TreeShapeStatistic.java

/*
 * TreeShapeStatistic.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.Tree;
import dr.evolution.tree.TreeShape;
import dr.evolution.tree.TreeUtils;
import dr.inference.model.Statistic;


/**
 * A statistic that returns the values of various tree shape statistics.
 *
 * @author Alexei Drummond
 * @version $Id: TreeShapeStatistic.java,v 1.4 2005/07/11 14:06:25 rambaut Exp $
 */
public class TreeShapeStatistic extends Statistic.Abstract implements TreeStatistic {

    public TreeShapeStatistic(String name, TreeModel target) {
        super(name);
        this.target = target;
        ultrametric = TreeUtils.isUltrametric(target);
    }

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

    public Tree getTree() {
        return target;
    }

    public int getDimension() {
        if (ultrametric) return 5;
        return 4;
    }

    public String getDimensionName(int dim) {
        switch (dim) {
            case 0:
                return "N-bar";
            case 1:
                return "N-bar-var";
            case 2:
                return "C";
            case 3:
                return "B1";
            case 4:
                return "gamma";
        }
        throw new IllegalArgumentException("Dimension doesn't exist!");
    }

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

        switch (dim) {
            case 0:
                return TreeShape.getNBarStatistic(target);
            case 1:
                return TreeShape.getVarNBarStatistic(target);
            case 2:
                return TreeShape.getCStatistic(target);
            case 3:
                return TreeShape.getB1Statistic(target);
            case 4:
                return TreeShape.getGammaStatistic(target);
        }
        throw new IllegalArgumentException("Dimension doesn't exist!");
    }

    private Tree target = null;
    private boolean ultrametric = false;
}