X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b2d41e8935bec20c6141000dd1cf9cc7e008d9bd;hb=12cc8cf9004b54db1b9fafa21d22d119bb874dfc;hp=08c1aa94a041ace080c816a955f25139056e7347;hpb=77c35fa912621cbadcf5ec74da4c6d45de6322e1;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 08c1aa9..b2d41e8 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -24,18 +24,18 @@ 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 jalview.analysis.*;
+import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
-import jalview.commands.*;
 import jalview.ws.*;
-import java.awt.dnd.*;
 
 /**
  * DOCUMENT ME!
@@ -43,7 +43,8 @@ import java.awt.dnd.*;
  * @author $author$
  * @version $Revision$
  */
-public class AlignFrame extends GAlignFrame implements DropTargetListener
+public class AlignFrame
+    extends GAlignFrame implements DropTargetListener
 {
   /** DOCUMENT ME!! */
   public static final int DEFAULT_WIDTH = 700;
@@ -56,13 +57,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   Vector alignPanels = new Vector();
 
-
   /** DOCUMENT ME!! */
   String currentFileFormat = null;
 
   String fileName = null;
 
-
   /**
    * Creates a new AlignFrame object.
    *
@@ -73,7 +72,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     this(al, null, width, height);
   }
 
-
   /**
    * new alignment window with hidden columns
    * @param al AlignmentI
@@ -87,7 +85,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     alignPanel = new AlignmentPanel(this, viewport);
 
-    if(al.getDataset()==null)
+    if (al.getDataset() == null)
     {
       al.setDataset(null);
     }
@@ -118,240 +116,269 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       BLOSUM62Colour.setEnabled(false);
       conservationMenuItem.setEnabled(false);
       modifyConservation.setEnabled(false);
-    //  PIDColour.setEnabled(false);
-    //  abovePIDThreshold.setEnabled(false);
-    //  modifyPID.setEnabled(false);
+      //  PIDColour.setEnabled(false);
+      //  abovePIDThreshold.setEnabled(false);
+      //  modifyPID.setEnabled(false);
     }
 
     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);
+    }
 
     if (Desktop.desktop != null)
-   {
-     addServiceListeners();
-     setGUINucleotide(viewport.alignment.isNucleotide());
-   }
+    {
+      addServiceListeners();
+      setGUINucleotide(viewport.alignment.isNucleotide());
+    }
 
-   setMenusFromViewport(viewport);
+    setMenusFromViewport(viewport);
 
-   if (viewport.wrapAlignment)
-   {
-     wrapMenuItem_actionPerformed(null);
-   }
+    if (viewport.wrapAlignment)
+    {
+      wrapMenuItem_actionPerformed(null);
+    }
 
-   addKeyListener();
+    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
+    {
+      this.overviewMenuItem_actionPerformed(null);
+    }
+
+    addKeyListener();
 
   }
 
   public void setFileName(String file, String format)
   {
-     fileName = file;
-     currentFileFormat = format;
-     reload.setEnabled(true);
+    fileName = file;
+    currentFileFormat = format;
+    reload.setEnabled(true);
   }
 
   void addKeyListener()
   {
-      addKeyListener(new KeyAdapter()
+    addKeyListener(new KeyAdapter()
+    {
+      public void keyPressed(KeyEvent evt)
       {
-        public void keyPressed(KeyEvent evt)
+        if (viewport.cursorMode
+            && evt.getKeyCode() >= KeyEvent.VK_0
+            && evt.getKeyCode() <= KeyEvent.VK_9)
         {
-          if (viewport.cursorMode
-              && evt.getKeyCode() >= KeyEvent.VK_0
-              && evt.getKeyCode() <= KeyEvent.VK_9)
-          {
-            alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-          }
+          alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+        }
 
-          switch (evt.getKeyCode())
-          {
+        switch (evt.getKeyCode())
+        {
 
-            case 27: // escape key
-              deselectAllSequenceMenuItem_actionPerformed(null);
+          case 27: // escape key
+            deselectAllSequenceMenuItem_actionPerformed(null);
 
-              break;
+            break;
 
-            case KeyEvent.VK_DOWN:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.moveCursor(0, 1);
-              }
-              else
-                moveSelectedSequences(false);
-              break;
+          case KeyEvent.VK_DOWN:
+            if (viewport.cursorMode)
+            {
+              alignPanel.seqPanel.moveCursor(0, 1);
+            }
+            else
+            {
+              moveSelectedSequences(false);
+            }
+            break;
 
-            case KeyEvent.VK_UP:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.moveCursor(0, -1);
-              }
-              else
-                moveSelectedSequences(true);
-              break;
+          case KeyEvent.VK_UP:
+            if (viewport.cursorMode)
+            {
+              alignPanel.seqPanel.moveCursor(0, -1);
+            }
+            else
+            {
+              moveSelectedSequences(true);
+            }
+            break;
 
-            case KeyEvent.VK_LEFT:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.moveCursor( -1, 0);
-              }
-              break;
+          case KeyEvent.VK_LEFT:
+            if (viewport.cursorMode)
+            {
+              alignPanel.seqPanel.moveCursor( -1, 0);
+            }
+            break;
 
