From b5d69834ef8b11df514d5b4c08c82945f15f8a2e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 11 Sep 2006 16:24:41 +0000
Subject: [PATCH] Comment out lower case colouring for bug fix release

---
 src/jalview/gui/UserDefinedColours.java    |   12 +++++++++++-
 src/jalview/jbgui/GUserDefinedColours.java |    3 ++-
 src/jalview/schemes/UserColourScheme.java  |   20 ++++++++++++--------
 3 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 2369049..d2741a9 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -66,6 +66,11 @@ public class UserDefinedColours extends GUserDefinedColours
     public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
     {
         super();
+
+        //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
+        casePanel.setVisible(false);
+
+
         lcaseColour.setEnabled(false);
 
         this.ap = ap;
@@ -132,6 +137,9 @@ public class UserDefinedColours extends GUserDefinedColours
 
     void resetButtonPanel(boolean caseSensitive)
     {
+      //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
+      caseSensitive = false;
+
       buttonPanel.removeAll();
 
 
@@ -348,10 +356,12 @@ public class UserDefinedColours extends GUserDefinedColours
           {    }
         }
 
+      /* //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
         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.setMargin(new java.awt.Insets(2,14,2,14));
+      */
 
         button.setBackground(col);
         button.setText(label);
diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 60ce4f4..661b962 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -56,7 +56,7 @@ public class GUserDefinedColours extends JPanel
   JPanel jPanel4 = new JPanel();
   BorderLayout borderLayout5 = new BorderLayout();
   JLabel label = new JLabel();
-  JPanel casePanel = new JPanel();
+  protected JPanel casePanel = new JPanel();
   protected JCheckBox caseSensitive = new JCheckBox();
   protected JButton lcaseColour = new JButton();
   /**
@@ -72,6 +72,7 @@ public class GUserDefinedColours extends JPanel
         {
             e.printStackTrace();
         }
+
     }
 
     /**
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 95e9a32..41fc6c9 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -134,7 +134,7 @@ public class UserColourScheme
   {
     StringTokenizer st = new StringTokenizer(paramValue, ";");
     StringTokenizer st2;
-    String token=null, colour, residues, residue;
+    String token=null, colour, residues;
     try{
       while (st.hasMoreElements())
       {
@@ -146,6 +146,13 @@ public class UserColourScheme
         while (st2.hasMoreTokens())
         {
           token = st2.nextToken();
+
+          int colIndex =
+              ( (Integer) ResidueProperties.aaHash.
+               get(token)).intValue();
+
+           //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
+           /*
           if(token.equalsIgnoreCase("lowerCase"))
           {
             if (lowerCaseColours == null)
@@ -157,10 +164,6 @@ public class UserColourScheme
               continue;
           }
 
-          int colIndex =
-              ( (Integer) ResidueProperties.aaHash.
-               get(token)).intValue();
-
           if(token.equals(token.toLowerCase()))
           {
             if(lowerCaseColours==null)
@@ -169,7 +172,7 @@ public class UserColourScheme
             }
             lowerCaseColours[colIndex] = getColourFromString(colour);
           }
-          else
+          else*/
             colors[colIndex] = getColourFromString(colour);
         }
       }
@@ -190,9 +193,10 @@ public class UserColourScheme
 
       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
       {
-        if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
+       //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
+       /* if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
           currentColour = lowerCaseColours[index];
-        else
+        else*/
           currentColour = colors[index];
       }
       else
-- 
1.7.10.2