lower case available

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 41fc6c9..bd70c5d 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -147,12 +147,15 @@ public class UserColourScheme
         {\r
           token = st2.nextToken();\r
 \r
+          if (ResidueProperties.aaHash.get(token) == null)\r
+            continue;\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
+\r
           if(token.equalsIgnoreCase("lowerCase"))\r
           {\r
             if (lowerCaseColours == null)\r
@@ -172,7 +175,7 @@ public class UserColourScheme
             }\r
             lowerCaseColours[colIndex] = getColourFromString(colour);\r
           }\r
-          else*/\r
+          else\r
             colors[colIndex] = getColourFromString(colour);\r
         }\r
       }\r
@@ -194,9 +197,9 @@ public class UserColourScheme
       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))\r
       {\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
+        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