How to use

commonLeaves

method

in

phylo.tree.model.TreeUtils

/**
 * Returns the list of leaves contained in all trees
 *
 * @param trees the trees
 * @return sharedLeaves the leaves common to all trees
 */
public static List<String> commonLeaves(Collection<Tree> trees) {
  return commonLeaves(trees.toArray(new Tree[trees.size()]));
}

for (int i = 0; i < trees.size() - 1; i++) {
  for (int j = i + 1; j < trees.size(); j++) {
    List<String> commonTaxa = TreeUtils.commonLeaves(Arrays.asList(trees.get(i), trees.get(j)));
    if (commonTaxa.size() > 1) {
      double[] distances = new double[commonTaxa.size() - 1];