X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b0d1b3250fe9556dee6384b24e035d578fe4a578;hb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;hp=9d0f60c951c510b8d23cc8c494922db9d34f3ee1;hpb=eac90472b9bedf5a147bf33c635492cdefc4ef23;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9d0f60c..4b28166 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,141 +1,391 @@
-/********************
- * 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 Softwarechang
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.jbgui.GAlignFrame;
-import jalview.schemes.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.io.*;
-import MCview.*;
+import java.beans.*;
+import java.io.*;
+import java.util.*;
+
 import java.awt.*;
+import java.awt.datatransfer.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
-import java.util.*;
+import javax.swing.event.*;
 
-public class AlignFrame extends GAlignFrame
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.ws.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignFrame
+    extends GAlignFrame
 {
+  /** 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)
   {
-    super();
-    viewport = new AlignViewport(al,true,true,true,false);
+    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());
+
+    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+
+    if(sortby.equals("Id"))
+      sortIDMenuItem_actionPerformed(null);
+    else if(sortby.equals("Pairwise Identity"))
+      sortPairwiseMenuItem_actionPerformed(null);
+
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
-    fontNameMenuItem.setText(viewport.getFont().getName());
-    fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
+
+    viewport.addPropertyChangeListener(new PropertyChangeListener()
+    {
+     public void propertyChange(PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
+     }
+   });
+
+    addServiceListeners();
+  }
+
+  /* Set up intrinsic listeners for dynamically generated GUI bits. */
+  private void addServiceListeners()
+  {
+    final java.beans.PropertyChangeListener thisListener;
+    // Do this once to get current state
+    BuildWebServiceMenu();
+    Desktop.discoverer.addPropertyChangeListener(
+        thisListener = new java.beans.PropertyChangeListener()
+    {
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        // System.out.println("Discoverer property change.");
+        if (evt.getPropertyName().equals("services"))
+        {
+          // System.out.println("Rebuilding web service menu");
+          BuildWebServiceMenu();
+        }
+      }
+    });
+    addInternalFrameListener(new javax.swing.event.
+                             InternalFrameAdapter()
+    {
+      public void internalFrameClosed(
+          javax.swing.event.InternalFrameEvent evt)
+      {
+        // System.out.println("deregistering discoverer listener");
+        Desktop.discoverer.removePropertyChangeListener(thisListener);
+        closeMenuItem_actionPerformed(null);
+      }
+      ;
+    });
+
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param String DOCUMENT ME!
+   */
+
+  public void parseGroupsFile(String file)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
-    chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
+    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 == JFileChooser.APPROVE_OPTION)
-    {
-      String choice =  chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.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();
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      currentFileFormat = chooser.getSelectedFormat();
+      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+                                    currentFileFormat);
+
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+
+      saveAlignment(choice, currentFileFormat);
+    }
+  }
+
+  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);
       }
-      catch(Exception ex){}
+
+      Jalview2XML.SaveAlignment(this, file, shortName);
+
+      // USE Jalview2XML to save this file
+      return true;
     }
+    else
+    {
+      String output = FormatAdapter.formatSequences(format,
+          viewport.getAlignment().
+          getSequences());
+      if (output == null)
+      {
+        return false;
+      }
 
+      try
+      {
+        java.io.PrintWriter out = new java.io.PrintWriter(
+            new java.io.FileWriter(file));
+
+        out.print(output);
+        out.close();
+        return true;
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+    return false;
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   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()));
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
+    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+                                              viewport.getAlignment().
+                                              getSequences()));
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport);
-    htmlOutput = null;
+    new HTMLOutput(viewport);
   }
 
-  public void printMenuItem_actionPerformed(ActionEvent e)
+  public void createImageMap(File file, String image)
   {
-    //Putting in a thread avoids Swing painting problems
-    PrintThread thread = new PrintThread();
-    thread.start();
+    alignPanel.makePNGImageMap(file, image);
   }
 
