X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdnaTest.java;h=d2559ae0df0a113fd4f71b00a0647ce11e6a50d8;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;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..d2559ae 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;
@@ -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
@@ -209,31 +211,32 @@ 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
-    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 +256,30 @@ 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()