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.Confidence;
32 import org.forester.phylogeny.data.Event;
33 import org.forester.phylogeny.data.PhylogenyData;
34 import org.forester.util.ForesterUtil;
36 public class EventParser implements PhylogenyDataPhyloXmlParser {
38 private static final PhylogenyDataPhyloXmlParser _instance;
41 _instance = new EventParser();
43 catch ( final Throwable e ) {
44 throw new RuntimeException( e.getMessage() );
48 private EventParser() {
52 public PhylogenyData parse( final XmlElement element ) throws PhylogenyParserException {
54 Confidence conf = null;
55 int duplications = Event.DEFAULT_VALUE;
56 int speciations = Event.DEFAULT_VALUE;
57 int losses = Event.DEFAULT_VALUE;
58 for( int i = 0; i < element.getNumberOfChildElements(); ++i ) {
59 final XmlElement child_element = element.getChildElement( i );
60 if ( child_element.getQualifiedName().equals( PhyloXmlMapping.EVENT_TYPE ) ) {
61 type = child_element.getValueAsString();
63 else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.CONFIDENCE ) ) {
64 conf = ( ( Confidence ) ConfidenceParser.getInstance().parse( child_element ) );
66 else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.EVENT_DUPLICATIONS ) ) {
67 duplications = child_element.getValueAsInt();
69 else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.EVENT_SPECIATIONS ) ) {
70 speciations = child_element.getValueAsInt();
72 else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.EVENT_LOSSES ) ) {
73 losses = child_element.getValueAsInt();
77 if ( ForesterUtil.isEmpty( type ) ) {
78 event = new Event( duplications, speciations, losses );
82 event = new Event( duplications, speciations, losses, type );
84 catch ( final Exception e ) {
85 throw new PhylogenyParserException( "problem with " + element.toString() + ": " + e.getMessage() );
89 event.setConfidence( conf );
94 public static PhylogenyDataPhyloXmlParser getInstance() {