X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5c3193127c60acead39d4e40653eeaf7ef148ae3;hb=1d6ae39a6442c455d362b933f1da89b0a481e5f5;hp=9566bb5731cf47301aecacb1e299a9f2c8b27436;hpb=6e9da2b0461e97e7d72711a61c9c8a982c548822;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9566bb5..5c31931 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,110 +1,171 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
-
-
-
-
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.jbgui.GAlignFrame;
-import jalview.schemes.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.io.*;
-import jalview.ws.*;
+import java.beans.*;
+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.*;
 
-public class AlignFrame extends GAlignFrame
+public class AlignFrame
+    extends GAlignFrame
 {
+  public static final int NEW_WINDOW_WIDTH = 700;
+  public static final int NEW_WINDOW_HEIGHT = 500;
   final AlignmentPanel alignPanel;
   final AlignViewport viewport;
+  public String currentFileFormat = "Jalview";
+  Stack historyList = new Stack();
+  Stack redoList = new Stack();
+  private int treeCount = 0;
+
   public AlignFrame(AlignmentI al)
   {
-    super();
-    viewport = new AlignViewport(al,true,true,true,false);
+    viewport = new AlignViewport(al);
+
     alignPanel = new AlignmentPanel(this, viewport);
+    alignPanel.annotationPanel.adjustPanelHeight();
+    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
+        annotationPanel.getPreferredSize());
+    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
+        getPreferredSize());
+    alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
+
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
 
     addInternalFrameListener(new InternalFrameAdapter()
-   {
-     public void internalFrameActivated(InternalFrameEvent evt)
-     {
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void internalFrameActivated(InternalFrameEvent evt)
+      {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
           {
-            public void run()
-            {      alignPanel.requestFocus();    }
-          });
-
-     }
-   });
-
+            alignPanel.requestFocus();
+          }
+        });
+      }
+    });
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-    chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"),
+        new String[]
+        {
+        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+        "jar"
+    },
+        new String[]
+        {
+        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+    }, currentFileFormat);
+
+    chooser.setAcceptAllFileFilterUsed(false);
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
+
     int value = chooser.showSaveDialog(this);
-    if(value == JFileChooser.APPROVE_OPTION)
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String choice =  chooser.getSelectedFile().getPath();
+      currentFileFormat = chooser.getSelectedFormat();
+      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+                                    currentFileFormat);
+
+      if (currentFileFormat.equals("Jalview"))
+      {
+        String shortName = title;
+
+        if (shortName.indexOf(java.io.File.separatorChar) > -1)
+        {
+          shortName = shortName.substring(shortName.lastIndexOf(
+              java.io.File.separatorChar) + 1);
+        }
+
+        String choice = chooser.getSelectedFile().getPath();
+        Jalview2XML.SaveState(this, choice, shortName);
+
+        // USE Jalview2XML to save this file
+        return;
+      }
+
+      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 )  );
+
+      String output = FormatAdapter.formatSequences(currentFileFormat,
+          viewport.getAlignment().getSequences());
+
+      try
+      {
+        java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
+            FileWriter(
+                choice));
         out.println(output);
         out.close();
       }
-      catch(Exception ex){}
+      catch (Exception ex)
+      {
+      }
     }
-
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     JInternalFrame frame = new JInternalFrame();
-     cap.formatForOutput();
-     frame.setContentPane(cap);
-     Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
-     cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
+    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+                                              viewport.getAlignment().
+                                              getSequences()));
   }
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport);
-    htmlOutput = null;
+    new HTMLOutput(viewport);
   }
 
-  protected void createJPG_actionPerformed(ActionEvent e)
+  protected void createPNG_actionPerformed(ActionEvent e)
   {
-
-    int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
-    int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
-
-
-    if(!viewport.getWrapAlignment())
-    {
-      height = viewport.alignment.getHeight() * viewport.charHeight;
-      width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
-    }
-
-    alignPanel.makeJPG( width, height);
+    alignPanel.makePNG();
   }
 
+  protected void epsFile_actionPerformed(ActionEvent e)
+  {
+    alignPanel.makeEPS();
+  }
 
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
@@ -113,61 +174,39 @@ 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();
-        }
-      }
-    }
-
-  }
-
-
-
-
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       this.setClosed(true);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
   }
 
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
-
   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);
@@ -175,59 +214,105 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
-  public void addHistoryItem(String type)
+  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();
   }
 
   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);
+  }
+
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+    HistoryItem hi = (HistoryItem) redoList.pop();
+    restoreHistoryItem(hi);
+    updateEditMenuBar();
+    viewport.updateConsensus();
+    alignPanel.repaint();
+    alignPanel.repaint();
+  }
+
+  // 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();
-      alignPanel.RefreshPanels();
+    viewport.updateConsensus();
+    viewport.updateConservation();
+    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null,
+                                viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
   {
-    SequenceGroup sg = viewport.getRubberbandGroup();
+    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);
@@ -238,44 +323,78 @@ 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);
       }
     }
 
