X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=ad1fe4e9b7911137ac7fd5e086d47b135b0c9a7b;hb=58e82de6951f919828899de75b908cd1114d8511;hp=0841bf21304df1290ece958777c6fe340af8eafe;hpb=5e0d83cae421154f0cd70e2296ce6dbcbc4207a4;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 0841bf2..ad1fe4e 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -18,8 +18,6 @@
 */
 package jalview.analysis;
 
-import jalview.analysis.*;
-
 import jalview.datamodel.*;
 
 import java.util.*;
@@ -43,7 +41,7 @@ public class AAFrequency
     * the values being the count of each residue in that column.
     * This class is used extensively in calculating alignment colourschemes
     * that depend on the amount of conservation in each alignment column. */
-    public static Vector calculate(Vector sequences, int start, int end)
+    public static final Vector calculate(Vector sequences, int start, int end)
     {
       Vector result = new Vector();
       Hashtable residueHash;
@@ -66,7 +64,7 @@ public class AAFrequency
 
                     if (sequence.length() > i)
                     {
-                        res = sequence.substring(i,i+1);
+                        res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));
 
                         if (jalview.util.Comparison.isGap(res.charAt(0)))
                         {