/* * ARGTotalLengthStatistic.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.evomodel.arg.ARGModel.Node; import dr.inference.model.Statistic; import dr.xml.*; public class ARGTotalLengthStatistic extends Statistic.Abstract{ public static final String ARG_TOTAL_LENGTH = "argTotalLengthStatistic"; private ARGModel arg; public ARGTotalLengthStatistic(String id, ARGModel arg){ super(id); this.arg = arg; } public int getDimension() { return 1; } public double getStatisticValue(int dim) { double length = 0; for(int i = 0; i < arg.getNodeCount(); i++){ Node x = (Node) arg.getNode(i); if(!x.isRoot()){ length += x.getParent(ARGModel.LEFT).getHeight() - x.getHeight(); if(x.isReassortment()){ length += x.getParent(ARGModel.RIGHT).getHeight() - x.getHeight(); } } } return length; } public static XMLObjectParser PARSER = new AbstractXMLObjectParser(){ @Override public String getParserDescription() { // TODO Auto-generated method stub return null; } @Override public Class getReturnType() { return ARGTotalLengthStatistic.class; } @Override public XMLSyntaxRule[] getSyntaxRules() { // TODO Auto-generated method stub return null; } @Override public Object parseXMLObject(XMLObject xo) throws XMLParseException { String id = xo.getId(); ARGModel a = (ARGModel) xo.getChild(ARGModel.class); return new ARGTotalLengthStatistic(id,a); } public String getParserName() { // TODO Auto-generated method stub return ARG_TOTAL_LENGTH; } }; }