Method createNodes

src/figtree/treeviewer/ReRootedTree.java:85–127

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

(RootedTree tree, Node parent, Node child)

     * @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));
                }
                length = tree.getEdgeLength(adjacencies.get(0), child) +
                        tree.getEdgeLength(adjacencies.get(1), child);

            } else {
                List<Node> children = new ArrayList<Node>();

                for (Node child2 : adjacencies) {
                    if (child2 != parent) {
                        children.add(createNodes(tree, child, child2));
                    }
                }

                if (tree.getParent(parent) == child) {
                    newNode = createInternalNode(parent, children);
                } else {
                    newNode = createInternalNode(child, children);
                }
                length = tree.getEdgeLength(parent, child);
            }
        }

        setLength(newNode, length);

        return newNode;
    }

    /**
     * Creates a new external node with the given taxon. See createInternalNode