/* * TreeLengthStatistic.java * * Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard * * This file is part of BEAST. * See the NOTICE file distributed with this work for additional * information regarding copyright ownership and licensing. * * BEAST is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as * published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * BEAST is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with BEAST; if not, write to the * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, * Boston, MA 02110-1301 USA */ package dr.evomodel.tree; import dr.evolution.tree.NodeRef; import dr.evolution.tree.Tree; import dr.inference.model.Statistic; /** * A statistic that reports the total length of all the branches in the tree * * @author Alexei Drummond * @version $Id: RateStatistic.java,v 1.9 2005/07/11 14:06:25 rambaut Exp $ */ public class TreeLengthStatistic extends Statistic.Abstract implements TreeStatistic { public TreeLengthStatistic(String name, Tree tree) { super(name); this.tree = tree; } public void setTree(Tree tree) { this.tree = tree; } public Tree getTree() { return tree; } public int getDimension() { return 1; } /** * @return the total length of all the branches in the tree */ public double getStatisticValue(int dim) { double treeLength = 0.0; for (int i = 0; i < tree.getNodeCount(); i++) { NodeRef node = tree.getNode(i); if (node != tree.getRoot()) { NodeRef parent = tree.getParent(node); treeLength += tree.getNodeHeight(parent) - tree.getNodeHeight(node); } } return treeLength; } private Tree tree = null; }