diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
old mode 100755
new mode 100644
index a104ad9..bf5c561
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,945 +1,962 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
  *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
 import jalview.datamodel.SequenceGroup;
 import jalview.io.JalviewFileChooser;
 import jalview.jbgui.GUserDefinedColours;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
 import java.awt.event.MouseEvent;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.Hashtable;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
 import javax.swing.JButton;
 import javax.swing.JInternalFrame;
 import javax.swing.JOptionPane;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 
 /**
  * DOCUMENT ME!
  * 
  * @author $author$
  * @version $Revision$
  */
 public class UserDefinedColours extends GUserDefinedColours implements
         ChangeListener
 {
   AlignmentPanel ap;
 
   SequenceGroup seqGroup;
 
-  Vector selectedButtons;
+  Vector<JButton> selectedButtons;
 
   ColourSchemeI oldColourScheme;
 
   JInternalFrame frame;
 
   AppJmol jmol;
 
-  Vector upperCaseButtons;
+  Vector<JButton> upperCaseButtons;
 
-  Vector lowerCaseButtons;
+  Vector<JButton> lowerCaseButtons;
 
   /**
    * Creates a new UserDefinedColours object.
    * 
    * @param ap
    *          DOCUMENT ME!
    * @param sg
    *          DOCUMENT ME!
    */
   public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
   {
     super();
 
     lcaseColour.setEnabled(false);
 
     this.ap = ap;
     seqGroup = sg;
 
     if (seqGroup != null)
     {
       oldColourScheme = seqGroup.cs;
     }
     else
     {
       oldColourScheme = ap.av.getGlobalColourScheme();
     }
 
     if (oldColourScheme instanceof UserColourScheme)
     {
       schemeName.setText(((UserColourScheme) oldColourScheme).getName());
       if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
       {
         caseSensitive.setSelected(true);
         lcaseColour.setEnabled(true);
         resetButtonPanel(true);
       }
       else
       {
         resetButtonPanel(false);
       }
     }
     else
     {
       resetButtonPanel(false);
     }
 
     showFrame();
   }
 
   public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs)
   {
     super();
     this.jmol = jmol;
 
     colorChooser.getSelectionModel().addChangeListener(this);
 
     oldColourScheme = oldcs;
 
     if (oldColourScheme instanceof UserColourScheme)
     {
       schemeName.setText(((UserColourScheme) oldColourScheme).getName());
     }
 
     resetButtonPanel(false);
 
     showFrame();
 
   }
 
   void showFrame()
   {
     colorChooser.getSelectionModel().addChangeListener(this);
     frame = new JInternalFrame();
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
 
     if (seqGroup != null)
     {
       frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
     }
 
     if (new jalview.util.Platform().isAMac())
     {
       frame.setSize(760, 370);
     }
   }
 
   void resetButtonPanel(boolean caseSensitive)
   {
     buttonPanel.removeAll();
 
     if (upperCaseButtons == null)
     {
       upperCaseButtons = new Vector();
     }
 
     JButton button;
     String label;
     for (int i = 0; i < 20; i++)
     {
       if (caseSensitive)
       {
         label = ResidueProperties.aa[i];
       }
       else
       {
         label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
                 .toString();
       }
 
       button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
               i);
 
       buttonPanel.add(button);
     }
 
     buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
     buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
     buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
     buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
 
     if (!caseSensitive)
     {
       gridLayout.setRows(6);
       gridLayout.setColumns(4);
     }
     else
     {
       gridLayout.setRows(7);
       int cols = 7;
       gridLayout.setColumns(cols + 1);
 
       if (lowerCaseButtons == null)
       {
         lowerCaseButtons = new Vector();
       }
 
       for (int i = 0; i < 20; i++)
       {
         int row = i / cols + 1;
         int index = (row * cols) + i;
         button = makeButton(ResidueProperties.aa[i].toLowerCase(),
                 ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
 
         buttonPanel.add(button, index);
       }
     }
 
     if (caseSensitive)
     {
       buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
       buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
       buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
     }
 
