JAL-4196 make very sure we avoid CME by defensively copying the Map.values() to anoth...

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

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index addb372..fc28e53 100644 (file)
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -25,6 +25,7 @@ import jalview.api.AlignCalcWorkerI;
 import jalview.datamodel.AlignmentAnnotation;
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.Hashtable;
@@ -68,12 +69,12 @@ 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>>());
+    updating = Collections.synchronizedMap(
+            new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
     canUpdate = new HashSet<AlignCalcWorkerI>();
   }
 
@@ -85,10 +86,8 @@ public class AlignCalcManager implements AlignCalcManagerI
       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)
       {
@@ -202,11 +201,29 @@ public class AlignCalcManager implements AlignCalcManagerI
   @Override
   public boolean isWorking()
   {
+    boolean working=false;
     synchronized (inProgress)
     {
       // System.err.println("isWorking "+hashCode());
-      return inProgress.size() > 0;
+      working |= inProgress.size() > 0;
     }
+    synchronized (updating)
+    {
+      Collection<List<AlignCalcWorkerI>> workersLists = updating.values();
+      synchronized (workersLists)
+      {
+        for (List<AlignCalcWorkerI> workers : workersLists)
+        {
+          if (workers!=null)
+          {
+            synchronized (workers) {
+              working |= workers.size() > 0;
+            }
+          }
+        }
+      }
+    }
+    return working;
   }
 
   @Override
@@ -235,7 +252,8 @@ public class AlignCalcManager implements AlignCalcManagerI
   }
 
   @Override
-  public boolean workingInvolvedWith(AlignmentAnnotation alignmentAnnotation)
+  public boolean workingInvolvedWith(
+          AlignmentAnnotation alignmentAnnotation)
   {
     synchronized (inProgress)
     {