boolean matchesOverlap(PfamHmmer3RawMatch one,PfamHmmer3RawMatch two){
  return !((one.getLocationStart() > two.getLocationEnd()) || (two.getLocationStart() > one.getLocationEnd()));
}

boolean matchesOverlap ( PfamHmmer3RawMatch one , PfamHmmer3RawMatch two ) { return ! ( ( one . getLocationStart ( ) > two . getLocationEnd ( ) ) || ( two . getLocationStart ( ) > one . getLocationEnd ( ) ) ) ; }
determines if two domains overlap .
