X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=9d58c7badef5f205da54936e314b68d820a49115;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=ee9eb274277cdfee1091d90f0199c235880595b6;hpb=631729455dcde5766a5d307f2c15d553bc32cb3e;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ee9eb27..9d58c7b 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,14 +18,13 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
 import jalview.io.*;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.dnd.*;
 import java.awt.event.*;
+import java.util.*;
 
 import javax.swing.*;
 
@@ -37,19 +36,27 @@ import javax.swing.*;
  * @version $Revision$
  */
 public class Desktop extends jalview.jbgui.GDesktop
-    implements DropTargetListener
+    implements DropTargetListener, ClipboardOwner
 {
     /** DOCUMENT ME!! */
+    public static Desktop instance;
     public static JDesktopPane desktop;
     static int openFrameCount = 0;
     static final int xOffset = 30;
     static final int yOffset = 30;
+    public static jalview.ws.Discoverer discoverer;
+
+    public static Object [] jalviewClipboard;
+
+    static int fileLoadingCount= 0;
 
     /**
      * Creates a new Desktop object.
      */
     public Desktop()
     {
+        instance = this;
+
         Image image = null;
 
         try
@@ -70,11 +77,12 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
         }
 
-        setTitle("Jalview 2005");
+        setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
         setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
         desktop = new JDesktopPane();
         desktop.setBackground(Color.white);
-        setContentPane(desktop);
+        getContentPane().setLayout(new BorderLayout());
+        getContentPane().add(desktop, BorderLayout.CENTER);
         desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
 
         // This line prevents Windows Look&Feel resizing all new windows to maximum
@@ -115,9 +123,13 @@ public class Desktop extends jalview.jbgui.GDesktop
         SplashScreen splash = new SplashScreen(frame, image);
         frame.setContentPane(splash);
         frame.setLayer(JLayeredPane.PALETTE_LAYER);
-        addInternalFrame(frame, "", 750, 160, false);
         frame.setLocation((int) ((getWidth() - 750) / 2),
             (int) ((getHeight() - 160) / 2));
+
+        addInternalFrame(frame, "", 750, 160, false);
+
+        discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+
     }
 
     /**
@@ -128,7 +140,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      * @param w DOCUMENT ME!
      * @param h DOCUMENT ME!
      */
-    public static void addInternalFrame(final JInternalFrame frame,
+    public static synchronized void addInternalFrame(final JInternalFrame frame,
         String title, int w, int h)
     {
         addInternalFrame(frame, title, w, h, true);
@@ -143,38 +155,60 @@ public class Desktop extends jalview.jbgui.GDesktop
      * @param h DOCUMENT ME!
      * @param resizable DOCUMENT ME!
      */
-    public static void addInternalFrame(final JInternalFrame frame,
+    public static synchronized void addInternalFrame(final JInternalFrame frame,
         String title, int w, int h, boolean resizable)
     {
-        desktop.add(frame);
-        openFrameCount++;
 
-        try
-        {
-            frame.setSelected(true);
-        }
-        catch (java.beans.PropertyVetoException e)
-        {
-        }
-
-        frame.setTitle(title);
+      frame.setTitle(title);
+      if(frame.getWidth()<1 || frame.getHeight()<1)
+      {
         frame.setSize(w, h);
+      }
+      // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
+      // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
+      // IF JALVIEW IS RUNNING HEADLESS
+      /////////////////////////////////////////////////
+      if (System.getProperty("java.awt.headless") != null
+          && System.getProperty("java.awt.headless").equals("true"))
+      {
+        return;
+      }
+
+
+        openFrameCount++;
+
+        frame.setVisible(true);
         frame.setClosable(true);
         frame.setResizable(resizable);
         frame.setMaximizable(resizable);
         frame.setIconifiable(resizable);
         frame.setFrameIcon(null);
-        frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);
-        frame.toFront();
+
+        if (frame.getX()<1 && frame.getY()<1)
+       {
+         frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
+       }
 
