/* * RateCovarianceStatisticParser.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.tree; import dr.evolution.tree.Tree; import dr.evomodel.branchratemodel.BranchRateModel; import dr.evomodel.tree.RateCovarianceStatistic; import dr.evomodel.tree.TreeModel; import dr.inference.model.Statistic; import dr.xml.*; /** */ public class RateCovarianceStatisticParser extends AbstractXMLObjectParser { public static final String RATE_COVARIANCE_STATISTIC = "rateCovarianceStatistic"; public String getParserName() { return RATE_COVARIANCE_STATISTIC; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { String name = xo.getAttribute(Statistic.NAME, xo.getId()); Tree tree = (Tree) xo.getChild(Tree.class); BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class); return new RateCovarianceStatistic(name, tree, branchRateModel); } //************************************************************************ // AbstractXMLObjectParser implementation //************************************************************************ public String getParserDescription() { return "A statistic that has as its value the covariance of parent and child branch rates"; } public Class getReturnType() { return RateCovarianceStatistic.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private final XMLSyntaxRule[] rules = { new ElementRule(TreeModel.class), new ElementRule(BranchRateModel.class), new StringAttributeRule("name", "A name for this statistic primarily for the purposes of logging", true), }; }