/* * NNIParser.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.operators; import dr.evomodel.operators.NNI; import dr.evomodel.tree.TreeModel; import dr.inference.operators.MCMCOperator; import dr.xml.*; /** */ public class NNIParser extends AbstractXMLObjectParser { public static final String NNI = "NearestNeighborInterchange"; public String getParserName() { return NNI; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class); double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); return new NNI(treeModel, weight); } // ************************************************************************ // AbstractXMLObjectParser // implementation // ************************************************************************ public String getParserDescription() { return "This element represents a NNI operator. " + "This operator swaps a random subtree with its uncle."; } public Class getReturnType() { return NNI.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private final XMLSyntaxRule[] rules = { AttributeRule.newDoubleRule(MCMCOperator.WEIGHT), new ElementRule(TreeModel.class) }; }