-            case KeyEvent.VK_RIGHT:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.moveCursor(1, 0);
-              }
-              break;
+          case KeyEvent.VK_RIGHT:
+            if (viewport.cursorMode)
+            {
+              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_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());
+          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;
+            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_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_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_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_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);
+          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:
+              javax.help.HelpBroker hb = hs.createHelpBroker();
+              hb.setCurrentID("home");
+              hb.setDisplayed(true);
+            }
+            catch (Exception ex)
             {
-              boolean toggleSeqs = !evt.isControlDown();
-              boolean toggleCols = !evt.isShiftDown();
+              ex.printStackTrace();
+            }
+            break
+                ;
+          case KeyEvent.VK_H:
+          {
+            boolean toggleSeqs = !evt.isControlDown();
+            boolean toggleCols = !evt.isShiftDown();
 
-              boolean hide = false;
+            boolean hide = false;
 
-              SequenceGroup sg = viewport.getSelectionGroup();
-              if (toggleSeqs)
+            SequenceGroup sg = viewport.getSelectionGroup();
+            if (toggleSeqs)
+            {
+              if (sg != null && sg.getSize() != viewport.alignment.getHeight())
               {
-                if (sg != null && sg.getSize() != viewport.alignment.getHeight())
-                {
-                  hideSelSequences_actionPerformed(null);
-                  hide = true;
-                }
-                else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
-                  showAllSeqs_actionPerformed(null);
+                hideSelSequences_actionPerformed(null);
+                hide = true;
+              }
+              else if (! (toggleCols &&
+                          viewport.colSel.getSelected().size() > 0))
+              {
+                showAllSeqs_actionPerformed(null);
               }
+            }
 
-              if (toggleCols)
+            if (toggleCols)
+            {
+              if (viewport.colSel.getSelected().size() > 0)
               {
-                if (viewport.colSel.getSelected().size() > 0)
+                hideSelColumns_actionPerformed(null);
+                if (!toggleSeqs)
                 {
-                  hideSelColumns_actionPerformed(null);
-                  if (!toggleSeqs)
-                    viewport.selectionGroup = sg;
+                  viewport.selectionGroup = sg;
                 }
-                else if (!hide)
-                  showAllColumns_actionPerformed(null);
               }
-              break;
+              else if (!hide)
+              {
+                showAllColumns_actionPerformed(null);
+              }
             }
-            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;
+            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;
         }
-      });
+      }
+    });
   }
 
-
   public void addAlignmentPanel(final AlignmentPanel ap,
                                 boolean newPanel)
   {
@@ -363,9 +390,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     int aSize = alignPanels.size();
 
-    tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+    tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 
-    if (aSize == 1 && ap.av.viewName==null)
+    if (aSize == 1 && ap.av.viewName == null)
     {
       this.getContentPane().add(ap, BorderLayout.CENTER);
     }
@@ -383,10 +410,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       ap.setVisible(false);
     }
 
-    if(newPanel)
+    if (newPanel)
     {
       if (ap.av.padGaps)
+      {
         ap.av.alignment.padGaps();
+      }
       ap.av.updateConservation(ap);
       ap.av.updateConsensus(ap);
     }
@@ -398,11 +427,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     gatherViews.setEnabled(true);
     tabbedPane.setVisible(true);
     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
-    tabbedPane.addTab(first.av.viewName,first);
+    tabbedPane.addTab(first.av.viewName, first);
     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
 
-
   public AlignViewport getViewport()
   {
     return viewport;
@@ -444,14 +472,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public void setGUINucleotide(boolean nucleotide)
   {
-    showTranslation.setVisible( nucleotide );
-    conservationMenuItem.setEnabled( !nucleotide );
-    modifyConservation.setEnabled(   !nucleotide );
+    showTranslation.setVisible(nucleotide);
+    conservationMenuItem.setEnabled(!nucleotide);
+    modifyConservation.setEnabled(!nucleotide);
 
     //Remember AlignFrame always starts as protein
-    if(!nucleotide)
+    if (!nucleotide)
     {
-      calculateMenu.remove(calculateMenu.getItemCount()-2);
+      calculateMenu.remove(calculateMenu.getItemCount() - 2);
     }
   }
 
@@ -487,26 +515,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     updateEditMenuBar();
   }
 
-
   Hashtable progressBars;
   public void setProgressBar(String message, long id)
   {
-    if(progressBars == null)
+    if (progressBars == null)
+    {
       progressBars = new Hashtable();
+    }
 
     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);
-     }
+    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
     {
       progressPanel = new JPanel(new BorderLayout(10, 5));
@@ -526,15 +557,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     validate();
   }
 
-
-
-
   /*
    Added so Castor Mapping file can obtain Jalview Version
-  */
+   */
   public String getVersion()
   {
-    return  jalview.bin.Cache.getProperty("VERSION");
+    return jalview.bin.Cache.getProperty("VERSION");
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -542,7 +570,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
   }
 
-
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
@@ -555,21 +582,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public void reload_actionPerformed(ActionEvent e)
   {
-    if(fileName!=null)
+    if (fileName != null)
     {
-      if(currentFileFormat.equals("Jalview"))
+      if (currentFileFormat.equals("Jalview"))
       {
-        JInternalFrame [] frames = Desktop.desktop.getAllFrames();
-        for(int i=0; i<frames.length; i++)
+        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{
+            try
+            {
               frames[i].setSelected(true);
               Desktop.instance.closeAssociatedWindows();
-            }catch(java.beans.PropertyVetoException ex){}
+            }
+            catch (java.beans.PropertyVetoException ex)
+            {}
           }
 
