@Test
public void testWithMarkupsNullAdditionalMarkups() {
Sequence withMarkups = sequence.withMarkups(null);
assertNotNull(withMarkups.getMarkups());
assertEquals(1, withMarkups.getMarkups().size());
assertEquals(24, withMarkups.getMarkups().get(0).getStart());
}
@Test
public void testWithMarkupsEmptyAdditionalMarkups() {
List<Markup> empty = Collections.emptyList();
Sequence withMarkups = sequence.withMarkups(empty);
assertNotNull(withMarkups.getMarkups());
assertEquals(1, withMarkups.getMarkups().size());
assertEquals(24, withMarkups.getMarkups().get(0).getStart());
}
@Test
public void testWithMarkups() {
Markup markup = new Markup();
markup.setStart(13);
Sequence withMarkups = sequence.withMarkups(ImmutableList.of(markup));
assertNotNull(withMarkups.getMarkups());
assertEquals(2, withMarkups.getMarkups().size());
for (Markup m : withMarkups.getMarkups()) {
assertTrue(m.getStart() == 13 || m.getStart() == 24);
}
}
@Test
public void testDeepCopy() {
Sequence copy = sequence.deepCopy();
assertNotSame(sequence, copy);
assertEquals(sequence.getLength(), copy.getLength());
assertEquals(sequence.getMarkups(), copy.getMarkups());
assertNotSame(sequence.getMarkups(), copy.getMarkups());
assertEquals(sequence.getMetadata(), copy.getMetadata());
assertNotSame(sequence.getMetadata(), copy.getMetadata());
assertEquals(sequence.getMotifs(), copy.getMotifs());
assertNotSame(sequence.getMotifs(), copy.getMotifs());
assertEquals(sequence.getOptions().getBaseUrl(), copy.getOptions().getBaseUrl());
assertNotSame(sequence.getOptions(), copy.getOptions());
assertEquals(sequence.getRegions(), copy.getRegions());
assertNotSame(sequence.getRegions(), copy.getRegions());
}
@Test
public void testDeserializeFromJsonO14640() throws Exception {
ObjectMapper objectMapper = new ObjectMapper();
objectMapper.configure(ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
TypeFactory typeFactory = objectMapper.getTypeFactory();
InputStream inputStream = getClass().getResourceAsStream("/O14640.json");
List<Sequence> sequences =
objectMapper.readValue(
inputStream, typeFactory.constructCollectionType(List.class, Sequence.class));
assertNotNull(sequences);
assertEquals(1, sequences.size());
Sequence s = sequences.get(0);
assertEquals(695, s.getLength());
assertEquals(5, s.getRegions().size());
assertEquals(0, s.getMarkups().size());
assertEquals(7, s.getMotifs().size());
assertEquals("uniprot", s.getMetadata().get("database"));
}
@Test
public void testWithMarkupsNullMarkups() {
sequence.setMarkups(null);
Sequence withMarkups = sequence.withMarkups(null);
assertNull(withMarkups.getMarkups());
}
@Test
public void testDeepCopyNullMarkups() {
sequence.setMarkups(null);
Sequence copy = sequence.deepCopy();
assertNull(copy.getMarkups());
}