/*
* GammaParameterPrior.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.prior;
//
//import dr.inference.model.Parameter;
//import dr.math.distributions.GammaDistribution;
//import org.w3c.dom.Document;
//import org.w3c.dom.Element;
/**
* This prior provides a gamma distributed expectation on a single parameter
*
* @author Alexei Drummond
* @version $Id: GammaParameterPrior.java,v 1.4 2005/05/24 20:26:00 rambaut Exp $
*/
//public class GammaParameterPrior extends AbstractParameterPrior {
//
// /**
// * the gamma distribution
// */
// GammaDistribution gammaDistribution;
//
// public GammaParameterPrior(Parameter parameter, double gammaMean, double gammaShape) {
// this(parameter, -1, gammaMean, gammaShape);
// }
//
// public GammaParameterPrior(Parameter parameter, int dimension, double gammaMean, double gammaShape) {
// gammaDistribution = new GammaDistribution(gammaShape, gammaMean / gammaShape);
// setParameter(parameter);
// setDimension(dimension);
// }
//
// public double getLogPriorComponent(double value) {
// return gammaDistribution.logPdf(value);
// // return Math.log(gammaDistribution.pdf(value));
// }
//
// public Element createElement(Document d) {
// Element e = d.createElement("gammaPrior");
// e.setAttribute("mean", gammaDistribution.mean() + "");
// e.setAttribute("shape", gammaDistribution.getShape() + "");
// return e;
// }
//
// public final double getMean() {
// return gammaDistribution.mean();
// }
//
// public final double getShape() {
// return gammaDistribution.getShape();
// }
//
//
// public String toString() {
// return "Gamma(" + formatter.format(getMean()).trim() + ", " + formatter.format(getShape()).trim() + ")";
// }
//
// public String toHTML() {
// return "<font color=\"#FF00FF\">" + toString() + "</font>";
// }
//}