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
-
-
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getRubberbandGroup()==null)
-     return;
+    if (viewport.getSelectionGroup() == null)
+    {
+      return;
+    }
 
-   SequenceGroup sg = viewport.getRubberbandGroup();
+    SequenceGroup sg = viewport.getSelectionGroup();
 
-     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-     StringBuffer buffer= new StringBuffer();
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    StringBuffer buffer = new StringBuffer();
 
-       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();
 
-  }
+    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;
+
+    for (int i = 0; i < sg.getSize(); i++)
+    {
+      SequenceI seq = null;
+
+      while (seq == null)
+      {
+        if (orderedSeqs.containsKey(index + ""))
+        {
+          seq = (SequenceI) orderedSeqs.get(index + "");
+          index++;
+
+          break;
+        }
+        else
+        {
+          index++;
+        }
+      }
+
+      buffer.append(seq.getName() + "\t" +
+                    seq.findPosition(sg.getStartRes()) + "\t" +
+                    seq.findPosition(sg.getEndRes()) + "\t" +
+                    sg.getSequenceAt(i).getSequence(sg.getStartRes(),
+          sg.getEndRes() + 1) + "\n");
+    }
 
+    c.setContents(new StringSelection(buffer.toString()), null);
+  }
 
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
@@ -284,56 +403,83 @@ public class AlignFrame extends GAlignFrame
 
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Paste");
+    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+                                   HistoryItem.PASTE));
     paste(false);
   }
 
   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())
       {
         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);
+        Sequence sequence = new Sequence(name, st.nextToken(), start,
+                                         end);
 
-        if(!newAlignment)
+        if (!newAlignment)
+        {
           viewport.alignment.addSequence(sequence);
+        }
         else
+        {
           seqs.add(sequence);
+        }
       }
 
-      if(newAlignment)
+      if (newAlignment)
       {
         SequenceI[] newSeqs = new SequenceI[seqs.size()];
         seqs.toArray(newSeqs);
+
         AlignFrame af = new AlignFrame(new Alignment(newSeqs));
-        int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
-        if (newHeight > 500)
-          newHeight = 500;
-        Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
+        String newtitle = new String("Copied sequences");
+
+        if (title.startsWith("Copied sequences"))
+        {
+          newtitle = title;
+        }
+        else
+        {
+          newtitle = newtitle.concat("- from " + title);
+        }
+
+        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
+                                 NEW_WINDOW_HEIGHT);
       }
       else
       {
+        viewport.firePropertyChange("alignment", null,
+                                    viewport.getAlignment().getSequences());
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        alignPanel.RefreshPanels();
+        viewport.updateConservation();
+        viewport.updateConsensus();
+        alignPanel.repaint();
       }
+    }
+    catch (Exception ex)
+    {
+    }
 
-    }catch(Exception ex){}// could be anything being pasted in here
-
+    // could be anything being pasted in here
   }
 
-
   protected void cut_actionPerformed(ActionEvent e)
   {
     copy_actionPerformed(null);
@@ -342,283 +488,377 @@ public class AlignFrame extends GAlignFrame
 
   protected void delete_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Delete");
-    if (viewport.getRubberbandGroup() == null)
+    boolean seqsdeleted = false;
+
+    if (viewport.getSelectionGroup() == null)
+    {
       return;
+    }
 
-     SequenceGroup sg = viewport.getRubberbandGroup();
-     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);
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                                   HistoryItem.HIDE));
 
-       if(seq.getSequence().length()<1)
-          viewport.getAlignment().deleteSequence(seq);
-      else
-          viewport.getAlignment().getSequences().setElementAt(seq, index);
-     }
+    SequenceGroup sg = viewport.getSelectionGroup();
 
-     viewport.setRubberbandGroup(null);
-     viewport.alignment.deleteGroup(sg);
-     viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
-     if(viewport.getAlignment().getHeight()<1)
-     try
-     {
-       this.setClosed(true);
-     }catch(Exception ex){}
-     alignPanel.RefreshPanels();
+    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)
+      {
+        seqsdeleted = true;
+        viewport.getAlignment().deleteSequence(seq);
+      }
+      else
+      {
+        viewport.getAlignment().getSequences().setElementAt(seq, index);
+      }
+    }
 
+    viewport.setSelectionGroup(null);
+    viewport.alignment.deleteGroup(sg);
 
+    if (seqsdeleted)
+    {
+      viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+    }
 
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
-  {
-     Object [] history = (Object[])redoList.remove(0);
-     SequenceI[] seq = (SequenceI[]) history[1];
-     viewport.setAlignment( new Alignment(seq) );
-     updateEditMenuBar();
-     alignPanel.RefreshPanels();
-  }
+    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
 
