X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FAlignCalcManager.java;h=77908b61e7575087cf315bbd0ab2348e17d5c7b5;hb=970956e40635fd5a86d46e399532abda64ccdf92;hp=b829a730dbd2033197c09ece43ea2a177ed1dfea;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index b829a73..77908b6 100644
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -22,6 +22,7 @@ package jalview.workers;
 
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentAnnotation;
 
 import java.util.ArrayList;
@@ -34,6 +35,10 @@ import java.util.Set;
 
 public class AlignCalcManager implements AlignCalcManagerI
 {
+  public static final String STARTED = "started";
+
+  public static final String FINISHED = "finished";
+
   /*
    * list of registered workers
    */
@@ -68,13 +73,13 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     restartable = Collections
             .synchronizedList(new ArrayList<AlignCalcWorkerI>());
-    blackList = Collections
-            .synchronizedList(new ArrayList<Class<? extends AlignCalcWorkerI>>());
+    blackList = Collections.synchronizedList(
+            new ArrayList<Class<? extends AlignCalcWorkerI>>());
     inProgress = Collections
             .synchronizedList(new ArrayList<AlignCalcWorkerI>());
-    updating = Collections
-            .synchronizedMap(new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
-    canUpdate = new HashSet<AlignCalcWorkerI>();
+    updating = Collections.synchronizedMap(
+            new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
+    canUpdate = new HashSet<>();
   }
 
   @Override
@@ -82,13 +87,12 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     synchronized (updating)
     {
+      Jalview.getInstance().notifyWorker(worker, STARTED);
       List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
       if (upd == null)
       {
-        updating.put(
-                worker.getClass(),
-                upd = Collections
-                        .synchronizedList(new ArrayList<AlignCalcWorkerI>()));
+        updating.put(worker.getClass(), upd = Collections
+                .synchronizedList(new ArrayList<AlignCalcWorkerI>()));
       }
       synchronized (upd)
       {
@@ -146,6 +150,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     synchronized (inProgress)
     {
+      Jalview.getInstance().notifyWorker(worker, FINISHED);
       // System.err.println("Worker " + worker + " marked as complete.");
       inProgress.remove(worker);
       List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
@@ -185,7 +190,8 @@ public class AlignCalcManager implements AlignCalcManagerI
     {
       Thread tw = new Thread(worker);
       tw.setName(worker.getClass().toString());
-      tw.start();
+      Jalview.execThread(tw); // JAL-3563
+      // tw.start();
     }
   }
 
@@ -235,7 +241,8 @@ public class AlignCalcManager implements AlignCalcManagerI
   }
 
   @Override
-  public boolean workingInvolvedWith(AlignmentAnnotation alignmentAnnotation)
+  public boolean workingInvolvedWith(
+          AlignmentAnnotation alignmentAnnotation)
   {
     synchronized (inProgress)
     {
@@ -286,7 +293,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
           Class<? extends AlignCalcWorkerI> workerClass)
   {
-    List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
+    List<AlignCalcWorkerI> workingClass = new ArrayList<>();
     synchronized (canUpdate)
     {
       for (AlignCalcWorkerI worker : canUpdate)
@@ -313,8 +320,8 @@ public class AlignCalcManager implements AlignCalcManagerI
   public void removeRegisteredWorkersOfClass(
           Class<? extends AlignCalcWorkerI> typeToRemove)
   {
-    List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
-    Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
+    List<AlignCalcWorkerI> removable = new ArrayList<>();
+    Set<AlignCalcWorkerI> toremovannot = new HashSet<>();
     synchronized (restartable)
     {
       for (AlignCalcWorkerI worker : restartable)
@@ -364,7 +371,7 @@ public class AlignCalcManager implements AlignCalcManagerI
      * first just find those to remove (to avoid
      * ConcurrentModificationException)
      */
-    List<AlignCalcWorkerI> toRemove = new ArrayList<AlignCalcWorkerI>();
+    List<AlignCalcWorkerI> toRemove = new ArrayList<>();
     for (AlignCalcWorkerI worker : restartable)
     {
       if (worker.involves(ann))