Simulator.java

/*
 * Simulator.java
 *
 * Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
 *
 * 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.simulator;

import dr.evolution.tree.Tree;
import dr.evolution.util.TaxonList;
import dr.evomodel.coalescent.CoalescentSimulator;
import dr.evomodel.coalescent.DemographicModel;
import dr.evomodel.tree.TreeStatistic;
import dr.inference.loggers.Logger;
import dr.xml.*;

import java.util.ArrayList;


/**
 * Runs a coalescent simulator multiple times, logging statistics.
 *
 * @version $Id: Simulator.java,v 1.5 2004/10/01 22:40:04 alexei Exp $
 *
 * @author Andrew Rambaut
 * @author Alexei Drummond
 */
public class Simulator implements Runnable {

	public static final String SIMULATOR = "simulator";
	public static final String REPEATS = "repeats";
	
	/** the coalescent simulator */
	private final DemographicModel demographicModel;
	private final TaxonList taxa;
	private final int simulationCount;
	private final TreeStatistic[] statistics;
	private final Logger[] loggers;
		
	/**
	 *
	 */
	public Simulator(
		int simulationCount,
		DemographicModel demographicModel,
		TaxonList taxa,
		TreeStatistic[] statistics,
		Logger[] loggers) {
	
		this.simulationCount = simulationCount;
		this.demographicModel = demographicModel;
		this.taxa = taxa;
		this.loggers = loggers;
		this.statistics = statistics;
	}

	public void run() {
		simulate();
	}
	
	/**
	 * This method actually intiates the MCMC analysis.
	 * @return a sample of the posterior distribution. Note that
	 * the site patterns have been dropped from the site model
	 * to reduce the footprint of the sample.
	 */
	public void simulate() {
		
		if (loggers != null) {
            for(Logger logger : loggers) {
                logger.startLogging();
            }
		}
		
		CoalescentSimulator coalSim = new CoalescentSimulator();
		
		timer.start();
			
		for (int i = 0; i < simulationCount; i++) {
		
			Tree tree = coalSim.simulateTree(taxa, demographicModel);

			if (loggers != null) {
                for(TreeStatistic statistic : statistics) {
                    statistic.setTree(tree);
                }

                for(Logger logger : loggers) {
                    logger.log(i);
                }
			}
		
		}
		
		if (loggers != null) {
            for(Logger logger : loggers) {
                logger.stopLogging();
            }
		}
				
		timer.stop();
	}	

	/** @return the timer. */
	public dr.util.Timer getTimer() { return timer; }
	
	/** @return the length of this analysis.*/
	public final int getSimulationCount() { return simulationCount; }
	
	/** 
	 * @return a tree object based on the XML element it was passed.
	 */
	public static XMLObjectParser getXMLObjectParser() {
	
		return new AbstractXMLObjectParser() {
		
			public String getParserName() { return SIMULATOR; }
		
			public Object parseXMLObject(XMLObject xo) throws XMLParseException {
		
				DemographicModel demoModel = (DemographicModel)xo.getChild(DemographicModel.class);
				TaxonList taxa = (TaxonList)xo.getChild(TaxonList.class);
				ArrayList<TreeStatistic> statistics = new ArrayList<TreeStatistic>();
				ArrayList<Logger> loggers = new ArrayList<Logger>();
	
				int repeats = xo.getIntegerAttribute(REPEATS);
				
				for (int i = 0; i < xo.getChildCount(); i++) {	
					final Object child = xo.getChild(i);
					if (child instanceof TreeStatistic) {
						statistics.add((TreeStatistic) child);
					} else if (child instanceof Logger) {
						loggers.add((Logger) child);
					}
				}
				
				TreeStatistic[] statArray = new TreeStatistic[statistics.size()];
				statistics.toArray(statArray);
				
				Logger[] logArray = new Logger[loggers.size()];
				loggers.toArray(logArray);

				Simulator simulator = new Simulator(repeats, demoModel, taxa, statArray, logArray);
			
				return simulator;
			}
			
			//************************************************************************
			// AbstractXMLObjectParser implementation
			//************************************************************************
			
			public String getParserDescription() {
				return "A simulator.";
			}

			public Class getReturnType() { return Simulator.class; }

			public XMLSyntaxRule[] getSyntaxRules() { return rules; }
		
			private final XMLSyntaxRule[] rules = {
				AttributeRule.newIntegerRule(REPEATS),
				new ElementRule(DemographicModel.class),
				new ElementRule(TaxonList.class),
				new ElementRule(TreeStatistic.class, 1, Integer.MAX_VALUE),
				new ElementRule(Logger.class, 1, Integer.MAX_VALUE)
			};
		};
	}

	// PRIVATE TRANSIENTS 
	private final dr.util.Timer timer = new dr.util.Timer();
	
}