-  class PrintThread extends Thread
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void createPNG(File f)
   {
-    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();
-        }
-      }
-    }
-
+    alignPanel.makePNG(f);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void createEPS(File f)
+  {
+    alignPanel.makeEPS(f);
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void printMenuItem_actionPerformed(ActionEvent e)
+  {
+    //Putting in a thread avoids Swing painting problems
+    PrintThread thread = new PrintThread();
+    thread.start();
+  }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
+      PaintRefresher.components.remove(viewport.alignment);
       this.setClosed(true);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
   }
 
-  ArrayList  historyList = new ArrayList();
-  ArrayList redoList = new ArrayList();
-
+  /**
+   * DOCUMENT ME!
+   */
   void updateEditMenuBar()
   {
-    if(historyList.size()>0)
-     {
-       undoMenuItem.setEnabled(true);
-       Object [] history = (Object[])historyList.get(0);
-       undoMenuItem.setText("Undo "+history[0]);
-     }
+    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);
-       Object [] history = (Object[])redoList.get(0);
-       redoMenuItem.setText("Redo "+history[0]);
-     }
+    if (redoList.size() > 0)
+    {
+      redoMenuItem.setEnabled(true);
+
+      HistoryItem hi = (HistoryItem) redoList.peek();
+      redoMenuItem.setText("Redo " + hi.getDescription());
+    }
     else
     {
       redoMenuItem.setEnabled(false);
@@ -143,477 +393,1394 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
-  public void addHistoryItem(String type)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param hi DOCUMENT ME!
+   */
+  public void addHistoryItem(HistoryItem hi)
   {
-    // 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++)
+    historyList.push(hi);
+    updateEditMenuBar();
+  }
+
+  /**
+   * 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);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+    HistoryItem hi = (HistoryItem) redoList.pop();
+    restoreHistoryItem(hi);
+    updateEditMenuBar();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
+
+  // used by undo and redo
+  void restoreHistoryItem(HistoryItem hi)
+  {
+    if (hi.getType() == HistoryItem.SORT)
     {
-      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
-                             viewport.getAlignment().getSequenceAt(i).getSequence());
+      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);
+        }
+      }
     }
 
-    historyList.add(0, new Object[]{type,  seq} );
     updateEditMenuBar();
+
+    viewport.firePropertyChange("alignment", null,
+                                viewport.getAlignment().getSequences());
   }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param up DOCUMENT ME!
+   */
+  public void moveSelectedSequences(boolean up)
   {
-    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++)
+    SequenceGroup sg = viewport.getSelectionGroup();
+
+    if (sg == null)
+    {
+      return;
+    }
+
+    if (up)
     {
-      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
-                            viewport.getAlignment().getSequenceAt(i).
-                            getSequence());
+      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;
+        }
 
-    redoList.add(0, new Object[] {history[0], seq});
+        viewport.alignment.getSequences().setElementAt(temp, i);
+        viewport.alignment.getSequences().setElementAt(seq, i + 1);
+      }
+    }
 
-      seq = (SequenceI[]) history[1];
-      viewport.setAlignment( new Alignment(seq) );
-      updateEditMenuBar();
-      alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void copy_actionPerformed(ActionEvent e)
+  {
+    if (viewport.getSelectionGroup() == null)
+    {
+      return;
+    }
+
+    SequenceGroup sg = viewport.getSelectionGroup();
 
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    StringBuffer buffer = new StringBuffer();
+
+    Hashtable orderedSeqs = new Hashtable();
+
+    for (int i = 0; i < sg.getSize(); i++)
+    {
+      SequenceI seq = sg.getSequenceAt(i);
+      int index = viewport.alignment.findIndex(seq);
+      orderedSeqs.put(index + "", seq);
+    }
+
+    int index = 0, startRes, endRes;
+    char ch;
+
+    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++;
+        }
+      }
+      //FIND START RES
+      //Returns residue following index if gap
+      startRes = seq.findPosition(sg.getStartRes());
+
+      //FIND END RES
+      //Need to find the residue preceeding index if gap
+      endRes = 0;
+
+      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
+      {
+        ch = seq.getCharAt(j);
+        if (!jalview.util.Comparison.isGap( (ch)))
+        {
+          endRes++;
+        }
+      }
+
+      if (endRes > 0)
+      {
+        endRes += seq.getStart() - 1;
+      }
+
+      buffer.append(seq.getName() + "\t" +
+                    startRes + "\t" +
+                    endRes + "\t" +
+                    seq.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)
   {
-     Object [] history = (Object[])redoList.remove(0);
-     SequenceI[] seq = (SequenceI[]) history[1];
-     viewport.setAlignment( new Alignment(seq) );
-     updateEditMenuBar();
-     alignPanel.RefreshPanels();
+    paste(true);
   }
 
