/*
* CladeMeanAttributeStatistic.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.app.treestat.statistics;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.evolution.tree.TreeUtils;
import dr.evolution.util.*;
import java.util.*;
/**
*
* @version $Id: TMRCASummaryStatistic.java,v 1.3 2006/05/09 10:24:27 rambaut Exp $
*
* @author Alexei Drummond
*/
public class CladeMeanAttributeStatistic extends AbstractTreeSummaryStatistic {
private CladeMeanAttributeStatistic() {
this.attributeName = "";
}
public void setTaxonList(TaxonList taxonList) {
this.taxonList = taxonList;
}
public void setString(String value) {
this.attributeName = value;
}
public double[] getSummaryStatistic(Tree tree) {
NodeRef node;
if (taxonList == null) {
node = tree.getRoot();
} else {
try {
Set<String> leafSet = TreeUtils.getLeavesForTaxa(tree, taxonList);
node = TreeUtils.getCommonAncestorNode(tree, leafSet);
if (node == null) throw new RuntimeException("No clade found that contains " + leafSet);
} catch (TreeUtils.MissingTaxonException e) {
throw new RuntimeException("Missing taxon!");
}
}
sumAttribute = 0.0;
nodeCount = 0;
getAttribute(tree, node);
return new double[] { sumAttribute / nodeCount };
}
private double sumAttribute;
private int nodeCount;
private void getAttribute(Tree tree, NodeRef node) {
if (!tree.isExternal(node)) {
for (int i = 0; i < tree.getChildCount(node); i++) {
getAttribute(tree, tree.getChild(node, i));
}
}
Object item = tree.getNodeAttribute(node, attributeName);
if (item != null && item instanceof Number) {
sumAttribute += ((Number)item).doubleValue();
nodeCount ++;
} else {
// just ignore it
}
}
public String getSummaryStatisticName() {
if (taxonList != null) {
return attributeName + "(" + taxonList.getId() + ")";
} else {
return attributeName + "(root)";
}
}
public String getSummaryStatisticDescription() {
if (taxonList != null) {
return "Gets the mean of an attribute for a clade defined by a taxon set";
}
return "Gets the mean of an attribute across the tree.";
}
public String getSummaryStatisticReference() { return FACTORY.getSummaryStatisticReference(); }
public boolean allowsPolytomies() { return FACTORY.allowsPolytomies(); }
public boolean allowsNonultrametricTrees() { return FACTORY.allowsNonultrametricTrees(); }
public boolean allowsUnrootedTrees() { return FACTORY.allowsUnrootedTrees(); }
public Category getCategory() { return FACTORY.getCategory(); }
public static final Factory FACTORY = new Factory() {
public TreeSummaryStatistic createStatistic() {
return new CladeMeanAttributeStatistic();
}
public String getSummaryStatisticName() {
return "Mean Clade Attribute";
}
public String getSummaryStatisticDescription() {
return "Extracts the mean of a named attribute for a clade defined by a taxon set";
}
public String getSummaryStatisticReference() {
return "-";
}
public String getValueName() { return "The attribute name:"; }
public boolean allowsPolytomies() { return true; }
public boolean allowsNonultrametricTrees() { return true; }
public boolean allowsUnrootedTrees() { return false; }
public Category getCategory() { return Category.GENERAL; }
public boolean allowsWholeTree() { return true; }
public boolean allowsTaxonList() { return true; }
public boolean allowsString() { return true; }
};
private String attributeName = null;
private TaxonList taxonList = null;
}