apply jalview code style

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 46264d6..4bff6ef 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -204,13 +204,22 @@ public class AAFrequency
           boolean includeAllConsSymbols, char[] alphabet)
   {
     float tval, value;
-    if (consensus==null || consensus.annotations==null || consensus.annotations.length<width)
+    if (consensus == null || consensus.annotations == null
+            || consensus.annotations.length < width)
     {
-      // called with a bad alignment annotation row - wait for it to be initialised properly
+      // called with a bad alignment annotation row - wait for it to be
+      // initialised properly
       return;
     }
     for (int i = iStart; i < width; i++)
     {
+      if (i >= hconsensus.length)
+      {
+        // happens if sequences calculated over were shorter than alignment
+        // width
+        consensus.annotations[i] = null;
+        continue;
+      }
       value = 0;
       if (ignoreGapsInConsensusCalculation)
       {