-  protected void modifyAlignmentMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void pasteThis_actionPerformed(ActionEvent e)
   {
-    viewport.groupDefiningMode = !modifyAlignmentMenuItem.isSelected();
+    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+                                   HistoryItem.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);
 
-  public void groupsMenuItem_actionPerformed(ActionEvent e)
+        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.setEndSeq(viewport.alignment.getHeight());
+        viewport.alignment.getWidth();
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+      }
+    }
+    catch (Exception ex)
+    {
+        // could be anything being pasted in here
+    }
+
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void cut_actionPerformed(ActionEvent e)
   {
-    GroupEditor geditor = new GroupEditor(viewport, alignPanel);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(geditor);
-    Desktop.addInternalFrame(frame, "Group editor", 710, 410);
-    frame.setResizable(false);
+    copy_actionPerformed(null);
+    delete_actionPerformed(null);
   }
 
-  public void groupEditingMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void delete_actionPerformed(ActionEvent e)
   {
-    viewport.setGroupEdit( groupEditingMenuItem.isSelected() );
+    boolean seqsdeleted = false;
+
+    if (viewport.getSelectionGroup() == null)
+    {
+      return;
+    }
+
+    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);
+      }
+    }
+
+    viewport.setSelectionGroup(null);
+    viewport.alignment.deleteGroup(sg);
+
+    if (seqsdeleted)
+    {
+      viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+    }
+
+
+    if (viewport.getAlignment().getHeight() < 1)
+    {
+      try
+      {
+        this.setClosed(true);
+      }
+      catch (Exception ex)
+      {
+      }
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void deleteGroups_actionPerformed(ActionEvent e)
+  {
+    viewport.alignment.deleteAllGroups();
+    viewport.setSelectionGroup(null);
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sel.addElement( viewport.getAlignment().getSequenceAt(i));
-    PaintRefresher.Refresh(null);
+    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() - 1);
+    viewport.setSelectionGroup(sg);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.getSelection().clear();
-    PaintRefresher.Refresh(null);
+    viewport.setSelectionGroup(null);
+    viewport.getColumnSelection().clear();
+    viewport.setSelectionGroup(null);
+    alignPanel.annotationPanel.activeRes = null;
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+    SequenceGroup sg = viewport.getSelectionGroup();
+
+    if (sg == null)
     {
-      if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
-        sel.removeElement(viewport.getAlignment().getSequenceAt(i));
-      else
-        sel.addElement(viewport.getAlignment().getSequenceAt(i));
+      selectAllSequenceMenuItem_actionPerformed(null);
+
+      return;
     }
-    PaintRefresher.Refresh(null);
-  }
 
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
+    {
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+    }
 
-  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.getColumnSelection().clear();
-    repaint();
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
+
     if (colSel.size() > 0)
     {
+      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
+                                     HistoryItem.HIDE));
+
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0,min);
-      alignPanel.RefreshPanels();
+      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);
+        }
+      }
+
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
+
     if (colSel.size() > 0)
     {
+      addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
+                                     HistoryItem.HIDE));
+
       int max = colSel.getMax();
-      if(max>1)
-        viewport.getAlignment().trimRight(max);
+      viewport.getAlignment().trimRight(max);
 
-      alignPanel.RefreshPanels();
-    }
+      if (viewport.getSelectionGroup() != null)
+      {
+        viewport.getSelectionGroup().adjustForRemoveRight(max);
+      }
+
+      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);
+        }
+      }
 
