X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=33492839133bb297f794bedf8348ed6da6a8c544;hb=bc39ee8df9694f820a8a8bd2430f527b87c07f31;hp=95e9a32e44f50c83d71960a8dbc7f0b43928e2b9;hpb=9e46fb6245b28f14f01cb84d46d03cf5453e7010;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 95e9a32..3349283 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 +146,12 @@ public class UserColourScheme
         while (st2.hasMoreTokens())
         {
           token = st2.nextToken();
+
+          if (ResidueProperties.aaIndex[token.charAt(0)]==-1)
+            continue;
+
+          int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
+
           if(token.equalsIgnoreCase("lowerCase"))
           {
             if (lowerCaseColours == null)
@@ -157,10 +163,6 @@ public class UserColourScheme
               continue;
           }
 
-          int colIndex =
-              ( (Integer) ResidueProperties.aaHash.
-               get(token)).intValue();
-
           if(token.equals(token.toLowerCase()))
           {
             if(lowerCaseColours==null)
@@ -186,7 +188,7 @@ public class UserColourScheme
 
   public Color findColour(String s, int j)
   {
-      int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
+      int index = ResidueProperties.aaIndex[s.charAt(0)];
 
       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
       {