X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2f7e5a89a5ecf3f867bac15c750c7a133f2e895b;hb=effd8d76f34bc7fd4e069603d80565b7ea9d3ff0;hp=c1a710508c5e432e088c227d37101a6206167db7;hpb=ac07859006686a2c62bcf57b24742eb610bc46f0;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c1a7105..2f7e5a8 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,1272 +1,2146 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
 
+import jalview.analysis.*;
 
+import jalview.datamodel.*;
 
+import jalview.io.*;
 
-package jalview.gui;
+import jalview.jbgui.*;
 
-import jalview.jbgui.GAlignFrame;
 import jalview.schemes.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.io.*;
+
 import jalview.ws.*;
+
 import java.awt.*;
+import java.awt.datatransfer.*;
 import java.awt.event.*;
 import java.awt.print.*;
+
+import java.io.*;
+
+import java.beans.*;
+
+import java.util.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
-import java.util.*;
-import java.awt.datatransfer.*;
 
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class AlignFrame extends GAlignFrame
 {
-  final AlignmentPanel alignPanel;
-  final AlignViewport viewport;
-  public static final int NEW_WINDOW_WIDTH = 700;
-  public static final int NEW_WINDOW_HEIGHT = 500;
-
-  public AlignFrame(AlignmentI al)
-  {
-    try{
-      String ip = java.net.InetAddress.getLocalHost().getHostAddress();
-      if( !ip.startsWith("10."))
-        alignMenu.setVisible(false);
+    /** DOCUMENT ME!! */
+    public static final int NEW_WINDOW_WIDTH = 700;
+
+    /** DOCUMENT ME!! */
+    public static final int NEW_WINDOW_HEIGHT = 500;
+    final AlignmentPanel alignPanel;
+    final AlignViewport viewport;
+
+    /** DOCUMENT ME!! */
+    public String currentFileFormat = null;
+    Stack historyList = new Stack();
+    Stack redoList = new Stack();
+    private int treeCount = 0;
+
+    /**
+     * Creates a new AlignFrame object.
+     *
+     * @param al DOCUMENT ME!
+     */
+    public AlignFrame(AlignmentI al)
+    {
+        viewport = new AlignViewport(al);
+
+        alignPanel = new AlignmentPanel(this, viewport);
+        alignPanel.annotationPanel.adjustPanelHeight();
+        alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+        alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+        alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
+
+        getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+
+        addInternalFrameListener(new InternalFrameAdapter()
+            {
+                public void internalFrameActivated(InternalFrameEvent evt)
+                {
+                    javax.swing.SwingUtilities.invokeLater(new Runnable()
+                        {
+                            public void run()
+                            {
+                                alignPanel.requestFocus();
+                            }
+                        });
+                }
+            });
     }
-    catch(java.net.UnknownHostException e){}
-    viewport = new AlignViewport(al,true,true,false);
 
-    String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
-    String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");
-    String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");
-    if(fontName!=null && fontStyle!=null && fontSize!=null)
-      viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
 
-    // add conservation graph to alignment
-    viewport.updateConservation();
-    viewport.updateConsensus();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void parseGroupsFile(String file)
+    {
+      try{
+        BufferedReader in = new BufferedReader(new FileReader(file));
+        SequenceI seq=null;
+        String line, text, token;
+        UserColourScheme ucs;
+        int index, start, end;
+        StringTokenizer st;
+        SequenceGroup sg;
+        while( (line = in.readLine())!=null)
+        {
+          st = new StringTokenizer(line, "\t");
+          if(st.countTokens()!=6)
+          {
+            System.out.println("Groups file "+file+" is invalid. Read help file.");
+            System.exit(1);
+          }
+
+          while(st.hasMoreElements())
+          {
+            text = st.nextToken();
+            token = st.nextToken();
+            if(!token.equals("ID_NOT_SPECIFIED"))
+            {
+              index = viewport.alignment.findIndex(viewport.alignment.findName(
+                  token));
+              st.nextToken();
+            }
+            else
+              index = Integer.parseInt( st.nextToken() );
+
+            start=Integer.parseInt( st.nextToken() );
+            end = Integer.parseInt( st.nextToken() );
+            ucs = new UserColourScheme(st.nextToken());
+
+            seq = viewport.alignment.getSequenceAt(index);
+            start = seq.findIndex(start)-1;
+            end = seq.findIndex(end)-1;
+
+            sg = new SequenceGroup(text,ucs,true,true,false,start,end);
+            sg.addSequence( seq,true);
+
+            viewport.alignment.addGroup(sg);
+          }
+        }
+
+      }catch(Exception ex){System.out.println("Error parsing groups file: "+ex);}
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+    {
+        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"
+                }, currentFileFormat);
+
+        chooser.setAcceptAllFileFilterUsed(false);
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save Alignment to file");
+        chooser.setToolTipText("Save");
+
+        int value = chooser.showSaveDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            currentFileFormat = chooser.getSelectedFormat();
+            jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+                currentFileFormat);
 
-    alignPanel = new AlignmentPanel(this, viewport);
+            String choice = chooser.getSelectedFile().getPath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
 
-    alignPanel.annotationPanel.adjustPanelHeight();
-    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
-    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+            saveAlignment(choice, currentFileFormat);
+        }
+    }
 
-    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+    public boolean saveAlignment(String file, String format)
+    {
+      if (format.equalsIgnoreCase("Jalview"))
+      {
+        String shortName = title;
 
+        if (shortName.indexOf(java.io.File.separatorChar) > -1)
+        {
+          shortName = shortName.substring(shortName.lastIndexOf(
+              java.io.File.separatorChar) + 1);
+        }
 
-    addInternalFrameListener(new InternalFrameAdapter()
-   {
-     public void internalFrameActivated(InternalFrameEvent evt)
-     {
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            public void run()
-            {      alignPanel.requestFocus();    }
-          });
-
-     }
-   });
-
-  }
-
-  protected void saveAs_actionPerformed(ActionEvent e)
-  {
-    String suffix [] = null;
-    if(e.getActionCommand().equals("FASTA"))
-      suffix = new String[]{"fa", "fasta"};
-    else if(e.getActionCommand().equals("MSF"))
-      suffix = new String[]{"msf"};
-    else if(e.getActionCommand().equals("CLUSTAL"))
-      suffix = new String[]{"aln"};
-    else if(e.getActionCommand().equals("BLC"))
-      suffix = new String[]{"blc"};
-    else if(e.getActionCommand().equals("PIR"))
-      suffix = new String[]{"pir"};
-    else if(e.getActionCommand().equals("PFAM"))
-      suffix = new String[]{"pfam"};
-
-
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
-        , suffix, e.getActionCommand()+" file");
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
-    chooser.setToolTipText("Save");
-    int value = chooser.showSaveDialog(this);
-    if(value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      String choice =  chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
-      try{
-        java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
-        out.println(output);
-        out.close();
+        Jalview2XML.SaveAlignment(this, file, shortName);
+
+        // USE Jalview2XML to save this file
+        return true;
       }
-      catch(Exception ex){}
-    }
-
-  }
-
-  protected void outputText_actionPerformed(ActionEvent e)
-  {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     JInternalFrame frame = new JInternalFrame();
-     cap.formatForOutput();
-     frame.setContentPane(cap);
-     Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
-     cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
-  }
-
-  protected void htmlMenuItem_actionPerformed(ActionEvent e)
-  {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport);
-    htmlOutput = null;
-  }
-
-  protected void createPNG_actionPerformed(ActionEvent e)
-  {
-    alignPanel.makePNG();
-  }
-
-  protected void epsFile_actionPerformed(ActionEvent e)
-  {
-    alignPanel.makeEPS();
-  }
-
-
-  public void printMenuItem_actionPerformed(ActionEvent e)
-  {
-    //Putting in a thread avoids Swing painting problems
-    PrintThread thread = new PrintThread();
-    thread.start();
-  }
-
-  class PrintThread extends Thread
-  {
-    public void run()
-    {
-      PrinterJob printJob = PrinterJob.getPrinterJob();
-      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
-      printJob.setPrintable(alignPanel, pf);
-      if (printJob.printDialog())
+      else
       {
+        String output = FormatAdapter.formatSequences(format,
+            viewport.getAlignment().
+            getSequences());
+        if(output==null)
+          return false;
+
         try
         {
-          printJob.print();
+          java.io.PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(file));
+          out.println(output);
+          out.close();
+          return true;
         }
-        catch (Exception PrintException)
+        catch (Exception ex)
         {
-          PrintException.printStackTrace();
+          ex.printStackTrace();
         }
       }
+      return false;
     }
 
