X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=7031e992a59df6342faf52acb971853987e8fb0d;hb=f09f33647e90a6376ffcf096d003afa59f2b41fc;hp=3acefe7752d19dfc2e3d06946d876da23bddf3fc;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 3acefe7..7031e99 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
@@ -24,6 +24,7 @@ import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.dnd.*;
 import java.awt.event.*;
+import java.util.*;
 
 import javax.swing.*;
 
@@ -35,9 +36,10 @@ 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;
@@ -46,15 +48,17 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     public static Object [] jalviewClipboard;
 
+    static int fileLoadingCount= 0;
 
     /**
      * Creates a new Desktop object.
      */
     public Desktop()
     {
+        instance = this;
+        doVamsasClientCheck();
         Image image = null;
 
-
         try
         {
             java.net.URL url = getClass().getResource("/images/logo.gif");
@@ -77,7 +81,8 @@ public class Desktop extends jalview.jbgui.GDesktop
         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
@@ -124,6 +129,13 @@ public class Desktop extends jalview.jbgui.GDesktop
         addInternalFrame(frame, "", 750, 160, false);
 
         discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+    }
+
+    private void doVamsasClientCheck() {
+      if (jalview.bin.Cache.vamsasJarsPresent()) {
+        VamsasMenu.setVisible(true);
+        vamsasLoad.setVisible(true);
+      }
 
     }
 
@@ -187,9 +199,20 @@ public class Desktop extends jalview.jbgui.GDesktop
         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)
                 {
+                    PaintRefresher.RemoveComponent(frame);
                     openFrameCount--;
                     windowMenu.remove(menuItem);
                     JInternalFrame itf = desktop.getSelectedFrame();
@@ -223,45 +246,25 @@ public class Desktop extends jalview.jbgui.GDesktop
           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!
@@ -271,40 +274,72 @@ 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;
+          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;
+              }
+
+              java.net.URI uri = new java.net.URI(s);
+              java.io.File file = new java.io.File(uri);
+              files.add(file);
+            }
+          }
         }
+        catch (Exception e)
+        {      }
 
-        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-
-        try
+        if (files != null)
         {
-            java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
-
+          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)
-        {
-            ex.printStackTrace();
+          }
+          catch (Exception ex)
+          {      }
         }
     }
 
@@ -313,7 +348,7 @@ 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"),
@@ -342,58 +377,77 @@ 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)
-    {
-      FileLoader fileLoader = new FileLoader();
-      fileLoader.LoadFile(file, protocol, format);
-    }
+
 
     /**
      * DOCUMENT ME!
      *
      * @param e DOCUMENT ME!
      */
-    public void inputURLMenuItem_actionPerformed(ActionEvent e)
+    public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
     {
-        Object reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
-                "Enter url of input file", "Input alignment from URL",
-                JOptionPane.QUESTION_MESSAGE, null, null, "http://www.");
+      // 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.");
 
-        if (reply == null)
+      String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+
+      StringTokenizer st;
+
+      if (historyItems != null)
+      {
+        st = new StringTokenizer(historyItems, "\t");
+
+        while (st.hasMoreTokens())
+        {
+          history.addItem(st.nextElement());
+        }
+      }
+
+       int reply = JOptionPane.showInternalConfirmDialog(desktop,
+          panel, "Input Alignment From URL",
+          JOptionPane.OK_CANCEL_OPTION );
+
+
+        if (reply != JOptionPane.OK_OPTION )
         {
             return;
         }
 
-        String url = reply.toString().trim();
+        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"))
           {
@@ -405,7 +459,10 @@ 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);
         }
     }
 
@@ -414,10 +471,10 @@ 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);
     }
 
@@ -461,7 +518,7 @@ 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,
 
@@ -487,11 +544,93 @@ public class Desktop extends jalview.jbgui.GDesktop
             hb.setDisplayed(true);
         }
         catch (Exception ex)
+        {     }
+    }
+
+    public void closeAll_actionPerformed(ActionEvent e)
+    {
+      JInternalFrame [] frames = desktop.getAllFrames();
+      for(int i=0; i<frames.length; i++)
+      {
+        try{
+        frames[i].setClosed(true);
+      }catch(java.beans.PropertyVetoException ex){}
+      }
+    }
+
+    public void raiseRelated_actionPerformed(ActionEvent e)
+    {
+      reorderAssociatedWindows(false, false);
+    }
+
+    public void minimizeAssociated_actionPerformed(ActionEvent e)
+    {
+      reorderAssociatedWindows(true, false);
+    }
+
+    void closeAssociatedWindows()
+    {
+      reorderAssociatedWindows(false, true);
+    }
+
+    void reorderAssociatedWindows(boolean minimize, boolean close)
+    {
+      JInternalFrame[] frames = desktop.getAllFrames();
+      if (frames == null || frames.length<1)
+        return;
+
+      AlignViewport source = null, target = null;
+      if (frames[0] instanceof AlignFrame)
+        source = ( (AlignFrame) frames[0]).getCurrentView();
+      else if (frames[0] instanceof TreePanel)
+        source = ( (TreePanel) frames[0]).getViewPort();
+      else if (frames[0] instanceof PCAPanel)
+        source = ( (PCAPanel) frames[0]).av;
+      else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
+        source = ((PairwiseAlignPanel)frames[0].getContentPane()).av;
+
+
+      if (source != null)
+        for (int i = 0; i < frames.length; i++)
         {
-            ex.printStackTrace();
+          target = null;
+          if(frames[i]==null)
+          {
+            continue;
+          }
+          if (frames[i] instanceof AlignFrame)
+            target = ( (AlignFrame) frames[i]).getCurrentView();
+          else if (frames[i] instanceof TreePanel)
+            target = ( (TreePanel) frames[i]).getViewPort();
+          else if (frames[i] instanceof PCAPanel)
+            target = ( (PCAPanel) frames[i]).av;
+          else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
+            target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av;
+
+          if (source == target)
+          {
+            try
+            {
+              if (close)
+                frames[i].setClosed(true);
+              else
+              {
+                frames[i].setIcon(minimize);
+                if (!minimize)
+                {
+                  frames[i].toFront();
+                }
+              }
+
+            }
+            catch (java.beans.PropertyVetoException ex)
+            {       }
+          }
         }
     }
 
