X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=001b2323d34be58ef353804711951da2efa357ab;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=e85a74cb7873bc5524cbe536b13787e07aa59c25;hpb=fd621a25427a759de0268471f753083bed5e1b53;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index e85a74c..001b232 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
@@ -18,25 +18,18 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import java.awt.*;
+import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
 
-
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -44,508 +37,893 @@ import javax.swing.event.*;
  * @author $author$
  * @version $Revision$
  */
-public class UserDefinedColours extends GUserDefinedColours
-    implements ChangeListener
+public class UserDefinedColours
+    extends GUserDefinedColours implements ChangeListener
 {
-    AlignmentPanel ap;
-    SequenceGroup seqGroup;
-    Vector selectedButtons;
-    ColourSchemeI oldColourScheme;
-    JInternalFrame frame;
-
-    /**
-     * Creates a new UserDefinedColours object.
-     *
-     * @param ap DOCUMENT ME!
-     * @param sg DOCUMENT ME!
-     */
-    public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
-    {
-        super();
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
-
-        if (System.getProperty("os.name").startsWith("Mac"))
-        {
-            frame.setSize(450, 560);
-        }
+  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();
+
+    lcaseColour.setEnabled(false);
+
+    this.ap = ap;
+    seqGroup = sg;
+
+    if (seqGroup != null)
+    {
+      oldColourScheme = seqGroup.cs;
+    }
+    else
+    {
+      oldColourScheme = ap.av.getGlobalColourScheme();
+    }
 
-        if (sg != null)
-        {
-            frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");
-        }
+    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);
+    }
 
-        colorChooser.getSelectionModel().addChangeListener(this);
+    showFrame();
+  }
 
-        this.ap = ap;
-        seqGroup = sg;
+  public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
+  {
+    super();
+    pdbcanvas = pdb;
 
-        if (seqGroup != null)
-        {
-            oldColourScheme = seqGroup.cs;
-        }
-        else
-        {
-            oldColourScheme = ap.av.getGlobalColourScheme();
-        }
+    colorChooser.getSelectionModel().addChangeListener(this);
 
-        if (oldColourScheme instanceof UserColourScheme)
-        {
-              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
-        }
-        for (int i = 0; i < 20; i++)
-        {
-            makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
-                "", ResidueProperties.aa[i]);
-        }
+    oldColourScheme = oldcs;
 
-        makeButton("B", "B");
-        makeButton("Z", "Z");
-        makeButton("X", "X");
-        makeButton("Gap", "-");
+    if (oldColourScheme instanceof UserColourScheme)
+    {
+      schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void stateChanged(ChangeEvent evt)
+    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)
     {
-        if (selectedButtons != null)
-        {
-          JButton button;
-          for(int i=0; i<selectedButtons.size(); i++)
-          {
-            button = (JButton)selectedButtons.elementAt(i);
-            button.setBackground(colorChooser.getColor());
-            button.setForeground( button.getBackground().brighter().brighter().brighter());
-          }
-        }
+      frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void colourButtonPressed(MouseEvent e)
+    if (System.getProperty("os.name").startsWith("Mac"))
     {
-      if(selectedButtons == null)
-        selectedButtons = new Vector();
+      frame.setSize(760, 370);
+    }
+  }
+
+  void resetButtonPanel(boolean caseSensitive)
+  {
+    buttonPanel.removeAll();
 
-      JButton pressed = (JButton) e.getSource();
+    if (upperCaseButtons == null)
+    {
+      upperCaseButtons = new Vector();
+    }
 
-      if(e.isShiftDown())
+    JButton button;
+    String label;
+    for (int i = 0; i < 20; i++)
+    {
+      if (caseSensitive)
       {
-        JButton start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
-        JButton end = (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;
-        }
+        label = ResidueProperties.aa[i];
+      }
+      else
+      {
+        label = ResidueProperties.aa2Triplet.get
+            (ResidueProperties.aa[i]).toString();
+      }
 
