GMRFSkyrideFixedEffectsGibbsOperatorParser.java

/*
 * GMRFSkyrideFixedEffectsGibbsOperatorParser.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.evomodelxml.coalescent.operators;

import dr.evomodel.coalescent.GMRFSkyrideLikelihood;
import dr.evomodel.coalescent.operators.GMRFSkyrideFixedEffectsGibbsOperator;
import dr.inference.distribution.MultivariateDistributionLikelihood;
import dr.inference.model.Parameter;
import dr.inference.operators.MCMCOperator;
import dr.math.distributions.MultivariateDistribution;
import dr.math.distributions.MultivariateNormalDistribution;
import dr.xml.*;

/**
 *
 */
public class GMRFSkyrideFixedEffectsGibbsOperatorParser extends AbstractXMLObjectParser {

    public static final String GMRF_GIBBS_OPERATOR = "gmrfFixedEffectsGibbsOperator";

    public String getParserName() {
        return GMRF_GIBBS_OPERATOR;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {


        double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);

        GMRFSkyrideLikelihood gmrfLikelihood = (GMRFSkyrideLikelihood) xo.getChild(GMRFSkyrideLikelihood.class);

        MultivariateDistributionLikelihood likelihood =
                (MultivariateDistributionLikelihood) xo.getChild(MultivariateDistributionLikelihood.class);

        MultivariateDistribution prior = likelihood.getDistribution();

        if (prior.getType().compareTo(MultivariateNormalDistribution.TYPE) != 0)
            throw new XMLParseException("Only a multivariate normal distribution is conjugate for the regression coefficients in a GMRF");

        Parameter param = (Parameter) xo.getChild(Parameter.class);

        return new GMRFSkyrideFixedEffectsGibbsOperator(param,
                gmrfLikelihood, prior, weight);

    }

    //************************************************************************
    // AbstractXMLObjectParser implementation
    //************************************************************************

    public String getParserDescription() {
        return "This element returns a Gibbs operator for regression coefficients in a GMRF.";
    }

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

    public XMLSyntaxRule[] getSyntaxRules() {
        return rules;
//            return null;
    }

    private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
            AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
            new ElementRule(MultivariateDistributionLikelihood.class),
            new ElementRule(Parameter.class),
            new ElementRule(GMRFSkyrideLikelihood.class)
    };
}