// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
import org.forester.util.ForesterUtil;
-public class Identifier implements PhylogenyData {
+public final class Identifier implements PhylogenyData {
- final String _value;
- final String _provider;
+ final public static String NCBI = "ncbi";
+ final public static String REFSEQ = "refseq";
+ final public static String SP = "sp";
+ final private String _value;
+ final private String _provider;
+ final private String _value_provider;
public Identifier() {
_value = "";
_provider = "";
+ _value_provider = "";
}
public Identifier( final String value ) {
_value = value;
_provider = "";
+ _value_provider = value;
}
public Identifier( final String value, final String provider ) {
_value = value;
_provider = provider;
+ if ( provider != null ) {
+ _value_provider = value + provider;
+ }
+ else {
+ _value_provider = value;
+ }
}
+ @Override
public StringBuffer asSimpleText() {
return new StringBuffer( getValue() );
}
+ @Override
public StringBuffer asText() {
final StringBuffer sb = new StringBuffer();
if ( !ForesterUtil.isEmpty( getProvider() ) ) {
return sb;
}
+ public String getValuePlusProvider() {
+ return _value_provider;
+ }
+
+ @Override
public PhylogenyData copy() {
return new Identifier( getValue(), getProvider() );
}
@Override
public int hashCode() {
- if ( getProvider() != null ) {
- return ( getProvider() + getValue() ).hashCode();
- }
- return getValue().hashCode();
+ return _value_provider.hashCode();
}
+ @Override
public boolean isEqual( final PhylogenyData data ) {
if ( this == data ) {
return true;
return ( a.getValue().equals( getValue() ) );
}
+ @Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
sb.append( ":" );
return sb;
}
+ @Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
if ( !org.forester.util.ForesterUtil.isEmpty( getProvider() ) ) {
PhylogenyDataUtil.appendElement( writer,