     buttonPanel.validate();
     validate();
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param evt
    *          DOCUMENT ME!
    */
   public void stateChanged(ChangeEvent evt)
   {
     if (selectedButtons != null)
     {
       JButton button = null;
       for (int i = 0; i < selectedButtons.size(); i++)
       {
         button = (JButton) selectedButtons.elementAt(i);
         button.setBackground(colorChooser.getColor());
         button.setForeground(button.getBackground().brighter().brighter()
                 .brighter());
       }
       if (button == lcaseColour)
       {
         for (int i = 0; i < lowerCaseButtons.size(); i++)
         {
           button = (JButton) lowerCaseButtons.elementAt(i);
           button.setBackground(colorChooser.getColor());
           button.setForeground(button.getBackground().brighter().brighter()
                   .brighter());
         }
       }
     }
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
    */
   public void colourButtonPressed(MouseEvent e)
   {
     if (selectedButtons == null)
     {
       selectedButtons = new Vector();
     }
 
     JButton pressed = (JButton) e.getSource();
 
     if (e.isShiftDown())
     {
       JButton start, end = (JButton) e.getSource();
       if (selectedButtons.size() > 0)
       {
         start = (JButton) selectedButtons
                 .elementAt(selectedButtons.size() - 1);
       }
       else
       {
         start = (JButton) e.getSource();
       }
 
       int startIndex = 0, endIndex = 0;
       for (int b = 0; b < buttonPanel.getComponentCount(); b++)
       {
         if (buttonPanel.getComponent(b) == start)
         {
           startIndex = b;
         }
         if (buttonPanel.getComponent(b) == end)
         {
           endIndex = b;
         }
       }
 
       if (startIndex > endIndex)
       {
         int temp = startIndex;
         startIndex = endIndex;
         endIndex = temp;
       }
 
       for (int b = startIndex; b <= endIndex; b++)
       {
         JButton button = (JButton) buttonPanel.getComponent(b);
         if (!selectedButtons.contains(button))
         {
           button.setForeground(button.getBackground().brighter().brighter());
           selectedButtons.add(button);
         }
       }
     }
     else if (!e.isControlDown())
     {
       for (int b = 0; b < selectedButtons.size(); b++)
       {
         JButton button = (JButton) selectedButtons.elementAt(b);
         button.setForeground(button.getBackground().darker().darker());
       }
       selectedButtons.clear();
       pressed.setForeground(pressed.getBackground().brighter().brighter());
       selectedButtons.addElement(pressed);
 
     }
     else if (e.isControlDown())
     {
       if (selectedButtons.contains(pressed))
       {
         pressed.setForeground(pressed.getBackground().darker().darker());
         selectedButtons.remove(pressed);
       }
       else
       {
         pressed.setForeground(pressed.getBackground().brighter().brighter());
         selectedButtons.addElement(pressed);
       }
     }
 
     if (selectedButtons.size() > 0)
     {
       colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
               .getBackground());
     }
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param label
    *          DOCUMENT ME!
    * @param aa
    *          DOCUMENT ME!
    */
   JButton makeButton(String label, String aa, Vector caseSensitiveButtons,
           int buttonIndex)
   {
     final JButton button;
     Color col;
 
     if (buttonIndex < caseSensitiveButtons.size())
     {
       button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
       col = button.getBackground();
     }
     else
     {
       button = new JButton();
       button.addMouseListener(new java.awt.event.MouseAdapter()
       {
         public void mouseClicked(MouseEvent e)
         {
           colourButtonPressed(e);
         }
       });
 
       caseSensitiveButtons.addElement(button);
 
       col = Color.white;
       if (oldColourScheme != null)
       {
         try
         {
           col = oldColourScheme.findColour(aa.charAt(0), -1, null);
         } catch (Exception ex)
         {
         }
       }
     }
 
     if (caseSensitive.isSelected())
     {
       button.setMargin(new java.awt.Insets(2, 2, 2, 2));
     }
     else
     {
       button.setMargin(new java.awt.Insets(2, 14, 2, 14));
     }
 
     button.setBackground(col);
     button.setText(label);
     button.setForeground(col.darker().darker().darker());
     button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
 