-  }
-
-
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void outputText_actionPerformed(ActionEvent e)
+    {
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();
+        Desktop.addInternalFrame(cap,
+            "Alignment output - " + e.getActionCommand(), 600, 500);
+        cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+                viewport.getAlignment().getSequences()));
+    }
 
-  public void closeMenuItem_actionPerformed(ActionEvent e)
-  {
-    try{
-      this.setClosed(true);
-    }catch(Exception ex){}
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void htmlMenuItem_actionPerformed(ActionEvent e)
+    {
+        new HTMLOutput(viewport);
+    }
 
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
-  JMenuBar jMenuBar1 = new JMenuBar();
+    public void createImageMap(File file, String image)
+    {
+      alignPanel.makePNGImageMap(file, image);
+    }
 
-  void updateEditMenuBar()
-  {
-    if(historyList.size()>0)
-     {
-       undoMenuItem.setEnabled(true);
-       Object [] history = (Object[])historyList.get(0);
-       undoMenuItem.setText("Undo "+history[0]);
-     }
-    else
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void createPNG(File f)
     {
-      undoMenuItem.setEnabled(false);
-      undoMenuItem.setText("Undo");
+        alignPanel.makePNG(f);
     }
 
-    if(redoList.size()>0)
-     {
-       redoMenuItem.setEnabled(true);
-       Object [] history = (Object[])redoList.get(0);
-       redoMenuItem.setText("Redo "+history[0]);
-     }
-    else
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void createEPS(File f)
     {
-      redoMenuItem.setEnabled(false);
-      redoMenuItem.setText("Redo");
+        alignPanel.makeEPS(f);
     }
-  }
 
-  public void addHistoryItem(String type)
-  {
-    // must make sure we add new sequence objects her, not refs to the existing sequences
-    redoList.clear();
-    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
-    for(int i=0; i<viewport.getAlignment().getHeight(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void printMenuItem_actionPerformed(ActionEvent e)
     {
-      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
-                             viewport.getAlignment().getSequenceAt(i).getSequence());
+        //Putting in a thread avoids Swing painting problems
+        PrintThread thread = new PrintThread();
+        thread.start();
     }
 
-    historyList.add(0, new Object[]{type,  seq} );
-    updateEditMenuBar();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void closeMenuItem_actionPerformed(ActionEvent e)
+    {
+        try
+        {
+            this.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
+    }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
-  {
-    Object [] history = (Object[])historyList.remove(0);
-    // add the redo state before continuing!!
-    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
-    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
+    /**
+     * DOCUMENT ME!
+     */
+    void updateEditMenuBar()
     {
-      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
-                            viewport.getAlignment().getSequenceAt(i).
-                            getSequence());
+        if (historyList.size() > 0)
+        {
+            undoMenuItem.setEnabled(true);
+
+            HistoryItem hi = (HistoryItem) historyList.peek();
+            undoMenuItem.setText("Undo " + hi.getDescription());
+        }
+        else
+        {
+            undoMenuItem.setEnabled(false);
+            undoMenuItem.setText("Undo");
+        }
+
+        if (redoList.size() > 0)
+        {
+            redoMenuItem.setEnabled(true);
+
+            HistoryItem hi = (HistoryItem) redoList.peek();
+            redoMenuItem.setText("Redo " + hi.getDescription());
+        }
+        else
+        {
+            redoMenuItem.setEnabled(false);
+            redoMenuItem.setText("Redo");
+        }
     }
-    /////////
 
-    redoList.add(0, new Object[] {history[0], seq});
+    /**
+     * DOCUMENT ME!
+     *
+     * @param hi DOCUMENT ME!
+     */
+    public void addHistoryItem(HistoryItem hi)
+    {
+        historyList.push(hi);
+        updateEditMenuBar();
+    }
 
-      seq = (SequenceI[]) history[1];
-      viewport.setAlignment( new Alignment(seq) );
-      updateEditMenuBar();
-      viewport.updateConsensus();
-      alignPanel.RefreshPanels();
-      alignPanel.RefreshPanels();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void undoMenuItem_actionPerformed(ActionEvent e)
+    {
+        HistoryItem hi = (HistoryItem) historyList.pop();
+        redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
+                HistoryItem.HIDE));
+        restoreHistoryItem(hi);
+    }
 
-  public void moveSelectedSequences(boolean up)
-  {
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg == null)
-      return;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void redoMenuItem_actionPerformed(ActionEvent e)
+    {
+        HistoryItem hi = (HistoryItem) redoList.pop();
+        restoreHistoryItem(hi);
+        updateEditMenuBar();
+        viewport.updateConsensus();
+        alignPanel.repaint();
+        alignPanel.repaint();
+    }
 
-    if (up)
+    // used by undo and redo
+    void restoreHistoryItem(HistoryItem hi)
     {
-      for (int i = 1; i < viewport.alignment.getHeight(); i++)
-      {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.sequences.contains(seq))
-          continue;
+        if (hi.getType() == HistoryItem.SORT)
+        {
+            for (int i = 0; i < hi.getSequences().size(); i++)
+            {
+                viewport.alignment.getSequences().setElementAt(hi.getSequences()
+                                                                 .elementAt(i),
+                    i);
+            }
+        }
+        else
+        {
+            for (int i = 0; i < hi.getSequences().size(); i++)
+            {
+                SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
+
+                if (restore.getLength() == 0)
+                {
+                    restore.setSequence(hi.getHidden().elementAt(i).toString());
+                    viewport.alignment.getSequences().insertElementAt(restore,
+                        hi.getAlignIndex(i));
+                }
+                else
+                {
+                    restore.setSequence(hi.getHidden().elementAt(i).toString());
+                }
+            }
+
+            if (hi.getType() == HistoryItem.PASTE)
+            {
+                for (int i = viewport.alignment.getHeight() - 1;
+                        i > (hi.getSequences().size() - 1); i--)
+                {
+                    viewport.alignment.deleteSequence(i);
+                }
+            }
+        }
 
-        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
-        if (sg.sequences.contains(temp))
-          continue;
+        updateEditMenuBar();
 
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i - 1);
-      }
+        viewport.updateConsensus();
+        viewport.updateConservation();
+        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null,
+            viewport.getAlignment().getSequences());
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param up DOCUMENT ME!
+     */
+    public void moveSelectedSequences(boolean up)
     {
-      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
-      {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.sequences.contains(seq))
-          continue;
+        SequenceGroup sg = viewport.getSelectionGroup();
 
-        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
-        if (sg.sequences.contains(temp))
-          continue;
+        if (sg == null)
+        {
+            return;
+        }
 
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i + 1);
-      }
+        if (up)
+        {
+            for (int i = 1; i < viewport.alignment.getHeight(); i++)
+            {
+                SequenceI seq = viewport.alignment.getSequenceAt(i);
+
+                if (!sg.sequences.contains(seq))
+                {
+                    continue;
+                }
+
+                SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+
+                if (sg.sequences.contains(temp))
+                {
+                    continue;
+                }
+
+                viewport.alignment.getSequences().setElementAt(temp, i);
+                viewport.alignment.getSequences().setElementAt(seq, i - 1);
+            }
+        }
+        else
+        {
+            for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+            {
+                SequenceI seq = viewport.alignment.getSequenceAt(i);
+
+                if (!sg.sequences.contains(seq))
+                {
+                    continue;
+                }
+
+                SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+
+                if (sg.sequences.contains(temp))
+                {
+                    continue;
+                }
+
+                viewport.alignment.getSequences().setElementAt(temp, i);
+                viewport.alignment.getSequences().setElementAt(seq, i + 1);
+            }
+        }
+
+        alignPanel.repaint();
     }
 
-    alignPanel.RefreshPanels();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void copy_actionPerformed(ActionEvent e)
+    {
+        if (viewport.getSelectionGroup() == null)
+        {
+            return;
+        }
 
+        SequenceGroup sg = viewport.getSelectionGroup();
 
+        Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+        StringBuffer buffer = new StringBuffer();
 
-  protected void copy_actionPerformed(ActionEvent e)
-  {
-   if(viewport.getSelectionGroup()==null)
-     return;
+        Hashtable orderedSeqs = new Hashtable();
 
