARENS);
+                        }
+                        let subtree2 = {};
+                        ancs[ancs.length - 1].children.push(subtree2);
+                        x = subtree2;
+                    } else if (element === ')') {
+                        x = ancs.pop();
+                    } else if (element === ':') {
+                    } else {
+                        let e = ss[i - 1];
+                        if (e) {
+                            e = e.trim();
+                            if ((e === ')') || (e === '(') || (e === ',')) {
+                                if (element && element.length > 0) {
+                                    if (element.charAt(element.length - 1) === "]") {
+                                        let o = element.indexOf('[');
+                                        if (o > -1) {
+                                            if (confidenceValuesInBrackets === true) {
+                                                addConfidence(x, element);
+                                            }
+                                            x.name = element.substring(0, o);
+                                        } else {
+                                            x.name = element;
+                                        }
+                                    } else {
+                                        x.name = element;
+                                        let op = x.name.indexOf('[');
+                                        if (op > -1) {
+                                            let cl = x.name.indexOf(']');
+                                            if (cl > op) {
+                                                x.name = x.name.substring(0, op) + x.name.substring(cl + 1, x.name.length);
+                                            }
+                                        }
+                                    }
+                                }
+                            } else if (e === ':') {
+                                if (element && element.length > 0) {
+                                    if (element.charAt(element.length - 1) === ']') {
+                                        let o1 = element.indexOf('[');
+                                        if (o1 > -1) {
+                                            if (confidenceValuesInBrackets === true) {
+                                                addConfidence(x, element);
+                                            }
+                                            let bl = parseFloat(element.substring(0, o1));
+                                            if (forester.isNumber(bl)) {
+                                                x.branch_length = bl;
+                                            }
+                                        }
+                                    } else {
+                                        let b = parseFloat(element);
+                                        if (forester.isNumber(b)) {
+                                            x.branch_length = b;
+                                        } else {
+                                            throw (NH_FORMAT_ERR + 'could not parse branch-length from "' + element + '"');
+                                        }
+                                    }
+                                }
+                            } else if (e === '"' || e === "'") {
+                                if ((element && element.length > 0) && (x.name && x.name.length > 0)) {
+                                    if (element.charAt(element.length - 1) === "]") {
+                                        let opp = element.indexOf('[');
+                                        if (opp > -1) {
+                                            if (confidenceValuesInBrackets === true) {
+                                                addConfidence(x, element);
+                                            }
+                                            x.name = x.name + element.substring(0, opp);
+                                        } else {
+                                            x.name = x.name + element;
+                                        }
+                                    } else {
+                                        x.name = x.name + element;
+                                    }
+                                }
+                            }
+                        }
+
+                    }
+                }
+            }
+        }
+        if (ancs.length !== 0) {
+            throw (NH_FORMAT_ERR_OPEN_PARENS);
+        }
+        if (!x) {
+            throw (NH_FORMAT_ERR_CLOSE_PARENS);
+        }
+
+        let phy = {};
+        phy.children = [x];
+
+        forester.addParents(phy);
+
+        if (confidenceValuesAsInternalNames === true) {
+            moveInternalNodeNamesToConfidenceValues(phy);
+        }
+
+        return phy;
+
+        function addConfidence(x, element) {
+            let confValue = parseConfidence(element);
+            if (confValue != null) {
+                x.confidences = [];
+                let conf = {};
+                conf.value = confValue;
+                conf.type = 'unknown';
+                x.confidences.push(conf);
+            }
+        }
+
+        function parseConfidence(element) {
+            let o = element.indexOf('[');
+            if (o > -1) {
+                let s = element.substring(o + 1, element.length - 1);
+                if (NUMBERS_ONLY_PATTERN.test(s)) {
+                    let confValue = parseFloat(s);
+                    if (forester.isNumber(confValue)) {
+                        return confValue;
+                    } else {
+                        throw (NH_FORMAT_ERR + 'could not parse confidence value from "' + element + '"');
+                    }
+                }
+            }
+            return null;
+        }
+
+        function moveInternalNodeNamesToConfidenceValues(node) {
+            forester.preOrderTraversalAll(node, function (n) {
+                if (n.children || n._children) {
+                    if (n.name) {
+                        let s = n.name;
+                        if (NUMBERS_ONLY_PATTERN.test(s)) {
+                            let confValue = parseFloat(s);
+                            if ((confValue != null) && (forester.isNumber(confValue))) {
+                                n.confidences = [];
+                                let conf1 = {};
+                                conf1.value = confValue;
+                                conf1.type = 'unknown';
+                                n.confidences.push(conf1);
+                                n.name = undefined;
+                            }
+                        }
+                    }
+                }
+            });
+        }
+    };
+
+    forester.isNumber = function (v) {
+        if (v === undefined || v === null) {
+            return false;
+        }
+        if (v != v) {
+            // This can only be true if the v is NaN
+            return false;
+        }
+        return true;
+    };
+
+    forester.getOneDistinctTaxonomy = function (node) {
+        let id = null;
+        let code = null;
+        let sn = null;
+        let cn = null;
+        let result = true;
+        let sawTax = false;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n.taxonomies && n.taxonomies.length === 1) {
+                let tax = n.taxonomies[0];
+                if (tax.code && tax.code.length > 0) {
+                    sawTax = true;
+                    if (code === null) {
+                        code = tax.code;
+                    } else if (code !== tax.code) {
+                        result = false;
+                        return;
+                    }
+                }
+                if (tax.scientific_name && tax.scientific_name.length > 0) {
+                    sawTax = true;
+                    if (sn === null) {
+                        sn = tax.scientific_name;
+                    } else if (sn !== tax.scientific_name) {
+                        result = false;
+                        return;
+                    }
+                }
+                if (tax.common_name && tax.common_name.length > 0) {
+                    sawTax = true;
+                    if (cn === null) {
+                        cn = tax.common_name;
+                    } else if (cn !== tax.common_name) {
+                        result = false;
+                        return;
+                    }
+                }
+                if (tax.id && tax.id.value && tax.id.value.length > 0) {
+                    sawTax = true;
+                    let myid;
+                    if (tax.id.provider && tax.id.provider.length > 0) {
+                        myid = tax.id.provider + ':' + tax.id.value;
+                    } else {
+                        myid = tax.id.value;
+                    }
+                    if (id === null) {
+                        id = myid;
+                    } else if (id !== myid) {
+                        result = false;
+
+                    }
+                }
+            } else if (!n.children && !n._children) {
+                // If an external node lacks taxonomy, return false.
