/*
* AncestralTrait.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.NodeRef;
import dr.evolution.tree.Tree;
import dr.evolution.tree.TreeTrait;
import dr.evolution.tree.TreeUtils;
import dr.evolution.util.TaxonList;
import dr.inference.loggers.LogColumn;
import dr.inference.loggers.Loggable;
import java.util.Set;
/**
* A statistic that logs the inferred trait at the MRCA of a set of taxa
*
* @author Alexei Drummond
* @author Andrew Rambaut
* @version $Id: TMRCAStatistic.java,v 1.21 2005/07/11 14:06:25 rambaut Exp $
*/
public class AncestralTrait implements Loggable {
public AncestralTrait(String name, TreeTrait ancestralTrait, Tree tree, TaxonList taxa) throws TreeUtils.MissingTaxonException {
this.name = name;
this.tree = tree;
this.ancestralTrait = ancestralTrait;
if (taxa != null) {
this.leafSet = TreeUtils.getLeavesForTaxa(tree, taxa);
}
}
public Tree getTree() {
return tree;
}
/**
* @return the ancestral state of the MRCA node.
*/
public String getAncestralState() {
NodeRef node;
if (leafSet != null) {
node = TreeUtils.getCommonAncestorNode(tree, leafSet);
if (node == null) throw new RuntimeException("No node found that is MRCA of " + leafSet);
} else {
node = tree.getRoot();
}
return ancestralTrait.getTraitString(tree, node);
}
// **************************************************************
// Loggable IMPLEMENTATION
// **************************************************************
/**
* @return the log columns.
*/
public LogColumn[] getColumns() {
LogColumn[] columns = new LogColumn[1];
columns[0] = new LogColumn.Abstract(name) {
protected String getFormattedValue() {
return getAncestralState();
}
};
return columns;
}
private final Tree tree;
private final TreeTrait ancestralTrait;
private final String name;
private Set<String> leafSet = null;
}