X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGenomeTest.java;h=0652dd6a872bfa499ad47cadc34bf397aab500a7;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;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..0652dd6 100644
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@ -75,29 +75,29 @@ public class EnsemblGenomeTest
     String transcriptId = "ABC123";
 
     // transcript at (start+10000) length 501
-    SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
-            20500, 0f, null);
-    sf.setValue("ID", "transcript:" + transcriptId);
+    SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
+            0f, null);
+    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);
 
     // Ensembl treats NMD_transcript_variant as if transcript
     // 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 = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000, 0f,
+            null);
+    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
@@ -133,16 +133,16 @@ public class EnsemblGenomeTest
     String accId = "ABC123";
     EnsemblGenome testee = new EnsemblGenome();
 
-    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("mature_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 kept
@@ -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()