+    if (viewport.getAlignment().getHeight() < 1)
+    {
+      try
+      {
+        this.setClosed(true);
+      }
+      catch (Exception ex)
+      {
+      }
+    }
 
-  public void groupsMenuItem_actionPerformed(ActionEvent e)
-  {
-    GroupEditor geditor = new GroupEditor(viewport, alignPanel);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(geditor);
-    Desktop.addInternalFrame(frame, "Group editor", 710, 410);
-    frame.setResizable(false);
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
   }
 
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
-    viewport.getSelection().clear();
-
-    alignPanel.RefreshPanels();
+    viewport.setSelectionGroup(null);
+    alignPanel.repaint();
   }
 
-
-
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sel.addElement( viewport.getAlignment().getSequenceAt(i));
+    SequenceGroup sg = new SequenceGroup();
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
+    {
+      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
+    }
+
+    sg.setEndRes(viewport.alignment.getWidth());
+    viewport.setSelectionGroup(sg);
     PaintRefresher.Refresh(null);
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setRubberbandGroup(null);
-    viewport.getSelection().clear();
+    viewport.setSelectionGroup(null);
+    viewport.getColumnSelection().clear();
+    viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(null);
   }
 
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+    SequenceGroup sg = viewport.getSelectionGroup();
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
     {
-      if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
-        sel.removeElement(viewport.getAlignment().getSequenceAt(i));
-      else
-        sel.addElement(viewport.getAlignment().getSequenceAt(i));
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
-    PaintRefresher.Refresh(null);
-  }
-
 
-  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.getColumnSelection().clear();
-    repaint();
+    PaintRefresher.Refresh(null);
   }
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
+
     if (colSel.size() > 0)
     {
+      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
+                                     HistoryItem.HIDE));
+
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0,min);
-      alignPanel.RefreshPanels();
+      colSel.compensateForEdit(0, min);
+
+      if (viewport.getSelectionGroup() != null)
+      {
+        viewport.getSelectionGroup().adjustForRemoveLeft(min);
+      }
+
+      Vector groups = viewport.alignment.getGroups();
+
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+
+        if (!sg.adjustForRemoveLeft(min))
+        {
+          viewport.alignment.deleteGroup(sg);
+        }
+      }
+
+      alignPanel.repaint();
     }
   }
 
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
+
     if (colSel.size() > 0)
     {
+      addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
+                                     HistoryItem.HIDE));
+
       int max = colSel.getMax();
-      if(max>1)
-        viewport.getAlignment().trimRight(max);
+      viewport.getAlignment().trimRight(max);
 
-      alignPanel.RefreshPanels();
-    }
+      if (viewport.getSelectionGroup() != null)
+      {
+        viewport.getSelectionGroup().adjustForRemoveRight(max);
+      }
 
-  }
+      Vector groups = viewport.alignment.getGroups();
 
-  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("delete gapped columns");
-    viewport.getAlignment().removeGaps();
-    alignPanel.RefreshPanels();
-  }
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
 
-  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+        if (!sg.adjustForRemoveRight(max))
+        {
+          viewport.alignment.deleteGroup(sg);
+        }
+      }
+
+      alignPanel.repaint();
+    }
+  }
+
+  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+  {
+    addHistoryItem(new HistoryItem("Remove Gapped Columns",
+                                   viewport.alignment, HistoryItem.HIDE));
+
+    viewport.getAlignment().removeGaps();
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
+  }
+
+  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete all gaps");
+    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
+                                   HistoryItem.HIDE));
+
     SequenceI current;
     int jSize;
-    for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
     {
       current = viewport.getAlignment().getSequenceAt(i);
       jSize = current.getLength();
-      for (int j=0; j < jSize; j++)
-        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
+
+      for (int j = 0; j < jSize; j++)
+      {
+        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
           current.deleteCharAt(j);
           j--;
           jSize--;
         }
+      }
     }
 
-    alignPanel.RefreshPanels();
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
   }
 
