X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=3d910809599f89392380403f7495a659789719c4;hb=410dfa093c4150aeadc02710c2a70eb862e3b2d8;hp=5b9a2a4be5eee5d0d5fa7134b5a312d19e37bfa1;hpb=702d861516f9f04118c97f36ae4d4e08017dde68;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 5b9a2a4..3d91080 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -55,7 +55,7 @@ public class AAFrequency
 
      if(end>=width)
      {
-       end = width-1;
+       end = width;
      }
 
      calculate(seqs, start, end, reply);
@@ -75,7 +75,7 @@ public static final void calculate(SequenceI[] sequences,
 
   int[] values = new int[132];
 
-  String seq;
+  char [] seq;
 
   for (i = start; i < end; i++)
   {
@@ -88,9 +88,9 @@ public static final void calculate(SequenceI[] sequences,
     for (j = 0; j < jSize; j++)
     {
       seq = sequences[j].getSequence();
-      if (seq.length() > i)
+      if (seq.length > i)
       {
-        c = seq.charAt(i);
+        c = seq[i];
 
         if(c == '.' || c==' ')
           c = '-';