code: public KAlignerParameters2 setScoring(AffineGapAlignmentScoring<NucleotideSequence> scoring) {
          if (scoring != null && !scoring.uniformBasicMatchScore())
              throw new IllegalArgumentException("Use scoring with common match score.");
          this.scoring = scoring;
          return this;
      }
docs: Sets scoring system used for building alignments
  
  @param scoring scoring system
  @return parameters object