boolean seqlimits = suffix.equalsIgnoreCase("true");\r
if (alf.viewport.getSelectionGroup() != null)\r
{\r
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data\r
+ // TODO consider using getSequenceSelection instead here\r
String reply = new AppletFormatAdapter().formatSequences(format,\r
new Alignment(alf.viewport.getSelectionAsNewSequence()),\r
seqlimits);\r