/*
* ARGPartitionLikelihood.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.AbstractModelLikelihood;
import dr.inference.model.Model;
public abstract class ARGPartitionLikelihood extends AbstractModelLikelihood {
private final ARGModel arg;
public abstract double[] generatePartition();
public abstract double getLogLikelihood(double[] partition);
public double getLogLikelihood() {
double logPrior = 0;
for(int i = 0, n = getReassortmentNodeCount(); i < n; i++){
logPrior += getLogLikelihood(getPartition(i));
}
return logPrior;
}
public double[] getPartition(int i){
if(arg.getReassortmentNodeCount() == 0){
return null;
}
return arg.getPartitioningParameters().getParameter(i).getParameterValues();
}
public ARGPartitionLikelihood(String id, ARGModel arg){
super(id);
this.arg = arg;
}
public int getNumberOfPartitionsMinusOne(){
return arg.getNumberOfPartitions() - 1;
}
public int getReassortmentNodeCount(){
return arg.getReassortmentNodeCount();
}
public Model getModel() {
return this;
}
public void makeDirty() {
}
}