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: https://sites.google.com/site/cmzmasek/home/software/forester
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.Annotation;
32 import org.forester.phylogeny.data.Confidence;
33 import org.forester.phylogeny.data.PhylogenyData;
34 import org.forester.phylogeny.data.PropertiesMap;
35 import org.forester.phylogeny.data.Property;
36 import org.forester.phylogeny.data.Uri;
38 public class AnnotationParser implements PhylogenyDataPhyloXmlParser {
40 private static final PhylogenyDataPhyloXmlParser _instance;
43 _instance = new AnnotationParser();
45 catch ( final Throwable e ) {
46 throw new RuntimeException( e.getMessage() );
50 private AnnotationParser() {
54 public PhylogenyData parse( final XmlElement element ) throws PhyloXmlDataFormatException {
55 final Annotation annotation;
56 if ( element.isHasAttribute( PhyloXmlMapping.ANNOTATION_REF_ATTR ) ) {
57 annotation = new Annotation( element.getAttribute( PhyloXmlMapping.ANNOTATION_REF_ATTR ) );
60 annotation = new Annotation();
62 if ( element.isHasAttribute( PhyloXmlMapping.ANNOTATION_TYPE_ATTR ) ) {
63 annotation.setType( element.getAttribute( PhyloXmlMapping.ANNOTATION_TYPE_ATTR ) );
65 if ( element.isHasAttribute( PhyloXmlMapping.ANNOTATION_EVIDENCE_ATTR ) ) {
66 annotation.setEvidence( element.getAttribute( PhyloXmlMapping.ANNOTATION_EVIDENCE_ATTR ) );
68 if ( element.isHasAttribute( PhyloXmlMapping.ANNOTATION_SOURCE_ATTR ) ) {
69 annotation.setSource( element.getAttribute( PhyloXmlMapping.ANNOTATION_SOURCE_ATTR ) );
71 for( int i = 0; i < element.getNumberOfChildElements(); ++i ) {
72 final XmlElement child_element = element.getChildElement( i );
73 if ( child_element.getQualifiedName().equals( PhyloXmlMapping.ANNOTATION_DESC ) ) {
74 annotation.setDesc( child_element.getValueAsString() );
76 else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.CONFIDENCE ) ) {
77 annotation.setConfidence( ( Confidence ) ConfidenceParser.getInstance().parse( child_element ) );
79 else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.URI ) ) {
80 annotation.addUri( ( Uri ) UriParser.getInstance().parse( child_element ) );
82 else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.PROPERTY ) ) {
83 if ( annotation.getProperties() == null ) {
84 annotation.setProperties( new PropertiesMap() );
86 annotation.getProperties()
87 .addProperty( ( Property ) PropertyParser.getInstance().parse( child_element ) );
93 public static PhylogenyDataPhyloXmlParser getInstance() {