X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGenomeTest.java;h=8687da94338b18b03bac698e28b0466ccdfe4a48;hb=d8720fc191cba996c440171ef8e07462ef9f7035;hp=991cd965c26a559ab364258df82f28ff1237597f;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index 991cd96..8687da9 100644
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.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;
@@ -39,6 +40,14 @@ import org.testng.annotations.Test;
 
 public class EnsemblGenomeTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
@@ -127,14 +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
@@ -170,19 +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));
   }