X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdsTest.java;h=4521d9b698cd8d32fd054857aaebe113925db139;hb=55ebdfcc6bd979605c9bb2b4092a422b035bc27e;hp=a44ab7f0ca58030bc9e0cdcb731a16638d322dee;hpb=a4f2a7f356b8edab17a9a5bb6f2e71a1419792a9;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index a44ab7f..4521d9b 100644
--- a/test/jalview/ext/ensembl/EnsemblCdsTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdsTest.java
@@ -53,13 +53,13 @@ public class EnsemblCdsTest
   @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);
   }
 
   /**
@@ -78,19 +78,19 @@ public class EnsemblCdsTest
     // CDS at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
             null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // CDS (sub-type) at (start + 10500) length 101
     sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // CDS belonging to a different transcript doesn't count
     sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
-    sf.setValue("Parent", "transcript:anotherOne");
+    sf.setValue("Parent", "anotherOne");
     genomic.addSequenceFeature(sf);
 
     // exon feature doesn't count
@@ -135,16 +135,16 @@ public class EnsemblCdsTest
     assertFalse(testee.retainFeature(sf, accId));
 
     // other feature with no parent is retained
-    sf = new SequenceFeature("CDS_psequence_variantredicted", "", 20000,
+    sf = new SequenceFeature("anotherType", "", 20000,
             20500, 0f, null);
     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));
 
     // feature with wrong parent is not retained
-    sf.setValue("Parent", "transcript:XYZ");
+    sf.setValue("Parent", "XYZ");
     assertFalse(testee.retainFeature(sf, accId));
   }
 
@@ -164,29 +164,29 @@ public class EnsemblCdsTest
 
     // cds with wrong parent not valid
     SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
-    sf2.setValue("Parent", "transcript:XYZ");
+    sf2.setValue("Parent", "XYZ");
     seq.addSequenceFeature(sf2);
 
     // cds with right parent is valid
     SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
-    sf3.setValue("Parent", "transcript:" + accId);
+    sf3.setValue("Parent", accId);
     seq.addSequenceFeature(sf3);
 
     // cds sub-type with right parent is valid
     SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 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);
 
     // exon not valid:
     SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
-    sf6.setValue("Parent", "transcript:" + accId);
+    sf6.setValue("Parent", accId);
     seq.addSequenceFeature(sf6);
 
     List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,