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.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 Identifier implements PhylogenyData {
37 final public static String NCBI = "ncbi";
38 final public static String REFSEQ = "refseq";
39 final public static String SP = "sp";
40 final private String _value;
41 final private String _provider;
42 final private String _value_provider;
50 public Identifier( final String value ) {
53 _value_provider = value;
56 public Identifier( final String value, final String provider ) {
59 if ( provider != null ) {
60 _value_provider = value + provider;
63 _value_provider = value;
68 public StringBuffer asSimpleText() {
69 return new StringBuffer( getValue() );
73 public StringBuffer asText() {
74 final StringBuffer sb = new StringBuffer();
75 if ( !ForesterUtil.isEmpty( getProvider() ) ) {
77 sb.append( getProvider() );
80 sb.append( getValue() );
84 public String getValuePlusProvider() {
85 return _value_provider;
89 public PhylogenyData copy() {
90 return new Identifier( getValue(), getProvider() );
94 public boolean equals( final Object o ) {
98 else if ( o == null ) {
101 else if ( o.getClass() != this.getClass() ) {
102 throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to " + o + " ["
103 + o.getClass() + "]" );
106 return isEqual( ( Identifier ) o );
110 public String getProvider() {
114 public String getValue() {
119 public int hashCode() {
120 return _value_provider.hashCode();
124 public boolean isEqual( final PhylogenyData data ) {
125 if ( this == data ) {
128 if ( ( data == null ) || ( getValue() == null ) ) {
131 final Identifier a = ( Identifier ) data;
132 if ( ( getProvider() != null ) && ( a.getProvider() != null ) ) {
133 return ( a.getValue().equals( getValue() ) && a.getProvider().equals( getProvider() ) );
135 return ( a.getValue().equals( getValue() ) );
139 public StringBuffer toNHX() {
140 final StringBuffer sb = new StringBuffer();
142 sb.append( NHXtags.NODE_IDENTIFIER );
143 sb.append( ForesterUtil.replaceIllegalNhxCharacters( getValue() ) );
148 public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
149 if ( !org.forester.util.ForesterUtil.isEmpty( getProvider() ) ) {
150 PhylogenyDataUtil.appendElement( writer,
151 PhyloXmlMapping.IDENTIFIER,
153 PhyloXmlMapping.IDENTIFIER_PROVIDER_ATTR,
158 PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.IDENTIFIER, getValue(), indentation );
163 public String toString() {
164 return asText().toString();