/*
* RateSampleOperatorParser.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.evomodelxml.operators;
import dr.oldevomodel.clock.RateEvolutionLikelihood;
import dr.evomodel.operators.RateSampleOperator;
import dr.evomodel.tree.TreeModel;
import dr.inference.operators.MCMCOperator;
import dr.xml.*;
/**
*/
public class RateSampleOperatorParser extends AbstractXMLObjectParser {
public static final String SAMPLE_OPERATOR = "rateSampleOperator";
public static final String SAMPLE_ALL = "sampleAll";
public String getParserName() {
return SAMPLE_OPERATOR;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
final boolean sampleAll = xo.getBooleanAttribute(SAMPLE_ALL);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
RateEvolutionLikelihood rateEvolution = (RateEvolutionLikelihood) xo.getChild(RateEvolutionLikelihood.class);
RateSampleOperator operator = new RateSampleOperator(treeModel, sampleAll, rateEvolution);
operator.setWeight(weight);
return operator;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element returns a rateSample operator on a given parameter.";
}
public Class getReturnType() {
return RateSampleOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
AttributeRule.newBooleanRule(SAMPLE_ALL, true),
new ElementRule(TreeModel.class),
new ElementRule(RateEvolutionLikelihood.class, true),
};
}