X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=aefc9c80630964b5f4f28388e4e59e4ae4643a24;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=077a2683e5a866fed21e4477ce740666d2cb2453;hpb=10764f0aed2b33ca4620c457c5a31b780af5c663;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 077a268..aefc9c8 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,251 +1,932 @@
-package jalview.gui;
-
-import jalview.jbgui.GUserDefinedColours;
-import jalview.datamodel.*;
-import jalview.io.*;
-import javax.swing.*;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.event.*;
-import jalview.schemes.*;
-import java.io.*;
-import java.util.*;
-
-
-public class UserDefinedColours extends GUserDefinedColours implements ChangeListener
-{
-
-  AlignmentPanel ap;
-  SequenceGroup seqGroup;
-  JButton selectedButton;
-  Vector oldColours = new Vector();
-  ColourSchemeI oldColourScheme;
-  JInternalFrame frame;
-
-  public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
-  {
-    super();
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "User defined colours", 450,530, false );
-    if(System.getProperty("os.name").startsWith("Mac"))
-      frame.setSize(450,560);
-
-    if(sg!=null)
-        frame.setTitle( frame.getTitle()+ " ("+sg.getName()+")");
-
-    colorChooser.getSelectionModel().addChangeListener(this);
-
-    this.ap = ap;
-    seqGroup = sg;
-
-
-      if (seqGroup != null)
-        oldColourScheme = seqGroup.cs;
-      else
-        oldColourScheme = ap.av.getGlobalColourScheme();
-
-      for (int i = 0; i < 20; i++)
-        makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
-                   "", ResidueProperties.aa[i]);
-
-      makeButton("B", "B");
-      makeButton("Z", "Z");
-      makeButton("X", "X");
-      makeButton("Gap", "'.','-',' '");
-
-      if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
-      {
-        loadColour(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
-      }
-  }
-
- public void stateChanged(ChangeEvent evt)
- {
-   if(selectedButton!=null)
-     selectedButton.setBackground( colorChooser.getColor() );
- }
-
-  public void colourButtonPressed(MouseEvent e)
-  {
-     selectedButton = (JButton)e.getSource();
-     colorChooser.setColor(selectedButton.getBackground());
-  }
-
-  void makeButton(String label, String aa)
-  {
-    final JButton button = new JButton();
-    Color col = Color.white;
-
-
-    try{
-      col = oldColourScheme.findColour(aa, -1);
-    }catch(Exception ex){}
-
-    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)
-      {
-        colourButtonPressed(e);
-      }
-    });
-
-    buttonPanel.add(button, null);
-  }
-
-
-  protected void okButton_actionPerformed(ActionEvent e)
-  {
-    applyButton_actionPerformed(null);
-    try{
-      frame.setClosed(true);
-    }catch(Exception ex){}
-  }
-
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
-
-    Color [] newColours = new Color[24];
-    for(int i=0; i<24; i++)
-    {
-          JButton button = (JButton)buttonPanel.getComponent(i);
-          newColours[i] = button.getBackground();
-    }
-
-    UserColourScheme ucs = new UserColourScheme();
-    ucs.setThreshold(0);
-    ucs.setColourScheme( newColours );
-
-    if(seqGroup!=null)
-      seqGroup.cs = ucs;
-    else
-      ap.av.setGlobalColourScheme(ucs);
-
-    ap.repaint();
-  }
-
-  protected void loadbutton_actionPerformed(ActionEvent e)
-  {
-    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());
-      loadColour(choice.getAbsolutePath());
-    }
-
-  }
-
-  public static UserColourScheme loadDefaultColours(String file)
-  {
-    UserColourScheme ucs = null;
-    try
-    {
-      BufferedReader in = new BufferedReader(new FileReader(file));
-      Color [] newColours = new Color[24];
-      for (int i = 0; i < 24; i++)
-      {
-        newColours[i] = new Color(Integer.parseInt(in.readLine()));
-      }
-
-      ucs = new UserColourScheme();
-      ucs.setThreshold(0);
-      ucs.setColourScheme(newColours);
-
-    }
-    catch (Exception ex)
-    {}
-
-    return ucs;
-  }
-
-  void loadColour(String file)
-  {
-    try
-    {
-      BufferedReader in = new BufferedReader(new FileReader(file));
-      for (int i = 0; i < 24; i++)
-      {
-        JButton button = (JButton) buttonPanel.getComponent(i);
-        Color c = new Color(Integer.parseInt(in.readLine()));
-        button.setBackground(c);
-      }
-
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", file);
-    }
-    catch (Exception ex)
-    {}
-
-  }
-
-  protected void savebutton_actionPerformed(ActionEvent e)
-  {
-    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();
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);
-
-      try{
-        PrintWriter out = new PrintWriter(new FileWriter(choice));
-        for(int i=0; i<24; i++)
-        {
-          JButton button = (JButton)buttonPanel.getComponent(i);
-          out.println(button.getBackground().getRGB() + "");
-        }
-
-        out.close();
-      }
-      catch(Exception ex)
-      {ex.printStackTrace();}
-    }
-
-  }
-
-  protected void cancelButton_actionPerformed(ActionEvent e)
-  {
-    UserColourScheme ucs = new UserColourScheme();
-    Color [] newColours = new Color[24];
-    for(int i=0; i<24; i++)
-    {
-          newColours[i] = (Color)oldColours.elementAt(i);
-          buttonPanel.getComponent(i).setBackground(newColours[i]);
-    }
-
-    ucs.setColourScheme( newColours );
-    if (seqGroup != null)
-      seqGroup.cs = ucs;
-    else
-      ap.av.setGlobalColourScheme(ucs);
-
-    ap.repaint();
-
-    try{
-      frame.setClosed(true);
-    }catch(Exception ex){}
-  }
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 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!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class UserDefinedColours extends GUserDefinedColours implements
+        ChangeListener
+{
+  AlignmentPanel ap;
+
+  SequenceGroup seqGroup;
+
+  Vector selectedButtons;
+
+  ColourSchemeI oldColourScheme;
+
+  JInternalFrame frame;
+
+  AppJmol jmol;
+
+  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 (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);
+        } 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();
+    }
+
+    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;
+  }
+
+  /**
+   * 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,
+              "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);
+
+    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);
+  }
+
+}