/* * 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; } }