X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAlignCalcWorker.java;h=48e3604f03d53cce5d60d23989a9bda441ac9a6e;hb=60073d3f838affacd3f4158c3e7d069652d26602;hp=18bff533378816f053ec30a97de8e544a1a7e1a9;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index 18bff53..48e3604 100644
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -1,25 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.List;
-
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
@@ -27,6 +27,8 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 
+import java.util.List;
+
 /**
  * Base class for alignment calculation workers
  * 
@@ -44,7 +46,7 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
 
   protected AlignmentViewPanel ap;
 
-  protected List<AlignmentAnnotation> ourAnnots = null;
+  protected List<AlignmentAnnotation> ourAnnots;
 
   public AlignCalcWorker(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
@@ -66,17 +68,18 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
 
   }
 
+  @Override
   public boolean involves(AlignmentAnnotation i)
   {
     return ourAnnots != null && ourAnnots.contains(i);
   }
 
   /**
-   * permanently remove from the alignment all annotation rows managed by this
+   * Permanently removes from the alignment all annotation rows managed by this
    * worker
    */
   @Override
-  public void removeOurAnnotation()
+  public void removeAnnotation()
   {
     if (ourAnnots != null && alignViewport != null)
     {
@@ -88,6 +91,7 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
           alignment.deleteAnnotation(aa, true);
         }
       }
+      ourAnnots.clear();
     }
   }
   // TODO: allow GUI to query workers associated with annotation to add items to