JAL-885; Implementation of StructureFrequency.java and according

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index bc178df..16754a1 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.
@@ -85,6 +85,7 @@ public class AAFrequency
   public static final void calculate(SequenceI[] sequences, int start,
           int end, Hashtable[] result, boolean profile)
   {
+       System.out.println("AAFrequence.calculate");
     Hashtable residueHash;
     int maxCount, nongap, i, j, v, jSize = sequences.length;
     String maxResidue;
@@ -105,6 +106,11 @@ 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 +210,22 @@ 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)
       {