X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b714aea53cabf9b96dea336328ca497d1ca28d14;hb=366b11bb8e79ff5bb1a9e6c50b648c3d4101862c;hp=cabb24f502198a6fa7270cebee2df895268d041e;hpb=9bea55eea55110a19b17d0127903802013fa60ea;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index cabb24f..b714aea 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,137 +1,358 @@
-/********************
- * 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 jalview.ws.*;
+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 javax.swing.event.*;
-import java.util.*;
-import java.awt.datatransfer.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.ws.*;
+import java.awt.dnd.*;
 
 
-public class AlignFrame extends GAlignFrame
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignFrame
+    extends GAlignFrame implements ClipboardOwner, DropTargetListener
 {
-  final AlignmentPanel alignPanel;
-  final AlignViewport viewport;
+  /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
+
+  /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_HEIGHT = 500;
+  AlignmentPanel alignPanel;
+  AlignViewport viewport;
 
+  Vector viewports = new Vector();
+  Vector alignPanels = new Vector();
+
+  /** 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)
   {
-    try{
-      String ip = java.net.InetAddress.getLocalHost().getHostAddress();
-      if( !ip.startsWith("10."))
-        webService.setVisible(false);
-    }
-    catch(java.net.UnknownHostException e){}
     viewport = new AlignViewport(al);
+    viewports.add(viewport);
 
+    this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+
+    if(viewport.vconsensus==null)
+    {
+      //Out of memory calculating consensus.
+      BLOSUM62Colour.setEnabled(false);
+      PIDColour.setEnabled(false);
+      conservationMenuItem.setEnabled(false);
+      modifyConservation.setEnabled(false);
+      abovePIDThreshold.setEnabled(false);
+      modifyPID.setEnabled(false);
+    }
 
     alignPanel = new AlignmentPanel(this, viewport);
-    alignPanel.annotationPanel.adjustPanelHeight();
-    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
-    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
-    alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
+    alignPanels.add(alignPanel);
+
+    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);
+
+   // remove(tabbedPane);
+    getContentPane().add(alignPanel, BorderLayout.CENTER);
 
-    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();    }
-          });
 
+  //  tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
+
+    ///Dataset tab
+    /////////////////////////
+    if(al.getDataset()==null)
+    {
+      al.setDataset(null);
+    }
+   // AlignViewport ds = new AlignViewport(al.getDataset(), true);
+   // AlignmentPanel dap = new AlignmentPanel(this, ds);
+  //  tabbedPane.add("Dataset", dap);
+  //  viewports.add(ds);
+  //  alignPanels.add(dap);
+    /////////////////////////
+
+
+    viewport.addPropertyChangeListener(new PropertyChangeListener()
+    {
+     public void propertyChange(PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
      }
    });
 
+
+  if (Desktop.desktop != null)
+  {
+    addServiceListeners();
+    setGUINucleotide(al.isNucleotide());
+  }
+  }
+
+  /* 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);
+      }
+      ;
+    });
+
+  }
+
+  public void setGUINucleotide(boolean nucleotide)
+  {
+    showTranslation.setVisible( nucleotide );
+    //sequenceFeatures.setVisible(!nucleotide );
+    //featureSettings.setVisible( !nucleotide );
+    conservationMenuItem.setVisible( !nucleotide );
+    modifyConservation.setVisible(   !nucleotide );
+
+    //Remember AlignFrame always starts as protein
+    if(!nucleotide)
+    {
+      calculateMenu.remove(calculateMenu.getItemCount()-2);
+    }
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+
+  /*
+   Added so Castor Mapping file can obtain Jalview Version
+  */
+  public String getVersion()
   {
-    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"};
+    return  jalview.bin.Cache.getProperty("VERSION");
+  }
 
 
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
-        , suffix, e.getActionCommand()+" file");
+  public void fetchSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(this);
+  }
+  /**
+   * 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 - "+e.getActionCommand() +" format.");
+    chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
+
     int value = chooser.showSaveDialog(this);
-    if(value == JalviewFileChooser.APPROVE_OPTION)
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String choice =  chooser.getSelectedFile().getPath();
+        currentFileFormat = chooser.getSelectedFormat();
+
+        if (currentFileFormat == null)
+        {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "You must select a file format before saving!",
+                                                "File format not specified",
+                                                JOptionPane.WARNING_MESSAGE);
+          value = chooser.showSaveDialog(this);
+          return;
+        }
+
+      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+                                    currentFileFormat);
+
+      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();
+
+      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 = new 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(new 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,
+                   alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
   }
 
-  protected void createPNG_actionPerformed(ActionEvent e)
+  public void createImageMap(File file, String image)
   {
-    alignPanel.makePNG();
+    alignPanel.makePNGImageMap(file, image);
   }
 
