X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=7db8f01805fec6f67eb2650b1b925eb7e018c4ef;hb=1146ae7f678127be7796772b228d5fc6823435d4;hp=1ff77e620ff9f005e4cdc51bc57f3082659632f5;hpb=33c59ebddbc51bbd26bc4c8576ec17c1498b19e8;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1ff77e6..7db8f01 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,902 +1,2559 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.dnd.*;
 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.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.ws.*;
 
-public class AlignFrame extends GAlignFrame
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignFrame
+    extends GAlignFrame implements DropTargetListener
 {
-  final AlignmentPanel alignPanel;
-  final AlignViewport viewport;
-  public static final int NEW_WINDOW_WIDTH = 700;
-  public static final int NEW_WINDOW_HEIGHT = 500;
-  public String currentFileFormat = "Jalview";
+  /** DOCUMENT ME!! */
+  public static final int DEFAULT_WIDTH = 700;
 
-  public AlignFrame(AlignmentI al)
-  {
-    viewport = new AlignViewport(al);
+  /** DOCUMENT ME!! */
+  public static final int DEFAULT_HEIGHT = 500;
+  public AlignmentPanel alignPanel;
 
-    alignPanel = new AlignmentPanel(this, viewport);
-    alignPanel.annotationPanel.adjustPanelHeight();
-    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
-    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
-    alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
+  AlignViewport viewport;
 
-    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+  Vector alignPanels = new Vector();
 
-    addInternalFrameListener(new InternalFrameAdapter()
-   {
-     public void internalFrameActivated(InternalFrameEvent evt)
-     {
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            public void run()
-            {      alignPanel.requestFocus();    }
-          });
 
-     }
-   });
+  /** DOCUMENT ME!! */
+  String currentFileFormat = null;
+
+  String fileName = null;
 
-  }
 
-  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  /**
+   * Creates a new AlignFrame object.
+   *
+   * @param al DOCUMENT ME!
+   */
+  public AlignFrame(AlignmentI al, int width, int height)
   {
-    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);
+    this(al, null, width, height);
+  }
 
-    chooser.setAcceptAllFileFilterUsed(false);
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Alignment to file");
-    chooser.setToolTipText("Save");
-    int value = chooser.showSaveDialog(this);
-    if(value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      currentFileFormat  = chooser.getSelectedFormat();
 
-      if (currentFileFormat.equals("Jalview"))
-      {
-        String shortName = title.replace('/', '_');
-        title = title.replace('\\', '_');
-        String choice = chooser.getSelectedFile().getPath();
-        Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,
-                              choice);
-        // USE Jalview2XML to save this file
-        return;
-      }
+  /**
+   * new alignment window with hidden columns
+   * @param al AlignmentI
+   * @param hiddenColumns ColumnSelection or null
+   */
+  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+                    int width, int height)
+  {
+    this.setSize(width, height);
+    viewport = new AlignViewport(al, hiddenColumns);
 
-      String choice =  chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", 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){}
+    alignPanel = new AlignmentPanel(this, viewport);
+
+    if(al.getDataset()==null)
+    {
+      al.setDataset(null);
     }
 
+    addAlignmentPanel(alignPanel, true);
+    init();
   }
 
-  protected void outputText_actionPerformed(ActionEvent e)
+  /**
+   * Make a new AlignFrame from exisiting alignmentPanels
+   * @param ap AlignmentPanel
+   * @param av AlignViewport
+   */
+  public AlignFrame(AlignmentPanel ap)
   {
-     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.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
+    viewport = ap.av;
+    alignPanel = ap;
+    addAlignmentPanel(ap, false);
+    init();
   }
 
-  protected void htmlMenuItem_actionPerformed(ActionEvent e)
+  void init()
   {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport);
-    htmlOutput = null;
-  }
+    this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
-  protected void createPNG_actionPerformed(ActionEvent e)
-  {
-    alignPanel.makePNG();
-  }
+    if (viewport.conservation == null)
+    {
+      BLOSUM62Colour.setEnabled(false);
+      conservationMenuItem.setEnabled(false);
+      modifyConservation.setEnabled(false);
+    //  PIDColour.setEnabled(false);
+    //  abovePIDThreshold.setEnabled(false);
+    //  modifyPID.setEnabled(false);
+    }
 
-  protected void epsFile_actionPerformed(ActionEvent e)
-  {
-    alignPanel.makeEPS();
-  }
+    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);
+    }
 
-  public void printMenuItem_actionPerformed(ActionEvent e)
+    if (Desktop.desktop != null)
+   {
+     addServiceListeners();
+     setGUINucleotide(viewport.alignment.isNucleotide());
+   }
+
+   setMenusFromViewport(viewport);
+
+   if (viewport.wrapAlignment)
+   {
+     wrapMenuItem_actionPerformed(null);
+   }
+
+    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
+    {
+      this.overviewMenuItem_actionPerformed(null);
+    }
+
+   addKeyListener();
+
+  }
+
+  public void setFileName(String file, String format)
   {
-    //Putting in a thread avoids Swing painting problems
-    PrintThread thread = new PrintThread();
-    thread.start();
+     fileName = file;
+     currentFileFormat = format;
+     reload.setEnabled(true);
   }
 
-  class PrintThread extends Thread
+  void addKeyListener()
   {
-    public void run()
-    {
-      PrinterJob printJob = PrinterJob.getPrinterJob();
-      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
-      printJob.setPrintable(alignPanel, pf);
-      if (printJob.printDialog())
+      addKeyListener(new KeyAdapter()
       {
-        try
+        public void keyPressed(KeyEvent evt)
         {
-          printJob.print();
+          if (viewport.cursorMode
+              && evt.getKeyCode() >= KeyEvent.VK_0
+              && evt.getKeyCode() <= KeyEvent.VK_9)
+          {
+            alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+          }
+
+          switch (evt.getKeyCode())
+          {
+
+            case 27: // escape key
+              deselectAllSequenceMenuItem_actionPerformed(null);
+
+              break;
+
+            case KeyEvent.VK_DOWN:
+             if (evt.isAltDown() || !viewport.cursorMode)
+              moveSelectedSequences(false);
+              if (viewport.cursorMode)
+                alignPanel.seqPanel.moveCursor(0, 1);
+              break;
+
+            case KeyEvent.VK_UP:
+            if (evt.isAltDown() || !viewport.cursorMode)
+              moveSelectedSequences(true);
+              if (viewport.cursorMode)
+                alignPanel.seqPanel.moveCursor(0, -1);
+
+              break;
+
+            case KeyEvent.VK_LEFT:
+            if (evt.isAltDown() || !viewport.cursorMode)
+              slideSequences(false,
+                             alignPanel.seqPanel.getKeyboardNo1());
+            else
+                alignPanel.seqPanel.moveCursor( -1, 0);
+
+
+              break;
+
+            case KeyEvent.VK_RIGHT:
+            if (evt.isAltDown() || !viewport.cursorMode)
+              slideSequences(true,
+                             alignPanel.seqPanel.getKeyboardNo1());
+            else
+                alignPanel.seqPanel.moveCursor(1, 0);
+              break;
+
+            case KeyEvent.VK_SPACE:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+                                           || evt.isShiftDown()
+                                           || evt.isAltDown());
+              }
+              break;
+
+            case KeyEvent.VK_DELETE:
+            case KeyEvent.VK_BACK_SPACE:
+              if (!viewport.cursorMode)
+              {
+                cut_actionPerformed(null);
+              }
+              else
+            {
+                alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+                                           || evt.isShiftDown()
+                                           || evt.isAltDown());
+            }
+
+              break;
+
+            case KeyEvent.VK_S:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setCursorRow();
+              }
+              break;
+            case KeyEvent.VK_C:
+              if (viewport.cursorMode && !evt.isControlDown())
+              {
+                alignPanel.seqPanel.setCursorColumn();
+              }
+              break;
+            case KeyEvent.VK_P:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setCursorPosition();
+              }
+              break;
+
+            case KeyEvent.VK_ENTER:
+            case KeyEvent.VK_COMMA:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setCursorRowAndColumn();
+              }
+              break;
+
+            case KeyEvent.VK_Q:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+              }
+              break;
+            case KeyEvent.VK_M:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+              }
+              break;
+
+            case KeyEvent.VK_F2:
+              viewport.cursorMode = !viewport.cursorMode;
+              statusBar.setText("Keyboard editing mode is " +
+                                           (viewport.cursorMode ? "on" : "off"));
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+                alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+              }
+              alignPanel.seqPanel.seqCanvas.repaint();
+              break;
+
+            case KeyEvent.VK_F1:
+              try
+              {
+                ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+                java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+                javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+                javax.help.HelpBroker hb = hs.createHelpBroker();
+                hb.setCurrentID("home");
+                hb.setDisplayed(true);
+              }
+              catch (Exception ex)
+              {
+                ex.printStackTrace();
+              }
+              break
+                  ;
+            case KeyEvent.VK_H:
+            {
+              boolean toggleSeqs = !evt.isControlDown();
+              boolean toggleCols = !evt.isShiftDown();
+
+              boolean hide = false;
+
+              SequenceGroup sg = viewport.getSelectionGroup();
+              if (toggleSeqs)
+              {
+                if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+                {
+                  hideSelSequences_actionPerformed(null);
+                  hide = true;
+                }
+              else if (! (toggleCols &&
+                          viewport.colSel.getSelected().size() > 0))
+              {
+                  showAllSeqs_actionPerformed(null);
+              }
+            }
+
+              if (toggleCols)
+              {
+                if (viewport.colSel.getSelected().size() > 0)
+                {
+                  hideSelColumns_actionPerformed(null);
+                  if (!toggleSeqs)
+                {
+                    viewport.selectionGroup = sg;
+                }
+              }
+                else if (!hide)
+              {
+                  showAllColumns_actionPerformed(null);
+              }
+            }
+              break;
+            }
+            case KeyEvent.VK_PAGE_UP:
+              if (viewport.wrapAlignment)
+            {
+                alignPanel.scrollUp(true);
+            }
+              else
+            {
+                alignPanel.setScrollValues(viewport.startRes,
+                                           viewport.startSeq
+                                           - viewport.endSeq + viewport.startSeq);
+            }
+              break;
+            case KeyEvent.VK_PAGE_DOWN:
+              if (viewport.wrapAlignment)
+            {
+                alignPanel.scrollUp(false);
+            }
+              else
+            {
+                alignPanel.setScrollValues(viewport.startRes,
+                                           viewport.startSeq
+                                           + viewport.endSeq - viewport.startSeq);
+            }
+              break;
+          }
         }
-        catch (Exception PrintException)
+
+      public void keyReleased(KeyEvent evt)
+      {
+        switch(evt.getKeyCode())
         {
-          PrintException.printStackTrace();
+          case KeyEvent.VK_LEFT:
+            if (evt.isAltDown() || !viewport.cursorMode)
+              viewport.firePropertyChange("alignment", null,
+                                          viewport.getAlignment().getSequences());
+            break;
+
+          case KeyEvent.VK_RIGHT:
+            if (evt.isAltDown() || !viewport.cursorMode)
+              viewport.firePropertyChange("alignment", null,
+                                          viewport.getAlignment().getSequences());
+            break;
         }
       }
-    }
-
+      });
   }
 
