From 5874ca652d08909c74d422552eb03a996112316d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 11 May 2006 13:53:49 +0000
Subject: [PATCH] Recently loaded files, urls, append sequences to Alignment

---
 src/jalview/bin/Jalview.java             |    2 +-
 src/jalview/datamodel/Alignment.java     |   25 +++--
 src/jalview/gui/AlignFrame.java          |   32 +++---
 src/jalview/gui/CutAndPasteTransfer.java |   20 +++-
 src/jalview/gui/Desktop.java             |   69 ++++++++-----
 src/jalview/io/FileLoader.java           |  164 +++++++++++++++++++++---------
 src/jalview/io/JalviewFileChooser.java   |   69 ++++++++++++-
 src/jalview/jbgui/GAlignFrame.java       |   48 +++++++++
 src/jalview/jbgui/GDesktop.java          |   12 +--
 9 files changed, 326 insertions(+), 115 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3e8018b..bdfe3ae 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -252,7 +252,7 @@ public class Jalview
             else
             {
               format = new jalview.io.IdentifyFile().Identify(file, protocol);
-              desktop.LoadFile(file, protocol, format);
+              new jalview.io.FileLoader().LoadFile(file, protocol, format);
             }
           }
     }
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index c62d707..f3d17b4 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -96,22 +96,21 @@ public class Alignment implements AlignmentI
      */
     public void addSequence(SequenceI snew)
     {
-        sequences.addElement(snew);
-    }
+      if(dataset!=null)
+      {
+        Sequence ds = new Sequence(snew.getName(),
+                                   AlignSeq.extractGaps("-. ", snew.getSequence()),
+                                   snew.getStart(),
+                                   snew.getEnd());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void addSequence(SequenceI[] seq)
-    {
-        for (int i = 0; i < seq.length; i++)
-        {
-            addSequence(seq[i]);
-        }
+        snew.setDatasetSequence(ds);
+        getDataset().addSequence(ds);
+      }
+
+      sequences.addElement(snew);
     }
 
+
     /** Adds a sequence to the alignment.  Recalculates maxLength and size.
      *
      * @param snew
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 151eb5e..4b1f1f1 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -200,6 +200,22 @@ public class AlignFrame
   {
     new SequenceFetcher(this);
   }
+
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport.alignment);
+  }
+
+  public void addFromText_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport.alignment);
+  }
+
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.inputURLMenuItem_actionPerformed(viewport.alignment);
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -716,22 +732,6 @@ public class AlignFrame
               sequences[i].getEnd());
 
           alignment.addSequence(newseq);
-          if(sequences[i].getDatasetSequence()==null)
-          {
-             ////////////////////////////
-            //Datset needs extension;
-            /////////////////////////////
-            Sequence ds = new Sequence(sequences[i].getName(),
-                                       AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
-                                       sequences[i].getStart(),
-                                       sequences[i].getEnd());
-            newseq.setDatasetSequence(ds);
-            alignment.getDataset().addSequence(ds);
-          }
-          else
-          {
-            newseq.setDatasetSequence(sequences[i].getDatasetSequence());
-          }
         }
         viewport.setEndSeq(alignment.getHeight());
         alignment.getWidth();
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 7a3eb98..5d48ea3 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -40,6 +40,8 @@ import javax.swing.*;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer
 {
 
+  AlignmentI addToThisAlignment;
+
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -55,9 +57,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     /**
      * DOCUMENT ME!
      */
-    public void setForInput()
+    public void setForInput(AlignmentI alignment)
     {
-        getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
+      addToThisAlignment = alignment;
+      getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
     }
 
     /**
@@ -147,20 +150,29 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
         if (sequences != null)
         {
+          if(addToThisAlignment!=null)
+          {
+            for(int i=0; i<sequences.length; i++)
+              addToThisAlignment.addSequence(sequences[i]);
+          }
+          else
+          {
             AlignFrame af = new AlignFrame(new Alignment(sequences));
             af.currentFileFormat = format;
             Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
-                AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+                                     AlignFrame.NEW_WINDOW_WIDTH,
+                                     AlignFrame.NEW_WINDOW_HEIGHT);
             af.statusBar.setText("Successfully pasted alignment file");
 
             try
             {
-                af.setMaximum( jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
             }
             catch (Exception ex)
             {
             }
 
+          }
             try
             {
                 this.setClosed(true);
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ab686ff..fdb19d5 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -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.*;
 
