/*
* ManyUniformGeoDistributionModelParser.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.geo;
import dr.geo.operators.UniformGeoSpatialOperator;
import dr.inference.distribution.AbstractDistributionLikelihood;
import dr.inference.distribution.CachedDistributionLikelihood;
import dr.inference.distribution.MultivariateDistributionLikelihood;
import dr.inference.model.Likelihood;
import dr.inference.model.Parameter;
import dr.inference.operators.MCMCOperator;
import dr.inference.operators.UniformOperator;
import dr.math.distributions.MultivariateDistribution;
import dr.xml.*;
import java.util.ArrayList;
import java.util.List;
/**
*/
public class ManyUniformGeoDistributionModelParser extends AbstractXMLObjectParser {
public final static String MANY_PARSER = "geoDistributionCollection";
public String getParserName() {
return MANY_PARSER;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
List<GeoSpatialDistribution> distributions = new ArrayList<GeoSpatialDistribution>();
List<Parameter> parameters = new ArrayList<Parameter>();
List<Likelihood> oldLikelihood = new ArrayList<Likelihood>();
for (int i = 0; i < xo.getChildCount(); ++i) {
Object cxo = xo.getChild(i);
MultivariateDistributionLikelihood ab = null;
if (cxo instanceof MultivariateDistributionLikelihood) {
ab = (MultivariateDistributionLikelihood) cxo;
} else if (cxo instanceof CachedDistributionLikelihood) {
ab = (MultivariateDistributionLikelihood)
((CachedDistributionLikelihood) cxo).getDistributionLikelihood();
}
if (ab != null) {
parameters.add(ab.getDataParameter());
MultivariateDistribution md = ab.getDistribution();
oldLikelihood.add((Likelihood)cxo);
if (md instanceof GeoSpatialDistribution) {
distributions.add((GeoSpatialDistribution)md);
} else {
throw new XMLParseException("Unhandled distribution type in '" + xo.getId() + "'");
}
}
}
return new ManyUniformGeoDistributionModel(xo.getId(), parameters, distributions, oldLikelihood);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "An operator that picks new parameter values uniformly at random.";
}
public Class getReturnType() {
return UniformOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(MultivariateDistributionLikelihood.class, 0, Integer.MAX_VALUE),
new ElementRule(CachedDistributionLikelihood.class, 0, Integer.MAX_VALUE),
};
}