/* * AlloppHybPopSizesScaleParser.java * * Copyright (c) 2002-2017 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.evomodel.alloppnet.parsers; import dr.evomodel.alloppnet.operators.AlloppHybPopSizesScale; import dr.evomodel.alloppnet.speciation.AlloppSpeciesBindings; import dr.evomodel.alloppnet.speciation.AlloppSpeciesNetworkModel; import dr.inference.operators.MCMCOperator; import dr.inferencexml.operators.ScaleOperatorParser; import dr.xml.*; /** * Created with IntelliJ IDEA. * User: Graham * Date: 03/08/12 */ public class AlloppHybPopSizesScaleParser extends AbstractXMLObjectParser { public static final String HYB_POP_SIZES_SCALE = "hybPopSizesScaleOperator"; public String getParserName() { return HYB_POP_SIZES_SCALE; } @Override public Object parseXMLObject(XMLObject xo) throws XMLParseException { AlloppSpeciesBindings apsp = (AlloppSpeciesBindings) xo.getChild(AlloppSpeciesBindings.class); AlloppSpeciesNetworkModel apspnet = (AlloppSpeciesNetworkModel) xo.getChild(AlloppSpeciesNetworkModel.class); final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); final double scalingfactor = xo.getDoubleAttribute(ScaleOperatorParser.SCALE_FACTOR); return new AlloppHybPopSizesScale(apspnet, apsp, scalingfactor, weight); } @Override public XMLSyntaxRule[] getSyntaxRules() { return new XMLSyntaxRule[]{ AttributeRule.newDoubleRule(MCMCOperator.WEIGHT), AttributeRule.newDoubleRule(ScaleOperatorParser.SCALE_FACTOR), new ElementRule(AlloppSpeciesBindings.class), new ElementRule(AlloppSpeciesNetworkModel.class) }; } @Override public String getParserDescription() { return "Operator which scales the population size of a newly formed hybrid."; } @Override public Class getReturnType() { return AlloppHybPopSizesScale.class; } }