-        if(startIndex > endIndex)
-        {
-          int temp = startIndex;
-          startIndex = endIndex;
-          endIndex = temp;
-        }
+      button = makeButton(label,
+                          ResidueProperties.aa[i],
+                          upperCaseButtons, i);
 
-        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);
-          }
-        }
+      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();
       }
-      else if(!e.isControlDown())
+
+      for (int i = 0; i < 20; i++)
       {
-        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);
+        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());
       }
-      else if(e.isControlDown())
+      if (button == lcaseColour)
       {
-        if(selectedButtons.contains(pressed))
-        {
-          pressed.setForeground(pressed.getBackground().darker().darker());
-          selectedButtons.remove(pressed);
-        }
-        else
+        for (int i = 0; i < lowerCaseButtons.size(); i++)
         {
-          pressed.setForeground( pressed.getBackground().brighter().brighter());
-          selectedButtons.addElement(pressed);
+          button = (JButton) lowerCaseButtons.elementAt(i);
+          button.setBackground(colorChooser.getColor());
+          button.setForeground(button.getBackground().brighter().brighter().
+                               brighter());
         }
       }
-
-      if(selectedButtons.size()>0)
-      colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void colourButtonPressed(MouseEvent e)
+  {
+    if (selectedButtons == null)
+    {
+      selectedButtons = new Vector();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param label DOCUMENT ME!
-     * @param aa DOCUMENT ME!
-     */
-    void makeButton(String label, String aa)
+    JButton pressed = (JButton) e.getSource();
+
+    if (e.isShiftDown())
     {
-        final JButton button = new JButton();
-        Color col = Color.white;
+      JButton start, end = (JButton) e.getSource();
+      if (selectedButtons.size() > 0)
+      {
+        start = (JButton) selectedButtons.elementAt(selectedButtons.size() - 1);
+      }
+      else
+      {
+        start = (JButton) e.getSource();
+      }
 
-        try
+      int startIndex = 0, endIndex = 0;
+      for (int b = 0; b < buttonPanel.getComponentCount(); b++)
+      {
+        if (buttonPanel.getComponent(b) == start)
         {
-            col = oldColourScheme.findColour(aa, -1);
+          startIndex = b;
         }
-        catch (Exception ex)
+        if (buttonPanel.getComponent(b) == end)
         {
-        //  ex.printStackTrace();
+          endIndex = b;
         }
+      }
 
-        button.setBackground(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)
-                {
-                    colourButtonPressed(e);
-                }
-            });
+      if (startIndex > endIndex)
+      {
+        int temp = startIndex;
+        startIndex = endIndex;
+        endIndex = temp;
+      }
 
-        buttonPanel.add(button, null);
+      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);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void okButton_actionPerformed(ActionEvent e)
+    }
+    else if (e.isControlDown())
     {
-        applyButton_actionPerformed(null);
+      if (selectedButtons.contains(pressed))
+      {
+        pressed.setForeground(pressed.getBackground().darker().darker());
+        selectedButtons.remove(pressed);
+      }
+      else
+      {
+        pressed.setForeground(pressed.getBackground().brighter().brighter());
+        selectedButtons.addElement(pressed);
+      }
+    }
 
-        try
-        {
-            frame.setClosed(true);
-        }
-        catch (Exception ex)
+    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;
+
+      try
+      {
+        col = oldColourScheme.findColour(aa.charAt(0), -1);
+      }
+      catch (Exception ex)
+      {}
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void applyButton_actionPerformed(ActionEvent e)
+    if (caseSensitive.isSelected())
+    {
+      button.setMargin(new java.awt.Insets(2, 2, 2, 2));
+    }
+    else
     {
-        UserColourScheme ucs = getSchemeFromGUI();
-        ucs.setName(schemeName.getText());
+      button.setMargin(new java.awt.Insets(2, 14, 2, 14));
+    }
 
-        if (seqGroup != null)
-        {
-            seqGroup.cs = ucs;
-            ap.repaint();
-        }
-        else
-        {
-            ap.alignFrame.changeColour(ucs);
-        }
+    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();
+    }
+  }
 
