From 9e46fb6245b28f14f01cb84d46d03cf5453e7010 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 30 Aug 2006 16:08:36 +0000
Subject: [PATCH] User colours are case sensitive

---
 src/jalview/gui/Jalview2XML.java           |   33 ++-
 src/jalview/gui/UserDefinedColours.java    |  331 +++++++++++++++++++++-------
 src/jalview/jbgui/GUserDefinedColours.java |   73 ++++--
 src/jalview/schemes/UserColourScheme.java  |   66 +++++-
 4 files changed, 395 insertions(+), 108 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index e65f37d..be03a9c 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -719,9 +719,21 @@ public class Jalview2XML
             for (int i = 0; i < colours.length; i++)
             {
                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+                col.setName(ResidueProperties.aa[i]);
                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
                 jbucs.addColour(col);
             }
+            if(ucs.getLowerCaseColours()!=null)
+            {
+              colours = ucs.getLowerCaseColours();
+              for (int i = 0; i < colours.length; i++)
+             {
+                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+                 col.setName(ResidueProperties.aa[i].toLowerCase());
+                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
+                 jbucs.addColour(col);
+             }
+            }
 
             id = "ucs" + userColours.indexOf(ucs);
             uc.setId(id);
@@ -748,16 +760,29 @@ public class Jalview2XML
             }
         }
 
-        int csize = colours.getUserColourScheme().getColourCount();
-        java.awt.Color[] newColours = new java.awt.Color[csize];
+        java.awt.Color[] newColours = new java.awt.Color[24];
 
-        for (int i = 0; i < csize; i++)
+        for (int i = 0; i < 24; i++)
         {
             newColours[i] = new java.awt.Color(Integer.parseInt(
                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
         }
 
-        return new jalview.schemes.UserColourScheme(newColours);
+        jalview.schemes.UserColourScheme ucs =
+            new jalview.schemes.UserColourScheme(newColours);
+
+        if (colours.getUserColourScheme().getColourCount() > 24)
+        {
+          newColours = new java.awt.Color[23];
+          for (int i = 0; i < 23; i++)
+          {
+            newColours[i] = new java.awt.Color(Integer.parseInt(
+                colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
+          }
+          ucs.setLowerCaseColours(newColours);
+        }
+
+        return ucs;
     }
 
     /**
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 8deec8e..2369049 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -53,6 +53,9 @@ public class UserDefinedColours extends GUserDefinedColours
     ColourSchemeI oldColourScheme;
     JInternalFrame frame;
     MCview.PDBCanvas pdbcanvas;
+    Vector upperCaseButtons;
+    Vector lowerCaseButtons;
+
 
     /**
      * Creates a new UserDefinedColours object.
@@ -63,63 +66,39 @@ public class UserDefinedColours extends GUserDefinedColours
     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(760, 370);
-        }
-
-        if (sg != null)
-        {
-            frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");
-        }
-
-        colorChooser.getSelectionModel().addChangeListener(this);
+        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());
-        }
-        for (int i = 0; i < 20; i++)
-        {
-            makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
-                "", ResidueProperties.aa[i]);
+          schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+          if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)
+          {
+            caseSensitive.setSelected(true);
+            lcaseColour.setEnabled(true);
+            resetButtonPanel(true);
+          }
+          else
+            resetButtonPanel(false);
         }
+        else
+           resetButtonPanel(false);
 
-        makeButton("B", "B");
-        makeButton("Z", "Z");
-        makeButton("X", "X");
-        makeButton("Gap", "-");
+        showFrame();
     }
 
     public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
     {
         super();
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
         pdbcanvas = pdb;
 
-        if (System.getProperty("os.name").startsWith("Mac"))
-        {
-            frame.setSize(760, 370);
-        }
-
         colorChooser.getSelectionModel().addChangeListener(this);
 
         oldColourScheme = oldcs;
@@ -128,16 +107,98 @@ public class UserDefinedColours extends GUserDefinedColours
         {
               schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
         }
-        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", "-");
+        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 (System.getProperty("os.name").startsWith("Mac"))
+      {
+        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();
     }
 
 
@@ -150,13 +211,22 @@ public class UserDefinedColours extends GUserDefinedColours
     {
         if (selectedButtons != null)
         {
-          JButton button;
+          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());
+            }
+          }
         }
     }
 
