/*
* GeneralF81ModelParser.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.FrequencyModel;
import dr.oldevomodel.substmodel.GeneralF81Model;
import dr.xml.*;
import java.util.logging.Logger;
/**
* Parses a GeneralF81Model
*/
public class GeneralF81ModelParser extends AbstractXMLObjectParser {
public static final String GENERAL_F81_MODEL = "generalF81Model";
public static final String FREQUENCIES = "frequencies";
public String getParserName() {
return GENERAL_F81_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
FrequencyModel freqModel = null;
if (xo.hasChildNamed(FREQUENCIES)) {
XMLObject cxo = xo.getChild(FREQUENCIES);
freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
}
Logger.getLogger("dr.evomodel").info(" General F81 Model from frequencyModel '"+ freqModel.getId() + "' (stateCount=" + freqModel.getFrequencyCount() + ")");
return new GeneralF81Model(freqModel);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A general F81 model for an arbitrary number of states.";
}
public Class getReturnType() {
return GeneralF81ModelParser.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(FREQUENCIES, FrequencyModel.class)
};
}