X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=a8afd43ba49fd21069d9347c66a951a7f3d34519;hb=7f7fc2e5533f7b00c86465f964e37c55bcf12fd7;hp=a96cf526a285ac27b53951b152c92191d6469a6c;hpb=577f505f54fe343e89f581461e780ea8308c20ec;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a96cf52..a8afd43 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,206 +1,862 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.jbgui.GUserDefinedColours;
 import jalview.datamodel.*;
-import javax.swing.*;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import javax.swing.event.*;
-import jalview.schemes.*;
+
 import java.io.*;
+
 import java.util.*;
 
+import javax.swing.*;
+import javax.swing.event.*;
+
 
-public class UserDefinedColours extends GUserDefinedColours implements ChangeListener
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class UserDefinedColours extends GUserDefinedColours
+    implements ChangeListener
 {
+    AlignmentPanel ap;
+    SequenceGroup seqGroup;
+    Vector selectedButtons;
+    ColourSchemeI oldColourScheme;
+    JInternalFrame frame;
+    MCview.PDBCanvas pdbcanvas;
+    Vector upperCaseButtons;
+    Vector lowerCaseButtons;
+
+
+    /**
+     * Creates a new UserDefinedColours object.
+     *
+     * @param ap DOCUMENT ME!
+     * @param sg DOCUMENT ME!
+     */
+    public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
+    {
+        super();
 
-  AlignmentPanel ap;
-  SequenceGroup seqGroup;
-  JButton selectedButton;
-  Vector oldColours = new Vector();
-  ColourSchemeI oldColourScheme;
-  JInternalFrame frame;
+        lcaseColour.setEnabled(false);
 
+        this.ap = ap;
+        seqGroup = sg;
 
-  public UserDefinedColours(JInternalFrame f, AlignmentPanel ap, SequenceGroup sg)
-  {
-    super();
-    colorChooser.getSelectionModel().addChangeListener(this);
-    this.ap = ap;
-    frame = f;
-    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);
 
-      if (seqGroup != null)
-        oldColourScheme = seqGroup.cs;
-      else
-        oldColourScheme = ap.av.getGlobalColourScheme();
+        showFrame();
+    }
 
-      for (int i = 0; i < 20; i++)
-        makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
-                   "", ResidueProperties.aa[i]);
+    public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
+    {
+        super();
+        pdbcanvas = pdb;
+
+        colorChooser.getSelectionModel().addChangeListener(this);
+
+        oldColourScheme = oldcs;
+
+        if (oldColourScheme instanceof UserColourScheme)
+        {
+              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+        }
+
+        resetButtonPanel(false);
+
+        showFrame();
 
-      makeButton("B", "B");
-      makeButton("Z", "Z");
-      makeButton("X", "X");
-      makeButton("'.','-',' '", "-");
+    }
+
+    void showFrame()
+    {
+      colorChooser.getSelectionModel().addChangeListener(this);
+      frame = new JInternalFrame();
+      frame.setContentPane(this);
+      Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
 
-      if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
+      if (seqGroup != null)
+            frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
+
+      if (System.getProperty("os.name").startsWith("Mac"))
       {
-        loadColour(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
+        frame.setSize(760, 370);
       }
+    }
 
+    void resetButtonPanel(boolean caseSensitive)
+    {
+      buttonPanel.removeAll();
 
-  }
 
- public void stateChanged(ChangeEvent evt)
- {
-   if(selectedButton!=null)
-     selectedButton.setBackground( colorChooser.getColor() );
- }
+      if(upperCaseButtons==null)
+        upperCaseButtons = new Vector();
 
-  public void colourButtonPressed(MouseEvent e)
-  {
-     selectedButton = (JButton)e.getSource();
-     colorChooser.setColor(selectedButton.getBackground());
-  }
+      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();
 
-  void makeButton(String label, String aa)
-  {
-    final JButton button = new JButton();
-    Color col = Color.white;
+        button = makeButton(label,
+                              ResidueProperties.aa[i],
+                              upperCaseButtons, i);
 
+        buttonPanel.add(button);
+      }
 
-    try{
-      col = oldColourScheme.findColour(aa, -1, null);
-    }catch(Exception ex){}
+        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));
 
-    button.setBackground(  col );
-    oldColours.addElement( col );
-    button.setText( label );
-    button.setForeground( col.darker().darker().darker() );
-    button.setFont(new java.awt.Font("Verdana", 1, 10));
-    button.addMouseListener(new java.awt.event.MouseAdapter()
-    {
-      public void mouseClicked(MouseEvent e)
+      if(!caseSensitive)
+      {
+        gridLayout.setRows(6);
+        gridLayout.setColumns(4);
+      }
+      else
       {
-        colourButtonPressed(e);
+        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);
+          }
       }
-    });
 
