X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=8882b5399057a279af967ee7858eeae5117a2ea7;hb=refs%2Fheads%2Fbug%2FJAL-4290_headless_alignment_figure_with_sse;hp=335529c71f2395aac83628a51140601cb2d3c98e;hpb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 335529c..8882b53 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -46,7 +46,7 @@ public class ConsensusThread extends AlignCalcWorker
       return;
     }
     calcMan.notifyStart(this);
-    long started = System.currentTimeMillis();
+    // long started = System.currentTimeMillis();
     try
     {
       AlignmentAnnotation consensus = getConsensusAnnotation();
@@ -58,7 +58,7 @@ public class ConsensusThread extends AlignCalcWorker
       }
       while (!calcMan.notifyWorking(this))
       {
-        // System.err.println("Thread
+        // jalview.bin.Console.errPrintln("Thread
         // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
         try
         {
@@ -118,7 +118,10 @@ public class ConsensusThread extends AlignCalcWorker
   protected void eraseConsensus(int aWidth)
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
-    consensus.annotations = new Annotation[aWidth];
+    if (consensus != null)
+    {
+      consensus.annotations = new Annotation[aWidth];
+    }
     AlignmentAnnotation gap = getGapAnnotation();
     if (gap != null)
     {