X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FAlignCalcManager.java;h=cdf8ea4d77fc08de067185aa1b69fddae4c5d51e;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=d81db8c93aa9c7b0d9335923eb97e9ae79ae212e;hpb=340ebd50b63087b4f8b2c4a26d94112dc51ada9c;p=jalview.git

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index d81db8c..cdf8ea4 100644
--- 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;
@@ -144,7 +145,8 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     synchronized (inProgress)
     {
-      // System.err.println("Worker " + worker + " marked as complete.");
+      // jalview.bin.Console.errPrintln("Worker " + worker + " marked as
+      // complete.");
       inProgress.remove(worker);
       List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
       if (upd != null)
@@ -191,7 +193,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   public boolean isWorking(AlignCalcWorkerI worker)
   {
     synchronized (inProgress)
-    {// System.err.println("isWorking : worker "+(worker!=null ?
+    {// jalview.bin.Console.errPrintln("isWorking : worker "+(worker!=null ?
      // worker.getClass():"null")+ " "+hashCode());
       return worker != null && inProgress.contains(worker);
     }
@@ -200,17 +202,27 @@ public class AlignCalcManager implements AlignCalcManagerI
   @Override
   public boolean isWorking()
   {
-    boolean working=false;
+    boolean working = false;
     synchronized (inProgress)
     {
-      // System.err.println("isWorking "+hashCode());
+      // jalview.bin.Console.errPrintln("isWorking "+hashCode());
       working |= inProgress.size() > 0;
     }
     synchronized (updating)
     {
-      for (List<AlignCalcWorkerI> workers : updating.values())
+      Collection<List<AlignCalcWorkerI>> workersLists = updating.values();
+      synchronized (workersLists)
       {
-        working |= workers.size() > 0;
+        for (List<AlignCalcWorkerI> workers : workersLists)
+        {
+          if (workers != null)
+          {
+            synchronized (workers)
+            {
+              working |= workers.size() > 0;
+            }
+          }
+        }
       }
     }
     return working;
@@ -295,14 +307,16 @@ public class AlignCalcManager implements AlignCalcManagerI
           Class<? extends AlignCalcWorkerI> workerClass)
   {
     List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
+    AlignCalcWorkerI[] workers;
     synchronized (canUpdate)
     {
-      for (AlignCalcWorkerI worker : canUpdate)
+      workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
+    }
+    for (AlignCalcWorkerI worker : workers)
+    {
+      if (workerClass.equals(worker.getClass()))
       {
-        if (workerClass.equals(worker.getClass()))
-        {
-          workingClass.add(worker);
-        }
+        workingClass.add(worker);
       }
     }
     return (workingClass.size() == 0) ? null : workingClass;
@@ -357,7 +371,7 @@ public class AlignCalcManager implements AlignCalcManagerI
      * {
      * 
      * if (isPending(worker)) { worker.abortAndDestroy(); startWorker(worker); }
-     * else { System.err.println("Pending exists for " + workerClass); } }
+     * else { jalview.bin.Console.errPrintln("Pending exists for " + workerClass); } }
      */
   }