How to use

getIndex

method

in

phylo.tree.model.TreeNode

/**
 * Returns true if this tree contains the given node
 *
 * @param node the node
 * @return true if tree contains node
 */
public boolean containsVertex(TreeNode node) {
  if (node == null) return false;
  return nodes.get(node.getIndex()) != null && nodes.get(node.getIndex()) == node;
}

public Map<Integer, BCNNode> getResult() {
  //compare(compareTree);
  HashMap<Integer, BCNNode> sscores = new HashMap<Integer, BCNNode>();
  for (TreeNode n : sourceScrores.keySet()) {
    BCNScore score = sourceScrores.get(n);
    sscores.put(n.getIndex(), new BCNNode(score.getScore(), score.getTargetIndex()));
  }
  return sscores;
}

/**
 * Adds a node to the tree.
 */
public int addVertex(TreeNode n) {
  n.setGraph(this);
  nodes.put(n);
  return n.getIndex();
}

/**
 * Create a new {@link Tree} that represents the subtree of this tree rooted at the given
 * node and removes this subtree from this tree. The returned tree is a new tree that contains the original {@link TreeNode}s of this tree.
 * <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 List<TreeNode> removeSubtree(TreeNode n) {
  if (n == null) throw new NullPointerException();
  if (nodes.get(n.getIndex()) != n) {
    return null;
  }
  LinkedList<TreeNode> nodes = new LinkedList<>();
  for (TreeNode node : n.depthFirstIterator()) {
    nodes.push(node);
    this.nodes.remove(node.getIndex());
  }
  if (n.incompingEdge != null) {
    n.incompingEdge.getSource().removeEdge(n.incompingEdge);
    n.incompingEdge = null;
  }
  nodes.push(n);
  this.nodes.remove(n.getIndex());
  return nodes;
}

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

if (this.getIndex() == object.getIndex()) {
  return true;
} else {

s.setTargetIndex(bcnNode.getIndex());

/**
 * 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;
}

score.setScore(r.getIndex());