         }
@@ -592,7 +622,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   public void addFromText_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
@@ -603,16 +632,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
-
   public void save_actionPerformed(ActionEvent e)
   {
-    if(fileName==null
-       || currentFileFormat==null
-       || fileName.startsWith("http")
+    if (fileName == null
+        || currentFileFormat == null
+        || fileName.startsWith("http")
         )
+    {
       saveAs_actionPerformed(null);
+    }
     else
+    {
       saveAlignment(fileName, currentFileFormat);
+    }
   }
 
   /**
@@ -623,15 +655,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty( "LAST_DIRECTORY"),
+        getProperty("LAST_DIRECTORY"),
         new String[]
-        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
+        {"fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar"},
         new String[]
-        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+        {"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
         currentFileFormat,
         false);
 
-
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
@@ -640,18 +671,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     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;
-        }
+      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;
+      }
 
-        fileName = chooser.getSelectedFile().getPath();
+      fileName = chooser.getSelectedFile().getPath();
 
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
                                     currentFileFormat);
@@ -679,8 +710,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       success = new Jalview2XML().SaveAlignment(this, file, shortName);
 
       statusBar.setText("Successfully saved to file: "
-                          +fileName+" in "
-                          +format +" format.");
+                        + fileName + " in "
+                        + format + " format.");
 
     }
     else
@@ -697,7 +728,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
 
         if (reply == JOptionPane.YES_OPTION)
+        {
           omitHidden = viewport.getViewAsString(false);
+        }
       }
 
       String output = new FormatAdapter().formatSequences(
@@ -732,10 +765,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
 
     if (!success)
+    {
       JOptionPane.showInternalMessageDialog(
           this, "Couldn't save file: " + fileName,
           "Error Saving File",
           JOptionPane.WARNING_MESSAGE);
+    }
 
     return success;
   }
@@ -747,17 +782,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    String [] omitHidden = null;
+    String[] omitHidden = null;
 
-    if(viewport.hasHiddenColumns)
+    if (viewport.hasHiddenColumns)
     {
       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);
+          + "\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)
+      if (reply == JOptionPane.YES_OPTION)
       {
         omitHidden = viewport.getViewAsString(false);
       }
@@ -769,7 +804,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
 
-
     cap.setText(new FormatAdapter().formatSequences(
         e.getActionCommand(),
         viewport.alignment.getSequencesArray(),
@@ -785,7 +819,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     new HTMLOutput(viewport,
                    alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
-        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+                   alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
   }
 
   public void createImageMap(File file, String image)
@@ -813,7 +847,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.makeEPS(f);
   }
 
-
   public void pageSetup_actionPerformed(ActionEvent e)
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -837,7 +870,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
-
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(
@@ -847,7 +879,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         );
   }
 
-
   public void associatedData_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
@@ -869,7 +900,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -877,14 +907,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
-    if(alignPanels!=null && alignPanels.size()<2)
+    if (alignPanels != null && alignPanels.size() < 2)
+    {
       closeAllTabs = true;
+    }
 
     try
     {
-      if(alignPanels!=null)
+      if (alignPanels != null)
       {
         if (closeAllTabs)
+        {
           for (int i = 0; i < alignPanels.size(); i++)
           {
             AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
@@ -892,6 +925,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
             PaintRefresher.RemoveComponent(ap);
           }
+        }
         else
         {
           int index = tabbedPane.getSelectedIndex();
@@ -906,15 +940,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           tabbedPane.removeTabAt(index);
           tabbedPane.validate();
 
-          if(index==tabbedPane.getTabCount())
-            index --;
+          if (index == tabbedPane.getTabCount())
+          {
+            index--;
+          }
 
           this.tabSelectionChanged(index);
         }
       }
 
       if (closeAllTabs)
+      {
         this.setClosed(true);
+      }
     }
     catch (Exception ex)
     {
@@ -922,7 +960,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   /**
    * DOCUMENT ME!
    */
@@ -955,10 +992,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   public void addHistoryItem(CommandI command)
   {
-    if(command.getSize()>0)
+    if (command.getSize() > 0)
     {
       viewport.historyList.push(command);
       viewport.redoList.clear();
@@ -967,8 +1003,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
-
   /**
    * DOCUMENT ME!
    *
@@ -976,14 +1010,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
-    CommandI command = (CommandI)viewport.historyList.pop();
+    CommandI command = (CommandI) viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand();
 
     AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
-    if(originalSource!=null)
+    if (originalSource != null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
       originalSource.firePropertyChange("alignment",
@@ -999,8 +1033,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.redoList.size()<1)
+    if (viewport.redoList.size() < 1)
+    {
       return;
+    }
 
     CommandI command = (CommandI) viewport.redoList.pop();
     viewport.historyList.push(command);
@@ -1009,7 +1045,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
-    if(originalSource!=null)
+    if (originalSource != null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
       originalSource.firePropertyChange("alignment",
@@ -1022,9 +1058,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     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;
+    //the property change event FROM the viewport where the
+    //original alignment was altered
+    AlignmentI al = null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
@@ -1050,7 +1086,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       //The original view is closed, we must validate
       //the current view against the closed view first
       if (al != null)
+      {
         PaintRefresher.validateSequences(al, viewport.alignment);
+      }
 
       originalSource = viewport;
     }
@@ -1120,8 +1158,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
-
-
   /**
    * DOCUMENT ME!
    *
@@ -1135,7 +1171,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       return;
     }
 