 
+  public void addAlignmentPanel(final AlignmentPanel ap,
+                                boolean newPanel)
+  {
+    ap.alignFrame = this;
 
+    alignPanels.addElement(ap);
 
-  public void closeMenuItem_actionPerformed(ActionEvent e)
-  {
-    try{
-      this.setClosed(true);
-    }catch(Exception ex){}
-  }
+    PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
+    int aSize = alignPanels.size();
 
-  void updateEditMenuBar()
-  {
-    if(historyList.size()>0)
-     {
-       undoMenuItem.setEnabled(true);
-       Object [] history = (Object[])historyList.get(0);
-       undoMenuItem.setText("Undo "+history[0]);
-     }
+    tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+
+    if (aSize == 1 && ap.av.viewName==null)
+    {
+      this.getContentPane().add(ap, BorderLayout.CENTER);
+    }
     else
     {
-      undoMenuItem.setEnabled(false);
-      undoMenuItem.setText("Undo");
+      if (aSize == 2)
+      {
+        setInitialTabVisible();
+      }
+
+      expandViews.setEnabled(true);
+      gatherViews.setEnabled(true);
+      tabbedPane.addTab(ap.av.viewName, ap);
+
+      ap.setVisible(false);
     }
 
-    if(redoList.size()>0)
-     {
-       redoMenuItem.setEnabled(true);
-       Object [] history = (Object[])redoList.get(0);
-       redoMenuItem.setText("Redo "+history[0]);
-     }
-    else
+    if(newPanel)
     {
-      redoMenuItem.setEnabled(false);
-      redoMenuItem.setText("Redo");
+      if (ap.av.padGaps)
+      {
+        ap.av.alignment.padGaps();
+      }
+      ap.av.updateConservation(ap);
+      ap.av.updateConsensus(ap);
     }
   }
 
-  public void addHistoryItem(String type)
+  public void setInitialTabVisible()
+  {
+    expandViews.setEnabled(true);
+    gatherViews.setEnabled(true);
+    tabbedPane.setVisible(true);
+    AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+    tabbedPane.addTab(first.av.viewName,first);
+    this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+  }
+
+
+  public AlignViewport getViewport()
   {
-    // must make sure we add new sequence objects her, not refs to the existing sequences
-    redoList.clear();
+    return viewport;
+  }
 
-    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
-    for(int i=0; i<viewport.getAlignment().getHeight(); i++)
+  /* 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()
     {
-      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
-                             viewport.getAlignment().getSequenceAt(i).getSequence());
-    }
-
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        // System.out.println("Discoverer property change.");
+        if (evt.getPropertyName().equals("services"))
+        {
+          // System.out.println("Rebuilding web service menu");
+          BuildWebServiceMenu();
+        }
+      }
+    });
 
-    historyList.add(0, new Object[]{type,  seq} );
-    updateEditMenuBar();
+    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(true);
+      }
+      ;
+    });
   }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  public void setGUINucleotide(boolean nucleotide)
   {
-    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++)
+    showTranslation.setVisible( nucleotide );
+    conservationMenuItem.setEnabled( !nucleotide );
+    modifyConservation.setEnabled(   !nucleotide );
+
+    //Remember AlignFrame always starts as protein
+    if(!nucleotide)
     {
-      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
-                            viewport.getAlignment().getSequenceAt(i).
-                            getSequence());
+      calculateMenu.remove(calculateMenu.getItemCount()-2);
     }
-    /////////
+  }
 
-    redoList.add(0, new Object[] {history[0], seq});
+  /**
+   * Need to call this method when tabs are selected for multiple views,
+   * or when loading from Jalview2XML.java
+   * @param av AlignViewport
+   */
+  void setMenusFromViewport(AlignViewport av)
+  {
+    padGapsMenuitem.setSelected(av.padGaps);
+    colourTextMenuItem.setSelected(av.showColourText);
+    abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+    conservationMenuItem.setSelected(av.getConservationSelected());
+    seqLimits.setSelected(av.getShowJVSuffix());
+    idRightAlign.setSelected(av.rightAlignIds);
+    renderGapsMenuItem.setSelected(av.renderGaps);
+    wrapMenuItem.setSelected(av.wrapAlignment);
+    scaleAbove.setVisible(av.wrapAlignment);
+    scaleLeft.setVisible(av.wrapAlignment);
+    scaleRight.setVisible(av.wrapAlignment);
+    annotationPanelMenuItem.setState(av.showAnnotation);
+    viewBoxesMenuItem.setSelected(av.showBoxes);
+    viewTextMenuItem.setSelected(av.showText);
+
+    setColourSelected(ColourSchemeProperty.
+                      getColourName(av.getGlobalColourScheme()));
+
+    showSeqFeatures.setSelected(av.showSequenceFeatures);
+    hiddenMarkers.setState(av.showHiddenMarkers);
+    applyToAllGroups.setState(av.colourAppliesToAllGroups);
 
-      seq = (SequenceI[]) history[1];
-      AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
-      viewport.setAlignment( new Alignment(seq) );
-      viewport.alignment.setGapCharacter( Preferences.gapSymbol );
-      updateEditMenuBar();
-      for(int i=0; i<old.length; i++)
-        viewport.alignment.addAnnotation(old[i]);
-      viewport.updateConsensus();
-      viewport.updateConservation();
-      alignPanel.repaint();
+    updateEditMenuBar();
   }
 
-  public void moveSelectedSequences(boolean up)
-  {
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg == null)
-      return;
 
-    if (up)
+  Hashtable progressBars;
+  public void setProgressBar(String message, long id)
+  {
+    if(progressBars == null)
     {
-      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;
+      progressBars = new Hashtable();
+    }
 
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i - 1);
+    JPanel progressPanel;
+    GridLayout layout = (GridLayout) statusPanel.getLayout();
+    if(progressBars.get( new Long(id) )!=null)
+     {
+       progressPanel = (JPanel)progressBars.get( new Long(id) );
+       statusPanel.remove(progressPanel);
+       progressBars.remove( progressPanel );
+       progressPanel = null;
+       if(message!=null)
+      {
+         statusBar.setText(message);
       }
-    }
+
+       layout.setRows(layout.getRows() - 1);
+     }
     else
     {
-      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
-      {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.sequences.contains(seq))
-          continue;
+      progressPanel = new JPanel(new BorderLayout(10, 5));
 
-        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
-        if (sg.sequences.contains(temp))
-          continue;
-
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i + 1);
-      }
-    }
-
-    alignPanel.repaint();
-  }
+      JProgressBar progressBar = new JProgressBar();
+      progressBar.setIndeterminate(true);
 
+      progressPanel.add(new JLabel(message), BorderLayout.WEST);
+      progressPanel.add(progressBar, BorderLayout.CENTER);
 
+      layout.setRows(layout.getRows() + 1);
+      statusPanel.add(progressPanel);
 
-  protected void copy_actionPerformed(ActionEvent e)
-  {
-     if(viewport.getSelectionGroup()==null)
-       return;
+      progressBars.put(new Long(id), progressPanel);
+    }
 
-     SequenceGroup sg = viewport.getSelectionGroup();
+    validate();
+  }
 
-     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-     StringBuffer buffer= new StringBuffer();
 
-     Hashtable orderedSeqs = new Hashtable();
-     for(int i=0; i<sg.getSize(); i++)
-     {
-        SequenceI seq = sg.getSequenceAt(i);
-        int index = viewport.alignment.findIndex(seq);
-        orderedSeqs.put(index+"", seq);
-     }
 
-     int index=0;
-     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 ) ;
+  /*
+   Added so Castor Mapping file can obtain Jalview Version
+  */
+  public String getVersion()
+  {
+    return  jalview.bin.Cache.getProperty("VERSION");
+  }
 
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
   }
 
 
-  protected void pasteNew_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
-    paste(true);
+    new SequenceFetcher(this);
   }
 
-  protected void pasteThis_actionPerformed(ActionEvent e)
+  public void addFromFile_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Paste");
-    paste(false);
+    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
   }
 
