/*
* MarkovJumpsLikelihoodLoggerParser.java
*
* Copyright (c) 2002-2016 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.evomodelxml.treelikelihood;
import dr.evomodel.treelikelihood.MarkovJumpsTraitProvider;
import dr.inference.loggers.LogColumn;
import dr.inference.loggers.Loggable;
import dr.inference.loggers.NumberColumn;
import dr.xml.*;
/**
* @author Marc A. Suchard
*/
public class MarkovJumpsLikelihoodLoggerParser extends AbstractXMLObjectParser {
public static final String PARSER_NAME = "dataLikelihood";
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final MarkovJumpsTraitProvider dataLikelihood =
(MarkovJumpsTraitProvider) xo.getChild(MarkovJumpsTraitProvider.class);
return new Loggable() {
public LogColumn[] getColumns() {
return new LogColumn[]{
new LikelihoodColumn(dataLikelihood, "dataLike")
};
}
};
}
protected class LikelihoodColumn extends NumberColumn {
final private MarkovJumpsTraitProvider tree;
public LikelihoodColumn(MarkovJumpsTraitProvider tree, String label) {
super(label);
this.tree = tree;
}
public double getDoubleValue() {
return tree.getLogLikelihood();
}
}
@Override
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private static XMLSyntaxRule[] rules = {
new ElementRule(MarkovJumpsTraitProvider.class),
};
@Override
public String getParserDescription() {
return null;
}
@Override
public Class getReturnType() {
return Loggable.class;
}
public String getParserName() {
return PARSER_NAME;
}
}