/*
* DirichletProcessPriorParser.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.evomodel.branchmodel.lineagespecific;
import dr.inference.distribution.ParametricMultivariateDistributionModel;
import dr.inference.model.CompoundParameter;
import dr.inference.model.Parameter;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
public class DirichletProcessPriorParser extends AbstractXMLObjectParser {
public static final String DIRICHLET_PROCESS_PRIOR = "dirichletProcessPrior";
public static final String BASE_MODEL = "baseModel";
public static final String CONCENTRATION = "concentration";
public static final String CATEGORIES = "categories";
@Override
public String getParserName() {
return DIRICHLET_PROCESS_PRIOR;
}
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Parameter categoriesParameter = (Parameter)xo.getElementFirstChild(CATEGORIES);
CompoundParameter uniquelyRealizedParameters = (CompoundParameter)xo.getChild(CompoundParameter.class);
ParametricMultivariateDistributionModel baseModel = (ParametricMultivariateDistributionModel) xo.getElementFirstChild(BASE_MODEL);
Parameter gamma = (Parameter) xo.getElementFirstChild(CONCENTRATION);
return new DirichletProcessPrior(categoriesParameter, //
uniquelyRealizedParameters, //
baseModel, //
gamma);
}//END: parseXMLObject
@Override
public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[]{
new ElementRule(CATEGORIES,
new XMLSyntaxRule[] { new ElementRule(Parameter.class, false) }), // categories assignments
new ElementRule(CompoundParameter.class, false), // realized parameters
new ElementRule(BASE_MODEL,
new XMLSyntaxRule[] {
new ElementRule(ParametricMultivariateDistributionModel.class, 1, Integer.MAX_VALUE),
}
), // base models
new ElementRule(CONCENTRATION,
new XMLSyntaxRule[] { new ElementRule(Parameter.class, false) }),// gamma
};
}
@Override
public String getParserDescription() {
return DIRICHLET_PROCESS_PRIOR;
}
@Override
public Class getReturnType() {
return DirichletProcessPrior.class;
}
}//END: class