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.nhx.NHXtags;
32 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
33 import org.forester.util.ForesterUtil;
35 public final class Accession implements PhylogenyData {
37 final private String _value;
38 final private String _source;
39 final private String _value_source;
41 public Accession( final String value, final String source ) {
44 if ( source != null ) {
45 _value_source = value + source;
48 _value_source = value;
53 public StringBuffer asSimpleText() {
54 return new StringBuffer( getValue() );
58 public StringBuffer asText() {
59 final StringBuffer sb = new StringBuffer();
60 if ( !ForesterUtil.isEmpty( getSource() ) ) {
62 sb.append( getSource() );
65 sb.append( getValue() );
70 public PhylogenyData copy() {
71 return new Accession( getValue() , getSource() );
75 public boolean equals( final Object o ) {
79 else if ( o == null ) {
82 else if ( o.getClass() != this.getClass() ) {
83 throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to " + o + " ["
84 + o.getClass() + "]" );
87 return isEqual( ( Accession ) o );
91 public String getSource() {
95 public String getValue() {
100 public int hashCode() {
101 //if ( getSource() != null ) {
102 // return ( getSource() + getValue() ).hashCode();
104 return _value_source.hashCode();
108 public boolean isEqual( final PhylogenyData data ) {
109 if ( this == data ) {
112 if ( ( data == null ) || ( getValue() == null ) ) {
115 final Accession a = ( Accession ) data;
116 if ( ( getSource() != null ) && ( a.getSource() != null ) ) {
117 return ( a.getValue().equals( getValue() ) && a.getSource().equals( getSource() ) );
119 return ( a.getValue().equals( getValue() ) );
123 public StringBuffer toNHX() {
124 final StringBuffer sb = new StringBuffer();
126 sb.append( NHXtags.SEQUENCE_ACCESSION );
127 sb.append( ForesterUtil.replaceIllegalNhxCharacters( getValue() ) );
132 public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
133 if ( ForesterUtil.isEmpty( getSource() ) ) {
134 PhylogenyDataUtil.appendElement( writer,
135 PhyloXmlMapping.ACCESSION,
137 PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
142 PhylogenyDataUtil.appendElement( writer,
143 PhyloXmlMapping.ACCESSION,
145 PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
152 public String toString() {
153 return asText().toString();