/*
* MutationDeathModelParser.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.substmodel;
import dr.evolution.datatype.MutationDeathType;
import dr.oldevomodel.substmodel.AbstractSubstitutionModel;
import dr.oldevomodel.substmodel.FrequencyModel;
import dr.oldevomodel.substmodel.MutationDeathModel;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
/**
*
*/
public class MutationDeathModelParser extends AbstractXMLObjectParser {
public static final String MD_MODEL = "mutationDeathModel";
public static final String MUTATION_RATE = "mutationRate";
public String getParserName() {
return MD_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Parameter dummyFreqParameter;
Parameter delParam = (Parameter) xo.getChild(Parameter.class);
Logger.getLogger("dr.evomodel").info("Creating MutationDeath substitution model.\n\tInitial death rate is "
+ delParam.getParameterValue(0));
MutationDeathType dT = (MutationDeathType) xo.getChild(MutationDeathType.class);
AbstractSubstitutionModel evoModel = (AbstractSubstitutionModel) xo.getChild(AbstractSubstitutionModel.class);
if (evoModel == null) { // Assuming pure survival model
Logger.getLogger("dr.evomodel").info("\tSubstitutionModel not provided assuming pure death/survival model.");
dummyFreqParameter = new Parameter.Default(new double[]{1.0, 0.0});
} else {
dummyFreqParameter = new Parameter.Default(dT.getStateCount());
double freqs[] = evoModel.getFrequencyModel().getFrequencies();
for (int i = 0; i < freqs.length; ++i) {
dummyFreqParameter.setParameterValueQuietly(i, freqs[i]);
}
dummyFreqParameter.setParameterValueQuietly(dT.getStateCount() - 1, 0.0);
}
FrequencyModel dummyFrequencies = new FrequencyModel(dT, dummyFreqParameter);
Parameter mutationRate;
if (xo.hasChildNamed(MUTATION_RATE)) {
mutationRate = (Parameter) xo.getElementFirstChild(MUTATION_RATE);
} else {
mutationRate = new Parameter.Default(new double[]{1.0});
}
Logger.getLogger("dr.evomodel").info("\tInitial mutation rate is " + mutationRate.getParameterValue(0));
return new MutationDeathModel(delParam, dT, evoModel, dummyFrequencies, mutationRate);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element represents an instance of the MutationDeath model of CTMC evolution with deletions.";
}
public Class getReturnType() {
return MutationDeathModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(AbstractSubstitutionModel.class, true),
new ElementRule(Parameter.class),
new ElementRule(MutationDeathType.class),
new ElementRule(MUTATION_RATE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}, true)
};
}