-  public void setGapCharMenuItem_actionPerformed(ActionEvent e)
+  public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
-    char thisChar = '-';
-    char nextChar = '.';
-    if(viewport.getGapCharacter()=='-')
+    addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
+                                   HistoryItem.HIDE));
+
+    SequenceI current;
+    int Width = viewport.getAlignment().getWidth() - 1;
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
     {
-      thisChar = '.';
-      nextChar = '-';
+      current = viewport.getAlignment().getSequenceAt(i);
+
+      if (current.getLength() < Width)
+      {
+        current.insertCharAt(Width, viewport.getGapCharacter());
+      }
     }
-    setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
-    viewport.setGapCharacter(thisChar);
-    alignPanel.RefreshPanels();
+
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
   }
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    JOptionPane op = new JOptionPane();
-    JInternalFrame frame =  op.createInternalFrame(this, "Find");
+    JInternalFrame frame = new JInternalFrame();
     Finder finder = new Finder(viewport, alignPanel, frame);
-    frame.setClosable(true);
     frame.setContentPane(finder);
-    frame.setSize(340,110);
-    frame.setVisible(true);
+    Desktop.addInternalFrame(frame, "Find", 340, 110);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
-
   public void font_actionPerformed(ActionEvent e)
   {
-    JOptionPane op = new JOptionPane();
-    JInternalFrame frame = op.createInternalFrame(this, "Change Font");
-    FontChooser fc = new FontChooser( alignPanel );
-    frame.setClosable(true);
-    frame.setContentPane(fc);
-    frame.setSize(480, 100);
-    frame.setVisible(true);
+    FontChooser fc = new FontChooser(alignPanel);
+  }
+
+  protected void fullSeqId_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowFullId(fullSeqId.isSelected());
+
+    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+    alignPanel.repaint();
   }
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-      viewport.setColourText( colourTextMenuItem.isSelected() );
-      alignPanel.RefreshPanels();
+    viewport.setColourText(colourTextMenuItem.isSelected());
+    alignPanel.repaint();
   }
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
-    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
+    viewport.setWrapAlignment(wrapMenuItem.isSelected());
+    alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+    scaleAbove.setVisible(wrapMenuItem.isSelected());
+    scaleLeft.setVisible(wrapMenuItem.isSelected());
+    scaleRight.setVisible(wrapMenuItem.isSelected());
+    alignPanel.repaint();
   }
 
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+    alignPanel.repaint();
+  }
+
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.repaint();
+  }
+
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.repaint();
+  }
 
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
+    alignPanel.repaint();
   }
 
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowText( viewTextMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+    viewport.setShowText(viewTextMenuItem.isSelected());
+    alignPanel.repaint();
   }
 
-
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.RefreshPanels();
+    alignPanel.repaint();
   }
 
   public void sequenceFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
-    if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
+
+    if (viewport.showSequenceFeatures &&
+        ! ( (Alignment) viewport.alignment).featuresAdded)
     {
-         AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
-         ((Alignment)viewport.alignment).featuresAdded = true;
+      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
+          alignment,
+          alignPanel);
+      ( (Alignment) viewport.alignment).featuresAdded = true;
     }
-    alignPanel.RefreshPanels();
+
+    alignPanel.repaint();
   }
 
-  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
+    if (annotationPanelMenuItem.isSelected() &&
+        viewport.getWrapAlignment())
+    {
+      annotationPanelMenuItem.setSelected(false);
+
+      return;
+    }
+
+    viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
+    alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
     if (alignPanel.overviewPanel != null)
+    {
       return;
+    }
 
     JInternalFrame frame = new JInternalFrame();
-    OverviewPanel overview = alignPanel.getOverviewPanel();
-   try{
-     overview = new OverviewPanel(alignPanel, viewport);
-     frame.setContentPane(overview);
+    OverviewPanel overview = new OverviewPanel(alignPanel);
+    frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
                              frame.getWidth(), frame.getHeight());
     frame.pack();
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+    {
+      public void internalFrameClosed(
+          javax.swing.event.InternalFrameEvent evt)
       {
-            alignPanel.setOverviewPanel(null);
-      };
+        alignPanel.setOverviewPanel(null);
+      }
+      ;
     });
-    alignPanel.setOverviewPanel( overview );
-
-  }catch(java.lang.OutOfMemoryError ex)
-   {
-     JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
-                                   +"\nTry reducing the font size.",
-                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
-   }
-
 
+    alignPanel.setOverviewPanel(overview);
   }
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    changeColour( null );
+    changeColour(null);
   }
 
-
   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()));
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
@@ -631,33 +871,29 @@ public class AlignFrame extends GAlignFrame
     changeColour(new TaylorColourScheme());
   }
 
-
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    changeColour( new HydrophobicColourScheme() );
+    changeColour(new HydrophobicColourScheme());
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new HelixColourScheme() );
+    changeColour(new HelixColourScheme());
   }
 
-
   public void strandColour_actionPerformed(ActionEvent e)
   {
     changeColour(new StrandColourScheme());
   }
 
-
   public void turnColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TurnColourScheme());
   }
 
-
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new BuriedColourScheme() );
+    changeColour(new BuriedColourScheme());
   }
 
   public void nucleotideColour_actionPerformed(ActionEvent e)
@@ -665,114 +901,195 @@ public class AlignFrame extends GAlignFrame
     changeColour(new NucleotideColourScheme());
   }
 
-
   protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
   }
 
-
-
   void changeColour(ColourSchemeI cs)
   {
+    int threshold = 0;
 