-  void paste(boolean newAlignment)
+  public void reload_actionPerformed(ActionEvent e)
   {
-    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(fileName!=null)
+    {
+      if(currentFileFormat.equals("Jalview"))
       {
-        String name = st.nextToken();
-        int start = Integer.parseInt(st.nextToken());
-        int end = Integer.parseInt(st.nextToken());
-        Sequence sequence = new Sequence(name,st.nextToken(), start, end);
-
-        if(!newAlignment)
-          viewport.alignment.addSequence(sequence);
-        else
-          seqs.add(sequence);
-      }
+        JInternalFrame [] frames = Desktop.desktop.getAllFrames();
+        for(int i=0; i<frames.length; i++)
+        {
+          if (frames[i] instanceof AlignFrame
+              && frames[i] != this
+              && ( (AlignFrame) frames[i]).fileName.equals(fileName))
+          {
+            try
+            {
+              frames[i].setSelected(true);
+              Desktop.instance.closeAssociatedWindows();
+          }
+            catch (java.beans.PropertyVetoException ex)
+            {}
+          }
 
-      if(newAlignment)
-      {
-        SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        seqs.toArray(newSeqs);
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs));
-        String newtitle = new String("Copied sequences");
-        if( title.startsWith("Copied sequences"))
-         newtitle = title;
-       else
-         newtitle = newtitle.concat("- from "+title);
+        }
+        Desktop.instance.closeAssociatedWindows();
 
-        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+        FileLoader loader = new FileLoader();
+        String protocol = fileName.startsWith("http:")? "URL":"File";
+        loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
       else
       {
-        viewport.setEndSeq(viewport.alignment.getHeight());
-        viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.repaint();
-      }
+        Rectangle bounds = this.getBounds();
 
-    }catch(Exception ex){}// could be anything being pasted in here
+        FileLoader loader = new FileLoader();
+        String protocol = fileName.startsWith("http:") ? "URL" : "File";
+        AlignFrame newframe =
+            loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
 
+        newframe.setBounds(bounds);
+
+        this.closeMenuItem_actionPerformed(true);
+      }
+    }
   }
 
 
-  protected void cut_actionPerformed(ActionEvent e)
+  public void addFromText_actionPerformed(ActionEvent e)
   {
-    copy_actionPerformed(null);
-    delete_actionPerformed(null);
+    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
   }
 
-  protected void delete_actionPerformed(ActionEvent e)
+  public void addFromURL_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Delete");
-    if (viewport.getSelectionGroup() == null)
-      return;
-
-     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);
-      else
-          viewport.getAlignment().getSequences().setElementAt(seq, index);
-     }
-
-     viewport.setSelectionGroup(null);
-     viewport.alignment.deleteGroup(sg);
-     viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
-     if(viewport.getAlignment().getHeight()<1)
-     try
-     {
-       this.setClosed(true);
-     }catch(Exception ex){}
-   viewport.updateConservation();
-   viewport.updateConsensus();
-     alignPanel.repaint();
-
+    Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
 
-
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  public void save_actionPerformed(ActionEvent e)
   {
-     Object [] history = (Object[])redoList.remove(0);
-     SequenceI[] seq = (SequenceI[]) history[1];
-     viewport.setAlignment( new Alignment(seq) );
-     viewport.alignment.setGapCharacter( Preferences.gapSymbol );
-     updateEditMenuBar();
-     viewport.updateConsensus();
-     alignPanel.repaint();
-     alignPanel.repaint();
+    if(fileName==null
+       || currentFileFormat==null
+       || fileName.startsWith("http")
+        )
+    {
+      saveAs_actionPerformed(null);
+    }
+    else
+    {
+      saveAlignment(fileName, currentFileFormat);
+  }
   }
 
-
-  protected void deleteGroups_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void saveAs_actionPerformed(ActionEvent e)
   {
-    viewport.alignment.deleteAllGroups();
-    viewport.setSelectionGroup(null);
-    alignPanel.repaint();
-  }
+    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,
+        false);
 
 
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save Alignment to file");
+    chooser.setToolTipText("Save");
 
-  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = new SequenceGroup();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
-    sg.setEndRes(viewport.alignment.getWidth());
-    viewport.setSelectionGroup(sg);
-    PaintRefresher.Refresh(null);
-  }
+    int value = chooser.showSaveDialog(this);
 
-  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setSelectionGroup(null);
-    viewport.getColumnSelection().clear();
-    viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(null);
-  }
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+        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;
+        }
 
-  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));
+        fileName = chooser.getSelectedFile().getPath();
+
+      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+                                    currentFileFormat);
 
-    PaintRefresher.Refresh(null);
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
+
+      saveAlignment(fileName, currentFileFormat);
+    }
   }
 
-  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+  public boolean saveAlignment(String file, String format)
   {
-    addHistoryItem("delete columns");
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
-    {
-      int min = colSel.getMin();
-      viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0,min);
+    boolean success = true;
 
-      if(viewport.getSelectionGroup()!=null)
-        viewport.getSelectionGroup().adjustForRemoveLeft(min);
+    if (format.equalsIgnoreCase("Jalview"))
+    {
+      String shortName = title;
 
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+      if (shortName.indexOf(java.io.File.separatorChar) > -1)
       {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
-        if(!sg.adjustForRemoveLeft(min))
-          viewport.alignment.deleteGroup(sg);
+        shortName = shortName.substring(shortName.lastIndexOf(
+            java.io.File.separatorChar) + 1);
       }
 
-      alignPanel.repaint();
-    }
-  }
+      success = new Jalview2XML().SaveAlignment(this, file, shortName);
 
-  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("delete columns");
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
+      statusBar.setText("Successfully saved to file: "
+                          +fileName+" in "
+                          +format +" format.");
+
+    }
+    else
     {
-      int max = colSel.getMax();
-      viewport.getAlignment().trimRight(max);
-      if(viewport.getSelectionGroup()!=null)
-        viewport.getSelectionGroup().adjustForRemoveRight(max);
 
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+      String[] omitHidden = null;
+
+      if (viewport.hasHiddenColumns)
       {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
-        if(!sg.adjustForRemoveRight(max))
-          viewport.alignment.deleteGroup(sg);
+        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+            "The Alignment contains hidden columns."
+            + "\nDo you want to save only the visible alignment?",
+            "Save / Omit Hidden Columns",
+            JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+        if (reply == JOptionPane.YES_OPTION)
+        {
+          omitHidden = viewport.getViewAsString(false);
+      }
       }
 
+      String output = new FormatAdapter().formatSequences(
+          format,
+          viewport.alignment.getSequencesArray(),
+          omitHidden);
 
+      if (output == null)
+      {
+        success = false;
+      }
+      else
+      {
+        try
+        {
+          java.io.PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(file));
+
+          out.print(output);
+          out.close();
+          this.setTitle(file);
+          statusBar.setText("Successfully saved to file: "
+                            + fileName + " in "
+                            + format + " format.");
+        }
+        catch (Exception ex)
+        {
+          success = false;
+          ex.printStackTrace();
+        }
+      }
+    }
 
-      alignPanel.repaint();
+    if (!success)
+    {
+      JOptionPane.showInternalMessageDialog(
+          this, "Couldn't save file: " + fileName,
+          "Error Saving File",
+          JOptionPane.WARNING_MESSAGE);
     }
 
+    return success;
   }
 
-  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void outputText_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete gapped columns");
-    viewport.getAlignment().removeGaps();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-  }
+    String [] omitHidden = null;
 
-  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem("delete all gaps");
-    SequenceI current;
-    int jSize;
-    for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
+    if(viewport.hasHiddenColumns)
     {
-      current = viewport.getAlignment().getSequenceAt(i);
-      jSize = current.getLength();
-      for (int j=0; j < jSize; j++)
-        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
-        {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
-        }
+      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          "The Alignment contains hidden columns."
+      +"\nDo you want to output only the visible alignment?",
+      "Save / Omit Hidden Columns",
+      JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+      if(reply==JOptionPane.YES_OPTION)
+      {
+        omitHidden = viewport.getViewAsString(false);
+      }
     }
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-  }
 
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
 
-  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);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
+    cap.setText(new FormatAdapter().formatSequences(
+        e.getActionCommand(),
+        viewport.alignment.getSequencesArray(),
+        omitHidden));
   }
 
-
-  public void font_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    FontChooser fc = new FontChooser( alignPanel );
+    new HTMLOutput(viewport,
+                   alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  public void createImageMap(File file, String image)
   {
-    viewport.setShowFullId( fullSeqId.isSelected() );
-
-    alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
-    alignPanel.repaint();
+    alignPanel.makePNGImageMap(file, image);
   }
 
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void createPNG(File f)
   {
-      viewport.setColourText( colourTextMenuItem.isSelected() );
-      alignPanel.repaint();
+    alignPanel.makePNG(f);
   }
 
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void createEPS(File f)
   {
-    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
-    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
-    scaleAbove.setVisible( wrapMenuItem.isSelected() );
-    scaleLeft.setVisible( wrapMenuItem.isSelected() );
-    scaleRight.setVisible( wrapMenuItem.isSelected() );
-    alignPanel.repaint();
+    alignPanel.makeEPS(f);
   }
 
-  protected void scaleAbove_actionPerformed(ActionEvent e)
-  {
-    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    alignPanel.repaint();
-  }
 
-  protected void scaleLeft_actionPerformed(ActionEvent e)
+  public void pageSetup_actionPerformed(ActionEvent e)
   {
-    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
-    alignPanel.repaint();
+    PrinterJob printJob = PrinterJob.getPrinterJob();
+    PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
   }
 
-  protected void scaleRight_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void printMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setScaleRightWrapped(scaleRight.isSelected());
-    alignPanel.repaint();
+    //Putting in a thread avoids Swing painting problems
+    PrintThread thread = new PrintThread(alignPanel);
+    thread.start();
   }
 
-
-
-  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  public void exportFeatures_actionPerformed(ActionEvent e)
   {
-    viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
-    alignPanel.repaint();
+    new AnnotationExporter().exportFeatures(alignPanel);
   }
 
-  public void viewTextMenuItem_actionPerformed(ActionEvent e)
+
+  public void exportAnnotations_actionPerformed(ActionEvent e)
   {
-    viewport.setShowText( viewTextMenuItem.isSelected() );
-    alignPanel.repaint();
+    new AnnotationExporter().exportAnnotations(
+      alignPanel,
+        viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
+      viewport.alignment.getGroups()
+        );
   }
 
