Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

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

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index 08ef3a2..1967375 100644 (file)
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -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;
@@ -74,9 +75,22 @@ public class AlignCalcManager implements AlignCalcManagerI
             .synchronizedList(new ArrayList<AlignCalcWorkerI>());
     updating = Collections.synchronizedMap(
             new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
-    canUpdate = new HashSet<AlignCalcWorkerI>();
+    canUpdate = new HashSet<>();
   }
 
+  private static boolean listContains(List<AlignCalcWorkerI> upd,
+          AlignCalcWorkerI worker)
+  {
+    // avoid use of 'Contains' in case
+    for (AlignCalcWorkerI _otherworker : upd)
+    {
+      if (_otherworker == upd)
+      {
+        return true;
+      }
+    }
+    return false;
+  }
   @Override
   public void notifyStart(AlignCalcWorkerI worker)
   {
@@ -90,7 +104,16 @@ public class AlignCalcManager implements AlignCalcManagerI
       }
       synchronized (upd)
       {
-        upd.add(worker);
+        if (listContains(upd, worker))
+        {
+          Cache.log.debug(
+                    "Ignoring second call to notifyStart for worker "
+                            + worker);
+        }
+        else
+        {
+          upd.add(worker);
+        }
       }
     }
   }
@@ -127,7 +150,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     synchronized (inProgress)
     {
-      if (inProgress.contains(worker))
+      if (listContains(inProgress, worker))
       {
         return false; // worker is already working, so ask caller to wait around
       }
@@ -144,7 +167,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     synchronized (inProgress)
     {
-      // System.err.println("Worker " + worker + " marked as complete.");
+      Cache.log.debug("Worker " + worker + " marked as complete.");
       inProgress.remove(worker);
       List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
       if (upd != null)
@@ -212,7 +235,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   {
     synchronized (restartable)
     {
-      if (!restartable.contains(worker))
+      if (!listContains(restartable, worker))
       {
         restartable.add(worker);
       }
@@ -285,7 +308,7 @@ 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)
@@ -312,8 +335,8 @@ 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)
@@ -363,7 +386,7 @@ 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))