@@ -242,33 +312,53 @@ public class UserDefinedColours extends GUserDefinedColours
      * @param label DOCUMENT ME!
      * @param aa DOCUMENT ME!
      */
-    void makeButton(String label, String aa)
+    JButton makeButton(String label,
+                       String aa,
+                       Vector caseSensitiveButtons,
+                       int buttonIndex)
     {
-        final JButton button = new JButton();
-        Color col = Color.white;
+        final JButton button;
+        Color col;
 
-        try
+        if(buttonIndex<caseSensitiveButtons.size())
         {
-            col = oldColourScheme.findColour(aa, -1);
+          button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
+          col = button.getBackground();
         }
-        catch (Exception ex)
+        else
         {
-        //  ex.printStackTrace();
+          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", 1, 10));
-        button.addMouseListener(new java.awt.event.MouseAdapter()
-            {
-                public void mouseClicked(MouseEvent e)
-                {
-                    colourButtonPressed(e);
-                }
-            });
+        button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
 
-        buttonPanel.add(button, null);
+        return button;
     }
 
     /**
@@ -296,7 +386,7 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     protected void applyButton_actionPerformed(ActionEvent e)
     {
-        UserColourScheme ucs = getSchemeFromGUI();
+        UserColourScheme ucs = getSchemeFromButtons();
         ucs.setName(schemeName.getText());
 
         if (seqGroup != null)
@@ -315,17 +405,31 @@ public class UserDefinedColours extends GUserDefinedColours
         }
     }
 
-    UserColourScheme getSchemeFromGUI()
+    UserColourScheme getSchemeFromButtons()
     {
+
       Color[] newColours = new Color[24];
 
       for (int i = 0; i < 24; i++)
       {
-        JButton button = (JButton) buttonPanel.getComponent(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());
 
@@ -342,6 +446,9 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     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");
@@ -367,11 +474,31 @@ public class UserDefinedColours extends GUserDefinedColours
             Color[] colors = ucs.getColours();
             schemeName.setText(ucs.getName());
 
-            for (int i = 0; i < colors.length; i++)
+            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) buttonPanel.getComponent(i);
+                JButton button = (JButton) upperCaseButtons.elementAt(i);
                 button.setBackground(colors[i]);
             }
+
         }
     }
 
@@ -417,7 +544,6 @@ public class UserDefinedColours extends GUserDefinedColours
     {
          UserColourScheme ucs = null;
          Color[]  newColours = null;
-
         try
         {
             InputStreamReader in = new InputStreamReader(new FileInputStream(
@@ -430,17 +556,51 @@ public class UserDefinedColours extends GUserDefinedColours
                   = new org.exolab.castor.xml.Unmarshaller(jucs);
               jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );
 
-              newColours = new Color[jucs.getColourCount()];
+              newColours = new Color[24];
+
+              Color [] lowerCase = null;
+              boolean caseSensitive = false;
+
 
-            for (int i = 0; i < 24; i++)
+            String name;
+            int index;
+            for (int i = 0; i < jucs.getColourCount(); i++)
             {
-              newColours[i] = new Color(Integer.parseInt(
+              name =  jucs.getColour(i).getName();
+              if(ResidueProperties.aa3Hash.containsKey(name))
+              {
+                index = ((Integer)ResidueProperties.aa3Hash.get(name)).intValue();
+              }
+              else
+              {
+                index = ((Integer)ResidueProperties.aaHash.get(name)).intValue();
+              }
+              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);
+              }
             }
 
         }
@@ -525,23 +685,26 @@ public class UserDefinedColours extends GUserDefinedColours
               defaultColours = defaultColours.concat(choice);
             }
 
-            userColourSchemes.put(schemeName.getText(), getSchemeFromGUI());
+            userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
 
             ap.alignFrame.updateUserColourMenu();
 
             jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
-            jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
+            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 < 24; i++)
+                for (int i = 0; i < buttonPanel.getComponentCount(); i++)
                 {
                     JButton button = (JButton) buttonPanel.getComponent(i);
-                    jalview.binding.Colour col = new jalview.binding.Colour();
+                    jalview.schemabinding.version2.Colour col
+                        = new jalview.schemabinding.version2.Colour();
                     col.setName(button.getText());
                     col.setRGB(jalview.util.Format.getHexString(
                             button.getBackground()));
@@ -679,4 +842,20 @@ public class UserDefinedColours extends GUserDefinedColours
         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);
+    }
+
 }
diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 31bc09c..60ce4f4 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -22,7 +22,7 @@ import java.awt.*;
 import java.awt.event.*;
 
 import javax.swing.*;
-
+import java.awt.Dimension;
 
