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

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 41fc6c9..3349283 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -147,12 +147,11 @@ public class UserColourScheme
         {\r
           token = st2.nextToken();\r
 \r
-          int colIndex =\r
-              ( (Integer) ResidueProperties.aaHash.\r
-               get(token)).intValue();\r
+          if (ResidueProperties.aaIndex[token.charAt(0)]==-1)\r
+            continue;\r
+\r
+          int colIndex = ResidueProperties.aaIndex[token.charAt(0)];\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
@@ -172,7 +171,7 @@ public class UserColourScheme
             }\r
             lowerCaseColours[colIndex] = getColourFromString(colour);\r
           }\r
-          else*/\r
+          else\r
             colors[colIndex] = getColourFromString(colour);\r
         }\r
       }\r
@@ -189,14 +188,13 @@ public class UserColourScheme
 \r
   public Color findColour(String s, int j)\r
   {\r
-      int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();\r
+      int index = ResidueProperties.aaIndex[s.charAt(0)];\r
 \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
+        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