コード例 #1
0
 @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"));
 }
コード例 #2
0
 @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"));
 }
コード例 #3
0
 @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());
 }