JAL-2446 merged to spike branch

[jalview.git] / test / MCview / PDBChainTest.java

diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index 907c500..defcdbc 100644 (file)
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package MCview;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -10,17 +30,29 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.TaylorColourScheme;
+import jalview.structure.StructureImportSettings;
 
 import java.awt.Color;
+import java.util.List;
 import java.util.Vector;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class PDBChainTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   PDBChain c;
 
   final Atom a1 = new Atom(1f, 2f, 3f);
@@ -35,6 +67,7 @@ public class PDBChainTest
   public void setUp()
   {
     System.out.println("setup");
+    StructureImportSettings.setShowSeqFeatures(true);
     c = new PDBChain("1GAQ", "A");
   }
 
@@ -226,19 +259,19 @@ public class PDBChainTest
     /*
      * check sequence features
      */
-    SequenceFeature[] sfs = c.sequence.getSequenceFeatures();
-    assertEquals(3, sfs.length);
-    assertEquals("RESNUM", sfs[0].type);
-    assertEquals("MET:4 1gaqA", sfs[0].description);
-    assertEquals(4, sfs[0].begin);
-    assertEquals(4, sfs[0].end);
-    assertEquals("RESNUM", sfs[0].type);
-    assertEquals("LYS:5 1gaqA", sfs[1].description);
-    assertEquals(5, sfs[1].begin);
-    assertEquals(5, sfs[1].end);
-    assertEquals("LEU:6 1gaqA", sfs[2].description);
-    assertEquals(6, sfs[2].begin);
-    assertEquals(6, sfs[2].end);
+    List<SequenceFeature> sfs = c.sequence.getSequenceFeatures();
+    assertEquals(3, sfs.size());
+    assertEquals("RESNUM", sfs.get(0).type);
+    assertEquals("MET:4 1gaqA", sfs.get(0).description);
+    assertEquals(4, sfs.get(0).begin);
+    assertEquals(4, sfs.get(0).end);
+    assertEquals("RESNUM", sfs.get(0).type);
+    assertEquals("LYS:5 1gaqA", sfs.get(1).description);
+    assertEquals(5, sfs.get(1).begin);
+    assertEquals(5, sfs.get(1).end);
+    assertEquals("LEU:6 1gaqA", sfs.get(2).description);
+    assertEquals(6, sfs.get(2).begin);
+    assertEquals(6, sfs.get(2).end);
   }
 
   private Atom makeAtom(int resnum, String name, String resname)