/*
* BeastImporter.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.beauti.util;
import dr.evolution.alignment.Alignment;
import dr.evolution.alignment.SimpleAlignment;
import dr.evolution.io.Importer;
import dr.evolution.sequence.Sequence;
import dr.evolution.util.*;
import dr.evoxml.AlignmentParser;
import dr.evoxml.DateParser;
import dr.evoxml.SequenceParser;
import dr.evoxml.TaxaParser;
import dr.evoxml.TaxonParser;
import dr.xml.AttributeParser;
import dr.xml.XMLParser;
import org.jdom.Document;
import org.jdom.Element;
import org.jdom.JDOMException;
import org.jdom.input.SAXBuilder;
import java.io.IOException;
import java.io.Reader;
import java.text.DateFormat;
import java.text.ParseException;
import java.util.Calendar;
import java.util.List;
import java.util.Locale;
/**
* @author Andrew Rambaut
* @version $Id$
*/
public class BeastImporter {
private final Element root;
private final DateFormat dateFormat;
private final java.util.Date origin;
public BeastImporter(Reader reader) throws IOException, JDOMException, Importer.ImportException {
SAXBuilder builder = new SAXBuilder();
Document doc = builder.build(reader);
root = doc.getRootElement();
if (!root.getName().equalsIgnoreCase("beast")) {
throw new Importer.ImportException("Unrecognized root element in XML file");
}
dateFormat = DateFormat.getDateInstance(java.text.DateFormat.SHORT, Locale.UK);
dateFormat.setLenient(true);
Calendar cal = Calendar.getInstance(Locale.getDefault());
// set uses a zero based month (Jan = 0):
cal.set(0000, 00, 01);
// origin = cal.getTime();
cal.setTimeInMillis(0);
origin = cal.getTime();
}
public void importBEAST(List<TaxonList> taxonLists, List<Alignment> alignments) throws Importer.ImportException {
TaxonList taxa = null;
List children = root.getChildren();
for(Object aChildren : children) {
Element child = (Element) aChildren;
if( child.getName().equalsIgnoreCase(TaxaParser.TAXA) ) {
if( taxa == null ) {
taxa = readTaxa(null, child);
taxonLists.add(taxa);
} else {
taxonLists.add(readTaxa(taxa, child));
}
} else if( child.getName().equalsIgnoreCase(AlignmentParser.ALIGNMENT) ) {
if( taxa == null ) {
throw new Importer.ImportException("taxa not defined");
}
alignments.add(readAlignment(child, taxa));
}
}
}
private TaxonList readTaxa(TaxonList primaryTaxa, Element e) throws Importer.ImportException {
Taxa taxa = new Taxa();
String id = e.getAttributeValue("id");
if (id != null) {
taxa.setId(id);
} else {
taxa.setId("taxa");
}
List children = e.getChildren();
for(Object aChildren : children) {
Element child = (Element) aChildren;
if( child.getName().equalsIgnoreCase(TaxonParser.TAXON) ) {
taxa.addTaxon(readTaxon(primaryTaxa, child));
}
}
return taxa;
}
private Taxon readTaxon(TaxonList primaryTaxa, Element e) throws Importer.ImportException {
String id = e.getAttributeValue(XMLParser.ID);
Taxon taxon = null;
if (id != null) {
taxon = new Taxon(id);
List children = e.getChildren();
for(Object aChildren : children) {
Element child = (Element) aChildren;
if( child.getName().equalsIgnoreCase(dr.evolution.util.Date.DATE) ) {
Date date = readDate(child);
taxon.setAttribute(dr.evolution.util.Date.DATE, date);
} else if( child.getName().equalsIgnoreCase(AttributeParser.ATTRIBUTE) ) {
String name = child.getAttributeValue(AttributeParser.NAME);
String value = child.getAttributeValue(AttributeParser.VALUE);
if (value == null) {
value = child.getTextTrim();
}
taxon.setAttribute(name, value);
}
}
} else {
String idref = e.getAttributeValue(XMLParser.IDREF);
int index = primaryTaxa.getTaxonIndex(idref);
if (index >= 0) {
taxon = primaryTaxa.getTaxon(index);
}
}
return taxon;
}
private Alignment readAlignment(Element e, TaxonList taxa) throws Importer.ImportException {
SimpleAlignment alignment = new SimpleAlignment();
List children = e.getChildren();
for(Object aChildren : children) {
Element child = (Element) aChildren;
if( child.getName().equalsIgnoreCase(SequenceParser.SEQUENCE) ) {
alignment.addSequence(readSequence(child, taxa));
}
}
return alignment;
}
private Sequence readSequence(Element e, TaxonList taxa) throws Importer.ImportException {
String taxonID = e.getChild(TaxonParser.TAXON).getAttributeValue(XMLParser.IDREF);
int index = taxa.getTaxonIndex(taxonID);
if (index < 0) {
throw new Importer.ImportException("Unknown taxon, " + taxonID + ", in alignment");
}
Taxon taxon = taxa.getTaxon(index);
String[] seq = e.getTextTrim().split("\\s");
StringBuilder sb = new StringBuilder();
for (String part : seq) {
sb.append(part);
}
return new Sequence(taxon, sb.toString());
}
private Date readDate(Element e) throws Importer.ImportException {
String value = e.getAttributeValue(DateParser.VALUE);
boolean backwards = true;
String direction = e.getAttributeValue(DateParser.DIRECTION);
if (direction != null && direction.equalsIgnoreCase(DateParser.FORWARDS)) {
backwards = false;
}
try {
return new Date(dateFormat.parse(value));
} catch (ParseException e1) {
// ignore the parse exception and try it just as a number
}
// try just parsing it as a number
return new Date(Double.valueOf(value), Units.Type.YEARS, backwards);
}
}