         final JMenuItem menuItem = new JMenuItem(title);
         frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
             {
+              public void internalFrameActivated(javax.swing.event.
+                                                 InternalFrameEvent evt)
+              {
+                JInternalFrame itf = desktop.getSelectedFrame();
+                if (itf != null)
+                  itf.requestFocus();
+
+              }
+
                 public void internalFrameClosed(
                     javax.swing.event.InternalFrameEvent evt)
                 {
                     openFrameCount--;
                     windowMenu.remove(menuItem);
+                    JInternalFrame itf = desktop.getSelectedFrame();
+                       if (itf != null)
+                        itf.requestFocus();
                 }
                 ;
             });
@@ -190,51 +224,38 @@ public class Desktop extends jalview.jbgui.GDesktop
                     }
                     catch (java.beans.PropertyVetoException ex)
                     {
-                    }
 
-                    ;
+                    }
                 }
             });
 
-        frame.setVisible(true);
         windowMenu.add(menuItem);
+
+        desktop.add(frame);
+        frame.toFront();
+        try{
+          frame.setSelected(true);
+          frame.requestFocus();
+        }catch(java.beans.PropertyVetoException ve)
+        {}
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void dragEnter(DropTargetDragEvent evt)
+    public void lostOwnership(Clipboard clipboard, Transferable contents)
     {
+      Desktop.jalviewClipboard = null;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
+    public void dragEnter(DropTargetDragEvent evt)
+    {}
+
     public void dragExit(DropTargetEvent evt)
-    {
-    }
+    {}
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
     public void dragOver(DropTargetDragEvent evt)
-    {
-    }
+    {}
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
     public void dropActionChanged(DropTargetDragEvent evt)
-    {
-    }
+    {}
 
     /**
      * DOCUMENT ME!
@@ -244,40 +265,76 @@ public class Desktop extends jalview.jbgui.GDesktop
     public void drop(DropTargetDropEvent evt)
     {
         Transferable t = evt.getTransferable();
+        java.util.List files = null;
 
-        if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+        try
         {
-            return;
-        }
-
-        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+          DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+          if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+          {
+            //Works on Windows and MacOSX
+            evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+            files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+          }
+          else if (t.isDataFlavorSupported(uriListFlavor))
+          {
+            // This is used by Unix drag system
+            evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+            String data = (String) t.getTransferData(uriListFlavor);
+            files = new java.util.ArrayList(1);
+            for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+                data,
+                "\r\n");
+                 st.hasMoreTokens(); )
+            {
+              String s = st.nextToken();
+              if (s.startsWith("#"))
+              {
+                // the line is a comment (as per the RFC 2483)
+                continue;
+              }
 
-        try
+              java.net.URI uri = new java.net.URI(s);
+              java.io.File file = new java.io.File(uri);
+              files.add(file);
+            }
+          }
+        }
+        catch (Exception e)
         {
-            java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+          e.printStackTrace();
+        }
 
+        if (files != null)
+        {
+          try
+          {
             for (int i = 0; i < files.size(); i++)
             {
-                String file = files.get(i).toString();
-                String protocol = "File";
-                String format = null;
+              String file = files.get(i).toString();
+              String protocol = FormatAdapter.FILE;
+              String format = null;
 
-                if (file.endsWith(".jar"))
-                {
-                  format = "Jalview";
+              if (file.endsWith(".jar"))
+              {
+                format = "Jalview";
+
+              }
+              else
+              {
+                format = new IdentifyFile().Identify(file,
+                                                          protocol);
+              }
+
+
+              new FileLoader().LoadFile(file, protocol, format);
 
-                }
-                else
-                {
-                    format = jalview.io.IdentifyFile.Identify(file,
-                            protocol);
-                }
-                LoadFile(file, protocol, format);
             }
-        }
-        catch (Exception ex)
-        {
+          }
+          catch (Exception ex)
+          {
             ex.printStackTrace();
+          }
         }
     }
 
