/*
* MkModelParser.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.DataType;
import dr.oldevomodel.substmodel.FrequencyModel;
import dr.oldevomodel.substmodel.GeneralSubstitutionModel;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Alexander V Alekseyenko (alexander.alekseyenko@gmail.com)
* <p/>
* MkModelParser implements Lewis's Mk Model Syst. Biol. 50(6):913-925, 2001
*/
public class MkModelParser extends AbstractXMLObjectParser {
public static final String MK_SUBSTITUTION_MODEL = "mkSubstitutionModel";
public String getParserName() {
return MK_SUBSTITUTION_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
XMLObject cxo = xo.getChild(GeneralSubstitutionModelParser.FREQUENCIES);
FrequencyModel freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
DataType dataType = freqModel.getDataType();
int rateCount = ((dataType.getStateCount() - 1) * dataType.getStateCount()) / 2 - 1;
Parameter ratesParameter = new Parameter.Default(rateCount, 1.0);
Logger.getLogger("dr.evolution").info("Creating an Mk substitution model with data type: " + dataType.getType() + "on " + dataType.getStateCount() + " states.");
int relativeTo = 1;
return new GeneralSubstitutionModel(dataType, freqModel, ratesParameter, relativeTo);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "An Mk model of substitution. This model can also accomodate arbitrary orderings of changes.";
}
public Class getReturnType() {
return GeneralSubstitutionModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(GeneralSubstitutionModelParser.FREQUENCIES, FrequencyModel.class),
};
}