TreeMetricStatistic.java

/*
 * TreeMetricStatistic.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.BranchScoreMetric;
import dr.evolution.tree.CladeMetric;
import dr.evolution.tree.Tree;
import dr.evolution.tree.TreeUtils;
import dr.inference.model.Statistic;
import jebl.evolution.treemetrics.BilleraMetric;
import jebl.evolution.treemetrics.CladeHeightMetric;
import jebl.evolution.treemetrics.RobinsonsFouldMetric;
import jebl.evolution.treemetrics.RootedTreeMetric;
import jebl.evolution.trees.SimpleRootedTree;

/**
 * A statistic that returns the distance between two trees.
 * <p/>
 * Currently supports the following metrics,
 * 1. compare - returns a 0 for identity of topology, 1 otherwise.
 * 2. Billera tree distance.
 * 3. ROBINSONS FOULD
 * 4. Clade height
 * 5. Branch Score
 *
 * @author Alexei Drummond
 * @author Andrew Rambaut
 * @author Joseph Heled
 * @author Sebastian Hoehna
 * @version $Id: TreeMetricStatistic.java,v 1.14 2005/07/11 14:06:25 rambaut Exp $
 */
public class TreeMetricStatistic extends Statistic.Abstract implements TreeStatistic {

    public enum Method {
        TOPOLOGY, BILLERA, ROBINSONSFOULD, CLADEHEIGHTM, BRANCHSCORE, CLADEMETRIC
    }

    public TreeMetricStatistic(String name, Tree target, Tree reference, Method method) {
        super(name);

        this.target = target;
        this.method = method;

        switch (method) {
            case TOPOLOGY: {
                this.referenceNewick = TreeUtils.uniqueNewick(reference, reference.getRoot());
                break;
            }
            default: {
                jreference = TreeUtils.asJeblTree(reference);
                break;
            }
        }

        switch (method) {
            case BILLERA:
                metric = new BilleraMetric();
                break;
            case ROBINSONSFOULD:
                metric = new RobinsonsFouldMetric();
                break;
            case CLADEHEIGHTM:
                metric = new CladeHeightMetric();
                break;
            case BRANCHSCORE:
                metric = new BranchScoreMetric();
                break;
            case CLADEMETRIC:
                metric = new CladeMetric();
                break;
        }
    }

    public void setTree(Tree tree) {
        this.target = tree;
    }

    public Tree getTree() {
        return target;
    }

    public int getDimension() {
        return 1;
    }

    /**
     * @return value.
     */
    public double getStatisticValue(int dim) {

        if (method == Method.TOPOLOGY) {
            return compareTreesByTopology();
        }

        return metric.getMetric(jreference, TreeUtils.asJeblTree(target));
    }

    private double compareTreesByTopology() {
        final String tar = TreeUtils.uniqueNewick(target, target.getRoot());
        return tar.equals(referenceNewick) ? 0.0 : 1.0;
    }

    public static String methodNames(String s) {
        String r = "";
        for (Method m : Method.values()) {
            if (r.length() > 0)
                r = r + s;
            r = r + m.name();
        }
        return r;
    }

    private final Method method;

    private Tree target = null;

    private String referenceNewick = null;

    private SimpleRootedTree jreference = null;

    RootedTreeMetric metric = null;
}