X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=3d910809599f89392380403f7495a659789719c4;hb=410dfa093c4150aeadc02710c2a70eb862e3b2d8;hp=f409f8c59e50d43aa675c63aedda44a0e46799f8;hpb=49b625d7c10b85425059a51706a2aca96deed955;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index f409f8c..3d91080 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -53,6 +53,11 @@ public class AAFrequency
 
      Hashtable [] reply = new Hashtable[width];
 
+     if(end>=width)
+     {
+       end = width;
+     }
+
      calculate(seqs, start, end, reply);
 
      return reply;
@@ -70,7 +75,7 @@ public static final void calculate(SequenceI[] sequences,
 
   int[] values = new int[132];
 
-  String seq;
+  char [] seq;
 
   for (i = start; i < end; i++)
   {
@@ -83,9 +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 = '-';