/* * 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)}) }; }