X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=a8c33ce7874f81bc9539ef5d050c3a319fc050dc;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=97d1236ac33b482e47c5dd83b8c7b3e474cd5121;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 97d1236..a8c33ce 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.workers;
@@ -33,7 +35,7 @@ import java.util.Hashtable;
 public class ConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
 {
-  private long nseq=-1;
+  private long nseq = -1;
 
   public ConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
@@ -77,6 +79,7 @@ public class ConsensusThread extends AlignCalcWorker implements
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -100,8 +103,8 @@ public class ConsensusThread extends AlignCalcWorker implements
       {
         SequenceI aseqs[] = alignment.getSequencesArray();
         nseq = aseqs.length;
-        AAFrequency.calculate(aseqs, 0,
-                alignment.getWidth(), hconsensus, true);
+        AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus,
+                true);
       } catch (ArrayIndexOutOfBoundsException x)
       {
         // this happens due to a race condition -