Class ReRootedTree

src/figtree/treeviewer/ReRootedTree.java:44–846

A rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree. @author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$

 * $LastChangedRevision$
 */
final public class ReRootedTree implements RootedTree {

    /**
     * Make a copy of the given unrooted tree
     * @param source an unrooted source tree
     * @param ingroupNode the node on one side of the root
     * @param outgroupNode the node on the other side of the root
     * @param ingroupBranchLength the branch length from the root to the ingroup node
     * @throws jebl.evolution.graphs.Graph.NoEdgeException
     */
    public ReRootedTree(RootedTree source, Node ingroupNode, Node outgroupNode, double ingroupBranchLength) throws NoEdgeException {

        this.source = source;
        List<Node> children = new ArrayList<Node>();

        Node node1 = createNodes(source, outgroupNode, ingroupNode);
        setLength(node1, ingroupBranchLength);
        children.add(node1);

        Node node2 = createNodes(source, ingroupNode, outgroupNode);
        double l = source.getEdgeLength(ingroupNode, outgroupNode);
        if (outgroupNode == source.getRootNode()) {
            // the tree is already rooted at the required location
            for (Node adj : source.getAdjacencies(outgroupNode)) {
                if (adj != ingroupNode) {
                   l += source.getEdgeLength(outgroupNode, adj);
                }
            }
        }
        setLength(node2, Math.max(l - ingroupBranchLength, 0.0));
        children.add(node2);

        createInternalNode(null, children);
    }

    /**
     * Clones the entire tree structure from the given (unrooted) Tree.
     * @param tree the unrooted tree
     * @param parent the parent node
     * @param child the child node
     */
    public Node createNodes(RootedTree tree, Node parent, Node child) throws NoEdgeException {

        Node newNode = null;
        double length;

        if (tree.isExternal(child)) {
            newNode = createExternalNode(child, tree.getTaxon(child));
            length = tree.getEdgeLength(parent, child);
        } else {
            List<Node> adjacencies = tree.getAdjacencies(child);

            if (adjacencies.size() == 2) {
                // this is the root node so skip over it...
                if (adjacencies.get(0) == parent) {
                    newNode = createNodes(tree, child, adjacencies.get(1));
                } else {
                    newNode = createNodes(tree, child, adjacencies.get(0));