2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/
26 package org.forester.io.parsers.phyloxml.data;
28 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
29 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
30 import org.forester.io.parsers.phyloxml.XmlElement;
31 import org.forester.phylogeny.data.PhylogenyData;
32 import org.forester.phylogeny.data.Reference;
33 import org.forester.util.ForesterUtil;
35 public class ReferenceParser implements PhylogenyDataPhyloXmlParser {
37 private static final PhylogenyDataPhyloXmlParser _instance;
40 _instance = new ReferenceParser();
42 catch ( final Throwable e ) {
43 throw new RuntimeException( e.getMessage() );
47 private ReferenceParser() {
51 public PhylogenyData parse( final XmlElement element ) throws PhyloXmlDataFormatException {
54 if ( element.isHasAttribute( PhyloXmlMapping.REFERENCE_DOI_ATTR ) ) {
55 doi = element.getAttribute( PhyloXmlMapping.REFERENCE_DOI_ATTR );
57 for( int i = 0; i < element.getNumberOfChildElements(); ++i ) {
58 final XmlElement child_element = element.getChildElement( i );
59 if ( child_element.getQualifiedName().equals( PhyloXmlMapping.REFERENCE_DESC ) ) {
60 desc = child_element.getValueAsString();
64 if ( !ForesterUtil.isEmpty( doi ) ) {
65 return new Reference( desc, doi );
68 return new Reference( desc );
72 public static PhylogenyDataPhyloXmlParser getInstance() {