/*
* TaxaParser.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.util.Taxa;
import dr.evolution.util.Taxon;
import dr.evolution.util.TaxonList;
import dr.xml.*;
/**
* @author Alexei Drummond
* @author Andrew Rambaut
*
* @version $Id: TaxaParser.java,v 1.2 2005/05/24 20:25:59 rambaut Exp $
*/
public class TaxaParser extends AbstractXMLObjectParser {
public static final String TAXA = "taxa";
public String getParserName() { return TAXA; }
public String getExample() {
return "<!-- A list of six taxa -->\n"+
"<taxa id=\"greatApes\">\n"+
" <taxon id=\"human\"/>\n"+
" <taxon id=\"chimp\"/>\n"+
" <taxon id=\"bonobo\"/>\n"+
" <taxon id=\"gorilla\"/>\n"+
" <taxon id=\"orangutan\"/>\n"+
" <taxon id=\"siamang\"/>\n"+
"</taxa>\n" +
"\n" +
"<!-- A list of three taxa by references to above taxon objects -->\n"+
"<taxa id=\"humanAndChimps\">\n"+
" <taxon idref=\"human\"/>\n"+
" <taxon idref=\"chimp\"/>\n"+
" <taxon idref=\"bonobo\"/>\n"+
"</taxa>\n";
}
/** @return an instance of Node created from a DOM element */
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Taxa taxonList = new Taxa();
for (int i = 0; i < xo.getChildCount(); i++) {
Object child = xo.getChild(i);
if (child instanceof Taxon) {
Taxon taxon = (Taxon)child;
taxonList.addTaxon(taxon);
} else if (child instanceof TaxonList) {
TaxonList taxonList1 = (TaxonList)child;
for (int j = 0; j < taxonList1.getTaxonCount(); j++) {
taxonList.addTaxon(taxonList1.getTaxon(j));
}
} else {
throwUnrecognizedElement(xo);
}
}
return taxonList;
}
public XMLSyntaxRule[] getSyntaxRules() { return rules; }
private final XMLSyntaxRule[] rules = {
new OrRule(
new ElementRule(Taxa.class, 1, Integer.MAX_VALUE),
new ElementRule(Taxon.class, 1, Integer.MAX_VALUE)
)
};
public String getParserDescription() {
return "Defines a set of taxon objects.";
}
public Class getReturnType() { return Taxa.class; }
}