-    if(viewport.getColourAppliesToAllGroups())
-    {
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-        sg.cs = cs;
-
-        if(abovePIDThreshold.isSelected())
-          abovePIDThreshold_actionPerformed(null);
-        else if( viewport.getConservationSelected() )
-        {
-          Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.sequences, sg.getStartRes(),
-                                            sg.getEndRes());
-          c.calculate();
-          c.verdict(false, 100);
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-          sg.cs = ccs;
-        }
-
-      }
-    }
-
-
-    if ( viewport.getAbovePIDThreshold())
+    if (viewport.getAbovePIDThreshold())
     {
-      int threshold = 0;
-      threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
-      Desktop.hideConservationSlider();
+      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)
+    else if (cs instanceof ResidueColourScheme)
+    {
       ( (ResidueColourScheme) cs).setThreshold(0);
+    }
     else if (cs instanceof ScoreColourScheme)
+    {
       ( (ScoreColourScheme) cs).setThreshold(0);
+    }
+
+    if (viewport.getConservationSelected())
+    {
+      ConservationColourScheme ccs = null;
+
+      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);
+
+      ccs = new ConservationColourScheme(c, cs);
+
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      ccs.setConsensus(viewport.vconsensus);
+      viewport.setGlobalColourScheme(ccs);
+
+      ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
+                                                  "Background");
+    }
+    else
+    {
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      if (cs != null)
+      {
+        cs.setConsensus(viewport.vconsensus);
+      }
 
+      viewport.setGlobalColourScheme(cs);
+    }
 
+    if (viewport.getColourAppliesToAllGroups())
+    {
+      Vector groups = viewport.alignment.getGroups();
 
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-if ( viewport.getConservationSelected() )
- {
-   ConservationColourScheme ccs = null;
+        if (cs == null)
+        {
+          sg.cs = null;
+        }
+        else if (cs instanceof ClustalxColourScheme)
+        {
+          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+        }
+        else if (cs instanceof UserColourScheme)
+        {
+          sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
+        }
+        else
+        {
+          try
+          {
+            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+          }
+          catch (Exception ex)
+          {
+          }
+        }
 
-   Alignment al = (Alignment) viewport.alignment;
-   Conservation c = new Conservation("All",
-                                     ResidueProperties.propHash, 3,
-                                     al.getSequences(), 0,
-                                     al.getWidth());
+        if (viewport.getAbovePIDThreshold())
+        {
+          if (sg.cs instanceof ResidueColourScheme)
+          {
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+          }
+          else if (sg.cs instanceof ScoreColourScheme)
+          {
+            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+          }
 
-   c.calculate();
-   c.verdict(false, 100);
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+              sg.getWidth()));
+        }
 
-   ccs = new ConservationColourScheme(c, cs);
+        if (viewport.getConservationSelected())
+        {
+          Conservation c = new Conservation("Group",
+                                            ResidueProperties.propHash, 3,
+                                            sg.sequences, 0,
+                                            viewport.alignment.getWidth() - 1);
+          c.calculate();
+          c.verdict(false, viewport.ConsPercGaps);
 
-   int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
-       "Background");
+          ConservationColourScheme ccs = new ConservationColourScheme(c,
+              sg.cs);
 
-   ccs.inc = threshold;
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                                                 sg.getWidth()));
+          sg.cs = ccs;
+        }
+        else if (cs != null)
+        {
+          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+              sg.getWidth()));
+        }
+      }
+    }
 
-   viewport.setGlobalColourScheme(ccs);
+    if (alignPanel.getOverviewPanel() != null)
+    {
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    }
 
+    alignPanel.repaint();
   }
-  else
-       viewport.setGlobalColourScheme( cs );
 
-    alignPanel.RefreshPanels();
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+    if (viewport.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(alignPanel,
+                                     viewport.getGlobalColourScheme(),
+                                     "Background");
+      SliderPanel.showPIDSlider();
+    }
   }
 
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+    if (viewport.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(alignPanel,
+                                        viewport.globalColourScheme,
+                                        "Background");
+      SliderPanel.showConservationSlider();
+    }
+  }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
-    Desktop.hidePIDSlider();
-    if(!viewport.getConservationSelected())
-      Desktop.hideConservationSlider();
 
-   ColourSchemeI cs = viewport.getGlobalColourScheme();
-   if(cs instanceof ConservationColourScheme )
-     changeColour( ((ConservationColourScheme)cs).cs );
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
+
+    if (cs instanceof ConservationColourScheme)
+    {
+      changeColour( ( (ConservationColourScheme) cs).cs);
+    }
     else
-      changeColour( cs );
-  }
+    {
+      changeColour(cs);
+    }
 
