ContinuousLikelihood.java

/*
 * ContinuousLikelihood.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.continuous;

import dr.evolution.continuous.ContinuousTraitLikelihood;
import dr.evolution.continuous.Contrastable;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Likelihood;
import dr.xml.*;

import java.util.ArrayList;


/**
 * Calculates the likelihood of a set of continuous attributes on a tree.
 *
 * @version $Id: ContinuousLikelihood.java,v 1.6 2006/06/18 16:20:58 alexei Exp $
 *
 * @author Alexei Drummond
 */
public class ContinuousLikelihood extends Likelihood.Abstract {
		
	public static final String CONTINUOUS_LIKELIHOOD = "continuousLikelihood";	
	public static final String TRAIT = "trait";	
	public static final String NAME = "name";	
		
	public ContinuousLikelihood(TreeModel treeModel, String[] traitNames) {
		super(treeModel);
		this.treeModel = treeModel;
		this.traitNames = traitNames;
	    mles = new Contrastable[traitNames.length];
	}
	
	/**
	 * Get the log likelihood.
	 * @return the log likelihood.
	 */
	public double calculateLogLikelihood() {
		
		return contTraitLikelihood.calculateLikelihood(treeModel, traitNames, mles, 1.0);
	}
	
	public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
		
		public String getParserName() { return CONTINUOUS_LIKELIHOOD; }
		
		public Object parseXMLObject(XMLObject xo) throws XMLParseException {
			
			TreeModel treeModel = (TreeModel)xo.getChild(TreeModel.class);
			ArrayList<String> traits = new ArrayList<String>();
			
			for (int i = 0; i < xo.getChildCount(); i++) {
			
				Object child = xo.getChild(i);
				if  (child instanceof XMLObject) {
			
					XMLObject cxo = (XMLObject)child;
					
					if (cxo.getName().equals(TRAIT)) {
						traits.add(cxo.getStringAttribute(NAME));
					}
						
				} else {
					 throw new XMLParseException("unknown child element found in continuousLikelihood");
				}
			}
			
			if (treeModel == null)
				throw new XMLParseException("tree model element missing from continuousLikelihood element");
			
			String[] traitNames = new String[traits.size()];
			for (int i =0; i < traitNames.length; i++) { traitNames[i] = traits.get(i); }
				
			ContinuousLikelihood cl = new ContinuousLikelihood(treeModel, traitNames);
	
			return cl;
		}
		
		//************************************************************************
		// AbstractXMLObjectParser implementation
		//************************************************************************
		
		public String getParserDescription() {
			return "A likelihood for continuous traits.";
		}
		
		public Class getReturnType() { return ContinuousLikelihood.class; }
					
		public XMLSyntaxRule[] getSyntaxRules() { return rules; }
			
		private XMLSyntaxRule[] rules = new XMLSyntaxRule[] {
			new ElementRule(TreeModel.class )
		};
	};
	
	private String[] traitNames = null;
	private Contrastable[] mles = null;
	private TreeModel treeModel = null;
	private ContinuousTraitLikelihood contTraitLikelihood = new ContinuousTraitLikelihood();
}