X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGeneTest.java;h=4e815d11841615a06b2792d85adf7e63f88be21c;hb=993d8ed7d398dd3f48838f8accf4a9f151bb9923;hp=d1c7e2fc6ed07306c9a59e280bd1905df6a065e3;hpb=550c391f0c113658e540783dc89034a34280ef18;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index d1c7e2f..4e815d1 100644
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -5,6 +5,7 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -12,6 +13,7 @@ import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyLite;
 import jalview.util.MapList;
 
+import java.awt.Color;
 import java.util.List;
 
 import org.testng.annotations.AfterClass;
@@ -20,13 +22,13 @@ import org.testng.annotations.Test;
 
 public class EnsemblGeneTest
 {
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);
@@ -233,4 +235,31 @@ public class EnsemblGeneTest
     sf.setType("exon");
     assertFalse(testee.identifiesSequence(sf, accId));
   }
+
+  /**
+   * 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.
+   */
+  @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());
+    assertTrue(fc.getFeatureColour("exon").isColourByLabel());
+    assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
+    assertEquals(1, fc.compare("sequence_variant", "exon"));
+    assertEquals(-1, fc.compare("exon", "sequence_variant"));
+    assertEquals(1, fc.compare("feature_variant", "coding_exon"));
+    assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
+    assertEquals(1f, fc.getTransparency());
+  }
 }