@@ -286,7 +343,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      *
      * @param e DOCUMENT ME!
      */
-    public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
+    public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
     {
         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
                     "LAST_DIRECTORY"),
@@ -315,81 +372,77 @@ public class Desktop extends jalview.jbgui.GDesktop
             String format = null;
             if (chooser.getSelectedFormat().equals("Jalview"))
             {
-              format = "Jalview";
+                format = "Jalview";
             }
             else
             {
-                format = IdentifyFile.Identify(choice, "File");
+                format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
             }
 
-            jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
-            LoadFile(choice, "File", format);
+            if (viewport != null)
+              new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
+            else
+              new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
         }
     }
 
+
+
     /**
      * DOCUMENT ME!
      *
-     * @param file DOCUMENT ME!
-     * @param protocol DOCUMENT ME!
-     * @param format DOCUMENT ME!
-     */
-    public void LoadFile(String file, String protocol, String format)
-    {
-        LoadingThread loader = new LoadingThread(file, protocol, format);
-        loader.start();
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param file DOCUMENT ME!
-     * @param protocol DOCUMENT ME!
-     * @param format DOCUMENT ME!
+     * @param e DOCUMENT ME!
      */
-    public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, String format)
+    public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
     {
-        LoadingThread loader = new LoadingThread(file, protocol, format);
-        loader.start();
+      // This construct allows us to have a wider textfield
+      // for viewing
+      JLabel label = new JLabel("Enter URL of Input File");
+      final JComboBox history = new JComboBox();
+
+      JPanel panel = new JPanel(new GridLayout(2,1));
+      panel.add(label);
+      panel.add(history);
+      history.setPreferredSize(new Dimension(400,20));
+      history.setEditable(true);
+      history.addItem("http://www.");
 
-        while (loader.isAlive())
+      String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+
+      StringTokenizer st;
+
+      if (historyItems != null)
+      {
+        st = new StringTokenizer(historyItems, "\t");
+
+        while (st.hasMoreTokens())
         {
-          try
-          {
-            Thread.sleep(50);
-          }
-          catch (Exception ex)
-          {}
+          history.addItem(st.nextElement());
         }
+      }
 
-      return loader.af;
-    }
+       int reply = JOptionPane.showInternalConfirmDialog(desktop,
+          panel, "Input Alignment From URL",
+          JOptionPane.OK_CANCEL_OPTION );
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputURLMenuItem_actionPerformed(ActionEvent e)
-    {
-        String url = JOptionPane.showInternalInputDialog(Desktop.desktop,
-                "Enter url of input file", "Input alignment from URL",
-                JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")
-                                .toString();
 
-        if (url == null)
+        if (reply != JOptionPane.OK_OPTION )
         {
             return;
         }
 
-        if (url.trim().toLowerCase().endsWith(".jar"))
+        String url = history.getSelectedItem().toString();
+
+        if (url.toLowerCase().endsWith(".jar"))
         {
-               jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
-               Jalview2XML.LoadJalviewAlign(url);
+          if (viewport != null)
+            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
+          else
+            new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
         }
         else
         {
-
-          String format = IdentifyFile.Identify(url, "URL");
+          String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
 
           if (format.equals("URL NOT FOUND"))
           {
@@ -401,7 +454,10 @@ public class Desktop extends jalview.jbgui.GDesktop
             return;
           }
 
-          LoadFile(url, "URL", format);
+          if (viewport != null)
+            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+          else
+            new FileLoader().LoadFile(url, FormatAdapter.URL, format);
         }
     }
 
@@ -410,10 +466,10 @@ public class Desktop extends jalview.jbgui.GDesktop
      *
      * @param e DOCUMENT ME!
      */
-    public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
+    public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
     {
         CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setForInput();
+        cap.setForInput(viewport);
         Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
     }
 
