/* * ARGRelaxedClock.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.evomodel.arg; import dr.evolution.tree.NodeRef; import dr.evolution.tree.Tree; import dr.evomodel.arg.ARGModel.Node; import dr.evomodel.branchratemodel.AbstractBranchRateModel; import dr.inference.model.Model; import dr.inference.model.Parameter; import dr.inference.model.Variable; import dr.inference.model.Variable.ChangeType; import dr.xml.*; public class ARGRelaxedClock extends AbstractBranchRateModel { public static final String ARG_LOCAL_CLOCK = "argLocalClock"; public static final String PARTITION = "partition"; private Parameter globalRateParameter; private ARGModel arg; private int partition; public ARGRelaxedClock(String name) { super(name); } public ARGRelaxedClock(String name, ARGModel arg, int partition, Parameter rate) { super(name); this.arg = arg; this.partition = partition; globalRateParameter = rate; addModel(arg); addVariable(rate); } protected void acceptState() { } protected void handleModelChangedEvent(Model model, Object object, int index) { //do nothing } protected void handleVariableChangedEvent(Variable variable, int index, ChangeType type) { //do nothing } protected void restoreState() { } protected void storeState() { } public double getBranchRate(Tree tree, NodeRef nodeRef) { Node treeNode = (Node) nodeRef; Node argNode = (Node) treeNode.mirrorNode; return globalRateParameter.getParameterValue(0) * argNode.getRate(partition); } public static XMLObjectParser PARSER = new AbstractXMLObjectParser() { public String getParserDescription() { return null; } public Class getReturnType() { return ARGRelaxedClock.class; } public XMLSyntaxRule[] getSyntaxRules() { return null; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { ARGModel arg = (ARGModel) xo.getChild(ARGModel.class); int partition = xo.getAttribute(PARTITION, 0); Parameter rate = (Parameter) xo.getChild(Parameter.class); return new ARGRelaxedClock("", arg, partition, rate); } public String getParserName() { return ARG_LOCAL_CLOCK; } }; }