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete gapped columns");
+    addHistoryItem(new HistoryItem("Remove Gapped Columns",
+                                   viewport.alignment, HistoryItem.HIDE));
+
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
     viewport.getAlignment().removeGaps();
-    alignPanel.RefreshPanels();
+
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete all gaps");
+    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
+                                   HistoryItem.HIDE));
+
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
+
     SequenceI current;
     int jSize;
-    for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
+
+    Vector seqs = null;
+
+    int start = 0;
+    int end = viewport.alignment.getWidth();
+
+    if (viewport.getSelectionGroup() != null
+        && viewport.getSelectionGroup().sequences != null
+        && viewport.getSelectionGroup().sequences.size() > 0)
     {
-      current = viewport.getAlignment().getSequenceAt(i);
+      seqs = viewport.getSelectionGroup().sequences;
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+    {
+      seqs = viewport.alignment.getSequences();
+    }
+
+    for (int i = 0; i < seqs.size(); i++)
+    {
+      current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
-      for (int j=0; j < jSize; j++)
-        if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
+
+      int j = start;
+
+      do
+      {
+        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
           current.deleteCharAt(j);
           j--;
           jSize--;
         }
+        j++;
+      }
+      while (j < end && j < jSize);
+    }
+
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
+
+ public void alignmentChanged()
+ {
+   viewport.updateConsensus();
+   viewport.updateConservation();
+   resetAllColourSchemes();
+   alignPanel.repaint();
+ }
+
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
+    {
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+            resetClustalX(viewport.alignment.getSequences(),
+                          viewport.alignment.getWidth());
+      }
+
+      cs.setConsensus(viewport.vconsensus);
+      if (cs.conservationApplied())
+      {
+        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);
+
+        cs.setConservation(c);
+      }
     }
 
-    alignPanel.RefreshPanels();
+    int s, sSize = viewport.alignment.getGroups().size();
+    for(s=0; s<sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+      }
+      sg.recalcConservation();
+    }
   }
 
-  public void setGapCharMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
-    char thisChar = '-';
-    char nextChar = '.';
-    if(viewport.getGapCharacter()=='-')
+    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++)
     {
-      thisChar = '.';
-      nextChar = '-';
+      current = viewport.getAlignment().getSequenceAt(i);
+
+      if (current.getLength() < Width)
+      {
+        current.insertCharAt(Width - 1, viewport.getGapCharacter());
+      }
     }
-    setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
-    viewport.setGapCharacter(thisChar);
-    alignPanel.RefreshPanels();
+
+    alignmentChanged();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    JOptionPane op = new JOptionPane();
-    JInternalFrame frame =  op.createInternalFrame(this, "Find");
+    JInternalFrame frame = new JInternalFrame();
     Finder finder = new Finder(viewport, alignPanel, frame);
     frame.setContentPane(finder);
-    frame.setSize(300,110);
-    frame.setVisible(true);
+    Desktop.addInternalFrame(frame, "Find", 340, 110);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void font_actionPerformed(ActionEvent e)
+  {
+    FontChooser fc = new FontChooser(alignPanel);
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fullSeqId_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowFullId(fullSeqId.isSelected());
 
-  public void fontNameMenuItem_actionPerformed(ActionEvent e)
+    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
+    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();
+  }
 
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font",
-                                "Font selection",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null,fonts
-                                ,fontNameMenuItem.getText()).toString();
-    if(selection!=null)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void viewTextMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowText(viewTextMenuItem.isSelected());
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void sequenceFeatures_actionPerformed(ActionEvent evt)
+  {
+    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
+
+    if (viewport.showSequenceFeatures &&
+        ! ( (Alignment) viewport.alignment).featuresAdded)
     {
-       fontNameMenuItem.setText(selection);
-       SetFont();
-     }
+      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
+          alignment,
+          alignPanel);
+      ( (Alignment) viewport.alignment).featuresAdded = true;
+    }
 
+    alignPanel.repaint();
   }
 
-  public void fontSizeMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font size",
-                                "Font size",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
-                                ,fontSizeMenuItem.getText()).toString();
-    if(selection!=null)
-     {
-       fontSizeMenuItem.setText(selection);
-       SetFont();
-     }
+    if (annotationPanelMenuItem.isSelected() &&
+        viewport.getWrapAlignment())
+    {
+      annotationPanelMenuItem.setSelected(false);
+
+      return;
+    }
+
+    viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
+    alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
   }
 
