/* * ImportanceSubtreeSwapParser.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.ImportanceSubtreeSwap; import dr.evomodel.tree.TreeModel; import dr.inference.operators.MCMCOperator; import dr.xml.*; /** */ public class ImportanceSubtreeSwapParser extends AbstractXMLObjectParser { public static final String IMPORTANCE_SUBTREE_SWAP = "ImportanceSubtreeSwap"; public String getParserName() { return IMPORTANCE_SUBTREE_SWAP; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { final TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class); final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); final int samples = xo.getIntegerAttribute("samples"); return new ImportanceSubtreeSwap(treeModel, weight, samples); } // ************************************************************************ // AbstractXMLObjectParser implementation // ************************************************************************ public String getParserDescription() { return "This element represents a importance guided subtree swap operator. " + "This operator swaps a random subtree with a second subtree guided by an importance distribution."; } public Class getReturnType() { return ImportanceSubtreeSwap.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private final XMLSyntaxRule[] rules;{ rules = new XMLSyntaxRule[]{ AttributeRule.newDoubleRule(MCMCOperator.WEIGHT), AttributeRule.newIntegerRule("samples"), new ElementRule(TreeModel.class) }; } }