+                result = false;
+            }
+        });
+        if (!sawTax) {
+            return null;
+        }
+        if (result === true) {
+
+            if (sn) {
+                return sn;
+            } else if (code) {
+                return code;
+            } else if (cn) {
+                return cn;
+            } else if (id) {
+                return id;
+            }
+        }
+        return null;
+    };
+
+    forester.getOneDistinctNodePropertyValue = function (node, propertyRef) {
+        let propValue = null;
+        let result = true;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n.properties && n.properties.length > 0) {
+                let propertiesLength = n.properties.length;
+                let gotIt = false;
+                for (let i = 0; i < propertiesLength; ++i) {
+                    let property = n.properties[i];
+                    if (property.ref && property.value && (property.applies_to === 'node') && (property.ref === propertyRef) && (property.value.length > 0)) {
+                        if (propValue === null) {
+                            propValue = property.value;
+                        } else if (propValue !== property.value) {
+                            result = false;
+                            return;
+                        }
+                        gotIt = true;
+                    }
+                }
+                if (!gotIt && !n.children && !n._children) {
+                    // If an external node lacks propertyRef, return false.
+                    result = false;
+
+                }
+            }
+        });
+        if (propValue === null) {
+            return null;
+        }
+        if (result === true) {
+            return propValue;
+        } else {
+            return null;
+        }
+    };
+
+    /**
+     * To be deprecated!
+     *
+     * @param phy
+     * @returns {{}}
+     */
+    forester.moveSimpleCharacteristicsToProperties = function (phy) {
+        let apptype;
+        if (phy.desc) {
+            apptype = 'ird:'
+        } else {
+            apptype = 'vipr:'
+        }
+
+        let HOST = apptype + 'Host';
+        let COUNTRY = apptype + 'Country';
+        let YEAR = apptype + 'Year';
+        let HA = apptype + 'HA';
+        let NA = apptype + 'NA';
+        let NODE = 'node';
+        let STRING = 'xsd:string';
+        let INT = 'xsd:integer';
+
+        forester.preOrderTraversalAll(phy, function (n) {
+            if (n.simple_characteristics) {
+                let sc = n.simple_characteristics;
+                let props;
+                if (sc.country && sc.country.length > 0) {
+                    props = {};
+                    props.ref = COUNTRY;
+                    props.datatype = STRING;
+                    props.applies_to = NODE;
+                    props.value = sc.country;
+                    addProperties(n, props);
+                }
+                if (sc.host && sc.host.length > 0) {
+                    props = {};
+                    props.ref = HOST;
+                    props.datatype = STRING;
+                    props.applies_to = NODE;
+                    props.value = sc.host;
+                    addProperties(n, props);
+                }
+                if (sc.year && sc.year.length > 0) {
+                    props = {};
+                    props.ref = YEAR;
+                    props.datatype = INT;
+                    props.applies_to = NODE;
+                    props.value = parseInt(sc.year);
+                    addProperties(n, props);
+                }
+                if (sc.ha && sc.ha.length > 0) {
+                    props = {};
+                    props.ref = HA;
+                    props.datatype = INT;
+                    props.applies_to = NODE;
+                    props.value = parseInt(sc.ha);
+                    addProperties(n, props);
+                }
+                if (sc.na && sc.na.length > 0) {
+                    props = {};
+                    props.ref = NA;
+                    props.datatype = INT;
+                    props.applies_to = NODE;
+                    props.value = parseInt(sc.na);
+                    addProperties(n, props);
+                }
+                n.simple_characteristics = undefined;
+            }
+        });
+
+        function addProperties(n, props) {
+            if (props) {
+                if (!n.properties) {
+                    n.properties = [];
+                }
+                let alreadyHave = false;
+                let l = n.properties.length;
+                for (let i = 0; i < l; ++i) {
+                    if (n.properties[i].ref === props.ref) {
+                        alreadyHave = true;
+                        break;
+                    }
+                }
+                if (!alreadyHave) {
+                    n.properties.push(props);
+                }
+            }
+        }
+    };
+
+
+    /**
+     * To convert a phylogentic tree object to a New Hampshire (Newick) formatted string.
