1 package jalview.ext.so;
3 import static org.testng.AssertJUnit.assertFalse;
4 import static org.testng.AssertJUnit.assertTrue;
6 import jalview.io.gff.SequenceOntologyI;
8 import org.testng.annotations.BeforeClass;
9 import org.testng.annotations.Test;
11 public class SequenceOntologyTest
13 private SequenceOntologyI so;
15 @BeforeClass(alwaysRun = true)
17 long now = System.currentTimeMillis();
20 so = new SequenceOntology();
23 System.out.println("SOTest error ");
24 t.printStackTrace(System.err);
26 long elapsed = System.currentTimeMillis() - now;
27 System.out.println("Load and cache of Sequence Ontology took "
31 @Test(groups = "Functional")
34 assertFalse(so.isA(null, null));
35 assertFalse(so.isA(null, "SO:0000087"));
36 assertFalse(so.isA("SO:0000087", null));
37 assertFalse(so.isA("complete", "garbage"));
39 assertTrue(so.isA("SO:0000087", "SO:0000704"));
40 assertFalse(so.isA("SO:0000704", "SO:0000087"));
41 assertTrue(so.isA("SO:0000736", "SO:0000735"));
44 assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
46 assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
48 assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
50 assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
52 // same thing by name / description:
53 assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
54 assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
55 assertTrue(so.isA("SO:0000084", "SO:0000084"));
57 // SO name to description:
58 assertTrue(so.isA("SO:0000084", "organelle_sequence"));
59 assertTrue(so.isA("SO:0000084", "sequence_location"));
60 assertTrue(so.isA("SO:0000084", "sequence_attribute"));
62 // description to SO name:
63 assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
64 assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
65 assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
68 @Test(groups = "Functional")
69 public void testIsCDS()
71 assertTrue(so.isA("CDS", "CDS"));
72 assertTrue(so.isA("CDS_predicted", "CDS"));
73 assertTrue(so.isA("transposable_element_CDS", "CDS"));
74 assertTrue(so.isA("edited_CDS", "CDS"));
75 assertTrue(so.isA("CDS_independently_known", "CDS"));
76 assertTrue(so.isA("CDS_fragment", "CDS"));
77 assertFalse(so.isA("CDS_region", "CDS"));// part_of
78 assertFalse(so.isA("polypeptide", "CDS")); // derives_from