/*
* SingleTipObservationProcessParser.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.MSSD;
import dr.evolution.alignment.PatternList;
import dr.evolution.util.Taxon;
import dr.oldevomodel.MSSD.SingleTipObservationProcess;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.oldevomodel.sitemodel.SiteModel;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
/**
*
*/
public class SingleTipObservationProcessParser extends AbstractXMLObjectParser {
public final static String MODEL_NAME = "singleTipObservationProcess";
public String getParserName() {
return MODEL_NAME;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Parameter mu = (Parameter) xo.getElementFirstChild(AnyTipObservationProcessParser.DEATH_RATE);
Parameter lam = (Parameter) xo.getElementFirstChild(AnyTipObservationProcessParser.IMMIGRATION_RATE);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
PatternList patterns = (PatternList) xo.getChild(PatternList.class);
Taxon sourceTaxon = (Taxon) xo.getChild(Taxon.class);
SiteModel siteModel = (SiteModel) xo.getChild(SiteModel.class);
BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
Logger.getLogger("dr.evomodel.MSSD").info("Creating SingleTipObservationProcess model. All traits are assumed extant in " + sourceTaxon.getId() + "Initial mu = " + mu.getParameterValue(0) + " initial lam = " + lam.getParameterValue(0));
return new SingleTipObservationProcess(treeModel, patterns, siteModel, branchRateModel, mu, lam, sourceTaxon);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element represents an instance of the SingleTipObservationProcess for ALSTreeLikelihood calculations";
}
public Class getReturnType() {
return SingleTipObservationProcess.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(TreeModel.class),
new ElementRule(PatternList.class),
new ElementRule(Taxon.class),
new ElementRule(SiteModel.class),
new ElementRule(BranchRateModel.class),
new ElementRule(AnyTipObservationProcessParser.DEATH_RATE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
new ElementRule(AnyTipObservationProcessParser.IMMIGRATION_RATE, new XMLSyntaxRule[]{new ElementRule(Parameter.class)})
};
}