 
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  public void associatedData_actionPerformed(ActionEvent e)
   {
-    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.repaint();
-  }
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Load Jalview Annotations or Features File");
+    chooser.setToolTipText("Load Jalview Annotations / Features file");
 
-  public void sequenceFeatures_actionPerformed(ActionEvent evt)
-  {
-    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
-    if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-         SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
-         ((Alignment)viewport.alignment).featuresAdded = true;
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      loadJalviewDataFile(choice);
     }
-    alignPanel.repaint();
+
   }
 
-  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
-    if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+    if(alignPanels!=null && alignPanels.size()<2)
     {
-      annotationPanelMenuItem.setSelected(false);
-      return;
+      closeAllTabs = true;
     }
-    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 = 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)
+    try
+    {
+      if(alignPanels!=null)
       {
-            alignPanel.setOverviewPanel(null);
-      };
-    });
-
-    alignPanel.setOverviewPanel( overview );
+        if (closeAllTabs)
+        {
+          for (int i = 0; i < alignPanels.size(); i++)
+          {
+            AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+            jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+                .removeStructureViewerListener(ap.seqPanel, null);
+            PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
+            PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
+            PaintRefresher.RemoveComponent(ap);
+            ap.av.alignment = null;
+          }
+        }
+        else
+        {
+          int index = tabbedPane.getSelectedIndex();
 
+          alignPanels.removeElement(alignPanel);
+          PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+          PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+          PaintRefresher.RemoveComponent(alignPanel);
+          viewport.alignment = null;
+          alignPanel = null;
+          viewport = null;
 
-  }
+          tabbedPane.removeTabAt(index);
+          tabbedPane.validate();
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    changeColour( null );
-  }
+          if(index==tabbedPane.getTabCount())
+          {
+            index --;
+          }
 
+          this.tabSelectionChanged(index);
+        }
+      }
 
-  public void clustalColour_actionPerformed(ActionEvent e)
-  {
-    abovePIDThreshold.setSelected(false);
-    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+      if (closeAllTabs)
+      {
+        this.setClosed(true);
+    }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
   }
 
-  public void zappoColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new ZappoColourScheme());
-  }
 
-  public void taylorColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   */
+  void updateEditMenuBar()
   {
-    changeColour(new TaylorColourScheme());
-  }
 
+    if (viewport.historyList.size() > 0)
+    {
+      undoMenuItem.setEnabled(true);
+      CommandI command = (CommandI) viewport.historyList.peek();
+      undoMenuItem.setText("Undo " + command.getDescription());
+    }
+    else
+    {
+      undoMenuItem.setEnabled(false);
+      undoMenuItem.setText("Undo");
+    }
 
-  public void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    changeColour( new HydrophobicColourScheme() );
-  }
+    if (viewport.redoList.size() > 0)
+    {
+      redoMenuItem.setEnabled(true);
 
-  public void helixColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new HelixColourScheme() );
+      CommandI command = (CommandI) viewport.redoList.peek();
+      redoMenuItem.setText("Redo " + command.getDescription());
+    }
+    else
+    {
+      redoMenuItem.setEnabled(false);
+      redoMenuItem.setText("Redo");
+    }
   }
 
 
-  public void strandColour_actionPerformed(ActionEvent e)
+  public void addHistoryItem(CommandI command)
   {
-    changeColour(new StrandColourScheme());
+    if(command.getSize()>0)
+    {
+      viewport.historyList.push(command);
+      viewport.redoList.clear();
+      updateEditMenuBar();
+      viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    }
   }
 
 
-  public void turnColour_actionPerformed(ActionEvent e)
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
-    changeColour(new TurnColourScheme());
-  }
+    CommandI command = (CommandI)viewport.historyList.pop();
+    viewport.redoList.push(command);
+    command.undoCommand();
 
+    AlignViewport originalSource = getOriginatingSource(command);
+    updateEditMenuBar();
 
-  public void buriedColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new BuriedColourScheme() );
+    if(originalSource!=null)
+    {
+      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
+    }
   }
 
-  public void nucleotideColour_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-    changeColour(new NucleotideColourScheme());
-  }
-
+    if(viewport.redoList.size()<1)
+    {
+      return;
+    }
 
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
-  {
-    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
-  }
+    CommandI command = (CommandI) viewport.redoList.pop();
+    viewport.historyList.push(command);
+    command.doCommand();
 
+    AlignViewport originalSource = getOriginatingSource(command);
+    updateEditMenuBar();
 
+    if(originalSource!=null)
+    {
+      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
+    }
+  }
 
-  void changeColour(ColourSchemeI cs)
+  AlignViewport getOriginatingSource(CommandI command)
   {
-    int threshold = 0;
-
-    if ( viewport.getAbovePIDThreshold() )
+    AlignViewport originalSource = null;
+    //For sequence removal and addition, we need to fire
+   //the property change event FROM the viewport where the
+   //original alignment was altered
+    AlignmentI al=null;
+    if (command instanceof EditCommand)
     {
-      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
+      EditCommand editCommand = (EditCommand) command;
+      al = editCommand.getAlignment();
+      Vector comps = (Vector) PaintRefresher.components
+          .get(viewport.getSequenceSetId());
 
-      if (cs instanceof ResidueColourScheme)
-        ( (ResidueColourScheme) cs).setThreshold(threshold);
-      else if (cs instanceof ScoreColourScheme)
-        ( (ScoreColourScheme) cs).setThreshold(threshold);
-
-      viewport.setGlobalColourScheme(cs);
+      for (int i = 0; i < comps.size(); i++)
+      {
+        if (comps.elementAt(i) instanceof AlignmentPanel)
+        {
+          if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+          {
+            originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+            break;
+          }
+        }
+      }
     }
-    else if (cs instanceof ResidueColourScheme)
-      ( (ResidueColourScheme) cs).setThreshold(0);
-    else if (cs instanceof ScoreColourScheme)
-      ( (ScoreColourScheme) cs).setThreshold(0);
-
 
-
-    if (viewport.getConservationSelected())
+    if (originalSource == null)
     {
-      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);
+      //The original view is closed, we must validate
+      //the current view against the closed view first
+      if (al != null)
+      {
+        PaintRefresher.validateSequences(al, viewport.alignment);
+      }
 
-      ccs = new ConservationColourScheme(c, cs);
+      originalSource = viewport;
+    }
 
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus( viewport.vconsensus );
-      viewport.setGlobalColourScheme(ccs);
+    return originalSource;
+  }
 
-      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+  /**
+   * DOCUMENT ME!
+   *
+   * @param up DOCUMENT ME!
+   */
+  public void moveSelectedSequences(boolean up)
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
 
-    }
-    else
+    if (sg == null)
     {
-        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-        if (cs != null)
-          cs.setConsensus(viewport.vconsensus);
-        viewport.setGlobalColourScheme(cs);
+      return;
     }
 
-
-    if(viewport.getColourAppliesToAllGroups())
+    if (up)
     {
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+      for (int i = 1; i < viewport.alignment.getHeight(); i++)
       {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-
-        if (cs instanceof ClustalxColourScheme)
-        {
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
-        }
-        else if(cs!=null)
-        {
-          try{
-            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
-          }catch(Exception ex){ex.printStackTrace();}
-        }
+        SequenceI seq = viewport.alignment.getSequenceAt(i);
 
-        if(viewport.getAbovePIDThreshold())
+        if (!sg.getSequences(null).contains(seq))
         {
-          if (sg.cs instanceof ResidueColourScheme)
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-          else if (sg.cs instanceof ScoreColourScheme)
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-
-           sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+          continue;
         }
 
-        if( viewport.getConservationSelected() )
-        {
-          Conservation c = new Conservation("Group",
-                                            ResidueProperties.propHash, 3,
-                                            sg.sequences, 0, viewport.alignment.getWidth()-1);
-          c.calculate();
-          c.verdict(false, viewport.ConsPercGaps);
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
 
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
-          sg.cs = ccs;
-        }
-        else if(cs!=null)
+        if (sg.getSequences(null).contains(temp))
         {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          continue;
         }
 
