1 package jalview.ext.so;
3 import static org.testng.AssertJUnit.assertFalse;
4 import static org.testng.AssertJUnit.assertTrue;
6 import jalview.ext.so.SequenceOntology;
7 import jalview.io.gff.SequenceOntologyFactory;
8 import jalview.io.gff.SequenceOntologyI;
10 import org.testng.annotations.AfterClass;
11 import org.testng.annotations.BeforeClass;
12 import org.testng.annotations.Test;
14 public class SequenceOntologyTest
16 private SequenceOntologyI so;
20 long now = System.currentTimeMillis();
21 SequenceOntologyFactory.setInstance(new SequenceOntology());
22 long elapsed = System.currentTimeMillis() - now;
23 System.out.println("Load and cache of Sequence Ontology took "
25 so = SequenceOntologyFactory.getInstance();
29 public void tearDown()
31 SequenceOntologyFactory.setInstance(null);
34 @Test(groups = "Functional")
37 assertFalse(so.isA(null, null));
38 assertFalse(so.isA(null, "SO:0000087"));
39 assertFalse(so.isA("SO:0000087", null));
40 assertFalse(so.isA("complete", "garbage"));
42 assertTrue(so.isA("SO:0000087", "SO:0000704"));
43 assertFalse(so.isA("SO:0000704", "SO:0000087"));
44 assertTrue(so.isA("SO:0000736", "SO:0000735"));
47 assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
49 assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
51 assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
53 assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
55 // same thing by name / description:
56 assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
57 assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
58 assertTrue(so.isA("SO:0000084", "SO:0000084"));
60 // SO name to description:
61 assertTrue(so.isA("SO:0000084", "organelle_sequence"));
62 assertTrue(so.isA("SO:0000084", "sequence_location"));
63 assertTrue(so.isA("SO:0000084", "sequence_attribute"));
65 // description to SO name:
66 assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
67 assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
68 assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
71 @Test(groups = "Functional")
72 public void testIsCDS()
74 assertTrue(so.isA("CDS", "CDS"));
75 assertTrue(so.isA("CDS_predicted", "CDS"));
76 assertTrue(so.isA("transposable_element_CDS", "CDS"));
77 assertTrue(so.isA("edited_CDS", "CDS"));
78 assertTrue(so.isA("CDS_independently_known", "CDS"));
79 assertTrue(so.isA("CDS_fragment", "CDS"));
80 assertFalse(so.isA("CDS_region", "CDS"));// part_of
81 assertFalse(so.isA("polypeptide", "CDS")); // derives_from