X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FDesktop.java;h=36183bb1f9804df638bec763214e0d3f1d7c197f;hb=0306c5b7a2aa4cc232ad0590a8ef285022eabd51;hp=3b130166a31d2ba85ee813f37d2d6ea2368c20d3;hpb=180faccf15c5358f8e456a98d63ccf4d50aef376;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 3b13016..36183bb 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -12,13 +12,16 @@ 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 jalview.bin.Cache;
 
 
-public class Desktop extends jalview.jbgui.GDesktop
+public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener
 {
   public static JDesktopPane desktop;
   static int openFrameCount = 0;
@@ -28,7 +31,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     Image image =null;
     try{
-      java.net.URL url = getClass().getResource("/images/BartonGroupBanner.gif");
+      java.net.URL url = getClass().getResource("/images/logo.gif");
       if(url!=null)
       {
         image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
@@ -42,73 +45,93 @@ 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 = 900, height = 650;
-    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
    /////////Add a splashscreen on startup
     JInternalFrame frame = new JInternalFrame();
 
     SplashScreen splash = new SplashScreen(frame, image);
     frame.setContentPane(splash);
-    desktop.add(frame);
-    frame.setVisible(true);
-    openFrameCount++;
-    try
-    {
-      frame.setSelected(true);
-    }
-    catch (java.beans.PropertyVetoException e)
-    {}
-    frame.setResizable(true);
-    frame.setSize(845, 200);
-    frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));
-    frame.setClosable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
-    frame.setFrameIcon(null);
-
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    addInternalFrame(frame, "", 750,160, false);
+    frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));
   }
-
   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);
    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-                                   { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
-                                     {
-                                       openFrameCount--;
-                                       windowMenu.remove(menuItem);
-                                     };
-                                   });
+   {
+     public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+     {
+       openFrameCount--;
+       windowMenu.remove(menuItem);
+     };
+   });
 
    menuItem.addActionListener(new ActionListener()
     {
@@ -119,62 +142,126 @@ 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";
+       if(file.endsWith(".jar"))
+                Jalview2XML.LoadJalviewAlign(file);
+      else
+      {
+        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.getProperty("LAST_DIRECTORY"));
+   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+       new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},
+       new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}
+       ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+
    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)
    {
+     jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
      String choice =  chooser.getSelectedFile().getPath();
-     jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-     String format = IdentifyFile.Identify(choice, "File");
-     LoadFile(choice, "File", format);
+     jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
+     if(chooser.getSelectedFormat().equals("Jalview"))
+     {
+       Jalview2XML.LoadJalviewAlign(choice);
+     }
+     else
+     {
+       String format = IdentifyFile.Identify(choice, "File");
+       LoadFile(choice, "File", format);
+     }
    }
  }
 
  public void LoadFile(String file, String protocol,  String format)
  {
-   SequenceI [] sequences = null;
+   LoadingThread loader = new LoadingThread(file, protocol, format);
+   loader.start();
+ }
 
-   if (FormatProperties.contains(format))
-       sequences = FormatAdapter.read(file, protocol, format);
+ class LoadingThread extends Thread
+ {
+   String file, protocol, format;
 
-   if (sequences != null)
+   public LoadingThread(String file, String protocol,  String format)
    {
-     AlignFrame af = new AlignFrame(new Alignment(sequences));
-     addInternalFrame(af, file, 700, 500);
-     af.statusBar.setText("Successfully loaded file " + file);
-
-
+     this.file = file;
+     this.protocol = protocol;
+     this.format = format;
    }
-   else
-     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",
-                                   JOptionPane.WARNING_MESSAGE);
+   public void run()
+   {
+     SequenceI [] sequences = null;
+
+     if (FormatAdapter.formats.contains(format))
+         sequences = FormatAdapter.readFile(file, protocol, format);
+
+     if (sequences != null && sequences.length>0)
+     {
+       AlignFrame af = new AlignFrame(new Alignment(sequences));
+       addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+       af.currentFileFormat = format;
+       af.statusBar.setText("Successfully loaded file " + file);
+       try{
+           af.setMaximum(Preferences.showFullscreen);
+       }catch(Exception ex){}
+
+     }
+     else
+       JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"
+                            + "Formats currently supported are\n"
+                            + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!
+                            ,"Error loading file",
+                                     JOptionPane.WARNING_MESSAGE);
 