-   SequenceGroup sg = viewport.getSelectionGroup();
+        for (int i = 0; i < sg.getSize(); i++)
+        {
+            SequenceI seq = sg.getSequenceAt(i);
+            int index = viewport.alignment.findIndex(seq);
+            orderedSeqs.put(index + "", seq);
+        }
 
-     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-     StringBuffer buffer= new StringBuffer();
+        int index = 0;
 
-       for(int i=0; i<sg.getSize(); i++)
-       {
-         SequenceI seq = sg.getSequenceAt(i);
-         buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
-                        +seq.findPosition( sg.getEndRes() )+ "\t"
-                        +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
-       }
-     c.setContents( new StringSelection( buffer.toString()) , null ) ;
+        for (int i = 0; i < sg.getSize(); i++)
+        {
+            SequenceI seq = null;
+
+            while (seq == null)
+            {
+                if (orderedSeqs.containsKey(index + ""))
+                {
+                    seq = (SequenceI) orderedSeqs.get(index + "");
+                    index++;
+
+                    break;
+                }
+                else
+                {
+                    index++;
+                }
+            }
+
+            buffer.append(seq.getName() + "\t" +
+                seq.findPosition(sg.getStartRes()) + "\t" +
+                seq.findPosition(sg.getEndRes()) + "\t" +
+                sg.getSequenceAt(i).getSequence(sg.getStartRes(),
+                    sg.getEndRes() + 1) + "\n");
+        }
 
-  }
+        c.setContents(new StringSelection(buffer.toString()), null);
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void pasteNew_actionPerformed(ActionEvent e)
+    {
+        paste(true);
+    }
 
-  protected void pasteNew_actionPerformed(ActionEvent e)
-  {
-    paste(true);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void pasteThis_actionPerformed(ActionEvent e)
+    {
+        addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+                HistoryItem.PASTE));
+        paste(false);
+    }
 
-  protected void pasteThis_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("Paste");
-    paste(false);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param newAlignment DOCUMENT ME!
+     */
+    void paste(boolean newAlignment)
+    {
+        try
+        {
+            Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+            Transferable contents = c.getContents(this);
+
+            if (contents == null)
+            {
+                return;
+            }
+
+            String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+            StringTokenizer st = new StringTokenizer(str);
+            ArrayList seqs = new ArrayList();
+
+            while (st.hasMoreElements())
+            {
+                String name = st.nextToken();
+                int start = Integer.parseInt(st.nextToken());
+                int end = Integer.parseInt(st.nextToken());
+                Sequence sequence = new Sequence(name, st.nextToken(), start,
+                        end);
+
+                if (!newAlignment)
+                {
+                    viewport.alignment.addSequence(sequence);
+                }
+                else
+                {
+                    seqs.add(sequence);
+                }
+            }
+
+            if (newAlignment)
+            {
+                SequenceI[] newSeqs = new SequenceI[seqs.size()];
+                seqs.toArray(newSeqs);
+
+                AlignFrame af = new AlignFrame(new Alignment(newSeqs));
+                String newtitle = new String("Copied sequences");
+
+                if (title.startsWith("Copied sequences"))
+                {
+                    newtitle = title;
+                }
+                else
+                {
+                    newtitle = newtitle.concat("- from " + title);
+                }
+
+                Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
+                    NEW_WINDOW_HEIGHT);
+            }
+            else
+            {
+                viewport.firePropertyChange("alignment", null,
+                    viewport.getAlignment().getSequences());
+                viewport.setEndSeq(viewport.alignment.getHeight());
+                viewport.alignment.getWidth();
+                viewport.updateConservation();
+                viewport.updateConsensus();
+                alignPanel.repaint();
+            }
+        }
+        catch (Exception ex)
+        {
+        }
 
-  void paste(boolean newAlignment)
-  {
-    try{
-      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-      Transferable contents = c.getContents(this);
-      if (contents == null)
-        return;
+        // could be anything being pasted in here
+    }
 
-      String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
-      StringTokenizer st = new StringTokenizer(str);
-      ArrayList seqs = new ArrayList();
-      while (st.hasMoreElements())
-      {
-        String name = st.nextToken();
-        int start = Integer.parseInt(st.nextToken());
-        int end = Integer.parseInt(st.nextToken());
-        Sequence sequence = new Sequence(name,st.nextToken(), start, end);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void cut_actionPerformed(ActionEvent e)
+    {
+        copy_actionPerformed(null);
+        delete_actionPerformed(null);
+    }
 
-        if(!newAlignment)
-          viewport.alignment.addSequence(sequence);
-        else
-          seqs.add(sequence);
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void delete_actionPerformed(ActionEvent e)
+    {
+        boolean seqsdeleted = false;
 
-      if(newAlignment)
-      {
-        SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        seqs.toArray(newSeqs);
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs));
-        Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
-      }
-      else
-      {
-        viewport.setEndSeq(viewport.alignment.getHeight());
-        viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.RefreshPanels();
-      }
+        if (viewport.getSelectionGroup() == null)
+        {
+            return;
+        }
 
-    }catch(Exception ex){}// could be anything being pasted in here
+        addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                HistoryItem.HIDE));
 
-  }
+        SequenceGroup sg = viewport.getSelectionGroup();
+        boolean allSequences = false;
+        if(sg.sequences.size()==viewport.alignment.getHeight())
+          allSequences = true;
 
+        for (int i = 0; i < sg.sequences.size(); i++)
+        {
+            SequenceI seq = sg.getSequenceAt(i);
+            int index = viewport.getAlignment().findIndex(seq);
+            seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+
+            // If the cut affects all sequences, remove highlighted columns
+            if(allSequences)
+            {
+              viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1);
+            }
+
+
+            if (seq.getSequence().length() < 1)
+            {
+                seqsdeleted = true;
+                viewport.getAlignment().deleteSequence(seq);
+            }
+            else
+            {
+                viewport.getAlignment().getSequences().setElementAt(seq, index);
+            }
+        }
 
-  protected void cut_actionPerformed(ActionEvent e)
-  {
-    copy_actionPerformed(null);
-    delete_actionPerformed(null);
-  }
+        viewport.setSelectionGroup(null);
+        viewport.alignment.deleteGroup(sg);
 
-  protected void delete_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("Delete");
-    if (viewport.getSelectionGroup() == null)
-      return;
+        if (seqsdeleted)
+        {
+            viewport.firePropertyChange("alignment", null,
+                viewport.getAlignment().getSequences());
+        }
 
-     SequenceGroup sg = viewport.getSelectionGroup();
-     for (int i=0;i < sg.sequences.size(); i++)
-     {
-       SequenceI seq = sg.getSequenceAt(i);
-       int index = viewport.getAlignment().findIndex(seq);
-       seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
+        viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
 
-       if(seq.getSequence().length()<1)
-          viewport.getAlignment().deleteSequence(seq);
-      else
-          viewport.getAlignment().getSequences().setElementAt(seq, index);
-     }
-
-     viewport.setSelectionGroup(null);
-     viewport.alignment.deleteGroup(sg);
-     viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
-     if(viewport.getAlignment().getHeight()<1)
-     try
-     {
-       this.setClosed(true);
-     }catch(Exception ex){}
-   viewport.updateConservation();
-   viewport.updateConsensus();
-     alignPanel.RefreshPanels();
-
-  }
-
-
-
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
-  {
-     Object [] history = (Object[])redoList.remove(0);
-     SequenceI[] seq = (SequenceI[]) history[1];
-     viewport.setAlignment( new Alignment(seq) );
-     updateEditMenuBar();
-     viewport.updateConsensus();
-     alignPanel.RefreshPanels();
-     alignPanel.RefreshPanels();
-  }
-
-
-  protected void deleteGroups_actionPerformed(ActionEvent e)
-  {
-    viewport.alignment.deleteAllGroups();
-    viewport.setSelectionGroup(null);
-
-    alignPanel.RefreshPanels();
-  }
-
-
-
-  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = new SequenceGroup();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
-    sg.setEndRes(viewport.alignment.getWidth());
-    viewport.setSelectionGroup(sg);
-    PaintRefresher.Refresh(null);
-  }
-
-  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(null);
-  }
-
-  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = viewport.getSelectionGroup();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
-
-    PaintRefresher.Refresh(null);
-  }
-
-
-  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.getColumnSelection().clear();
-    repaint();
-  }
-
-  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("delete columns");
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
-    {
-      int min = colSel.getMin();
-      viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0,min);
-
-      if(viewport.getSelectionGroup()!=null)
-        viewport.getSelectionGroup().adjustForRemoveLeft(min);
-
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
-        if(!sg.adjustForRemoveLeft(min))
-          viewport.alignment.deleteGroup(sg);
-      }
+        if (viewport.getAlignment().getHeight() < 1)
+        {
+            try
+            {
+                this.setClosed(true);
+            }
+            catch (Exception ex)
+            {
+            }
+        }
 