-      }
+        viewport.alignment.getSequences().setElementAt(temp, i);
+        viewport.alignment.getSequences().setElementAt(seq, i - 1);
+      }
+    }
+    else
+    {
+      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+      {
+        SequenceI seq = viewport.alignment.getSequenceAt(i);
+
+        if (!sg.getSequences(null).contains(seq))
+        {
+          continue;
+        }
+
+        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+
+        if (sg.getSequences(null).contains(temp))
+        {
+          continue;
+        }
+
+        viewport.alignment.getSequences().setElementAt(temp, i);
+        viewport.alignment.getSequences().setElementAt(seq, i + 1);
+      }
+    }
+
+    alignPanel.paintAlignment(true);
+  }
+
+
+
+
+  synchronized void slideSequences(boolean right, int size)
+  {
+    Vector sg = new Vector();
+    if(viewport.cursorMode)
+    {
+      sg.addElement(viewport.alignment.getSequenceAt(
+          alignPanel.seqPanel.seqCanvas.cursorY));
+    }
+    else if(viewport.getSelectionGroup()!=null
+        && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
+   {
+     sg = viewport.getSelectionGroup().getSequences(
+         viewport.hiddenRepSequences);
+   }
+
+    if(sg.size()<1)
+    {
+      return;
+    }
+
+    Vector invertGroup = new Vector();
+
+    for (int i = 0; i < viewport.alignment.getHeight(); i++)
+    {
+      if(!sg.contains(viewport.alignment.getSequenceAt(i)))
+         invertGroup.add(viewport.alignment.getSequenceAt(i));
+    }
+
+    SequenceI[] seqs1 = new SequenceI[sg.size()];
+    for (int i = 0; i < sg.size(); i++)
+      seqs1[i] = (SequenceI) sg.elementAt(i);
+
+    SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+    for (int i = 0; i < invertGroup.size(); i++)
+      seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+
+    SlideSequencesCommand ssc;
+    if (right)
+      ssc = new SlideSequencesCommand("Slide Sequences",
+                                      seqs2, seqs1, size,
+                                      viewport.getGapCharacter()
+          );
+    else
+      ssc = new SlideSequencesCommand("Slide Sequences",
+                                      seqs1, seqs2, size,
+                                      viewport.getGapCharacter()
+          );
+
+    int groupAdjustment = 0;
+    if (ssc.getGapsInsertedBegin() && right)
+    {
+      if (viewport.cursorMode)
+        alignPanel.seqPanel.moveCursor(size, 0);
+      else
+        groupAdjustment = size;
+    }
+    else if (!ssc.getGapsInsertedBegin() && !right)
+    {
+      if (viewport.cursorMode)
+        alignPanel.seqPanel.moveCursor( -size, 0);
+      else
+        groupAdjustment = -size;
+    }
+
+    if (groupAdjustment != 0)
+    {
+      viewport.getSelectionGroup().setStartRes(
+          viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+      viewport.getSelectionGroup().setEndRes(
+          viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+    }
+
+
+    boolean appendHistoryItem = false;
+    if(viewport.historyList!=null
+       && viewport.historyList.size()>0
+      && viewport.historyList.peek() instanceof SlideSequencesCommand)
+    {
+      appendHistoryItem = ssc.appendSlideCommand(
+          (SlideSequencesCommand)viewport.historyList.peek())
+          ;
+    }
+
+    if(!appendHistoryItem)
+      addHistoryItem(ssc);
+
+    repaint();
+  }
+
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void copy_actionPerformed(ActionEvent e)
+  {
+    System.gc();
+    if (viewport.getSelectionGroup() == null)
+    {
+      return;
+    }
+
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    String[] omitHidden = null;
+
+    if (viewport.hasHiddenColumns)
+    {
+      omitHidden = viewport.getViewAsString(true);
+    }
+
+    String output = new FormatAdapter().formatSequences(
+        "Fasta",
+        seqs,
+        omitHidden);
+
+    StringSelection ss = new StringSelection(output);
+
+    try
+    {
+      jalview.gui.Desktop.internalCopy = true;
+      //Its really worth setting the clipboard contents
+      //to empty before setting the large StringSelection!!
+      Toolkit.getDefaultToolkit().getSystemClipboard()
+          .setContents(new StringSelection(""), null);
+
+      Toolkit.getDefaultToolkit().getSystemClipboard()
+          .setContents(ss, Desktop.instance);
+    }
+    catch (OutOfMemoryError er)
+    {
+      er.printStackTrace();
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  "Out of memory copying region!!"
+                  +
+                  "\nSee help files for increasing Java Virtual Machine memory."
+                  , "Out of memory",
+                  javax.swing.JOptionPane.WARNING_MESSAGE);
+            }
+          });
+
+      return;
+    }
+
+    Vector hiddenColumns = null;
+    if(viewport.hasHiddenColumns)
+    {
+      hiddenColumns =new Vector();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
+           i++)
+      {
+        int[] region = (int[])
+            viewport.getColumnSelection().getHiddenColumns().elementAt(i);
+
+        hiddenColumns.addElement(new int[]
+                                 {region[0] - hiddenOffset,
+                          region[1]-hiddenOffset});
+      }
+    }
+
+    Desktop.jalviewClipboard = new Object[]
+        {
+        seqs,
+        viewport.alignment.getDataset(),
+        hiddenColumns};
+    statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
+  }
+
+  /**
+   * 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)
+  {
+    paste(false);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param newAlignment DOCUMENT ME!
+   */
+  void paste(boolean newAlignment)
+  {
+    try
+    {
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
+
+      if (contents == null)
+      {
+        return;
+      }
+
+      String str, format;
+      try
+      {
+        str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+        if (str.length() < 1)
+        {
+          return;
+        }
+
+        format = new IdentifyFile().Identify(str, "Paste");
+
+      }
+      catch (OutOfMemoryError er)
+      {
+        er.printStackTrace();
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory pasting sequences!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
+        return;
+      }
+
+      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).
+            getSequencesArray();
+     }
+
+     AlignmentI alignment = null;
+
+      if (newAlignment)
+      {
+          alignment = new Alignment(sequences);
+
+          if (Desktop.jalviewClipboard != null)
+        {
+            alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
+        }
+          else
+        {
+            alignment.setDataset(null);
+      }
+      }
+      else
+      {
+        alignment = viewport.getAlignment();
+
+        //!newAlignment
+        SequenceI [] newseqs = new SequenceI[sequences.length];
+        for (int i = 0; i < sequences.length; i++)
+        {
+          newseqs[i] = new Sequence(sequences[i].getName(),
+                                    sequences[i].getSequence(),
+                                    sequences[i].getStart(),
+              sequences[i].getEnd());
+
+          alignment.addSequence(newseqs[i]);
+        }
+
+        /*
+         //ADD HISTORY ITEM
+         */
+        addHistoryItem(new EditCommand(
+            "Add sequences",
+            EditCommand.PASTE,
+            newseqs,
+            0,
+            alignment.getWidth(),
+            alignment)
+            );
+
+
+        viewport.setEndSeq(alignment.getHeight());
+        alignment.getWidth();
+        viewport.firePropertyChange("alignment", null, alignment.getSequences());
+      }
+
+
+
+      // Add any annotations attached to sequences
+      for (int i = 0; i < sequences.length; i++)
+     {
+       if (sequences[i].getAnnotation() != null)
+       {
+         for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+         {
+           AlignmentAnnotation newAnnot =
+               new AlignmentAnnotation(
+                   sequences[i].getAnnotation()[a].label,
+                   sequences[i].getAnnotation()[a].description,
+                   sequences[i].getAnnotation()[a].annotations,
+                   sequences[i].getAnnotation()[a].graphMin,
+                   sequences[i].getAnnotation()[a].graphMax,
+                   sequences[i].getAnnotation()[a].graph);
+
+           sequences[i].getAnnotation()[a] = newAnnot;
+           newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
+               sequenceMapping;
+           newAnnot.sequenceRef = sequences[i];
+           newAnnot.adjustForAlignment();
+           alignment.addAnnotation(newAnnot);
+           alignment.setAnnotationIndex(newAnnot, a);
+         }
+
+         alignPanel.annotationPanel.adjustPanelHeight();
+       }
+     }
+
+     if(newAlignment)
+     {
+       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+       String newtitle = new String("Copied sequences");
+
+       if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
+         {
+           Vector hc = (Vector)Desktop.jalviewClipboard[2];
+           for(int i=0; i<hc.size(); i++)
+           {
+             int [] region = (int[]) hc.elementAt(i);
+             af.viewport.hideColumns(region[0], region[1]);
+           }
+         }
+
+
+       //>>>This is a fix for the moment, until a better solution is found!!<<<
+       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+           alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
+       if (title.startsWith("Copied sequences"))
+       {
+         newtitle = title;
+       }
+       else
+       {
+         newtitle = newtitle.concat("- from " + title);
+       }
+
+       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+                                DEFAULT_HEIGHT);
+
+     }
+
+
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+        System.out.println("Exception whilst pasting: "+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 evt)
+  {
+
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg == null)
+    {
+      return;
+    }
+
+    Vector seqs = new Vector();
+    SequenceI seq;
+    for (int i = 0; i < sg.getSize(); i++)
+    {
+      seq = sg.getSequenceAt(i);
+      seqs.addElement(seq);
+    }
+
+
+   // If the cut affects all sequences, remove highlighted columns
+   if (sg.getSize() == viewport.alignment.getHeight())
+   {
+     viewport.getColumnSelection().removeElements(sg.getStartRes(),
+         sg.getEndRes() + 1);
+   }
+
+
+    SequenceI [] cut = new SequenceI[seqs.size()];
+    for(int i=0; i<seqs.size(); i++)
+    {
+      cut[i] = (SequenceI)seqs.elementAt(i);
+    }
+
+
+    /*
+    //ADD HISTORY ITEM
+    */
+    addHistoryItem(new EditCommand("Cut Sequences",
+                                      EditCommand.CUT,
+                                      cut,
+                                      sg.getStartRes(),
+                                      sg.getEndRes()-sg.getStartRes()+1,
+                                      viewport.alignment));
+
+
+    viewport.setSelectionGroup(null);
+    viewport.alignment.deleteGroup(sg);
+
+    viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+
+    if (viewport.getAlignment().getHeight() < 1)
+    {
+      try
+      {
+        this.setClosed(true);
+      }
+      catch (Exception ex)
+      {
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void deleteGroups_actionPerformed(ActionEvent e)
+  {
+    viewport.alignment.deleteAllGroups();
+    viewport.sequenceColours = null;
+    viewport.setSelectionGroup(null);
+    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = new SequenceGroup();
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
+    {
+      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
+    }
+
+    sg.setEndRes(viewport.alignment.getWidth() - 1);
+    viewport.setSelectionGroup(sg);
+    alignPanel.paintAlignment(true);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+    if(viewport.cursorMode)
+    {
+      alignPanel.seqPanel.keyboardNo1 = null;
+      alignPanel.seqPanel.keyboardNo2 = null;
+    }
+    viewport.setSelectionGroup(null);
+    viewport.getColumnSelection().clear();
+    viewport.setSelectionGroup(null);
+    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
+    alignPanel.idPanel.idCanvas.searchResults = null;
+    alignPanel.paintAlignment(true);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
+
+    if (sg == null)
+    {
+      selectAllSequenceMenuItem_actionPerformed(null);
