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/forester
26 package org.forester.io.parsers.phyloxml.data;
28 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
29 import org.forester.io.parsers.phyloxml.XmlElement;
30 import org.forester.io.parsers.util.PhylogenyParserException;
31 import org.forester.phylogeny.data.ProteinDomain;
33 public class ProteinDomainParser implements PhylogenyDataPhyloXmlParser {
35 private static final PhylogenyDataPhyloXmlParser _instance;
38 _instance = new ProteinDomainParser();
40 catch ( final Throwable e ) {
41 throw new RuntimeException( e.getMessage() );
45 private ProteinDomainParser() {
49 public ProteinDomain parse( final XmlElement element ) throws PhylogenyParserException {
53 double conf = ProteinDomain.CONFIDENCE_DEFAULT;
54 String id = ProteinDomain.IDENTIFIER_DEFAULT;
57 .parseInt( element.getAttribute( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM ) );
58 t = Integer.parseInt( element.getAttribute( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO ) );
59 conf = Double.parseDouble( element
60 .getAttribute( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE ) );
61 if ( element.isHasAttribute( PhyloXmlMapping.IDENTIFIER ) ) {
62 id = element.getAttribute( PhyloXmlMapping.IDENTIFIER );
65 catch ( final Exception e ) {
66 throw new PhylogenyParserException( "failed to parse element [" + element + "]: " + e.getMessage() );
68 name = element.getValueAsString();
69 if ( ( f == -1 ) || ( t == -1 ) || ( conf == ProteinDomain.CONFIDENCE_DEFAULT ) ) {
70 throw new PhylogenyParserException( "from, to, or confidence attribute not set in: " + element );
72 return new ProteinDomain( name, f, t, id, conf );
75 public static PhylogenyDataPhyloXmlParser getInstance() {