@Test
public void testParseReferenceGoAnnotations()
throws IOException, MissingAccessionException, MissingProteinException, SAXException,
ParsingException {
ahrd.setup(false);
assertNotNull(ahrd.getReferenceGoAnnotations());
assertTrue(!ahrd.getReferenceGoAnnotations().isEmpty());
assertEquals(4, ahrd.getReferenceGoAnnotations().size());
Set<String> refGos = ahrd.getReferenceGoAnnotations().get("AT1G01040.1");
assertTrue(refGos.contains("GO:0003824"));
assertTrue(refGos.contains("GO:0003870"));
}
@Test
public void testAnnotatesGoTerms()
throws IOException, MissingAccessionException, MissingProteinException, SAXException,
ParsingException, MissingInterproResultException, SQLException {
ahrd.setup(false);
ahrd.assignHumanReadableDescriptions();
Protein p = ahrd.getProteins().get("gene:chr01.1056:mRNA:chr01.1056");
assertNotNull(p.getGoResults());
assertEquals(2, p.getGoResults().size());
assertTrue(p.getGoResults().contains("GO:0006355"));
assertTrue(p.getGoResults().contains("GO:0043401"));
}
@Test
public void testUniqueShortAccessions()
throws IOException, MissingAccessionException, MissingProteinException, SAXException,
ParsingException {
ahrd.setup(false);
assertNotNull(ahrd.getUniqueBlastResultShortAccessions());
// Somehow assertEquals does not work on Collections as expected, hence
// the following work-around:
List<String> expectedUniqueShortAccessions =
Utils.fromFile("./test/resources/all_blast_hits_blast8_tabular_searches.txt");
for (String sa : expectedUniqueShortAccessions) {
assertTrue(ahrd.getUniqueBlastResultShortAccessions().contains(sa));
}
assertEquals(
expectedUniqueShortAccessions.size(), ahrd.getUniqueBlastResultShortAccessions().size());
ahrd.getUniqueBlastResultShortAccessions().removeAll(expectedUniqueShortAccessions);
assertEquals(0, ahrd.getUniqueBlastResultShortAccessions().size());
}