+    modifyConservation_actionPerformed(null);
+  }
 
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
@@ -780,93 +1097,82 @@ if ( viewport.getConservationSelected() )
 
     conservationMenuItem.setSelected(false);
     viewport.setConservationSelected(false);
-    Desktop.hideConservationSlider();
-
-    if(!viewport.getAbovePIDThreshold())
-      Desktop.hidePIDSlider();
-
 
     ColourSchemeI cs = viewport.getGlobalColourScheme();
-    if(cs instanceof ConservationColourScheme )
-        changeColour( ((ConservationColourScheme)cs).cs );
+
+    if (cs instanceof ConservationColourScheme)
+    {
+      changeColour( ( (ConservationColourScheme) cs).cs);
+    }
     else
-        changeColour( cs );
+    {
+      changeColour(cs);
+    }
 
+    modifyPID_actionPerformed(null);
   }
 
-
-
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
-    frame.setResizable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
+    new UserDefinedColours(alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    changeColour( new PIDColourScheme() );
+    changeColour(new PIDColourScheme());
   }
 
-
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme(viewport) );
+    changeColour(new Blosum62ColourScheme());
   }
 
-
-
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
-    alignPanel.RefreshPanels();
+    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
+                                   HistoryItem.SORT));
+    AlignmentSorter.sortByPID(viewport.getAlignment(),
+                              viewport.getAlignment().getSequenceAt(0));
+    alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByID( viewport.getAlignment() );
-    alignPanel.RefreshPanels();
+    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+                                   HistoryItem.SORT));
+    AlignmentSorter.sortByID(viewport.getAlignment());
+    alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByGroup(viewport.getAlignment());
-    AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.RefreshPanels();
-  }
-
-  public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("sort");
-    if(viewport.getCurrentTree()==null)
-      return;
+    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+                                   HistoryItem.SORT));
 
-    AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
-    alignPanel.RefreshPanels();
+    //  AlignmentSorter.sortByGroup(viewport.getAlignment());
+    AlignmentSorter.sortGroups(viewport.getAlignment());
+    alignPanel.repaint();
   }
 
   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);
-    frame.setMaximizable(false);
-    frame.setResizable(false);
-
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
+                             100, false);
   }
 
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelection().size()<2)
-      JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
+    if ( (viewport.getSelectionGroup() == null) ||
+        (viewport.getSelectionGroup().getSize() < 2))
+    {
+      JOptionPane.showInternalMessageDialog(this,
+                                            "You must select at least 2 sequences.",
+                                            "Invalid Selection",
+                                            JOptionPane.WARNING_MESSAGE);
+    }
     else
     {
       JInternalFrame frame = new JInternalFrame();
@@ -877,28 +1183,35 @@ if ( viewport.getConservationSelected() )
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-    if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
-       || viewport.getAlignment().getHeight()<4)
+    if ( ( (viewport.getSelectionGroup() != null) &&
+          (viewport.getSelectionGroup().getSize() < 4) &&
+          (viewport.getSelectionGroup().getSize() > 0)) ||
+        (viewport.getAlignment().getHeight() < 4))
     {
-      JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
-                                    +"at least 4 input sequences.",
-                                    "Sequence selection insufficient",
-                                    JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(this,
+                                            "Principal component analysis must take\n" +
+                                            "at least 4 input sequences.",
+                                            "Sequence selection insufficient",
+                                            JOptionPane.WARNING_MESSAGE);
+
       return;
     }
 
-    try{
+    try
+    {
       PCAPanel pcaPanel = new PCAPanel(viewport, null);
       JInternalFrame frame = new JInternalFrame();
       frame.setContentPane(pcaPanel);
-      Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
-   }catch(java.lang.OutOfMemoryError ex)
-   {
-     JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
-                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
-   }
-
-
+      Desktop.addInternalFrame(frame, "Principal component analysis",
+                               400, 400);
+    }
+    catch (java.lang.OutOfMemoryError ex)
+    {
+      JOptionPane.showInternalMessageDialog(this,
+                                            "Too many sequences selected\nfor Principal Component Analysis!!",
+                                            "Out of memory",
+                                            JOptionPane.WARNING_MESSAGE);
+    }
   }
 
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
@@ -911,7 +1224,6 @@ if ( viewport.getConservationSelected() )
     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
   }
 
-
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
@@ -919,139 +1231,400 @@ if ( viewport.getConservationSelected() )
 
