JAL-3878 update branch from 2.12 merge from 2.11.2

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

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index c927f04..fb80a35 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -56,13 +56,13 @@ public class EnsemblCdnaTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
-    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+    SequenceOntologyFactory.setSequenceOntology(new SequenceOntologyLite());
   }
 
   @AfterClass(alwaysRun = true)
   public void tearDown()
   {
-    SequenceOntologyFactory.setInstance(null);
+    SequenceOntologyFactory.setSequenceOntology(null);
   }
 
   /**
@@ -211,20 +211,21 @@ public class EnsemblCdnaTest
     String accId = "ABC123";
     EnsemblCdna testee = new EnsemblCdna();
 
-    SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
-            20500, 0f, null);
+    SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
+            0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
     sf = new SequenceFeature("aberrant_processed_transcript", "", 20000,
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
-            0f, null);
+    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
+            null);
     assertFalse(testee.retainFeature(sf, accId));
 
     // other feature with no parent is retained
-    sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null);
+    sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f,
+            null);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with desired parent is retained