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.phylogeny.data;
28 import java.io.IOException;
29 import java.io.Writer;
31 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
32 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
33 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
34 import org.forester.util.ForesterUtil;
36 public class Reference implements PhylogenyData {
41 public Reference( final String desc ) {
46 public Reference( final String desc, final String doi ) {
52 public StringBuffer asSimpleText() {
53 return new StringBuffer( getDescription() );
57 public StringBuffer asText() {
58 final StringBuffer sb = new StringBuffer();
59 if ( !ForesterUtil.isEmpty( getDoi() ) ) {
61 sb.append( getDoi() );
64 sb.append( getDescription() );
69 public PhylogenyData copy() {
70 return new Reference( getDescription(), getDoi() );
73 public String getDoi() {
77 public String getDescription() {
82 public boolean isEqual( final PhylogenyData data ) {
83 if ( ( data == null ) || ( getDescription() == null ) ) {
86 return ( ( Reference ) data ).getDescription().equals( getDescription() )
87 && ( ( Reference ) data ).getDoi().equals( getDoi() );
90 public void setDoi( final String doi ) {
91 if ( !ForesterUtil.isEmpty( doi ) && !PhyloXmlUtil.LIT_REF_DOI_PATTERN.matcher( doi ).matches() ) {
92 throw new PhyloXmlDataFormatException( "illegal doi: [" + doi + "]" );
97 public void setValue( final String value ) {
102 public StringBuffer toNHX() {
103 throw new UnsupportedOperationException();
107 public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
108 writer.write( ForesterUtil.LINE_SEPARATOR );
109 writer.write( indentation );
110 PhylogenyDataUtil.appendOpen( writer, PhyloXmlMapping.REFERENCE, PhyloXmlMapping.REFERENCE_DOI_ATTR, getDoi() );
111 if ( !ForesterUtil.isEmpty( getDescription() ) ) {
112 PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.REFERENCE_DESC, getDescription(), indentation );
114 writer.write( ForesterUtil.LINE_SEPARATOR );
115 writer.write( indentation );
116 PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.REFERENCE );
120 public String toString() {
121 return asText().toString();