-    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    SequenceI[] seqs = viewport.getSelectionAsNewSequence();
     String[] omitHidden = null;
 
     if (viewport.hasHiddenColumns)
@@ -1165,42 +1201,44 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       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);
-            }
-          });
+      {
+        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)
+    if (viewport.hasHiddenColumns)
     {
-      hiddenColumns =new Vector();
+      hiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
+      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});
+        hiddenColumns.addElement(new int[]
+                                 {region[0] - hiddenOffset,
+                                 region[1] - hiddenOffset});
       }
     }
 
-
-
-    Desktop.jalviewClipboard = new Object[]{ seqs,
+    Desktop.jalviewClipboard = new Object[]
+        {
+        seqs,
         viewport.alignment.getDataset(),
         hiddenColumns};
-    statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
+    statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
   }
 
   /**
@@ -1245,7 +1283,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
         if (str.length() < 1)
+        {
           return;
+        }
 
         format = new IdentifyFile().Identify(str, "Paste");
 
@@ -1271,40 +1311,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       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();
+      }
 
-     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;
+      AlignmentI alignment = null;
 
       if (newAlignment)
       {
-          alignment = new Alignment(sequences);
+        alignment = new Alignment(sequences);
 
-          if (Desktop.jalviewClipboard != null)
-            alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
-          else
-            alignment.setDataset(null);
+        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];
+        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());
+                                    sequences[i].getSequence(),
+                                    sequences[i].getStart(),
+                                    sequences[i].getEnd());
 
           alignment.addSequence(newseqs[i]);
         }
@@ -1321,88 +1366,81 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             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]);
-           }
-         }
+      {
+        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();
+        }
+      }
 
-       //>>>This is a fix for the moment, until a better solution is found!!<<<
-       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
-           alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+      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]);
+          }
+        }
 
-       if (title.startsWith("Copied sequences"))
-       {
-         newtitle = title;
-       }
-       else
-       {
-         newtitle = newtitle.concat("- from " + title);
-       }
+        //>>>This is a fix for the moment, until a better solution is found!!<<<
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
 
-       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
-                                DEFAULT_HEIGHT);
+        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
+      System.out.println("Exception whilst pasting: " + ex);
+      // could be anything being pasted in here
     }
 
-
   }
 
   /**
@@ -1438,36 +1476,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       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);
+    }
 
-   // 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);
-
+    SequenceI[] cut = new SequenceI[seqs.size()];
+    for (int i = 0; i < seqs.size(); i++)
+    {
+      cut[i] = (SequenceI) seqs.elementAt(i);
+    }
 
     /*
-    //ADD HISTORY ITEM
-    */
+         //ADD HISTORY ITEM
+     */
     addHistoryItem(new EditCommand("Cut Sequences",
-                                      EditCommand.CUT,
-                                      cut,
-                                      sg.getStartRes(),
-                                      sg.getEndRes()-sg.getStartRes()+1,
-                                      viewport.alignment));
-
+                                   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());
+                                viewport.getAlignment().getSequences());
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -1523,7 +1559,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.cursorMode)
+    if (viewport.cursorMode)
     {
       alignPanel.seqPanel.keyboardNo1 = null;
       alignPanel.seqPanel.keyboardNo2 = null;
@@ -1570,7 +1606,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -1588,7 +1623,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-      trimAlignment(false);
+    trimAlignment(false);
   }
 
   void trimAlignment(boolean trimLeft)
@@ -1598,43 +1633,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     if (colSel.size() > 0)
     {
-      if(trimLeft)
+      if (trimLeft)
+      {
         column = colSel.getMin();
+      }
       else
+      {
         column = colSel.getMax();
+      }
 
-      SequenceI [] seqs;
-      if(viewport.getSelectionGroup()!=null)
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
+      SequenceI[] seqs;
+      if (viewport.getSelectionGroup() != null)
+      {
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+            hiddenRepSequences);
+      }
       else
+      {
         seqs = viewport.alignment.getSequencesArray();
-
+      }
 
       TrimRegionCommand trimRegion;
-      if(trimLeft)
+      if (trimLeft)
       {
         trimRegion = new TrimRegionCommand("Remove Left",
-                                    TrimRegionCommand.TRIM_LEFT,
-                                    seqs,
-                                    column,
-                                    viewport.alignment,
-                                    viewport.colSel,
-                                    viewport.selectionGroup);
+                                           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.");
+      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);
 
@@ -1663,18 +1705,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth()-1;
+    int start = 0, end = viewport.alignment.getWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
+      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",
@@ -1684,19 +1728,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     addHistoryItem(removeGapCols);
 
-    statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
+    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());
+    // 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());
 
   }
 
@@ -1707,17 +1752,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth()-1;
+    int start = 0, end = viewport.alignment.getWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
+      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
@@ -1729,9 +1777,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                                          start, end,
                                          viewport.alignment));
 
-    viewport.setStartRes(seq.findIndex(startRes)-1);
+    viewport.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null,
+                                viewport.getAlignment().getSequences());
 
