JAL-4150 test and quick patch copying code from AlignFrame.paste() to Desktop.paste...

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 7b4af59..1521d0a 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -105,6 +105,10 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 import jalview.gui.ImageExporter.ImageWriterI;
 import jalview.gui.QuitHandler.QResponse;
 import jalview.io.BackupFiles;
@@ -799,6 +803,41 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public void paste()
   {
+    // quick patch for JAL-4150 - needs some more work and test coverage
+    // TODO - unify below and AlignFrame.paste()
+    // TODO - write tests and fix AlignFrame.paste() which doesn't track if
+    // clipboard has come from a different alignment window than the one where
+    // paste has been called! JAL-4151
+    
+    if (Desktop.jalviewClipboard != null)
+    {
+      // The clipboard was filled from within Jalview, we must use the
+      // sequences
+      // And dataset from the copied alignment
+      SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+      // be doubly sure that we create *new* sequence objects.
+      SequenceI[] sequences = new SequenceI[newseq.length];
+      for (int i = 0; i < newseq.length; i++)
+      {
+        sequences[i] = new Sequence(newseq[i]);
+      }
+      Alignment alignment = new Alignment(sequences);
+      // dataset is inherited
+      alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+      AlignFrame af = new AlignFrame(alignment, AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
+      String newtitle = new String("Copied sequences");
+
+      if (Desktop.jalviewClipboard[2] != null)
+      {
+        HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+        af.viewport.setHiddenColumns(hc);
+      }
+
+      Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT);
+
+    } else {
     try
     {
       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -820,6 +859,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       System.out.println(
               "Unable to paste alignment from system clipboard:\n" + ex);
     }
+    }
   }
 
   /**

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 06be982..92db223 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1591,4 +1591,14 @@ public class AlignmentTest
     // ?
 
   }
+  @Test(groups = {"Functional"})
+  public void testEquals()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+    a.setDataset(null);
+    assertEquals(a.getDataset(),a.getDataset());
+  }
 }

diff --git a/test/jalview/gui/DesktopTests.java b/test/jalview/gui/DesktopTests.java
new file mode 100644 (file)
index 0000000..897f28e
--- /dev/null
+++ b/test/jalview/gui/DesktopTests.java
@@ -0,0 +1,153 @@
+/*
+ * 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 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 javax.swing.SwingUtilities;
+
+import org.junit.Assert;
+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;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.project.Jalview2xmlTests;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.util.MessageManager;
+
+public class DesktopTests
+{
+
+  @BeforeClass(alwaysRun = true)
+  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
+   */
+  public AlignFrame loadTestFile()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.TRUE.toString());
+    AlignFrame 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());
+    return af;
+  }
+
+  public static void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testInternalCopyPaste()
+  {
+    AlignFrame internalSource = loadTestFile();
+
+    try
+    {
+      SwingUtilities.invokeAndWait(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+          internalSource.selectAllSequenceMenuItem_actionPerformed(null);
+          internalSource.copy_actionPerformed();
+          Desktop.instance.paste();
+        }
+      });
+    } catch (Exception x)
+    {
+      Assert.fail("Unexpected exception " + x);
+    }
+    AlignFrame[] alfs = Desktop.getAlignFrames();
+    Assert.assertEquals("Expect just 2 alignment frames", 2, alfs.length);
+    // internal paste should yield a new alignment window with shared dataset
+    AlignmentI dataset = internalSource.getViewport().getAlignment()
+            .getDataset();
+    Assert.assertNotNull(dataset);
+
+    for (AlignFrame alf : alfs)
+    {
+      Assert.assertTrue(
+              "Internal paste should yield alignment with same dataset.",
+              dataset == alf.getViewport().getAlignment().getDataset());
+    }
+
+  }
+}