JAL-3143 unit tests updated for code changes!

[jalview.git] / test / jalview / ext / ensembl / EnsemblCdnaTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index c9d8deb..9e9d9a4 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -79,19 +79,19 @@ 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 +134,19 @@ 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 +226,14 @@ 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()));
 
     // feature with wrong parent is not retained
-    sf.setValue("Parent", "transcript:XYZ");
+    sf.setValue("Parent", "XYZ");
     assertFalse(testee.retainFeature(sf, accId));
   }
 
@@ -253,30 +253,30 @@ 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()