Submissions for secondary structure prediction are now filtered to remove empty seque...

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index a705386..8323320 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -43,6 +43,10 @@ public class Desktop extends jalview.jbgui.GDesktop
     static final int xOffset = 30;
     static final int yOffset = 30;
     public static jalview.ws.Discoverer discoverer;
+
+    public static Object [] jalviewClipboard;
+
+
     /**
      * Creates a new Desktop object.
      */
@@ -50,6 +54,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
         Image image = null;
 
+
         try
         {
             java.net.URL url = getClass().getResource("/images/logo.gif");
@@ -68,7 +73,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
         }
 
-        setTitle("Jalview 2005");
+        setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
         setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
         desktop = new JDesktopPane();
         desktop.setBackground(Color.white);
@@ -115,9 +120,11 @@ public class Desktop extends jalview.jbgui.GDesktop
         frame.setLayer(JLayeredPane.PALETTE_LAYER);
         frame.setLocation((int) ((getWidth() - 750) / 2),
             (int) ((getHeight() - 160) / 2));
+
         addInternalFrame(frame, "", 750, 160, false);
 
         discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+
     }
 
     /**
@@ -128,7 +135,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      * @param w DOCUMENT ME!
      * @param h DOCUMENT ME!
      */
-    public static void addInternalFrame(final JInternalFrame frame,
+    public static synchronized void addInternalFrame(final JInternalFrame frame,
         String title, int w, int h)
     {
         addInternalFrame(frame, title, w, h, true);
@@ -143,7 +150,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      * @param h DOCUMENT ME!
      * @param resizable DOCUMENT ME!
      */
-    public static void addInternalFrame(final JInternalFrame frame,
+    public static synchronized void addInternalFrame(final JInternalFrame frame,
         String title, int w, int h, boolean resizable)
     {
 
@@ -163,17 +170,9 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
 
 
-        desktop.add(frame);
         openFrameCount++;
 
-        try
-        {
-            frame.setSelected(true);
-        }
-        catch (java.beans.PropertyVetoException e)
-        {
-        }
-
+        frame.setVisible(true);
         frame.setClosable(true);
         frame.setResizable(resizable);
         frame.setMaximizable(resizable);
@@ -182,10 +181,9 @@ public class Desktop extends jalview.jbgui.GDesktop
 
         if (frame.getX()<1 && frame.getY()<1)
        {
-         frame.setLocation(xOffset * openFrameCount, yOffset * (openFrameCount%10)+yOffset);
+         frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
        }
 
-        frame.toFront();
         final JMenuItem menuItem = new JMenuItem(title);
         frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
             {
@@ -194,6 +192,9 @@ public class Desktop extends jalview.jbgui.GDesktop
                 {
                     openFrameCount--;
                     windowMenu.remove(menuItem);
+                    JInternalFrame itf = desktop.getSelectedFrame();
+                       if (itf != null)
+                        itf.requestFocus();
                 }
                 ;
             });
@@ -209,16 +210,23 @@ public class Desktop extends jalview.jbgui.GDesktop
                     }
                     catch (java.beans.PropertyVetoException ex)
                     {
-                    }
 
-                    ;
+                    }
                 }
             });
 
-        frame.setVisible(true);
         windowMenu.add(menuItem);
+
+        desktop.add(frame);
+        frame.toFront();
+        try{
+          frame.setSelected(true);
+          frame.requestFocus();
+        }catch(java.beans.PropertyVetoException ve)
+        {}
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -366,17 +374,18 @@ public class Desktop extends jalview.jbgui.GDesktop
      */
     public void inputURLMenuItem_actionPerformed(ActionEvent e)
     {
-        String url = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        Object reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
                 "Enter url of input file", "Input alignment from URL",
-                JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")
-                                .toString();
+                JOptionPane.QUESTION_MESSAGE, null, null, "http://www.");
 
-        if (url == null)
+        if (reply == null)
         {
             return;
         }
 
-        if (url.trim().toLowerCase().endsWith(".jar"))
+        String url = reply.toString().trim();
+
+        if (url.toLowerCase().endsWith(".jar"))
         {
                jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
                Jalview2XML.LoadJalviewAlign(url);
@@ -474,8 +483,6 @@ public class Desktop extends jalview.jbgui.GDesktop
             javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
 
             javax.help.HelpBroker hb = hs.createHelpBroker();
-            hb.setLocation(new Point(200, 50));
-            hb.setSize(new Dimension(800, 700));
             hb.setCurrentID("home");
             hb.setDisplayed(true);
         }
@@ -543,5 +550,31 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
     }
 
+  /*  public void vamsasLoad_actionPerformed(ActionEvent e)
+    {
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+          getProperty("LAST_DIRECTORY"));
+
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle("Load Vamsas file");
+      chooser.setToolTipText("Import");
+
+      int value = chooser.showOpenDialog(this);
+
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
+        vs.load(
+            chooser.getSelectedFile().getAbsolutePath()
+            );
+      }
+
+    }*/
+
+
+    public void inputSequence_actionPerformed(ActionEvent e)
+    {
+      SequenceFetcher sf = new SequenceFetcher(null);
+    }
 }