-  protected void epsFile_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void createPNG(File f)
   {
-    alignPanel.makeEPS();
+    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
@@ -139,61 +360,48 @@ public class AlignFrame extends GAlignFrame
     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())
-      {
-        try
-        {
-          printJob.print();
-        }
-        catch (Exception PrintException)
-        {
-          PrintException.printStackTrace();
-        }
-      }
-    }
-
-  }
-
-
-
-
+  /**
+   * 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)
+    {
+    }
   }
 
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
-
+  /**
+   * 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);
@@ -201,60 +409,121 @@ 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++)
-    {
-      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
-                             viewport.getAlignment().getSequenceAt(i).getSequence());
-    }
-
-    historyList.add(0, new Object[]{type,  seq} );
+    historyList.push(hi);
     updateEditMenuBar();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   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++)
+    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)
+    {
+      for (int i = 0; i < hi.getSequences().size(); i++)
+      {
+        viewport.alignment.getSequences().setElementAt(hi.getSequences()
+            .elementAt(i),
+            i);
+      }
+    }
+    else
     {
-      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
-                            viewport.getAlignment().getSequenceAt(i).
-                            getSequence());
+      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);
+        }
+      }
     }
-    /////////
 
-    redoList.add(0, new Object[] {history[0], seq});
+    updateEditMenuBar();
 
-      seq = (SequenceI[]) history[1];
-      viewport.setAlignment( new Alignment(seq) );
-      updateEditMenuBar();
-      viewport.updateConsensus();
-      alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null,
+                                viewport.getAlignment().getSequences());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param up DOCUMENT ME!
+   */
   public void moveSelectedSequences(boolean up)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
+
     if (sg == null)
+    {
       return;
+    }
 
     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);
@@ -265,12 +534,18 @@ public class AlignFrame extends GAlignFrame
       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);
@@ -280,597 +555,1168 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();
   }
 
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    Desktop.jalviewClipboard = null;
+  }
 
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getSelectionGroup()==null)
-     return;
+    if (viewport.getSelectionGroup() == null)
+    {
+      return;
+    }
 
-   SequenceGroup sg = viewport.getSelectionGroup();
+    SequenceGroup sg = viewport.getSelectionGroup();
 
-     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-     StringBuffer buffer= new StringBuffer();
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 
-       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 ) ;
+    Hashtable orderedSeqs = new Hashtable();
+    SequenceI[] seqs = new SequenceI[sg.getSize()];
 
-  }
+    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;
+      }
+
+      seqs[i] = new Sequence(seq.getName(),
+                             seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
+                             startRes,
+                             endRes);
+      seqs[i].setDescription(seq.getDescription());
+      seqs[i].setDBRef(seq.getDBRef());
+      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
+      seqs[i].setDatasetSequence(seq.getDatasetSequence());
+
+    }
 
+    FastaFile ff = new FastaFile();
+    ff.addJVSuffix( viewport.showJVSuffix );
+    c.setContents(new StringSelection( ff.print(seqs)), this);
+    Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
     paste(true);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Paste");
+    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+                                   HistoryItem.PASTE));
     paste(false);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param newAlignment DOCUMENT ME!
+   */
   void paste(boolean newAlignment)
   {
-    try{
+    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())
+      if(str.length()<1)
+        return;
+
+      String format = new IdentifyFile().Identify(str, "Paste");
+      SequenceI[] sequences;
+
+     if(Desktop.jalviewClipboard!=null)
+     {
+       // The clipboard was filled from within Jalview, we must use the sequences
+       // And dataset from the copied alignment
+       sequences = (SequenceI[])Desktop.jalviewClipboard[0];
+     }
+     else
+     {
+       sequences = new FormatAdapter().readFile(str, "Paste", format);
+     }
+
+      if (newAlignment)
       {
-        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);
+        Alignment alignment = new Alignment(sequences);
+
+        if(Desktop.jalviewClipboard!=null)
+           alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
         else
-          seqs.add(sequence);
-      }
+           alignment.setDataset( null );
 
-      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);
+
+        AlignFrame af = new AlignFrame(alignment);
+        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
       {
+        //!newAlignment
+        for (int i = 0; i < sequences.length; i++)
+        {
+          Sequence newseq = new Sequence(sequences[i].getName(),
+              sequences[i].getSequence(), sequences[i].getStart(),
+              sequences[i].getEnd());
+          viewport.alignment.addSequence(newseq);
+          if(sequences[i].getDatasetSequence()==null)
+          {
+             ////////////////////////////
+            //Datset needs extension;
+            /////////////////////////////
+            Sequence ds = new Sequence(sequences[i].getName(),
+                                       AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
+                                       sequences[i].getStart(),
+                                       sequences[i].getEnd());
+            newseq.setDatasetSequence(ds);
+            viewport.alignment.getDataset().addSequence(ds);
+          }
+          else
+          {
+            newseq.setDatasetSequence(sequences[i].getDatasetSequence());
+            if(sequences[i].getDatasetSequence().getAnnotation()!=null)
+            {
+              for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)
+              {
+                viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);
+              }
+            }
+          }
+        }
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
       }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+        System.out.println("Exception whilst pasting: "+ex);
+        // could be anything being pasted in here
+    }
 
