/*
* ScaledTreeLengthRateModelParser.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.evomodelxml.branchratemodel;
import dr.evomodel.branchratemodel.ScaledTreeLengthRateModel;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
/**
*/
public class ScaledTreeLengthRateModelParser extends AbstractXMLObjectParser {
public static final String MODEL_NAME = "scaledTreeLengthModel";
public static final String SCALING_FACTOR = "scalingFactor";
public String getParserName() {
return MODEL_NAME;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
Parameter totalLength = (Parameter) xo.getElementFirstChild(SCALING_FACTOR);
if (totalLength == null) {
totalLength = new Parameter.Default(1, 1.0);
}
Logger.getLogger("dr.evomodel.branchratemodel").info("\n ---------------------------------\nCreating ScaledTreeLengthRateModel model.");
Logger.getLogger("dr.evomodel.branchratemodel").info("\tTotal tree length will be scaled to " + totalLength.getParameterValue(0) + ".");
Logger.getLogger("dr.evomodel.branchratemodel").info("\tIf you publish results using this rate model, please cite Alekseyenko, Lee and Suchard (2008) Syst. Biol 57: 772-784." +
"\n---------------------------------\n");
return new ScaledTreeLengthRateModel(tree, totalLength);
}
public String getParserDescription() {
return "This element returns a branch rate model that scales the total length " +
"of the tree to specified valued (default=1.0).";
}
public Class getReturnType() {
return ScaledTreeLengthRateModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(SCALING_FACTOR,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}, true),
new ElementRule(TreeModel.class)
};
}