/*
* NewickParser.java
*
* Copyright (C) 2002-2009 Alexei Drummond and Andrew Rambaut
*
* 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.io.Importer;
import dr.evolution.io.NewickImporter;
import dr.evolution.tree.*;
import dr.evolution.util.Taxon;
import dr.evolution.util.TimeScale;
import dr.evolution.util.Units;
import dr.evoxml.util.XMLUnits;
import dr.xml.*;
import java.io.IOException;
/**
* @author Alexei Drummond
* @author Andrew Rambaut
* @version $Id: NewickParser.java,v 1.7 2006/04/25 14:41:08 rambaut Exp $
*/
public class NewickParser extends AbstractXMLObjectParser {
public static final String NEWICK = "newick";
public static final String UNITS = "units";
public static final String RESCALE_HEIGHT = "rescaleHeight";
public static final String RESCALE_LENGTH = "rescaleLength";
public NewickParser() {
rules = new XMLSyntaxRule[]{
AttributeRule.newBooleanRule(SimpleTreeParser.USING_DATES, true),
AttributeRule.newDoubleRule(RESCALE_HEIGHT, true, "Attempt to rescale the tree to the given root height"),
AttributeRule.newDoubleRule(RESCALE_LENGTH, true, "Attempt to rescale the tree to the given total length"),
new StringAttributeRule(UNITS, "The branch length units of this tree", Units.UNIT_NAMES, true),
new ElementRule(String.class, "The NEWICK format tree. Tip labels are taken to be Taxon IDs")
};
}
public String getParserName() {
return NEWICK;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
boolean usingDates = xo.getAttribute(SimpleTreeParser.USING_DATES, true);
StringBuffer buffer = new StringBuffer();
for (int i = 0; i < xo.getChildCount(); i++) {
if (xo.getChild(i) instanceof String) {
buffer.append((String) xo.getChild(i));
} else {
throw new XMLParseException("illegal element in newick element");
}
}
java.io.Reader reader = new java.io.StringReader(buffer.toString());
NewickImporter importer = new NewickImporter(reader);
FlexibleTree tree;
try {
tree = (FlexibleTree) importer.importTree(null);
} catch (IOException ioe) {
throw new XMLParseException("error parsing tree in newick element");
} catch (NewickImporter.BranchMissingException bme) {
throw new XMLParseException("branch missing in tree in newick element");
} catch (Importer.ImportException ime) {
throw new XMLParseException("error parsing tree in newick element - " + ime.getMessage());
}
if (tree == null) {
throw new XMLParseException("Failed to read tree");
}
tree.setUnits(units);
for (int i = 0; i < tree.getTaxonCount(); i++) {
FlexibleNode node = (FlexibleNode) tree.getExternalNode(i);
String id = node.getTaxon().getId();
Taxon taxon = null;
try {
Object obj = getStore().getObjectById(id);
if (obj instanceof Taxon) {
taxon = (Taxon) obj;
}
} catch (ObjectNotFoundException e) { /**/}
if (taxon != null) {
node.setTaxon(taxon);
} else {
throw new XMLParseException("unknown taxon, " + id + ", in newick tree");
}
}
if (usingDates) {
for (int i = 0; i < tree.getTaxonCount(); i++) {
NodeRef node = tree.getExternalNode(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);
}
double height = 0.0;
double nodeHeight = tree.getNodeHeight(node);
if (date != null) {
height = Taxon.getHeightFromDate(date);
}
if (Math.abs(nodeHeight - height) > 1e-5) {
System.out.println(" Changing height of node " + tree.getTaxon(node.getNumber()) + " from " + nodeHeight + " to " + height);
tree.setNodeHeight(node, 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 = Taxon.getHeightFromDate(date);
tree.setNodeHeight(tree.getInternalNode(i), height);
}
}
MutableTree.Utils.correctHeightsForTips(tree);
} else {
// not using dates
for (int i = 0; i < tree.getTaxonCount(); i++) {
final NodeRef leaf = tree.getExternalNode(i);
final double h = tree.getNodeHeight(leaf);
if (h != 0.0) {
tree.setNodeHeight(leaf, 0.0);
}
}
}
if (xo.hasAttribute(RESCALE_HEIGHT)) {
double rescaleHeight = xo.getDoubleAttribute(RESCALE_HEIGHT);
double scale = rescaleHeight / tree.getNodeHeight(tree.getRoot());
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef n = tree.getInternalNode(i);
tree.setNodeHeight(n, tree.getNodeHeight(n) * scale);
}
}
if (xo.hasAttribute(RESCALE_LENGTH)) {
double rescaleLength = xo.getDoubleAttribute(RESCALE_LENGTH);
double scale = rescaleLength / Tree.Utils.getTreeLength(tree, tree.getRoot());
for (int i = 0; i < tree.getInternalNodeCount(); i++) {
NodeRef n = tree.getInternalNode(i);
tree.setNodeHeight(n, tree.getNodeHeight(n) * scale);
}
}
//System.out.println("Constructed newick tree = " + Tree.Utils.uniqueNewick(tree, tree.getRoot()));
return tree;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "Constructs a tree from a NEWICK format tree description";
}
public String getExample() {
return "<" + getParserName() + " " + UNITS + "=\"" + Units.Utils.getDefaultUnitName(Units.Type.YEARS) + "\">" + " ((A:1.0, B:1.0):1.0,(C:2.0, D:2.0):1.0); </" + getParserName() + ">";
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules;
public Class getReturnType() {
return Tree.class;
}
}