X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=990f724fdb500d27613d9f9f57abcfc2dcb296a0;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=681007e1bc473bda00f8df1f05132e81ff59359a;hpb=8f1b417b654a575bf7a368b4edeffee813042a5c;p=jalview.git

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 681007e..990f724 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -1,33 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignmentViewPanel;
 import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public class ConservationThread extends AlignCalcWorker implements
         AlignCalcWorkerI
 {
@@ -72,6 +74,7 @@ public class ConservationThread extends AlignCalcWorker implements
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
       AlignmentI alignment = alignViewport.getAlignment();
@@ -80,7 +83,7 @@ public class ConservationThread extends AlignCalcWorker implements
       ourAnnot.add(conservation);
       ourAnnot.add(quality);
       ourAnnots = ourAnnot;
-
+      ConsPercGaps = alignViewport.getConsPercGaps();
       // AlignViewport.UPDATING_CONSERVATION = true;
 
       if (alignment == null || (alWidth = alignment.getWidth()) < 0)