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
+    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
   }
 
   void NewTreePanel(String type, String pwType, String title)
   {
-    //are the sequences aligned?
-    if(!viewport.alignment.isAligned())
+    String ltitle;
+    final TreePanel tp;
+
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 3))
     {
-      JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
-                                    "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
-      return;
+      int s = 0;
+      SequenceGroup sg = viewport.getSelectionGroup();
+
+      /* Decide if the selection is a column region */
+      while (s < sg.sequences.size())
+      {
+        if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
+            sg.getEndRes())
+        {
+          JOptionPane.showMessageDialog(Desktop.desktop,
+                                        "The selected region to create a tree may\nonly contain residues or gaps.\n" +
+                                        "Try using the Pad function in the edit menu,\n" +
+                                        "or one of the multiple sequence alignment web services.",
+                                        "Sequences in selection are not aligned",
+                                        JOptionPane.WARNING_MESSAGE);
+
+          return;
+        }
+      }
+
+      title = title + " on region";
+      tp = new TreePanel(viewport,
+                         viewport.getSelectionGroup().sequences, type, pwType,
+                         sg.getStartRes(), sg.getEndRes());
+    }
+    else
+    {
+      //are the sequences aligned?
+      if (!viewport.alignment.isAligned())
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "The sequences must be aligned before creating a tree.\n" +
+                                      "Try using the Pad function in the edit menu,\n" +
+                                      "or one of the multiple sequence alignment web services.",
+                                      "Sequences not aligned",
+                                      JOptionPane.WARNING_MESSAGE);
+
+        return;
+      }
+
+      tp = new TreePanel(viewport,
+                         viewport.getAlignment().getSequences(), type, pwType,
+                         0,
+                         viewport.alignment.getWidth());
     }
 
-    TreePanel tp=null;
-   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
-   {
-     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
-                         0, viewport.alignment.getWidth());
-   }
-   else
-   {
-     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType,  0, viewport.alignment.getWidth());
-   }
+    addTreeMenuItem(tp, title);
+    viewport.setCurrentTree(tp.getTree());
 
-   Desktop.addInternalFrame(tp, title, 600, 500);
+    Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
   }
 
+  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();
+      }
+    });
+  }
+
+  void addTreeMenuItem(final TreePanel treePanel, String title)
+  {
+    final JMenuItem item = new JMenuItem(title);
+
+    treeCount++;
 
+    if (treeCount == 1)
+    {
+      sort.add(sortByTreeMenu);
+    }
 
+    sortByTreeMenu.add(item);
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addHistoryItem(new HistoryItem("Tree Sort",
+                                       viewport.alignment, HistoryItem.SORT));
+        AlignmentSorter.sortByTree(viewport.getAlignment(),
+                                   treePanel.getTree());
+        alignPanel.repaint();
+      }
+    });
+
+    treePanel.addInternalFrameListener(new javax.swing.event.
+                                       InternalFrameAdapter()
+    {
+      public void internalFrameClosed(
+          javax.swing.event.InternalFrameEvent evt)
+      {
+        treeCount--;
+        sortByTreeMenu.remove(item);
+
+        if (treeCount == 0)
+        {
+          sort.remove(sortByTreeMenu);
+        }
+      }
+      ;
+    });
+    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+    {
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        if (evt.getPropertyName().equals("alignment"))
+        {
+          treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
+          treePanel.repaint();
+        }
+      }
+    });
+  }
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    ClustalThread ct = new ClustalThread(frame);
-    Thread t = new Thread(ct);
-    t.start();
-    frame.setContentPane(ct);
-     Desktop.addInternalFrame(frame, title, 300, 80);
+    // TODO:resolve which menu item was actually selected
+    // Now, check we have enough sequences
+    SequenceI[] msa = null;
+
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 1))
+    {
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+      int sz;
+      msa = new SequenceI[sz = seqs.getSize()];
+
+      for (int i = 0; i < sz; i++)
+      {
+        msa[i] = (SequenceI) seqs.getSequenceAt(i);
+      }
+    }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if (seqs.size() > 1)
+      {
+        msa = new SequenceI[seqs.size()];
+
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          msa[i] = (SequenceI) seqs.elementAt(i);
+        }
+      }
+    }
+
+    if (msa != null)
+    {
+      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
+          title, msa, false, true);
+    }
+  }
+
+  public void ClustalRealign_actionPerformed(ActionEvent e)
+  {
+    // TODO:resolve which menu item was actually selected
+    // Now, check we have enough sequences
+    SequenceI[] msa = null;
+
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 1))
+    {
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+      int sz;
+      msa = new SequenceI[sz = seqs.getSize()];
+
+      for (int i = 0; i < sz; i++)
+      {
+        msa[i] = (SequenceI) seqs.getSequenceAt(i);
+      }
+    }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if (seqs.size() > 1)
+      {
+        msa = new SequenceI[seqs.size()];
+
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          msa[i] = (SequenceI) seqs.elementAt(i);
+        }
+      }
+    }
 
+    if (msa != null)
+    {
+      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
+          title, msa, true, true);
+    }
   }
 
