/*
* TKF91LikelihoodParser.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.indel;
import dr.evolution.alignment.Alignment;
import dr.oldevomodel.indel.TKF91Likelihood;
import dr.oldevomodel.indel.TKF91Model;
import dr.oldevomodel.sitemodel.GammaSiteModel;
import dr.evomodel.tree.TreeModel;
import dr.xml.*;
/**
*
*/
public class TKF91LikelihoodParser extends AbstractXMLObjectParser {
public static final String TKF91_LIKELIHOOD = "tkf91Likelihood";
public static final String TKF91_DEATH = "deathRate";
//public static final String MU = "mutationRate";
public String getParserName() {
return TKF91_LIKELIHOOD;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
Alignment alignment = (Alignment) xo.getChild(Alignment.class);
GammaSiteModel siteModel = (GammaSiteModel) xo.getChild(GammaSiteModel.class);
TKF91Model tkfModel = (TKF91Model) xo.getChild(TKF91Model.class);
return new TKF91Likelihood(tree, alignment, siteModel, tkfModel);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "Returns the total likelihood of a single alignment under the TKF91 model, for a given tree. " +
"In particular all possible ancestral histories of insertions and deletions leading to the " +
"alignment of sequences at the tips are taken into account.";
}
public Class getReturnType() {
return TKF91Likelihood.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(TreeModel.class),
new ElementRule(Alignment.class),
new ElementRule(GammaSiteModel.class),
new ElementRule(TKF91Model.class)
};
}