public int write(Protein protein) throws IOException {
  int sequenceLength=protein.getSequenceLength();
  String md5=protein.getMd5();
  String date=dmyFormat.format(new Date());
  Set<Match> matches=protein.getMatches();
  String proteinIdForGFF=null;
  List<String> proteinIdsFromGetOrf=getProteinAccessions(protein);
  for (  String proteinIdFromGetorf : proteinIdsFromGetOrf) {
    if (matches.size() > 0) {
      proteinIdFromGetorf=getValidGFF3SeqId(proteinIdFromGetorf);
      writeSequenceRegionPart(protein,sequenceLength,md5,proteinIdFromGetorf);
      processMatches(matches,proteinIdForGFF,date,protein,getNucleotideId());
    }
  }
  return 0;
}

public int write ( Protein protein ) throws IOException { int sequenceLength = protein . getSequenceLength ( ) ; String md5 = protein . getMd5 ( ) ; String date = dmyFormat . format ( new Date ( ) ) ; Set < Match > matches = protein . getMatches ( ) ; String proteinIdForGFF = null ; List < String > proteinIdsFromGetOrf = getProteinAccessions ( protein ) ; for ( String proteinIdFromGetorf : proteinIdsFromGetOrf ) { if ( matches . size ( ) > 0 ) { proteinIdFromGetorf = getValidGFF3SeqId ( proteinIdFromGetorf ) ; writeSequenceRegionPart ( protein , sequenceLength , md5 , proteinIdFromGetorf ) ; processMatches ( matches , proteinIdForGFF , date , protein , getNucleotideId ( ) ) ; } } return 0 ; }
writes out a protein object to a gff version 3 file
