/*
* 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;
}
};
}