-  public void fontStyleMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
-    String selection = JOptionPane.showInternalInputDialog(this,
-                                "Select font style",
-                                "Font style",
-                                JOptionPane.QUESTION_MESSAGE,
-                                null, new String[]{"plain", "bold", "italic"}
-                                ,fontStyleMenuItem.getText()).toString();
-    if(selection!=null)
+    if (alignPanel.overviewPanel != null)
     {
-      fontStyleMenuItem.setText(selection);
-      SetFont();
+      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);
   }
 
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-      viewport.setColourText( colourTextMenuItem.isSelected() );
-      alignPanel.RefreshPanels();
+    changeColour(null);
   }
 
-  void SetFont()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void clustalColour_actionPerformed(ActionEvent e)
   {
-      int style = java.awt.Font.PLAIN;
-      if(fontStyleMenuItem.getText().equals("bold"))
-        style = java.awt.Font.BOLD;
-      else if(fontStyleMenuItem.getText().equals("italic"))
-        style = java.awt.Font.ITALIC;
+    changeColour(new ClustalxColourScheme(
+        viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+  }
 
-      viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
-                                           style,
-                                           Integer.parseInt(fontSizeMenuItem.getText())));
-      alignPanel.RefreshPanels();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void zappoColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new ZappoColourScheme());
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void taylorColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new TaylorColourScheme());
   }
 
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    changeColour(new HydrophobicColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void helixColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new HelixColourScheme());
+  }
 
-  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void strandColour_actionPerformed(ActionEvent e)
   {
-    viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    changeColour(new StrandColourScheme());
   }
 
-  public void viewTextMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void turnColour_actionPerformed(ActionEvent e)
   {
-    viewport.setShowText( viewTextMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    changeColour(new TurnColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void buriedColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new BuriedColourScheme());
+  }
 
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void nucleotideColour_actionPerformed(ActionEvent e)
   {
-    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.RefreshPanels();
+    changeColour(new NucleotideColourScheme());
   }
 
+  /**
+   * 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(cs!=null)
+    {
+      if (viewport.getAbovePIDThreshold())
+      {
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+                                                   "Background");
+
+        cs.setThreshold(threshold,
+                        viewport.getIgnoreGapsConsensus());
+
+        viewport.setGlobalColourScheme(cs);
+      }
+      else
+      {
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+      }
+
+      if (viewport.getConservationSelected())
+      {
+
+        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);
+
+        cs.setConservation(c);
+
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
+      }
+      else
+      {
+        cs.setConservation(null);
+      }
+
+      cs.setConsensus(viewport.vconsensus);
+    }
 
-  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
-  {
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
-  }
+    viewport.setGlobalColourScheme(cs);
 
-  public void overviewMenuItem_actionPerformed(ActionEvent e)
-  {
+    if (viewport.getColourAppliesToAllGroups())
+    {
+      Vector groups = viewport.alignment.getGroups();
 
-    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)
+      for (int i = 0; i < groups.size(); i++)
       {
-            alignPanel.setOverviewPanel(null);
-      };
-    });
-    alignPanel.setOverviewPanel( overview );
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-  }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);
-   }
+        if (cs == null)
+        {
+          sg.cs = null;
+          continue;
+        }
 
+        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()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
+        {
+         sg.cs.setThreshold(threshold,
+                viewport.getIgnoreGapsConsensus());
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( null );
-    alignPanel.setColourScheme();
-  }
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+              sg.getWidth()));
+        }
+        else
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
 
 
-  public void clustalColour_actionPerformed(ActionEvent e)
-  {
-   // alignPanel.setColourScheme( new ClustalxColourScheme() );
-  }
+        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);
+          sg.cs.setConservation(c);
+        }
+        else
+          sg.cs.setConservation(null);
+      }
+    }
 
-  public void zappoColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new ZappoColourScheme() );
-    alignPanel.setColourScheme(  );
+    if (alignPanel.getOverviewPanel() != null)
+    {
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    }
+
+    alignPanel.repaint();
   }
 
