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 4bff6ef..16754a1 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -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)
         {