SmithWaterman extends AbstractPairwiseSequenceAligner<S, C> { public SmithWaterman() { super(null, null, null, null, true); } SmithWaterman();  SmithWaterman(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix);   }
@Test public void testSmithWaterman() { SmithWaterman<ProteinSequence, AminoAcidCompound> alig = new SmithWaterman<ProteinSequence, AminoAcidCompound>(); alig.setQuery(query); alig.setTarget(target); alig.setGapPenalty(gaps); alig.setSubstitutionMatrix(blosum62); assertEquals(alig.getPair().toString(), String.format("ERNDKK%nER-DNK%n")); }