-      alignPanel.RefreshPanels();
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
     }
-  }
 
-  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("delete columns");
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void deleteGroups_actionPerformed(ActionEvent e)
     {
-      int max = colSel.getMax();
-      viewport.getAlignment().trimRight(max);
-      if(viewport.getSelectionGroup()!=null)
-        viewport.getSelectionGroup().adjustForRemoveRight(max);
+        viewport.alignment.deleteAllGroups();
+        viewport.setSelectionGroup(null);
+        alignPanel.repaint();
+    }
 
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
-        if(!sg.adjustForRemoveRight(max))
-          viewport.alignment.deleteGroup(sg);
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = new SequenceGroup();
 
+        for (int i = 0; i < viewport.getAlignment().getSequences().size();
+                i++)
+        {
+            sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
+        }
 
+        sg.setEndRes(viewport.alignment.getWidth());
+        viewport.setSelectionGroup(sg);
+        PaintRefresher.Refresh(null, viewport.alignment);
+    }
 
-      alignPanel.RefreshPanels();
-    }
-
-  }
-
-  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("delete gapped columns");
-    viewport.getAlignment().removeGaps();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.RefreshPanels();
-  }
-
-  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("delete all gaps");
-    SequenceI current;
-    int jSize;
-    for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
-    {
-      current = viewport.getAlignment().getSequenceAt(i);
-      jSize = current.getLength();
-      for (int j=0; j < jSize; j++)
-        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
-        {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
-        }
-    }
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.RefreshPanels();
-  }
-
-  public void setGapCharMenuItem_actionPerformed(ActionEvent e)
-  {
-    char thisChar = '-';
-    char nextChar = '.';
-    if(viewport.getGapCharacter()=='-')
-    {
-      thisChar = '.';
-      nextChar = '-';
-    }
-    setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
-    viewport.setGapCharacter(thisChar);
-    alignPanel.RefreshPanels();
-  }
-
-  public void findMenuItem_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    Finder finder = new Finder(viewport, alignPanel, frame);
-    frame.setContentPane(finder);
-    Desktop.addInternalFrame(frame, "Find", 340,110, false);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-
-  }
-
-
-  public void font_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    FontChooser fc = new FontChooser( alignPanel, frame );
-    frame.setContentPane(fc);
-    Desktop.addInternalFrame(frame, "Change Font", 480,100);
-  }
-
-  protected void fullSeqId_actionPerformed(ActionEvent e)
-  {
-    viewport.setShowFullId( fullSeqId.isSelected() );
-
-    alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
-    alignPanel.RefreshPanels();
-  }
-
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
-  {
-      viewport.setColourText( colourTextMenuItem.isSelected() );
-      alignPanel.RefreshPanels();
-  }
-
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
-    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
-    scaleAbove.setVisible( wrapMenuItem.isSelected() );
-    scaleLeft.setVisible( wrapMenuItem.isSelected() );
-    scaleRight.setVisible( wrapMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
-  }
-
-  protected void scaleAbove_actionPerformed(ActionEvent e)
-  {
-    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    alignPanel.repaint();
-  }
-
-  protected void scaleLeft_actionPerformed(ActionEvent e)
-  {
-    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
-    alignPanel.repaint();
-  }
-
-  protected void scaleRight_actionPerformed(ActionEvent e)
-  {
-    viewport.setScaleRightWrapped(scaleRight.isSelected());
-    alignPanel.repaint();
-  }
-
-
-
-  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
-  }
-
-  public void viewTextMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setShowText( viewTextMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
-  }
-
-
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.RefreshPanels();
-  }
-
-  public void sequenceFeatures_actionPerformed(ActionEvent evt)
-  {
-    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
-    if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
-    {
-         AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
-         ((Alignment)viewport.alignment).featuresAdded = true;
-    }
-    alignPanel.RefreshPanels();
-  }
-
-  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
-  {
-    if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
-    {
-      annotationPanelMenuItem.setSelected(false);
-      return;
-    }
-    viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
-    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
-  }
-
-  public void overviewMenuItem_actionPerformed(ActionEvent e)
-  {
-    if (alignPanel.overviewPanel != null)
-      return;
-
-    JInternalFrame frame = new JInternalFrame();
-    OverviewPanel overview = alignPanel.getOverviewPanel();
-   try{
-     overview = new OverviewPanel(alignPanel, viewport);
-     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
-                             frame.getWidth(), frame.getHeight());
-    frame.pack();
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
-      {
-            alignPanel.setOverviewPanel(null);
-      };
-    });
-    alignPanel.setOverviewPanel( overview );
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+    {
+        viewport.setSelectionGroup(null);
+        viewport.getColumnSelection().clear();
+        viewport.setSelectionGroup(null);
+        alignPanel.annotationPanel.activeRes = null;
+        PaintRefresher.Refresh(null, viewport.alignment);
+    }
 
-  }catch(java.lang.OutOfMemoryError ex)
-   {
-     JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
-                                   +"\nTry reducing the font size.",
-                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
-   }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+    {
+        SequenceGroup sg = viewport.getSelectionGroup();
 
+        if (sg == null)
+        {
+            selectAllSequenceMenuItem_actionPerformed(null);
 
-  }
+            return;
+        }
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    changeColour( null );
-  }
+        for (int i = 0; i < viewport.getAlignment().getSequences().size();
+                i++)
+        {
+            sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+        }
 
+        PaintRefresher.Refresh(null, viewport.alignment);
+    }
 
-  public void clustalColour_actionPerformed(ActionEvent e)
-  {
-    abovePIDThreshold.setSelected(false);
-    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+    {
+        ColumnSelection colSel = viewport.getColumnSelection();
 
-  public void zappoColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new ZappoColourScheme());
-  }
+        if (colSel.size() > 0)
+        {
+            addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
+                    HistoryItem.HIDE));
 
-  public void taylorColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new TaylorColourScheme());
-  }
+            int min = colSel.getMin();
+            viewport.getAlignment().trimLeft(min);
+            colSel.compensateForEdit(0, min);
 
+            if (viewport.getSelectionGroup() != null)
+            {
+                viewport.getSelectionGroup().adjustForRemoveLeft(min);
+            }
 
-  public void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    changeColour( new HydrophobicColourScheme() );
-  }
+            Vector groups = viewport.alignment.getGroups();
 
-  public void helixColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new HelixColourScheme() );
-  }
+            for (int i = 0; i < groups.size(); i++)
+            {
+                SequenceGroup sg = (SequenceGroup) groups.get(i);
 
+                if (!sg.adjustForRemoveLeft(min))
+                {
+                    viewport.alignment.deleteGroup(sg);
+                }
+            }
 
-  public void strandColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new StrandColourScheme());
-  }
+            alignPanel.repaint();
+        }
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void remove2RightMenuItem_actionPerformed(ActionEvent e)
+    {
+        ColumnSelection colSel = viewport.getColumnSelection();
 
-  public void turnColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new TurnColourScheme());
-  }
+        if (colSel.size() > 0)
+        {
+            addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
+                    HistoryItem.HIDE));
 
+            int max = colSel.getMax();
+            viewport.getAlignment().trimRight(max);
 
-  public void buriedColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new BuriedColourScheme() );
-  }
+            if (viewport.getSelectionGroup() != null)
+            {
+                viewport.getSelectionGroup().adjustForRemoveRight(max);
+            }
 
-  public void nucleotideColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new NucleotideColourScheme());
-  }
+            Vector groups = viewport.alignment.getGroups();
 
+            for (int i = 0; i < groups.size(); i++)
+            {
+                SequenceGroup sg = (SequenceGroup) groups.get(i);
 
