X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fso%2FSequenceOntologyTest.java;h=31e1887d4b673f2c76f5a1dfb13bd27e2f964410;hb=6536eebed40b833ad60803e8f2a4b0a9bd395035;hp=1bc802ece1ec5938838aaff444e3137b6780ea97;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/test/jalview/ext/so/SequenceOntologyTest.java b/test/jalview/ext/so/SequenceOntologyTest.java
index 1bc802e..31e1887 100644
--- a/test/jalview/ext/so/SequenceOntologyTest.java
+++ b/test/jalview/ext/so/SequenceOntologyTest.java
@@ -23,6 +23,7 @@ package jalview.ext.so;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.gui.JvOptionPane;
 import jalview.io.gff.SequenceOntologyI;
 
 import org.testng.annotations.BeforeClass;
@@ -30,6 +31,14 @@ import org.testng.annotations.Test;
 
 public class SequenceOntologyTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   private SequenceOntologyI so;
 
   @BeforeClass(alwaysRun = true)
@@ -98,4 +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"));
+  }
 }