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)
18 long now = System.currentTimeMillis();
21 so = new SequenceOntology();
24 System.out.println("SOTest error ");
25 t.printStackTrace(System.err);
27 long elapsed = System.currentTimeMillis() - now;
28 System.out.println("Load and cache of Sequence Ontology took "
32 @Test(groups = "Functional")
35 assertFalse(so.isA(null, null));
36 assertFalse(so.isA(null, "SO:0000087"));
37 assertFalse(so.isA("SO:0000087", null));
38 assertFalse(so.isA("complete", "garbage"));
40 assertTrue(so.isA("SO:0000087", "SO:0000704"));
41 assertFalse(so.isA("SO:0000704", "SO:0000087"));
42 assertTrue(so.isA("SO:0000736", "SO:0000735"));
45 assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
47 assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
49 assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
51 assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
53 // same thing by name / description:
54 assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
55 assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
56 assertTrue(so.isA("SO:0000084", "SO:0000084"));
58 // SO name to description:
59 assertTrue(so.isA("SO:0000084", "organelle_sequence"));
60 assertTrue(so.isA("SO:0000084", "sequence_location"));
61 assertTrue(so.isA("SO:0000084", "sequence_attribute"));
63 // description to SO name:
64 assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
65 assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
66 assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
69 @Test(groups = "Functional")
70 public void testIsCDS()
72 assertTrue(so.isA("CDS", "CDS"));
73 assertTrue(so.isA("CDS_predicted", "CDS"));
74 assertTrue(so.isA("transposable_element_CDS", "CDS"));
75 assertTrue(so.isA("edited_CDS", "CDS"));
76 assertTrue(so.isA("CDS_independently_known", "CDS"));
77 assertTrue(so.isA("CDS_fragment", "CDS"));
78 assertFalse(so.isA("CDS_region", "CDS"));// part_of
79 assertFalse(so.isA("polypeptide", "CDS")); // derives_from