/*
* BetaSplittingModelParser.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.speciation;
import dr.evolution.tree.Tree;
import dr.evomodel.speciation.BetaSplittingModel;
import dr.inference.model.Parameter;
import dr.xml.*;
/**
* Parses an element from an DOM document into a SpeciationModel. Recognises YuleModel.
*/
public class BetaSplittingModelParser extends AbstractXMLObjectParser {
public static final String BETA_SPLITTING_MODEL = "betaSplittingModel";
public static final String PHI = "phi";
public static final String TREE = "branchingTree";
public String getParserName() {
return BETA_SPLITTING_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
XMLObject cxo = xo.getChild(PHI);
Parameter phiParameter = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(TREE);
Tree tree = (Tree) cxo.getChild(Tree.class);
return new BetaSplittingModel(phiParameter, tree);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "The beta-splitting family of tree branching models (Aldous, 1996;2001).";
}
public Class getReturnType() {
return BetaSplittingModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(PHI,
new XMLSyntaxRule[]{new ElementRule(Parameter.class)}, "A parameter that ranges from -infinity (comb-tree) to +infinity (balanced tree)"),
new ElementRule(TREE,
new XMLSyntaxRule[]{new ElementRule(Tree.class)})
};
}