/*
* ARGReassortmentNodeCountStatistic.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.inference.model.Statistic;
import dr.xml.*;
/**
* @author Marc Suchard
*/
public class ARGReassortmentNodeCountStatistic extends Statistic.Abstract {
public static final String REASSORTMENT_STATISTIC = "argReassortmentNodeCount";
public ARGReassortmentNodeCountStatistic(String name, ARGModel arg) {
super(name);
this.arg = arg;
}
public int getDimension() {
return 1;
}
public double getStatisticValue(int dim) {
return arg.getReassortmentNodeCount();
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return REASSORTMENT_STATISTIC;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
String name = xo.getAttribute(NAME, xo.getId());
ARGModel arg = (ARGModel) xo.getChild(ARGModel.class);
return new ARGReassortmentNodeCountStatistic(name,arg);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "A statistic that returns the number of reassortment nodes in an ARG";
}
public Class getReturnType() {
return Statistic.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new StringAttributeRule(NAME, "A name for this statistic for the purpose of logging", true),
new ElementRule(ARGModel.class),
};
};
private ARGModel arg;
}