X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=aadd8f0e82ab8ec034b49f7fd0fd0d00f45bbb9d;hb=a81cd4fa55b7cade14dc0ee9a0875c63e96d3f44;hp=bc178dfdcf68cd3a6caebd93d99ab1ddfb38b72a;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index bc178df..aadd8f0 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -105,6 +105,11 @@ public class AAFrequency
 
       for (j = 0; j < jSize; j++)
       {
+        if (sequences[j]==null)
+        {
+          System.err.println("WARNING: Consensus skipping null sequence - possible race condition.");
+          continue;
+        }
         seq = sequences[j].getSequence();
         if (seq.length > i)
         {
@@ -204,8 +209,22 @@ public class AAFrequency
           boolean includeAllConsSymbols, char[] alphabet)
   {
     float tval, value;
+    if (consensus == null || consensus.annotations == null
+            || consensus.annotations.length < width)
+    {
+      // 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)
       {