/*
* BifractionalDiffusionModelParser.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.evoxml;
import dr.xml.*;
import dr.inference.model.Parameter;
import dr.evomodel.continuous.MultivariateDiffusionModel;
import dr.evomodel.continuous.BifractionalDiffusionModel;
/**
* @author Marc Suchard
*/
public class BifractionalDiffusionModelParser extends AbstractXMLObjectParser {
public static final String BIFRACTIONAL_DIFFUSION_PROCESS = "bifractionalDiffusionModel";
public static final String ALPHA_PARAMETER = "alpha";
public static final String BETA_PARAMETER = "beta";
public String getParserName() {
return BIFRACTIONAL_DIFFUSION_PROCESS;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
XMLObject cxo = xo.getChild(ALPHA_PARAMETER);
Parameter alpha = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(BETA_PARAMETER);
Parameter beta = (Parameter) cxo.getChild(Parameter.class);
return new BifractionalDiffusionModel(alpha, beta);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "Describes a bivariate diffusion process using a bifractional random walk";
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(ALPHA_PARAMETER,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(BETA_PARAMETER,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
};
public Class getReturnType() {
return MultivariateDiffusionModel.class;
}
}