     return button;
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
    */
   protected void okButton_actionPerformed(ActionEvent e)
   {
     applyButton_actionPerformed(null);
 
     try
     {
       frame.setClosed(true);
     } catch (Exception ex)
     {
     }
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
    */
   protected void applyButton_actionPerformed(ActionEvent e)
   {
     UserColourScheme ucs = getSchemeFromButtons();
     ucs.setName(schemeName.getText());
 
     if (seqGroup != null)
     {
       seqGroup.cs = ucs;
       ap.paintAlignment(true);
     }
     else if (ap != null)
     {
       ap.alignFrame.changeColour(ucs);
     }
     else if (jmol != null)
     {
       jmol.setJalviewColourScheme(ucs);
     }
   }
 
   UserColourScheme getSchemeFromButtons()
   {
 
     Color[] newColours = new Color[24];
 
-    for (int i = 0; i < 24; i++)
-    {
-      JButton button = (JButton) upperCaseButtons.elementAt(i);
-      newColours[i] = button.getBackground();
+    int length = upperCaseButtons.size();
+    if (length<24){
+    	int i = 0;
+    	for (JButton btn:upperCaseButtons){
+    		newColours[i] = btn.getBackground();
+    		i++;
+    	}
+    }else{
+	    for (int i = 0; i < 24; i++)
+	    {
+	      JButton button = (JButton) upperCaseButtons.elementAt(i);
+	      newColours[i] = button.getBackground();
+	    }
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
 
     if (caseSensitive.isSelected())
     {
-      newColours = new Color[23];
-      for (int i = 0; i < 23; i++)
-      {
-        JButton button = (JButton) lowerCaseButtons.elementAt(i);
-        newColours[i] = button.getBackground();
-      }
-      ucs.setLowerCaseColours(newColours);
+    	newColours = new Color[23];
+        length = lowerCaseButtons.size();
+        if (length<23){
+        	int i = 0;
+        	for (JButton btn:lowerCaseButtons){
+        		newColours[i] = btn.getBackground();
+        		i++;
+        	}
+        }else{
+    	    for (int i = 0; i < 23; i++)
+    	    {
+    	      JButton button = (JButton) lowerCaseButtons.elementAt(i);
+    	      newColours[i] = button.getBackground();
+    	    }
+        }
     }
 
     if (ap != null)
     {
       ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
 
     return ucs;
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
    */
   protected void loadbutton_actionPerformed(ActionEvent e)
   {
     upperCaseButtons = new Vector();
     lowerCaseButtons = new Vector();
 
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "jc" }, new String[]
             { "Jalview User Colours" }, "Jalview User Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Load colour scheme");
     chooser.setToolTipText("Load");
 
     int value = chooser.showOpenDialog(this);
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       File choice = chooser.getSelectedFile();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
       String defaultColours = jalview.bin.Cache.getDefault(
               "USER_DEFINED_COLOURS", choice.getPath());
       if (defaultColours.indexOf(choice.getPath()) == -1)
       {
         defaultColours = defaultColours.concat("|")
                 .concat(choice.getPath());
       }
 
       jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
       UserColourScheme ucs = loadColours(choice.getAbsolutePath());
       Color[] colors = ucs.getColours();
       schemeName.setText(ucs.getName());
 
       if (ucs.getLowerCaseColours() != null)
       {
         caseSensitive.setSelected(true);
         lcaseColour.setEnabled(true);
         resetButtonPanel(true);
         for (int i = 0; i < lowerCaseButtons.size(); i++)
         {
           JButton button = (JButton) lowerCaseButtons.elementAt(i);
           button.setBackground(ucs.getLowerCaseColours()[i]);
         }
 
       }
       else
       {
         caseSensitive.setSelected(false);
         lcaseColour.setEnabled(false);
         resetButtonPanel(false);
       }
 
       for (int i = 0; i < upperCaseButtons.size(); i++)
       {
         JButton button = (JButton) upperCaseButtons.elementAt(i);
         button.setBackground(colors[i]);
       }
 
     }
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
   public static UserColourScheme loadDefaultColours()
   {
     UserColourScheme ret = null;
 
