X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGeneTest.java;h=33bb189ac8b7dc30f784abd9dc25de77c15a769c;hb=0a9a0c390bce6a5b374f4d559d0b93797e5d36d0;hp=1f1a84e3f1302eb691159d6ec666106d47b1e10d;hpb=e96f5e8ce137e879dd4b4f37fb5c4d134e2778e2;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 1f1a84e..33bb189 100644
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -5,6 +25,7 @@ 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 +33,7 @@ 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 +42,13 @@ 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);
@@ -129,27 +151,35 @@ public class EnsemblGeneTest
     SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
             20500, 0f, null);
     sf1.setValue("Parent", "gene:" + geneId);
+    sf1.setValue("transcript_id", "transcript1");
     genomic.addSequenceFeature(sf1);
 
     // transcript sub-type feature
-    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000,
-            20500, 0f, null);
+    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000, 20500,
+            0f, null);
     sf2.setValue("Parent", "gene:" + geneId);
+    sf2.setValue("transcript_id", "transcript2");
     genomic.addSequenceFeature(sf2);
 
     // NMD_transcript_variant treated like transcript in Ensembl
     SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
             20000, 20500, 0f, null);
     sf3.setValue("Parent", "gene:" + geneId);
+    sf3.setValue("transcript_id", "transcript3");
     genomic.addSequenceFeature(sf3);
 
     // transcript for a different gene - ignored
     SequenceFeature sf4 = new SequenceFeature("snRNA", "", 20000, 20500,
             0f, null);
     sf4.setValue("Parent", "gene:XYZ");
+    sf4.setValue("transcript_id", "transcript4");
     genomic.addSequenceFeature(sf4);
 
     EnsemblGene testee = new EnsemblGene();
+
+    /*
+     * with no filter
+     */
     List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
             genomic);
     assertEquals(3, features.size());
@@ -167,8 +197,8 @@ public class EnsemblGeneTest
   {
     String geneId = "ABC123";
     EnsemblGene testee = new EnsemblGene();
-    SequenceFeature sf = new SequenceFeature("gene", "", 20000,
-            20500, 0f, null);
+    SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
+            null);
     sf.setValue("ID", "gene:" + geneId);
     assertFalse(testee.retainFeature(sf, geneId));
 
@@ -200,29 +230,56 @@ public class EnsemblGeneTest
   {
     String accId = "ABC123";
     EnsemblGene testee = new EnsemblGene();
-  
+
     // gene with no ID not valid
     SequenceFeature sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // gene with wrong ID not valid
     sf.setValue("ID", "gene:XYZ");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // gene with right ID is valid
     sf.setValue("ID", "gene:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // gene sub-type with right ID is valid
     sf.setType("snRNA_gene");
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // transcript not valid:
     sf.setType("transcript");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // exon not valid:
     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());
+  }
 }