-    }catch(Exception ex){}// could be anything being pasted in here
 
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void cut_actionPerformed(ActionEvent e)
   {
     copy_actionPerformed(null);
     delete_actionPerformed(null);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void delete_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Delete");
+
     if (viewport.getSelectionGroup() == null)
+    {
       return;
+    }
+
+
+    SequenceGroup sg = viewport.getSelectionGroup();
+
+
+
+    //Jalview no longer allows deletion of residues.
+    //Check here whether any residues are in selection area
+    if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
+    {
+      for (int i = 0; i < sg.sequences.size(); i++)
+      {
+        SequenceI seq = sg.getSequenceAt(i);
+        int j = sg.getStartRes();
+        do
+        {
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+          {
+            JOptionPane.showInternalMessageDialog(
+                Desktop.desktop, "Cannot delete residues from alignment!\n"
+                + "Try hiding columns instead.",
+                "Deletion of residues not permitted",
+                JOptionPane.WARNING_MESSAGE);
+
+            return;
+          }
+          j++;
+        }while(j<=sg.getEndRes());
+      }
+    }
+
+
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                                   HistoryItem.HIDE));
 
-     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);
 
-       if(seq.getSequence().length()<1)
-          viewport.getAlignment().deleteSequence(seq);
+    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 (sg.sequences.size() == viewport.alignment.getHeight())
+      {
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),
+            sg.getEndRes() + 1);
+      }
+
+      if (seq.getSequence().length() < 1)
+      {
+        viewport.getAlignment().deleteSequence(seq);
+      }
       else
-          viewport.getAlignment().getSequences().setElementAt(seq, index);
-     }
+      {
+        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.repaint();
+    viewport.setSelectionGroup(null);
+    viewport.alignment.deleteGroup(sg);
 
-  }
+    viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
 
 
 
-  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.repaint();
-     alignPanel.repaint();
+    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)
   {
     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());
+
+    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);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(null);
+    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
+    alignPanel.idPanel.idCanvas.searchResults = null;
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   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);
+    if (sg == null)
+    {
+      selectAllSequenceMenuItem_actionPerformed(null);
+
+      return;
+    }
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
+    {
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+    }
+
+    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);
+      colSel.compensateForEdit(0, min);
 
-      if(viewport.getSelectionGroup()!=null)
+      if (viewport.getSelectionGroup() != null)
+      {
         viewport.getSelectionGroup().adjustForRemoveLeft(min);
+      }
 
       Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+
+      for (int i = 0; i < groups.size(); i++)
       {
         SequenceGroup sg = (SequenceGroup) groups.get(i);
-        if(!sg.adjustForRemoveLeft(min))
+
+        if (!sg.adjustForRemoveLeft(min))
+        {
           viewport.alignment.deleteGroup(sg);
+        }
       }
 
-      alignPanel.repaint();
+      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();
       viewport.getAlignment().trimRight(max);
-      if(viewport.getSelectionGroup()!=null)
+
+      if (viewport.getSelectionGroup() != null)
+      {
         viewport.getSelectionGroup().adjustForRemoveRight(max);
+      }
 
       Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+
+      for (int i = 0; i < groups.size(); i++)
       {
         SequenceGroup sg = (SequenceGroup) groups.get(i);
-        if(!sg.adjustForRemoveRight(max))
+
+        if (!sg.adjustForRemoveRight(max))
+        {
           viewport.alignment.deleteGroup(sg);
+        }
       }
 
