SimpleProfileProfileAligner extends AbstractProfileProfileAligner<S, C> { public SimpleProfileProfileAligner() { } SimpleProfileProfileAligner();  SimpleProfileProfileAligner(Profile<S, C> query, Profile<S, C> target, GapPenalty gapPenalty,
            SubstitutionMatrix<C> subMatrix);  SimpleProfileProfileAligner(Future<ProfilePair<S, C>> query, Future<ProfilePair<S, C>> target,
            GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix);  SimpleProfileProfileAligner(Profile<S, C> query, Future<ProfilePair<S, C>> target, GapPenalty gapPenalty,
            SubstitutionMatrix<C> subMatrix);  SimpleProfileProfileAligner(Future<ProfilePair<S, C>> query, Profile<S, C> target, GapPenalty gapPenalty,
            SubstitutionMatrix<C> subMatrix);   }
@Test public void testSimpleProfileProfileAligner() { SimpleProfileProfileAligner<ProteinSequence, AminoAcidCompound> alig = new SimpleProfileProfileAligner<ProteinSequence, AminoAcidCompound>(); alig.setQuery(prof1); alig.setTarget(prof2); alig.setGapPenalty(gaps); alig.setSubstitutionMatrix(blosum62); assertEquals(alig.getScore(), sppa1.getScore()); }