X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=4a68f819e8a7dd7cf1fd28d964c67e6a75a53f0e;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=c1c4f71cfb5922eeb5139fb861895800615fc5ed;hpb=9832a6ac361db1a51c020ef1ebdb7f495676c72d;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index c1c4f71..4a68f81 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;
@@ -68,24 +73,24 @@ public static final void calculate(SequenceI[] sequences,
   char c;
   float percentage;
 
-  int[] values = new int[132];
+  int[] values = new int[255];
 
-  String seq;
+  char [] seq;
 
   for (i = start; i < end; i++)
   {
     residueHash = new Hashtable();
     maxCount = 0;
-    maxResidue = "-";
+    maxResidue = "";
     nongap = 0;
-    values = new int[132];
+    values = new int[255];
 
     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 = '-';
@@ -112,7 +117,7 @@ public static final void calculate(SequenceI[] sequences,
 
     for (v = 'A'; v < 'Z'; v++)
     {
-      if (values[v] == 0 || values[v] < maxCount)
+      if (values[v] < 2 || values[v] < maxCount)
         continue;
 
       if (values[v] > maxCount)
@@ -126,6 +131,8 @@ public static final void calculate(SequenceI[] sequences,
       maxCount = values[v];
     }
 
+    if(maxResidue.length()==0)
+      maxResidue = "-";
 
     residueHash.put(MAXCOUNT, new Integer(maxCount));
     residueHash.put(MAXRESIDUE, maxResidue);