X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdnaTest.java;h=6611e057bc5064938723fdee5678bb97cd0e436b;hb=086ba94444cd5748b76a4236149af998022ed240;hp=95d371a65ad749f2f9bf58b4afc3554ea012b611;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index 95d371a..6611e05 100644
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -28,6 +28,7 @@ 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;
@@ -41,6 +42,14 @@ import org.testng.annotations.Test;
 
 public class EnsemblCdnaTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
@@ -203,14 +212,16 @@ public class EnsemblCdnaTest
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("aberrant_processed_transcript");
+    sf = new SequenceFeature("aberrant_processed_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 retained
-    sf.setType("sequence_variant");
+    sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with desired parent is retained
@@ -245,15 +256,18 @@ public class EnsemblCdnaTest
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // exon sub-type with right parent is valid
-    sf.setType("coding_exon");
+    sf = new SequenceFeature("coding_exon", "", 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));
 
     // CDS not valid:
-    sf.setType("CDS");
+    sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
+    sf.setValue("Parent", "transcript:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
   }