/*
* terminalBranchStatistic.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 branch lengths of external branches in the tree
*
* @author Luiz Carvalho
*/
public class TerminalBranchStatistic extends Statistic.Abstract implements TreeStatistic {
public TerminalBranchStatistic(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 tree.getExternalNodeCount();
}
/**
* @returns external branch lengths
*/
public double getStatisticValue(int dim) {
final double[] terminalBranches = new double [tree.getExternalNodeCount()] ;
int k = 0;
for (int i = 0; i < tree.getNodeCount(); i++) {
NodeRef node = tree.getNode(i);
if(tree.isExternal(node)){
terminalBranches[k] = tree.getBranchLength(node) ;
k = k + 1 ;
}
}
return terminalBranches[dim];
}
private Tree tree = null;
}