X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FDesktop.java;h=331f8828c0636e3ca532c2a8394e45c685c27172;hb=ac07859006686a2c62bcf57b24742eb610bc46f0;hp=ad7cb847643442b58f66d4f030656599227101b8;hpb=2a15dbb3db1c89edd6bbc0d1ddf80863feb2203f;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ad7cb84..331f882 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -12,12 +12,17 @@ package jalview.gui;
 import jalview.gui.*;
 import jalview.io.*;
 import jalview.datamodel.*;
+import jalview.schemes.*;
 import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
+import java.awt.dnd.*;
+import javax.swing.*;
+import java.awt.datatransfer.*;
+import java.io.*;
 
 
-public class Desktop extends jalview.jbgui.GDesktop
+public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener
 {
   public static JDesktopPane desktop;
   static int openFrameCount = 0;
@@ -27,7 +32,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     Image image =null;
     try{
-      java.net.URL url = getClass().getResource("/BartonGroupBanner.gif");
+      java.net.URL url = getClass().getResource("/images/logo.gif");
       if(url!=null)
       {
         image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
@@ -41,22 +46,49 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     setTitle("Jalview 2005");
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-    setVisible(true);
     desktop = new JDesktopPane();
+ //   desktop.setBackground(Color.white);
     setContentPane(desktop);
     desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
 
+
+    // This line prevents Windows Look&Feel resizing all new windows to maximum
+    // if previous window was maximised
+    desktop.setDesktopManager( new DefaultDesktopManager() );
+
+
     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-    int width = 1200, height = 800;
-    if(screenSize.getWidth()<width)
-      width = screenSize.width;
-    if(screenSize.getHeight()<height)
-      height = screenSize.height;
+    String x = jalview.bin.Cache.getProperty("SCREEN_X");
+    String y = jalview.bin.Cache.getProperty("SCREEN_Y");
+    String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
+    String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
 
-    setBounds( (int)(screenSize.width-width)/2,
-               (int)(screenSize.height-height)/2,
-              width ,
-              height);
+    if(x!=null && y!=null && width!=null && height!=null)
+    {
+      setBounds( Integer.parseInt(x), Integer.parseInt(y),
+                 Integer.parseInt(width), Integer.parseInt(height));
+    }
+    else
+      setBounds( (int)(screenSize.width-900)/2,
+           (int)(screenSize.height-650)/2,
+          900 ,
+          650);
+
+this.addWindowListener(new WindowAdapter()
+{
+public void windowClosing(WindowEvent evt)
+{
+ jalview.bin.Cache.setProperty("SCREEN_X",
+                               getBounds().x + "");
+ jalview.bin.Cache.setProperty("SCREEN_Y",
+                               getBounds().y + "");
+ jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
+ jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
+}
+});
+setVisible(true);
+
+this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 
 
    /////////Add a splashscreen on startup
@@ -65,7 +97,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     SplashScreen splash = new SplashScreen(frame, image);
     frame.setContentPane(splash);
     desktop.add(frame);
-    frame.setVisible(true);
+
     openFrameCount++;
     try
     {
@@ -74,29 +106,37 @@ public class Desktop extends jalview.jbgui.GDesktop
     catch (java.beans.PropertyVetoException e)
     {}
     frame.setResizable(true);
-    frame.setSize(845, 200);
-    frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));
+    frame.setSize(750, 160);
+    frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));
     frame.setClosable(false);
     frame.setIconifiable(false);
     frame.setMaximizable(false);
     frame.setFrameIcon(null);
+    frame.setVisible(true);
 
   }
-
   public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
   {
+    addInternalFrame(frame, title, w, h, true);
+  }
+
+  public static void addInternalFrame(final JInternalFrame frame, String title,
+                                      int w,
+                                      int h,
+                                      boolean resizable )
+  {
    desktop.add(frame);
-   frame.setVisible(true);
    openFrameCount++;
    try {
        frame.setSelected(true);
    } catch (java.beans.PropertyVetoException e) {}
    frame.setTitle(title);
-   frame.setResizable(true);
    frame.setSize(w,h);
    frame.setClosable(true);
-   frame.setMaximizable(true);
-   frame.setIconifiable(true);
+   frame.setResizable(resizable);
+   frame.setMaximizable(resizable);
+   frame.setIconifiable(resizable);
+   frame.setFrameIcon(null);
    frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
    frame.toFront();
    final JMenuItem menuItem = new JMenuItem(title);
@@ -105,7 +145,6 @@ public class Desktop extends jalview.jbgui.GDesktop
                                      {
                                        openFrameCount--;
                                        windowMenu.remove(menuItem);
-                                       System.out.println(openFrameCount);
                                      };
                                    });
 
@@ -118,21 +157,47 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
     });
 
+   frame.setVisible(true);
    windowMenu.add(menuItem);
  }
 
+ public void dragEnter(DropTargetDragEvent evt){}
+ public void dragExit(DropTargetEvent evt){}
+ public void dragOver(DropTargetDragEvent evt){}
+ public void dropActionChanged(DropTargetDragEvent evt){}
+ public void drop(DropTargetDropEvent evt)
+{
+   Transferable t = evt.getTransferable();
+   if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+     return;
 
+   evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+   try{
+     java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+
+     for (int i = 0; i < files.size(); i++)
+     {
+       String file = files.get(i).toString();
+       String protocol = "File";
+       String format = jalview.io.IdentifyFile.Identify(file, protocol);
+       LoadFile(file, protocol, format);
+     }
+
+   }catch(Exception ex){ex.printStackTrace();}
+  }
 
