Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures

[jalview.git] / test / jalview / ext / so / SequenceOntologyTest.java

diff --git a/test/jalview/ext/so/SequenceOntologyTest.java b/test/jalview/ext/so/SequenceOntologyTest.java
index b76a295..31e1887 100644 (file)
--- a/test/jalview/ext/so/SequenceOntologyTest.java
+++ b/test/jalview/ext/so/SequenceOntologyTest.java
@@ -107,4 +107,29 @@ public class SequenceOntologyTest
     assertFalse(so.isA("CDS_region", "CDS"));// part_of
     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
   }
+
+  @Test(groups = "Functional")
+  public void testIsSequenceVariant()
+  {
+    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"));
+  }
 }