NeedlemanWunsch extends AbstractPairwiseSequenceAligner<S, C> { public NeedlemanWunsch() { } NeedlemanWunsch();  NeedlemanWunsch(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix);   }
@Test public void testNeedlemanWunsch() { NeedlemanWunsch<ProteinSequence, AminoAcidCompound> nw = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(); nw.setQuery(query); nw.setTarget(target); nw.setGapPenalty(gaps); nw.setSubstitutionMatrix(blosum62); assertEquals(nw.getScore(), alignment.getScore()); }