     String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
     if (colours != null)
     {
       if (colours.indexOf("|") > -1)
       {
         colours = colours.substring(0, colours.indexOf("|"));
       }
 
       ret = loadColours(colours);
     }
 
     if (ret == null)
     {
       Color[] newColours = new Color[24];
       for (int i = 0; i < 24; i++)
       {
         newColours[i] = Color.white;
       }
       ret = new UserColourScheme(newColours);
     }
 
     return ret;
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param file
    *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
   static UserColourScheme loadColours(String file)
   {
     UserColourScheme ucs = null;
     Color[] newColours = null;
     try
     {
       InputStreamReader in = new InputStreamReader(
               new FileInputStream(file), "UTF-8");
 
       jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
 
       org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
               jucs);
       jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
               .unmarshal(in);
 
       newColours = new Color[24];
 
       Color[] lowerCase = null;
       boolean caseSensitive = false;
 
       String name;
       int index;
       for (int i = 0; i < jucs.getColourCount(); i++)
       {
         name = jucs.getColour(i).getName();
         if (ResidueProperties.aa3Hash.containsKey(name))
         {
           index = ((Integer) ResidueProperties.aa3Hash.get(name))
                   .intValue();
         }
         else
         {
           index = ResidueProperties.aaIndex[name.charAt(0)];
         }
         if (index == -1)
         {
           continue;
         }
 
         if (name.toLowerCase().equals(name))
         {
           if (lowerCase == null)
           {
             lowerCase = new Color[23];
           }
           caseSensitive = true;
           lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
                   .getRGB(), 16));
         }
         else
         {
           newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
                   .getRGB(), 16));
         }
       }
 
       if (newColours != null)
       {
         ucs = new UserColourScheme(newColours);
         ucs.setName(jucs.getSchemeName());
         if (caseSensitive)
         {
           ucs.setLowerCaseColours(lowerCase);
         }
       }
 
     } catch (Exception ex)
     {
       // Could be Archive Jalview format
       try
       {
         InputStreamReader in = new InputStreamReader(new FileInputStream(
                 file), "UTF-8");
 
         jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
 
         jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
 
         newColours = new Color[jucs.getColourCount()];
 
         for (int i = 0; i < 24; i++)
         {
           newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
                   .getRGB(), 16));
         }
         if (newColours != null)
         {
           ucs = new UserColourScheme(newColours);
           ucs.setName(jucs.getSchemeName());
         }
       } catch (Exception ex2)
       {
         ex2.printStackTrace();
       }
 
       if (newColours == null)
       {
         System.out.println("Error loading User ColourFile\n" + ex);
       }
     }
 
     return ucs;
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
    */
   protected void savebutton_actionPerformed(ActionEvent e)
   {
     if (schemeName.getText().trim().length() < 1)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager.getString("label.user_colour_scheme_must_have_name"),
               MessageManager.getString("label.no_name_colour_scheme"), JOptionPane.WARNING_MESSAGE);
       return;
     }
 
     if (userColourSchemes != null
             && userColourSchemes.containsKey(schemeName.getText()))
     {
       int reply = JOptionPane.showInternalConfirmDialog(
               Desktop.desktop,
               MessageManager.formatMessage("label.colour_scheme_exists_overwrite", new String[]{schemeName.getText(),schemeName.getText()}),
               MessageManager.getString("label.duplicate_scheme_name"), JOptionPane.YES_NO_OPTION);
       if (reply != JOptionPane.YES_OPTION)
       {
         return;
       }
 
       userColourSchemes.remove(schemeName.getText());
     }
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "jc" }, new String[]
             { "Jalview User Colours" }, "Jalview User Colours");
 
