+package jalview.io.gff;
+
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import org.testng.annotations.Test;
+
+public class SequenceOntologyLiteTest
+{
+ @Test(groups = "Functional")
+ public void testIsA_sequenceVariant()
+ {
+ SequenceOntologyI so = new SequenceOntologyLite();
+
+ assertFalse(so.isA("CDS", "sequence_variant"));
+ assertTrue(so.isA("sequence_variant", "sequence_variant"));
+
+ /*
+ * these should all be sub-types of sequence_variant
+ */
+ assertTrue(so.isA("structural_variant", "sequence_variant"));
+ assertTrue(so.isA("feature_variant", "sequence_variant"));
+ assertTrue(so.isA("gene_variant", "sequence_variant"));
+ assertTrue(so.isA("transcript_variant", "sequence_variant"));
+ assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
+ assertTrue(so.isA("missense_variant", "sequence_variant"));
+ assertTrue(so.isA("synonymous_variant", "sequence_variant"));
+ assertTrue(so.isA("frameshift_variant", "sequence_variant"));
+ assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
+ assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
+ assertTrue(so.isA("stop_gained", "sequence_variant"));
+ assertTrue(so.isA("stop_lost", "sequence_variant"));
+ assertTrue(so.isA("inframe_deletion", "sequence_variant"));
+ assertTrue(so.isA("inframe_insertion", "sequence_variant"));
+ assertTrue(so.isA("splice_region_variant", "sequence_variant"));
+ }
+}