Merge remote-tracking branch 'origin/develop' into bug/JAL-2665-2.10.3

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

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index 654797c..8687da9 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@ -136,14 +136,16 @@ public class EnsemblGenomeTest
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("mature_transcript");
+    sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
+            null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("NMD_transcript_variant");
+    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
+            0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
     // other feature with no parent is kept
-    sf.setType("anything");
+    sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with correct parent is kept
@@ -179,19 +181,23 @@ public class EnsemblGenomeTest
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // transcript sub-type with right ID is valid
-    sf.setType("ncRNA");
+    sf = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
+    sf.setValue("ID", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // Ensembl treats NMD_transcript_variant as if a transcript
-    sf.setType("NMD_transcript_variant");
+    sf = new SequenceFeature("NMD_transcript_variant", "", 1, 2, 0f, null);
+    sf.setValue("ID", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // gene not valid:
-    sf.setType("gene");
+    sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
+    sf.setValue("ID", "transcript:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
 
     // exon not valid:
-    sf.setType("exon");
+    sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf.setValue("ID", "transcript:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
   }