code: public static <S extends Sequence<S>> int calculateScore(S seq1, Mutations<S> mutations,
                                                               AlignmentScoring<S> scoring) {
          return calculateScore(seq1, new Range(0, seq1.size()), mutations, scoring);
      }
docs: Calculates score of alignment
  
  @param seq1      target sequence
  @param mutations mutations (alignment)
  @param scoring   scoring
  @param <S>       sequence type
  @return score