lower case available

[jalview.git] / src / jalview / schemes / UserColourScheme.java

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 95e9a32..bd70c5d 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 +146,16 @@ public class UserColourScheme
         while (st2.hasMoreTokens())\r
         {\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
           if(token.equalsIgnoreCase("lowerCase"))\r
           {\r
             if (lowerCaseColours == null)\r
@@ -157,10 +167,6 @@ 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
@@ -190,6 +196,7 @@ public class UserColourScheme
 \r
       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
           currentColour = lowerCaseColours[index];\r
         else\r