/*
* LinkedGroup.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.evolution;
import dr.evolution.util.TaxonList;
import dr.util.Identifiable;
/**
* @author Aaron Darling (koadman)
*/
public class LinkedGroup implements Identifiable {
protected String id = null;
TaxonList taxa;
double probability; // probability that reads in this group are linked to each other
public LinkedGroup(TaxonList taxa, double probability){
this.taxa = taxa;
this.probability = probability;
}
public LinkedGroup(TaxonList taxa){
// default constructor assumes probability of linkage is 1
this(taxa, 1.0);
}
public double getLinkageProbability(){
return probability;
}
public TaxonList getLinkedReads(){
return taxa;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
}