-
-
-      alignPanel.repaint();
+      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();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+
+    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)
+    {
+      seqs = viewport.getSelectionGroup().sequences;
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
+    }
+    else
+    {
+      seqs = viewport.alignment.getSequences();
+    }
+
+    for (int i = 0; i < seqs.size(); i++)
     {
-      current = viewport.getAlignment().getSequenceAt(i);
+      current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
-      for (int j=0; j < jSize; j++)
-        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
+
+      // Removing a range is much quicker than removing gaps
+      // one by one for long sequences
+      int j = start;
+      int rangeStart=-1, rangeEnd=-1;
+
+      do
+      {
+        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
+        {
+          if(rangeStart==-1)
+           {
+             rangeStart = j;
+             rangeEnd = j+1;
+           }
+           else
+           {
+             rangeEnd++;
+           }
+           j++;
+        }
+        else
         {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
+          if(rangeStart>-1)
+          {
+            current.deleteChars(rangeStart, rangeEnd);
+            j-=rangeEnd-rangeStart;
+            jSize-=rangeEnd-rangeStart;
+            rangeStart = -1;
+            rangeEnd = -1;
+          }
+          else
+            j++;
         }
+      }
+      while (j < end && j < jSize);
+      if(rangeStart>-1)
+      {
+       current.deleteChars(rangeStart, rangeEnd);
+      }
+    }
+
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
+
+ public void alignmentChanged()
+ {
+   if(viewport.vconsensus!=null)
+   {
+     viewport.updateConsensus();
+     viewport.updateConservation();
+   }
+   resetAllColourSchemes();
+   if(alignPanel.overviewPanel!=null)
+     alignPanel.overviewPanel.updateOverviewImage();
+
+   viewport.alignment.adjustSequenceAnnotations();
+
+   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);
+      }
+    }
+
+    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();
     }
-    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));
+    if (viewport.getAlignment().padGaps())
+      alignmentChanged();
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   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);
-
+    Desktop.addInternalFrame(frame, "Find", 340, 110);
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void font_actionPerformed(ActionEvent e)
   {
-    FontChooser fc = new FontChooser( alignPanel );
+    new FontChooser(alignPanel);
+  }
+
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+    viewport.antiAlias = smoothFont.isSelected();
+    alignPanel.annotationPanel.image = null;
+    alignPanel.repaint();
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void seqLimit_actionPerformed(ActionEvent e)
   {
-    viewport.setShowFullId( fullSeqId.isSelected() );
+    viewport.setShowJVSuffix(seqLimits.isSelected());
 
-    alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
+    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
     alignPanel.repaint();
   }
 
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-      viewport.setColourText( colourTextMenuItem.isSelected() );
-      alignPanel.repaint();
+    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() );
+    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();
   }
 
+  /**
+   * 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() );
+    viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowText( viewTextMenuItem.isSelected() );
+    viewport.setShowText(viewTextMenuItem.isSelected());
     alignPanel.repaint();
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
     alignPanel.repaint();
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent evt)
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
   {
-    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
-    if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
+    if (!viewport.alignment.isNucleotide())
     {
-         AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
-         ((Alignment)viewport.alignment).featuresAdded = true;
+      new SequenceFeatureFetcher(viewport.
+                                 alignment,
+                                 alignPanel);
+      viewport.setShowSequenceFeatures(true);
+      showSeqFeatures.setSelected(true);
     }
-    alignPanel.repaint();
   }
 
-  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+
+  public void featureSettings_actionPerformed(ActionEvent e)
   {
-    if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+    new FeatureSettings(viewport, alignPanel);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void showSeqFeatures_actionPerformed(ActionEvent evt)
+  {
+    viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
+    alignPanel.repaint();
+    if (alignPanel.getOverviewPanel() != null)
     {
-      annotationPanelMenuItem.setSelected(false);
-      return;
+      alignPanel.getOverviewPanel().updateOverviewImage();
     }
-    viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
-    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+  {
+    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;
+    }
 
     JInternalFrame frame = new JInternalFrame();
     OverviewPanel overview = new OverviewPanel(alignPanel);
-     frame.setContentPane(overview);
+    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)
+    {
+      public void internalFrameClosed(
+          javax.swing.event.InternalFrameEvent evt)
       {
-            alignPanel.setOverviewPanel(null);
-      };
+        alignPanel.setOverviewPanel(null);
+      }
+      ;
     });
 
-    alignPanel.setOverviewPanel( overview );
-
-
+    alignPanel.setOverviewPanel(overview);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    changeColour( null );
+    changeColour(null);
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    abovePIDThreshold.setSelected(false);
-    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+    changeColour(new ClustalxColourScheme(
+        viewport.alignment.getSequences(), viewport.alignment.getWidth()));
   }
 
+  /**
+   * 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());
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    changeColour( new HydrophobicColourScheme() );
+    changeColour(new HydrophobicColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new HelixColourScheme() );
+    changeColour(new HelixColourScheme());
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void strandColour_actionPerformed(ActionEvent e)
   {
     changeColour(new StrandColourScheme());
   }
 
-
+  /**
+   * 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() );
+    changeColour(new BuriedColourScheme());
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void nucleotideColour_actionPerformed(ActionEvent e)
   {
     changeColour(new NucleotideColourScheme());
   }
 
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+    new AnnotationColourChooser(viewport, alignPanel);
+  }
+
 
+  /**
+   * 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() )
+    if(cs!=null)
     {
-      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);
-
+      if (viewport.getAbovePIDThreshold())
+      {
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+                                                   "Background");
 