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
-  {
-    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
-  }
+                if (!sg.adjustForRemoveRight(max))
+                {
+                    viewport.alignment.deleteGroup(sg);
+                }
+            }
 
+            alignPanel.repaint();
+        }
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+    {
+        addHistoryItem(new HistoryItem("Remove Gapped Columns",
+                viewport.alignment, HistoryItem.HIDE));
 
-  void changeColour(ColourSchemeI cs)
-  {
+        viewport.getAlignment().removeGaps();
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
+    }
 
-    if(viewport.getColourAppliesToAllGroups())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
     {
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-        sg.cs = cs;
+        addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
+                HistoryItem.HIDE));
+
+        SequenceI current;
+        int jSize;
+
+        Vector seqs = null;
 
-        if(abovePIDThreshold.isSelected())
-          abovePIDThreshold_actionPerformed(null);
-        else if( viewport.getConservationSelected() )
+        int start = 0;
+        int end = viewport.alignment.getWidth();
+
+        if (viewport.getSelectionGroup() != null)
+        {
+            seqs = viewport.getSelectionGroup().sequences;
+            start = viewport.getSelectionGroup().getStartRes();
+            end = viewport.getSelectionGroup().getEndRes();
+        }
+        else
         {
-          Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.sequences, sg.getStartRes(),
-                                            sg.getEndRes());
-          c.calculate();
-          c.verdict(false, viewport.ConsPercGaps);
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+            seqs = viewport.alignment.getSequences();
+        }
 
-          sg.cs = ccs;
+        for (int i = 0; i < seqs.size(); i++)
+        {
+            current = (SequenceI) seqs.elementAt(i);
+            jSize = current.getLength();
+
+            int j = start;
+
+            do
+            {
+                if (jalview.util.Comparison.isGap(current.getCharAt(j)))
+                {
+                    current.deleteCharAt(j);
+                    j--;
+                    jSize--;
+                }
+
+                j++;
+            }
+            while (j < end && j < jSize);
         }
 
-      }
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void padGapsMenuitem_actionPerformed(ActionEvent e)
+    {
+        addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
+                HistoryItem.HIDE));
+
+        SequenceI current;
+        int Width = viewport.getAlignment().getWidth();
+
+        for (int i = 0; i < viewport.getAlignment().getSequences().size();
+                i++)
+        {
+            current = viewport.getAlignment().getSequenceAt(i);
 
-    if ( viewport.getAbovePIDThreshold() )
+            if (current.getLength() < Width)
+            {
+                current.insertCharAt(Width - 1, viewport.getGapCharacter());
+            }
+        }
+
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findMenuItem_actionPerformed(ActionEvent e)
     {
- //     int threshold = 0;
-   //   threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
-      Desktop.hideConservationSlider();
+        JInternalFrame frame = new JInternalFrame();
+        Finder finder = new Finder(viewport, alignPanel, frame);
+        frame.setContentPane(finder);
+        Desktop.addInternalFrame(frame, "Find", 340, 110);
+        frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
 
- //     if (cs instanceof ResidueColourScheme)
- //       ( (ResidueColourScheme) cs).setThreshold(threshold);
-  //    else if (cs instanceof ScoreColourScheme)
-   //     ( (ScoreColourScheme) cs).setThreshold(threshold);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void font_actionPerformed(ActionEvent e)
+    {
+        FontChooser fc = new FontChooser(alignPanel);
+    }
 
-      viewport.setGlobalColourScheme(cs);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void fullSeqId_actionPerformed(ActionEvent e)
+    {
+        viewport.setShowFullId(fullSeqId.isSelected());
 
+        alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+        alignPanel.repaint();
     }
-    else
-    if (cs instanceof ResidueColourScheme)
-      ( (ResidueColourScheme) cs).setThreshold(0);
-    else if (cs instanceof ScoreColourScheme)
-      ( (ScoreColourScheme) cs).setThreshold(0);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+    {
+        viewport.setColourText(colourTextMenuItem.isSelected());
+        alignPanel.repaint();
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void wrapMenuItem_actionPerformed(ActionEvent e)
+    {
+        viewport.setWrapAlignment(wrapMenuItem.isSelected());
+        alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+        scaleAbove.setVisible(wrapMenuItem.isSelected());
+        scaleLeft.setVisible(wrapMenuItem.isSelected());
+        scaleRight.setVisible(wrapMenuItem.isSelected());
+        alignPanel.repaint();
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void scaleAbove_actionPerformed(ActionEvent e)
+    {
+        viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+        alignPanel.repaint();
+    }
 
-if ( viewport.getConservationSelected() )
- {
-   ConservationColourScheme ccs = null;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void scaleLeft_actionPerformed(ActionEvent e)
+    {
+        viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+        alignPanel.repaint();
+    }
 
-   Alignment al = (Alignment) viewport.alignment;
-   Conservation c = new Conservation("All",
-                                     ResidueProperties.propHash, 3,
-                                     al.getSequences(), 0,
-                                     al.getWidth());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void scaleRight_actionPerformed(ActionEvent e)
+    {
+        viewport.setScaleRightWrapped(scaleRight.isSelected());
+        alignPanel.repaint();
+    }
 
-   c.calculate();
-   c.verdict(false, viewport.ConsPercGaps);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+    {
+        viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
+        alignPanel.repaint();
+    }
 
-   ccs = new ConservationColourScheme(c, cs);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void viewTextMenuItem_actionPerformed(ActionEvent e)
+    {
+        viewport.setShowText(viewTextMenuItem.isSelected());
+        alignPanel.repaint();
+    }
 
- //  int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,    "Background");
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+    {
+        viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+        alignPanel.repaint();
+    }
 
- //  ccs.inc = threshold;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void sequenceFeatures_actionPerformed(ActionEvent evt)
+    {
+        viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 
-   viewport.setGlobalColourScheme(ccs);
+        if (viewport.showSequenceFeatures &&
+                !((Alignment) viewport.alignment).featuresAdded)
+        {
+            SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,
+                    alignPanel);
+            ((Alignment) viewport.alignment).featuresAdded = true;
+        }
 
-  }
-  else
-       viewport.setGlobalColourScheme( cs );
+        alignPanel.repaint();
+    }
 
-    alignPanel.RefreshPanels();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+    {
+        if (annotationPanelMenuItem.isSelected() &&
+                viewport.getWrapAlignment())
+        {
+            annotationPanelMenuItem.setSelected(false);
 
-  protected void modifyPID_actionPerformed(ActionEvent e)
-  {
-    Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");
-  }
+            return;
+        }
 
-  protected void modifyConservation_actionPerformed(ActionEvent e)
-  {
-    Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme,    "Background");
-  }
+        viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
+        alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void overviewMenuItem_actionPerformed(ActionEvent e)
+    {
+        if (alignPanel.overviewPanel != null)
+        {
+            return;
+        }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setConservationSelected(conservationMenuItem.isSelected());
-    if(coloursChanging)
-      return;
+        JInternalFrame frame = new JInternalFrame();
+        OverviewPanel overview = new OverviewPanel(alignPanel);
+        frame.setContentPane(overview);
+        Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+            frame.getWidth(), frame.getHeight());
+        frame.pack();
+        frame.setLayer(JLayeredPane.PALETTE_LAYER);
+        frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+                public void internalFrameClosed(
+                    javax.swing.event.InternalFrameEvent evt)
+                {
+                    alignPanel.setOverviewPanel(null);
+                }
+                ;
+            });
+
+        alignPanel.setOverviewPanel(overview);
+    }
 
-    coloursChanging = true;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void noColourmenuItem_actionPerformed(ActionEvent e)
+    {
+        changeColour(null);
+    }
 
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setSelected(false);
-    Desktop.hidePIDSlider();
-    if(!viewport.getConservationSelected())
-      Desktop.hideConservationSlider();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void clustalColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new ClustalxColourScheme(
+                viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+    }
 
-   ColourSchemeI cs = viewport.getGlobalColourScheme();
-   if(cs instanceof ConservationColourScheme )
-     changeColour( ((ConservationColourScheme)cs).cs );
-    else
-      changeColour( cs );
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void zappoColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new ZappoColourScheme());
+    }
 
-    coloursChanging = false;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void taylorColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new TaylorColourScheme());
+    }
 
-  boolean coloursChanging = false;
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)
-  {
-    if(coloursChanging)
-      return;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void hydrophobicityColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new HydrophobicColourScheme());
+    }
 