+
+      return;
+    }
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
+    {
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+    }
+
+    alignPanel.paintAlignment(true);
+
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+  }
+
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+    viewport.invertColumnSelection();
+    alignPanel.paintAlignment(true);
+  }
+
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+  {
+    trimAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
+  {
+      trimAlignment(false);
+  }
+
+  void trimAlignment(boolean trimLeft)
+  {
+    ColumnSelection colSel = viewport.getColumnSelection();
+    int column;
+
+    if (colSel.size() > 0)
+    {
+      if(trimLeft)
+      {
+        column = colSel.getMin();
+      }
+      else
+      {
+        column = colSel.getMax();
+      }
+
+      SequenceI [] seqs;
+      if(viewport.getSelectionGroup()!=null)
+      {
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+            hiddenRepSequences);
+      }
+      else
+      {
+        seqs = viewport.alignment.getSequencesArray();
+      }
+
+
+      TrimRegionCommand trimRegion;
+      if(trimLeft)
+      {
+        trimRegion = new TrimRegionCommand("Remove Left",
+                                    TrimRegionCommand.TRIM_LEFT,
+                                    seqs,
+                                    column,
+                                    viewport.alignment,
+                                    viewport.colSel,
+                                    viewport.selectionGroup);
+        viewport.setStartRes(0);
+      }
+     else
+     {
+       trimRegion = new TrimRegionCommand("Remove Right",
+                                   TrimRegionCommand.TRIM_RIGHT,
+                                   seqs,
+                                   column,
+                                   viewport.alignment,
+                                   viewport.colSel,
+                                   viewport.selectionGroup);
+     }
+
+     statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+
+
+      addHistoryItem(trimRegion);
+
+      Vector groups = viewport.alignment.getGroups();
+
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+
+        if ( (trimLeft && !sg.adjustForRemoveLeft(column))
+            || (!trimLeft && !sg.adjustForRemoveRight(column)))
+        {
+          viewport.alignment.deleteGroup(sg);
+        }
+      }
+
+      viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+  {
+    int start = 0, end = viewport.alignment.getWidth()-1;
+
+    SequenceI[] seqs;
+    if (viewport.getSelectionGroup() != null)
+    {
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+          hiddenRepSequences);
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+    {
+      seqs = viewport.alignment.getSequencesArray();
+    }
+
+
+    RemoveGapColCommand removeGapCols =
+        new RemoveGapColCommand("Remove Gapped Columns",
+                                seqs,
+                                start, end,
+                                viewport.alignment);
+
+    addHistoryItem(removeGapCols);
+
+    statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
+
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+   // ShiftList shifts;
+   // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+   // edit.alColumnChanges=shifts.getInverse();
+   // if (viewport.hasHiddenColumns)
+   //   viewport.getColumnSelection().compensateForEdits(shifts);
+   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)
+  {
+    int start = 0, end = viewport.alignment.getWidth()-1;
+
+    SequenceI[] seqs;
+    if (viewport.getSelectionGroup() != null)
+    {
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+          hiddenRepSequences);
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+    {
+      seqs = viewport.alignment.getSequencesArray();
+    }
+
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
+    addHistoryItem(new RemoveGapsCommand("Remove Gaps",
+                                         seqs,
+                                         start, end,
+                                         viewport.alignment));
+
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+    viewport.firePropertyChange("alignment", null,
+                                viewport.getAlignment().getSequences());
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void padGapsMenuitem_actionPerformed(ActionEvent e)
+  {
+    viewport.padGaps = padGapsMenuitem.isSelected();
+
+    viewport.firePropertyChange("alignment",
+                                null,
+                                viewport.getAlignment().getSequences());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void findMenuItem_actionPerformed(ActionEvent e)
+  {
+    new Finder();
+  }
+
+  public void newView_actionPerformed(ActionEvent e)
+  {
+    AlignmentPanel newap =
+        new Jalview2XML().copyAlignPanel(alignPanel, true);
+
+    newap.av.gatherViewsHere = false;
+
+    if (viewport.viewName == null)
+    {
+      viewport.viewName = "Original";
+    }
+
+    newap.av.historyList = viewport.historyList;
+    newap.av.redoList = viewport.redoList;
+
+    int index = Desktop.getViewCount(viewport.getSequenceSetId());
+    String newViewName = "View " +index;
+
+    Vector comps = (Vector) PaintRefresher.components.get(viewport.
+        getSequenceSetId());
+    Vector existingNames = new Vector();
+    for(int i=0; i<comps.size(); i++)
+    {
+      if(comps.elementAt(i) instanceof AlignmentPanel)
+      {
+        AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
+        if(!existingNames.contains(ap.av.viewName))
+        {
+          existingNames.addElement(ap.av.viewName);
+      }
+    }
+    }
+
+    while(existingNames.contains(newViewName))
+    {
+      newViewName = "View "+ (++index);
+    }
+
+    newap.av.viewName = newViewName;
+
+    addAlignmentPanel(newap, false);
+
+    if(alignPanels.size()==2)
+    {
+      viewport.gatherViewsHere = true;
+    }
+    tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+  }
+
+  public void expandViews_actionPerformed(ActionEvent e)
+  {
+        Desktop.instance.explodeViews(this);
+  }
+
+  public void gatherViews_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.gatherViews(this);
+  }
+
+
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void font_actionPerformed(ActionEvent e)
+  {
+    new FontChooser(alignPanel);
+  }
+
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void seqLimit_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowJVSuffix(seqLimits.isSelected());
+
+    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+    alignPanel.paintAlignment(true);
+  }
+
+  public void idRightAlign_actionPerformed(ActionEvent e)
+  {
+    viewport.rightAlignIds = idRightAlign.isSelected();
+    alignPanel.paintAlignment(true);
+  }
+
+
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setColourText(colourTextMenuItem.isSelected());
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void wrapMenuItem_actionPerformed(ActionEvent e)
+  {
+    scaleAbove.setVisible(wrapMenuItem.isSelected());
+    scaleLeft.setVisible(wrapMenuItem.isSelected());
+    scaleRight.setVisible(wrapMenuItem.isSelected());
+    viewport.setWrapAlignment(wrapMenuItem.isSelected());
+    alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+  }
+
+  public void showAllSeqs_actionPerformed(ActionEvent e)
+  {
+    viewport.showAllHiddenSeqs();
+  }
+
+  public void showAllColumns_actionPerformed(ActionEvent e)
+  {
+    viewport.showAllHiddenColumns();
+    repaint();
+  }
+
+  public void hideSelSequences_actionPerformed(ActionEvent e)
+  {
+    viewport.hideAllSelectedSeqs();
+    alignPanel.paintAlignment(true);
+  }
+
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
+    viewport.hideSelectedColumns();
+    alignPanel.paintAlignment(true);
+  }
+
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
+    viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void viewTextMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowText(viewTextMenuItem.isSelected());
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+    alignPanel.paintAlignment(true);
+  }
+
+
+  public FeatureSettings featureSettings;
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+    if(featureSettings !=null )
+    {
+      featureSettings.close();
+      featureSettings = null;
+    }
+    featureSettings = new FeatureSettings(this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void showSeqFeatures_actionPerformed(ActionEvent evt)
+  {
+    viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
+    alignPanel.paintAlignment(true);
+    if (alignPanel.getOverviewPanel() != null)
+    {
+      alignPanel.getOverviewPanel().updateOverviewImage();
+    }
+  }
+
+  /**
+   * 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);
+    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+                             frame.getWidth(), frame.getHeight());
+    frame.pack();
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      public void internalFrameClosed(
+          javax.swing.event.InternalFrameEvent evt)
+      {
+        alignPanel.setOverviewPanel(null);
+      }
+      ;
+    });
+
+    alignPanel.setOverviewPanel(overview);
+  }
+
+  public void textColour_actionPerformed(ActionEvent e)
+  {
+    new TextColourChooser().chooseColour(alignPanel, null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  {
+    changeColour(null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void clustalColour_actionPerformed(ActionEvent e)
+  {
+    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());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void helixColour_actionPerformed(ActionEvent e)
+  {
+    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());
+  }
+
+  /**
+   * 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!
+   */
+  public void changeColour(ColourSchemeI cs)
+  {
+    int threshold = 0;
+
+    if(cs!=null)
+    {
+      if (viewport.getAbovePIDThreshold())
+      {
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+                                                   "Background");
+
+        cs.setThreshold(threshold,
+                        viewport.getIgnoreGapsConsensus());
+
+        viewport.setGlobalColourScheme(cs);
+      }
+      else
+      {
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+      }
+
+      if (viewport.getConservationSelected())
+      {
+
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
+
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
+
+        cs.setConservation(c);
+
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
+      }
+      else
+      {
+        cs.setConservation(null);
+      }
+
+      cs.setConsensus(viewport.hconsensus);
+    }
+
+    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 (cs == null)
+        {
+          sg.cs = null;
+          continue;
+        }
+
+        if (cs instanceof ClustalxColourScheme)
+        {
+          sg.cs = new ClustalxColourScheme(
+              sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
+        }
+        else if (cs instanceof UserColourScheme)
+        {
+          sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
+        }
+        else
+        {
+          try
+          {
+            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+          }
+          catch (Exception ex)
+          {
+          }
+        }
+
+        if (viewport.getAbovePIDThreshold()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
+        {
+         sg.cs.setThreshold(threshold,
+                viewport.getIgnoreGapsConsensus());
+
+         sg.cs.setConsensus(AAFrequency.calculate(
+             sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
+             sg.getEndRes()+1));
+       }
+        else
+        {
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+        }
+
+
+        if (viewport.getConservationSelected())
+        {
+          Conservation c = new Conservation("Group",
+                                            ResidueProperties.propHash, 3,
+                                            sg.getSequences(viewport.
+              hiddenRepSequences),
+                                            sg.getStartRes(),
+                                            sg.getEndRes()+1);
+          c.calculate();
+          c.verdict(false, viewport.ConsPercGaps);
+          sg.cs.setConservation(c);
+        }
+        else
+        {
+          sg.cs.setConservation(null);
+      }
+    }
     }
 
