X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FDesktop.java;h=8bf7523984f21e9206952c4dfbd2ef922848cb3a;hb=bb920f9f8878f5c60a2a06997eacb8937d0fa797;hp=a1e88bef30861ed83d9fec0dd30737a1273e8b3e;hpb=dba30c55e191417596da163caeef250c78de132d;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index a1e88be..8bf7523 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -12,6 +12,7 @@ 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.*;
@@ -22,13 +23,12 @@ public class Desktop extends jalview.jbgui.GDesktop
   public static JDesktopPane desktop;
   static int openFrameCount = 0;
   static final int xOffset = 30, yOffset = 30;
-  static boolean splashScreenVisible = false;
 
   public Desktop()
   {
     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);
@@ -44,44 +44,71 @@ public class Desktop extends jalview.jbgui.GDesktop
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
     setVisible(true);
     desktop = new JDesktopPane();
+    desktop.setBackground(Color.white);
     setContentPane(desktop);
     desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
 
     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-    setBounds( (int)(screenSize.getWidth()-1200)/2,
-               (int)(screenSize.getHeight()-800)/2,
-              1200 ,
-              800);
+    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");
+
+    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() + "");
+}
+});
+
+/////////Add a splashscreen on startup
 
 
    /////////Add a splashscreen on startup
-  /*  JInternalFrame frame = new JInternalFrame();
+    JInternalFrame frame = new JInternalFrame();
 
     SplashScreen splash = new SplashScreen(frame, image);
     frame.setContentPane(splash);
-    addInternalFrame(frame, "",820,200);
-    splashScreenVisible = true;
-
-    frame.setLocation( (int)((getWidth()-820) /2), (int)((getHeight()-240) /2));
+    desktop.add(frame);
+    frame.setVisible(true);
+    openFrameCount++;
+    try
+    {
+      frame.setSelected(true);
+    }
+    catch (java.beans.PropertyVetoException e)
+    {}
+    frame.setResizable(true);
+    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.setFrameIcon(null);
 
-  public static void splashScreenClosing()
-  {
-    splashScreenVisible = false;
-    JInternalFrame [] frames  = desktop.getAllFrames();
-    for(int i=0; i<frames.length; i++)
-      frames[i].setVisible(true);
   }
 
   public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
   {
-   if(!splashScreenVisible)
-      frame.setVisible(true); //necessary as of 1.3
    desktop.add(frame);
+   frame.setVisible(true);
    openFrameCount++;
    try {
        frame.setSelected(true);
@@ -92,6 +119,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    frame.setClosable(true);
    frame.setMaximizable(true);
    frame.setIconifiable(true);
+   frame.setFrameIcon(null);
    frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
    frame.toFront();
    final JMenuItem menuItem = new JMenuItem(title);
@@ -119,14 +147,16 @@ public class Desktop extends jalview.jbgui.GDesktop
 
  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);
    }
@@ -148,7 +178,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
    }
    else
-     JOptionPane.showInternalMessageDialog(this,  "Couldn't open file.\n"
+     JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"
                           + "Formats currently supported are\n"
                           + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"
                           ,"Error loading file",
@@ -158,7 +188,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
  public void inputURLMenuItem_actionPerformed(ActionEvent e)
  {
-   String url = JOptionPane.showInternalInputDialog(this,"Enter url of input file",
+   String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
                                             "Input alignment from URL",
                                             JOptionPane.QUESTION_MESSAGE);
    if (url == null)
@@ -169,7 +199,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    System.out.println(format +" format");
    if (format.equals("URL NOT FOUND"))
    {
-     JOptionPane.showInternalMessageDialog(this,"Couldn't locate " + url,
+     JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
                                    "URL not found",
                                    JOptionPane.WARNING_MESSAGE);
      return;
@@ -181,7 +211,7 @@ public class Desktop extends jalview.jbgui.GDesktop
  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
  {
    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
-   int accept =  JOptionPane.showInternalOptionDialog(desktop, cap, "Cut & paste Alignment File",
+   int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",
                                        JOptionPane.YES_NO_CANCEL_OPTION,
                                        JOptionPane.PLAIN_MESSAGE,
                                        null,
@@ -204,12 +234,11 @@ public class Desktop extends jalview.jbgui.GDesktop
         af.statusBar.setText("Successfully pasted alignment file");
       }
       else
-        JOptionPane.showInternalMessageDialog(this, "Couldn't read the pasted text.\n"
+        JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
                                       +"Formats currently supported are\n"
                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);
 
-
    }
  }
 
@@ -218,23 +247,19 @@ 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,
-                                         "JalView 2005"
-                                       +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse and Geoff Barton."
+   JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                         "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\"",
                                          "About Jalview",
@@ -243,10 +268,104 @@ public class Desktop extends jalview.jbgui.GDesktop
 
  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;
+
+   if(conservationSlider == null)
+   {
+     sp = new SliderPanel(ap, 30, true, cs);
+     conservationSlider = new JInternalFrame();
+     conservationSlider.setContentPane(sp);
+     conservationSlider.setResizable(false);
+     addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90);
+     conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+                  {
+                    public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)
+                    {
+                      conservationSlider = null;
+                    }
+                  });
+   }
+   else
+   {
+       conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");
+       sp = (SliderPanel)conservationSlider.getContentPane();
+       sp.cs = cs;
+   }
+
+   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://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);
+     PIDSlider.setResizable(false);
+     addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);
+   }
+   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();
+
+ }
 
 }