/*
* UCLikelihoodParser.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.oldevomodelxml.clock;
import dr.oldevomodel.clock.RateEvolutionLikelihood;
import dr.oldevomodel.clock.UCLikelihood;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
*/
public class UCLikelihoodParser extends AbstractXMLObjectParser {
public static final String UC_LIKELIHOOD = "UCLikelihood";
public static final String VARIANCE = "variance";
public String getParserName() {
return UC_LIKELIHOOD;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
Parameter ratesParameter = (Parameter) xo.getElementFirstChild(RateEvolutionLikelihood.RATES);
Parameter rootRate = (Parameter) xo.getElementFirstChild(RateEvolutionLikelihood.ROOTRATE);
Parameter variance = (Parameter) xo.getElementFirstChild(VARIANCE);
boolean isLogSpace = xo.getAttribute(RateEvolutionLikelihood.LOGSPACE, false);
return new UCLikelihood(tree, ratesParameter, variance, rootRate, isLogSpace);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return
"This element returns an object that can calculate the likelihood " +
"of rates in a tree under the assumption of " +
"(log)normally distributed rates. ";
}
public Class getReturnType() {
return UCLikelihood.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(TreeModel.class),
new ElementRule(RateEvolutionLikelihood.RATES, Parameter.class, "The branch rates parameter", false),
AttributeRule.newBooleanRule(RateEvolutionLikelihood.LOGSPACE, true, "true if model considers the log of the rates."),
new ElementRule(RateEvolutionLikelihood.ROOTRATE, Parameter.class, "The root rate parameter"),
new ElementRule(VARIANCE, Parameter.class, "The standard deviation of the (log)normal distribution"),
};
}