NeighborJoiningTree.java

/*
 * NeighborJoiningTree.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.evolution.tree;

import dr.evolution.distance.DistanceMatrix;

/**
 * constructs a neighbor-joining tree from pairwise distances
 * 
 * @version $Id: NeighborJoiningTree.java,v 1.15 2005/05/24 20:25:56 rambaut Exp $
 *
 * @author Andrew Rambaut
 * @author Alexei Drummond
 */
public class NeighborJoiningTree extends ClusteringTree {

	/**
	 * construct NJ tree
	 *
	 * @param distanceMatrix distance matrix
	 */
	public NeighborJoiningTree(DistanceMatrix distanceMatrix) {
	
		super(distanceMatrix, 3);
	}


	//
	// Private stuff
	//
	
	private double[] r;
	private double scale, maxHeight;

	protected void init(DistanceMatrix distanceMatrix) {
	
		super.init(distanceMatrix);

		r = new double[numClusters];
		maxHeight = 0.0;
	}

	protected void findNextPair() {
	
		for (int i = 0; i < numClusters; i++) {
			r[i] = 0;
			for (int j = 0; j < numClusters; j++) {
				r[i] += getDist(i,j);
			}
		}

		besti = 0;
		bestj = 1;
		double smax = -1.0;
		scale = 1.0/(numClusters-2);
		for (int i = 0; i < numClusters-1; i++) {
			for (int j = i+1; j < numClusters; j++) {
				double sij = (r[i] + r[j] ) * scale - getDist(i, j);
			
				if (sij > smax) {
					smax = sij;
					besti = i;
					bestj = j;
				}
			}
		}
		abi = alias[besti];
		abj = alias[bestj];
	}

	protected void finish() {
		
		// Connect up the final two clusters
		abi = alias[0];
		abj = alias[1];
	
		newCluster = new SimpleNode();
		
		double dij = getDist(0, 1);
		double l = dij * 0.5;
		if (l < 0.0)
			l = 0.0;
		appendHeight(clusters[abi], l);
		appendHeight(clusters[abj], l);

		newCluster.setHeight(0.0);
		
		newCluster.addChild(clusters[abi]);
		newCluster.addChild(clusters[abj]);
				
		reverseHeights(newCluster, maxHeight);
		
		super.finish();
	}

	private void reverseHeights(SimpleNode node, double totalHeight) {
	
		double height = totalHeight - node.getHeight();
		node.setHeight(height);
		
		if (!node.isExternal()) {
			int i, n = node.getChildCount();
			for (i = 0; i < n; i++) {
				reverseHeights(node.getChild(i), totalHeight);
			}
		}
	}

	protected double newNodeHeight() {
	
		double dij = getDist(besti, bestj);
		double li = (dij + (r[besti] - r[bestj]) * scale) * 0.5;
		double lj = dij - li; // = (dij + (r[bestj]-r[besti])*scale)*0.5

		if (li < 0.0)
			li = 0.0;
			
		if (lj < 0.0)
			lj = 0.0;
		
		appendHeight(clusters[abi], li);
		appendHeight(clusters[abj], lj);
		
		return 0.0;
	}

	private void appendHeight(SimpleNode node, double delta) {
	
		double height = node.getHeight() + delta;
		node.setHeight(height);
		
		if (!node.isExternal()) {
			int i, n = node.getChildCount();
			for (i = 0; i < n; i++) {
				appendHeight(node.getChild(i), delta);
			}
		} else {	
			if (height > maxHeight)
				maxHeight = height;
		}
	}

	/**
	 * compute updated distance between the new cluster (i,j)
	 * to any other cluster k
	 */
	protected double updatedDistance(int i, int j, int k) {
	
		return (getDist(k, i) + getDist(k, j) - getDist(i, j)) * 0.5;
	}
}