 /**
  * DOCUMENT ME!
@@ -35,7 +35,7 @@ public class GUserDefinedColours extends JPanel
     protected JColorChooser colorChooser = new JColorChooser();
     protected JPanel buttonPanel = new JPanel();
     protected GridLayout gridLayout = new GridLayout();
-    JPanel jPanel2 = new JPanel();
+    JPanel lowerPanel = new JPanel();
     protected JButton okButton = new JButton();
     protected JButton applyButton = new JButton();
     protected JButton loadbutton = new JButton();
@@ -46,8 +46,8 @@ public class GUserDefinedColours extends JPanel
   protected JTextField schemeName = new JTextField();
   BorderLayout borderLayout1 = new BorderLayout();
   JPanel panel1 = new JPanel();
-  JPanel jPanel1 = new JPanel();
-  JPanel jPanel3 = new JPanel();
+  JPanel okCancelPanel = new JPanel();
+  JPanel saveLoadPanel = new JPanel();
   BorderLayout borderLayout3 = new BorderLayout();
   GridBagLayout gridBagLayout1 = new GridBagLayout();
   BorderLayout borderLayout2 = new BorderLayout();
@@ -55,8 +55,10 @@ public class GUserDefinedColours extends JPanel
   BorderLayout borderLayout4 = new BorderLayout();
   JPanel jPanel4 = new JPanel();
   BorderLayout borderLayout5 = new BorderLayout();
-  JPanel jPanel6 = new JPanel();
   JLabel label = new JLabel();
+  JPanel casePanel = new JPanel();
+  protected JCheckBox caseSensitive = new JCheckBox();
+  protected JButton lcaseColour = new JButton();
   /**
      * Creates a new GUserDefinedColours object.
      */
@@ -82,7 +84,7 @@ public class GUserDefinedColours extends JPanel
         this.setLayout(borderLayout4);
         buttonPanel.setLayout(gridLayout);
         gridLayout.setColumns(4);
-        gridLayout.setRows(6);
+        gridLayout.setRows(5);
         okButton.setFont(new java.awt.Font("Verdana", 0, 11));
         okButton.setText("OK");
         okButton.addActionListener(new java.awt.event.ActionListener()
@@ -129,8 +131,8 @@ public class GUserDefinedColours extends JPanel
                 }
             });
         this.setBackground(new Color(212, 208, 223));
-        jPanel2.setOpaque(false);
-    jPanel2.setLayout(borderLayout3);
+    lowerPanel.setOpaque(false);
+    lowerPanel.setLayout(borderLayout3);
     colorChooser.setOpaque(false);
     jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     jLabel1.setText("Name");
@@ -145,38 +147,51 @@ public class GUserDefinedColours extends JPanel
     schemeName.setHorizontalAlignment(SwingConstants.CENTER);
     panel1.setLayout(flowLayout1);
     panel1.setOpaque(false);
-    jPanel1.setOpaque(false);
-    jPanel3.setOpaque(false);
+    okCancelPanel.setOpaque(false);
+    saveLoadPanel.setOpaque(false);
     jPanel4.setLayout(borderLayout5);
-    jPanel6.setBackground(Color.pink);
-    jPanel6.setMinimumSize(new Dimension(10, 70));
-    jPanel6.setOpaque(false);
-    jPanel6.setPreferredSize(new Dimension(10, 45));
-    jPanel6.setLayout(null);
     label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
     label.setOpaque(false);
     label.setPreferredSize(new Dimension(260, 34));
     label.setText(
         "<html>Save your colour scheme with a unique name and it will be added " +
         "to the Colour menu.</html>");
+    caseSensitive.setText("Case Sensitive");
+    caseSensitive.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        caseSensitive_actionPerformed(e);
+      }
+    });
+    lcaseColour.setText("Lower Case Colour");
+    lcaseColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        lcaseColour_actionPerformed(e);
+      }
+    });
 
