public static < S extends Sequence < S > > Alignment < S > alignLocal ( AlignmentScoring < S > alignmentScoring , S seq1 , S seq2 ) { if ( alignmentScoring instanceof AffineGapAlignmentScoring ) return alignLocalAffine ( ( AffineGapAlignmentScoring < S > ) alignmentScoring , seq1 , seq2 ) ; if ( alignmentScoring instanceof LinearGapAlignmentScoring ) return alignLocalLinear ( ( LinearGapAlignmentScoring < S > ) alignmentScoring , seq1 , seq2 ) ; throw new RuntimeException ( "Unknown scoring type." ) ; }
Performs local alignment