X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FAlignCalcManager.java;h=79ca8632e376052ca14249a61b557504021a4d25;hb=6a6fb5010c2cd06b14a1e055eabaeb4848e65d2d;hp=19673753ac029aa1b83fc4551c6191a605a1a650;hpb=b13d4ee2f7839be680d23ce157aff4e204377a8f;p=jalview.git

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index 1967375..79ca863 100644
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -27,6 +27,7 @@ import jalview.datamodel.AlignmentAnnotation;
 
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
@@ -38,45 +39,33 @@ public class AlignCalcManager implements AlignCalcManagerI
   /*
    * list of registered workers
    */
-  private volatile List<AlignCalcWorkerI> restartable;
+  private final List<AlignCalcWorkerI> restartable = Collections
+          .synchronizedList(new ArrayList<AlignCalcWorkerI>());
 
   /*
    * types of worker _not_ to run (for example, because they have
    * previously thrown errors)
    */
-  private volatile List<Class<? extends AlignCalcWorkerI>> blackList;
+  private final List<Class<? extends AlignCalcWorkerI>> blackList = Collections
+          .synchronizedList(new ArrayList<Class<? extends AlignCalcWorkerI>>());
 
   /*
    * global record of calculations in progress
    */
-  private volatile List<AlignCalcWorkerI> inProgress;
+  private final List<AlignCalcWorkerI> inProgress = Collections
+          .synchronizedList(new ArrayList<AlignCalcWorkerI>());
 
   /*
    * record of calculations pending or in progress in the current context
    */
-  private volatile Map<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>> updating;
+  private final Map<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>> updating =
+          new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>();
 
   /*
    * workers that have run to completion so are candidates for visual-only 
    * update of their results
    */
-  private HashSet<AlignCalcWorkerI> canUpdate;
-
-  /**
-   * Constructor
-   */
-  public AlignCalcManager()
-  {
-    restartable = Collections
-            .synchronizedList(new ArrayList<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<>();
-  }
+  private HashSet<AlignCalcWorkerI> canUpdate = new HashSet<>();;
 
   private static boolean listContains(List<AlignCalcWorkerI> upd,
           AlignCalcWorkerI worker)
@@ -92,7 +81,7 @@ public class AlignCalcManager implements AlignCalcManagerI
     return false;
   }
   @Override
-  public void notifyStart(AlignCalcWorkerI worker)
+  public void notifyStarted(AlignCalcWorkerI worker)
   {
     synchronized (updating)
     {
@@ -126,22 +115,10 @@ public class AlignCalcManager implements AlignCalcManagerI
   @Override
   public boolean isPending(AlignCalcWorkerI workingClass)
   {
-    List<AlignCalcWorkerI> upd;
     synchronized (updating)
     {
-      upd = updating.get(workingClass.getClass());
-      if (upd == null)
-      {
-        return false;
-      }
-      synchronized (upd)
-      {
-        if (upd.size() > 1)
-        {
-          return true;
-        }
-      }
-      return false;
+      List<AlignCalcWorkerI> upd = updating.get(workingClass.getClass());
+      return upd != null && upd.size() > 1;
     }
   }
 
@@ -204,7 +181,15 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     if (!isDisabled(worker))
     {
-      Thread tw = new Thread(worker);
+      Thread tw = new Thread(() -> {
+        try
+        {
+          worker.run();
+        } catch (Exception e)
+        {
+          e.printStackTrace();
+        }
+      });
       tw.setName(worker.getClass().toString());
       tw.start();
     }
@@ -332,7 +317,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   }
 
   @Override
-  public void removeRegisteredWorkersOfClass(
+  public void removeWorkersOfClass(
           Class<? extends AlignCalcWorkerI> typeToRemove)
   {
     List<AlignCalcWorkerI> removable = new ArrayList<>();