X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=00f8f6f6bb1c597eb1af80cf05d222367bc12052;hb=d70d7e5bc8da1189f44709b6ec59ea1e23f6f557;hp=9d61279ffdf679deb1643f7b6f2c9ad6b0aa8aa7;hpb=3d941a02a998676a12f8ff43fa98d9e1f4c27142;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 9d61279..00f8f6f 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -186,14 +186,14 @@ public class UserColourScheme
 
 
 
-  public Color findColour(String s, int j)
+  public Color findColour(char c, int j)
   {
       Color currentColour;
-      int index = ResidueProperties.aaIndex[s.charAt(0)];
+      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];
@@ -204,7 +204,7 @@ public class UserColourScheme
       }
 
       if(conservationColouring)
-        applyConservation(currentColour, j);
+       currentColour =  applyConservation(currentColour, j);
 
 
       return currentColour;