X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=00f8f6f6bb1c597eb1af80cf05d222367bc12052;hb=f78ed026becc8e143d5b5953fce6c0961428d2a7;hp=007d35875e1b1384d6e443e18518351063becd53;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 007d358..00f8f6f 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -152,8 +152,6 @@ public class UserColourScheme
 
           int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
 
-           //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
-
           if(token.equalsIgnoreCase("lowerCase"))
           {
             if (lowerCaseColours == null)
@@ -188,14 +186,14 @@ public class UserColourScheme
 
 
 
-  public Color findColour(String s, int j)
+  public Color findColour(char c, int j)
   {
-      int index = ResidueProperties.aaIndex[s.charAt(0)];
+      Color currentColour;
+      int index = ResidueProperties.aaIndex[c];
 
-      if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+      if ((threshold == 0) || aboveThreshold(c, 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' <= c && c <= 'z')
           currentColour = lowerCaseColours[index];
         else
           currentColour = colors[index];
@@ -206,7 +204,7 @@ public class UserColourScheme
       }
 
       if(conservationColouring)
-        applyConservation(j);
+       currentColour =  applyConservation(currentColour, j);
 
 
       return currentColour;