+     *
+     * @param phy - A phylogentic tree object.
+     * @param decPointsMax - Maximal number of decimal points for branch lengths (optional)
+     * @param replaceChars - To replace illegal characters (),:;"' instead of surrounding with quotation marks
+     * @param writeConfidences - to write confidence values in brackets
+     * @returns {*} - a New Hampshire (Newick) formatted string.
+     */
+    forester.toNewHampshire = function (phy, decPointsMax, replaceChars, writeConfidences) {
+        let nh = "";
+        if (phy.children && phy.children.length === 1) {
+            toNewHampshireHelper(phy.children[0], true);
+        }
+        if (nh.length > 0) {
+            return nh + ";";
+        }
+        return nh;
+
+        function toNewHampshireHelper(node, last) {
+            if (node.children) {
+                let l = node.children.length;
+                nh += "(";
+                for (let i = 0; i < l; ++i) {
+                    toNewHampshireHelper(node.children[i], i === l - 1);
+                }
+                nh += ")";
+            } else if (node._children) {
+                let ll = node._children.length;
+                nh += "(";
+                for (let ii = 0; ii < ll; ++ii) {
+                    toNewHampshireHelper(node._children[ii], ii === ll - 1);
+                }
+                nh += ")";
+            }
+            if (node.name && node.name.length > 0) {
+                if (replaceChars === true) {
+                    nh += replaceUnsafeChars(node.name);
+                } else {
+                    let myName = node.name.replace(/\s+/g, ' ');
+                    if (/[\s,():;'"\[\]]/.test(myName)) {
+                        if ((myName.indexOf('"') > -1) && (myName.indexOf("'") > -1)) {
+                            nh += '"' + myName.replace(/"/g, "'") + '"';
+                        } else if (myName.indexOf('"') > -1) {
+                            nh += "'" + myName + "'";
+                        } else {
+                            nh += '"' + myName + '"';
+                        }
+                    } else {
+                        nh += myName;
+                    }
+                }
+            }
+            if (node.branch_length !== undefined && node.branch_length !== null) {
+                if (decPointsMax && decPointsMax > 0) {
+                    nh += ":" + forester.roundNumber(node.branch_length, decPointsMax);
+                } else {
+                    nh += ":" + node.branch_length;
+                }
+            }
+            if (writeConfidences && node.confidences && node.confidences.length === 1 && node.confidences[0].value !== undefined && node.confidences[0].value !== null) {
+                if (decPointsMax && decPointsMax > 0) {
+                    nh += "[" + forester.roundNumber(node.confidences[0].value, decPointsMax) + "]";
+                } else {
+                    nh += "[" + node.confidences[0].value + "]";
+                }
+            }
+            if (!last) {
+                nh += ",";
+            }
+        }
+
+        function replaceUnsafeChars(str) {
+            return str.replace(/[\s,():;'"\[\]]+/g, '_');
+        }
+    };
+
+    forester.getMolecularSequencesAsFasta = function (node, sep) {
+        let fasta_all = '';
+        let ext_nodes = forester.getAllExternalNodes(node).reverse();
+        for (let j = 0, l = ext_nodes.length; j < l; ++j) {
+            let n = ext_nodes[j];
+            if (n.sequences) {
+                for (let i = 0; i < n.sequences.length; ++i) {
+                    let s = n.sequences[i];
+                    if (s.mol_seq && s.mol_seq.value && s.mol_seq.value.length > 0) {
+                        let seq = s.mol_seq.value;
+                        let seqname = j;
+                        if (s.name && s.name.length > 0) {
+                            seqname = s.name
+                        } else if (n.name && n.name.length > 0) {
+                            seqname = n.name
+                        }
+                        let split_seq_ary = seq.match(/.{1,80}/g);
+                        let split_seq = '';
+                        for (let ii = 0; ii < split_seq_ary.length; ++ii) {
+                            split_seq += split_seq_ary[ii] + sep;
+                        }
+
+                        let fasta = '>' + seqname + sep + split_seq;
+                        fasta_all += fasta;
+                    }
+                }
+            }
+        }
+        return fasta_all;
+    }
+
+    forester.roundNumber = function (num, dec) {
+        return Math.round(num * Math.pow(10, dec)) / Math.pow(10, dec);
+    };
+
+    forester.isString = function (s) {
+        return (typeof s === 'string' || s instanceof String);
+    };
+
+
+    // --------------------------------------------------------------
+    // For exporting
+    // --------------------------------------------------------------
+    if (typeof module !== 'undefined' && module.exports && !global.xmldocAssumeBrowser) module.exports.forester = forester; else if (typeof window !== "undefined") window.forester = forester; else this.forester = forester;
+})();