AbstractPairwiseAlignment implements PairwiseAlignment { @Override public Iterable<AlignmentPair> local(final Sequence query, final Sequence subject) { return local(ImmutableList.of(query), ImmutableList.of(subject), DEFAULT_LOCAL_GAP_PENALTIES); } protected  AbstractPairwiseAlignment(final SubstitutionMatrix substitutionMatrix); final SubstitutionMatrix getSubstitutionMatrix(); @Override Iterable<AlignmentPair> local(final Sequence query, final Sequence subject); @Override Iterable<AlignmentPair> local(final Sequence query,
                                         final Sequence subject,
                                         final GapPenalties gapPenalties); @Override Iterable<AlignmentPair> local(final Sequence query, final List<Sequence> subjects); @Override Iterable<AlignmentPair> local(final Sequence query,
                                         final List<Sequence> subjects,
                                         final GapPenalties gapPenalties); @Override Iterable<AlignmentPair> local(final List<Sequence> queries, final List<Sequence> subjects); @Override Iterable<AlignmentPair> global(final Sequence query, final Sequence subject); @Override Iterable<AlignmentPair> global(final Sequence query,
                                          final Sequence subject,
                                          final GapPenalties gapPenalties); @Override Iterable<AlignmentPair> global(final Sequence query, final List<Sequence> subjects); @Override Iterable<AlignmentPair> global(final Sequence query,
                                          final List<Sequence> subjects,
                                          final GapPenalties gapPenalties); @Override Iterable<AlignmentPair> global(final List<Sequence> queries, final List<Sequence> subjects);  }
@Test(expected=NullPointerException.class) public void testLocalNullQuery() { align.local(null, subject); }
@Test(expected=NullPointerException.class) public void testLocalNullSubject() { align.local(query, (Sequence) null); }
@Test(expected=NullPointerException.class) public void testLocalGapPenaltiesNullQuery() { align.local(null, subject, gapPenalties); }
@Test(expected=NullPointerException.class) public void testLocalGapPenaltiesNullSubject() { align.local(query, (Sequence) null, gapPenalties); }
@Test(expected=NullPointerException.class) public void testLocalNullGapPenalties() { align.local(query, subject, null); }
@Test(expected=NullPointerException.class) public void testLocalNullSubjects() { align.local(query, (List<Sequence>) null); }
@Test(expected=NullPointerException.class) public void testLocalNullQueries() { align.local((List<Sequence>) null, subjects); }
@Test public void testLocal() { for (AlignmentPair alignmentPair : align.local(query, subject)) { assertNotNull(alignmentPair); } }
@Test public void testLocalGapPenalties() { for (AlignmentPair alignmentPair : align.local(query, subject, gapPenalties)) { assertNotNull(alignmentPair); } }
@Test public void testLocalSubjects() { for (AlignmentPair alignmentPair : align.local(query, subjects)) { assertNotNull(alignmentPair); } }
@Test public void testLocalSubjectsGapPenalties() { for (AlignmentPair alignmentPair : align.local(query, subjects, gapPenalties)) { assertNotNull(alignmentPair); } }
@Test public void testLocalQueries() { for (AlignmentPair alignmentPair : align.local(queries, subjects)) { assertNotNull(alignmentPair); } }
@Test public void testLocalQueriesGapPenalties() { for (AlignmentPair alignmentPair : align.local(queries, subjects, gapPenalties)) { assertNotNull(alignmentPair); } }