JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / jalview / workers / AlignCalcWorker.java

diff --git a/src/jalview/workers/AlignCalcWorker.java b/src/jalview/workers/AlignCalcWorker.java
index f1b3019..6bdf1c2 100644 (file)
--- a/src/jalview/workers/AlignCalcWorker.java
+++ b/src/jalview/workers/AlignCalcWorker.java
@@ -1,10 +1,25 @@
-/**
+/*
+ * 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.
+ *  
+ * 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/>.
+ * 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;
@@ -12,10 +27,13 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 
+import java.util.List;
+
 /**
- * Base class for alignment calculation workers 
+ * Base class for alignment calculation workers
+ * 
  * @author jimp
- *
+ * 
  */
 public abstract class AlignCalcWorker implements AlignCalcWorkerI
 {
@@ -23,49 +41,58 @@ public abstract class AlignCalcWorker implements AlignCalcWorkerI
    * manager and data source for calculations
    */
   protected AlignViewportI alignViewport;
+
   protected AlignCalcManagerI calcMan;
+
   protected AlignmentViewPanel ap;
-  protected List<AlignmentAnnotation> ourAnnots=null;
-  
+
+  protected List<AlignmentAnnotation> ourAnnots = null;
+
   public AlignCalcWorker(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
     this.alignViewport = alignViewport;
-    calcMan=alignViewport.getCalcManager();
-    ap = alignPanel;    
+    calcMan = alignViewport.getCalcManager();
+    ap = alignPanel;
   }
+
   protected void abortAndDestroy()
   {
-    if (calcMan!=null) {
+    if (calcMan != null)
+    {
       calcMan.workerComplete(this);
     }
-    alignViewport=null;
-    calcMan=null;
-    ap=null;
-    
+    alignViewport = null;
+    calcMan = null;
+    ap = null;
+
   }
+
   public boolean involves(AlignmentAnnotation i)
   {
-    return ourAnnots!=null && ourAnnots.contains(i);
+    return ourAnnots != null && ourAnnots.contains(i);
   }
 
   /**
-   * permanently remove from the alignment all annotation rows managed by this worker
+   * permanently remove from the alignment all annotation rows managed by this
+   * worker
    */
   @Override
   public void removeOurAnnotation()
   {
-    if (ourAnnots!=null && alignViewport!=null)
+    if (ourAnnots != null && alignViewport != null)
     {
-      AlignmentI alignment=alignViewport.getAlignment();
-      synchronized (ourAnnots) {
-        for (AlignmentAnnotation aa:ourAnnots)
+      AlignmentI alignment = alignViewport.getAlignment();
+      synchronized (ourAnnots)
+      {
+        for (AlignmentAnnotation aa : ourAnnots)
         {
           alignment.deleteAnnotation(aa, true);
         }
       }
     }
   }
-  // TODO: allow GUI to query workers associated with annotation to add items to annotation label panel popup menu
+  // TODO: allow GUI to query workers associated with annotation to add items to
+  // annotation label panel popup menu
 
 }