X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=d362d35c1d5a2ee1bcb58f3f6db121fcaa2ae28e;hb=bf5bc203579d7a291844f3b34d5e8431984ee8e2;hp=bdda48d95c6c6ca6a3483b1e5ab6168a66d1d12f;hpb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;p=jalview.git

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index bdda48d..d362d35 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -20,12 +20,21 @@
  */
 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;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.util.Iterator;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
@@ -48,20 +57,55 @@ import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.util.MessageManager;
 
-import java.awt.Color;
-import java.util.Iterator;
-
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 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
+     */
+    do
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+      }
+    } while (af.getViewport().getCalcManager().isWorking());
+  }
+
+  public static void setUpJvOptionPane()
   {
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
@@ -118,7 +162,8 @@ public class AlignFrameTest
      * seq1 feature in columns 1-5 is hidden
      * seq2 feature in columns 6-10 is shown
      */
-    FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+    FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+            0f, 10f);
     fc.setAboveThreshold(true);
     fc.setThreshold(5f);
     alignFrame.getFeatureRenderer().setColour("Metal", fc);
@@ -149,52 +194,6 @@ 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>
@@ -259,8 +258,11 @@ 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);
@@ -353,7 +355,7 @@ public class AlignFrameTest
 
     /*
      * inspect the colour of 
-     * FER_CAPAN.9(I), column 14 (14 base 0)
+     * FER_CAPAN.9(I), column 15 (14 base 0)
      * FER_CAPAN.10(SER), column 16 (15 base 0)
      */
     SequenceI ferCapan = al.findName("FER_CAPAN");
@@ -372,10 +374,14 @@ public class AlignFrameTest
     SliderPanel sp = SliderPanel.getSliderPanel();
     assertTrue(sp.isForConservation());
     assertEquals(sp.getValue(), 30); // initial slider setting
+    c = rs.findColour('I', 14, ferCapan);
+    Color i_faded = new Color(255, 255, 255);
+    assertEquals(c, i_faded);
     sp.valueChanged(10);
     assertSame(rs, av.getResidueShading());
+    assertEquals(rs.getConservationInc(), 10);
     c = rs.findColour('I', 14, ferCapan);
-    Color i_faded = new Color(196, 186, 196);
+    i_faded = new Color(196, 186, 196);
     assertEquals(c, i_faded);
     c = rs.findColour('S', 15, ferCapan);
     Color s_faded = new Color(144, 225, 144);
@@ -538,7 +544,8 @@ 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);
@@ -599,4 +606,26 @@ 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");
+  }
 }