X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAlignCalcWorker.java;h=48e3604f03d53cce5d60d23989a9bda441ac9a6e;hb=1070450e1afee97a5b4567416f5b7655fbfa59f1;hp=566891f5801b8909db8f79fb643ba08e005a88f1;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index 566891f..48e3604 100644
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -20,8 +20,6 @@
  */
 package jalview.workers;
 
-import java.util.List;
-
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
@@ -29,6 +27,8 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 
+import java.util.List;
+
 /**
  * Base class for alignment calculation workers
  * 
@@ -46,7 +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)
@@ -68,17 +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)
     {
@@ -90,6 +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