-  public void taylorColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new TaylorColourScheme() );
-    alignPanel.setColourScheme(  );
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+    {
+      SliderPanel.setPIDSliderSource(alignPanel,
+                                     viewport.getGlobalColourScheme(),
+                                     "Background");
+      SliderPanel.showPIDSlider();
+    }
   }
 
-
-  public void hydrophobicityColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
-    alignPanel.setColourScheme( );
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+    {
+      SliderPanel.setConservationSlider(alignPanel,
+                                        viewport.globalColourScheme,
+                                        "Background");
+      SliderPanel.showConservationSlider();
+    }
   }
 
-  public void helixColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new HelixColourScheme()  );
-    alignPanel.setColourScheme();
-  }
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
 
+    viewport.setAbovePIDThreshold(false);
+    abovePIDThreshold.setSelected(false);
 
-  public void strandColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme(new StrandColourScheme() );
-    alignPanel.setColourScheme(  );
-  }
+    changeColour(viewport.getGlobalColourScheme());
 
+    modifyConservation_actionPerformed(null);
+  }
 
-  public void turnColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new TurnColourScheme() );
-    alignPanel.setColourScheme(  );
-  }
+    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 
+    conservationMenuItem.setSelected(false);
+    viewport.setConservationSelected(false);
 
-  public void buriedColour_actionPerformed(ActionEvent e)
-  {
-    viewport.setGlobalColourScheme( new BuriedColourScheme() );
-    alignPanel.setColourScheme( );
-  }
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
 
+    changeColour(viewport.getGlobalColourScheme());
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setConservationSelected(conservationMenuItem.isSelected());
-    conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
-    alignPanel.setColourScheme();
+    modifyPID_actionPerformed(null);
   }
 
-  public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
- {
-   ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
-   JInternalFrame frame = new JInternalFrame();
-   frame.setContentPane(cip);
-   Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
-   frame.setMaximizable(false);
- }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void userDefinedColour_actionPerformed(ActionEvent e)
+  {
+    if (e.getActionCommand().equals("User Defined..."))
+    {
+      new UserDefinedColours(alignPanel, null);
+    }
+    else
+    {
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+          getUserColourSchemes().get(e.getActionCommand());
 
+      changeColour(udc);
+    }
+  }
 
-  public void abovePIDColour_actionPerformed(ActionEvent e)
+  public void updateUserColourMenu()
   {
-    viewport.setGlobalColourScheme(new PIDColourScheme());
-    alignPanel.setColourScheme( );
-  }
 
+    Component[] menuItems = colourMenu.getMenuComponents();
+    int i, iSize = menuItems.length;
+    for (i = 0; i < iSize; i++)
+    {
+      if (menuItems[i].getName() != null &&
+          menuItems[i].getName().equals("USER_DEFINED"))
+      {
+        colourMenu.remove(menuItems[i]);
+        iSize--;
+      }
+    }
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
 
-  public void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, viewport );
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
+      while (userColours.hasMoreElements())
+      {
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+            nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addMouseListener(new MouseAdapter()
+            {
+              public void mousePressed(MouseEvent evt)
+              {
+                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                {
+                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
+                  if(option == JOptionPane.YES_OPTION)
+                  {
+                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+                    colourMenu.remove(radioItem);
+                  }
+                  else
+                    radioItem.addActionListener(new ActionListener()
+                    {
+                      public void actionPerformed(ActionEvent evt)
+                      {
+                        userDefinedColour_actionPerformed(evt);
+                      }
+                    });
+                }
+              }
+            });
+        radioItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+
+        colourMenu.insert(radioItem, 15);
+        colours.add(radioItem);
+      }
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme(new PIDColourScheme() );
-    alignPanel.setColourScheme( );
+    changeColour(new PIDColourScheme());
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
-    alignPanel.setColourScheme();
-  }
-
-
-
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
-  {
-    ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
-    Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
+    changeColour(new Blosum62ColourScheme());
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
-    alignPanel.RefreshPanels();
+    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
+                                   HistoryItem.SORT));
+    AlignmentSorter.sortByPID(viewport.getAlignment(),
+                              viewport.getAlignment().getSequenceAt(0));
+    alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByID( viewport.getAlignment() );
-    alignPanel.RefreshPanels();
+    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("sort");
-    AlignmentSorter.sortByGroup(viewport.getAlignment());
-    AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.RefreshPanels();
-  }
-
-  public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    if(viewport.getCurrentTree()==null)
-      return;
+    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+                                   HistoryItem.SORT));
 