-    if(alignPanel.getOverviewPanel()!=null)
+    if (alignPanel.getOverviewPanel() != null)
+    {
       alignPanel.getOverviewPanel().updateOverviewImage();
-    alignPanel.repaint();
+    }
+
+
+
+
+    alignPanel.paintAlignment(true);
   }
 
+  /**
+   * 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());
@@ -904,405 +2561,1002 @@ 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)
+  {
+    if (e.getActionCommand().equals("User Defined..."))
+    {
+      new UserDefinedColours(alignPanel, null);
+    }
+    else
+    {
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+          getUserColourSchemes().get(e.getActionCommand());
 
+      changeColour(udc);
+    }
+  }
 
-  public void userDefinedColour_actionPerformed(ActionEvent e)
+  public void updateUserColourMenu()
   {
-    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
+
+    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() );
+    changeColour(new PIDColourScheme());
   }
 
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme() );
+    changeColour(new Blosum62ColourScheme());
   }
 
-
-
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
-    alignPanel.repaint();
+    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByPID(viewport.getAlignment(),
+                              viewport.getAlignment().getSequenceAt(0));
+    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+                                    viewport.alignment));
+    alignPanel.paintAlignment(true);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByID( viewport.getAlignment() );
-    alignPanel.repaint();
+    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByID(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+    alignPanel.paintAlignment(true);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByGroup(viewport.getAlignment());
-    AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.repaint();
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
+
+    alignPanel.paintAlignment(true);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
+    new RedundancyPanel(alignPanel, this);
+  }
+
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+  {
+    if ( (viewport.getSelectionGroup() == null) ||
+        (viewport.getSelectionGroup().getSize() < 2))
+    {
+      JOptionPane.showInternalMessageDialog(this,
+                                            "You must select at least 2 sequences.",
+                                            "Invalid Selection",
+                                            JOptionPane.WARNING_MESSAGE);
+    }
+    else
+    {
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(new PairwiseAlignPanel(viewport));
+      Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+    }
+  }
+
+  /**
+   * 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))
+    {
+      JOptionPane.showInternalMessageDialog(this,
+                                            "Principal component analysis must take\n" +
+                                            "at least 4 input sequences.",
+                                            "Sequence selection insufficient",
+                                            JOptionPane.WARNING_MESSAGE);
+
+      return;
+    }
+
+     new PCAPanel(alignPanel);
+  }
+
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+    viewport.autoCalculateConsensus = autoCalculate.isSelected();
+    if(viewport.autoCalculateConsensus)
+    {
+      viewport.firePropertyChange("alignment",
+                                  null,
+                                  viewport.getAlignment().getSequences());
+    }
+  }
+
+
+  /**
+   * 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 BLOSUM62");
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param type DOCUMENT ME!
+   * @param pwType DOCUMENT ME!
+   * @param title DOCUMENT ME!
+   */
+  void NewTreePanel(String type, String pwType, String title)
+  {
+    TreePanel tp;
+
+    if (viewport.getSelectionGroup() != null)
+    {
+      if (viewport.getSelectionGroup().getSize() < 3)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "You need to have more than two sequences selected to build a tree!",
+                                      "Not enough sequences",
+                                      JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
+      int s = 0;
+      SequenceGroup sg = viewport.getSelectionGroup();
+
+      /* Decide if the selection is a column region */
+      while (s < sg.getSize())
+      {
+        if ( ( (SequenceI) sg.getSequences(null).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(alignPanel, type, pwType);
+    }
+    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;
+      }
+
+      if(viewport.alignment.getHeight()<2)
+      {
+        return;
+      }
+
+      tp = new TreePanel(alignPanel, type, pwType);
+    }
+
+    title += " from ";
+
+    if(viewport.viewName!=null)
+    {
+      title+= viewport.viewName+" of ";
+    }
+
+    title += this.title;
+
+    Desktop.addInternalFrame(tp, 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)
+      {
+        SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
 
+        // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+        AlignmentSorter.sortBy(viewport.getAlignment(), order);
+
+        addHistoryItem(new OrderCommand(order.getName(), oldOrder,
+                                        viewport.alignment));
+
+        alignPanel.paintAlignment(true);
+      }
+    });
+  }
+
+  /**
+   * 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.
+   */
+  public void buildTreeMenu()
+  {
+    sortByTreeMenu.removeAll();
+
+    Vector comps = (Vector) PaintRefresher.components.get(viewport.
+        getSequenceSetId());
+    Vector treePanels = new Vector();
+    int i, iSize = comps.size();
+    for(i=0; i<iSize; i++)
+    {
+      if(comps.elementAt(i) instanceof TreePanel)
+      {
+        treePanels.add(comps.elementAt(i));
+      }
+    }
+
+    iSize = treePanels.size();
+
+    if(iSize<1)
+    {
+      sortByTreeMenu.setVisible(false);
+      return;
+    }
+
+    sortByTreeMenu.setVisible(true);
+
+    for(i=0; i<treePanels.size(); i++)
+    {
+      TreePanel tp = (TreePanel)treePanels.elementAt(i);
+      final JMenuItem item = new JMenuItem(tp.getTitle());
+      final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
+      item.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+          AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
+
+          addHistoryItem(new OrderCommand("Tree Sort",
+                                          oldOrder,
+                                          viewport.alignment));
+
+          alignPanel.paintAlignment(true);
+        }
+      });
+
+      sortByTreeMenu.add(item);
+    }
   }
 
-  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);
+  /**
+   * Work out whether the whole set of sequences
+   * or just the selected set will be submitted for multiple alignment.
+   *
+   */
+  private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
+  {
+    // Now, check we have enough sequences
+    AlignmentView 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(false)];
+
+      for (int i = 0; i < sz; i++)
+      {
+        msa[i] = (SequenceI) seqs.getSequenceAt(i);
+      } */
+      msa = viewport.getAlignmentView(true);
+    }
     else
     {
-      JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(new PairwiseAlignPanel(viewport));
-      Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+      /*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);
+        }
+      }*/
+      msa = viewport.getAlignmentView(false);
     }
+    return msa;
   }
 
-  public void PCAMenuItem_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).
+   */
+  AlignmentView gatherSeqOrMsaForSecStrPrediction()
   {
+   AlignmentView seqs = null;
 
-    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
-       || viewport.getAlignment().getHeight()<4)
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 0))
     {
-      JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
-                                    +"at least 4 input sequences.",
-                                    "Sequence selection insufficient",
-                                    JOptionPane.WARNING_MESSAGE);
-      return;
+      seqs = viewport.getAlignmentView(true);
     }
+    else
+    {
+      seqs = viewport.getAlignmentView(false);
+    }
+    // limit sequences - JBPNote in future - could spawn multiple prediction jobs
+    // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
+    if (!viewport.alignment.isAligned())
+    {
+      seqs.setSequences(new SeqCigar[]
+                        {seqs.getSequences()[0]});
+    }
+    return seqs;
+  }
+  /**
+   * 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");
 
-    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);
-   }
+    int value = chooser.showOpenDialog(null);
 
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
 
+      try
+      {
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
+            "File");
+        viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "Problem reading tree file",
+                                      ex.getMessage(),
+                                      JOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+    }
   }
 
-  public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    NewTreePanel("AV", "PID", "Average distance tree using PID");
-  }
 
-  public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+  public TreePanel ShowNewickTree(NewickFile nf, String title)
   {
-    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+    return ShowNewickTree(nf,title,600,500,4,5);
   }
 
-
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  public TreePanel ShowNewickTree(NewickFile nf, String title,
+                                  AlignmentView input)
   {
-    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+    return ShowNewickTree(nf,title, input, 600,500,4,5);
   }
 
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
+                                  int x, int y)
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
+    return ShowNewickTree(nf, title, null, w, h, x, y);
   }
-
-  void NewTreePanel(String type, String pwType, String title)
+  /**
+   * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
+   *
+   * @param nf the tree
+   * @param title tree viewer title
+   * @param input Associated alignment input data (or null)
+   * @param w width
+   * @param h height
+   * @param x position
+   * @param y position
+   * @return TreePanel handle
+   */
+  public TreePanel ShowNewickTree(NewickFile nf, String title,
+                                  AlignmentView input, int w, int h, int x,
+                                  int y)
   {
-    //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;
-    }
+    TreePanel tp = null;
 
-    final TreePanel tp;
-    if (viewport.getSelectionGroup() != null &&
-        viewport.getSelectionGroup().getSize() > 3)
-    {
-      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
-                         pwType,
-                         0, viewport.alignment.getWidth());
-    }
-    else
+    try
     {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, 0, viewport.alignment.getWidth());
-    }
+      nf.parse();
 
-   addTreeMenuItem(tp, title);
+      if (nf.getTree() != null)
+      {
+        tp = new TreePanel(alignPanel,
+                           "FromFile",
+                           title,
+                           nf, input);
 
-   Desktop.addInternalFrame(tp, title, 600, 500);
-  }
+        tp.setSize(w,h);
 
-  public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
-    final JMenuItem item = new JMenuItem(title);
-    sortByTreeMenu.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        addHistoryItem("sort");
-        AlignmentSorter.sortBy(viewport.getAlignment(), order);
-        alignPanel.repaint();
-      }
-    });
-  }
+        if(x>0 && y>0)
+        {
+          tp.setLocation(x,y);
+        }
 
-  void addTreeMenuItem(final TreePanel treePanel, String title)
-  {
-    final JMenuItem item = new JMenuItem(title);
-    sortByTreeMenu.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        addHistoryItem("sort");
-        AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
-        alignPanel.repaint();
-      }
-    });
 