-    UserColourScheme getSchemeFromGUI()
+  UserColourScheme getSchemeFromButtons()
+  {
+
+    Color[] newColours = new Color[24];
+
+    for (int i = 0; i < 24; i++)
     {
-      Color[] newColours = new Color[24];
+      JButton button = (JButton) upperCaseButtons.elementAt(i);
+      newColours[i] = button.getBackground();
+    }
 
-      for (int i = 0; i < 24; i++)
+    UserColourScheme ucs = new UserColourScheme(newColours);
+
+    if (caseSensitive.isSelected())
+    {
+      newColours = new Color[23];
+      for (int i = 0; i < 23; i++)
       {
-        JButton button = (JButton) buttonPanel.getComponent(i);
+        JButton button = (JButton) lowerCaseButtons.elementAt(i);
         newColours[i] = button.getBackground();
       }
+      ucs.setLowerCaseColours(newColours);
+    }
 
-      UserColourScheme ucs = new UserColourScheme(newColours);
+    if (ap != null)
+    {
       ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
-
-      return ucs;
     }
 
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void loadbutton_actionPerformed(ActionEvent e)
+    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)
     {
-        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");
+      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);
 
-        int value = chooser.showOpenDialog(this);
+      UserColourScheme ucs = loadColours(choice.getAbsolutePath());
+      Color[] colors = ucs.getColours();
+      schemeName.setText(ucs.getName());
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
+      if (ucs.getLowerCaseColours() != null)
+      {
+        caseSensitive.setSelected(true);
+        lcaseColour.setEnabled(true);
+        resetButtonPanel(true);
+        for (int i = 0; i < lowerCaseButtons.size(); i++)
         {
-            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());
+          JButton button = (JButton) lowerCaseButtons.elementAt(i);
+          button.setBackground(ucs.getLowerCaseColours()[i]);
+        }
 
-            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
+      }
+      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]);
+      }
 
-            UserColourScheme ucs = loadColours(choice.getAbsolutePath());
-            Color[] colors = ucs.getColours();
-            schemeName.setText(ucs.getName());
+    }
+  }
+
+  /**
+   * 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("|"));
+      }
 
-            for (int i = 0; i < colors.length; i++)
-            {
-                JButton button = (JButton) buttonPanel.getComponent(i);
-                button.setBackground(colors[i]);
-            }
-        }
+      ret = loadColours(colours);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static UserColourScheme loadDefaultColours()
+    if (ret == null)
     {
-        String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
-        if ( colours != null)
-        {
-          if(colours.indexOf("|")>-1)
-            colours = colours.substring(0, colours.indexOf("|"));
+      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();
 
-            return loadColours(colours);
+      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
         {
-          Color[] newColours = new Color[24];
-          for (int i = 0; i < 24; i++)
+          index = ResidueProperties.aaIndex[name.charAt(0)];
+        }
+        if (index == -1)
+        {
+          continue;
+        }
+
+        if (name.toLowerCase().equals(name))
+        {
+          if (lowerCase == null)
           {
-            newColours[i] = Color.white;
+            lowerCase = new Color[23];
           }
-          return new UserColourScheme(newColours);
+          caseSensitive = true;
+          lowerCase[index] = new Color(Integer.parseInt(
+              jucs.getColour(i).getRGB(), 16));
         }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param file DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    static UserColourScheme loadColours(String file)
-    {
-         UserColourScheme ucs = null;
-         Color[]  newColours = null;
+        else
+        {
+          newColours[index] = new Color(Integer.parseInt(
+              jucs.getColour(i).getRGB(), 16));
+        }
+      }
 
-        try
+      if (newColours != null)
+      {
+        ucs = new UserColourScheme(newColours);
+        ucs.setName(jucs.getSchemeName());
+        if (caseSensitive)
         {
-            InputStreamReader in = new InputStreamReader(new FileInputStream(
-                        file), "UTF-8");
+          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);
+        jalview.binding.JalviewUserColours jucs
+            = new jalview.binding.JalviewUserColours();
 