+
+
     /**
      * DOCUMENT ME!
      *
@@ -522,7 +661,7 @@ 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);
         }
     }
 
@@ -546,7 +685,7 @@ 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);
         }
     }
 
@@ -574,7 +713,172 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     public void inputSequence_actionPerformed(ActionEvent e)
     {
-      SequenceFetcher sf = new SequenceFetcher(null);
+      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();
+    }
+
+    public static int getViewCount(String viewId)
+    {
+      int count = 0;
+      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+      for (int t = 0; t < frames.length; t++)
+      {
+        if (frames[t] instanceof AlignFrame)
+        {
+          AlignFrame af = (AlignFrame) frames[t];
+          for(int a=0; a<af.alignPanels.size(); a++)
+          {
+            if(viewId.equals(
+                ((AlignmentPanel)af.alignPanels.elementAt(a)).av.getSequenceSetId() )
+                )
+            count ++;
+          }
+        }
+      }
+
+      return count;
+    }
+
+    public void explodeViews(AlignFrame af)
+    {
+      int size = af.alignPanels.size();
+      if(size<2)
+        return;
+
+      for(int i=0; i<size; i++)
+      {
+        AlignmentPanel ap = (AlignmentPanel)af.alignPanels.elementAt(i);
+        AlignFrame newaf = new AlignFrame(ap);
+        if(ap.av.explodedPosition!=null)
+          newaf.setBounds(ap.av.explodedPosition);
+
+        ap.av.gatherViewsHere = false;
+
+        addInternalFrame(newaf, af.getTitle(),
+                         AlignFrame.DEFAULT_WIDTH,
+                         AlignFrame.DEFAULT_HEIGHT);
+      }
+
+      af.alignPanels.clear();
+      af.closeMenuItem_actionPerformed(true);
+
+    }
+
+    public void gatherViews(AlignFrame source)
+    {
+      source.viewport.gatherViewsHere = true;
+      source.viewport.explodedPosition = source.getBounds();
+      JInternalFrame[] frames = desktop.getAllFrames();
+      String viewId = source.viewport.sequenceSetID;
+
+      for (int t = 0; t < frames.length; t++)
+      {
+        if (frames[t] instanceof AlignFrame && frames[t] != source)
+        {
+          AlignFrame af = (AlignFrame) frames[t];
+          boolean gatherThis = false;
+          for (int a = 0; a < af.alignPanels.size(); a++)
+          {
+            AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
+            if (viewId.equals(ap.av.getSequenceSetId()))
+            {
+              gatherThis = true;
+              ap.av.gatherViewsHere = false;
+              ap.av.explodedPosition = af.getBounds();
+              source.addAlignmentPanel(ap, false);
+            }
+          }
+
+          if (gatherThis)
+          {
+            af.alignPanels.clear();
+            af.closeMenuItem_actionPerformed(true);
+          }
+        }
+      }
+
+    }
+
+    jalview.gui.VamsasClient v_client=null;
+    public void vamsasLoad_actionPerformed(ActionEvent e)
+    {
+      if (v_client==null) {
+        // Start a session.
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+            getProperty("LAST_DIRECTORY"));
+
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Load Vamsas file");
+        chooser.setToolTipText("Import");
+
+        int value = chooser.showOpenDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+          v_client = new jalview.gui.VamsasClient(this,
+              chooser.getSelectedFile());
+          this.vamsasLoad.setText("Session Update");
+          this.vamsasStop.setVisible(true);
+          v_client.initial_update();
+          v_client.startWatcher();
+        }
+      } else {
+        // store current data in session.
+        v_client.push_update();
+      }
+    }
+    public void vamsasStop_actionPerformed(ActionEvent e) {
+      if (v_client!=null) {
+        v_client.end_session();
+        v_client=null;
+        this.vamsasStop.setVisible(false);
+        this.vamsasLoad.setText("Start Vamsas Session...");
+      }
+    }
+    /**
+     * hide vamsas user gui bits when a vamsas document event is being handled.
+     * @param b true to hide gui, false to reveal gui
+     */
+    public void setVamsasUpdate(boolean b) {
+      jalview.bin.Cache.log.debug("Setting gui for Vamsas update "+(b ? "in progress" : "finished"));
+      vamsasLoad.setVisible(!b);
+      vamsasStop.setVisible(!b);
+
     }
 }