code: public static AffineGapAlignmentScoring<AminoAcidSequence> getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapOpenPenalty, int gapExtensionPenalty) {
          return new AffineGapAlignmentScoring<>(AminoAcidSequence.ALPHABET,
                  matrix.getMatrix(),
                  gapOpenPenalty, gapExtensionPenalty);
      }
docs: Returns AminoAcid BLAST scoring
  
  @param matrix              BLAST substitution matrix to be used
  @param gapOpenPenalty      penalty for opening gap to be used in system
  @param gapExtensionPenalty penalty for extending gap to be used in system
  @return AminoAcid BLAST scoring