@@ -436,18 +492,18 @@ public class Desktop extends jalview.jbgui.GDesktop
      */
     public void aboutMenuItem_actionPerformed(ActionEvent e)
     {
-      StringBuffer message = new StringBuffer("JalView 2005 version " +
+      StringBuffer message = new StringBuffer("JalView version " +
                                               jalview.bin.Cache.getProperty(
           "VERSION") +
                                               "; last updated: " +
                                               jalview.bin.
-                                              Cache.getProperty("BUILD_DATE"));
+                                              Cache.getDefault("BUILD_DATE", "unknown"));
 
-      if (!jalview.bin.Cache.getProperty("jalview.version").equals(
+      if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
           jalview.bin.Cache.getProperty("VERSION")))
       {
         message.append("\n\n!! Jalview version "
-                       + jalview.bin.Cache.getProperty("jalview.version")
+                       + jalview.bin.Cache.getProperty("LATEST_VERSION")
                        + " is available for download from http://www.jalview.org !!\n");
 
       }
@@ -457,7 +513,7 @@ public class Desktop extends jalview.jbgui.GDesktop
             "\nFor all issues relating to Jalview, email help@jalview.org" +
             "\n\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.");
+            "\nBioinformatics,  2004 20;426-7.");
 
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 
@@ -479,8 +535,6 @@ public class Desktop extends jalview.jbgui.GDesktop
             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);
         }
@@ -520,7 +574,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
             java.io.File choice = chooser.getSelectedFile();
             jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-            Jalview2XML.SaveState(choice);
+            new Jalview2XML().SaveState(choice);
         }
     }
 
@@ -544,64 +598,72 @@ public class Desktop extends jalview.jbgui.GDesktop
             String choice = chooser.getSelectedFile().getAbsolutePath();
             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
                 chooser.getSelectedFile().getParent());
-            Jalview2XML.LoadJalviewAlign(choice);
+            new Jalview2XML().LoadJalviewAlign(choice);
         }
     }
 
-    class LoadingThread extends Thread
+  /*  public void vamsasLoad_actionPerformed(ActionEvent e)
     {
-        String file;
-        String protocol;
-        String format;
-        AlignFrame af;
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+          getProperty("LAST_DIRECTORY"));
 
-        public LoadingThread(String file, String protocol, String format)
-        {
-            this.file = file;
-            this.protocol = protocol;
-            this.format = format;
-        }
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle("Load Vamsas file");
+      chooser.setToolTipText("Import");
 
-        public void run()
-        {
-            SequenceI[] sequences = null;
+      int value = chooser.showOpenDialog(this);
 
-            if(format.equalsIgnoreCase("Jalview"))
-            {
-              Jalview2XML.LoadJalviewAlign(file);
-            }
-            else
-            {
-              if (FormatAdapter.formats.contains(format))
-              {
-                sequences = FormatAdapter.readFile(file, protocol, format);
-              }
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
+        vs.load(
+            chooser.getSelectedFile().getAbsolutePath()
+            );
+      }
 
-              if ( (sequences != null) && (sequences.length > 0))
-              {
-                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 inputSequence_actionPerformed(ActionEvent e)
+    {
+      new SequenceFetcher(null);
+    }
+
+    JPanel progressPanel;
+
+    public void startLoading(final String fileName)
+    {
+      if (fileLoadingCount == 0)
+      {
+        progressPanel = new JPanel(new BorderLayout());
+        JProgressBar progressBar = new JProgressBar();
+        progressBar.setIndeterminate(true);
+
+        progressPanel.add(new JLabel("Loading File: " + fileName + "   "),
+                          BorderLayout.WEST);
+
+        progressPanel.add(progressBar, BorderLayout.CENTER);
+
+        instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+      }
+      fileLoadingCount++;
+      validate();
+    }
+
+    public void stopLoading()
+    {
+      fileLoadingCount--;
+      if (fileLoadingCount < 1)
+      {
+        if(progressPanel!=null)
+        {
+          this.getContentPane().remove(progressPanel);
+          progressPanel = null;
         }
+        fileLoadingCount = 0;
+      }
+      validate();
     }
+
 }
+