   }
 
@@ -1765,36 +1814,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         new Jalview2XML().copyAlignPanel(alignPanel, true);
 
     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;
+    String newViewName = "View " + index;
 
-    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector comps = (Vector) PaintRefresher.components.get(viewport.
+        getSequenceSetId());
     Vector existingNames = new Vector();
-    for(int i=0; i<comps.size(); i++)
+    for (int i = 0; i < comps.size(); i++)
     {
-      if(comps.elementAt(i) instanceof AlignmentPanel)
+      if (comps.elementAt(i) instanceof AlignmentPanel)
       {
-        AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
-        if(!existingNames.contains(ap.av.viewName))
+        AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
+        if (!existingNames.contains(ap.av.viewName))
+        {
           existingNames.addElement(ap.av.viewName);
+        }
       }
     }
 
-    while(existingNames.contains(newViewName))
+    while (existingNames.contains(newViewName))
     {
-      newViewName = "View "+ (++index);
+      newViewName = "View " + (++index);
     }
 
     newap.av.viewName = newViewName;
 
     addAlignmentPanel(newap, false);
 
-    if(alignPanels.size()==2)
+    if (alignPanels.size() == 2)
     {
       viewport.gatherViewsHere = true;
     }
@@ -1803,7 +1857,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public void expandViews_actionPerformed(ActionEvent e)
   {
-        Desktop.instance.explodeViews(this);
+    Desktop.instance.explodeViews(this);
   }
 
   public void gatherViews_actionPerformed(ActionEvent e)
@@ -1811,8 +1865,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     Desktop.instance.gatherViews(this);
   }
 
-
-
   /**
    * DOCUMENT ME!
    *
@@ -1823,7 +1875,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     new FontChooser(alignPanel);
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -1843,8 +1894,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
-
-
   /**
    * DOCUMENT ME!
    *
@@ -1965,11 +2014,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
-
   public FeatureSettings featureSettings;
   public void featureSettings_actionPerformed(ActionEvent e)
   {
-    if(featureSettings !=null )
+    if (featureSettings != null)
     {
       featureSettings.close();
       featureSettings = null;
@@ -2146,7 +2194,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     new AnnotationColourChooser(viewport, alignPanel);
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -2166,12 +2213,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     int threshold = 0;
 
-    if(cs!=null)
+    if (cs != null)
     {
       if (viewport.getAbovePIDThreshold())
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                                                   "Background");
+            "Background");
 
         cs.setThreshold(threshold,
                         viewport.getIgnoreGapsConsensus());
@@ -2248,30 +2295,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             || cs instanceof PIDColourScheme
             || cs instanceof Blosum62ColourScheme)
         {
-         sg.cs.setThreshold(threshold,
-                viewport.getIgnoreGapsConsensus());
+          sg.cs.setThreshold(threshold,
+                             viewport.getIgnoreGapsConsensus());
 
-         sg.cs.setConsensus(AAFrequency.calculate(
-             sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
-             sg.getEndRes()+1));
-       }
+          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.getSequences(viewport.
+              hiddenRepSequences),
                                             sg.getStartRes(),
-                                            sg.getEndRes()+1);
+                                            sg.getEndRes() + 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           sg.cs.setConservation(c);
         }
         else
+        {
           sg.cs.setConservation(null);
+        }
       }
     }
 
@@ -2290,7 +2341,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
                                      viewport.getGlobalColourScheme(),
@@ -2306,7 +2357,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+    if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
                                         viewport.globalColourScheme,
@@ -2390,37 +2441,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       while (userColours.hasMoreElements())
       {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+        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))
             {
-              public void mousePressed(MouseEvent 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
               {
-                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                radioItem.addActionListener(new ActionListener()
                 {
-                  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)
+                  public void actionPerformed(ActionEvent evt)
                   {
-                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
-                    colourMenu.remove(radioItem);
+                    userDefinedColour_actionPerformed(evt);
                   }
-                  else
-                    radioItem.addActionListener(new ActionListener()
-                    {
-                      public void actionPerformed(ActionEvent evt)
-                      {
-                        userDefinedColour_actionPerformed(evt);
-                      }
-                    });
-                }
+                });
               }
-            });
+            }
+          }
+        });
         radioItem.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -2462,10 +2518,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
-    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
+    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+                                    viewport.alignment));
     alignPanel.repaint();
   }
 
@@ -2476,7 +2533,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByID(viewport.getAlignment());
     addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
     alignPanel.repaint();
@@ -2489,7 +2546,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
 
@@ -2506,7 +2563,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     new RedundancyPanel(alignPanel, this);
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -2551,14 +2607,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       return;
     }
 
-     new PCAPanel(alignPanel);
+    new PCAPanel(alignPanel);
   }
 
-
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
     viewport.autoCalculateConsensus = autoCalculate.isSelected();
-    if(viewport.autoCalculateConsensus)
+    if (viewport.autoCalculateConsensus)
     {
       viewport.firePropertyChange("alignment",
                                   null,
@@ -2566,7 +2621,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -2618,8 +2672,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     TreePanel tp;
 
-    if (viewport.getSelectionGroup() != null) {
-      if (viewport.getSelectionGroup().getSize() < 3) {
+    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",
@@ -2665,16 +2721,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         return;
       }
 
