JAL-3364 align split frame sequence panels with wrapped view scale left
[jalview.git] / test / jalview / io / gff / SequenceOntologyLiteTest.java
1 package jalview.io.gff;
2
3 import static org.testng.AssertJUnit.assertFalse;
4 import static org.testng.AssertJUnit.assertTrue;
5
6 import org.testng.annotations.Test;
7
8 public class SequenceOntologyLiteTest
9 {
10   @Test(groups = "Functional")
11   public void testIsA_sequenceVariant()
12   {
13     SequenceOntologyI so = new SequenceOntologyLite();
14
15     assertFalse(so.isA("CDS", "sequence_variant"));
16     assertTrue(so.isA("sequence_variant", "sequence_variant"));
17
18     /*
19      * these should all be sub-types of sequence_variant
20      */
21     assertTrue(so.isA("structural_variant", "sequence_variant"));
22     assertTrue(so.isA("feature_variant", "sequence_variant"));
23     assertTrue(so.isA("gene_variant", "sequence_variant"));
24     assertTrue(so.isA("transcript_variant", "sequence_variant"));
25     assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
26     assertTrue(so.isA("missense_variant", "sequence_variant"));
27     assertTrue(so.isA("synonymous_variant", "sequence_variant"));
28     assertTrue(so.isA("frameshift_variant", "sequence_variant"));
29     assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
30     assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
31     assertTrue(so.isA("stop_gained", "sequence_variant"));
32     assertTrue(so.isA("stop_lost", "sequence_variant"));
33     assertTrue(so.isA("inframe_deletion", "sequence_variant"));
34     assertTrue(so.isA("inframe_insertion", "sequence_variant"));
35     assertTrue(so.isA("splice_region_variant", "sequence_variant"));
36   }
37 }