Paste menu item dispalyed on right click. Memory settings visible in this version

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 26b28e7..fd741be 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -39,7 +39,13 @@ public class Desktop
 {
   /** DOCUMENT ME!! */
   public static Desktop instance;
-  public static JDesktopPane desktop;
+
+  //Need to decide if the Memory Usage is to be included in
+  //Next release or not.
+  public static MyDesktopPane desktop;
+ //  public static JDesktopPane desktop;
+
+
   static int openFrameCount = 0;
   static final int xOffset = 30;
   static final int yOffset = 30;
@@ -59,6 +65,7 @@ public class Desktop
     doVamsasClientCheck();
     Image image = null;
 
+
     try
     {
       java.net.URL url = getClass().getResource("/images/logo.gif");
@@ -79,7 +86,9 @@ public class Desktop
 
     setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-    desktop = new JDesktopPane();
+
+    desktop = new MyDesktopPane(true);
+ //   desktop = new JDesktopPane();
     desktop.setBackground(Color.white);
     getContentPane().setLayout(new BorderLayout());
     getContentPane().add(desktop, BorderLayout.CENTER);
@@ -114,6 +123,18 @@ public class Desktop
       }
     });
 
+    this.addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent evt)
+          {
+            if(SwingUtilities.isRightMouseButton(evt))
+            {
+              showPasteMenu(evt.getX(), evt.getY());
+            }
+          }
+        });
+
+
     this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 
     /////////Add a splashscreen on startup
@@ -138,7 +159,48 @@ public class Desktop
       VamsasMenu.setVisible(true);
       vamsasLoad.setVisible(true);
     }
+  }
+
+  void showPasteMenu(int x, int y)
+  {
+    JPopupMenu popup = new JPopupMenu();
+    JMenuItem item = new JMenuItem("Paste To New Window");
+    item.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent evt)
+      {
+        paste();
+      }
+    });
 
+    popup.add(item);
+    popup.show(this, x, y);
+  }
+
+  public void paste()
+  {
+    try
+    {
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
+
+      if (contents != null)
+      {
+        String file = (String) contents
+            .getTransferData(DataFlavor.stringFlavor);
+
+        String format = new IdentifyFile().Identify(file,
+                                                    FormatAdapter.PASTE);
+
+        new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
+
+      }
+    }
+    catch (Exception ex)
+    {
+      System.out.println("Unable to paste alignment from system clipboard:\n"
+                         + ex);
+    }
   }
 
   /**
@@ -223,6 +285,7 @@ public class Desktop
         {
           itf.requestFocus();
         }
+        System.gc();
       }
       ;
     });
@@ -584,6 +647,8 @@ public class Desktop
       catch (java.beans.PropertyVetoException ex)
       {}
     }
+    System.out.println("ALL CLOSED");
+
   }
 
   public void raiseRelated_actionPerformed(ActionEvent e)
@@ -951,6 +1016,12 @@ public class Desktop
 
   }
 
+  public JInternalFrame[] getAllFrames()
+  {
+    return desktop.getAllFrames();
+  }
+
+
   /**
    * Checks the given url to see if it gives a response indicating that
    * the user should be informed of a new questionnaire.
@@ -962,4 +1033,75 @@ public class Desktop
     javax.swing.SwingUtilities.invokeLater(jvq);
   }
 
-}
+  class  MyDesktopPane extends JDesktopPane implements Runnable
+  {
+    boolean showMemoryUsage = false;
+    Runtime runtime;
+    java.text.NumberFormat df;
+
+    float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
+
+    public MyDesktopPane(boolean showMemoryUsage)
+    {
+      showMemoryUsage(showMemoryUsage);
+    }
+
+    public void showMemoryUsage(boolean showMemoryUsage)
+    {
+      this.showMemoryUsage = showMemoryUsage;
+      if (showMemoryUsage)
+      {
+        Thread worker = new Thread(this);
+        worker.start();
+      }
+    }
+
+    public void run()
+    {
+      df = java.text.NumberFormat.getNumberInstance();
+      df.setMaximumFractionDigits(2);
+      runtime = Runtime.getRuntime();
+
+      while (showMemoryUsage)
+      {
+        try
+        {
+          Thread.sleep(3000);
+          maxMemory = runtime.maxMemory() / 1048576f;
+          allocatedMemory = runtime.totalMemory() / 1048576f;
+          freeMemory = runtime.freeMemory() / 1048576f;
+          totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
+
+          percentUsage = (totalFreeMemory / maxMemory) * 100;
+
+        //  if (percentUsage < 20)
+          {
+            //   border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, Color.red);
+            //    instance.set.setBorder(border1);
+          }
+          repaint();
+
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+    }
+
+    public void paintComponent(Graphics g)
+    {
+      if(showMemoryUsage)
+      {
+        if (percentUsage < 20)
+          g.setColor(Color.red);
+
+        g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
+                     + "MB; Max Memory: " + df.format(maxMemory)
+                     + "MB; " + df.format(percentUsage) + "%", 10,
+                     getHeight() - g.getFontMetrics().getHeight());
+      }
+    }
+  }
+
+  }