@@ -322,7 +323,10 @@ public class Desktop extends jalview.jbgui.GDesktop
                 format = new IdentifyFile().Identify(file,
                                                           protocol);
               }
-              LoadFile(file, protocol, format);
+
+
+              new FileLoader().LoadFile(file, protocol, format);
+
             }
           }
           catch (Exception ex)
@@ -337,7 +341,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      *
      * @param e DOCUMENT ME!
      */
-    public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
+    public void inputLocalFileMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)
     {
         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
                     "LAST_DIRECTORY"),
@@ -366,46 +370,53 @@ public class Desktop extends jalview.jbgui.GDesktop
             String format = null;
             if (chooser.getSelectedFormat().equals("Jalview"))
             {
-              format = "Jalview";
+                format = "Jalview";
             }
             else
             {
                 format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
             }
 
-            jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
-            LoadFile(choice, FormatAdapter.FILE, format);
+            if (alignment != null)
+              new FileLoader().LoadFile(alignment, 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(jalview.datamodel.AlignmentI alignment)
     {
       // This construct allows us to have a wider textfield
       // for viewing
       JLabel label = new JLabel("Enter URL of Input File");
-      JTextField textinput = new JTextField("http://www.", 40);
+      final JComboBox history = new JComboBox();
       JPanel panel = new JPanel(new BorderLayout());
       panel.add(label, BorderLayout.NORTH);
-      panel.add(textinput, BorderLayout.SOUTH);
+      panel.add(history, BorderLayout.CENTER);
+      history.setPreferredSize(new Dimension(400,20));
+      history.setEditable(true);
+      history.addItem("http://www.");
+
+      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",
@@ -417,16 +428,17 @@ public class Desktop extends jalview.jbgui.GDesktop
             return;
         }
 
-        String url = textinput.getText();
+        String url = history.getSelectedItem().toString();
 
         if (url.toLowerCase().endsWith(".jar"))
         {
-               jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
-               new Jalview2XML().LoadJalviewAlign(url);
+          if (alignment != null)
+            new FileLoader().LoadFile(alignment, url, FormatAdapter.URL, "Jalview");
+          else
+            new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
         }
         else
         {
-
           String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
 
           if (format.equals("URL NOT FOUND"))
@@ -439,7 +451,10 @@ public class Desktop extends jalview.jbgui.GDesktop
             return;
           }
 
-          LoadFile(url, FormatAdapter.URL, format);
+          if (alignment != null)
+            new FileLoader().LoadFile(alignment, url, FormatAdapter.URL, format);
+          else
+            new FileLoader().LoadFile(url, FormatAdapter.URL, format);
         }
     }
 
@@ -448,10 +463,10 @@ public class Desktop extends jalview.jbgui.GDesktop
      *
      * @param e DOCUMENT ME!
      */
-    public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
+    public void inputTextboxMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)
     {
         CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setForInput();
+        cap.setForInput(alignment);
         Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
     }
 
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index a3ef237..1785e89 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -22,22 +22,43 @@ package jalview.io;
 import jalview.gui.AlignFrame;
 import jalview.gui.Jalview2XML;
 import javax.swing.JOptionPane;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.*;
 import jalview.gui.Desktop;
 import jalview.datamodel.SequenceI;
+import java.util.Vector;
+import java.util.StringTokenizer;
 
 public class FileLoader
 {
+  String file;
+  String protocol;
+  String format;
+  AlignmentI alignment;
+
+  public void LoadFile(AlignmentI alignment, String file, String protocol, String format)
+  {
+    this.alignment = alignment;
+    LoadFile(file, protocol, format);
+  }
+
   public void LoadFile(String file, String protocol, String format)
   {
-    LoadingThread loader = new LoadingThread(file, protocol, format);
+    this.file = file;
+    this.protocol = protocol;
+    this.format = format;
+
+    LoadingThread loader = new LoadingThread();
     loader.start();
   }
 
   public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
                                                   String format)
   {
-    LoadingThread loader = new LoadingThread(file, protocol, format);
+    this.file = file;
+    this.protocol = protocol;
+    this.format = format;
+
+    LoadingThread loader = new LoadingThread();
     loader.start();
     while (loader.isAlive())
     {
@@ -53,71 +74,120 @@ public class FileLoader
   }
 
 
-  class LoadingThread
-    extends Thread
-{
-  String file;
-  String protocol;
-  String format;
-  AlignFrame af;
 
-  public LoadingThread(String file, String protocol, String format)
+  public void updateRecentlyOpened()
   {
-    this.file = file;
-    this.protocol = protocol;
-    this.format = format;
-  }
+    Vector recent = new Vector();
 
-  public void run()
-  {
-    SequenceI[] sequences = null;
+    String type = protocol.equals(FormatAdapter.FILE)
+        ? "RECENT_FILE" : "RECENT_URL";
+
+    String historyItems = jalview.bin.Cache.getProperty(type);
 
