(JAL-965) new api methods to allow features to be loaded without automatically enabli...

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 3796b08..2a72e44 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -18,28 +18,68 @@
 package jalview.gui;
 
 import jalview.bin.Cache;
-import jalview.io.*;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
 import jalview.ws.params.ParamManager;
 
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.dnd.*;
-import java.awt.event.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+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.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyVetoException;
 import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileOutputStream;
-import java.io.InputStream;
 import java.lang.reflect.Constructor;
 import java.net.URL;
-import java.net.URLConnection;
-import java.nio.channels.ReadableByteChannel;
-import java.util.*;
-
-import javax.swing.*;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.DefaultDesktopManager;
+import javax.swing.DesktopManager;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JDesktopPane;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JProgressBar;
+import javax.swing.SwingUtilities;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
@@ -57,6 +97,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
   /**
+   * news reader - null if it was never started.
+   */
+  private BlogReader jvnews=null;
+
+  /**
    * @param listener
    * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
    */
@@ -267,6 +312,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     showConsole(showjconsole);
 
+    showNews.setVisible(false);
+    final Desktop me = this;
+    // Thread off the news reader, in case there are connection problems.
+    new Thread( new Runnable() {
+      @Override
+      public void run()
+      {
+        Cache.log.debug("Starting news thread.");
+
+        jvnews = new BlogReader(me);
+        showNews.setVisible(true);
+        Cache.log.debug("Completed news thread.");
+      }
+    }).start();
+    
     this.addWindowListener(new WindowAdapter()
     {
       public void windowClosing(WindowEvent evt)
@@ -285,7 +345,24 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         }
       }
     });
-
+    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()
@@ -328,6 +405,32 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             });
   }
 
+  protected void showNews_actionPerformed(ActionEvent e)
+  {
+    showNews(showNews.isSelected());
+  }
+  void showNews(boolean visible)
+  {
+    {
+      Cache.log.debug((visible?"Showing":"Hiding")+" news.");
+      showNews.setSelected(visible);
+      if (visible && !jvnews.isVisible())
+      {
+        new Thread(new Runnable() {
+          @Override
+          public void run()
+          {
+            long instance=System.currentTimeMillis();
+            Desktop.instance.setProgressBar("Refreshing news", instance);
+            jvnews.refreshNews();
+            Desktop.instance.setProgressBar(null, instance);
+            jvnews.showNews();
+          }
+        }).start();
+      }
+    }
+  }
+
   /**
    * recover the last known dimensions for a jalview window
    * 
@@ -914,6 +1017,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
       jconsole.stopConsole();
     }
+    if (jvnews!=null)
+    {
+      storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+      
+    }
+      
     System.exit(0);
   }
 
@@ -1946,6 +2055,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   }
 
+  /**
+   * fixes stacking order after a modal dialog to ensure windows that should be on top actually are
+   */
+  public void relayerWindows()
+  {
+    
+  }
+
   protected JMenuItem groovyShell;
 
   public void doGroovyCheck()