-    AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
-    alignPanel.RefreshPanels();
+    AlignmentSorter.sortByGroup(viewport.getAlignment());
+    alignPanel.repaint();
   }
 
+  /**
+   * 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);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelection().size()<2)
-      JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
+    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();
@@ -622,122 +1789,553 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-    if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
-       || viewport.getAlignment().getHeight()<4)
+    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);
+      JOptionPane.showInternalMessageDialog(this,
+                                            "Principal component analysis must take\n" +
+                                            "at least 4 input sequences.",
+                                            "Sequence selection insufficient",
+                                            JOptionPane.WARNING_MESSAGE);
+
       return;
     }
 
-    try{
+    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);
-   }
-
-
+      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 averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("AV", "PID", "Average distance tree using PID");
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
+    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param type DOCUMENT ME!
+   * @param pwType DOCUMENT ME!
+   * @param title DOCUMENT ME!
+   */
   void NewTreePanel(String type, String pwType, String title)
   {
-    JInternalFrame frame = new javax.swing.JInternalFrame();
-    TreePanel tp=null;
-   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
-   {
-     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
-                         viewport.getStartRes(), viewport.getEndRes());
-   }
-   else
-   {
-     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, viewport.getStartRes(),
-                         viewport.getEndRes());
-   }
+    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());
+
+    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));
 
-   frame.setContentPane(tp);
-   Desktop.addInternalFrame(frame, title, 600, 500);
+        // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+        AlignmentSorter.sortBy(viewport.getAlignment(), order);
+        alignPanel.repaint();
+      }
+    });
   }
 
+  /**
+   * Maintain the Order by->Displayed Tree menu.
+   * Creates a new menu item for a TreePanel with an appropriate
+   * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
+   * to remove the menu item when the treePanel is closed, and adjust
+   * the tree leaf to sequence mapping when the alignment is modified.
+   * @param treePanel Displayed tree window.
+   * @param title SortBy menu item title.
+   */
+  void addTreeMenuItem(final TreePanel treePanel, String title)
+  {
+    final JMenuItem item = new JMenuItem(title);
+
+    treeCount++;
+
+    if (treeCount == 1)
+    {
+      sort.add(sortByTreeMenu);
+    }
+
+    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();
+        }
+      }
+    });
+  }
 
-  public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * Work out whether the whole set of sequences
+   * or just the selected set will be submitted for multiple alignment.
+   *
+   */
+  private SequenceI[] gatherSequencesForAlignment()
   {
-    JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"
-                                  +"\nwithin the Barton Group, Dundee University."
-                                  +"\nThis will be available as a web service 2005",
-                                  "Web service", JOptionPane.INFORMATION_MESSAGE);
+    // 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);
+        }
+      }
+    }
+    return msa;
   }
 
-  public void pdbTest_actionPerformed(ActionEvent e)
+  /**
+   * Decides what is submitted to a secondary structure prediction service,
+   * the currently selected sequence, or the currently selected alignment
+   * (where the first sequence in the set is the one that the prediction
+   * will be for).
+   */
+  SequenceI[] gatherSeqOrMsaForSecStrPrediction()
   {
-   String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
+    SequenceI seq = null;
+    SequenceI[] msa = null;
+
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 0))
+    {
+      // 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()];
 
-   String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
-   if (reply.length()>1)
-     url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+      }
+    }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
 
-   try
-   {
-     PDBfile pdb = new PDBfile(url,
-                               "URL");
-    Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
-    seq.setPDBfile(pdb);
-     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
-     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
-  // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
+      if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
+      {
+        seq = (SequenceI) seqs.elementAt(0);
+      }
+      else
+      {
+        msa = new SequenceI[seqs.size()];
 
