JAL-4392 Consensus secondary structure: Display Secondary structure consensus for...

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

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index fc28e53..d64bf4d 100644 (file)
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -20,10 +20,6 @@
  */
 package jalview.workers;
 
-import jalview.api.AlignCalcManagerI;
-import jalview.api.AlignCalcWorkerI;
-import jalview.datamodel.AlignmentAnnotation;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -33,6 +29,10 @@ 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
 {
   /*
@@ -145,7 +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)
@@ -192,7 +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);
     }
@@ -201,10 +202,10 @@ 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)
@@ -214,9 +215,10 @@ public class AlignCalcManager implements AlignCalcManagerI
       {
         for (List<AlignCalcWorkerI> workers : workersLists)
         {
-          if (workers!=null)
+          if (workers != null)
           {
-            synchronized (workers) {
+            synchronized (workers)
+            {
               working |= workers.size() > 0;
             }
           }
@@ -305,14 +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;
@@ -367,7 +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); } }
      */
   }