Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

[jalview.git] / test / jalview / ext / ensembl / EnsemblGeneTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 8b1e840..e16197a 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -20,6 +20,8 @@
  */
 package jalview.ext.ensembl;
 
+import java.util.Locale;
+
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
@@ -161,7 +163,7 @@ public class EnsemblGeneTest
     SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
             22000, 22500, 0f, null);
     // id matching should not be case-sensitive
-    sf3.setValue("Parent", geneId.toLowerCase());
+    sf3.setValue("Parent", geneId.toLowerCase(Locale.ROOT));
     sf3.setValue("id", "transcript3");
     genomic.addSequenceFeature(sf3);
 
@@ -271,18 +273,24 @@ public class EnsemblGeneTest
 
   /**
    * Check behaviour of feature colour scheme for EnsemblGene sequences.
-   * Currently coded to display exon and sequence_variant (or sub-types) only,
-   * with sequence_variant in red above exon coloured by label.
+   * Currently coded to hide all except exon and sequence_variant (or sub-types)
+   * only, with sequence_variant in red above exon coloured by label.
    */
   @Test(groups = "Functional")
   public void testGetFeatureColourScheme()
   {
     FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
-    assertTrue(fc.isFeatureDisplayed("exon"));
-    assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
-    assertTrue(fc.isFeatureDisplayed("sequence_variant"));
-    assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
-    assertFalse(fc.isFeatureDisplayed("transcript"));
+    assertFalse(fc.isFeatureDisplayed("exon"));
+    assertFalse(fc.isFeatureHidden("exon"));
+    assertFalse(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
+    assertFalse(fc.isFeatureHidden("coding_exon")); // subtype of exon
+    assertFalse(fc.isFeatureDisplayed("sequence_variant"));
+    assertFalse(fc.isFeatureHidden("sequence_variant"));
+    assertFalse(fc.isFeatureDisplayed("feature_variant")); // subtype
+    assertFalse(fc.isFeatureHidden("feature_variant")); // subtype
+    assertTrue(fc.isFeatureHidden("transcript"));
+    assertTrue(fc.isFeatureHidden("CDS"));
+
     assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
             .getColour());
     assertEquals(Color.RED, fc.getFeatureColour("feature_variant")