/*
* UPGMATreeParser.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.evoxml;
import dr.evolution.distance.DistanceMatrix;
import dr.evolution.tree.MutableTree;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.UPGMATree;
import dr.evolution.util.TimeScale;
import dr.evomodelxml.tree.TreeModelParser;
import dr.math.MathUtils;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Alexei Drummond
* @author Andrew Rambaut
* @author Marc A. Suchard
* @version $Id: UPGMATreeParser.java,v 1.6 2006/07/28 11:27:32 rambaut Exp $
*/
public class UPGMATreeParser extends AbstractXMLObjectParser {
//
// Public stuff
//
public static final String UPGMA_TREE = "upgmaTree";
//public static final String DISTANCES = "distances";
public static final String ROOT_HEIGHT = TreeModelParser.ROOT_HEIGHT;
public static final String RANDOMIZE = "nonzeroBranchLengths";
public String getParserName() {
return UPGMA_TREE;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
boolean usingDatesSpecified = false;
boolean usingDates = true;
double rootHeight = xo.getAttribute(ROOT_HEIGHT, -1.0);
if (xo.hasAttribute(SimpleTreeParser.USING_DATES)) {
usingDatesSpecified = true;
usingDates = xo.getBooleanAttribute(SimpleTreeParser.USING_DATES);
}
DistanceMatrix distances = (DistanceMatrix) xo.getChild(DistanceMatrix.class);
UPGMATree tree = new UPGMATree(distances);
if (rootHeight > 0) {
double scaleFactor = rootHeight / tree.getNodeHeight(tree.getRoot());
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef node = tree.getInternalNode(i);
double height = tree.getNodeHeight(node);
tree.setNodeHeight(node, height * scaleFactor);
}
}
if (usingDates) {
dr.evolution.util.Date mostRecent = null;
for (int i = 0; i < tree.getTaxonCount(); i++) {
dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getTaxonAttribute(i, dr.evolution.util.Date.DATE);
if (date == null) {
date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getExternalNode(i), dr.evolution.util.Date.DATE);
}
if (date != null && ((mostRecent == null) || date.after(mostRecent))) {
mostRecent = date;
}
}
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getInternalNode(i), dr.evolution.util.Date.DATE);
if (date != null && ((mostRecent == null) || date.after(mostRecent))) {
mostRecent = date;
}
}
if (mostRecent == null) {
if (usingDatesSpecified) {
throw new XMLParseException("no date elements in tree (and usingDates attribute set)");
}
} else {
TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
for (int i = 0; i < tree.getTaxonCount(); i++) {
dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getTaxonAttribute(i, dr.evolution.util.Date.DATE);
if (date == null) {
date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getExternalNode(i), dr.evolution.util.Date.DATE);
}
if (date != null) {
double height = timeScale.convertTime(date.getTimeValue(), date);
tree.setNodeHeight(tree.getExternalNode(i), height);
}
}
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getInternalNode(i), dr.evolution.util.Date.DATE);
if (date != null) {
double height = timeScale.convertTime(date.getTimeValue(), date);
tree.setNodeHeight(tree.getInternalNode(i), height);
}
}
MutableTree.Utils.correctHeightsForTips(tree);
}
}
if (rootHeight > 0) {
double scaleFactor = rootHeight / tree.getNodeHeight(tree.getRoot());
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef node = tree.getInternalNode(i);
double height = tree.getNodeHeight(node);
tree.setNodeHeight(node, height * scaleFactor);
}
}
if (xo.getAttribute(RANDOMIZE, false)) {
shakeTree(tree);
}
return tree;
}
private boolean shakeNode(UPGMATree tree, NodeRef node) {
if (tree.isRoot(node) || tree.isExternal(node)) {
return false;
}
boolean shake = false;
if (tree.getBranchLength(node) <= tolerance) {
shake = true;
}
double maxHeight = tree.getNodeHeight(tree.getParent(node));
double minHeight = Double.NEGATIVE_INFINITY;
for (int i = 0; i < tree.getChildCount(node); i++) {
NodeRef child = tree.getChild(node, i);
if (tree.getBranchLength(child) <= tolerance) {
shake = true;
}
double thisHeight = tree.getNodeHeight(child);
if (thisHeight > minHeight) {
minHeight = thisHeight;
}
}
if (shake) {
double draw = minHeight + (maxHeight - minHeight) * MathUtils.nextDouble();
tree.setNodeHeight(node, draw);
}
return shake;
}
private void shakeTree(UPGMATree tree) {
boolean shake = true;
int[] permutation = new int[tree.getNodeCount()];
for (int i = 0; i < tree.getNodeCount(); i++) {
permutation[i] = i;
}
while (shake) {
Logger.getLogger("dr.evomodelxml").info("Adjusting heights in UPGMA tree");
MathUtils.permute(permutation);
shake = false;
for (int i = 0; i < tree.getNodeCount(); i++) {
NodeRef node = tree.getNode(permutation[i]);
if (shakeNode(tree, node)) {
shake = true;
}
}
}
}
private static double tolerance = 0.0;
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newBooleanRule(SimpleTreeParser.USING_DATES, true),
AttributeRule.newDoubleRule(ROOT_HEIGHT, true),
AttributeRule.newBooleanRule(RANDOMIZE, true),
new ElementRule(DistanceMatrix.class)
};
public String getParserDescription() {
return "This element returns a UPGMA tree generated from the given distances.";
}
public Class getReturnType() {
return UPGMATree.class;
}
}