X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdnaTest.java;h=59bab321920b21b6920202994c353ef4f7a511c4;hb=49db0dff1da16c3355b43a41498c1fc93ef47e91;hp=c9d8deb93308f43981f0c7b2d26fed6efdbc7e94;hpb=a4f2a7f356b8edab17a9a5bb6f2e71a1419792a9;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index c9d8deb..59bab32 100644
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -20,6 +20,8 @@
  */
 package jalview.ext.ensembl;
 
+import java.util.Locale;
+
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
@@ -54,13 +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);
   }
 
   /**
@@ -79,19 +81,19 @@ public class EnsemblCdnaTest
     // exon at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
             null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("-");
     genomic.addSequenceFeature(sf);
 
     // exon (sub-type) at (start + exon_variant) length 101
     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("-");
     genomic.addSequenceFeature(sf);
 
     // exon belonging to a different transcript doesn't count
     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
-    sf.setValue("Parent", "transcript:anotherOne");
+    sf.setValue("Parent", "anotherOne");
     genomic.addSequenceFeature(sf);
 
     // transcript feature doesn't count
@@ -134,19 +136,19 @@ public class EnsemblCdnaTest
     // exon at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
             null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // exon (sub-type) at (start + exon_variant) length 101
     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // exon belonging to a different transcript doesn't count
     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
-    sf.setValue("Parent", "transcript:anotherOne");
+    sf.setValue("Parent", "anotherOne");
     genomic.addSequenceFeature(sf);
 
     // transcript feature doesn't count
@@ -226,14 +228,14 @@ public class EnsemblCdnaTest
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with desired parent is retained
-    sf.setValue("Parent", "transcript:" + accId);
+    sf.setValue("Parent", accId);
     assertTrue(testee.retainFeature(sf, accId));
 
     // test is not case-sensitive
-    assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
+    assertTrue(testee.retainFeature(sf, accId.toLowerCase(Locale.ROOT)));
 
     // feature with wrong parent is not retained
-    sf.setValue("Parent", "transcript:XYZ");
+    sf.setValue("Parent", "XYZ");
     assertFalse(testee.retainFeature(sf, accId));
   }
 
@@ -253,30 +255,30 @@ public class EnsemblCdnaTest
 
     // exon with wrong parent: not valid
     SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
-    sf2.setValue("Parent", "transcript:XYZ");
+    sf2.setValue("Parent", "XYZ");
     seq.addSequenceFeature(sf2);
 
     // exon with right parent is valid
     SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
-    sf3.setValue("Parent", "transcript:" + accId);
+    sf3.setValue("Parent", accId);
     seq.addSequenceFeature(sf3);
 
     // exon sub-type with right parent is valid
     SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
             null);
-    sf4.setValue("Parent", "transcript:" + accId);
+    sf4.setValue("Parent", accId);
     seq.addSequenceFeature(sf4);
 
     // transcript not valid:
     SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
             null);
-    sf5.setValue("Parent", "transcript:" + accId);
+    sf5.setValue("Parent", accId);
     seq.addSequenceFeature(sf5);
 
     // CDS not valid:
     SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
             null);
-    sf6.setValue("Parent", "transcript:" + accId);
+    sf6.setValue("Parent", accId);
     seq.addSequenceFeature(sf6);
 
     List<SequenceFeature> sfs = new EnsemblCdna()