-    if (format.equalsIgnoreCase("Jalview"))
+    StringTokenizer st;
+
+    if (historyItems != null)
     {
-      af = new Jalview2XML().LoadJalviewAlign(file);
+      st = new StringTokenizer(historyItems, "\t");
+
+      while (st.hasMoreTokens())
+      {
+        recent.addElement(st.nextElement().toString().trim());
+      }
+    }
+
+    if (recent.contains(file))
+    {
+      recent.remove(file);
+    }
+
+    StringBuffer newHistory = new StringBuffer(file);
+    for (int i = 0; i < recent.size() && i < 10; i++)
+    {
+      newHistory.append("\t");
+      newHistory.append(recent.elementAt(i));
     }
-    else
+
+    jalview.bin.Cache.setProperty(type, newHistory.toString());
+
+    if(type.equals(FormatAdapter.FILE))
+      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+  }
+
+
+  class LoadingThread
+      extends Thread
+  {
+
+    AlignFrame af;
+
+
+    public void run()
     {
-      String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS;
+      SequenceI[] sequences = null;
 
-      if (FormatAdapter.formats.contains(format))
+      if (format.equalsIgnoreCase("Jalview"))
       {
-        try{
-          sequences = new FormatAdapter().readFile(file, protocol, format);
-        }catch(java.io.IOException ex)
-        {
-          errorMessage = ex.getMessage();
-        }
+        af = new Jalview2XML().LoadJalviewAlign(file);
       }
-
-      if ( (sequences != null) && (sequences.length > 0))
+      else
       {
-        af = new AlignFrame(new Alignment(sequences));
-        af.currentFileFormat = format;
-        af.statusBar.setText("Successfully loaded file " + file);
-
-        Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
-                           AlignFrame.NEW_WINDOW_HEIGHT);
+        String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS;
 
+        if (FormatAdapter.formats.contains(format))
+        {
+          try
+          {
+            sequences = new FormatAdapter().readFile(file, protocol, format);
+          }
+          catch (java.io.IOException ex)
+          {
+            errorMessage = ex.getMessage();
+          }
+        }
 
-        try
+        if ( (sequences != null) && (sequences.length > 0))
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+          if(alignment!=null)
+          {
+            for(int i=0; i<sequences.length; i++)
+              alignment.addSequence(sequences[i]);
+          }
+          else
+          {
+            af = new AlignFrame(new Alignment(sequences));
+            af.currentFileFormat = format;
+            af.statusBar.setText("Successfully loaded file " + file);
+
+            Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
+                                     AlignFrame.NEW_WINDOW_HEIGHT);
+
+            try
+            {
+              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+            }
+            catch (java.beans.PropertyVetoException ex)
+            {
+            }
+          }
+
         }
-        catch (Exception ex)
+        else
         {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "Couldn't load file " + file +
+                                                "\n"
+                                                + errorMessage,
+                                                "Error loading file",
+                                                JOptionPane.WARNING_MESSAGE);
         }
       }
-      else
+
+      if (af != null)
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                              "Couldn't load file "+file+"\n"
-                                              +errorMessage,
-                                              "Error loading file",
-                                              JOptionPane.WARNING_MESSAGE);
+        updateRecentlyOpened();
       }
     }
   }
-}
 
 }
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 2bac0de..b04a705 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -23,6 +23,8 @@ package jalview.io;
 import java.io.*;
 import java.awt.*;
 import javax.swing.*;
+import java.awt.event.*;
+import java.util.*;
 
 public class JalviewFileChooser
     extends JFileChooser
@@ -31,6 +33,7 @@ public class JalviewFileChooser
   public JalviewFileChooser(String dir)
   {
     super(dir);
+    setAccessory(new RecentlyOpened());
   }
 
   public JalviewFileChooser(String dir, String[] suffix, String[] desc,
@@ -55,8 +58,10 @@ public class JalviewFileChooser
     {
       setFileFilter(chosen);
     }
+    setAccessory(new RecentlyOpened());
   }
 
+
   public void setFileFilter(javax.swing.filechooser.FileFilter filter)
   {
     super.setFileFilter(filter);
@@ -91,7 +96,6 @@ public class JalviewFileChooser
     }
   }
 