-    buttonPanel.add(button);
-  }
 
+      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();
+    }
 
-  protected void okButton_actionPerformed(ActionEvent e)
-  {
-    applyButton_actionPerformed(null);
-    try{
-      frame.setClosed(true);
-    }catch(Exception ex){}
-  }
 
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
-    UserColourScheme ucs = new UserColourScheme();
-    Color [] newColours = new Color[24];
-    for(int i=0; i<24; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void stateChanged(ChangeEvent evt)
     {
-          JButton button = (JButton)buttonPanel.getComponent(i);
-          newColours[i] = button.getBackground();
+        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());
+            }
+          }
+        }
     }
 
-    ucs.setThreshold(0);
-    ucs.setColourScheme( newColours );
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void colourButtonPressed(MouseEvent e)
+    {
+      if(selectedButtons == null)
+        selectedButtons = new Vector();
 
-    if(seqGroup!=null)
-      seqGroup.cs = ucs;
-    else
-      ap.av.setGlobalColourScheme(ucs);
+      JButton pressed = (JButton) e.getSource();
 
-    ap.RefreshPanels();
-  }
+      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;
+        }
 
-  protected void loadbutton_actionPerformed(ActionEvent e)
-  {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-    chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle("Load colour scheme");
-    chooser.setToolTipText("Load");
-    int value = chooser.showOpenDialog(this);
-    if (value == JFileChooser.APPROVE_OPTION)
+        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)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",  choice);
-      loadColour(choice);
+        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;
+
+          try
+          {
+            col = oldColourScheme.findColour(aa, -1);
+          }
+          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.repaint();
+        }
+        else if(ap!=null)
+        {
+            ap.alignFrame.changeColour(ucs);
+        }
+        else if(pdbcanvas!=null)
+        {
+          pdbcanvas.pdb.setColours(ucs);
+          pdbcanvas.updateSeqColours();
+        }
+    }
 
-  void loadColour(String file)
-  {
-    try
+    UserColourScheme getSchemeFromButtons()
     {
-      BufferedReader in = new BufferedReader(new FileReader(file));
+
+      Color[] newColours = new Color[24];
+
       for (int i = 0; i < 24; i++)
       {
-        JButton button = (JButton) buttonPanel.getComponent(i);
-        Color c = new Color(Integer.parseInt(in.readLine()));
-        button.setBackground(c);
+        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);
+      }
+
+      if(ap!=null)
+        ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+
+
+      return ucs;
     }
-    catch (Exception ex)
-    {}
 
-  }
 
-  protected void savebutton_actionPerformed(ActionEvent e)
-  {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-    chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle("Save colour scheme");
-    chooser.setToolTipText("Save");
-    int value = chooser.showSaveDialog(this);
-    if (value == JFileChooser.APPROVE_OPTION)
+
+    /**
+     * 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)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);
+         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);
+              }
+            }
 
-      try{
-        PrintWriter out = new PrintWriter(new FileWriter(choice));
-        for(int i=0; i<24; i++)
+        }
+        catch (Exception ex)
         {
-          JButton button = (JButton)buttonPanel.getComponent(i);
-          out.println(button.getBackground().getRGB() + "");
+            //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);
         }
 
-        out.close();
+       return ucs;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void savebutton_actionPerformed(ActionEvent e)
+    {
+      if(schemeName.getText().trim().length()<1)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              "User colour scheme must have a name!",
+                                              "No name for colour scheme",
+                                              JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
+      if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )
+      {
+        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."
+            +"\nContinue saving colour scheme as "+schemeName.getText()+"?",
+           "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
+        if(reply != JOptionPane.YES_OPTION)
+          return;
+
+         userColourSchemes.remove(schemeName.getText());
       }
-      catch(Exception ex)
-      {ex.printStackTrace();}
+        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.repaint();
+      }
 
-  protected void cancelButton_actionPerformed(ActionEvent e)
-  {
-    UserColourScheme ucs = new UserColourScheme();
-    Color [] newColours = new Color[24];
-    for(int i=0; i<24; i++)
+      if(pdbcanvas!=null)
+      {
+        pdbcanvas.pdb.setColours(oldColourScheme);
+      }
+
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
+    }
+
+
+    static Hashtable userColourSchemes;
+
+    public static Hashtable getUserColourSchemes()
     {
-          newColours[i] = (Color)oldColours.elementAt(i);
-          buttonPanel.getComponent(i).setBackground(newColours[i]);
+      return userColourSchemes;
     }
 
-    ucs.setColourScheme( newColours );
-    if (seqGroup != null)
-      seqGroup.cs = ucs;
-    else
-      ap.av.setGlobalColourScheme(ucs);
+    public static void initUserColourSchemes(String files)
+    {
+      userColourSchemes = new Hashtable();
 
-    ap.RefreshPanels();
+      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);
+    }
 
 }