  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
  {
-   JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
+   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+       new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");
+   chooser.setFileView(new JalviewFileView());
    chooser.setDialogTitle("Open local file");
    chooser.setToolTipText("Open");
    int value = chooser.showOpenDialog(this);
-   if(value == JFileChooser.APPROVE_OPTION)
+   if(value == JalviewFileChooser.APPROVE_OPTION)
    {
      String choice =  chooser.getSelectedFile().getPath();
-     jalview.bin.Cache.LAST_DIRECTORY = choice;
+     jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
      String format = IdentifyFile.Identify(choice, "File");
      LoadFile(choice, "File", format);
    }
@@ -145,18 +210,17 @@ public class Desktop extends jalview.jbgui.GDesktop
    if (FormatProperties.contains(format))
        sequences = FormatAdapter.read(file, protocol, format);
 
-   if (sequences != null)
+   if (sequences != null && sequences.length>0)
    {
      AlignFrame af = new AlignFrame(new Alignment(sequences));
-     addInternalFrame(af, file, 700, 500);
+     addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
      af.statusBar.setText("Successfully loaded file " + file);
 
-
    }
    else
      JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"
                           + "Formats currently supported are\n"
-                          + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"
+                          + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" // JBPNote - message should be generated through FormatAdapter!
                           ,"Error loading file",
                                    JOptionPane.WARNING_MESSAGE);
 
@@ -172,7 +236,6 @@ public class Desktop extends jalview.jbgui.GDesktop
 
    String format = IdentifyFile.Identify(url, "URL");
 
-   System.out.println(format +" format");
    if (format.equals("URL NOT FOUND"))
    {
      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
@@ -206,7 +269,9 @@ public class Desktop extends jalview.jbgui.GDesktop
       if(sequences!=null)
       {
         AlignFrame af = new AlignFrame(new Alignment(sequences));
-        addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);
+        addInternalFrame(af, "Cut & Paste input - "+format,
+                         AlignFrame.NEW_WINDOW_WIDTH,
+                         AlignFrame.NEW_WINDOW_HEIGHT);
         af.statusBar.setText("Successfully pasted alignment file");
       }
       else
@@ -215,7 +280,6 @@ public class Desktop extends jalview.jbgui.GDesktop
                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);
 
-
    }
  }
 
@@ -224,35 +288,130 @@ public class Desktop extends jalview.jbgui.GDesktop
 */
  public void quit_actionPerformed(ActionEvent e)
  {
-   this.setVisible(false);
-   System.exit(0);
+   if(jalview.bin.Jalview.applet!=null)
+     jalview.bin.Jalview.applet.destroy();
+    else
+      System.exit(0);
  }
 
 
- protected void colourIndexMenuItem_actionPerformed(ActionEvent e)
- {
-   ColourKey colourKey = new ColourKey(null);
-   addInternalFrame(colourKey, "Colour scheme key", 400, 320);
- }
-
 
  public void aboutMenuItem_actionPerformed(ActionEvent e)
  {
    JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                         "JalView 2005"
+                                         "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE
                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."
                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."
-                                       +"\nIf  you use JalView, please cite:  \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
+                                       +"\nIf  you use JalView, please cite:  Bioinformatics,  2004 12;426-7."
+                                       +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
                                          "About Jalview",
                                          JOptionPane.INFORMATION_MESSAGE);
  }
 
  public void documentationMenuItem_actionPerformed(ActionEvent e)
  {
+   try
+   {
+      ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+      java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
+      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);
+   }
+   catch (Exception ex)
+   {
+     ex.printStackTrace();
+   }
+ }
+
+ static JInternalFrame conservationSlider;
+ static JInternalFrame PIDSlider;
+ public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
+ {
+   SliderPanel sp = null;
+   ConservationColourScheme ccs = (ConservationColourScheme)cs;
+   int value = ccs.inc;
+
+   if(conservationSlider == null)
+   {
+     sp = new SliderPanel(ap, value, true, cs);
+     conservationSlider = new JInternalFrame();
+     conservationSlider.setContentPane(sp);
+     addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90, false);
+     conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+                  {
+                    public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)
+                    {
+                      conservationSlider = null;
+                    }
+                  });
+      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+   }
+   else
+   {
+
+       conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");
+       sp = (SliderPanel)conservationSlider.getContentPane();
+       sp.cs = cs;
+       sp.setValue(value);
+   }
+
+   if(ap.av.alignment.getGroups()!=null)
+     sp.setAllGroupsCheckEnabled( true );
+   else
+     sp.setAllGroupsCheckEnabled( false);
+
+   return sp.getValue();
+
+ }
+
+ public static void hideConservationSlider()
+ {
+  try{
+    conservationSlider.setClosed(true);
+    conservationSlider = null;
+  }catch(Exception ex){}
+}
+
+
+ public static void hidePIDSlider()
+ {
    try{
-     jalview.util.BrowserLauncher.openURL("http://www.jalview.org/documentation.html");
+     PIDSlider.setClosed(true);
+     PIDSlider = null;
    }catch(Exception ex){}
  }
 
+ public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
+ {
+   SliderPanel pid = null;
+   if(PIDSlider == null)
+   {
+     pid = new SliderPanel(ap, 50, false, cs);
+     PIDSlider = new JInternalFrame();
+     PIDSlider.setContentPane(pid);
+     addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90, false);
+     PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+   }
+   else
+   {
+       PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
+       pid = (SliderPanel)PIDSlider.getContentPane();
+       pid.cs = cs;
+   }
+
+   if (ap.av.alignment.getGroups() != null)
+     pid.setAllGroupsCheckEnabled(true);
+   else
+     pid.setAllGroupsCheckEnabled(false);
+
+
+   return pid.getValue();
+
+ }
 
 }