/*
* PositiveDefiniteSubstitutionModelParser.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.oldevomodel.substmodel.PositiveDefiniteSubstitutionModel;
import dr.inference.model.MatrixParameter;
import dr.xml.*;
/**
*
*/
public class PositiveDefiniteSubstitutionModelParser extends AbstractXMLObjectParser {
public static final String SVS_GENERAL_SUBSTITUTION_MODEL = "positiveDefiniteSubstitutionModel";
public String getParserName() {
return SVS_GENERAL_SUBSTITUTION_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
MatrixParameter ratesParameter = (MatrixParameter) xo.getChild(MatrixParameter.class);
return new PositiveDefiniteSubstitutionModel(ratesParameter);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A general reversible model of sequence substitution for any data type with stochastic variable selection.";
}
public Class getReturnType() {
return PositiveDefiniteSubstitutionModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(MatrixParameter.class)
};
}