JAL-2189 apply license

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

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index daad8b1..991cd96 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.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;
@@ -19,13 +39,13 @@ import org.testng.annotations.Test;
 
 public class EnsemblGenomeTest
 {
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);
@@ -43,15 +63,14 @@ public class EnsemblGenomeTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // transcript at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
-            20500, 0f,
-            null);
+            20500, 0f, null);
     sf.setValue("ID", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // transcript (sub-type) at (start + 10500) length 101
     sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
     sf.setValue("ID", "transcript:" + transcriptId);
@@ -65,12 +84,12 @@ public class EnsemblGenomeTest
     sf.setValue("ID", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // transcript with a different ID doesn't count
     sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
     sf.setValue("ID", "transcript:anotherOne");
     genomic.addSequenceFeature(sf);
-  
+
     // parent of transcript feature doesn't count
     sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
             null);
@@ -107,13 +126,13 @@ public class EnsemblGenomeTest
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     sf.setType("mature_transcript");
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     sf.setType("NMD_transcript_variant");
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     // other feature with no parent is kept
     sf.setType("anything");
     assertTrue(testee.retainFeature(sf, accId));
@@ -136,20 +155,20 @@ public class EnsemblGenomeTest
   {
     String accId = "ABC123";
     EnsemblGenome testee = new EnsemblGenome();
-  
+
     // transcript with no ID not valid
     SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
             null);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // transcript with wrong ID not valid
     sf.setValue("ID", "transcript");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // transcript with right ID is valid
     sf.setValue("ID", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // transcript sub-type with right ID is valid
     sf.setType("ncRNA");
     assertTrue(testee.identifiesSequence(sf, accId));
@@ -157,11 +176,11 @@ public class EnsemblGenomeTest
     // Ensembl treats NMD_transcript_variant as if a transcript
     sf.setType("NMD_transcript_variant");
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // gene not valid:
     sf.setType("gene");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // exon not valid:
     sf.setType("exon");
     assertFalse(testee.identifiesSequence(sf, accId));