How to use

pruneInnerNode

method

in

phylo.tree.model.TreeUtils

/**
 * Deletes the specified node from the tree.The child of this node becomes child
 * of its parent.
 * If the node has more than one child, nothing have to be done.
 *
 * @param node: the node, that has to be deleted
 * @param tree: the tree, from that the tree has to be deleted
 */
public static void pruneInnerNode(TreeNode node, Tree tree) {
  pruneInnerNode(node, tree, true, false);
}

public static void pruneInnerNode(TreeNode node, Tree tree, boolean sumEdgeWeight) {
  pruneInnerNode(node, tree, sumEdgeWeight, false);
}

public static void pruneDegreeOneNodes(Tree tree, boolean sumEdgeWeight, boolean useParentWeight) {
  for (int i = 0; i < tree.getMaxIndex(); i++) {
    TreeNode n = tree.getVertex(i);
    if (n == null) {
      continue;
    }
    //prune the node, if it is not null
    pruneInnerNode(n, tree, sumEdgeWeight, useParentWeight);
  }
}

  supertree.removeVertex(cladeToCheck);
} else {
  TreeUtils.pruneInnerNode(cladeToCheck, supertree, false);

  supertree.removeVertex(cladeNodeToCheck);
} else {
  TreeUtils.pruneInnerNode(cladeNodeToCheck, supertree, false);