-  class ClustalThread extends JPanel implements Runnable
+  protected void jpred_actionPerformed(ActionEvent e)
   {
-    Image [] image;
-    int imageIndex = 0;
-    boolean webServiceRunning = false;
-    JInternalFrame frame;
-    public ClustalThread(JInternalFrame frame)
+    SequenceI seq = null;
+    SequenceI[] msa = null;
+
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 0))
+    {
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+
+      if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
+      {
+        seq = (SequenceI) seqs.getSequenceAt(0);
+      }
+      else
+      {
+        int sz;
+        msa = new SequenceI[sz = seqs.getSize()];
+
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+      }
+    }
+    else
     {
-      this.frame = frame;
-      image = new Image[9];
-      for(int i=0; i<9; i++)
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
+      {
+        seq = (SequenceI) seqs.elementAt(0);
+      }
+      else
       {
-        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
-        if (url != null)
+        msa = new SequenceI[seqs.size()];
+
+        for (int i = 0; i < seqs.size(); i++)
         {
-          image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-          MediaTracker mt = new MediaTracker(this);
-          mt.addImage(image[i], i);
-          try{mt.waitForID(i);}
-          catch(Exception ex){}
+          msa[i] = (SequenceI) seqs.elementAt(i);
         }
       }
-      DNATwirler twirler = new DNATwirler();
-      twirler.start();
-      webServiceRunning = true;
     }
 
-    class DNATwirler extends Thread
+    if (msa != null)
+    {
+      JPredClient ct = new JPredClient(title, msa);
+    }
+    else if (seq != null)
+    {
+      JPredClient ct = new JPredClient(title, seq);
+    }
+    else
+    {
+      System.err.print(
+          "JALVIEW ERROR! - Unexpected JPred selection state!\n");
+    }
+  }
+
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO:resolve which menu item was actually selected
+    // Now, check we have enough sequences
+    SequenceI[] msa = null;
+
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 1))
     {
-      public void run()
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+      int sz;
+      msa = new SequenceI[sz = seqs.getSize()];
+
+      for (int i = 0; i < sz; i++)
       {
-        while(webServiceRunning)
+        msa[i] = (SequenceI) seqs.getSequenceAt(i);
+      }
+    }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if (seqs.size() > 1)
+      {
+        msa = new SequenceI[seqs.size()];
+
+        for (int i = 0; i < seqs.size(); i++)
         {
-          try{
-            Thread.sleep(100);
-            imageIndex++;
-            imageIndex %=9;
-            repaint();
-          }
-          catch(Exception ex){}
+          msa[i] = (SequenceI) seqs.elementAt(i);
         }
       }
     }
 
-    // JBPNote
-    // Should check to see if the server settings are valid
-    // Need visual-delay indication here.
+    if (msa != null)
+    {
+      MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
+                                                  false, true);
+    }
+  }
+
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+  {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Select a newick-like tree file");
+    chooser.setToolTipText("Load a tree file");
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+
+      try
+      {
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
+            "File");
+        ShowNewickTree(fin, choice);
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "Problem reading tree file",
+                                      ex.getMessage(),
+                                      JOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+    }
+  }
+
+  public void ShowNewickTree(NewickFile nf, String title)
+  {
+    try
+    {
+      nf.parse();
+
+      if (nf.getTree() != null)
+      {
+        TreePanel tp = new TreePanel(viewport,
+                                     viewport.getAlignment().getSequences(), nf,
+                                     "FromFile",
+                                     title);
+        Desktop.addInternalFrame(tp, title, 600, 500);
+        addTreeMenuItem(tp, title);
+        viewport.setCurrentTree(tp.getTree());
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  class PrintThread
+      extends Thread
+  {
     public void run()
-       {
-         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
-         Vector sv = viewport.getAlignment().getSequences();
-         SequenceI[] seqs = new SequenceI[sv.size()];
-
-         int i = 0;
-         do
-         {
-           seqs[i] = (SequenceI) sv.elementAt(i);
-         }
-         while (++i < sv.size());
-
-         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
-
-         if (alignment != null)
-         {
-           AlignFrame af = new AlignFrame(new Alignment(alignment));
-          af.clustalColour.setSelected(true);
-          af.clustalColour_actionPerformed(null);
-           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
-                                    700, 500); // JBPNote - is there a new window geom. property ?
-         }
-         else
-           JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
-                                         JOptionPane.WARNING_MESSAGE);
-
-         webServiceRunning = false;
-         try{
-           frame.setClosed(true);
-         }catch(Exception ex){}
-       }
-
-       public void paintComponent(Graphics g)
-       {
-         g.setColor(Color.white);
-         g.fillRect(0,0,getWidth(), getHeight());
-         if(image!=null)
-         {
-           g.drawImage(image[imageIndex],10,10,this);
-         }
-         g.setFont(new Font("Arial", Font.BOLD, 12));
-         g.setColor(Color.black);
-         g.drawString("Clustal Alignment Web Service running", 30,30);
-       }
+    {
+      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();
+        }
+      }
+    }
   }
 }