-    jPanel3.add(savebutton);
-    jPanel3.add(loadbutton);
-    jPanel1.add(applyButton);
-    jPanel1.add(okButton);
-    jPanel1.add(cancelButton);
-    jPanel2.add(jPanel3, java.awt.BorderLayout.NORTH);
-    jPanel2.add(jPanel1, java.awt.BorderLayout.SOUTH);
+    saveLoadPanel.add(savebutton);
+    saveLoadPanel.add(loadbutton);
+    okCancelPanel.add(applyButton);
+    okCancelPanel.add(okButton);
+    okCancelPanel.add(cancelButton);
+    lowerPanel.add(saveLoadPanel, java.awt.BorderLayout.NORTH);
+    lowerPanel.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 
     namePanel.add(schemeName, java.awt.BorderLayout.CENTER);
     namePanel.add(jLabel1, java.awt.BorderLayout.WEST);
     panel1.add(namePanel, null);
     panel1.add(buttonPanel, null);
-    panel1.add(jPanel2, null);
+    panel1.add(casePanel);
+    casePanel.add(caseSensitive);
+    casePanel.add(lcaseColour);
+    panel1.add(lowerPanel, null);
     panel1.add(label);
 
     jPanel4.add(panel1, java.awt.BorderLayout.CENTER);
-    jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);
     this.add(jPanel4, java.awt.BorderLayout.CENTER);
     this.add(colorChooser, java.awt.BorderLayout.EAST);
   }
@@ -225,4 +240,14 @@ public class GUserDefinedColours extends JPanel
     protected void cancelButton_actionPerformed(ActionEvent e)
     {
     }
+
+    public void caseSensitive_actionPerformed(ActionEvent e)
+    {
+
+    }
+
+    public void lcaseColour_actionPerformed(ActionEvent e)
+    {
+
+    }
 }
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index e5efb1a..95e9a32 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -24,6 +24,8 @@ import java.util.StringTokenizer;
 public class UserColourScheme
     extends ResidueColourScheme
 {
+  Color [] lowerCaseColours;
+
   protected String schemeName;
 
   public UserColourScheme()
@@ -54,6 +56,11 @@ public class UserColourScheme
     return colors;
   }
 
+  public Color[] getLowerCaseColours()
+  {
+    return lowerCaseColours;
+  }
+
   public void setName(String name)
   {
     schemeName = name;
@@ -127,7 +134,7 @@ public class UserColourScheme
   {
     StringTokenizer st = new StringTokenizer(paramValue, ";");
     StringTokenizer st2;
-    String token=null, colour, residues;
+    String token=null, colour, residues, residue;
     try{
       while (st.hasMoreElements())
       {
@@ -138,11 +145,32 @@ public class UserColourScheme
         st2 = new StringTokenizer(residues, " ,");
         while (st2.hasMoreTokens())
         {
+          token = st2.nextToken();
+          if(token.equalsIgnoreCase("lowerCase"))
+          {
+            if (lowerCaseColours == null)
+              lowerCaseColours = new Color[23];
+            for (int i = 0; i < 23; i++)
+              if (lowerCaseColours[i] == null)
+                lowerCaseColours[i] = getColourFromString(colour);
+
+              continue;
+          }
+
           int colIndex =
               ( (Integer) ResidueProperties.aaHash.
-               get(st2.nextToken())).intValue();
-
-          colors[colIndex] = getColourFromString(colour);
+               get(token)).intValue();
+
+          if(token.equals(token.toLowerCase()))
+          {
+            if(lowerCaseColours==null)
+            {
+              lowerCaseColours = new Color[23];
+            }
+            lowerCaseColours[colIndex] = getColourFromString(colour);
+          }
+          else
+            colors[colIndex] = getColourFromString(colour);
         }
       }
     }
@@ -154,4 +182,34 @@ public class UserColourScheme
 
   }
 
+
+
+  public Color findColour(String s, int j)
+  {
+      int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
+
+      if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+      {
+        if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
+          currentColour = lowerCaseColours[index];
+        else
+          currentColour = colors[index];
+      }
+      else
+      {
+          currentColour = Color.white;
+      }
+
+      if(conservationColouring)
+        applyConservation(j);
+
+
+      return currentColour;
+   }
+
+   public void setLowerCaseColours(Color [] lcolours)
+   {
+     lowerCaseColours = lcolours;
+   }
+
 }
-- 
1.7.10.2