-    coloursChanging = true;
-    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void helixColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new HelixColourScheme());
+    }
 
-    conservationMenuItem.setSelected(false);
-    viewport.setConservationSelected(false);
-    Desktop.hideConservationSlider();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void strandColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new StrandColourScheme());
+    }
 
-    if(!viewport.getAbovePIDThreshold())
-      Desktop.hidePIDSlider();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void turnColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new TurnColourScheme());
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void buriedColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new BuriedColourScheme());
+    }
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-    if(cs instanceof ConservationColourScheme )
-        changeColour( ((ConservationColourScheme)cs).cs );
-    else
-        changeColour( cs );
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void nucleotideColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new NucleotideColourScheme());
+    }
 
-    coloursChanging = false;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void applyToAllGroups_actionPerformed(ActionEvent e)
+    {
+        viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     */
+    void changeColour(ColourSchemeI cs)
+    {
+        int threshold = 0;
 
+        if (viewport.getAbovePIDThreshold())
+        {
+            threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+                    "Background");
+
+            if (cs instanceof ResidueColourScheme)
+            {
+                ((ResidueColourScheme) cs).setThreshold(threshold);
+            }
+            else if (cs instanceof ScoreColourScheme)
+            {
+                ((ScoreColourScheme) cs).setThreshold(threshold);
+            }
+
+            viewport.setGlobalColourScheme(cs);
+        }
+        else if (cs instanceof ResidueColourScheme)
+        {
+            ((ResidueColourScheme) cs).setThreshold(0);
+        }
+        else if (cs instanceof ScoreColourScheme)
+        {
+            ((ScoreColourScheme) cs).setThreshold(0);
+        }
 
-  public void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );
-  }
+        if (viewport.getConservationSelected())
+        {
+            ConservationColourScheme ccs = null;
 
-  public void PIDColour_actionPerformed(ActionEvent e)
-  {
-    changeColour( new PIDColourScheme() );
-  }
+            Alignment al = (Alignment) viewport.alignment;
+            Conservation c = new Conservation("All",
+                    ResidueProperties.propHash, 3, al.getSequences(), 0,
+                    al.getWidth() - 1);
 
+            c.calculate();
+            c.verdict(false, viewport.ConsPercGaps);
 
-  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new Blosum62ColourScheme(viewport) );
-  }
+            ccs = new ConservationColourScheme(c, cs);
 
+            // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+            ccs.setConsensus(viewport.vconsensus);
+            viewport.setGlobalColourScheme(ccs);
 
+            ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
+                    "Background");
+        }
+        else
+        {
+            // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+            if (cs != null)
+            {
+                cs.setConsensus(viewport.vconsensus);
+            }
 
-  public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
-    alignPanel.RefreshPanels();
-  }
+            viewport.setGlobalColourScheme(cs);
+        }
 
-  public void sortIDMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByID( viewport.getAlignment() );
-    alignPanel.RefreshPanels();
-  }
+        if (viewport.getColourAppliesToAllGroups())
+        {
+            Vector groups = viewport.alignment.getGroups();
+
+            for (int i = 0; i < groups.size(); i++)
+            {
+                SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+                if (cs == null)
+                {
+                    sg.cs = null;
+                }
+                else if (cs instanceof ClustalxColourScheme)
+                {
+                    sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+                }
+                else if (cs instanceof UserColourScheme)
+                {
+                    sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
+                }
+                else
+                {
+                    try
+                    {
+                        sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+                    }
+                    catch (Exception ex)
+                    {
+                    }
+                }
+
+                if (viewport.getAbovePIDThreshold())
+                {
+                    if (sg.cs instanceof ResidueColourScheme)
+                    {
+                        ((ResidueColourScheme) sg.cs).setThreshold(threshold);
+                    }
+                    else if (sg.cs instanceof ScoreColourScheme)
+                    {
+                        ((ScoreColourScheme) sg.cs).setThreshold(threshold);
+                    }
+
+                    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                            sg.getWidth()));
+                }
+
+                if (viewport.getConservationSelected())
+                {
+                    Conservation c = new Conservation("Group",
+                            ResidueProperties.propHash, 3, sg.sequences, 0,
+                            viewport.alignment.getWidth() - 1);
+                    c.calculate();
+                    c.verdict(false, viewport.ConsPercGaps);
+
+                    ConservationColourScheme ccs = new ConservationColourScheme(c,
+                            sg.cs);
+
+                    // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+                    ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                            sg.getWidth()));
+                    sg.cs = ccs;
+                }
+                else if (cs != null)
+                {
+                    // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+                    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                            sg.getWidth()));
+                }
+            }
+        }
 
-  public void sortGroupMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByGroup(viewport.getAlignment());
-    AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.RefreshPanels();
-  }
+        if (alignPanel.getOverviewPanel() != null)
+        {
+            alignPanel.getOverviewPanel().updateOverviewImage();
+        }
 
-  public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
-  {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
+        alignPanel.repaint();
+    }
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void modifyPID_actionPerformed(ActionEvent e)
+    {
+        if (viewport.getAbovePIDThreshold())
+        {
+            SliderPanel.setPIDSliderSource(alignPanel,
+                viewport.getGlobalColourScheme(), "Background");
+            SliderPanel.showPIDSlider();
+        }
+    }
 
-  public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
-  {
-    if(viewport.getSelectionGroup().getSize()<2)
-      JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
-    else
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void modifyConservation_actionPerformed(ActionEvent e)
     {
-      JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(new PairwiseAlignPanel(viewport));
-      Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+        if (viewport.getConservationSelected())
+        {
+            SliderPanel.setConservationSlider(alignPanel,
+                viewport.globalColourScheme, "Background");
+            SliderPanel.showConservationSlider();
+        }
     }
-  }
 
-  public void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void conservationMenuItem_actionPerformed(ActionEvent e)
+    {
+        viewport.setConservationSelected(conservationMenuItem.isSelected());
+
+        viewport.setAbovePIDThreshold(false);
+        abovePIDThreshold.setSelected(false);
+
+        ColourSchemeI cs = viewport.getGlobalColourScheme();
+
+        if (cs instanceof ConservationColourScheme)
+        {
+            changeColour(((ConservationColourScheme) cs).cs);
+        }
+        else
+        {
+            changeColour(cs);
+        }
+
+        modifyConservation_actionPerformed(null);
+    }
 
-    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
-       || viewport.getAlignment().getHeight()<4)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void abovePIDThreshold_actionPerformed(ActionEvent e)
     {
-      JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
-                                    +"at least 4 input sequences.",
-                                    "Sequence selection insufficient",
-                                    JOptionPane.WARNING_MESSAGE);
-      return;
+        viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+
+        conservationMenuItem.setSelected(false);
+        viewport.setConservationSelected(false);
+
+        ColourSchemeI cs = viewport.getGlobalColourScheme();
+
+        if (cs instanceof ConservationColourScheme)
+        {
+            changeColour(((ConservationColourScheme) cs).cs);
+        }
+        else
+        {
+            changeColour(cs);
+        }
+
+        modifyPID_actionPerformed(null);
     }
 
-    try{
-      PCAPanel pcaPanel = new PCAPanel(viewport, null);
-      JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(pcaPanel);
-      Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
-   }catch(java.lang.OutOfMemoryError ex)
-   {
-     JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
-                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
-   }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void userDefinedColour_actionPerformed(ActionEvent e)
+    {
+        new UserDefinedColours(alignPanel, null);
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void PIDColour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new PIDColourScheme());
+    }
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+    {
+        changeColour(new Blosum62ColourScheme());
+    }
 
-  public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    NewTreePanel("AV", "PID", "Average distance tree using PID");
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+    {
+        addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
+                HistoryItem.SORT));
+        AlignmentSorter.sortByPID(viewport.getAlignment(),
+            viewport.getAlignment().getSequenceAt(0));
+        alignPanel.repaint();
+    }
 
-  public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void sortIDMenuItem_actionPerformed(ActionEvent e)
+    {
+        addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+                HistoryItem.SORT));
+        AlignmentSorter.sortByID(viewport.getAlignment());
+        alignPanel.repaint();
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void sortGroupMenuItem_actionPerformed(ActionEvent e)
+    {
+        addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+                HistoryItem.SORT));
 
