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

[jalview.git] / test / jalview / structure / StructureSelectionManagerTest.java

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 2556ab1..a59fbde 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -27,18 +27,28 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.util.MapList;
 
 import java.util.ArrayList;
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class StructureSelectionManagerTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   private StructureSelectionManager ssm;
 
   @BeforeMethod(alwaysRun = true)
@@ -124,7 +134,7 @@ public class StructureSelectionManagerTest
     sm.setProcessSecondaryStructure(true);
     sm.setAddTempFacAnnot(true);
     StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
-            new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
+            new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
     assertTrue(pmap != null);
 
     assertEquals(3, pmap.getSeqs().size());
@@ -135,7 +145,7 @@ public class StructureSelectionManagerTest
     /*
      * Verify a RESNUM sequence feature in the PDBfile sequence
      */
-    SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
+    SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0);
     assertEquals("RESNUM", sf.getType());
     assertEquals("1gaq", sf.getFeatureGroup());
     assertEquals("GLU:  19  1gaqA", sf.getDescription());
@@ -145,7 +155,7 @@ public class StructureSelectionManagerTest
      * sequence
      */
     StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
-    sf = map.sequence.getSequenceFeatures()[0];
+    sf = map.sequence.getSequenceFeatures().get(0);
     assertEquals("RESNUM", sf.getType());
     assertEquals("1gaq", sf.getFeatureGroup());
     assertEquals("ALA:   1  1gaqB", sf.getDescription());