+        cs.setThreshold(threshold,
+                        viewport.getIgnoreGapsConsensus());
 
-    if (viewport.getConservationSelected())
-    {
-      ConservationColourScheme ccs = null;
+        viewport.setGlobalColourScheme(cs);
+      }
+      else
+      {
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+      }
 
-      Alignment al = (Alignment) viewport.alignment;
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth() - 1);
+      if (viewport.getConservationSelected())
+      {
 
-      c.calculate();
-      c.verdict(false, viewport.ConsPercGaps);
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
 
-      ccs = new ConservationColourScheme(c, cs);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
 
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus( viewport.vconsensus );
-      viewport.setGlobalColourScheme(ccs);
+        cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
+      }
+      else
+      {
+        cs.setConservation(null);
+      }
 
-    }
-    else
-    {
-        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-        if (cs != null)
-          cs.setConsensus(viewport.vconsensus);
-        viewport.setGlobalColourScheme(cs);
+      cs.setConsensus(viewport.vconsensus);
     }
 
+    viewport.setGlobalColourScheme(cs);
 
-    if(viewport.getColourAppliesToAllGroups())
+    if (viewport.getColourAppliesToAllGroups())
     {
       Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+
+      for (int i = 0; i < groups.size(); i++)
       {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+        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)
           {
-            ex.printStackTrace();
-            sg.cs = cs;
           }
+        }
 
-        if(viewport.getAbovePIDThreshold())
+        if (viewport.getAbovePIDThreshold()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
         {
-          if (sg.cs instanceof ResidueColourScheme)
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-          else if (sg.cs instanceof ScoreColourScheme)
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+         sg.cs.setThreshold(threshold,
+                viewport.getIgnoreGapsConsensus());
 
-           sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+              sg.getWidth()));
         }
+        else
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+
 
-        if( viewport.getConservationSelected() )
+        if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.sequences, 0, viewport.alignment.getWidth()-1);
+                                            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;
+          sg.cs.setConservation(c);
         }
         else
-        {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
-        }
-
+          sg.cs.setConservation(null);
       }
     }
 
-    if(alignPanel.getOverviewPanel()!=null)
+    if (alignPanel.getOverviewPanel() != null)
+    {
       alignPanel.getOverviewPanel().updateOverviewImage();
+    }
+
     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();
-      }
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+    {
+      SliderPanel.setPIDSliderSource(alignPanel,
+                                     viewport.getGlobalColourScheme(),
+                                     "Background");
+      SliderPanel.showPIDSlider();
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if(viewport.getConservationSelected())
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
     {
-      SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
+      SliderPanel.setConservationSlider(alignPanel,
+                                        viewport.globalColourScheme,
                                         "Background");
       SliderPanel.showConservationSlider();
     }
   }
 
-
-  protected  void conservationMenuItem_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 );
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyConservation_actionPerformed(null);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -878,71 +1724,187 @@ public class AlignFrame extends GAlignFrame
     conservationMenuItem.setSelected(false);
     viewport.setConservationSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if(cs instanceof ConservationColourScheme )
-        changeColour( ((ConservationColourScheme)cs).cs );
-    else
-        changeColour( cs );
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyPID_actionPerformed(null);
   }
 
-
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
-  }
+    if (e.getActionCommand().equals("User Defined..."))
+    {
+      new UserDefinedColours(alignPanel, null);
+    }
+    else
+    {
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+          getUserColourSchemes().get(e.getActionCommand());
 
-  public void PIDColour_actionPerformed(ActionEvent e)
-  {
-    changeColour( new PIDColourScheme() );
+      changeColour(udc);
+    }
   }
 
+  public void updateUserColourMenu()
+  {
 
-  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new Blosum62ColourScheme() );
+    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();
+
+      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)
+  {
+    changeColour(new PIDColourScheme());
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  {
+    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));
+    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() );
+    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");
+    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+                                   HistoryItem.SORT));
+
     AlignmentSorter.sortByGroup(viewport.getAlignment());
-    AlignmentSorter.sortGroups(viewport.getAlignment());
     alignPanel.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel);
+    RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
     JInternalFrame frame = new JInternalFrame();
     frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
-
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
+                             100, false);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   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);
+    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();
@@ -951,274 +1913,859 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-
-    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>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{
-      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);
-   }
-
-
+     new PCAPanel(viewport);
   }
 
+  /**
+   * 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)
   {
-    //are the sequences aligned?
-    if(!viewport.alignment.isAligned())
-    {
-      JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
-                                    "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
-      return;
-    }
-
     final TreePanel tp;
-    if (viewport.getSelectionGroup() != null &&
-        viewport.getSelectionGroup().getSize() > 3)
+
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 3))
     {
-      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
-                         pwType,
-                         0, viewport.alignment.getWidth());
+      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
     {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, 0, viewport.alignment.getWidth());
+      //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);
+    addTreeMenuItem(tp, title);
+    viewport.setCurrentTree(tp.getTree());
 
