/*
* MonophylyStatistic.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.tree;
import dr.evolution.tree.Tree;
import dr.evolution.tree.TreeUtils;
import dr.evolution.util.TaxonList;
import dr.inference.model.BooleanStatistic;
import java.util.Collections;
import java.util.Set;
/**
* Performs monophyly test given a taxonList
*
* @author Roald Forsberg
* @author Alexei Drummond
* @author Andrew Rambaut
* @version $Id: MonophylyStatistic.java,v 1.16 2005/07/11 14:06:25 rambaut Exp $
*/
public class MonophylyStatistic extends BooleanStatistic implements TreeStatistic {
public MonophylyStatistic(String name, Tree tree, TaxonList taxa, TaxonList ignore) throws TreeUtils.MissingTaxonException {
this(name, tree, taxa, ignore, false);
}
public MonophylyStatistic(String name, Tree tree, TaxonList taxa, TaxonList ignore, boolean inverse) throws TreeUtils.MissingTaxonException {
super(name);
this.tree = tree;
this.leafSet = TreeUtils.getLeavesForTaxa(tree, taxa);
if (ignore != null) {
this.ignoreLeafSet = TreeUtils.getLeavesForTaxa(tree, ignore);
} else {
this.ignoreLeafSet = Collections.emptySet();
}
this.inverse = inverse;
}
public void setTree(Tree tree) {
this.tree = tree;
}
public Tree getTree() {
return tree;
}
public int getDimension() {
return 1;
}
/**
* @return boolean result of test.
*/
public boolean getBoolean(int dim) {
boolean monophyletic = TreeUtils.isMonophyletic(this.tree, this.leafSet, this.ignoreLeafSet);
if (inverse){
return !monophyletic;
} else {
return monophyletic;
}
}
private Tree tree = null;
private Set<String> leafSet = null;
private Set<String> ignoreLeafSet = null;
private boolean inverse = false;
}