X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FAlignCalcManager.java;h=10637063e3217a8448315cde0a4b2b9be2773bdb;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=59f84441a9976cbcebf978e623038df4c1e47452;hpb=ebec7bf5754da64c85a0b1f26511a503247f158f;p=jalview.git

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index 59f8444..1063706 100644
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -1,53 +1,132 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.workers;
 
+import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignCalcWorkerI;
+import jalview.datamodel.AlignmentAnnotation;
+
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
-
-import jalview.api.AlignCalcManagerI;
-import jalview.api.AlignCalcWorkerI;
-import jalview.datamodel.AlignmentAnnotation;
+import java.util.Set;
 
 public class AlignCalcManager implements AlignCalcManagerI
 {
-  private volatile List<AlignCalcWorkerI> restartable = new ArrayList<AlignCalcWorkerI>();
+  private volatile List<AlignCalcWorkerI> restartable = Collections
+          .synchronizedList(new ArrayList<AlignCalcWorkerI>());
 
-  private List<Class> blackList = new ArrayList<Class>();
+  private volatile List<Class> blackList = Collections
+          .synchronizedList(new ArrayList<Class>());
 
   /**
    * global record of calculations in progress
    */
-  private static Hashtable<Class, AlignCalcWorkerI> inProgress = new Hashtable<Class, AlignCalcWorkerI>();
+  private volatile Map<Class, AlignCalcWorkerI> inProgress = Collections
+          .synchronizedMap(new Hashtable<Class, AlignCalcWorkerI>());
 
   /**
    * record of calculations pending or in progress in the current context
    */
-  private Map<Class, List<AlignCalcWorkerI>> updating = new Hashtable<Class, List<AlignCalcWorkerI>>();
+  private volatile Map<Class, List<AlignCalcWorkerI>> updating = Collections
+          .synchronizedMap(new Hashtable<Class, List<AlignCalcWorkerI>>());
 
   @Override
   public void notifyStart(AlignCalcWorkerI worker)
   {
-    List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
-    if (upd == null)
+    synchronized (updating)
     {
-      updating.put(worker.getClass(),
-              upd = new ArrayList<AlignCalcWorkerI>());
+      List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
+      if (upd == null)
+      {
+        updating.put(
+                worker.getClass(),
+                upd = Collections
+                        .synchronizedList(new ArrayList<AlignCalcWorkerI>()));
+      }
+      synchronized (upd)
+      {
+        upd.add(worker);
+      }
     }
-    upd.add(worker);
   }
 
   @Override
-  public synchronized boolean alreadyDoing(AlignCalcWorkerI worker)
+  public boolean alreadyDoing(AlignCalcWorkerI worker)
   {
-    return inProgress.containsKey(worker.getClass());
+    synchronized (inProgress)
+    {
+      return inProgress.containsKey(worker.getClass());
+    }
   }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.api.AlignCalcManagerI#isPending(jalview.api.AlignCalcWorkerI)
+   */
   @Override
-  public synchronized boolean notifyWorking(AlignCalcWorkerI worker)
+  public boolean isPending(AlignCalcWorkerI workingClass)
   {
-    // synchronized (inProgress)
+    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;
+    }
+  }
+
+  // TODO make into api method if needed ?
+  public int numberLive(AlignCalcWorkerI worker)
+  {
+    synchronized (updating)
+    {
+      List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
+      if (upd == null)
+      {
+        return 0;
+      }
+      ;
+      return upd.size();
+    }
+  }
+
+  @Override
+  public boolean notifyWorking(AlignCalcWorkerI worker)
+  {
+    synchronized (inProgress)
     {
       // TODO: decide if we should throw exceptions here if multiple workers
       // start to work
@@ -66,92 +145,138 @@ public class AlignCalcManager implements AlignCalcManagerI
     return true;
   }
 
