X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGenomeTest.java;h=0a9cc644effd9d21d68d18c8bd840d9173716506;hb=e7e676ca075c5b2832be98b4544364e5d6adc4c1;hp=72ee492cccb683638cb9ba223034f49108e2ce23;hpb=a4f2a7f356b8edab17a9a5bb6f2e71a1419792a9;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index 72ee492..0a9cc64 100644
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@ -52,13 +52,13 @@ public class EnsemblGenomeTest
   @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);
   }
 
   /**
@@ -77,13 +77,13 @@ public class EnsemblGenomeTest
     // transcript at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
             20500, 0f, null);
-    sf.setValue("ID", "transcript:" + transcriptId);
+    sf.setValue("id", 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);
+    sf.setValue("id", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
@@ -91,13 +91,13 @@ public class EnsemblGenomeTest
     // although strictly it is a sequence_variant in SO
     sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
             0f, null);
-    sf.setValue("ID", "transcript:" + transcriptId);
+    sf.setValue("id", 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");
+    sf.setValue("id", "anotherOne");
     genomic.addSequenceFeature(sf);
 
     // parent of transcript feature doesn't count
@@ -150,11 +150,11 @@ public class EnsemblGenomeTest
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with correct parent is kept
-    sf.setValue("Parent", "transcript:" + accId);
+    sf.setValue("Parent", accId);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with wrong parent is not kept
-    sf.setValue("Parent", "transcript:XYZ");
+    sf.setValue("Parent", "XYZ");
     assertFalse(testee.retainFeature(sf, accId));
   }
 
@@ -174,36 +174,37 @@ public class EnsemblGenomeTest
     seq.addSequenceFeature(sf1);
 
     // transcript with wrong ID not valid
-    SequenceFeature sf2 = new SequenceFeature("transcript", "", 1, 2, 0f,
+    // NB change desc to avoid rejection of duplicate feature!
+    SequenceFeature sf2 = new SequenceFeature("transcript", "a", 1, 2, 0f,
             null);
-    sf2.setValue("ID", "transcript");
+    sf2.setValue("id", "transcript");
     seq.addSequenceFeature(sf2);
 
     // transcript with right ID is valid
-    SequenceFeature sf3 = new SequenceFeature("transcript", "", 1, 2, 0f,
+    SequenceFeature sf3 = new SequenceFeature("transcript", "b", 1, 2, 0f,
             null);
-    sf3.setValue("ID", "transcript:" + accId);
+    sf3.setValue("id", accId);
     seq.addSequenceFeature(sf3);
 
     // transcript sub-type with right ID is valid
     SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
-    sf4.setValue("ID", "transcript:" + accId);
+    sf4.setValue("id", accId);
     seq.addSequenceFeature(sf4);
 
     // Ensembl treats NMD_transcript_variant as if a transcript
     SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
             1, 2, 0f, null);
-    sf5.setValue("ID", "transcript:" + accId);
+    sf5.setValue("id", accId);
     seq.addSequenceFeature(sf5);
 
     // gene not valid:
     SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
-    sf6.setValue("ID", "transcript:" + accId);
+    sf6.setValue("id", accId);
     seq.addSequenceFeature(sf6);
 
     // exon not valid:
     SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
-    sf7.setValue("ID", "transcript:" + accId);
+    sf7.setValue("id", accId);
     seq.addSequenceFeature(sf7);
 
     List<SequenceFeature> sfs = new EnsemblGenome()