-            newColours = new Color[jucs.getColourCount()];
+        jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
 
-            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() );
-            }
+        newColours = new Color[jucs.getColourCount()];
 
+        for (int i = 0; i < 24; i++)
+        {
+          newColours[i] = new Color(Integer.parseInt(
+              jucs.getColour(i).getRGB(), 16));
         }
-        catch (Exception ex)
+        if (newColours != null)
         {
-            System.out.println("Error loading User ColourFile\n"+ex);
+          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;
+    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;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void savebutton_actionPerformed(ActionEvent e)
+    if (userColourSchemes != null &&
+        userColourSchemes.containsKey(schemeName.getText()))
     {
-      if(schemeName.getText().trim().length()<1)
+      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)
       {
-        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());
+    }
+    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);
 
-         userColourSchemes.remove(schemeName.getText());
+    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);
       }
-        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");
+      userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
 
-        int value = chooser.showSaveDialog(this);
+      ap.alignFrame.updateUserColourMenu();
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
+      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++)
         {
-            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(), getSchemeFromGUI());
-
-            ap.alignFrame.updateUserColourMenu();
-
-            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
-
-            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
-            ucs.setSchemeName(schemeName.getText());
-            try
-            {
-                PrintWriter out = new PrintWriter(new OutputStreamWriter(
-                            new FileOutputStream(choice), "UTF-8"));
-
-                for (int i = 0; i < 24; i++)
-                {
-                    JButton button = (JButton) buttonPanel.getComponent(i);
-                    jalview.binding.Colour col = new jalview.binding.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();
-            }
+          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);
         }
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void cancelButton_actionPerformed(ActionEvent e)
+        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
-        {
-            ap.av.setGlobalColourScheme(oldColourScheme);
-        }
+      if (seqGroup != null)
+      {
+        seqGroup.cs = oldColourScheme;
+      }
+      else if (ap != null)
+      {
+        ap.av.setGlobalColourScheme(oldColourScheme);
+      }
+      ap.repaint();
+    }
 
-        ap.repaint();
+    if (pdbcanvas != null)
+    {
+      pdbcanvas.pdb.setColours(oldColourScheme);
+    }
 
-        try
-        {
-            frame.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
+    try
+    {
+      frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {
     }
+  }
+
+  static Hashtable userColourSchemes;
 
+  public static Hashtable getUserColourSchemes()
+  {
+    return userColourSchemes;
+  }
 
-    static Hashtable userColourSchemes;
+  public static void initUserColourSchemes(String files)
+  {
+    userColourSchemes = new Hashtable();
 
-    public static Hashtable getUserColourSchemes()
+    if (files == null || files.length() == 0)
     {
-      return userColourSchemes;
+      return;
     }
 
-    public static void initUserColourSchemes(String files)
+    // 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())
     {
-      userColourSchemes = new Hashtable();
-
-      if(files==null)
-        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
       {
-        String file = st.nextToken();
-        try
+        UserColourScheme ucs = loadColours(file);
+        if (ucs != null)
         {
-          UserColourScheme ucs = loadColours(file);
-          if (ucs != null)
+          if (coloursFound.length() > 0)
           {
-            if (coloursFound.length() > 0)
-              coloursFound.append("|");
-            coloursFound.append(file);
-            userColourSchemes.put(ucs.getName(), ucs);
+            coloursFound.append("|");
           }
+          coloursFound.append(file);
+          userColourSchemes.put(ucs.getName(), ucs);
         }
-        catch (Exception ex)
+      }
+      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))
         {
-          System.out.println("Error loading User ColourFile\n" + ex);
+          if (coloursFound.length() > 0)
+          {
+            coloursFound.append("|");
+          }
+          coloursFound.append(file);
+          userColourSchemes.put(ucs.getName(), ucs);
         }
       }
-      if (!files.equals(coloursFound.toString()))
+      catch (Exception ex)
       {
-        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
+        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);
+  }
+
 }