// 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
getAnnotations().add( annotation );
}
+ @Override
public void addUri( final Uri uri ) {
if ( getUris() == null ) {
setUris( new ArrayList<Uri>() );
_seq_relations.add( sr );
}
+ @Override
public StringBuffer asSimpleText() {
final StringBuffer sb = new StringBuffer();
if ( getAccession() != null ) {
return sb;
}
+ @Override
public StringBuffer asText() {
return asSimpleText();
}
* Not a deep copy.
*
*/
+ @Override
public PhylogenyData copy() {
final Sequence seq = new Sequence();
seq.setAnnotations( getAnnotations() );
return _type;
}
+ @Override
public List<Uri> getUris() {
return _uris;
}
+ @Override
public Uri getUri( final int index ) {
return getUris().get( index );
}
setSourceId( null );
}
+ @Override
public boolean isEqual( final PhylogenyData data ) {
if ( this == data ) {
return true;
_type = type;
}
+ @Override
public void setUris( final List<Uri> uris ) {
_uris = uris;
}
+ @Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
if ( getName().length() > 0 ) {
return sb;
}
+ @Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
if ( isEmpty() ) {
return;