Merge develop to Release_2_8_3_Branch

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

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index 544c2c8..1063706 100644 (file)
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -1,5 +1,29 @@
+/*
+ * 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.
+ *  
+ * 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 jalview.api.AlignCalcManagerI;
+import jalview.api.AlignCalcWorkerI;
+import jalview.datamodel.AlignmentAnnotation;
+
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashSet;
@@ -8,10 +32,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import jalview.api.AlignCalcManagerI;
-import jalview.api.AlignCalcWorkerI;
-import jalview.datamodel.AlignmentAnnotation;
-
 public class AlignCalcManager implements AlignCalcManagerI
 {
   private volatile List<AlignCalcWorkerI> restartable = Collections
@@ -63,7 +83,7 @@ public class AlignCalcManager implements AlignCalcManagerI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.api.AlignCalcManagerI#isPending(jalview.api.AlignCalcWorkerI)
    */
   @Override
@@ -132,7 +152,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     synchronized (inProgress)
     {
-//      System.err.println("Worker "+worker.getClass()+" marked as complete.");
+      // System.err.println("Worker "+worker.getClass()+" marked as complete.");
       inProgress.remove(worker.getClass());
       List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
       if (upd != null)
@@ -166,8 +186,8 @@ public class AlignCalcManager implements AlignCalcManagerI
   @Override
   public void startWorker(AlignCalcWorkerI worker)
   {
-//    System.err.println("Starting "+worker.getClass());
-//    new Exception("").printStackTrace();
+    // System.err.println("Starting "+worker.getClass());
+    // new Exception("").printStackTrace();
     Thread tw = new Thread(worker);
     tw.setName(worker.getClass().toString());
     tw.start();
@@ -236,10 +256,12 @@ public class AlignCalcManager implements AlignCalcManagerI
       for (List<AlignCalcWorkerI> workers : updating.values())
       {
         for (AlignCalcWorkerI worker : workers)
+        {
           if (worker.involves(alignmentAnnotation))
           {
             return true;
           }
+        }
       }
     }
     return false;
@@ -271,7 +293,7 @@ public class AlignCalcManager implements AlignCalcManagerI
     AlignCalcWorkerI[] workers;
     synchronized (canUpdate)
     {
-      workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
+      workers = canUpdate.toArray(new AlignCalcWorkerI[canUpdate.size()]);
     }
     for (AlignCalcWorkerI worker : workers)
     {
@@ -322,11 +344,13 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     List<AlignCalcWorkerI> workers = getRegisteredWorkersOfClass(typeToRemove);
     List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
-    Set<AlignCalcWorkerI> toremovannot=new HashSet<AlignCalcWorkerI>();
+    Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
     synchronized (restartable)
     {
-      for (AlignCalcWorkerI worker:restartable) {
-        if (typeToRemove.equals(worker.getClass())) {
+      for (AlignCalcWorkerI worker : restartable)
+      {
+        if (typeToRemove.equals(worker.getClass()))
+        {
           removable.add(worker);
           toremovannot.add(worker);
         }
@@ -335,8 +359,10 @@ public class AlignCalcManager implements AlignCalcManagerI
     }
     synchronized (canUpdate)
     {
-      for (AlignCalcWorkerI worker:canUpdate) {
-        if (typeToRemove.equals(worker.getClass())) {
+      for (AlignCalcWorkerI worker : canUpdate)
+      {
+        if (typeToRemove.equals(worker.getClass()))
+        {
           removable.add(worker);
           toremovannot.add(worker);
         }
@@ -345,28 +371,15 @@ public class AlignCalcManager implements AlignCalcManagerI
     }
     // TODO: finish testing this extension
 
-/*    synchronized (inProgress)
-    {
-      // need to kill or mark as dead any running threads...
-      (inProgress.get(typeToRemove));
-    }
-    
-    if (workers == null)
-    {
-      return;
-    }
-    for (AlignCalcWorkerI worker : workers)
-    {
-      
-      if (isPending(worker))
-      {
-        worker.abortAndDestroy();
-        startWorker(worker);
-      }
-      else
-      {
-        System.err.println("Pending exists for " + workerClass);
-      }
-    }*/
+    /*
+     * synchronized (inProgress) { // need to kill or mark as dead any running
+     * threads... (inProgress.get(typeToRemove)); }
+     * 
+     * if (workers == null) { return; } for (AlignCalcWorkerI worker : workers)
+     * {
+     * 
+     * if (isPending(worker)) { worker.abortAndDestroy(); startWorker(worker); }
+     * else { System.err.println("Pending exists for " + workerClass); } }
+     */
   }
 }