X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=8882b5399057a279af967ee7858eeae5117a2ea7;hb=c1f3a352a553ccd40063b14336b27e5a2a7329cf;hp=284f1a164b28c03ca351b6214fe2cd9704cc43d3;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 284f1a1..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();
@@ -58,12 +58,13 @@ public class ConsensusThread extends AlignCalcWorker
       }
       while (!calcMan.notifyWorking(this))
       {
-        // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
+        // jalview.bin.Console.errPrintln("Thread
+        // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
         try
         {
           if (ap != null)
           {
-            ap.paintAlignment(false);
+            ap.paintAlignment(false, false);
           }
           Thread.sleep(200);
         } catch (Exception ex)
@@ -92,7 +93,7 @@ public class ConsensusThread extends AlignCalcWorker
 
       if (ap != null)
       {
-        ap.paintAlignment(true);
+        ap.paintAlignment(true, true);
       }
     } catch (OutOfMemoryError error)
     {
@@ -117,7 +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)
     {