X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=d2284f12593ae4b63b14ee0c15a26c6bcde552e6;hb=f2511dd2e8e37b8e999e924f8a53d150377b21b5;hp=afb61d09c444e5cacc178cfebd54512b8cbe5e84;hpb=e42eed3a0089a8a064560df4cf17a5021fd1e16a;p=jalview.git

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index afb61d0..d2284f1 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import static org.junit.Assert.assertNotEquals;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotSame;
@@ -38,7 +39,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.Jalview2xmlTests;
+import jalview.project.Jalview2xmlTests;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.FeatureColour;
@@ -61,7 +62,53 @@ public class AlignFrameTest
   AlignFrame af;
 
   @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
+  public static void setUpBeforeClass() throws Exception
+  {
+    setUpJvOptionPane();
+    /*
+     * use read-only test properties file
+     */
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Jalview.main(new String[] { "-nonews" });
+  }
+
+  @AfterMethod(alwaysRun = true)
+  public void tearDown()
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  /**
+   * configure (read-only) properties for test to ensure Consensus is computed for
+   * colour Above PID testing
+   */
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.TRUE.toString());
+    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+            DataSourceType.FILE);
+
+    /*
+     * wait for Consensus thread to complete
+     */
+    synchronized (this)
+    {
+      while (af.getViewport().getConsensusSeq() == null)
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      }
+    }
+  }
+
+  public static void setUpJvOptionPane()
   {
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
@@ -150,52 +197,6 @@ public class AlignFrameTest
     assertEquals(next[1], 8);
   }
 
-  @BeforeClass(alwaysRun = true)
-  public static void setUpBeforeClass() throws Exception
-  {
-    /*
-     * use read-only test properties file
-     */
-    Cache.loadProperties("test/jalview/io/testProps.jvprops");
-    Jalview.main(new String[] { "-nonews" });
-  }
-
-  @AfterMethod(alwaysRun = true)
-  public void tearDown()
-  {
-    Desktop.instance.closeAll_actionPerformed(null);
-  }
-
-  /**
-   * configure (read-only) properties for test to ensure Consensus is computed
-   * for colour Above PID testing
-   */
-  @BeforeMethod(alwaysRun = true)
-  public void setUp()
-  {
-    Cache.loadProperties("test/jalview/io/testProps.jvprops");
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
-            Boolean.TRUE.toString());
-    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
-            DataSourceType.FILE);
-
-    /*
-     * wait for Consensus thread to complete
-     */
-    synchronized (this)
-    {
-      while (af.getViewport().getConsensusSeq() == null)
-      {
-        try
-        {
-          wait(50);
-        } catch (InterruptedException e)
-        {
-        }
-      }
-    }
-  }
-
   /**
    * Test that changing background (alignment) colour scheme
    * <ul>
@@ -260,8 +261,11 @@ public class AlignFrameTest
 
     /*
      * apply 30% Conservation to group
+     * (notice menu action applies to selection group even if mouse click
+     * is at a sequence not in the group)
      */
-    PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+    PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
+            null);
     popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
             .toString());
     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
@@ -539,7 +543,8 @@ public class AlignFrameTest
     sg.setStartRes(15);
     sg.setEndRes(25);
     av.setSelectionGroup(sg);
-    PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+    PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0),
+            null);
     popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
             .toString());
     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
@@ -600,4 +605,26 @@ public class AlignFrameTest
     sp.valueChanged(22);
     assertEquals(av2.getResidueShading().getConservationInc(), 22);
   }
+
+  /**
+   * Verify that making a New View preserves the dataset reference for the
+   * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
+   * save alignments with multiple views, and codon mappings will not be shared
+   * across all panels in a split frame.
+   * 
+   * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
+   */
+  @Test(groups = "Functional")
+  public void testNewView_dsRefPreserved()
+  {
+    AlignViewport av = af.getViewport();
+    AlignmentI al = av.getAlignment();
+    AlignmentI original_ds = al.getDataset();
+    af.newView_actionPerformed(null);
+    assertNotEquals("New view didn't select the a new panel", av,
+            af.getViewport());
+    org.testng.Assert.assertEquals(original_ds,
+            af.getViewport().getAlignment().getDataset(),
+            "Dataset was not preserved in new view");
+  }
 }