X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=00f8f6f6bb1c597eb1af80cf05d222367bc12052;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=33492839133bb297f794bedf8348ed6da6a8c544;hpb=7f7fc2e5533f7b00c86465f964e37c55bcf12fd7;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 3349283..00f8f6f 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -186,13 +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))
       {
-        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];
@@ -203,7 +204,7 @@ public class UserColourScheme
       }
 
       if(conservationColouring)
-        applyConservation(j);
+       currentColour =  applyConservation(currentColour, j);
 
 
       return currentColour;