CherryStatistic.java

/*
 * CherryStatistic.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.app.treestat.statistics;

import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;

/**
 *
 * @version $Id: CherryStatistic.java,v 1.2 2005/09/28 13:50:56 rambaut Exp $
 *
 * @author Alexei Drummond
 */
public class CherryStatistic extends AbstractTreeSummaryStatistic {

	private CherryStatistic() { }

	public double[] getSummaryStatistic(Tree tree) {

		int cherryCount = 0;

		int internalNodeCount = tree.getInternalNodeCount();
		for (int i = 0; i < internalNodeCount; i++) {
			NodeRef node = tree.getInternalNode(i);
			boolean allChildrenExternal = true;
			for (int j = 0; j < tree.getChildCount(node); j++) {
				if (!tree.isExternal(tree.getChild(node, j))) {
					allChildrenExternal = false;
				}
			}
			if (allChildrenExternal) cherryCount += 1;
		}
		return new double[] { (double)cherryCount };
	}

	public String getSummaryStatisticName() { return FACTORY.getSummaryStatisticName(); }
	public String getSummaryStatisticDescription() { return FACTORY.getSummaryStatisticDescription(); }
	public String getSummaryStatisticReference() { return FACTORY.getSummaryStatisticReference(); }
	public boolean allowsPolytomies() { return FACTORY.allowsPolytomies(); }
	public boolean allowsNonultrametricTrees() { return FACTORY.allowsNonultrametricTrees(); }
	public boolean allowsUnrootedTrees() { return FACTORY.allowsUnrootedTrees(); }
	public SummaryStatisticDescription.Category getCategory() { return FACTORY.getCategory(); }

	public static final TreeSummaryStatistic.Factory FACTORY = new TreeSummaryStatistic.Factory() {

		public TreeSummaryStatistic createStatistic() {
			return new CherryStatistic();
		}

		public String getSummaryStatisticName() {
			return "Cherry count";
		}

		public String getSummaryStatisticDescription() {

			return "The number of internal nodes that have only tips as children.";
		}

		public String getSummaryStatisticReference() {
			return "Steel and McKenzie (2001)";
		}

		public boolean allowsPolytomies() { return true; }

		public boolean allowsNonultrametricTrees() { return true; }

		public boolean allowsUnrootedTrees() { return false; }

		public SummaryStatisticDescription.Category getCategory() { return SummaryStatisticDescription.Category.TREE_SHAPE; }
	};
}