-      if(viewport.alignment.getHeight()<2)
+      if (viewport.alignment.getHeight() < 2)
+      {
         return;
+      }
 
       tp = new TreePanel(alignPanel, type, pwType);
     }
 
     title += " from ";
 
-    if(viewport.viewName!=null)
-      title+= viewport.viewName+" of ";
+    if (viewport.viewName != null)
+    {
+      title += viewport.viewName + " of ";
+    }
 
     title += this.title;
 
@@ -2695,12 +2755,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       public void actionPerformed(ActionEvent e)
       {
-        SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+        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));
+        addHistoryItem(new OrderCommand(order.getName(), oldOrder,
+                                        viewport.alignment));
 
         alignPanel.repaint();
       }
@@ -2720,12 +2781,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     sortByTreeMenu.removeAll();
 
-    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector comps = (Vector) PaintRefresher.components.get(viewport.
+        getSequenceSetId());
     Vector treePanels = new Vector();
     int i, iSize = comps.size();
-    for(i=0; i<iSize; i++)
+    for (i = 0; i < iSize; i++)
     {
-      if(comps.elementAt(i) instanceof TreePanel)
+      if (comps.elementAt(i) instanceof TreePanel)
       {
         treePanels.add(comps.elementAt(i));
       }
@@ -2733,7 +2795,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     iSize = treePanels.size();
 
-    if(iSize<1)
+    if (iSize < 1)
     {
       sortByTreeMenu.setVisible(false);
       return;
@@ -2741,11 +2803,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     sortByTreeMenu.setVisible(true);
 
-    for(i=0; i<treePanels.size(); i++)
+    for (i = 0; i < treePanels.size(); i++)
     {
-      TreePanel tp = (TreePanel)treePanels.elementAt(i);
+      TreePanel tp = (TreePanel) treePanels.elementAt(i);
       final JMenuItem item = new JMenuItem(tp.getTitle());
-      final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
+      final NJTree tree = ( (TreePanel) treePanels.elementAt(i)).getTree();
       item.addActionListener(new java.awt.event.ActionListener()
       {
         public void actionPerformed(ActionEvent e)
@@ -2780,28 +2842,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       // 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)];
+             int sz;
+             msa = new SequenceI[sz = seqs.getSize(false)];
 
-      for (int i = 0; i < sz; i++)
-      {
+             for (int i = 0; i < sz; i++)
+             {
         msa[i] = (SequenceI) seqs.getSequenceAt(i);
-      } */
+             } */
       msa = viewport.getAlignmentView(true);
     }
     else
     {
       /*Vector seqs = viewport.getAlignment().getSequences();
-
-      if (seqs.size() > 1)
-      {
+             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;
@@ -2815,7 +2876,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   AlignmentView gatherSeqOrMsaForSecStrPrediction()
   {
-   AlignmentView seqs = null;
+    AlignmentView seqs = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize() > 0))
@@ -2830,10 +2891,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     // 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] } );
+      seqs.setSequences(new SeqCigar[]
+                        {seqs.getSequences()[0]});
     }
     return seqs;
   }
+
   /**
    * DOCUMENT ME!
    *
@@ -2873,18 +2936,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   public TreePanel ShowNewickTree(NewickFile nf, String title)
   {
-    return ShowNewickTree(nf,title,600,500,4,5);
+    return ShowNewickTree(nf, title, 600, 500, 4, 5);
   }
-  public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
+
+  public TreePanel ShowNewickTree(NewickFile nf, String title,
+                                  AlignmentView input)
   {
-    return ShowNewickTree(nf,title, input, 600,500,4,5);
+    return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
   }
-  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
+
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
+                                  int x, int y)
+  {
     return ShowNewickTree(nf, title, null, w, h, x, y);
   }
+
   /**
    * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
    *
@@ -2897,7 +2965,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    * @param y position
    * @return TreePanel handle
    */
-  public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
+  public TreePanel ShowNewickTree(NewickFile nf, String title,
+                                  AlignmentView input, int w, int h, int x,
+                                  int y)
+  {
     TreePanel tp = null;
 
     try
@@ -2911,11 +2982,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                            title,
                            nf, input);
 
-        tp.setSize(w,h);
-
-        if(x>0 && y>0)
-          tp.setLocation(x,y);
+        tp.setSize(w, h);
 
+        if (x > 0 && y > 0)
+        {
+          tp.setLocation(x, y);
+        }
 
         Desktop.addInternalFrame(tp, title, w, h);
       }
@@ -2928,7 +3000,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     return tp;
   }
 
-
   /**
    * Generates menu items and listener event actions for web service clients
    *
@@ -2957,7 +3028,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             {
               AlignmentView msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true, viewport.getAlignment().getDataset(), af);
+                                         false, true,
+                                         viewport.getAlignment().getDataset(),
+                                         af);
 
             }
 
@@ -2967,14 +3040,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           if (sh.getName().indexOf("lustal") > -1)
           {
             // We know that ClustalWS can accept partial alignments for refinement.
-            final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
+            final JMenuItem methodR = new JMenuItem(sh.getName() + " Realign");
             methodR.addActionListener(new ActionListener()
             {
               public void actionPerformed(ActionEvent e)
               {
                 AlignmentView msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true, viewport.getAlignment().getDataset(), af);
+                                           true, true,
+                                           viewport.getAlignment().getDataset(),
+                                           af);
 