-   Desktop.addInternalFrame(tp, title, 600, 500);
+    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();
+      }
+    });
   }
 
+  /**
+   * 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("sort");
-        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
+        addHistoryItem(new HistoryItem("Tree Sort",
+                                       viewport.alignment, HistoryItem.SORT));
+        AlignmentSorter.sortByTree(viewport.getAlignment(),
+                                   treePanel.getTree());
         alignPanel.repaint();
       }
     });
 
-    treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    treePanel.addInternalFrameListener(new javax.swing.event.
+                                       InternalFrameAdapter()
     {
-      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+      public void internalFrameClosed(
+          javax.swing.event.InternalFrameEvent evt)
       {
+        treeCount--;
         sortByTreeMenu.remove(item);
-      };
-    });
 
+        if (treeCount == 0)
+        {
+          sort.remove(sortByTreeMenu);
+        }
+      }
+      ;
+    });
   }
 
-
-  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()
   {
-     WebserviceInfo info = new WebserviceInfo("Clustal web service",
-     "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
-     " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
-    +" Nucleic Acids Research, submitted, June 1994.",
-     450, 150);
-
-    ClustalThread thread = new ClustalThread(info);
-    thread.start();
-  }
+    // Now, check we have enough sequences
+    SequenceI[] msa = null;
 
-    class ClustalThread extends Thread
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 1))
     {
-      WebserviceInfo info;
-      public ClustalThread(WebserviceInfo info)
-      {this.info = info; }
+      // 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()];
 
-      public void run()
+      for (int i = 0; i < sz; i++)
       {
-        info.setStatus(WebserviceInfo.STATE_RUNNING);
-        jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
-        Vector sv = viewport.getAlignment().getSequences();
-        SequenceI[] seqs = new SequenceI[sv.size()];
+        msa[i] = (SequenceI) seqs.getSequenceAt(i);
+      }
+    }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
 
-        int i = 0;
-        do
-        {
-          seqs[i] = (SequenceI) sv.elementAt(i);
-        }
-        while (++i < sv.size());
+      if (seqs.size() > 1)
+      {
+        msa = new SequenceI[seqs.size()];
 
-        SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
-        if (alignment != null)
-        {
-          AlignFrame af = new AlignFrame(new Alignment(alignment));
-          Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
-                                   NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
-          af.clustalColour_actionPerformed(null);
-          af.clustalColour.setSelected(true);
-          info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else
+        for (int i = 0; i < seqs.size(); i++)
         {
-            info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-            info.appendProgressText("Problem obtaining clustal alignment");
+          msa[i] = (SequenceI) seqs.elementAt(i);
         }
       }
     }
+    return msa;
+  }
 
-  protected void jpred_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()
+  {
+    SequenceI seq = null;
+    SequenceI[] msa = null;
 
-    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+    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())
+
+      if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
       {
-        JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
+        seq = (SequenceI) seqs.getSequenceAt(0);
       }
       else
       {
         int sz;
-        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        msa = new SequenceI[sz = seqs.getSize()];
+
         for (int i = 0; i < sz; i++)
         {
           msa[i] = (SequenceI) seqs.getSequenceAt(i);
         }
-
-        JPredClient ct = new JPredClient(msa);
       }
-
     }
     else
     {
       Vector seqs = viewport.getAlignment().getSequences();
 
-      if (seqs.size() == 1 || !viewport.alignment.isAligned())
+      if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
       {
-        JPredClient ct = new JPredClient( (SequenceI)
-                                         seqs.elementAt(0));
+        seq = (SequenceI) seqs.elementAt(0);
       }
       else
       {
-        SequenceI[] msa = new SequenceI[seqs.size()];
+        msa = new SequenceI[seqs.size()];
+
         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");
 
-        JPredClient ct = new JPredClient(msa);
+    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 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;
   }
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+
+  class PrintThread
+      extends Thread
   {
-    // TODO:resolve which menu item was actually selected
-    // Now, check we have enough sequences
-      if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+    public void run()
+    {
+      PrinterJob printJob = PrinterJob.getPrinterJob();
+      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+      printJob.setPrintable(alignPanel, pf);
+
+      if (printJob.printDialog())
       {
-        // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-        SequenceGroup seqs = viewport.getSelectionGroup();
-        int sz;
-        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
-        for (int i = 0; i < sz; i++)
+        try
         {
-          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+          printJob.print();
+        }
+        catch (Exception PrintException)
+        {
+          PrintException.printStackTrace();
         }
-
-        MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
       }
-      else
+    }
+  }
+
+  /**
+   * Generates menu items and listener event actions for web service clients
+   *
+   */
+  public void BuildWebServiceMenu()
+  {
+    if ( (Discoverer.services != null)
+        && (Discoverer.services.size() > 0))
+    {
+      Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+      Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
+      Vector wsmenu = new Vector();
+      if (msaws != null)
       {
-        Vector seqs = viewport.getAlignment().getSequences();
+        // 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();
+              new jalview.ws.MsaWSClient(sh, title, msa,
+                  false, true, viewport.getAlignment().getDataset());
+
+            }
 