-  private HashSet<AlignCalcWorkerI> canUpdate=new HashSet<AlignCalcWorkerI>();
+  private final HashSet<AlignCalcWorkerI> canUpdate = new HashSet<AlignCalcWorkerI>();
+
   @Override
-  public synchronized void workerComplete(AlignCalcWorkerI worker)
+  public void workerComplete(AlignCalcWorkerI worker)
   {
-    inProgress.remove(worker.getClass());
-    List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
-    if (upd != null)
+    synchronized (inProgress)
     {
-      upd.remove(worker);
-      canUpdate.add(worker);
+      // System.err.println("Worker "+worker.getClass()+" marked as complete.");
+      inProgress.remove(worker.getClass());
+      List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
+      if (upd != null)
+      {
+        synchronized (upd)
+        {
+          upd.remove(worker);
+        }
+        canUpdate.add(worker);
+      }
     }
-
   }
 
   @Override
   public void workerCannotRun(AlignCalcWorkerI worker)
   {
-    blackList.add(worker.getClass());
+    synchronized (blackList)
+    {
+      blackList.add(worker.getClass());
+    }
   }
 
   public boolean isBlackListed(Class workerType)
   {
-    return blackList.contains(workerType);
+    synchronized (blackList)
+    {
+      return blackList.contains(workerType);
+    }
   }
 
   @Override
   public void startWorker(AlignCalcWorkerI worker)
   {
-    new Thread(worker).start();
+    // System.err.println("Starting "+worker.getClass());
+    // new Exception("").printStackTrace();
+    Thread tw = new Thread(worker);
+    tw.setName(worker.getClass().toString());
+    tw.start();
   }
 
   @Override
-  public synchronized boolean isWorking(AlignCalcWorkerI worker)
+  public boolean isWorking(AlignCalcWorkerI worker)
   {
-    // System.err.println("isWorking : worker "+(worker!=null ?
-    // worker.getClass():"null")+ " "+hashCode());
-    return worker != null && inProgress.get(worker.getClass()) == worker;
+    synchronized (inProgress)
+    {// System.err.println("isWorking : worker "+(worker!=null ?
+     // worker.getClass():"null")+ " "+hashCode());
+      return worker != null && inProgress.get(worker.getClass()) == worker;
+    }
   }
 
   @Override
   public boolean isWorking()
   {
-    // System.err.println("isWorking "+hashCode());
-    return inProgress.size() > 0;
+    synchronized (inProgress)
+    {
+      // System.err.println("isWorking "+hashCode());
+      return inProgress.size() > 0;
+    }
   }
 
   @Override
   public void registerWorker(AlignCalcWorkerI worker)
   {
-    if (!restartable.contains(worker))
+    synchronized (restartable)
     {
-      restartable.add(worker);
+      if (!restartable.contains(worker))
+      {
+        restartable.add(worker);
+      }
+      startWorker(worker);
     }
-    startWorker(worker);
   }
 
   @Override
   public void restartWorkers()
   {
-    for (AlignCalcWorkerI worker : restartable)
+    synchronized (restartable)
     {
-      startWorker(worker);
+      for (AlignCalcWorkerI worker : restartable)
+      {
+        startWorker(worker);
+      }
     }
   }
 
   @Override
   public boolean workingInvolvedWith(AlignmentAnnotation alignmentAnnotation)
   {
-    if (isWorking())
+    synchronized (inProgress)
     {
-      for (List<AlignCalcWorkerI> workers: updating.values())
+      for (AlignCalcWorkerI worker : inProgress.values())
       {
-        for (AlignCalcWorkerI worker:workers)
         if (worker.involves(alignmentAnnotation))
         {
           return true;
         }
       }
     }
+    synchronized (updating)
+    {
+      for (List<AlignCalcWorkerI> workers : updating.values())
+      {
+        for (AlignCalcWorkerI worker : workers)
+        {
+          if (worker.involves(alignmentAnnotation))
+          {
+            return true;
+          }
+        }
+      }
+    }
     return false;
   }
 
