Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index c644e83..8482c90 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdsTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdsTest.java
@@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyLite;
 import jalview.util.MapList;
@@ -40,6 +41,14 @@ import org.testng.annotations.Test;
 
 public class EnsemblCdsTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
@@ -121,11 +130,12 @@ public class EnsemblCdsTest
             null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("CDS_predicted");
+    sf = new SequenceFeature("CDS_predicted", "", 20000, 20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
     // other feature with no parent is retained
-    sf.setType("sequence_variant");
+    sf = new SequenceFeature("CDS_psequence_variantredicted", "", 20000,
+            20500, 0f, null);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with desired parent is retained
@@ -160,15 +170,18 @@ public class EnsemblCdsTest
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // cds sub-type with right parent is valid
-    sf.setType("CDS_predicted");
+    sf = new SequenceFeature("CDS_predicted", "", 1, 2, 0f, null);
+    sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // transcript not valid:
-    sf.setType("transcript");
+    sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+    sf.setValue("Parent", "transcript:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
 
     // exon not valid:
-    sf.setType("exon");
+    sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf.setValue("Parent", "transcript:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
   }