X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=76d02e76837d57956907a70ea55eb6a09dbf193b;hb=69933be26034fbebe01d573a9290f0baa2b468b4;hp=fd741be605b4655f57a54426354a21e73be82c8d;hpb=c2404cecc845332c659d1a42bda51576235ba92b;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index fd741be..76d02e7 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -23,6 +23,7 @@ import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.dnd.*;
 import java.awt.event.*;
+import java.lang.reflect.Constructor;
 import java.util.*;
 
 import javax.swing.*;
@@ -42,8 +43,8 @@ public class 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;
+ // public static MyDesktopPane desktop;
+   public static JDesktopPane desktop;
 
 
   static int openFrameCount = 0;
@@ -63,32 +64,13 @@ public class Desktop
   {
     instance = this;
     doVamsasClientCheck();
-    Image image = null;
+    doGroovyCheck();
 
 
-    try
-    {
-      java.net.URL url = getClass().getResource("/images/logo.gif");
-
-      if (url != null)
-      {
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-        mt.waitForID(0);
-        setIconImage(image);
-      }
-    }
-    catch (Exception ex)
-    {
-    }
-
     setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 
-    desktop = new MyDesktopPane(true);
- //   desktop = new JDesktopPane();
+    desktop = new JDesktopPane();
     desktop.setBackground(Color.white);
     getContentPane().setLayout(new BorderLayout());
     getContentPane().add(desktop, BorderLayout.CENTER);
@@ -139,15 +121,8 @@ public class Desktop
 
     /////////Add a splashscreen on startup
     /////////Add a splashscreen on startup
-    JInternalFrame frame = new JInternalFrame();
-
-    SplashScreen splash = new SplashScreen(frame, image);
-    frame.setContentPane(splash);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    frame.setLocation( (int) ( (getWidth() - 750) / 2),
-                      (int) ( (getHeight() - 160) / 2));
+    new SplashScreen();
 
-    addInternalFrame(frame, "", 750, 160, false);
 
     discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
   }
@@ -807,28 +782,6 @@ public class Desktop
     }
   }
 
-  /*  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)
   {
     new SequenceFetcher(null);
@@ -960,12 +913,14 @@ public class Desktop
 
   }
 
-  jalview.gui.VamsasClient v_client = null;
+  jalview.gui.VamsasApplication v_client = null;
   public void vamsasLoad_actionPerformed(ActionEvent e)
   {
     if (v_client == null)
     {
       // Start a session.
+      // we just start a default session for moment.
+      /*
       JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
           getProperty("LAST_DIRECTORY"));
 
@@ -977,13 +932,14 @@ public class Desktop
 
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
-        v_client = new jalview.gui.VamsasClient(this,
+        v_client = new jalview.gui.VamsasApplication(this,
                                                 chooser.getSelectedFile());
-        this.vamsasLoad.setText("Session Update");
-        this.vamsasStop.setVisible(true);
-        v_client.initial_update();
-        v_client.startWatcher();
-      }
+                                                *
+                                                */
+      v_client = new VamsasApplication(this);
+      vamsasLoad.setText("Session Update");
+      vamsasStop.setVisible(true);
+      v_client.initial_update();
     }
     else
     {
@@ -1033,7 +989,8 @@ public class Desktop
     javax.swing.SwingUtilities.invokeLater(jvq);
   }
 
-  class  MyDesktopPane extends JDesktopPane implements Runnable
+  /*DISABLED
+   class  MyDesktopPane extends JDesktopPane implements Runnable
   {
     boolean showMemoryUsage = false;
     Runtime runtime;
@@ -1102,6 +1059,88 @@ public class Desktop
                      getHeight() - g.getFontMetrics().getHeight());
       }
     }
+  }*/
+  protected JMenuItem groovyShell;
+  public void doGroovyCheck() {
+    if (jalview.bin.Cache.groovyJarsPresent())
+    {
+      groovyShell = new JMenuItem();
+      groovyShell.setText("Groovy Shell...");
+      groovyShell.addActionListener(new ActionListener()
+      {
+          public void actionPerformed(ActionEvent e) {
+              groovyShell_actionPerformed(e);
+          }
+      });
+      toolsMenu.add(groovyShell);
+      groovyShell.setVisible(true);
+    }
   }
+  /**
+   * Accessor method to quickly get all the AlignmentFrames
+   * loaded.
+   */
+  protected AlignFrame[] getAlignframes() {
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
+    if (frames == null)
+    {
+      return null;
+      }
+      Vector avp=new Vector();
+      try
+      {
+          //REVERSE ORDER
+          for (int i = frames.length - 1; i > -1; i--)
+          {
+              if (frames[i] instanceof AlignFrame)
+              {
+                  AlignFrame af = (AlignFrame) frames[i];
+                  avp.addElement(af);
+              }
+          }
+      }
+      catch (Exception ex)
+      {
+          ex.printStackTrace();
+      }
+      if (avp.size()==0)
+      {
+          return null;
+      }
+      AlignFrame afs[] = new AlignFrame[avp.size()];
+      for (int i=0,j=avp.size(); i<j; i++) {
+          afs[i] = (AlignFrame) avp.elementAt(i);
+      }
+      avp.clear();
+      return afs;
+  }
+
+  /**
+    * Add Groovy Support to Jalview
+    */
+  public void groovyShell_actionPerformed(ActionEvent e) {
+    // use reflection to avoid creating compilation dependency.
+    if (!jalview.bin.Cache.groovyJarsPresent())
+    {
+      throw new Error("Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+    }
+    try {
+    Class gcClass = Desktop.class.getClassLoader().loadClass("groovy.ui.Console");
+    Constructor gccons = gcClass.getConstructor(null);
+    java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class} );
+    java.lang.reflect.Method run = gcClass.getMethod("run", null);
+    Object gc = gccons.newInstance(null);
+    setvar.invoke(gc, new Object[] { "Jalview", this});
+    run.invoke(gc, null);
+    }
+    catch (Exception ex)
+    {
+      jalview.bin.Cache.log.error("Groovy Shell Creation failed.",ex);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+              "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.", "Jalview Groovy Support Failed",
+              JOptionPane.ERROR_MESSAGE);
+    }
   }
+}