-    treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+        Desktop.addInternalFrame(tp, title, w, h);
+      }
+    }
+    catch (Exception ex)
     {
-      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
-      {
-        sortByTreeMenu.remove(item);
-      };
-    });
+      ex.printStackTrace();
+    }
 
+    return tp;
   }
 
 
-  public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+  /**
+   * Generates menu items and listener event actions for web service clients
+   *
+   */
+  public void BuildWebServiceMenu()
   {
-      // 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)
+    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();
+      final AlignFrame af = this;
+      if (msaws != null)
+      {
+        // Add any Multiple Sequence Alignment Services
+        final JMenu msawsmenu = new JMenu("Alignment");
+        for (int i = 0, j = msaws.size(); i < j; i++)
         {
-          // 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++)
+          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
+              get(i);
+          final JMenuItem method = new JMenuItem(sh.getName());
+          method.addActionListener(new ActionListener()
           {
-            msa[i] = (SequenceI) seqs.getSequenceAt(i);
-          }
+            public void actionPerformed(ActionEvent e)
+            {
+              AlignmentView msa = gatherSequencesForAlignment();
+              new jalview.ws.MsaWSClient(sh, title, msa,
+                                         false, true,
+                                         viewport.getAlignment().getDataset(),
+                                         af);
 
-          }
-        else
-        {
-          Vector seqs = viewport.getAlignment().getSequences();
+            }
 
-          if (seqs.size() > 1) {
-            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)
+          {
+            // We know that ClustalWS can accept partial alignments for refinement.
+            final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
+            methodR.addActionListener(new ActionListener()
             {
-              msa[i] = (SequenceI) seqs.elementAt(i);
-            }
+              public void actionPerformed(ActionEvent e)
+              {
+                AlignmentView msa = gatherSequencesForAlignment();
+                new jalview.ws.MsaWSClient(sh, title, msa,
+                                           true, true,
+                                           viewport.getAlignment().getDataset(),
+                                           af);
 
-          }
+              }
+
+            });
+            msawsmenu.add(methodR);
 
+          }
         }
-        if (msa!=null) {
-          jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
+        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)
+            {
+              AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
+              if (msa.getSequences().length == 1)
+              {
+                // Single Sequence prediction
+                new jalview.ws.JPredClient(sh, title, false, msa, af, true);
+              }
+              else
+              {
+                if (msa.getSequences().length > 1)
+                {
+                  // Sequence profile based prediction
+                  new jalview.ws.JPredClient(sh,
+                      title, true, msa, af, true);
+                }
+              }
+            }
+          });
+          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.
   }
-/* Old cLustalW
-       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();
-  }
+ /* public void vamsasStore_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Export to Vamsas file");
+    chooser.setToolTipText("Export");
 
-    class ClustalThread extends Thread
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      WebserviceInfo info;
-      public ClustalThread(WebserviceInfo info)
-      {this.info = info; }
+      jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
+      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+    }
+  }*/
 
-      public void run()
-      {
-        info.setStatus(WebserviceInfo.STATE_RUNNING);
-        jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
-        Vector sv = viewport.getAlignment().getSequences();
-        SequenceI[] seqs = new SequenceI[sv.size()];
 
-        int i = 0;
-        do
-        {
-          seqs[i] = (SequenceI) sv.elementAt(i);
-        }
-        while (++i < sv.size());
 
-        SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
-        if (alignment != null)
-        {
-          AlignFrame af = new AlignFrame(new Alignment(alignment));
-          Desktop.addInternalFrame(af, 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
-        {
-            info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-            info.appendProgressText("Problem obtaining clustal alignment");
-        }
-      }
+
+public void showTranslation_actionPerformed(ActionEvent e)
+{
+  ///////////////////////////////
+  // Collect Data to be translated/transferred
+
+  SequenceI [] selection = viewport.getSelectionAsNewSequence();
+  String [] seqstring = viewport.getViewAsString(true);
+  AlignmentI al  = null;
+  try {
+    al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
+        viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
+        viewport.alignment.getWidth());
+  } catch (Exception ex) {
+    al = null;
+    jalview.bin.Cache.log.debug("Exception during translation.",ex);
+  }
+  if (al==null)
+  {
+    JOptionPane.showMessageDialog(Desktop.desktop,
+        "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+        "Translation Failed",
+        JOptionPane.WARNING_MESSAGE);
+  } else {
+    AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+    Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+                             DEFAULT_WIDTH,
+                             DEFAULT_HEIGHT);
+  }
+}
+
+/**
+ * DOCUMENT ME!
+ *
+ * @param String DOCUMENT ME!
+ */
+public boolean parseFeaturesFile(String file, String type)
+{
+    boolean featuresFile = false;
+    try
+    {
+      featuresFile = new FeaturesFile(file,
+          type).parse(viewport.alignment.getDataset(),
+                                         alignPanel.seqPanel.seqCanvas.
+                                         getFeatureRenderer().featureColours,
+                                         false);
+    }
+    catch(Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    if(featuresFile)
+    {
+      viewport.showSequenceFeatures = true;
+      showSeqFeatures.setSelected(true);
+      alignPanel.paintAlignment(true);
     }
-*/
 
-  protected void jpred_actionPerformed(ActionEvent e)
+    return featuresFile;
+}
+
+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;
 
-    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+    try
     {
-      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
-      if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
+      DataFlavor uriListFlavor = new DataFlavor(
+          "text/uri-list;class=java.lang.String");
+      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
       {
-        JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
+        //Works on Windows and MacOSX
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        files = (java.util.List) t.getTransferData(DataFlavor.
+            javaFileListFlavor);
       }
-      else
+      else if (t.isDataFlavorSupported(uriListFlavor))
       {
-        int sz;
-        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
-        for (int i = 0; i < sz; i++)
+        // 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(); )
         {
-          msa[i] = (SequenceI) seqs.getSequenceAt(i);
-        }
+          String s = st.nextToken();
+          if (s.startsWith("#"))
+          {
+            // the line is a comment (as per the RFC 2483)
+            continue;
+          }
 
-        JPredClient ct = new JPredClient(msa);
+          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
+      {
 
+        for (int i = 0; i < files.size(); i++)
+        {
+          loadJalviewDataFile(files.get(i).toString());
+        }
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
     }
-    else
+}
+
+  // This method will attempt to load a "dropped" file first by testing
+  // whether its and Annotation file, then features file. If both are
+  // false then the user may have dropped an alignment file onto this
+  // AlignFrame
+   public void loadJalviewDataFile(String file)
+  {
+    try
     {
-      Vector seqs = viewport.getAlignment().getSequences();
+      String protocol = "File";
 
-      if (seqs.size() == 1 || !viewport.alignment.isAligned())
+      if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
       {
-        JPredClient ct = new JPredClient( (SequenceI)
-                                         seqs.elementAt(0));
+        protocol = "URL";
       }
-      else
+
+      boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
+          alignment, file, protocol);
+
+      if (!isAnnotation)
       {
-        SequenceI[] msa = new SequenceI[seqs.size()];
-        for (int i = 0; i < seqs.size(); i++)
+        boolean isGroupsFile = parseFeaturesFile(file,protocol);
+        if (!isGroupsFile)
         {
-          msa[i] = (SequenceI) seqs.elementAt(i);
-        }
+          String format = new IdentifyFile().Identify(file, protocol);
 
-        JPredClient ct = new JPredClient(msa);
+          if(format.equalsIgnoreCase("JnetFile"))
+          {
+            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                file, protocol);
+            new JnetAnnotationMaker().add_annotation(predictions,
+                viewport.getAlignment(),
+                0, false);
+            alignPanel.adjustAnnotationHeight();
+            alignPanel.paintAlignment(true);
+          }
+          else
+          {
+            new FileLoader().LoadFile(viewport, file, protocol, format);
+        }
+      }
+      }
+      else
+      {
+        // (isAnnotation)
+        alignPanel.adjustAnnotationHeight();
       }
 
     }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
   }
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+
+  public void tabSelectionChanged(int index)
   {
-    // 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);
-        }
+    if (index > -1)
+    {
+      alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
+      viewport = alignPanel.av;
+      setMenusFromViewport(viewport);
+    }
+  }
 
+  public void tabbedPane_mousePressed(MouseEvent e)
+  {
+    if(SwingUtilities.isRightMouseButton(e))
+    {
+      String reply = JOptionPane.showInternalInputDialog(this,
+          "Enter View Name",
+          "Edit View Name",
+          JOptionPane.QUESTION_MESSAGE);
 
-      }
-      else
+      if (reply != null)
       {
-        Vector seqs = viewport.getAlignment().getSequences();
+        viewport.viewName = reply;
+        tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+      }
+    }
+  }
 
-        if (seqs.size() > 1) {
-          msa = new SequenceI[seqs.size()];
-          for (int i = 0; i < seqs.size(); i++)
-          {
-            msa[i] = (SequenceI) seqs.elementAt(i);
-          }
 
-        }
+  public AlignViewport getCurrentView()
+  {
+    return viewport;
+  }
+}
 
-      }
-      if (msa!=null) {
-        MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, true, true);
-      }
+class PrintThread
+    extends Thread
+{
+  AlignmentPanel ap;
+  public PrintThread(AlignmentPanel ap)
+  {
+   this.ap = ap;
   }
-    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)
+  static PageFormat pf;
+  public void run()
+  {
+    PrinterJob printJob = PrinterJob.getPrinterJob();
+
+    if (pf != null)
+    {
+      printJob.setPrintable(ap, pf);
+    }
+    else
+    {
+      printJob.setPrintable(ap);
+    }
+
+    if (printJob.printDialog())
     {
-      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);
+        printJob.print();
       }
-      catch (Exception ex)
+      catch (Exception PrintException)
       {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                                      "Problem reading tree file",
-                                      ex.getMessage(),
-                                      JOptionPane.WARNING_MESSAGE);
-        ex.printStackTrace();
+        PrintException.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();}
-  }
-
-
 }