Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[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 da129ba..b0d447a 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;
@@ -151,8 +153,8 @@ public class EnsemblGeneTest
     genomic.addSequenceFeature(sf1);
 
     // transcript sub-type feature
-    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
-            0f, null);
+    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500, 0f,
+            null);
     sf2.setValue("Parent", geneId);
     sf2.setValue("id", "transcript2");
     genomic.addSequenceFeature(sf2);
@@ -161,13 +163,13 @@ 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);
 
     // transcript for a different gene - ignored
-    SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
-            0f, null);
+    SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500, 0f,
+            null);
     sf4.setValue("Parent", "XYZ");
     sf4.setValue("id", "transcript4");
     genomic.addSequenceFeature(sf4);
@@ -208,8 +210,8 @@ public class EnsemblGeneTest
     sf.setValue("Parent", geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
-    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
-            0f, null);
+    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
+            null);
     sf.setValue("Parent", geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
@@ -245,12 +247,14 @@ public class EnsemblGeneTest
     seq.addSequenceFeature(sf3);
 
     // gene sub-type with right ID is valid
-    SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
+    SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f,
+            null);
     sf4.setValue("id", accId);
     seq.addSequenceFeature(sf4);
 
     // transcript not valid:
-    SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+    SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
+            null);
     sf5.setValue("id", accId);
     seq.addSequenceFeature(sf5);
 
@@ -258,7 +262,7 @@ public class EnsemblGeneTest
     SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
     sf6.setValue("id", accId);
     seq.addSequenceFeature(sf6);
-    
+
     List<SequenceFeature> sfs = new EnsemblGene()
             .getIdentifyingFeatures(seq, accId);
     assertFalse(sfs.contains(sf1));
@@ -271,22 +275,28 @@ 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"));
-    assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
-            .getColour());
-    assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
-            .getColour());
+    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").getColour());
     assertTrue(fc.getFeatureColour("exon").isColourByLabel());
     assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
     assertEquals(1, fc.compare("sequence_variant", "exon"));
@@ -309,7 +319,6 @@ public class EnsemblGeneTest
     String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF";
     EnsemblGene testee = new EnsemblGene();
     List<String> geneIds = testee.getGeneIds(ids);
-    assertEquals(8, geneIds.size());
     assertTrue(geneIds.contains("ENSG00000158828"));
     assertTrue(geneIds.contains("ENSG00000136448"));
     assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human
@@ -318,5 +327,7 @@ public class EnsemblGeneTest
     assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
     assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
     assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
+    assertEquals(8, geneIds.size());
+
   }
 }