/*
* TwoPartsDistributionLikelihoodParser.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.inferencexml.distribution;
import dr.inference.distribution.DistributionLikelihood;
import dr.inference.distribution.TwoPartsDistributionLikelihood;
import dr.inference.model.Parameter;
import dr.xml.*;
import dr.math.distributions.Distribution;
/**
* @author Chieh-Hsi Wu
*
* Parser for TwoPartDistribution likelihood
*/
public class TwoPartsDistributionLikelihoodParser extends AbstractXMLObjectParser{
public static final String TWO_PART_DISTRIBUTION_LIKELIHOOD = "twoPartDistribution";
public static final String PRIOR = "priorLik";
public static final String PSEUDO_PRIOR = "pseudoPriorLik";
public static final String PARAMETER_VECTOR = "parameterVector";
public static final String PARAMETER_INDEX = "paramIndex";
public static final String SELECTED_VARIABLE = "selectedVariable";
public String getParserName() {
return TWO_PART_DISTRIBUTION_LIKELIHOOD;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
DistributionLikelihood priorLikelihood = (DistributionLikelihood)xo.getElementFirstChild(PRIOR);
DistributionLikelihood pseudoPriorLikelihood = (DistributionLikelihood)xo.getElementFirstChild(PSEUDO_PRIOR);
Distribution prior = priorLikelihood.getDistribution();
Distribution pseudoPrior = pseudoPriorLikelihood.getDistribution();
Parameter bitVector = (Parameter)xo.getElementFirstChild(PARAMETER_VECTOR);
int paramIndex = xo.getIntegerAttribute(PARAMETER_INDEX);
Parameter selectedVariable = (Parameter)xo.getElementFirstChild(SELECTED_VARIABLE);
TwoPartsDistributionLikelihood likelihood =
new TwoPartsDistributionLikelihood(
prior,
pseudoPrior,
bitVector,
paramIndex
);
likelihood.addData(selectedVariable);
return likelihood;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
};
public String getParserDescription() {
return "Calculates the likelihood of some data given some parametric or empirical distribution.";
}
public Class getReturnType() {
return TwoPartsDistributionLikelihood.class;
}
}