Comment out lower case colouring for bug fix release

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 2369049..d2741a9 100755 (executable)
--- 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)\r
     {\r
         super();\r
+\r
+        //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
+        casePanel.setVisible(false);\r
+\r
+\r
         lcaseColour.setEnabled(false);\r
 \r
         this.ap = ap;\r
@@ -132,6 +137,9 @@ public class UserDefinedColours extends GUserDefinedColours
 \r
     void resetButtonPanel(boolean caseSensitive)\r
     {\r
+      //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
+      caseSensitive = false;\r
+\r
       buttonPanel.removeAll();\r
 \r
 \r
@@ -348,10 +356,12 @@ public class UserDefinedColours extends GUserDefinedColours
           {    }\r
         }\r
 \r
+      /* //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
         if(caseSensitive.isSelected())\r
           button.setMargin(new java.awt.Insets(2,2,2,2));\r
         else\r
-          button.setMargin(new java.awt.Insets(2,14,2,14));\r
+         button.setMargin(new java.awt.Insets(2,14,2,14));\r
+      */\r
 \r
         button.setBackground(col);\r
         button.setText(label);\r

diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 60ce4f4..661b962 100755 (executable)
--- 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();\r
   BorderLayout borderLayout5 = new BorderLayout();\r
   JLabel label = new JLabel();\r
-  JPanel casePanel = new JPanel();\r
+  protected JPanel casePanel = new JPanel();\r
   protected JCheckBox caseSensitive = new JCheckBox();\r
   protected JButton lcaseColour = new JButton();\r
   /**\r
@@ -72,6 +72,7 @@ public class GUserDefinedColours extends JPanel
         {\r
             e.printStackTrace();\r
         }\r
+\r
     }\r
 \r
     /**\r

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 95e9a32..41fc6c9 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -134,7 +134,7 @@ public class UserColourScheme
   {\r
     StringTokenizer st = new StringTokenizer(paramValue, ";");\r
     StringTokenizer st2;\r
-    String token=null, colour, residues, residue;\r
+    String token=null, colour, residues;\r
     try{\r
       while (st.hasMoreElements())\r
       {\r
@@ -146,6 +146,13 @@ public class UserColourScheme
         while (st2.hasMoreTokens())\r
         {\r
           token = st2.nextToken();\r
+\r
+          int colIndex =\r
+              ( (Integer) ResidueProperties.aaHash.\r
+               get(token)).intValue();\r
+\r
+           //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
+           /*\r
           if(token.equalsIgnoreCase("lowerCase"))\r
           {\r
             if (lowerCaseColours == null)\r
@@ -157,10 +164,6 @@ public class UserColourScheme
               continue;\r
           }\r
 \r
-          int colIndex =\r
-              ( (Integer) ResidueProperties.aaHash.\r
-               get(token)).intValue();\r
-\r
           if(token.equals(token.toLowerCase()))\r
           {\r
             if(lowerCaseColours==null)\r
@@ -169,7 +172,7 @@ public class UserColourScheme
             }\r
             lowerCaseColours[colIndex] = getColourFromString(colour);\r
           }\r
-          else\r
+          else*/\r
             colors[colIndex] = getColourFromString(colour);\r
         }\r
       }\r
@@ -190,9 +193,10 @@ public class UserColourScheme
 \r
       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))\r
       {\r
-        if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')\r
+       //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
+       /* if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')\r
           currentColour = lowerCaseColours[index];\r
-        else\r
+        else*/\r
           currentColour = colors[index];\r
       }\r
       else\r