               }
 
@@ -3010,7 +3085,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 {
                   // Sequence profile based prediction
                   new jalview.ws.JPredClient(sh,
-                      title, true, msa, af, true);
+                                             title, true, msa, af, true);
                 }
               }
             }
@@ -3035,139 +3110,144 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     // TODO: group services by location as well as function.
   }
 
- /* 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");
-
-    int value = chooser.showSaveDialog(this);
+  /* public void vamsasStore_actionPerformed(ActionEvent e)
+   {
+     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+         getProperty("LAST_DIRECTORY"));
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
-      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
-      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
-    }
-  }*/
+     chooser.setFileView(new JalviewFileView());
+     chooser.setDialogTitle("Export to Vamsas file");
+     chooser.setToolTipText("Export");
 
+     int value = chooser.showSaveDialog(this);
 
+     if (value == JalviewFileChooser.APPROVE_OPTION)
+     {
+   jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+       //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
+       vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+     }
+   }*/
 
 
-public void showTranslation_actionPerformed(ActionEvent e)
-{
-  SequenceI [] selection = viewport.getSelectionAsNewSequence();
-  String [] seqstring = viewport.getViewAsString(true);
-
-  int s, sSize = selection.length;
-  SequenceI [] newSeq = new SequenceI[sSize];
-
-  int res, resSize;
-  StringBuffer protein;
-  String seq;
-  for(s=0; s<sSize; s++)
-  {
-    protein = new StringBuffer();
-    seq = AlignSeq.extractGaps("-. ", seqstring[s]);
-    resSize = seq.length();
-    resSize -= resSize%3;
-
-    for(res = 0; res < resSize; res+=3)
-    {
-      String codon = seq.substring(res, res+3);
-      codon = codon.replace('U', 'T');
-      String aa = ResidueProperties.codonTranslate(codon);
-      if(aa==null)
-        protein.append(viewport.getGapCharacter());
-      else if(aa.equals("STOP"))
-        protein.append("X");
-      else
-        protein.append( aa );
-    }
-    newSeq[s] = new Sequence(selection[s].getName(),
-                             protein.toString());
-  }
 
 
-  AlignmentI al = new Alignment(newSeq);
-  al.setDataset(null);
+  public void showTranslation_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] selection = viewport.getSelectionAsNewSequence();
+    String[] seqstring = viewport.getViewAsString(true);
 
+    int s, sSize = selection.length;
+    SequenceI[] newSeq = new SequenceI[sSize];
 
-  ////////////////////////////////
-  // Copy annotations across
-  jalview.datamodel.AlignmentAnnotation[] annotations
-      = viewport.alignment.getAlignmentAnnotation();
-  int a, aSize;
-  if(annotations!=null)
-  {
-    for (int i = 0; i < annotations.length; i++)
+    int res, resSize;
+    StringBuffer protein;
+    String seq;
+    for (s = 0; s < sSize; s++)
     {
-      if (annotations[i]==viewport.quality ||
-          annotations[i]==viewport.conservation ||
-          annotations[i]==viewport.consensus)
+      protein = new StringBuffer();
+      seq = AlignSeq.extractGaps("-. ", seqstring[s]);
+      resSize = seq.length();
+      resSize -= resSize % 3;
+
+      for (res = 0; res < resSize; res += 3)
       {
-        System.out.println("COPT HERE");
-        continue;
+        String codon = seq.substring(res, res + 3);
+        codon = codon.replace('U', 'T');
+        String aa = ResidueProperties.codonTranslate(codon);
+        if (aa == null)
+        {
+          protein.append(viewport.getGapCharacter());
+        }
+        else if (aa.equals("STOP"))
+        {
+          protein.append("X");
+        }
+        else
+        {
+          protein.append(aa);
+        }
       }
+      newSeq[s] = new Sequence(selection[s].getName(),
+                               protein.toString());
+    }
 
-      aSize = viewport.alignment.getWidth() / 3;
-      jalview.datamodel.Annotation[] anots =
-          new jalview.datamodel.Annotation[aSize];
+    AlignmentI al = new Alignment(newSeq);
+    al.setDataset(null);
 
-      for (a = 0; a < viewport.alignment.getWidth(); a++)
+    ////////////////////////////////
+    // Copy annotations across
+    jalview.datamodel.AlignmentAnnotation[] annotations
+        = viewport.alignment.getAlignmentAnnotation();
+    int a, aSize;
+    if (annotations != null)
+    {
+      for (int i = 0; i < annotations.length; i++)
       {
-        if (annotations[i].annotations[a] == null
-            || annotations[i].annotations[a] == null)
+        if (annotations[i] == viewport.quality ||
+            annotations[i] == viewport.conservation ||
+            annotations[i] == viewport.consensus)
+        {
+          System.out.println("COPT HERE");
           continue;
+        }
 
-        anots[a / 3] = new Annotation(
-            annotations[i].annotations[a].displayCharacter,
-            annotations[i].annotations[a].description,
-            annotations[i].annotations[a].secondaryStructure,
-            annotations[i].annotations[a].value,
-            annotations[i].annotations[a].colour);
-      }
+        aSize = viewport.alignment.getWidth() / 3;
+        jalview.datamodel.Annotation[] anots =
+            new jalview.datamodel.Annotation[aSize];
+
+        for (a = 0; a < viewport.alignment.getWidth(); a++)
+        {
+          if (annotations[i].annotations[a] == null
+              || annotations[i].annotations[a] == null)
+          {
+            continue;
+          }
+
+          anots[a / 3] = new Annotation(
+              annotations[i].annotations[a].displayCharacter,
+              annotations[i].annotations[a].description,
+              annotations[i].annotations[a].secondaryStructure,
+              annotations[i].annotations[a].value,
+              annotations[i].annotations[a].colour);
+        }
 