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
-  }
+        AlignmentSorter.sortByGroup(viewport.getAlignment());
+        alignPanel.repaint();
+    }
 
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+    {
+        RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
+        JInternalFrame frame = new JInternalFrame();
+        frame.setContentPane(sp);
+        Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
+            100, false);
+    }
 
-  void NewTreePanel(String type, String pwType, String title)
-  {
-    //are the sequences aligned?
-    if(!viewport.alignment.isAligned())
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
-                                    "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
-      return;
+        if ((viewport.getSelectionGroup() == null) ||
+                (viewport.getSelectionGroup().getSize() < 2))
+        {
+            JOptionPane.showInternalMessageDialog(this,
+                "You must select at least 2 sequences.", "Invalid Selection",
+                JOptionPane.WARNING_MESSAGE);
+        }
+        else
+        {
+            JInternalFrame frame = new JInternalFrame();
+            frame.setContentPane(new PairwiseAlignPanel(viewport));
+            Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+        }
     }
 
-    final TreePanel tp;
-    if (viewport.getSelectionGroup() != null &&
-        viewport.getSelectionGroup().getSize() > 3)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void PCAMenuItem_actionPerformed(ActionEvent e)
     {
-      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
-                         pwType,
-                         0, viewport.alignment.getWidth());
+        if (((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() < 4) &&
+                (viewport.getSelectionGroup().getSize() > 0)) ||
+                (viewport.getAlignment().getHeight() < 4))
+        {
+            JOptionPane.showInternalMessageDialog(this,
+                "Principal component analysis must take\n" +
+                "at least 4 input sequences.",
+                "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE);
+
+            return;
+        }
+
+        try
+        {
+            PCAPanel pcaPanel = new PCAPanel(viewport, null);
+            JInternalFrame frame = new JInternalFrame();
+            frame.setContentPane(pcaPanel);
+            Desktop.addInternalFrame(frame, "Principal component analysis",
+                400, 400);
+        }
+        catch (java.lang.OutOfMemoryError ex)
+        {
+            JOptionPane.showInternalMessageDialog(this,
+                "Too many sequences selected\nfor Principal Component Analysis!!",
+                "Out of memory", JOptionPane.WARNING_MESSAGE);
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
     {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, 0, viewport.alignment.getWidth());
+        NewTreePanel("AV", "PID", "Average distance tree using PID");
     }
 
-   addTreeMenuItem(tp, title);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+    {
+        NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+    }
 
-   Desktop.addInternalFrame(tp, title, 600, 500);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+    {
+        NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+    }
 
-  void addTreeMenuItem(final TreePanel treePanel, String title)
-  {
-    final JMenuItem item = new JMenuItem(title);
-    sortByTreeMenu.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        addHistoryItem("sort");
-        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
-        alignPanel.RefreshPanels();
-      }
-    });
+        NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+    }
 
-    treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    /**
+     * DOCUMENT ME!
+     *
+     * @param type DOCUMENT ME!
+     * @param pwType DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     */
+    void NewTreePanel(String type, String pwType, String title)
     {
-      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
-      {
-        sortByTreeMenu.remove(item);
-      };
-    });
+        final TreePanel tp;
 
-  }
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 3))
+        {
+            int s = 0;
+            SequenceGroup sg = viewport.getSelectionGroup();
+
+            /* Decide if the selection is a column region */
+            while (s < sg.sequences.size())
+            {
+                if (((SequenceI) sg.sequences.elementAt(s++)).getLength() < sg.getEndRes())
+                {
+                    JOptionPane.showMessageDialog(Desktop.desktop,
+                        "The selected region to create a tree may\nonly contain residues or gaps.\n" +
+                        "Try using the Pad function in the edit menu,\n" +
+                        "or one of the multiple sequence alignment web services.",
+                        "Sequences in selection are not aligned",
+                        JOptionPane.WARNING_MESSAGE);
+
+                    return;
+                }
+            }
+
+            title = title + " on region";
+            tp = new TreePanel(viewport,
+                    viewport.getSelectionGroup().sequences, type, pwType,
+                    sg.getStartRes(), sg.getEndRes());
+        }
+        else
+        {
+            //are the sequences aligned?
+            if (!viewport.alignment.isAligned())
+            {
+                JOptionPane.showMessageDialog(Desktop.desktop,
+                    "The sequences must be aligned before creating a tree.\n" +
+                    "Try using the Pad function in the edit menu,\n" +
+                    "or one of the multiple sequence alignment web services.",
+                    "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+
+                return;
+            }
+
+            tp = new TreePanel(viewport,
+                    viewport.getAlignment().getSequences(), type, pwType, 0,
+                    viewport.alignment.getWidth());
+        }
 
+        addTreeMenuItem(tp, title);
+        viewport.setCurrentTree(tp.getTree());
 
-  public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    ClustalThread ct = new ClustalThread(frame);
-    Thread t = new Thread(ct);
-    t.start();
-    frame.setContentPane(ct);
-     Desktop.addInternalFrame(frame, title, 320, 90);
+        Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
+    }
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param title DOCUMENT ME!
+     * @param order DOCUMENT ME!
+     */
+    public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
+    {
+        final JMenuItem item = new JMenuItem("by " + title);
+        sort.add(item);
+        item.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+                            HistoryItem.SORT));
+
+                    // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+                    AlignmentSorter.sortBy(viewport.getAlignment(), order);
+                    alignPanel.repaint();
+                }
+            });
+    }
 
-  class ClustalThread extends JPanel implements Runnable
-  {
-    Image image;
-    int angle = 0;
-    boolean webServiceRunning = false;
-    JInternalFrame frame;
-    public ClustalThread(JInternalFrame frame)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param treePanel DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     */
+    void addTreeMenuItem(final TreePanel treePanel, String title)
     {
-      this.frame = frame;
+        final JMenuItem item = new JMenuItem(title);
 
-      java.net.URL url = getClass().getResource("/images/logo.gif");
-      if (url != null)
-      {
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-        try
+        treeCount++;
+
+        if (treeCount == 1)
         {
-          mt.waitForID(0);
+            sort.add(sortByTreeMenu);
         }
-        catch (Exception ex)
-        {}
-      }
 
-      ImageSpinner spinner = new ImageSpinner();
-      spinner.start();
-      webServiceRunning = true;
+        sortByTreeMenu.add(item);
+        item.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    addHistoryItem(new HistoryItem("Tree Sort",
+                            viewport.alignment, HistoryItem.SORT));
+                    AlignmentSorter.sortByTree(viewport.getAlignment(),
+                        treePanel.getTree());
+                    alignPanel.repaint();
+                }
+            });
+
+        treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+                public void internalFrameClosed(
+                    javax.swing.event.InternalFrameEvent evt)
+                {
+                    treeCount--;
+                    sortByTreeMenu.remove(item);
+
+                    if (treeCount == 0)
+                    {
+                        sort.remove(sortByTreeMenu);
+                    }
+                }
+                ;
+            });
+        viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+            {
+                public void propertyChange(PropertyChangeEvent evt)
+                {
+                    if (evt.getPropertyName().equals("alignment"))
+                    {
+                        treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue());
+                        treePanel.repaint();
+                    }
+                }
+            });
     }
 
-    class ImageSpinner extends Thread
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
     {
-      public void run()
-      {
-        while(webServiceRunning)
+        // TODO:resolve which menu item was actually selected
+        // Now, check we have enough sequences
+        SequenceI[] msa = null;
+
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 1))
         {
-          try{
-            Thread.sleep(10);
-            angle+=1;
-            angle %=360;
-            repaint();
-          }
-          catch(Exception ex){}
+            // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+            SequenceGroup seqs = viewport.getSelectionGroup();
+            int sz;
+            msa = new SequenceI[sz = seqs.getSize()];
+
+            for (int i = 0; i < sz; i++)
+            {
+                msa[i] = (SequenceI) seqs.getSequenceAt(i);
+            }
         }
-      }
-    }
+        else
+        {
+            Vector seqs = viewport.getAlignment().getSequences();
 