-        if (seqs.size() > 1) {
-          SequenceI[] msa = new SequenceI[seqs.size()];
-          for (int i = 0; i < seqs.size(); i++)
+          });
+          msawsmenu.add(method);
+          // Deal with services that we know accept partial alignments.
+          if (sh.getName().indexOf("lustal") > -1)
           {
-            msa[i] = (SequenceI) seqs.elementAt(i);
-          }
+            // 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();
+                new jalview.ws.MsaWSClient(sh, title, msa,
+                    true, true, viewport.getAlignment().getDataset());
 
-          MsaWSClient ct = new MsaWSClient(msa);
-        }
+              }
 
+            });
+            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
+                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.
+  }
 
-    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
-    // Pick the tree file
+ /* public void vamsasStore_actionPerformed(ActionEvent e)
+  {
     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);
+    chooser.setDialogTitle("Export to Vamsas file");
+    chooser.setToolTipText("Export");
+
+    int value = chooser.showSaveDialog(this);
+
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      TreePanel treepanel = null;
+      jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
+      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+    }
+  }*/
+
+
+
+
+
+public void showTranslation_actionPerformed(ActionEvent e)
+{
+  int s, sSize = viewport.alignment.getHeight();
+  SequenceI [] newSeq = new SequenceI[sSize];
+
+  int res, resSize;
+  StringBuffer protein;
+  String seq;
+  for(s=0; s<sSize; s++)
+  {
+    protein = new StringBuffer();
+    seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
+    resSize = seq.length();
+    resSize -= resSize%3;
+
+    for(res = 0; res < resSize; res+=3)
+    {
+      String codon = seq.substring(res, res+3);
+      codon = codon.replace('U', 'T');
+      String aa = ResidueProperties.codonTranslate(codon);
+      if(aa==null)
+        protein.append(viewport.getGapCharacter());
+      else if(aa.equals("STOP"))
+        protein.append("X");
+      else
+        protein.append( aa );
+    }
+    newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
+  }
+
+
+  AlignmentI al = new Alignment(newSeq);
+  al.setDataset(null);
+
+
+  ////////////////////////////////
+  // Copy annotations across
+  jalview.datamodel.AlignmentAnnotation[] annotations
+      = viewport.alignment.getAlignmentAnnotation();
+  int a, aSize;
+  for (int i = 0; i < annotations.length; i++)
+  {
+
+    if (annotations[i].label.equals("Quality") ||
+        annotations[i].label.equals("Conservation") ||
+        annotations[i].label.equals("Consensus"))
+    {
+      continue;
+    }
+
+
+    aSize = viewport.alignment.getWidth()/3;
+    jalview.datamodel.Annotation [] anots =
+        new jalview.datamodel.Annotation[aSize];
+
+    for(a=0; a<viewport.alignment.getWidth(); a++)
+    {
+     if( annotations[i].annotations[a]==null
+      || annotations[i].annotations[a]==null)
+       continue;
+
+      anots[a/3] = new Annotation(
+     annotations[i].annotations[a].displayCharacter,
+     annotations[i].annotations[a].description,
+     annotations[i].annotations[a].secondaryStructure,
+     annotations[i].annotations[a].value,
+     annotations[i].annotations[a].colour);
+    }
+
+    jalview.datamodel.AlignmentAnnotation aa
+          = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
+       annotations[i].description, anots );
+     al.addAnnotation(aa);
+  }
+
+
+    AlignFrame af = new AlignFrame(al);
+    Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+                             NEW_WINDOW_WIDTH,
+                             NEW_WINDOW_HEIGHT);
+
+
+   // AlignViewport newViewport = new AlignViewport(al);
+   // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
+   // tabbedPane.add("Protein", ap);
+   // viewports.add(newViewport);
+  //  alignPanels.add(ap);
+
+    ///Dataset tab
+  /////////////////////////
+
+  //  AlignViewport ds = new AlignViewport(al.getDataset());
+  //  ds.setDataset(true);
+  //  AlignmentPanel dap = new AlignmentPanel(this, ds);
+  //  tabbedPane.add("Dataset", dap);
+  //  viewports.add(ds);
+  //  alignPanels.add(dap);
+  /////////////////////////
+
+
+}
+
+/*public void tabSelected()
+ {
+  int index = tabbedPane.getSelectedIndex();
+  viewport = (AlignViewport)viewports.elementAt(index);
+  alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
+ }*/
+
+/**
+ * DOCUMENT ME!
+ *
+ * @param String DOCUMENT ME!
+ */
+public boolean parseGroupsFile(String file)
+{
+    try
+    {
+      BufferedReader in = new BufferedReader(new FileReader(file));
+      SequenceI seq = null;
+      String line, type, desc, token;
+
+      int index, start, end;
+      StringTokenizer st;
+      SequenceFeature sf;
+      int lineNo = 0;
+      String featureGroup = null;
+      while ( (line = in.readLine()) != null)