-
   public String getSelectedFormat()
   {
     if(getFileFilter()==null)
@@ -136,6 +140,8 @@ public class JalviewFileChooser
   public int showSaveDialog(Component parent)
       throws HeadlessException
   {
+    this.setAccessory(null);
+
     setDialogType(SAVE_DIALOG);
 
     int ret = showDialog(parent, null);
@@ -168,7 +174,68 @@ public class JalviewFileChooser
 
     return ret;
   }
+
+  void recentListSelectionChanged(String selection)
+  {
+    setSelectedFile(null);
+
+    File file = new File(selection);
+    if (getFileFilter() instanceof JalviewFileFilter)
+    {
+      JalviewFileFilter jvf = (JalviewFileFilter)this.getFileFilter();
+
+      if (!jvf.accept(file))
+      {
+        setFileFilter(getChoosableFileFilters()[0]);
+      }
+    }
+
+     setSelectedFile( file );
+  }
+
+  class RecentlyOpened extends JPanel
+  {
+    JList list;
+    public RecentlyOpened()
+    {
+      String historyItems = jalview.bin.Cache.getProperty("RECENT_FILE");
+      StringTokenizer st;
+      Vector recent = new Vector();
+
+      if (historyItems != null)
+      {
+        st = new StringTokenizer(historyItems, "\t");
+
+        while (st.hasMoreTokens())
+        {
+          recent.addElement(st.nextElement());
+        }
+      }
+
+      list = new JList(recent);
+      list.addMouseListener(new MouseAdapter()
+          {
+            public void mousePressed(MouseEvent evt)
+            {
+              recentListSelectionChanged(list.getSelectedValue().toString());
+            }
+          });
+
+      this.setBorder(new javax.swing.border.TitledBorder("Recently Opened"));
+
+      JScrollPane scroller = new JScrollPane(list);
+      scroller.setPreferredSize(new Dimension(250, 200));
+      this.add(scroller);
+      scroller.getHorizontalScrollBar()
+          .setValue(scroller.getHorizontalScrollBar().getMaximum()
+          );
+
+    }
+
+  }
 }
 
 
 
+
+
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index f5df999..14975b7 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -125,6 +125,10 @@ public class GAlignFrame
 
   JMenuItem associatedData = new JMenuItem();
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+  JMenu addSequenceMenu = new JMenu();
+  JMenuItem addFromFile = new JMenuItem();
+  JMenuItem addFromText = new JMenuItem();
+  JMenuItem addFromURL = new JMenuItem();
   public GAlignFrame()
   {
 
@@ -988,6 +992,31 @@ public class GAlignFrame
         autoCalculate_actionPerformed(e);
       }
     });
+    addSequenceMenu.setText("Add Sequences");
+    addFromFile.setText("From File");
+    addFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromFile_actionPerformed(e);
+      }
+    });
+    addFromText.setText("From Textbox");
+    addFromText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromText_actionPerformed(e);
+      }
+    });
+    addFromURL.setText("From URL");
+    addFromURL.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromURL_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -995,6 +1024,7 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
+    fileMenu.add(addSequenceMenu);
     fileMenu.add(fetchSequence);
     fileMenu.addSeparator();
     fileMenu.add(vamsasStore);
@@ -1091,6 +1121,9 @@ public class GAlignFrame
     jMenu2.add(htmlMenuItem);
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
+    addSequenceMenu.add(addFromFile);
+    addSequenceMenu.add(addFromText);
+    addSequenceMenu.add(addFromURL);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
@@ -1419,4 +1452,19 @@ public class GAlignFrame
   {
 
   }
+
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromText_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+
+  }
 }
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 63f1836..b16c99e 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -83,7 +83,7 @@ public class GDesktop extends JFrame
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    inputLocalFileMenuItem_actionPerformed(e);
+                    inputLocalFileMenuItem_actionPerformed(null);
                 }
             });
         inputURLMenuItem.setMnemonic('U');
@@ -92,7 +92,7 @@ public class GDesktop extends JFrame
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    inputURLMenuItem_actionPerformed(e);
+                    inputURLMenuItem_actionPerformed(null);
                 }
             });
         inputTextboxMenuItem.setMnemonic('C');
@@ -101,7 +101,7 @@ public class GDesktop extends JFrame
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    inputTextboxMenuItem_actionPerformed(e);
+                    inputTextboxMenuItem_actionPerformed(null);
                 }
             });
         quit.setMnemonic('Q');
@@ -203,7 +203,7 @@ public class GDesktop extends JFrame
      *
      * @param e DOCUMENT ME!
      */
-    protected void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
+    protected void inputLocalFileMenuItem_actionPerformed(jalview.datamodel.AlignmentI al)
     {
     }
 
@@ -212,7 +212,7 @@ public class GDesktop extends JFrame
      *
      * @param e DOCUMENT ME!
      */
-    protected void inputURLMenuItem_actionPerformed(ActionEvent e)
+    protected void inputURLMenuItem_actionPerformed(jalview.datamodel.AlignmentI al)
     {
     }
 
@@ -221,7 +221,7 @@ public class GDesktop extends JFrame
      *
      * @param e DOCUMENT ME!
      */
-    protected void inputTextboxMenuItem_actionPerformed(ActionEvent e)
+    protected void inputTextboxMenuItem_actionPerformed(jalview.datamodel.AlignmentI al)
     {
     }
 
-- 
1.7.10.2