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Save colour scheme");
     chooser.setToolTipText("Save");
 
     int value = chooser.showSaveDialog(this);
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
       String defaultColours = jalview.bin.Cache.getDefault(
               "USER_DEFINED_COLOURS", choice);
       if (defaultColours.indexOf(choice) == -1)
       {
         if (defaultColours.length() > 0)
         {
           defaultColours = defaultColours.concat("|");
         }
         defaultColours = defaultColours.concat(choice);
       }
 
       userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
 
       ap.alignFrame.updateUserColourMenu();
 
       jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
       jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
 
       ucs.setSchemeName(schemeName.getText());
       try
       {
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
                 new FileOutputStream(choice), "UTF-8"));
 
         for (int i = 0; i < buttonPanel.getComponentCount(); i++)
         {
           JButton button = (JButton) buttonPanel.getComponent(i);
           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
           col.setName(button.getText());
           col.setRGB(jalview.util.Format.getHexString(button
                   .getBackground()));
           ucs.addColour(col);
         }
 
         ucs.marshal(out);
         out.close();
       } catch (Exception ex)
       {
         ex.printStackTrace();
       }
     }
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
    */
   protected void cancelButton_actionPerformed(ActionEvent e)
   {
     if (ap != null)
     {
       if (seqGroup != null)
       {
         seqGroup.cs = oldColourScheme;
       }
       else if (ap != null)
       {
         ap.av.setGlobalColourScheme(oldColourScheme);
       }
       ap.paintAlignment(true);
     }
 
     if (jmol != null)
     {
       jmol.setJalviewColourScheme(oldColourScheme);
     }
 
     try
     {
       frame.setClosed(true);
     } catch (Exception ex)
     {
     }
   }
 
   static Hashtable userColourSchemes;
 
   public static Hashtable getUserColourSchemes()
   {
     return userColourSchemes;
   }
 
   public static void initUserColourSchemes(String files)
   {
     userColourSchemes = new Hashtable();
 
     if (files == null || files.length() == 0)
     {
       return;
     }
 
     // In case colours can't be loaded, we'll remove them
     // from the default list here.
     StringBuffer coloursFound = new StringBuffer();
     StringTokenizer st = new StringTokenizer(files, "|");
     while (st.hasMoreElements())
     {
       String file = st.nextToken();
       try
       {
         UserColourScheme ucs = loadColours(file);
         if (ucs != null)
         {
           if (coloursFound.length() > 0)
           {
             coloursFound.append("|");
           }
           coloursFound.append(file);
           userColourSchemes.put(ucs.getName(), ucs);
         }
       } catch (Exception ex)
       {
         System.out.println("Error loading User ColourFile\n" + ex);
       }
     }
     if (!files.equals(coloursFound.toString()))
     {
       if (coloursFound.toString().length() > 1)
       {
         jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
                 coloursFound.toString());
       }
       else
       {
         jalview.bin.Cache.applicationProperties
                 .remove("USER_DEFINED_COLOURS");
       }
     }
   }
 
   public static void removeColourFromDefaults(String target)
   {
     // The only way to find colours by name is to load them in
     // In case colours can't be loaded, we'll remove them
     // from the default list here.
 
     userColourSchemes = new Hashtable();
 
     StringBuffer coloursFound = new StringBuffer();
     StringTokenizer st = new StringTokenizer(
             jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
 
     while (st.hasMoreElements())
     {
       String file = st.nextToken();
       try
       {
         UserColourScheme ucs = loadColours(file);
         if (ucs != null && !ucs.getName().equals(target))
         {
           if (coloursFound.length() > 0)
           {
             coloursFound.append("|");
           }
           coloursFound.append(file);
           userColourSchemes.put(ucs.getName(), ucs);
         }
       } catch (Exception ex)
       {
         System.out.println("Error loading User ColourFile\n" + ex);
       }
     }
 
     if (coloursFound.toString().length() > 1)
     {
       jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
               coloursFound.toString());
     }
     else
     {
       jalview.bin.Cache.applicationProperties
               .remove("USER_DEFINED_COLOURS");
     }
 
   }
 
   public void caseSensitive_actionPerformed(ActionEvent e)
   {
     resetButtonPanel(caseSensitive.isSelected());
     lcaseColour.setEnabled(caseSensitive.isSelected());
   }
 
   public void lcaseColour_actionPerformed(ActionEvent e)
   {
     if (selectedButtons == null)
     {
       selectedButtons = new Vector();
     }
     else
     {
       selectedButtons.clear();
     }
     selectedButtons.add(lcaseColour);
   }
 
 }