+   }
  }
 
+
  public void inputURLMenuItem_actionPerformed(ActionEvent e)
  {
    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
                                             "Input alignment from URL",
-                                            JOptionPane.QUESTION_MESSAGE);
+                                            JOptionPane.QUESTION_MESSAGE,
+                                            null, null,
+                                            "http://www.").toString();
    if (url == null)
      return;
 
    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,
@@ -201,20 +288,23 @@ public class Desktop extends jalview.jbgui.GDesktop
     String format = IdentifyFile.Identify(cap.getText(), "Paste");
     SequenceI [] sequences = null;
 
-    if (FormatProperties.contains( format ))
-      sequences = FormatAdapter.read(cap.getText(), "Paste", format);
+    if (FormatAdapter.formats.contains( format ))
+      sequences = FormatAdapter.readFile(cap.getText(), "Paste", format);
 
 
       if(sequences!=null)
       {
         AlignFrame af = new AlignFrame(new Alignment(sequences));
-        addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);
+        af.currentFileFormat = format;
+        addInternalFrame(af, "Cut & Paste input - "+format,
+                         AlignFrame.NEW_WINDOW_WIDTH,
+                         AlignFrame.NEW_WINDOW_HEIGHT);
         af.statusBar.setText("Successfully pasted alignment file");
       }
       else
         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
                                       +"Formats currently supported are\n"
-                                      +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
+                                      +"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",
                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);
 
    }
@@ -236,10 +326,12 @@ public class Desktop extends jalview.jbgui.GDesktop
  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:"
+                                       +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""
+                                       +"\nBioinformatics,  2004 12;426-7.",
                                          "About Jalview",
                                          JOptionPane.INFORMATION_MESSAGE);
  }
@@ -264,86 +356,45 @@ public class Desktop extends jalview.jbgui.GDesktop
    }
  }
 
- static JInternalFrame conservationSlider;
- static JInternalFrame PIDSlider;
- public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
+ protected void preferences_actionPerformed(ActionEvent e)
  {
-   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();
-
+   Preferences pref = new Preferences();
  }
 
- public static void hideConservationSlider()
+ public void saveState_actionPerformed(ActionEvent e)
  {
-  try{
-    conservationSlider.setClosed(true);
-    conservationSlider = null;
-  }catch(Exception ex){}
-}
+   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+       getProperty("LAST_DIRECTORY"),
+       new String[]
+       {"xml"}, new String[]{"Jalview Project"}, "Jalview Project");
 
+   chooser.setFileView(new JalviewFileView());
+   chooser.setDialogTitle("Save State");
+   int value = chooser.showSaveDialog(this);
+   if (value == JalviewFileChooser.APPROVE_OPTION)
+   {
+     java.io.File choice = chooser.getSelectedFile();
+     jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+     Jalview2XML.SaveState(choice);
+   }
 
- public static void hidePIDSlider()
- {
-   try{
-     PIDSlider.setClosed(true);
-     PIDSlider = null;
-   }catch(Exception ex){}
  }
 
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
+
+ public void loadState_actionPerformed(ActionEvent e)
  {
-   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
+   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+       new String[]{"xml"}, new String[]{"Jalview Project"}, "Jalview Project");
+   chooser.setFileView(new JalviewFileView());
+   chooser.setDialogTitle("Restore state");
+   int value = chooser.showOpenDialog(this);
+   if(value == JalviewFileChooser.APPROVE_OPTION)
    {
-       PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
-       pid = (SliderPanel)PIDSlider.getContentPane();
-       pid.cs = cs;
+     String choice =  chooser.getSelectedFile().getAbsolutePath();
+     jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
+     Jalview2XML.LoadState(choice);
    }
-
-   if (ap.av.alignment.getGroups() != null)
-     pid.setAllGroupsCheckEnabled(true);
-   else
-     pid.setAllGroupsCheckEnabled(false);
-
-
-   return pid.getValue();
-
  }
-
 }
+
+