How to use

setIndex

method

in

phylo.tree.model.TreeNode

/**
 * Adds a node to the tree and refreshes its vertex. this is useful to add vertices that were in another tree before.
 */
public int addVertex(TreeNode n, final boolean refreshIndex) {
  if (refreshIndex)
    n.setIndex(-1);
  return addVertex(n);
}

/**
 * Clones this node.
 *
 * @return node the new node
 */
public TreeNode cloneNode() {
  TreeNode n = new TreeNode();
  n.setLabel(getLabel());
  n.setIndex(getIndex());
  return n;
}

/**
 * Add subtree to existing tree, recursive iteration over the subtree to add
 *
 * @param tree    the target tree
 * @param parent  the parent node
 * @param newNode the current node to be added to the parent
 * @return node added node
 */
private TreeNode addSubtree(Tree tree, TreeNode parent, TreeNode newNode) {
  TreeNode nn = newNode.cloneNode();
  nn.setIndex(-1);
  tree.addVertex(nn);
  tree.addEdge(parent, nn);
  for (TreeNode child : newNode.children()) {
    addSubtree(tree, nn, child);
  }
  return nn;
}

@SuppressWarnings("unchecked")
private void hangIn(TreeNode newParent, TreeNode oldParent, Tree tree) {
  for (TreeNode n : oldParent.children()) {
    TreeNode newNode = n.cloneNode();
    newNode.setIndex(-1);
    tree.addVertex(newNode);
    Edge edge = tree.addEdge(newParent, newNode);
    edge.setWeight(n.getDistanceToParent());
    hangIn(newNode, n, tree);
  }
}

/**
 * Create a new {@link Tree} that represents the subtree of this tree rooted at the given
 * node. The returned tree is a new tree that contains clones of the {@link TreeNode}s of this tree.
 * The node copies are created using {@link TreeNode#cloneNode()} and are
 * new instances, so you will not have object equality ( n != n.cloneNode() ). Node equality using
 * {@link TreeNode#equals(Object)} will work at least for labeled nodes (because the labels are compared), but
 * for performance reasons we do not do deep checks.
 * <p>
 * If this tree does not contain the given node, null is returned.
 *
 * @param n the root node of the subtree
 * @return subtree rooted at the given node or null
 */
public Tree getSubtree(TreeNode n) {
  if (n == null) throw new NullPointerException();
  if (nodes.get(n.getIndex()) != n) {
    return null;
  }
  Tree r = new Tree();
  r.setName(getName());
  TreeNode root = n.cloneNode();
  root.setIndex(-1); // reset index
  r.addVertex(root);
  r.setRoot(root);
  hangIn(root, n, r);
  return r;
}