/*
 * MCMCCriterion.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.inference.mcmc;

import dr.math.MathUtils;
import dr.inference.markovchain.Acceptor;

/**
 * This class encapsulates the acception criterion for an MCMC proposal.
 *
 * @author Alexei Drummond
 *
 * @version $Id: MCMCCriterion.java,v 1.12 2005/05/24 20:25:59 rambaut Exp $
 */
public class MCMCCriterion implements Acceptor {

	protected double temperature = 1.0;

	public MCMCCriterion() {
		temperature = 1.0;
	}

	public MCMCCriterion(double t) {
		temperature = t;
	}

	public double getAcceptanceValue(double oldScore, double hastingsRatio) {

		double acceptanceValue = (Math.log(MathUtils.nextDouble()) + (oldScore * temperature) - hastingsRatio) / temperature;

		return acceptanceValue;
	}

	public boolean accept(double oldScore, double newScore, double hastingsRatio, double[] logr) {


		logr[0] = (newScore - oldScore) * temperature + hastingsRatio;

		// for coercedAcceptanceProbability
		if (logr[0] > 0) logr[0] = 0.0;

		boolean accept = (Math.log(MathUtils.nextDouble()) < logr[0]);

		return accept;
	}

	public double getTemperature() {
		return temperature;
	}

	public void setTemperature(double temperature) {
		this.temperature = temperature;
	}

}

@@ -1567,35 +1567,31 @@
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 Double()
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 t = 
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 Math
@@ -1946,20 +1946,25 @@
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@@ -1959,17 +1959,16 @@
 Double()
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@@ -1969,17 +1969,16 @@
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use randomLogDouble