   @Override
   public void updateAnnotationFor(Class workerClass)
   {
-    for (AlignCalcWorkerI worker:canUpdate.toArray(new AlignCalcWorkerI[1]))
+
+    AlignCalcWorkerI[] workers;
+    synchronized (canUpdate)
+    {
+      workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
+    }
+    for (AlignCalcWorkerI worker : workers)
     {
       if (workerClass.equals(worker.getClass()))
       {
@@ -164,37 +289,97 @@ public class AlignCalcManager implements AlignCalcManagerI
   public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
           Class workerClass)
   {
-    List<AlignCalcWorkerI> workingClass=new ArrayList<AlignCalcWorkerI>();
-    for (AlignCalcWorkerI worker:canUpdate.toArray(new AlignCalcWorkerI[0]))
+    List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
+    AlignCalcWorkerI[] workers;
+    synchronized (canUpdate)
+    {
+      workers = canUpdate.toArray(new AlignCalcWorkerI[canUpdate.size()]);
+    }
+    for (AlignCalcWorkerI worker : workers)
     {
       if (workerClass.equals(worker.getClass()))
       {
         workingClass.add(worker);
       }
     }
-    return (workingClass.size()==0) ? null : workingClass;
+    return (workingClass.size() == 0) ? null : workingClass;
   }
 
   @Override
   public boolean startRegisteredWorkersOfClass(Class workerClass)
   {
-	  List<AlignCalcWorkerI> workers=getRegisteredWorkersOfClass(workerClass);
-	  if (workers==null)
-	  {
-		  return false;
-	  }
-	  for (AlignCalcWorkerI worker: workers) {
-		  startWorker(worker);
-	  }
-	  return true;
+    List<AlignCalcWorkerI> workers = getRegisteredWorkersOfClass(workerClass);
+    if (workers == null)
+    {
+      return false;
+    }
+    for (AlignCalcWorkerI worker : workers)
+    {
+      if (!isPending(worker))
+      {
+        startWorker(worker);
+      }
+      else
+      {
+        System.err.println("Pending exists for " + workerClass);
+      }
+    }
+    return true;
   }
 
   @Override
   public void workerMayRun(AlignCalcWorkerI worker)
   {
-    if (blackList.contains(worker.getClass()))
+    synchronized (blackList)
     {
-      blackList.remove(worker.getClass());
+      if (blackList.contains(worker.getClass()))
+      {
+        blackList.remove(worker.getClass());
+      }
     }
   }
+
+  @Override
+  public void removeRegisteredWorkersOfClass(Class typeToRemove)
+  {
+    List<AlignCalcWorkerI> workers = getRegisteredWorkersOfClass(typeToRemove);
+    List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
+    Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
+    synchronized (restartable)
+    {
+      for (AlignCalcWorkerI worker : restartable)
+      {
+        if (typeToRemove.equals(worker.getClass()))
+        {
+          removable.add(worker);
+          toremovannot.add(worker);
+        }
+      }
+      restartable.removeAll(removable);
+    }
+    synchronized (canUpdate)
+    {
+      for (AlignCalcWorkerI worker : canUpdate)
+      {
+        if (typeToRemove.equals(worker.getClass()))
+        {
+          removable.add(worker);
+          toremovannot.add(worker);
+        }
+      }
+      canUpdate.removeAll(removable);
+    }
+    // TODO: finish testing this extension
+
+    /*
+     * synchronized (inProgress) { // need to kill or mark as dead any running
+     * threads... (inProgress.get(typeToRemove)); }
+     * 
+     * if (workers == null) { return; } for (AlignCalcWorkerI worker : workers)
+     * {
+     * 
+     * if (isPending(worker)) { worker.abortAndDestroy(); startWorker(worker); }
+     * else { System.err.println("Pending exists for " + workerClass); } }
+     */
+  }
 }