X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGeneTest.java;h=6cfd85b4f8f69be2e027864e487451f870c6fdf7;hb=45e015aabe8f35a4a13be26e7630641ef8c94fbb;hp=a262c1eb6ce9c82140a876cb5cfe09decc9c0a6c;hpb=ef9282b464dc189faf9ce40a4b7420a204266668;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index a262c1e..6cfd85b 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;
@@ -5,14 +25,16 @@ 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;
+import jalview.gui.JvOptionPane;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyLite;
 import jalview.util.MapList;
 
-import java.util.Arrays;
+import java.awt.Color;
 import java.util.List;
 
 import org.testng.annotations.AfterClass;
@@ -21,13 +43,21 @@ import org.testng.annotations.Test;
 
 public class EnsemblGeneTest
 {
-  @BeforeClass
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);
@@ -134,8 +164,8 @@ public class EnsemblGeneTest
     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);
@@ -160,21 +190,11 @@ public class EnsemblGeneTest
      * with no filter
      */
     List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
-            genomic, null);
+            genomic);
     assertEquals(3, features.size());
     assertSame(sf1, features.get(0));
     assertSame(sf2, features.get(1));
     assertSame(sf3, features.get(2));
-
-    /*
-     * with filter
-     */
-    List<String> ids = Arrays.asList(new String[] { "transcript2",
-        "transcript3" });
-    features = testee.getTranscriptFeatures(geneId, genomic, ids);
-    assertEquals(2, features.size());
-    assertSame(sf2, features.get(0));
-    assertSame(sf3, features.get(1));
   }
 
   /**
@@ -186,8 +206,8 @@ 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));
 
@@ -219,29 +239,56 @@ 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());
+  }
 }