JAL-3070 use identity equivalence for workers rather than relying on equals not being...

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

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index b829a73..3a3dc44 100644 (file)
--- 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.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 
 import java.util.ArrayList;
@@ -68,13 +69,13 @@ 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
@@ -85,14 +86,23 @@ 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)
       {
-        upd.add(worker);
+        // avoid use of 'Contains' in case
+        for (AlignCalcWorkerI _otherworker : upd)
+        {
+          if (_otherworker == upd)
+          {
+            Cache.log.debug(
+                    "Ignoring second call to notifyStart for worker "
+                            + worker);
+            return;
+          }
+        }
+          upd.add(worker);
       }
     }
   }
@@ -235,7 +245,8 @@ public class AlignCalcManager implements AlignCalcManagerI
   }
 
   @Override
-  public boolean workingInvolvedWith(AlignmentAnnotation alignmentAnnotation)
+  public boolean workingInvolvedWith(
+          AlignmentAnnotation alignmentAnnotation)
   {
     synchronized (inProgress)
     {
@@ -286,7 +297,7 @@ 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 +324,8 @@ 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 +375,7 @@ 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))