+      {
+        lineNo++;
+        st = new StringTokenizer(line, "\t");
+        if (st.countTokens() == 2)
+        {
+          type = st.nextToken();
+          if (type.equalsIgnoreCase("startgroup"))
+          {
+            featureGroup = st.nextToken();
+          }
+          else if (type.equalsIgnoreCase("endgroup"))
+          {
+            //We should check whether this is the current group,
+            //but at present theres no way of showing more than 1 group
+            st.nextToken();
+            featureGroup = null;
+          }
+          else
+          {
+            UserColourScheme ucs = new UserColourScheme(st.nextToken());
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type,
+                ucs.findColour("A"));
+          }
+          continue;
+        }
+
+        while (st.hasMoreElements())
+        {
+          desc = 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());
+
+          seq = viewport.alignment.getSequenceAt(index);
+
+          type = st.nextToken();
+
+          if (alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type) == null)
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
+          }
+
+          sf = new SequenceFeature(type, desc, "", start, end);
+          sf.setFeatureGroup(featureGroup);
+
+          seq.getDatasetSequence().addSequenceFeature(sf);
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+      System.out.println("Error parsing groups file: " + ex);
+      return false;
+    }
+
+    viewport.showSequenceFeatures = true;
+    showSeqFeatures.setSelected(true);
+    alignPanel.repaint();
+    return true;
+}
+
+public void dragEnter(DropTargetDragEvent evt)
+{}
+
+public void dragExit(DropTargetEvent evt)
+{}
+
+public void dragOver(DropTargetDragEvent evt)
+{}
+
+public void dropActionChanged(DropTargetDragEvent evt)
+{}
+
+public void drop(DropTargetDropEvent evt)
+{
+    Transferable t = evt.getTransferable();
+    java.util.List files = null;
+
+    try
+    {
+      DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+      {
+        //Works on Windows and MacOSX
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+      }
+      else if (t.isDataFlavorSupported(uriListFlavor))
+      {
+        // This is used by Unix drag system
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        String data = (String) t.getTransferData(uriListFlavor);
+        files = new java.util.ArrayList(1);
+        for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+            data,
+            "\r\n");
+             st.hasMoreTokens(); )
+        {
+          String s = st.nextToken();
+          if (s.startsWith("#"))
+          {
+            // the line is a comment (as per the RFC 2483)
+            continue;
+          }
+
+          java.net.URI uri = new java.net.URI(s);
+          java.io.File file = new java.io.File(uri);
+          files.add(file);
+        }
+      }
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    if (files != null)
+    {
       try
       {
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
-        fin.parse();
+        boolean isAnnotation = false;
+
+        for (int i = 0; i < files.size(); i++)
+        {
+          String file = files.get(i).toString();
+
+          isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);
+
+          if( !isAnnotation )
+          {
+            boolean isGroupsFile = parseGroupsFile(file);
+            if (!isGroupsFile)
+            {
+              String protocol = "File";
+              String format = new IdentifyFile().Identify(file, protocol);
+              SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);
+
+              FastaFile ff = new FastaFile();
+              Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+              c.setContents(new StringSelection(ff.print(sequences)), this);
+
+              this.paste(false);
+
+            }
+          }
+        }
 
-        if (fin.getTree() != null)
+        if(isAnnotation)
         {
-          TreePanel tp = null;
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", choice);
-          Desktop.addInternalFrame(tp, title, 600, 500);
-          addTreeMenuItem(tp, title);
+          int height = alignPanel.annotationPanel.adjustPanelHeight();
+          alignPanel.annotationScroller.setPreferredSize(
+              new Dimension(alignPanel.annotationScroller.getWidth(),
+                            height));
+
+          alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+              alignPanel.annotationSpaceFillerHolder.getWidth(),
+              height));
+
+          alignPanel.addNotify();
         }
       }
       catch (Exception ex)
       {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                                      "Problem reading tree file",
-                                      ex.getMessage(),
-                                      JOptionPane.WARNING_MESSAGE);
         ex.printStackTrace();
       }
     }
-  }
+}
 
 }