code: public void process() throws Exception {
  		// Loosely based on code from Howard Salis
  		// TODO - Force lower case?
  		// boolean closeit = false;
  		PrintWriter writer = new PrintWriter(os);
  		for (S sequence : sequences) {
  			String header = headerFormat.getHeader(sequence);
  			writer.format(header);
  			writer.println();
  			// os.write(lineSep);
  
  			/*
  			 * if isinstance(record.seq, UnknownSeq): #We have already recorded
  			 * the length, and there is no need #to record a long sequence of
  			 * NNNNNNN...NNN or whatever. if "contig" in record.annotations:
  			 * self._write_contig(record) else: self.handle.write("ORIGIN\n")
  			 * return
  			 */
  
  			String data = sequence.getSequenceAsString().toLowerCase();
  			int seq_len = data.length();
  			writer.println("ORIGIN");
  			// os.write(lineSep);
  
  			for (int line_number = 0; line_number < seq_len; line_number += lineLength) {
  				writer.print(StringManipulationHelper.padLeft(
  						Integer.toString(line_number + 1), SEQUENCE_INDENT));
  				for (int words = line_number; words < Math.min(line_number
  						+ lineLength, seq_len); words += 10) {
  					if ((words + 10) > data.length()) {
  						writer.print((" " + data.substring(words)));
  					} else {
  						writer.print((" " + data.substring(words, words + 10)));
  					}
  				}
  				// os.write(lineSep);
  				writer.println();
  			}
  
  			writer.println("//");
  
  		}
  
  		writer.flush();
  
  	}
docs: Allow an override of operating system line separator for programs that
  needs a specific CRLF or CR or LF option
  
  @param lineSeparator