Merge branch 'develop' into bug/JAL-2225mapMultipleChains

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index c8d900d..128481c 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -68,8 +68,6 @@ import java.awt.dnd.DropTargetEvent;
 import java.awt.dnd.DropTargetListener;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
@@ -269,12 +267,14 @@ public class Desktop extends jalview.jbgui.GDesktop
     public void endDraggingFrame(JComponent f)
     {
       delegate.endDraggingFrame(f);
+      desktop.repaint();
     }
 
     @Override
     public void endResizingFrame(JComponent f)
     {
       delegate.endResizingFrame(f);
+      desktop.repaint();
     }
 
     @Override
@@ -344,10 +344,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
             false);
     desktop = new MyDesktopPane(selmemusage);
-    if (Platform.isAMac())
-    {
-      desktop.setDoubleBuffered(false);
-    }
     showMemusage.setSelected(selmemusage);
     desktop.setBackground(Color.white);
     getContentPane().setLayout(new BorderLayout());
@@ -361,7 +357,12 @@ public class Desktop extends jalview.jbgui.GDesktop
     // This line prevents Windows Look&Feel resizing all new windows to maximum
     // if previous window was maximised
     desktop.setDesktopManager(
-            new MyDesktopManager(new DefaultDesktopManager()));
+            new MyDesktopManager(
+                    (Platform.isWindows() ? new DefaultDesktopManager()
+                            : Platform.isAMac()
+                                    ? new AquaInternalFrameManager(
+                                            desktop.getDesktopManager())
+                                    : desktop.getDesktopManager())));
 
     Rectangle dims = getLastKnownDimensions("");
     if (dims != null)
@@ -431,24 +432,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     });
     desktop.addMouseListener(ma);
 
-    this.addFocusListener(new FocusListener()
-    {
-
-      @Override
-      public void focusLost(FocusEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void focusGained(FocusEvent e)
-      {
-        Cache.log.debug("Relaying windows after focus gain");
-        // make sure that we sort windows properly after we gain focus
-        instance.relayerWindows();
-      }
-    });
     this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
     // Spawn a thread that shows the splashscreen
     SwingUtilities.invokeLater(new Runnable()
@@ -866,13 +849,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     frame.setResizable(resizable);
     frame.setMaximizable(resizable);
     frame.setIconifiable(resizable);
-    if (Platform.isAMac())
-    {
-      frame.setIconifiable(false);
-      frame.setFrameIcon(null);
-      // frame.setDesktopIcon(null);
-      frame.setDoubleBuffered(false);
-    }
+
     if (frame.getX() < 1 && frame.getY() < 1)
     {
       frame.setLocation(xOffset * openFrameCount,
@@ -892,6 +869,10 @@ public class Desktop extends jalview.jbgui.GDesktop
         JInternalFrame itf = desktop.getSelectedFrame();
         if (itf != null)
         {
+          if (itf instanceof AlignFrame)
+          {
+            Jalview.setCurrentAlignFrame((AlignFrame) itf);
+          }
           itf.requestFocus();
         }
       }
@@ -918,15 +899,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
         windowMenu.remove(menuItem);
-        JInternalFrame itf = desktop.getSelectedFrame();
-        if (itf != null)
-        {
-          itf.requestFocus();
-          if (itf instanceof AlignFrame)
-          {
-            Jalview.setCurrentAlignFrame((AlignFrame) itf);
-          }
-        }
+
         System.gc();
       };
     });
@@ -1011,8 +984,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     // Java's Transferable for native dnd
     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
-    List<String> files = new ArrayList<String>();
-    List<DataSourceType> protocols = new ArrayList<DataSourceType>();
+    List<String> files = new ArrayList<>();
+    List<DataSourceType> protocols = new ArrayList<>();
 
     try
     {
@@ -1720,7 +1693,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   JPanel progressPanel;
 
-  ArrayList<JPanel> fileLoadingPanels = new ArrayList<JPanel>();
+  ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
 
   public void startLoading(final String fileName)
   {
@@ -1812,7 +1785,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       // TODO: verify that frames are recoverable when in headless mode
       return null;
     }
-    List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>();
+    List<AlignmentPanel> aps = new ArrayList<>();
     AlignFrame[] frames = getAlignFrames();
     if (frames == null)
     {
@@ -1847,7 +1820,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    */
   public static AlignmentViewport[] getViewports(String sequenceSetId)
   {
-    List<AlignmentViewport> viewp = new ArrayList<AlignmentViewport>();
+    List<AlignmentViewport> viewp = new ArrayList<>();
     if (desktop != null)
     {
       AlignFrame[] frames = Desktop.getAlignFrames();
@@ -2360,12 +2333,12 @@ public class Desktop extends jalview.jbgui.GDesktop
           // SEQUENCE_ID which is not the default EMBL_EBI link
           ListIterator<String> li = links.listIterator();
           boolean check = false;
-          List<JLabel> urls = new ArrayList<JLabel>();
+          List<JLabel> urls = new ArrayList<>();
           while (li.hasNext())
           {
             String link = li.next();
             if (link.contains(SEQUENCE_ID)
-                    && !link.equals(UrlConstants.DEFAULT_STRING))
+                    && !UrlConstants.isDefaultString(link))
             {
               check = true;
               int barPos = link.indexOf("|");
@@ -2454,6 +2427,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         Thread worker = new Thread(this);
         worker.start();
       }
+      repaint();
     }
 
     public boolean isShowMemoryUsage()
@@ -2517,14 +2491,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
   }
 
-  /**
-   * fixes stacking order after a modal dialog to ensure windows that should be
-   * on top actually are
-   */
-  public void relayerWindows()
-  {
-
-  }
 
   /**
    * Accessor method to quickly get all the AlignmentFrames loaded.
@@ -2545,7 +2511,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
       return null;
     }
-    List<AlignFrame> avp = new ArrayList<AlignFrame>();
+    List<AlignFrame> avp = new ArrayList<>();
     // REVERSE ORDER
     for (int i = frames.length - 1; i > -1; i--)
     {
@@ -2590,7 +2556,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
       return null;
     }
-    List<GStructureViewer> avp = new ArrayList<GStructureViewer>();
+    List<GStructureViewer> avp = new ArrayList<>();
     // REVERSE ORDER
     for (int i = frames.length - 1; i > -1; i--)
     {
@@ -2733,8 +2699,8 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     if (progressBars == null)
     {
-      progressBars = new Hashtable<Long, JPanel>();
-      progressBarHandlers = new Hashtable<Long, IProgressIndicatorHandler>();
+      progressBars = new Hashtable<>();
+      progressBarHandlers = new Hashtable<>();
     }
 
     if (progressBars.get(new Long(id)) != null)