format = FileFormat.Fasta;
break;
}
- InputStream stream = new ByteArrayInputStream(
- fa.formatSequences(format, sequences.toArray(new SequenceI[0]))
+
+ // we avoid any use of Jalview's user facing export routines here
+
+ InputStream stream = new ByteArrayInputStream(format.getWriter(null)
+ .print(sequences.toArray(new SequenceI[0]), false)
.getBytes());
request.addFile(param.getId(), stream);
}