From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 5 Oct 2006 16:20:39 +0000 (+0000)
Subject: lower case available
X-Git-Tag: Release_2_2~320
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9451924e2cdf30878359420a35d669ccee881043

lower case available
---

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 41fc6c9..bd70c5d 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -147,12 +147,15 @@ public class UserColourScheme
         {
           token = st2.nextToken();
 
+          if (ResidueProperties.aaHash.get(token) == null)
+            continue;
+
           int colIndex =
               ( (Integer) ResidueProperties.aaHash.
                get(token)).intValue();
 
            //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
-           /*
+
           if(token.equalsIgnoreCase("lowerCase"))
           {
             if (lowerCaseColours == null)
@@ -172,7 +175,7 @@ public class UserColourScheme
             }
             lowerCaseColours[colIndex] = getColourFromString(colour);
           }
-          else*/
+          else
             colors[colIndex] = getColourFromString(colour);
         }
       }
@@ -194,9 +197,9 @@ public class UserColourScheme
       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
       {
        //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
-       /* if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
+        if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
           currentColour = lowerCaseColours[index];
-        else*/
+        else
           currentColour = colors[index];
       }
       else