-      jalview.datamodel.AlignmentAnnotation aa
-          = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-          annotations[i].description, anots);
-      al.addAnnotation(aa);
+        jalview.datamodel.AlignmentAnnotation aa
+            = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
+            annotations[i].description, anots);
+        al.addAnnotation(aa);
+      }
     }
-  }
 
     AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-    Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+    Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
                              DEFAULT_WIDTH,
                              DEFAULT_HEIGHT);
 
+  }
 
-
-
-}
-
-/**
- * DOCUMENT ME!
- *
- * @param String DOCUMENT ME!
- */
-public boolean parseFeaturesFile(String file, String type)
-{
+  /**
+   * 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);
+    try
+    {
+      featuresFile = new FeaturesFile(file,
+          type).parse(viewport.alignment.getDataset(),
+                      alignPanel.seqPanel.seqCanvas.
+                      getFeatureRenderer().featureColours,
+                      false);
     }
-    catch(Exception ex)
+    catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if(featuresFile)
+    if (featuresFile)
     {
       viewport.showSequenceFeatures = true;
       showSeqFeatures.setSelected(true);
@@ -3175,33 +3255,35 @@ public boolean parseFeaturesFile(String file, String type)
     }
 
     return featuresFile;
-}
+  }
 
-public void dragEnter(DropTargetDragEvent evt)
-{}
+  public void dragEnter(DropTargetDragEvent evt)
+  {}
 
-public void dragExit(DropTargetEvent evt)
-{}
+  public void dragExit(DropTargetEvent evt)
+  {}
 
-public void dragOver(DropTargetDragEvent evt)
-{}
+  public void dragOver(DropTargetDragEvent evt)
+  {}
 
-public void dropActionChanged(DropTargetDragEvent evt)
-{}
+  public void dropActionChanged(DropTargetDragEvent evt)
+  {}
 
-public void drop(DropTargetDropEvent evt)
-{
+  public void drop(DropTargetDropEvent evt)
+  {
     Transferable t = evt.getTransferable();
     java.util.List files = null;
 
     try
     {
-      DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+      DataFlavor uriListFlavor = new DataFlavor(
+          "text/uri-list;class=java.lang.String");
       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
       {
         //Works on Windows and MacOSX
         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+        files = (java.util.List) t.getTransferData(DataFlavor.
+            javaFileListFlavor);
       }
       else if (t.isDataFlavorSupported(uriListFlavor))
       {
@@ -3246,15 +3328,16 @@ public void drop(DropTargetDropEvent evt)
         ex.printStackTrace();
       }
     }
-}
+  }
 
   // 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)
+  public void loadJalviewDataFile(String file)
   {
-    try{
+    try
+    {
       String protocol = "File";
 
       if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
@@ -3267,12 +3350,12 @@ public void drop(DropTargetDropEvent evt)
 
       if (!isAnnotation)
       {
-        boolean isGroupsFile = parseFeaturesFile(file,protocol);
+        boolean isGroupsFile = parseFeaturesFile(file, protocol);
         if (!isGroupsFile)
         {
           String format = new IdentifyFile().Identify(file, protocol);
 
-          if(format.equalsIgnoreCase("JnetFile"))
+          if (format.equalsIgnoreCase("JnetFile"))
           {
             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
                 file, protocol);
@@ -3283,7 +3366,9 @@ public void drop(DropTargetDropEvent evt)
             alignPanel.repaint();
           }
           else
+          {
             new FileLoader().LoadFile(viewport, file, protocol, format);
+          }
         }
       }
       else
@@ -3292,7 +3377,8 @@ public void drop(DropTargetDropEvent evt)
         alignPanel.adjustAnnotationHeight();
       }
 
-    }catch(Exception ex)
+    }
+    catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -3310,7 +3396,7 @@ public void drop(DropTargetDropEvent evt)
 
   public void tabbedPane_mousePressed(MouseEvent e)
   {
-    if(SwingUtilities.isRightMouseButton(e))
+    if (SwingUtilities.isRightMouseButton(e))
     {
       String reply = JOptionPane.showInternalInputDialog(this,
           "Enter View Name",
@@ -3320,34 +3406,39 @@ public void drop(DropTargetDropEvent evt)
       if (reply != null)
       {
         viewport.viewName = reply;
-        tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+        tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
       }
     }
   }
 
-
   public AlignViewport getCurrentView()
   {
     return viewport;
   }
 }
 
-class PrintThread extends Thread
+class PrintThread
+    extends Thread
 {
   AlignmentPanel ap;
   public PrintThread(AlignmentPanel ap)
   {
-   this.ap = ap;
+    this.ap = ap;
   }
+
   static PageFormat pf;
   public void run()
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
 
     if (pf != null)
+    {
       printJob.setPrintable(ap, pf);
+    }
     else
+    {
       printJob.setPrintable(ap);
+    }
 
     if (printJob.printDialog())
     {