-     rotCanvas rc = new rotCanvas(pdb);
-     JInternalFrame frame = new JInternalFrame();
-     frame.setContentPane(rc);
-     Desktop.addInternalFrame(frame, url, 400,400);
-   }
-   catch (Exception ex)
-   {
-     ex.printStackTrace();
-   }
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          msa[i] = (SequenceI) seqs.elementAt(i);
+        }
+      }
+    }
+    if (msa != null)
+    {
+      return msa;
+    }
+    else
+    {
+      if (seq != null)
+      {
+        return new SequenceI[]
+            {
+            seq};
+      }
+    }
+    return null;
+  }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  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)
+    {
+      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();
+      }
+    }
   }
 
 
-  public void doKeyPressed(KeyEvent evt)
+  public TreePanel ShowNewickTree(NewickFile nf, String title)
+  {
+    return ShowNewickTree(nf,title,600,500,4,5);
+  }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param nf DOCUMENT ME!
+   * @param title DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
   {
+    TreePanel tp = null;
+
+    try
+    {
+      nf.parse();
+
+      if (nf.getTree() != null)
+      {
+        tp = new TreePanel(viewport,
+                           viewport.getAlignment().getSequences(), nf,
+                           "FromFile",
+                           title);
+
+        tp.setSize(w,h);
+
+        if(x>0 && y>0)
+          tp.setLocation(x,y);
+
+
+        Desktop.addInternalFrame(tp, title, w, h);
+        addTreeMenuItem(tp, title);
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    return tp;
+  }
 
-    System.out.println(evt.getKeyChar());
-    if(evt.isControlDown() && evt.getKeyChar()=='f')
-      findMenuItem_actionPerformed(null);
+  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();
+        }
+      }
+    }
   }
 
+  /**
+   * Generates menu items and listener event actions for web service clients
+   *
+   */
+  public void BuildWebServiceMenu()
+  {
+    if ( (Desktop.discoverer.services != null)
+        && (Desktop.discoverer.services.size() > 0))
+    {
+      Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
+      Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
+      Vector wsmenu = new Vector();
+      if (msaws != null)
+      {
+        // Add any Multiple Sequence Alignment Services
+        final JMenu msawsmenu = new JMenu("Alignment");
+        for (int i = 0, j = msaws.size(); i < j; i++)
+        {
+          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
+              get(i);
+          final JMenuItem method = new JMenuItem(sh.getName());
+          method.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              SequenceI[] msa = gatherSequencesForAlignment();
+              MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
+                  false, true);
+
+            }
+
+          });
+          msawsmenu.add(method);
+          // Deal with services that we know accept partial alignments.
+          if (sh.getName().indexOf("lustal") > -1)
+          {
+            // We know that ClustalWS can accept partial alignments for refinement.
+            final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
+            methodR.addActionListener(new ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                SequenceI[] msa = gatherSequencesForAlignment();
+                MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
+                    true, true);
+
+              }
+
+            });
+            msawsmenu.add(methodR);
+
+          }
+        }
+        wsmenu.add(msawsmenu);
+      }
+      if (secstrpr != null)
+      {
+        // Add any secondary structure prediction services
+        final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
+        for (int i = 0, j = secstrpr.size(); i < j; i++)
+        {
+          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
+              secstrpr.get(i);
+          final JMenuItem method = new JMenuItem(sh.getName());
+          method.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
+              if (msa.length == 1)
+              {
+                // Single Sequence prediction
+                jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
+                    title, msa[0]);
+              }
+              else
+              {
+                if (msa.length > 1)
+                {
+                  // Single Sequence prediction
+                  jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
+                      title, msa);
+                }
+              }
+            }
+          });
+          secstrmenu.add(method);
+        }
+        wsmenu.add(secstrmenu);
+      }
+      this.webService.removeAll();
+      for (int i = 0, j = wsmenu.size(); i < j; i++)
+      {
+        webService.add( (JMenu) wsmenu.get(i));
+      }
+    }
+    else
+    {
+      this.webService.removeAll();
+      this.webService.add(this.webServiceNoServices);
+    }
+    // TODO: add in rediscovery function
+    // TODO: reduce code redundancy.
+    // TODO: group services by location as well as function.
+  }
 
 }