GenBankHandler can parse and write GenBank and EMBL files. 

The GenBankParser or EmblParser can be used to parse either file types. 
The RecordBuilder build an accessible object out of the generated parse event. 
The GenBankWriter or EmblWriter can used to create the output file from the record generated by the RecordBuilder.
 
  RecordBuilder builder = new RecordBuilder();
  InsdcParser parser = null;
  if(isGenbank)
    parser = new GenBankParser(in,builder);
  else
    parser = new EmblParser(in,builder);
  parser.parse(true);
  InsdcWriter writer = null;
  if(isGenbank)
    writer = new GenBankWriter(buf);
  else
    writer = new EmblWriter(buf);
  writer.writeRecord(builder.getRecords().get(0));