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

[jalview.git] / test / jalview / io / gff / SequenceOntologyLiteTest.java

diff --git a/test/jalview/io/gff/SequenceOntologyLiteTest.java b/test/jalview/io/gff/SequenceOntologyLiteTest.java
new file mode 100644 (file)
index 0000000..0766666
--- /dev/null
+++ b/test/jalview/io/gff/SequenceOntologyLiteTest.java
@@ -0,0 +1,37 @@
+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"));
+  }
+}