private int computeNumberOfLettersInPerfectOverlap(Lane iLane,Lane jLane){
  final int firstCoordinate=Math.max(iLane.getFirstNonGapPosition(),jLane.getFirstNonGapPosition());
  final int lastCoordinate=Math.min(iLane.getLastNonGapPosition(),jLane.getLastNonGapPosition());
  int count=0;
  for (int i=firstCoordinate; i < lastCoordinate; i++) {
    char iChar=Character.toLowerCase(iLane.charAt(i));
    char jChar=Character.toLowerCase(jLane.charAt(i));
    if (iChar != jChar && iChar != 'n' && jChar != 'n')     return 0;
 else     if (Character.isLetter(iChar))     count++;
  }
  return count;
}

private int computeNumberOfLettersInPerfectOverlap ( Lane iLane , Lane jLane ) { final int firstCoordinate = Math . max ( iLane . getFirstNonGapPosition ( ) , jLane . getFirstNonGapPosition ( ) ) ; final int lastCoordinate = Math . min ( iLane . getLastNonGapPosition ( ) , jLane . getLastNonGapPosition ( ) ) ; int count = 0 ; for ( int i = firstCoordinate ; i < lastCoordinate ; i ++ ) { char iChar = Character . toLowerCase ( iLane . charAt ( i ) ) ; char jChar = Character . toLowerCase ( jLane . charAt ( i ) ) ; if ( iChar != jChar && iChar != 'n' && jChar != 'n' ) return 0 ; else if ( Character . isLetter ( iChar ) ) count ++ ; } return count ; }
count the number of letters in the overlap between two lanes .
