AbstractPairwiseAlignment implements PairwiseAlignment { @Override public Iterable<AlignmentPair> global(final Sequence query, final Sequence subject) { return global(ImmutableList.of(query), ImmutableList.of(subject), DEFAULT_GLOBAL_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 testGlobalNullQuery() { align.global(null, subject); }
@Test(expected=NullPointerException.class) public void testGlobalNullSubject() { align.global(query, (Sequence) null); }
@Test(expected=NullPointerException.class) public void testGlobalGapPenaltiesNullQuery() { align.global(null, subject, gapPenalties); }
@Test(expected=NullPointerException.class) public void testGlobalGapPenaltiesNullSubject() { align.global(query, (Sequence) null, gapPenalties); }
@Test(expected=NullPointerException.class) public void testGlobalNullGapPenalties() { align.global(query, subject, null); }
@Test(expected=NullPointerException.class) public void testGlobalNullSubjects() { align.global(query, (List<Sequence>) null); }
@Test(expected=NullPointerException.class) public void testGlobalNullQueries() { align.global((List<Sequence>) null, subjects); }
@Test public void testGlobal() { for (AlignmentPair alignmentPair : align.global(query, subject)) { assertNotNull(alignmentPair); } }
@Test public void testGlobalGapPenalties() { for (AlignmentPair alignmentPair : align.global(query, subject, gapPenalties)) { assertNotNull(alignmentPair); } }
@Test public void testGlobalSubjects() { for (AlignmentPair alignmentPair : align.global(query, subjects)) { assertNotNull(alignmentPair); } }
@Test public void testGlobalSubjectsGapPenalties() { for (AlignmentPair alignmentPair : align.global(query, subjects, gapPenalties)) { assertNotNull(alignmentPair); } }
@Test public void testGlobalQueries() { for (AlignmentPair alignmentPair : align.global(queries, subjects)) { assertNotNull(alignmentPair); } }
@Test public void testGlobalQueriesGapPenalties() { for (AlignmentPair alignmentPair : align.global(queries, subjects, gapPenalties)) { assertNotNull(alignmentPair); } }