/*
* NegativeBinomialDistributionModelParser.java
*
* Copyright (c) 2002-2016 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.NegativeBinomialDistributionModel;
import dr.inference.distribution.PoissonDistributionModel;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* Reads a Poisson distribution model from a DOM Document element.
*/
public class NegativeBinomialDistributionModelParser extends AbstractXMLObjectParser {
public static final String NEGATIVE_BINOMIAL_DISTRIBUTION_MODEL = "negativeBinomialDistributionModel";
public static final String MEAN = "mean";
public static final String ALPHA = "alpha";
public String getParserName() {
return NEGATIVE_BINOMIAL_DISTRIBUTION_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Parameter meanParam, alphaParameter;
XMLObject cxo = xo.getChild(MEAN);
if (cxo.getChild(0) instanceof Parameter) {
meanParam = (Parameter) cxo.getChild(Parameter.class);
} else {
meanParam = new Parameter.Default(cxo.getDoubleChild(0));
}
cxo = xo.getChild(ALPHA);
if (cxo.getChild(0) instanceof Parameter) {
alphaParameter = (Parameter) cxo.getChild(Parameter.class);
} else {
alphaParameter = new Parameter.Default(cxo.getDoubleChild(0));
}
return new NegativeBinomialDistributionModel(meanParam, alphaParameter);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(MEAN,
new XMLSyntaxRule[]{
new XORRule(
new ElementRule(Parameter.class),
new ElementRule(Double.class)
)}
),
new ElementRule(ALPHA,
new XMLSyntaxRule[]{
new XORRule(
new ElementRule(Parameter.class),
new ElementRule(Double.class)
)}
)
};
public String getParserDescription() {
return "Describes a Negative Binomial distribution with a given mean and scale " +
"that can be used in a distributionLikelihood element";
}
public Class getReturnType() {
return NegativeBinomialDistributionModel.class;
}
}