X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FAlignCalcManager.java;h=addb372bd9234a6127ba7dde80803b58163db1e4;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=473e31bf60843f8825ccbfe1a95f94c17ae06827;hpb=60805a2d20a347ef1958a7a5576cda7a186f8a8d;p=jalview.git

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index 473e31b..addb372 100644
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -1,73 +1,399 @@
+/*
+ * 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 java.util.Set;
 
 public class AlignCalcManager implements AlignCalcManagerI
 {
-  private List<Class> blackList=new ArrayList<Class>();
-  /**
+  /*
+   * list of registered workers
+   */
+  private volatile List<AlignCalcWorkerI> restartable;
+
+  /*
+   * types of worker _not_ to run (for example, because they have
+   * previously thrown errors)
+   */
+  private volatile List<Class<? extends AlignCalcWorkerI>> blackList;
+
+  /*
    * global record of calculations in progress
    */
-  private static Hashtable<Class,AlignCalcWorkerI> inProgress=new Hashtable<Class,AlignCalcWorkerI>();
-  /**
+  private volatile List<AlignCalcWorkerI> inProgress;
+
+  /*
    * 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<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>> updating;
+
+  /*
+   * 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<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);
   }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.api.AlignCalcManagerI#isPending(jalview.api.AlignCalcWorkerI)
+   */
   @Override
-  public boolean alreadyDoing(AlignCalcWorkerI worker)
+  public boolean isPending(AlignCalcWorkerI workingClass)
   {
-    return inProgress.containsKey(worker.getClass());
+    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;
+    }
   }
 
   @Override
-  public void notifyWorking(AlignCalcWorkerI worker)
+  public boolean notifyWorking(AlignCalcWorkerI worker)
   {
-    // TODO: decide if we should throw exceptions here if multiple workers start to work
-    if (inProgress.get(worker.getClass())!=null)
+    synchronized (inProgress)
     {
-      System.err.println("Warning: Multiple workers are running of type "+worker.getClass());
+      if (inProgress.contains(worker))
+      {
+        return false; // worker is already working, so ask caller to wait around
+      }
+      else
+      {
+        inProgress.add(worker);
+      }
     }
-    inProgress.put(worker.getClass(), worker);
-    
+    return true;
   }
 
   @Override
   public void workerComplete(AlignCalcWorkerI worker)
   {
-    inProgress.remove(worker);
+    synchronized (inProgress)
+    {
+      // System.err.println("Worker " + worker + " marked as complete.");
+      inProgress.remove(worker);
+      List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
+      if (upd != null)
+      {
+        synchronized (upd)
+        {
+          upd.remove(worker);
+        }
+        canUpdate.add(worker);
+      }
+    }
   }
 
   @Override
-  public void workerCannotRun(AlignCalcWorkerI worker)
+  public void disableWorker(AlignCalcWorkerI worker)
   {
-    blackList.add(worker.getClass());
+    synchronized (blackList)
+    {
+      blackList.add(worker.getClass());
+    }
   }
-  public boolean isBlackListed(Class workerType)
+
+  @Override
+  public boolean isDisabled(AlignCalcWorkerI worker)
   {
-    return blackList.contains(workerType);
+    synchronized (blackList)
+    {
+      return blackList.contains(worker.getClass());
+    }
   }
 
   @Override
   public void startWorker(AlignCalcWorkerI worker)
   {
-    new Thread(worker).start();
+    if (!isDisabled(worker))
+    {
+      Thread tw = new Thread(worker);
+      tw.setName(worker.getClass().toString());
+      tw.start();
+    }
+  }
+
+  @Override
+  public boolean isWorking(AlignCalcWorkerI worker)
+  {
+    synchronized (inProgress)
+    {// System.err.println("isWorking : worker "+(worker!=null ?
+     // worker.getClass():"null")+ " "+hashCode());
+      return worker != null && inProgress.contains(worker);
+    }
+  }
+
+  @Override
+  public boolean isWorking()
+  {
+    synchronized (inProgress)
+    {
+      // System.err.println("isWorking "+hashCode());
+      return inProgress.size() > 0;
+    }
+  }
+
+  @Override
+  public void registerWorker(AlignCalcWorkerI worker)
+  {
+    synchronized (restartable)
+    {
+      if (!restartable.contains(worker))
+      {
+        restartable.add(worker);
+      }
+      startWorker(worker);
+    }
+  }
+
+  @Override
+  public void restartWorkers()
+  {
+    synchronized (restartable)
+    {
+      for (AlignCalcWorkerI worker : restartable)
+      {
+        startWorker(worker);
+      }
+    }
+  }
+
+  @Override
+  public boolean workingInvolvedWith(AlignmentAnnotation alignmentAnnotation)
+  {
+    synchronized (inProgress)
+    {
+      for (AlignCalcWorkerI worker : inProgress)
+      {
+        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<? extends AlignCalcWorkerI> workerClass)
+  {
+
+    AlignCalcWorkerI[] workers;
+    synchronized (canUpdate)
+    {
+      workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
+    }
+    for (AlignCalcWorkerI worker : workers)
+    {
+      if (workerClass.equals(worker.getClass()))
+      {
+        worker.updateAnnotation();
+      }
+    }
+  }
+
+  @Override
+  public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
+          Class<? extends AlignCalcWorkerI> workerClass)
+  {
+    List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
+    synchronized (canUpdate)
+    {
+      for (AlignCalcWorkerI worker : canUpdate)
+      {
+        if (workerClass.equals(worker.getClass()))
+        {
+          workingClass.add(worker);
+        }
+      }
+    }
+    return (workingClass.size() == 0) ? null : workingClass;
+  }
+
+  @Override
+  public void enableWorker(AlignCalcWorkerI worker)
+  {
+    synchronized (blackList)
+    {
+      blackList.remove(worker.getClass());
+    }
+  }
+
+  @Override
+  public void removeRegisteredWorkersOfClass(
+          Class<? extends AlignCalcWorkerI> 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); } }
+     */
+  }
+
+  /**
+   * Deletes the worker that update the given annotation, provided it is marked
+   * as deletable.
+   */
+  @Override
+  public void removeWorkerForAnnotation(AlignmentAnnotation ann)
+  {
+    /*
+     * first just find those to remove (to avoid
+     * ConcurrentModificationException)
+     */
+    List<AlignCalcWorkerI> toRemove = new ArrayList<AlignCalcWorkerI>();
+    for (AlignCalcWorkerI worker : restartable)
+    {
+      if (worker.involves(ann))
+      {
+        if (worker.isDeletable())
+        {
+          toRemove.add(worker);
+        }
+      }
+    }
+
+    /*
+     * remove all references to deleted workers so any references 
+     * they hold to annotation data can be garbage collected 
+     */
+    for (AlignCalcWorkerI worker : toRemove)
+    {
+      restartable.remove(worker);
+      blackList.remove(worker.getClass());
+      inProgress.remove(worker);
+      canUpdate.remove(worker);
+      synchronized (updating)
+      {
+        List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
+        if (upd != null)
+        {
+          upd.remove(worker);
+        }
+      }
+    }
   }
 }