-    // JBPNote
-    // Should check to see if the server settings are valid
-    // Need visual-delay indication here.
-    public void run()
-       {
-         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
-         Vector sv = viewport.getAlignment().getSequences();
-         SequenceI[] seqs = new SequenceI[sv.size()];
-
-         int i = 0;
-         do
-         {
-           seqs[i] = (SequenceI) sv.elementAt(i);
-         }
-         while (++i < sv.size());
-
-         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
-
-         if (alignment != null)
-         {
-           AlignFrame af = new AlignFrame(new Alignment(alignment));
-           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
-           af.clustalColour_actionPerformed(null);
-           af.clustalColour.setSelected(true);
-         }
-         else
-           JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
-                                         JOptionPane.WARNING_MESSAGE);
-
-         webServiceRunning = false;
-         try{
-           frame.setClosed(true);
-         }catch(Exception ex){}
-       }
-
-       public void paintComponent(Graphics g1)
-       {
-         Graphics2D g = (Graphics2D)g1;
-         g.setColor(Color.white);
-         g.fillRect(0,0,getWidth(), getHeight());
-         if(image!=null)
-         {
-
-           g.rotate (Math.toRadians(angle), 28, 28);
-
-           g.drawImage(image,10,10,this);
-           g.rotate (-Math.toRadians(angle), 28, 28 );
-         }
-         g.setFont(new Font("Arial", Font.BOLD, 12));
-         g.setColor(Color.black);
-         g.drawString("Clustal Alignment Web Service running", 60,30);
-       }
-  }
-  protected void jpred_actionPerformed(ActionEvent e)
-{
+            if (seqs.size() > 1)
+            {
+                msa = new SequenceI[seqs.size()];
 
-    JInternalFrame frame = new JInternalFrame();
-    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+                for (int i = 0; i < seqs.size(); i++)
+                {
+                    msa[i] = (SequenceI) seqs.elementAt(i);
+                }
+            }
+        }
+
+        if (msa != null)
+        {
+            jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
+                    title, msa, false, true);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ClustalRealign_actionPerformed(ActionEvent e)
     {
-      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
-      if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
-      {
-        JPredClient ct = new JPredClient( (SequenceI)
-                                         seqs.getSequenceAt(0));
-      }
-      else
-      {
-        int sz;
-        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
-        for (int i = 0; i < sz; i++)
+        // TODO:resolve which menu item was actually selected
+        // Now, check we have enough sequences
+        SequenceI[] msa = null;
+
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 1))
         {
-          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+            // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+            SequenceGroup seqs = viewport.getSelectionGroup();
+            int sz;
+            msa = new SequenceI[sz = seqs.getSize()];
+
+            for (int i = 0; i < sz; i++)
+            {
+                msa[i] = (SequenceI) seqs.getSequenceAt(i);
+            }
         }
+        else
+        {
+            Vector seqs = viewport.getAlignment().getSequences();
 
-        JPredClient ct = new JPredClient(msa);
-      }
+            if (seqs.size() > 1)
+            {
+                msa = new SequenceI[seqs.size()];
 
+                for (int i = 0; i < seqs.size(); i++)
+                {
+                    msa[i] = (SequenceI) seqs.elementAt(i);
+                }
+            }
+        }
+
+        if (msa != null)
+        {
+            jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
+                    title, msa, true, true);
+        }
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void jpred_actionPerformed(ActionEvent e)
     {
-      Vector seqs = viewport.getAlignment().getSequences();
+        SequenceI seq = null;
+        SequenceI[] msa = null;
 
-      if (seqs.size() == 1 || !viewport.alignment.isAligned())
-      {
-        JPredClient ct = new JPredClient( (SequenceI)
-                                         seqs.elementAt(0));
-      }
-      else
-      {
-        SequenceI[] msa = new SequenceI[seqs.size()];
-        for (int i = 0; i < seqs.size(); i++)
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 0))
         {
-          msa[i] = (SequenceI) seqs.elementAt(i);
+            // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+            SequenceGroup seqs = viewport.getSelectionGroup();
+
+            if ((seqs.getSize() == 1) || !viewport.alignment.isAligned())
+            {
+                seq = (SequenceI) seqs.getSequenceAt(0);
+            }
+            else
+            {
+                int sz;
+                msa = new SequenceI[sz = seqs.getSize()];
+
+                for (int i = 0; i < sz; i++)
+                {
+                    msa[i] = (SequenceI) seqs.getSequenceAt(i);
+                }
+            }
+        }
+        else
+        {
+            Vector seqs = viewport.getAlignment().getSequences();
+
+            if ((seqs.size() == 1) || !viewport.alignment.isAligned())
+            {
+                seq = (SequenceI) seqs.elementAt(0);
+            }
+            else
+            {
+                msa = new SequenceI[seqs.size()];
+
+                for (int i = 0; i < seqs.size(); i++)
+                {
+                    msa[i] = (SequenceI) seqs.elementAt(i);
+                }
+            }
         }
 
-        JPredClient ct = new JPredClient(msa);
-      }
+        if (msa != null)
+        {
+            JPredClient ct = new JPredClient(title, msa);
+        }
+        else if (seq != null)
+        {
+            JPredClient ct = new JPredClient(title, seq);
+        }
+        else
+        {
+            System.err.print(
+                "JALVIEW ERROR! - Unexpected JPred selection state!\n");
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+    {
+        // TODO:resolve which menu item was actually selected
+        // Now, check we have enough sequences
+        SequenceI[] msa = null;
+
+        if ((viewport.getSelectionGroup() != null) &&
+                (viewport.getSelectionGroup().getSize() > 1))
+        {
+            // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+            SequenceGroup seqs = viewport.getSelectionGroup();
+            int sz;
+            msa = new SequenceI[sz = seqs.getSize()];
+
+            for (int i = 0; i < sz; i++)
+            {
+                msa[i] = (SequenceI) seqs.getSequenceAt(i);
+            }
+        }
+        else
+        {
+            Vector seqs = viewport.getAlignment().getSequences();
 
+            if (seqs.size() > 1)
+            {
+                msa = new SequenceI[seqs.size()];
+
+                for (int i = 0; i < seqs.size(); i++)
+                {
+                    msa[i] = (SequenceI) seqs.elementAt(i);
+                }
+            }
+        }
+
+        if (msa != null)
+        {
+            MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
+                    false, true);
+        }
     }
-  }
 
-    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
-    // Pick the tree file
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty("LAST_DIRECTORY"));
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Select a newick-like tree file");
-    chooser.setToolTipText("Load a tree file");
-    int value = chooser.showOpenDialog(null);
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      TreePanel treepanel = null;
-      try
-      {
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
-        fin.parse();
+        // Pick the tree file
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"));
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Select a newick-like tree file");
+        chooser.setToolTipText("Load a tree file");
+
+        int value = chooser.showOpenDialog(null);
 
-        if (fin.getTree() != null)
+        if (value == JalviewFileChooser.APPROVE_OPTION)
         {
-          TreePanel tp = null;
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", choice);
-          Desktop.addInternalFrame(tp, title, 600, 500);
-          addTreeMenuItem(tp, title);
+            String choice = chooser.getSelectedFile().getPath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+
+            try
+            {
+                jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
+                        "File");
+                viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
+            }
+            catch (Exception ex)
+            {
+                JOptionPane.showMessageDialog(Desktop.desktop,
+                    "Problem reading tree file", ex.getMessage(),
+                    JOptionPane.WARNING_MESSAGE);
+                ex.printStackTrace();
+            }
         }
-      }
-      catch (Exception ex)
-      {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                                      "Problem reading tree file",
-                                      ex.getMessage(),
-                                      JOptionPane.WARNING_MESSAGE);
-        ex.printStackTrace();
-      }
     }
-  }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param nf DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public TreePanel ShowNewickTree(NewickFile nf, String title)
+    {
+        TreePanel tp = null;
+
+        try
+        {
+            nf.parse();
+
+            if (nf.getTree() != null)
+            {
+                tp = new TreePanel(viewport,
+                        viewport.getAlignment().getSequences(), nf, "FromFile",
+                        title);
+                Desktop.addInternalFrame(tp, title, 600, 500);
+                addTreeMenuItem(tp, title);
+            }
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+
+        return tp;
+    }
+
+    class PrintThread extends Thread
+    {
+        public void run()
+        {
+            PrinterJob printJob = PrinterJob.getPrinterJob();
+            PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+            printJob.setPrintable(alignPanel, pf);
+
+            if (printJob.printDialog())
+            {
+                try
+                {
+                    printJob.print();
+                }
+                catch (Exception PrintException)
+                {
+                    PrintException.printStackTrace();
+                }
+            }
+        }
+    }
 }